Query 028022
Match_columns 215
No_of_seqs 76 out of 78
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 05:03:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028022.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028022hhsearch_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 5.3E-76 1.2E-80 474.7 11.9 124 37-160 9-132 (132)
2 PF08821 CGGC: CGGC domain; I 92.3 0.29 6.2E-06 38.3 4.8 66 58-133 30-98 (107)
3 PF02899 Phage_int_SAM_1: Phag 91.5 0.32 6.8E-06 33.1 3.7 40 50-90 21-60 (84)
4 cd00798 INT_XerDC XerD and Xer 87.7 2 4.4E-05 33.3 6.1 69 50-145 21-91 (284)
5 cd00799 INT_Cre Cre recombinas 86.8 5.7 0.00012 32.3 8.4 77 50-158 6-82 (287)
6 TIGR02225 recomb_XerD tyrosine 85.0 3.6 7.8E-05 32.3 6.2 70 49-146 19-90 (291)
7 PRK00283 xerD site-specific ty 84.3 2.7 5.8E-05 33.7 5.3 67 51-145 30-98 (299)
8 TIGR02224 recomb_XerC tyrosine 76.2 12 0.00025 29.6 6.4 69 52-146 22-92 (295)
9 COG1080 PtsA Phosphoenolpyruva 68.2 6 0.00013 39.5 3.8 40 117-156 306-367 (574)
10 cd01185 INT_Tn4399 Tn4399 and 62.7 33 0.00071 28.0 6.5 33 54-86 44-78 (299)
11 PF10865 DUF2703: Domain of un 60.7 3.4 7.4E-05 33.4 0.5 43 79-141 2-44 (120)
12 PF00539 Tat: Transactivating 57.8 4.4 9.4E-05 30.6 0.6 19 162-180 45-63 (68)
13 COG4974 XerD Site-specific rec 55.0 11 0.00025 34.9 2.9 38 52-91 31-69 (300)
14 PF13495 Phage_int_SAM_4: Phag 54.2 16 0.00035 24.9 3.0 54 53-135 24-77 (85)
15 PRK00236 xerC site-specific ty 50.5 64 0.0014 25.4 6.1 37 51-88 31-67 (297)
16 PRK10529 DNA-binding transcrip 47.6 16 0.00035 28.0 2.3 17 121-137 191-207 (225)
17 TIGR01418 PEP_synth phosphoeno 46.0 34 0.00074 34.6 4.8 42 123-164 547-618 (782)
18 cd00801 INT_P4 Bacteriophage P 46.0 39 0.00084 27.8 4.4 26 120-146 135-163 (357)
19 PF13276 HTH_21: HTH-like doma 41.3 46 0.00099 22.3 3.5 29 123-156 4-32 (60)
20 PF08544 GHMP_kinases_C: GHMP 40.4 6 0.00013 27.0 -1.0 75 51-134 6-84 (85)
21 PF05528 Coronavirus_5: Corona 40.0 4.9 0.00011 31.3 -1.6 18 140-157 4-24 (82)
22 PRK10816 DNA-binding transcrip 39.4 22 0.00047 27.3 1.9 23 114-136 174-204 (223)
23 PF06252 DUF1018: Protein of u 38.2 1.6E+02 0.0036 22.5 6.6 87 54-155 2-89 (119)
24 PF00486 Trans_reg_C: Transcri 37.9 33 0.00073 23.0 2.4 21 120-140 44-64 (77)
25 smart00259 ZnF_A20 A20-like zi 37.6 17 0.00037 22.6 0.9 16 97-112 7-22 (26)
26 cd04383 RhoGAP_srGAP RhoGAP_sr 36.2 1.1E+02 0.0025 25.1 5.7 35 124-159 47-88 (188)
27 cd01187 INT_SG4 INT_SG4, DNA b 35.7 1.5E+02 0.0032 24.3 6.2 30 53-86 24-53 (299)
28 PF00140 Sigma70_r1_2: Sigma-7 35.6 27 0.00059 22.5 1.6 12 148-159 2-13 (37)
29 PRK05084 xerS site-specific ty 34.9 82 0.0018 26.8 4.8 68 52-135 42-119 (357)
30 PF09336 Vps4_C: Vps4 C termin 34.2 34 0.00074 24.4 2.1 31 55-90 32-62 (62)
31 smart00862 Trans_reg_C Transcr 32.9 46 0.001 22.1 2.5 51 58-138 13-63 (78)
32 PF07700 HNOB: Heme NO binding 32.5 20 0.00043 28.8 0.7 37 52-88 64-103 (171)
33 PF11709 Mit_ribos_Mrp51: Mito 32.1 56 0.0012 29.7 3.6 64 43-106 147-229 (312)
34 smart00243 GAS2 Growth-Arrest- 31.7 32 0.00069 26.4 1.7 14 54-67 55-68 (73)
35 PF00667 FAD_binding_1: FAD bi 30.3 55 0.0012 27.2 3.0 45 76-120 56-100 (219)
36 PF14768 RPA_interact_C: Repli 30.1 47 0.001 24.6 2.3 35 110-144 18-56 (82)
37 KOG4670 Uncharacterized conser 30.1 21 0.00046 36.0 0.6 59 50-108 468-544 (602)
38 TIGR02249 integrase_gron integ 28.3 1.3E+02 0.0028 25.0 4.9 33 52-88 23-55 (315)
39 PF13099 DUF3944: Domain of un 28.1 31 0.00067 23.2 0.9 22 72-93 11-34 (35)
40 TIGR01417 PTS_I_fam phosphoeno 27.9 61 0.0013 31.7 3.3 36 121-156 308-365 (565)
41 PF12067 Sox_C_TAD: Sox C-term 27.6 33 0.00072 30.0 1.3 15 53-67 141-155 (197)
42 KOG4405 GDP dissociation inhib 27.6 29 0.00062 34.7 1.0 85 50-139 218-331 (547)
43 PF09107 SelB-wing_3: Elongati 27.4 26 0.00056 24.3 0.5 20 74-93 22-41 (50)
44 PF03732 Retrotrans_gag: Retro 26.6 1.5E+02 0.0033 19.9 4.2 36 115-155 56-92 (96)
45 cd07288 PX_SNX15 The phosphoin 26.1 75 0.0016 25.0 2.9 33 47-84 84-116 (118)
46 cd04385 RhoGAP_ARAP RhoGAP_ARA 25.9 1E+02 0.0022 25.2 3.8 39 120-159 41-85 (184)
47 cd04372 RhoGAP_chimaerin RhoGA 25.5 77 0.0017 26.1 3.0 36 124-159 45-87 (194)
48 cd01355 AcnX Putative Aconitas 25.5 73 0.0016 30.4 3.2 53 77-141 49-108 (389)
49 COG0606 Predicted ATPase with 25.1 3.7E+02 0.0081 26.9 8.0 45 97-143 336-380 (490)
50 PRK09279 pyruvate phosphate di 25.0 69 0.0015 33.4 3.2 36 129-164 636-685 (879)
51 PF10520 Kua-UEV1_localn: Kua- 23.8 38 0.00082 29.1 1.0 24 118-141 17-41 (178)
52 TIGR03190 benz_CoA_bzdN benzoy 23.7 5.7E+02 0.012 23.4 10.1 25 47-71 166-190 (377)
53 cd04436 DEP_fRgd2 DEP (Disheve 23.5 68 0.0015 25.0 2.2 41 56-96 33-77 (84)
54 PTZ00398 phosphoenolpyruvate c 23.4 1.3E+02 0.0029 31.8 4.9 42 119-160 264-336 (974)
55 cd04396 RhoGAP_fSAC7_BAG7 RhoG 23.4 3E+02 0.0064 23.4 6.2 37 123-159 60-103 (225)
56 PLN02837 threonine-tRNA ligase 23.3 38 0.00083 33.0 1.0 16 116-131 489-504 (614)
57 PRK11235 bifunctional antitoxi 23.1 1.9E+02 0.0041 22.0 4.5 38 124-171 11-48 (80)
58 smart00353 HLH helix loop heli 23.0 1.1E+02 0.0024 19.6 2.8 24 47-70 3-26 (53)
59 cd08793 Death_IRAK4 Death doma 22.8 92 0.002 24.9 2.9 63 54-138 23-85 (100)
60 PF09958 DUF2192: Uncharacteri 22.5 75 0.0016 28.8 2.6 21 121-141 27-47 (231)
61 cd00383 trans_reg_C Effector d 22.5 76 0.0017 21.9 2.1 19 120-138 62-80 (95)
62 TIGR01828 pyru_phos_dikin pyru 22.4 51 0.0011 34.1 1.7 26 139-164 651-679 (856)
63 KOG2731 DNA alkylation damage 22.4 38 0.00083 32.6 0.8 38 51-90 327-364 (378)
64 PRK10236 hypothetical protein; 22.1 64 0.0014 29.3 2.1 84 71-172 14-107 (237)
65 PRK13197 pyrrolidone-carboxyla 22.1 2.4E+02 0.0051 24.3 5.4 83 43-135 108-199 (215)
66 PF02187 GAS2: Growth-Arrest-S 22.0 18 0.00039 27.5 -1.2 13 55-67 56-68 (73)
67 PF07535 zf-DBF: DBF zinc fing 21.9 46 0.00099 23.4 0.9 12 119-130 37-48 (49)
68 COG4311 SoxD Sarcosine oxidase 21.9 39 0.00084 27.2 0.6 35 67-102 27-66 (97)
69 KOG1452 Predicted Rho GTPase-a 21.7 51 0.0011 32.1 1.5 30 128-158 233-270 (442)
70 cd00778 ProRS_core_arch_euk Pr 21.7 50 0.0011 28.4 1.3 17 115-131 244-260 (261)
71 COG4865 Glutamate mutase epsil 21.7 61 0.0013 31.9 2.0 22 125-146 196-217 (485)
72 cd07287 PX_RPK118_like The pho 21.6 1E+02 0.0023 24.3 3.0 35 45-84 82-116 (118)
73 COG0745 OmpR Response regulato 21.5 75 0.0016 27.1 2.3 29 112-140 176-212 (229)
74 cd04407 RhoGAP_myosin_IXB RhoG 21.3 2.1E+02 0.0046 23.6 4.8 36 124-159 44-83 (186)
75 PF02896 PEP-utilizers_C: PEP- 21.3 1.2E+02 0.0027 27.4 3.8 38 119-156 58-118 (293)
76 PF09674 DUF2400: Protein of u 21.2 84 0.0018 27.8 2.6 52 116-167 24-94 (232)
77 PF00179 UQ_con: Ubiquitin-con 21.1 2.1E+02 0.0046 21.9 4.5 45 118-165 90-137 (140)
78 cd04400 RhoGAP_fBEM3 RhoGAP_fB 21.1 1.4E+02 0.003 24.4 3.7 39 120-159 49-94 (190)
79 TIGR02384 RelB_DinJ addiction 20.6 2.5E+02 0.0053 21.0 4.6 39 124-172 12-50 (83)
80 PHA03019 hypothetical protein; 20.5 70 0.0015 24.8 1.7 21 52-72 45-65 (77)
81 PRK01381 Trp operon repressor; 20.2 1.4E+02 0.0031 23.8 3.5 28 49-84 3-30 (99)
82 PRK11061 fused phosphoenolpyru 20.2 1.5E+02 0.0033 30.0 4.4 35 121-155 475-530 (748)
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=5.3e-76 Score=474.75 Aligned_cols=124 Identities=77% Similarity=1.435 Sum_probs=120.1
Q ss_pred CCCCCCCCchhhHhhhhhHHHHHHHHHhcCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchh
Q 028022 37 PPAAAAPPSRYESQKRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLK 116 (215)
Q Consensus 37 ~~~~~~~~srYesQKRRdWntF~qyL~n~rPPlsL~~Csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlR 116 (215)
.+++++.+||||+|||||||||+|||+||+|||+|++|+++|||+||+|||||||||||.++|+|||||+||+||+||||
T Consensus 9 ~~~~~~~~SrYesQKrrdwntf~qyL~n~rPP~~L~~csg~hVl~FL~~~d~~GkTkVh~~~C~~~g~~~~p~~C~CPlr 88 (132)
T PF04852_consen 9 SRSPQPAPSRYESQKRRDWNTFGQYLRNHRPPLSLSRCSGNHVLEFLRYLDQFGKTKVHGQGCPFFGHPSPPAPCPCPLR 88 (132)
T ss_pred CCCCCCCCcccchhhhHHHHHHHHHHHccCCCcchhhcChHHHHHHHHHHhccCCeeecCCCCCCCCCCCCCCCCCCcHH
Confidence 34455688999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcchhHHHHHHHHHHHHHhCCCCCCCccchhHHHHHHHHHHHH
Q 028022 117 QAWGSLDALIGRLRAAYEENGGRPESNPFGARAVRIYLREVRES 160 (215)
Q Consensus 117 QAWGSLDALIGRLRAAfEE~Gg~pE~NPF~araVRlYLReVRd~ 160 (215)
||||||||||||||||||||||+||+|||++++||+|||||||+
T Consensus 89 qAwGSlDalIGrLraafee~Gg~pe~NPf~~~~vr~yLr~vr~~ 132 (132)
T PF04852_consen 89 QAWGSLDALIGRLRAAFEEHGGHPEANPFAARAVRLYLREVRDS 132 (132)
T ss_pred HHhccHHHHHHHHHHHHHHhCCCCCCCchhhHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999999999999985
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=92.33 E-value=0.29 Score=38.35 Aligned_cols=66 Identities=23% Similarity=0.530 Sum_probs=49.1
Q ss_pred HHHHHHhcCCCccccc---ccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 028022 58 FLQYLKNHKPPLTLAR---CSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRAAY 133 (215)
Q Consensus 58 F~qyL~n~rPPlsL~~---Csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAAf 133 (215)
|.+|=.+..--+.+.+ |.+..|+..++.+-.+|-..||...|.+.+.+.+ .||. +|.|+-.|+++|
T Consensus 30 F~~y~~~~~elvgf~~CgGCpg~~~~~~~~~l~~~~~d~IHlssC~~~~~~~~----~CP~------~~~~~~~I~~~~ 98 (107)
T PF08821_consen 30 FARYDDEDVELVGFFTCGGCPGRKLVRRIKKLKKNGADVIHLSSCMVKGNPHG----PCPH------IDEIKKIIEEKF 98 (107)
T ss_pred cccCCCCCeEEEEEeeCCCCChhHHHHHHHHHHHCCCCEEEEcCCEecCCCCC----CCCC------HHHHHHHHHHHh
Confidence 4444332222344445 4568999999999999999999999999987653 6666 899999999887
No 3
>PF02899 Phage_int_SAM_1: Phage integrase, N-terminal SAM-like domain; InterPro: IPR004107 Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104 from INTERPRO).; GO: 0003677 DNA binding, 0015074 DNA integration; PDB: 1Z1G_B 1Z19_A 1Z1B_A 2OXO_A 1P7D_B 3NRW_A 1A0P_A.
Probab=91.46 E-value=0.32 Score=33.08 Aligned_cols=40 Identities=28% Similarity=0.525 Sum_probs=31.7
Q ss_pred hhhhhHHHHHHHHHhcCCCcccccccchhHhHHhhhhcccC
Q 028022 50 QKRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFG 90 (215)
Q Consensus 50 QKRRdWntF~qyL~n~rPPlsL~~Csg~hVleFLrylDqfG 90 (215)
.-+++++.|.+||.+ ....++..++..||.+||.++-+.|
T Consensus 21 ~Y~~~l~~f~~~~~~-~~~~~~~~i~~~~v~~f~~~~~~~~ 60 (84)
T PF02899_consen 21 SYRRDLRRFIRWLEE-HGIIDWEDITEEDVRDFLEYLAKEG 60 (84)
T ss_dssp HHHHHHHHHHHHHHH-TTS-CGGG--HHHHHHHHHHHHCTT
T ss_pred HHHHHHHHHHHhhhh-hhhhhhhhhhhHHHHHHHHHHHccC
Confidence 456899999999999 5667788899999999999987766
No 4
>cd00798 INT_XerDC XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequen
Probab=87.74 E-value=2 Score=33.33 Aligned_cols=69 Identities=25% Similarity=0.300 Sum_probs=47.4
Q ss_pred hhhhhHHHHHHHHHhcCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHH
Q 028022 50 QKRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRL 129 (215)
Q Consensus 50 QKRRdWntF~qyL~n~rPPlsL~~Csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRL 129 (215)
+-+..|+.|.+|+.....+. +..-+..||.+|+.++.+.| ....++...++-|
T Consensus 21 ~~~~~~~~~~~~~~~~~~~~-~~~l~~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~l 73 (284)
T cd00798 21 AYRRDLERFLEFLEERGILF-PADVTPDDIRRFLAELKDQG--------------------------LSARSIARKLSAL 73 (284)
T ss_pred HHHHHHHHHHHHHHHcCCCc-hhhCCHHHHHHHHHHhhhcC--------------------------CCHHHHHHHHHHH
Confidence 44567899999998764433 56678999999999887644 1235677778888
Q ss_pred HHHHHHhC--CCCCCCcc
Q 028022 130 RAAYEENG--GRPESNPF 145 (215)
Q Consensus 130 RAAfEE~G--g~pE~NPF 145 (215)
+++|.-.. +.-+.||+
T Consensus 74 ~~~~~~~~~~~~~~~~p~ 91 (284)
T cd00798 74 RSFFKFLLREGLILANPA 91 (284)
T ss_pred HHHHHHHHHcCCccCChh
Confidence 88776321 23445776
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=86.77 E-value=5.7 Score=32.28 Aligned_cols=77 Identities=23% Similarity=0.303 Sum_probs=52.8
Q ss_pred hhhhhHHHHHHHHHhcCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHH
Q 028022 50 QKRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRL 129 (215)
Q Consensus 50 QKRRdWntF~qyL~n~rPPlsL~~Csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRL 129 (215)
.-.++++.|.+|+..+. +....-+..||.+||.||.+. .+..++-..++.|
T Consensus 6 ~y~~~l~~f~~~~~~~~--~~~~~~~~~~i~~~~~~l~~~---------------------------~s~~ti~~~~~~l 56 (287)
T cd00799 6 AYLSDWRRFAAWCQAHG--RTPLPASPETVTLYLTDLADS---------------------------LAPSTISRRLSAL 56 (287)
T ss_pred HHHHHHHHHHHHHHhcC--CCCCCCCHHHHHHHHHHHHhc---------------------------cChHHHHHHHHHH
Confidence 44568889999998752 222234589999999988531 1456888899999
Q ss_pred HHHHHHhCCCCCCCccchhHHHHHHHHHH
Q 028022 130 RAAYEENGGRPESNPFGARAVRIYLREVR 158 (215)
Q Consensus 130 RAAfEE~Gg~pE~NPF~araVRlYLReVR 158 (215)
+..|+..+. .||+....++.-|+.++
T Consensus 57 ~~~~~~~~~---~~p~~~~~~~~~~~~~~ 82 (287)
T cd00799 57 SQLHRRSGL---PSPADSPLVRLVLRGIR 82 (287)
T ss_pred HHHHHHcCC---CCCccCHHHHHHHHHHH
Confidence 999985432 58876655555555554
No 6
>TIGR02225 recomb_XerD tyrosine recombinase XerD. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK.
Probab=85.02 E-value=3.6 Score=32.34 Aligned_cols=70 Identities=26% Similarity=0.448 Sum_probs=47.5
Q ss_pred HhhhhhHHHHHHHHHhcCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHH
Q 028022 49 SQKRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGR 128 (215)
Q Consensus 49 sQKRRdWntF~qyL~n~rPPlsL~~Csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGR 128 (215)
.+-++.++.|.+||..+. ..+..-+..||.+|+.++.+.| ...-+++..+..
T Consensus 19 ~~~~~~~~~~~~~~~~~~--~~~~~it~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~ 70 (291)
T TIGR02225 19 EAYRRDLEKFLEFLEERG--IDLEEVDRGDIVDFLAELKEAG--------------------------LSARSIARALSA 70 (291)
T ss_pred HHHHHHHHHHHHHHHhcC--CChHHCCHHHHHHHHHHhhcCC--------------------------CCHhHHHHHHHH
Confidence 445567888999998543 2455567899999999887643 112367888899
Q ss_pred HHHHHHHh--CCCCCCCccc
Q 028022 129 LRAAYEEN--GGRPESNPFG 146 (215)
Q Consensus 129 LRAAfEE~--Gg~pE~NPF~ 146 (215)
|+++|+-. -+-.+.|||.
T Consensus 71 l~~~~~~a~~~~~~~~np~~ 90 (291)
T TIGR02225 71 LRSFYRFLLREGIREDDPSA 90 (291)
T ss_pred HHHHHHHHHhcccccCCchh
Confidence 99888732 2334567763
No 7
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=84.31 E-value=2.7 Score=33.68 Aligned_cols=67 Identities=25% Similarity=0.279 Sum_probs=46.8
Q ss_pred hhhhHHHHHHHHHhcCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHH
Q 028022 51 KRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLR 130 (215)
Q Consensus 51 KRRdWntF~qyL~n~rPPlsL~~Csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLR 130 (215)
-+++|+.|..||..+.- .+...+..||.+|+.++.+.+ .+.-++...+..|+
T Consensus 30 ~~~~~~~~~~~~~~~~~--~~~~l~~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~l~ 81 (299)
T PRK00283 30 YRRDLELFAEWLAARGL--SLAEATRDDLQAFLAELAEGG--------------------------YKATSSARRLSALR 81 (299)
T ss_pred HHHHHHHHHHHHHhcCC--ChHHCCHHHHHHHHHHHHhCC--------------------------CCHHHHHHHHHHHH
Confidence 46688999999986533 566778999999999885431 23347778888888
Q ss_pred HHHHHhC--CCCCCCcc
Q 028022 131 AAYEENG--GRPESNPF 145 (215)
Q Consensus 131 AAfEE~G--g~pE~NPF 145 (215)
++|+-.. +.-..|||
T Consensus 82 ~~~~~a~~~~~i~~np~ 98 (299)
T PRK00283 82 RFFQFLLREGLREDDPS 98 (299)
T ss_pred HHHHHHHHcCCcccCch
Confidence 8887331 23446776
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=76.20 E-value=12 Score=29.64 Aligned_cols=69 Identities=30% Similarity=0.400 Sum_probs=46.7
Q ss_pred hhhHHHHHHHHHhcCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHH
Q 028022 52 RRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRA 131 (215)
Q Consensus 52 RRdWntF~qyL~n~rPPlsL~~Csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRA 131 (215)
+.+++.|.+||......+.|..-+..||.+||.++.+.|. ...++...+..||+
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~l~~~~i~~~~~~~~~~~~--------------------------~~~T~~~~~~~l~~ 75 (295)
T TIGR02224 22 RRDLKAFLEFLEEEGGLASLAEVTAADLRSFLAELHARGL--------------------------SRRSLARKLSALRS 75 (295)
T ss_pred HHHHHHHHHHHHhcCCCCccccCcHHHHHHHHHHhcccCC--------------------------CHHHHHHHHHHHHH
Confidence 4566778889988666678888889999999998765321 22456667777777
Q ss_pred HHHHhC--CCCCCCccc
Q 028022 132 AYEENG--GRPESNPFG 146 (215)
Q Consensus 132 AfEE~G--g~pE~NPF~ 146 (215)
+|.-.. +.-+.|||.
T Consensus 76 ~~~~a~~~~~~~~np~~ 92 (295)
T TIGR02224 76 FYRFLVRRGLIKANPAA 92 (295)
T ss_pred HHHHHHHcCccccChHh
Confidence 776421 223457763
No 9
>COG1080 PtsA Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]
Probab=68.18 E-value=6 Score=39.52 Aligned_cols=40 Identities=38% Similarity=0.640 Sum_probs=31.2
Q ss_pred hhcchhHHHHHHHHHHHHHhCCC--------------------C-CCCcc-chhHHHHHHHH
Q 028022 117 QAWGSLDALIGRLRAAYEENGGR--------------------P-ESNPF-GARAVRIYLRE 156 (215)
Q Consensus 117 QAWGSLDALIGRLRAAfEE~Gg~--------------------p-E~NPF-~araVRlYLRe 156 (215)
..|=+.|..----++..|.+|++ | |.||| |-|+||+||..
T Consensus 306 ~~~P~EeEQ~~aY~~vlea~~g~pviiRTlDiGGDK~lpyl~lp~E~NPfLG~RaIRl~l~~ 367 (574)
T COG1080 306 DALPDEEEQFEAYKAVLEAMGGKPVIIRTLDIGGDKPLPYLNLPKEENPFLGYRAIRLSLER 367 (574)
T ss_pred CCCCChHHHHHHHHHHHHHcCCCceEEEecccCCCCcCCCCCCccccCchhhhHHHHHhhcc
Confidence 34556777777778888888887 3 79999 68999999853
No 10
>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=62.66 E-value=33 Score=28.00 Aligned_cols=33 Identities=12% Similarity=0.335 Sum_probs=26.5
Q ss_pred hHHHHHHHHHhcCC--CcccccccchhHhHHhhhh
Q 028022 54 DWNTFLQYLKNHKP--PLTLARCSGAHVIEFLKYL 86 (215)
Q Consensus 54 dWntF~qyL~n~rP--PlsL~~Csg~hVleFLryl 86 (215)
.++.|..||....+ .+.|..-+..||.+|+.|+
T Consensus 44 ~~~~~~~~~~~~~~~~~~~l~~i~~~~i~~~~~~l 78 (299)
T cd01185 44 HLKNLREFIECTYKEIDIALLELTREFILEFKLFL 78 (299)
T ss_pred HHHHHHHHHHHhcCccCCCHHHccHHHHHHHHHHH
Confidence 46678888876554 6778888899999999988
No 11
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=60.67 E-value=3.4 Score=33.35 Aligned_cols=43 Identities=28% Similarity=0.292 Sum_probs=33.1
Q ss_pred HhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHHHHhCCCCC
Q 028022 79 VIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRAAYEENGGRPE 141 (215)
Q Consensus 79 VleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAAfEE~Gg~pE 141 (215)
+|+|+ |||..|+| |... ...+.+|+..|-+|+.+|+..|..++
T Consensus 2 ~I~w~-~l~~~g~t------C~RC-------------~~Tg~~L~~av~~l~~~L~~~Giev~ 44 (120)
T PF10865_consen 2 VIEWQ-HLDLDGKT------CERC-------------GDTGETLREAVKELAPVLAPLGIEVR 44 (120)
T ss_pred eEEEE-EeecCCCc------CCch-------------hhHHHHHHHHHHHHHHHHHhCCcEEE
Confidence 46788 55555876 4433 36778999999999999999998754
No 12
>PF00539 Tat: Transactivating regulatory protein (Tat); InterPro: IPR001831 Like other lentiviruses, Human immunodeficiency virus 1 (HIV-1) encodes a trans-activating regulatory protein (Tat), which is essential for efficient transcription of the viral genome [, ]. Tat acts by binding to an RNA stem-loop structure, the trans-activating response element (TAR), found at the 5' ends of nascent HIV-1 transcripts. In binding to TAR, Tat alters the properties of the transcription complex, recruits a positive transcription elongation complex (P-TEFb) and hence increases the production of full-length viral RNA []. Tat protein also associates with RNA polymerase II complexes during early transcription elongation after the promoter clearance and before the synthesis of full-length TAR RNA transcript. This interaction of Tat with RNA polymerase II elongation complexes is P-TEFb-independent. There are two Tat binding sites on each transcription elongation complex; one is located on TAR RNA and the other one on RNA polymerase II near the exit site for nascent mRNA transcripts which suggests that two Tat molecules are involved in performing various functions during a single round of HIV-1 mRNA synthesis []. The minimum Tat sequence that can mediate specific TAR binding in vitro has been mapped to a basic domain of 10 amino acids, comprising mostly Arg and Lys residues. Regulatory activity, however, also requires the 47 N-terminal residues, which interact with components of the transcription complex and function as a transcriptional activation domain [, , ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 2W2H_D 1ZBN_B 1TVS_A 1TVT_A 3O6L_C 3O6M_C 3MI9_C 3MIA_C 1JFW_A 1TBC_A ....
Probab=57.80 E-value=4.4 Score=30.57 Aligned_cols=19 Identities=37% Similarity=0.655 Sum_probs=14.4
Q ss_pred HhhhCCchhhhhccCCCcc
Q 028022 162 AKARGIPYEKKKRKRPVVT 180 (215)
Q Consensus 162 AKARgi~y~kkkrkr~~~~ 180 (215)
.|.-||.|..|||||....
T Consensus 45 ~KgLGI~Y~r~rrRrr~~~ 63 (68)
T PF00539_consen 45 QKGLGISYGRKRRRRRTPQ 63 (68)
T ss_dssp CTSSSTSSSSSSCSCCCSS
T ss_pred eCCCcccccccccCcCCCC
Confidence 4788999998887665543
No 13
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=55.01 E-value=11 Score=34.91 Aligned_cols=38 Identities=32% Similarity=0.540 Sum_probs=33.9
Q ss_pred hhhHHHHHHHHHhcCCCc-ccccccchhHhHHhhhhcccCc
Q 028022 52 RRDWNTFLQYLKNHKPPL-TLARCSGAHVIEFLKYLDQFGK 91 (215)
Q Consensus 52 RRdWntF~qyL~n~rPPl-sL~~Csg~hVleFLrylDqfGK 91 (215)
|||-+.|.+||..+- + +|...+-.||.+||.|+-.+|.
T Consensus 31 rrDL~~f~~~L~~~~--~~~l~~~~~~di~~yl~~l~~~g~ 69 (300)
T COG4974 31 RRDLEDFREWLEERG--ITDLADATEADIREYLTELAEQGL 69 (300)
T ss_pred HHHHHHHHHHHHhcC--CCChhhcCHHHHHHHHHHHHhCCc
Confidence 789999999999886 4 6788889999999999999993
No 14
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=54.21 E-value=16 Score=24.94 Aligned_cols=54 Identities=17% Similarity=0.325 Sum_probs=32.3
Q ss_pred hhHHHHHHHHHhcCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHH
Q 028022 53 RDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRAA 132 (215)
Q Consensus 53 RdWntF~qyL~n~rPPlsL~~Csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAA 132 (215)
...+.|.+|+.+. .+...+..||.+||.||-..-+ .+..++...+.-||..
T Consensus 24 ~~l~~f~~~~~~~----~~~~it~~~i~~y~~~l~~~~~-------------------------~s~~T~~~~~~~l~~f 74 (85)
T PF13495_consen 24 YHLKRFLRFLGNK----PPDEITPEDIEQYLNYLQNERG-------------------------LSPSTINQYLSALRSF 74 (85)
T ss_dssp HHHHHHHTTSSS------GGG--HHHHHHHHHHHHTTT----------------------------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcccC----ccchhHHHHHHHHHHHHHHhcC-------------------------CCHHHHHHHHHHHHHH
Confidence 4456677777633 4566779999999998872211 3455666677777777
Q ss_pred HHH
Q 028022 133 YEE 135 (215)
Q Consensus 133 fEE 135 (215)
|+-
T Consensus 75 f~~ 77 (85)
T PF13495_consen 75 FRW 77 (85)
T ss_dssp HHC
T ss_pred HHH
Confidence 653
No 15
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=50.54 E-value=64 Score=25.45 Aligned_cols=37 Identities=30% Similarity=0.443 Sum_probs=28.0
Q ss_pred hhhhHHHHHHHHHhcCCCcccccccchhHhHHhhhhcc
Q 028022 51 KRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQ 88 (215)
Q Consensus 51 KRRdWntF~qyL~n~rPPlsL~~Csg~hVleFLrylDq 88 (215)
-+.+|+.|..|+..... ..+..-...||.+||.++-+
T Consensus 31 ~~~~~~~~~~~~~~~~~-~~~~~i~~~~i~~~~~~~~~ 67 (297)
T PRK00236 31 YRRDLRAFLAFLEEHGI-SSLQDLDAADLRSFLARRRR 67 (297)
T ss_pred HHHHHHHHHHHHHHcCC-CchhhCCHHHHHHHHHHHHh
Confidence 35678889999887543 55677788999999987754
No 16
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=47.62 E-value=16 Score=27.97 Aligned_cols=17 Identities=29% Similarity=0.485 Sum_probs=13.1
Q ss_pred hhHHHHHHHHHHHHHhC
Q 028022 121 SLDALIGRLRAAYEENG 137 (215)
Q Consensus 121 SLDALIGRLRAAfEE~G 137 (215)
+||.+|.|||.-+++.+
T Consensus 191 ~~~~~i~rlR~kl~~~~ 207 (225)
T PRK10529 191 YLRIYMGHLRQKLEQDP 207 (225)
T ss_pred CHHHHHHHHHHHhccCC
Confidence 58888888888887544
No 17
>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=46.00 E-value=34 Score=34.61 Aligned_cols=42 Identities=24% Similarity=0.283 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHhCCC-------------------------CCCCcc-chhHHHHHH----HHHHHHHHhh
Q 028022 123 DALIGRLRAAYEENGGR-------------------------PESNPF-GARAVRIYL----REVRESQAKA 164 (215)
Q Consensus 123 DALIGRLRAAfEE~Gg~-------------------------pE~NPF-~araVRlYL----ReVRd~QAKA 164 (215)
|.+.-.+|.+++.++++ .|.||| |.|.||+|| .++=+.|.+|
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 55556777777776443 378997 679999999 4566666655
No 18
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=45.97 E-value=39 Score=27.83 Aligned_cols=26 Identities=19% Similarity=0.276 Sum_probs=19.9
Q ss_pred chhHHHHHHHHHHHHH---hCCCCCCCccc
Q 028022 120 GSLDALIGRLRAAYEE---NGGRPESNPFG 146 (215)
Q Consensus 120 GSLDALIGRLRAAfEE---~Gg~pE~NPF~ 146 (215)
-++...+..|+++|+- +|.-+ .|||.
T Consensus 135 ~t~~~~~~~l~~~~~~a~~~g~i~-~nP~~ 163 (357)
T cd00801 135 ETARRVRQRLKQVFRYAIARGLIE-ANPAA 163 (357)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCcc-cCchH
Confidence 4788999999999984 45433 89985
No 19
>PF13276 HTH_21: HTH-like domain
Probab=41.33 E-value=46 Score=22.35 Aligned_cols=29 Identities=24% Similarity=0.430 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHhCCCCCCCccchhHHHHHHHH
Q 028022 123 DALIGRLRAAYEENGGRPESNPFGARAVRIYLRE 156 (215)
Q Consensus 123 DALIGRLRAAfEE~Gg~pE~NPF~araVRlYLRe 156 (215)
|+|+-.++++|+++.. =||.+-|..+|+.
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 20
>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=40.44 E-value=6 Score=27.03 Aligned_cols=75 Identities=15% Similarity=0.214 Sum_probs=45.5
Q ss_pred hhhhHHHHHHHHHhcCC--CcccccccchhHhHHhhhhcccC--ceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHH
Q 028022 51 KRRDWNTFLQYLKNHKP--PLTLARCSGAHVIEFLKYLDQFG--KTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALI 126 (215)
Q Consensus 51 KRRdWntF~qyL~n~rP--PlsL~~Csg~hVleFLrylDqfG--KTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALI 126 (215)
++.||..|.+.+.+..- +.....+...+|.+.+.++-+.| -.++ .|.- -.||-.=|=.--...|.++
T Consensus 6 ~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~Ga~~~~~-------sGsG--~G~~v~~l~~~~~~~~~v~ 76 (85)
T PF08544_consen 6 AEGDLELLGELMNENQENEPENYREVLTPEIDELKEAAEENGALGAKM-------SGSG--GGPTVFALCKDEDDAERVA 76 (85)
T ss_dssp HTTCHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHTTESEEEE-------ETTS--SSSEEEEEESSHHHHHHHH
T ss_pred HCcCHHHHHHHHHHhhhhcchHHHHHcCHHHHHHHHHHHHCCCCceec-------CCCC--CCCeEEEEECCHHHHHHHH
Confidence 56899999999995544 55556677888888888888888 2222 1110 0222222222234566677
Q ss_pred HHHHHHHH
Q 028022 127 GRLRAAYE 134 (215)
Q Consensus 127 GRLRAAfE 134 (215)
-+|++.|+
T Consensus 77 ~~l~~~~~ 84 (85)
T PF08544_consen 77 EALREHYK 84 (85)
T ss_dssp HHHHHHTH
T ss_pred HHHHHhCC
Confidence 77776664
No 21
>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=40.01 E-value=4.9 Score=31.35 Aligned_cols=18 Identities=61% Similarity=0.959 Sum_probs=14.2
Q ss_pred CCCCccc---hhHHHHHHHHH
Q 028022 140 PESNPFG---ARAVRIYLREV 157 (215)
Q Consensus 140 pE~NPF~---araVRlYLReV 157 (215)
..+|||+ ||-+|+||||=
T Consensus 4 ~k~NPfr~aiARKaRiyLr~G 24 (82)
T PF05528_consen 4 SKDNPFRGAIARKARIYLREG 24 (82)
T ss_pred cccCchhhhhhhheeeeeecC
Confidence 3489996 68899999863
No 22
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=39.38 E-value=22 Score=27.32 Aligned_cols=23 Identities=30% Similarity=0.564 Sum_probs=16.5
Q ss_pred chhhhcc--------hhHHHHHHHHHHHHHh
Q 028022 114 PLKQAWG--------SLDALIGRLRAAYEEN 136 (215)
Q Consensus 114 PlRQAWG--------SLDALIGRLRAAfEE~ 136 (215)
-+++.|| +||.+|.|||.-+++.
T Consensus 174 l~~~~w~~~~~~~~~~v~~~i~rLR~kl~~~ 204 (223)
T PRK10816 174 LMLQLYPDAELRESHTIDVLMGRLRKKIQAQ 204 (223)
T ss_pred HHHHhcCCCCCCCcCCHHHHHHHHHHHhccC
Confidence 3456666 6888888888888654
No 23
>PF06252 DUF1018: Protein of unknown function (DUF1018); InterPro: IPR009363 This family consists of several bacterial and phage proteins, related to Gp16 of phage Mu, of unknown function.
Probab=38.24 E-value=1.6e+02 Score=22.53 Aligned_cols=87 Identities=16% Similarity=0.206 Sum_probs=56.3
Q ss_pred hHHHHHHHHHhcCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 028022 54 DWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRAAY 133 (215)
Q Consensus 54 dWntF~qyL~n~rPPlsL~~Csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAAf 133 (215)
|-.++.++|.++.-=-+...|+-....++|.++.+.|-. +....=.+-. .|.. ...+.+.+|+|..
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 456778888888887788889999999999988888852 1111111111 1111 1778999999999
Q ss_pred HHhCCCCC-CCccchhHHHHHHH
Q 028022 134 EENGGRPE-SNPFGARAVRIYLR 155 (215)
Q Consensus 134 EE~Gg~pE-~NPF~araVRlYLR 155 (215)
.++|.... .|| ...++.-|++
T Consensus 68 ~~~~~~~~v~~~-s~~aL~~fvk 89 (119)
T PF06252_consen 68 KQLGKPGAVRDP-SEAALDAFVK 89 (119)
T ss_pred HHhhccCCccch-HHHHHHHHHH
Confidence 99997655 333 2334444443
No 24
>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=37.90 E-value=33 Score=22.95 Aligned_cols=21 Identities=52% Similarity=0.841 Sum_probs=18.0
Q ss_pred chhHHHHHHHHHHHHHhCCCC
Q 028022 120 GSLDALIGRLRAAYEENGGRP 140 (215)
Q Consensus 120 GSLDALIGRLRAAfEE~Gg~p 140 (215)
-+||.+|-|||..++..|..+
T Consensus 44 ~~l~~~I~rLR~kL~~~~~~~ 64 (77)
T PF00486_consen 44 NSLDVHISRLRKKLEDAGGDP 64 (77)
T ss_dssp HHHHHHHHHHHHHHHSSTTSS
T ss_pred hhHHHHHHHHHHHHhhcCCCC
Confidence 489999999999999987543
No 25
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=37.58 E-value=17 Score=22.58 Aligned_cols=16 Identities=38% Similarity=1.134 Sum_probs=13.5
Q ss_pred cCCCCCCCCCCCCCCC
Q 028022 97 SGCPYFGHPNPPAPCA 112 (215)
Q Consensus 97 ~~C~ffG~p~ppapC~ 112 (215)
.+|.|||.+..-..|.
T Consensus 7 ~~CgF~G~~~t~~~Cs 22 (26)
T smart00259 7 PGCGFFGNPATEGLCS 22 (26)
T ss_pred CCCCCcCChhhcccCH
Confidence 6999999998777774
No 26
>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=36.16 E-value=1.1e+02 Score=25.14 Aligned_cols=35 Identities=23% Similarity=0.532 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHhCCCC---CCCc----cchhHHHHHHHHHHH
Q 028022 124 ALIGRLRAAYEENGGRP---ESNP----FGARAVRIYLREVRE 159 (215)
Q Consensus 124 ALIGRLRAAfEE~Gg~p---E~NP----F~araVRlYLReVRd 159 (215)
.-|.+||..|+. |..+ +.+. -.+..++.||||..|
T Consensus 47 ~~i~~l~~~~d~-g~~~~~~~~~~~d~~~va~lLK~fLReLPe 88 (188)
T cd04383 47 VEVNDIKNAFER-GEDPLADDQNDHDINSVAGVLKLYFRGLEN 88 (188)
T ss_pred HHHHHHHHHHhc-CCCccccccccccHHHHHHHHHHHHHhCCC
Confidence 478999999986 3332 1122 258899999999754
No 27
>cd01187 INT_SG4 INT_SG4, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 4, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases for which not much biochemical characterization is available.
Probab=35.65 E-value=1.5e+02 Score=24.31 Aligned_cols=30 Identities=13% Similarity=0.228 Sum_probs=22.5
Q ss_pred hhHHHHHHHHHhcCCCcccccccchhHhHHhhhh
Q 028022 53 RDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYL 86 (215)
Q Consensus 53 RdWntF~qyL~n~rPPlsL~~Csg~hVleFLryl 86 (215)
+.-+.|.+||.++. +...+..||.+|+.++
T Consensus 24 ~~~~~f~~~~~~~~----~~~it~~~~~~~~~~~ 53 (299)
T cd01187 24 RLLRDFVRFLERHG----AGFITTDLALRWAASP 53 (299)
T ss_pred HHHHHHHHHHHhCC----CCCCCHHHHHHHHhcC
Confidence 44567888998754 5677889999988754
No 28
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=35.59 E-value=27 Score=22.46 Aligned_cols=12 Identities=33% Similarity=0.852 Sum_probs=10.1
Q ss_pred hHHHHHHHHHHH
Q 028022 148 RAVRIYLREVRE 159 (215)
Q Consensus 148 raVRlYLReVRd 159 (215)
-+|++||++|+.
T Consensus 2 D~l~~Yl~ei~~ 13 (37)
T PF00140_consen 2 DSLRLYLKEIGR 13 (37)
T ss_dssp HHHHHHHHHHHH
T ss_pred cHHHHHHHHHcC
Confidence 479999999974
No 29
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed
Probab=34.87 E-value=82 Score=26.84 Aligned_cols=68 Identities=16% Similarity=0.275 Sum_probs=43.7
Q ss_pred hhhHHHHHHHHHhcCC-----Cc-----ccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcch
Q 028022 52 RRDWNTFLQYLKNHKP-----PL-----TLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGS 121 (215)
Q Consensus 52 RRdWntF~qyL~n~rP-----Pl-----sL~~Csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGS 121 (215)
+++...|.+||..+.. +. .|...+..||.+|+.|+.+.-.. + ++.. +...+..+
T Consensus 42 ~~~l~~f~~~l~~~~~~~~~~~~~~~~~~l~~lt~~~i~~f~~~l~~~~~~------~---~~~~-------~~~~s~~T 105 (357)
T PRK05084 42 LTEYRRFFNWLISEGLSDASKIKDIPLSTLENLTKKDVEAFILYLRERPLL------N---GHST-------KKGNSQTT 105 (357)
T ss_pred HHHHHHHHHHHHHcCCCCcCCcccCCHHHHHhhhHHHHHHHHHHHHhcccc------c---cccc-------ccchhHHH
Confidence 4567788888876542 11 24567899999999998542100 0 0000 01246678
Q ss_pred hHHHHHHHHHHHHH
Q 028022 122 LDALIGRLRAAYEE 135 (215)
Q Consensus 122 LDALIGRLRAAfEE 135 (215)
+...+.-||+.|.-
T Consensus 106 i~~~l~~l~~~~~~ 119 (357)
T PRK05084 106 INRTLSALKSLFKY 119 (357)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999999984
No 30
>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=34.16 E-value=34 Score=24.37 Aligned_cols=31 Identities=26% Similarity=0.483 Sum_probs=24.8
Q ss_pred HHHHHHHHHhcCCCcccccccchhHhHHhhhhcccC
Q 028022 55 WNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFG 90 (215)
Q Consensus 55 WntF~qyL~n~rPPlsL~~Csg~hVleFLrylDqfG 90 (215)
-+.|.+=|++.+| +.+.+||..|..|-.+||
T Consensus 32 ~~DF~~Al~~~kp-----SVs~~dl~~ye~w~~~FG 62 (62)
T PF09336_consen 32 MEDFEEALKKVKP-----SVSQEDLKKYEEWTKEFG 62 (62)
T ss_dssp HHHHHHHHHTCGG-----SS-HHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHHcCC-----CCCHHHHHHHHHHHHHcC
Confidence 4567777888888 456889999999999998
No 31
>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=32.88 E-value=46 Score=22.14 Aligned_cols=51 Identities=25% Similarity=0.309 Sum_probs=33.7
Q ss_pred HHHHHHhcCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHHHHhC
Q 028022 58 FLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRAAYEENG 137 (215)
Q Consensus 58 F~qyL~n~rPPlsL~~Csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAAfEE~G 137 (215)
+..||-.+..- .++-.++++.| |-+.+ ...+-.+|+.+|-|||..+++.|
T Consensus 13 lL~~L~~~~~~----~vs~~~l~~~l-w~~~~-------------------------~~~~~~~l~~~i~~LR~~l~~~~ 62 (78)
T smart00862 13 LLELLLRNPGR----VVSREELLEAV-WGDDD-------------------------DDVDDNTLDVHISRLRKKLEDDG 62 (78)
T ss_pred HHHHHHhCCCC----ccCHHHHHHHH-cCCCC-------------------------CCCccchHHHHHHHHHHHHhcCC
Confidence 66777766542 25667788866 53322 00112579999999999999876
Q ss_pred C
Q 028022 138 G 138 (215)
Q Consensus 138 g 138 (215)
.
T Consensus 63 ~ 63 (78)
T smart00862 63 A 63 (78)
T ss_pred C
Confidence 5
No 32
>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=32.54 E-value=20 Score=28.81 Aligned_cols=37 Identities=24% Similarity=0.353 Sum_probs=29.9
Q ss_pred hhhHHHHHHHHHh---cCCCcccccccchhHhHHhhhhcc
Q 028022 52 RRDWNTFLQYLKN---HKPPLTLARCSGAHVIEFLKYLDQ 88 (215)
Q Consensus 52 RRdWntF~qyL~n---~rPPlsL~~Csg~hVleFLrylDq 88 (215)
.-.|..|++|+-. ..-|-.+.++.+.++.+||.-+|.
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 3468888888876 455777889999999999998875
No 33
>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=32.14 E-value=56 Score=29.66 Aligned_cols=64 Identities=23% Similarity=0.264 Sum_probs=45.4
Q ss_pred CCchhhHhhhhhHHHHHHHHHhcCCCccc--ccccchhHhHHhhh-----------------hcccCceeeeecCCCCCC
Q 028022 43 PPSRYESQKRRDWNTFLQYLKNHKPPLTL--ARCSGAHVIEFLKY-----------------LDQFGKTKVHISGCPYFG 103 (215)
Q Consensus 43 ~~srYesQKRRdWntF~qyL~n~rPPlsL--~~Csg~hVleFLry-----------------lDqfGKTkVH~~~C~ffG 103 (215)
.-.+|-++=|..-.+|.+||+.+.|-... ..--...|.|||.. ....|..++|-.+=-.|.
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 44678888899999999999999886621 22345678899975 334667777776666665
Q ss_pred CCC
Q 028022 104 HPN 106 (215)
Q Consensus 104 ~p~ 106 (215)
+++
T Consensus 227 ~~g 229 (312)
T PF11709_consen 227 RTG 229 (312)
T ss_pred CCc
Confidence 544
No 34
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=31.72 E-value=32 Score=26.43 Aligned_cols=14 Identities=43% Similarity=0.999 Sum_probs=13.1
Q ss_pred hHHHHHHHHHhcCC
Q 028022 54 DWNTFLQYLKNHKP 67 (215)
Q Consensus 54 dWntF~qyL~n~rP 67 (215)
-|.||.+||..|.|
T Consensus 55 GW~tL~~fL~khDP 68 (73)
T smart00243 55 GWETLDEYLLKHDP 68 (73)
T ss_pred cHHHHHHHHHhCCC
Confidence 49999999999999
No 35
>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=30.25 E-value=55 Score=27.16 Aligned_cols=45 Identities=20% Similarity=0.176 Sum_probs=34.4
Q ss_pred chhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcc
Q 028022 76 GAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWG 120 (215)
Q Consensus 76 g~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWG 120 (215)
..+|.+||..|.-.+.+.|.+....-.....++.|++|.++++--
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 467888999988888888877666544556678888999988753
No 36
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=30.13 E-value=47 Score=24.55 Aligned_cols=35 Identities=31% Similarity=0.504 Sum_probs=29.9
Q ss_pred CCCCchhhhcc----hhHHHHHHHHHHHHHhCCCCCCCc
Q 028022 110 PCACPLKQAWG----SLDALIGRLRAAYEENGGRPESNP 144 (215)
Q Consensus 110 pC~CPlRQAWG----SLDALIGRLRAAfEE~Gg~pE~NP 144 (215)
-|+|=||.--+ +||.|=-+|..+++||--+...+|
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 37777888888 999999999999999987766666
No 37
>KOG4670 consensus Uncharacterized conserved membrane protein [Function unknown]
Probab=30.07 E-value=21 Score=36.02 Aligned_cols=59 Identities=25% Similarity=0.375 Sum_probs=41.8
Q ss_pred hhhhhHHH------------HHHHHHhcCCCcccccccchhHhHHhhhhcccCcee-----ee-ecCCCCCCCCCCC
Q 028022 50 QKRRDWNT------------FLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTK-----VH-ISGCPYFGHPNPP 108 (215)
Q Consensus 50 QKRRdWnt------------F~qyL~n~rPPlsL~~Csg~hVleFLrylDqfGKTk-----VH-~~~C~ffG~p~pp 108 (215)
-|+|.|++ ||-||..|.+|..+--=.-.---.|++-+++.-++. || ...|.+-...+||
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 67888874 999999999998776422222345677888886654 55 4668887777764
No 38
>TIGR02249 integrase_gron integron integrase. Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family (pfam00589) that also includes recombinases XerC (TIGR02224) and XerD (TIGR02225), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961.
Probab=28.34 E-value=1.3e+02 Score=24.98 Aligned_cols=33 Identities=15% Similarity=0.164 Sum_probs=24.5
Q ss_pred hhhHHHHHHHHHhcCCCcccccccchhHhHHhhhhcc
Q 028022 52 RRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQ 88 (215)
Q Consensus 52 RRdWntF~qyL~n~rPPlsL~~Csg~hVleFLrylDq 88 (215)
+..++.|.+|+.+ +.+..-+..||.+||.++-+
T Consensus 23 ~~~~~~~~~~~g~----~~~~~it~~~i~~~l~~l~~ 55 (315)
T TIGR02249 23 LHWIKRFIRFHNK----RHPSTMGDTEVEAFLSDLAV 55 (315)
T ss_pred HHHHHHHHHHhCC----CChHhcCHHHHHHHHHHHHh
Confidence 4578888888642 34555689999999999854
No 39
>PF13099 DUF3944: Domain of unknown function (DUF3944)
Probab=28.06 E-value=31 Score=23.17 Aligned_cols=22 Identities=32% Similarity=0.631 Sum_probs=15.8
Q ss_pred ccccchhHhHHhhhh--cccCcee
Q 028022 72 ARCSGAHVIEFLKYL--DQFGKTK 93 (215)
Q Consensus 72 ~~Csg~hVleFLryl--DqfGKTk 93 (215)
..|+..|+-++..+| |..|+++
T Consensus 11 ~~cs~edL~~L~~~Lt~dkdG~~R 34 (35)
T PF13099_consen 11 AECSNEDLKDLVDILTHDKDGKKR 34 (35)
T ss_pred HHCCHHHHHHHHHHHhcCCCCCcC
Confidence 459998877765554 7888765
No 40
>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=27.92 E-value=61 Score=31.65 Aligned_cols=36 Identities=28% Similarity=0.474 Sum_probs=28.1
Q ss_pred hhHHHHHHHHHHHHHhCCC---------------------CCCCcc-chhHHHHHHHH
Q 028022 121 SLDALIGRLRAAYEENGGR---------------------PESNPF-GARAVRIYLRE 156 (215)
Q Consensus 121 SLDALIGRLRAAfEE~Gg~---------------------pE~NPF-~araVRlYLRe 156 (215)
+.|...-..|.+.+.++++ .|.||| |-|+||+||..
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 4467777788888888766 379997 77999999964
No 41
>PF12067 Sox_C_TAD: Sox C-terminal transactivation domain; InterPro: IPR021934 The Sox family of high mobility group (HMG) box transcription factors that are homologous to the Y-chromosome encoded sex- determining factor SRY plays important roles in embryonic development. Sox18, together with Sox7 and -17, constitutes the subgroup F within this family. Bioinformatic analysis of the C-termini of subgroup F Sox family members from different species including humans, mice, rat, chicken and Xenopus revealed three conserved blocks including highly conserved residues. They were termed proline, charged, and serine according to the predominance of the respective amino acids. The charged block comprises a strong transactivating domain []. This entry covers the entire Sox C-terminal domain, and was previously annotated as DUF3547.
Probab=27.59 E-value=33 Score=29.98 Aligned_cols=15 Identities=33% Similarity=0.448 Sum_probs=11.6
Q ss_pred hhHHHHHHHHHhcCC
Q 028022 53 RDWNTFLQYLKNHKP 67 (215)
Q Consensus 53 RdWntF~qyL~n~rP 67 (215)
=|.|+|.|||...+.
T Consensus 141 VDR~EFdQYLn~~~~ 155 (197)
T PF12067_consen 141 VDRTEFDQYLNSSRC 155 (197)
T ss_pred hhHHHHHHHhccccC
Confidence 468999999996444
No 42
>KOG4405 consensus GDP dissociation inhibitor [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.56 E-value=29 Score=34.72 Aligned_cols=85 Identities=29% Similarity=0.467 Sum_probs=62.8
Q ss_pred hhhhhHHHHHHHHHhcCCCcccccc--------cch---------hHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCC
Q 028022 50 QKRRDWNTFLQYLKNHKPPLTLARC--------SGA---------HVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCA 112 (215)
Q Consensus 50 QKRRdWntF~qyL~n~rPPlsL~~C--------sg~---------hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~ 112 (215)
++-|+. +|.+||+.++=+..|.+| +.. -...||..+.+||.|-. -=|.||+-..| .|-
T Consensus 218 ~~~~e~-~F~EyL~~~rltp~lqs~vl~aIaM~~~~~~tt~eGm~at~~fl~slGrfgntpf---LfPlYGqGELp-QcF 292 (547)
T KOG4405|consen 218 VEFRER-PFSEYLKTMRLTPKLQSIVLHAIAMLSESQLTTIEGMDATKNFLTSLGRFGNTPF---LFPLYGQGELP-QCF 292 (547)
T ss_pred HHhhcC-cHHHHHHhcCCChhhHHHHHHHHHhcCcccccHHHHHHHHHHHHHHhhccCCCcc---eeeccCCCcch-HHH
Confidence 333433 999999999988877654 221 24579999999999983 34678887755 688
Q ss_pred Cchhhhcch------------hHHHHHHHHHHHHHhCCC
Q 028022 113 CPLKQAWGS------------LDALIGRLRAAYEENGGR 139 (215)
Q Consensus 113 CPlRQAWGS------------LDALIGRLRAAfEE~Gg~ 139 (215)
|-+--..|+ ||.++++..++.+.+|-+
T Consensus 293 CRlcAVfGgIYcLr~~Vq~ivldk~s~~~~~~l~s~g~r 331 (547)
T KOG4405|consen 293 CRLCAVFGGIYCLRRPVQAIVLDKESLDCKAILDSFGQR 331 (547)
T ss_pred HHHHHHhcceEEeccchhheeecccccchhhhHhhhcch
Confidence 877777775 577788888999999965
No 43
>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=27.39 E-value=26 Score=24.32 Aligned_cols=20 Identities=40% Similarity=0.529 Sum_probs=17.0
Q ss_pred ccchhHhHHhhhhcccCcee
Q 028022 74 CSGAHVIEFLKYLDQFGKTK 93 (215)
Q Consensus 74 Csg~hVleFLrylDqfGKTk 93 (215)
.|=+-++-+|.|+|+.|-|+
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 56678999999999999987
No 44
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=26.60 E-value=1.5e+02 Score=19.90 Aligned_cols=36 Identities=22% Similarity=0.282 Sum_probs=26.4
Q ss_pred hhhhcchhHHHHHHHHHHHHHhCC-CCCCCccchhHHHHHHH
Q 028022 115 LKQAWGSLDALIGRLRAAYEENGG-RPESNPFGARAVRIYLR 155 (215)
Q Consensus 115 lRQAWGSLDALIGRLRAAfEE~Gg-~pE~NPF~araVRlYLR 155 (215)
++|.-.||+..+-|++......+. -+| .-.|..|++
T Consensus 56 l~Q~~esv~~y~~rf~~l~~~~~~~~~e-----~~~v~~f~~ 92 (96)
T PF03732_consen 56 LRQGNESVREYVNRFRELARRAPPPMDE-----EMLVERFIR 92 (96)
T ss_pred hhccCCcHHHHHHHHHHHHHHCCCCcCH-----HHHHHHHHH
Confidence 777677999999999999998885 222 445555554
No 45
>cd07288 PX_SNX15 The phosphoinositide binding Phox Homology domain of Sorting Nexin 15. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX15 contains an N-terminal PX domain and a C-terminal Microtubule Interacting and Trafficking (MIT) domain. It plays a role in protein trafficking processes in the endocytic pathway and the trans-Golgi network. The PX domain of SNX15 interacts with the PDGF receptor and is responsible for the membrane association of t
Probab=26.13 E-value=75 Score=24.98 Aligned_cols=33 Identities=21% Similarity=0.367 Sum_probs=26.6
Q ss_pred hhHhhhhhHHHHHHHHHhcCCCcccccccchhHhHHhh
Q 028022 47 YESQKRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLK 84 (215)
Q Consensus 47 YesQKRRdWntF~qyL~n~rPPlsL~~Csg~hVleFLr 84 (215)
.-.+.|+--+.|.+.|.|| | .-|...++.+||.
T Consensus 84 fIeeRR~~Le~fL~~i~~~-p----~l~~s~~~~~FL~ 116 (118)
T cd07288 84 VIEERRNAAEAMLLFTVNI-P----ALYNSPQLKEFFR 116 (118)
T ss_pred HHHHHHHHHHHHHHHHhCC-h----hhcCChHHHHHHh
Confidence 5577888899999999888 3 3367789999995
No 46
>cd04385 RhoGAP_ARAP RhoGAP_ARAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in ARAPs. ARAPs (also known as centaurin deltas) contain, besides the RhoGAP domain, an Arf GAP, ankyrin repeat ras-associating, and PH domains. Since their ArfGAP activity is PIP3-dependent, ARAPs are considered integration points for phosphoinositide, Arf and Rho signaling. 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=25.94 E-value=1e+02 Score=25.18 Aligned_cols=39 Identities=18% Similarity=0.354 Sum_probs=26.0
Q ss_pred chhHHHHHHHHHHHHHhCC--C---CCCCcc-chhHHHHHHHHHHH
Q 028022 120 GSLDALIGRLRAAYEENGG--R---PESNPF-GARAVRIYLREVRE 159 (215)
Q Consensus 120 GSLDALIGRLRAAfEE~Gg--~---pE~NPF-~araVRlYLReVRd 159 (215)
|+. .-|.+|+..|+.... . .+.+|. .+..++.||||.-+
T Consensus 41 g~~-~~i~~L~~~~~~~~~~~~~~~~~~d~~~va~llK~yLreLP~ 85 (184)
T cd04385 41 GKN-SSVKKLLEAFRKDARSVQLREGEYTVHDVADVLKRFLRDLPD 85 (184)
T ss_pred CcH-HHHHHHHHHHhcCCCcCCCCcccCCHHHHHHHHHHHHHhCCC
Confidence 444 457889999976431 1 124555 78899999998654
No 47
>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=25.52 E-value=77 Score=26.06 Aligned_cols=36 Identities=17% Similarity=0.460 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHhCCCCC---C---Cc-cchhHHHHHHHHHHH
Q 028022 124 ALIGRLRAAYEENGGRPE---S---NP-FGARAVRIYLREVRE 159 (215)
Q Consensus 124 ALIGRLRAAfEE~Gg~pE---~---NP-F~araVRlYLReVRd 159 (215)
.-|-+|+..|++.|...+ . ++ -.+..++.||||.-+
T Consensus 45 ~~i~~l~~~~d~~~~~~~~~~~~~~d~h~va~lLK~flReLP~ 87 (194)
T cd04372 45 EEIEDVKMAFDRDGEKADISATVYPDINVITGALKLYFRDLPI 87 (194)
T ss_pred HHHHHHHHHHcCCCCccCCcccccccHHHHHHHHHHHHHhCCC
Confidence 478889999998775332 1 22 267888999999754
No 48
>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=25.45 E-value=73 Score=30.37 Aligned_cols=53 Identities=34% Similarity=0.493 Sum_probs=35.1
Q ss_pred hhHhHHhhhhcccC-ceeeeecCCCCCCCCCCCCCCCCchhhhcchh--HH----HHHHHHHHHHHhCCCCC
Q 028022 77 AHVIEFLKYLDQFG-KTKVHISGCPYFGHPNPPAPCACPLKQAWGSL--DA----LIGRLRAAYEENGGRPE 141 (215)
Q Consensus 77 ~hVleFLrylDqfG-KTkVH~~~C~ffG~p~ppapC~CPlRQAWGSL--DA----LIGRLRAAfEE~Gg~pE 141 (215)
..=++||..|.+.| |-+|+. .-.|-.+.++ |..+ |. .--||..+|+++|-.|.
T Consensus 49 ~agl~f~e~l~~~gakv~VpT----------TlNp~~~D~~--w~~~gvd~~f~~~q~~i~~ay~~mG~~~t 108 (389)
T cd01355 49 DAGLEFLERLADQGAKVAVPT----------TLNPISMDLH--WRELGVDEEFAEKQARLVKAYKAMGVDPT 108 (389)
T ss_pred hhhHHHHHHHHhCCCeEeecC----------ccCCcccCcc--hhhcCCCHHHHHHHHHHHHHHHHcCCccc
Confidence 34479999886666 344433 3456667777 8755 22 34467899999998765
No 49
>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]
Probab=25.07 E-value=3.7e+02 Score=26.87 Aligned_cols=45 Identities=22% Similarity=0.355 Sum_probs=36.2
Q ss_pred cCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHHHHhCCCCCCC
Q 028022 97 SGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRAAYEENGGRPESN 143 (215)
Q Consensus 97 ~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAAfEE~Gg~pE~N 143 (215)
-.|.+++.+. ..|+|--+|--=-++-|.|=|+--++..+--|.-|
T Consensus 336 cpcG~~~~~~--~~C~c~~~~~~~Y~~klSgp~lDRiDl~vev~~~~ 380 (490)
T COG0606 336 CPCGNLGAPL--RRCPCSPRQIKRYLNKLSGPFLDRIDLMVEVPRLS 380 (490)
T ss_pred CCccCCCCCC--CCcCCCHHHHHHHHHHhhHHHHhhhhheecccCCC
Confidence 4688887654 67999999998889999999999888888665544
No 50
>PRK09279 pyruvate phosphate dikinase; Provisional
Probab=24.97 E-value=69 Score=33.43 Aligned_cols=36 Identities=36% Similarity=0.453 Sum_probs=0.0
Q ss_pred HHHHHHHhCCC-----------CCCCcc-chhHHHHHH--HHHHHHHHhh
Q 028022 129 LRAAYEENGGR-----------PESNPF-GARAVRIYL--REVRESQAKA 164 (215)
Q Consensus 129 LRAAfEE~Gg~-----------pE~NPF-~araVRlYL--ReVRd~QAKA 164 (215)
++..-++.|+. -|.||| +.|.+|+|| .|+=++|.+|
T Consensus 636 ~~~~a~~~g~~~~k~~~~~~~~~E~NPmLG~RG~Rl~l~~pei~~~QlrA 685 (879)
T PRK09279 636 IEELAEALGLSLEELKARVEALHEFNPMLGHRGCRLGITYPEIYEMQARA 685 (879)
T ss_pred HHHHHHHcCCCHHHHHHHhcCCCCCCCccccchhhcccCChHHHHHHHHH
No 51
>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=23.82 E-value=38 Score=29.09 Aligned_cols=24 Identities=33% Similarity=0.749 Sum_probs=21.8
Q ss_pred hcchhHH-HHHHHHHHHHHhCCCCC
Q 028022 118 AWGSLDA-LIGRLRAAYEENGGRPE 141 (215)
Q Consensus 118 AWGSLDA-LIGRLRAAfEE~Gg~pE 141 (215)
-|||+|- |||+.-..|.||-.+|-
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 99999999999999875
No 52
>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=23.68 E-value=5.7e+02 Score=23.36 Aligned_cols=25 Identities=24% Similarity=0.335 Sum_probs=20.8
Q ss_pred hhHhhhhhHHHHHHHHHhcCCCccc
Q 028022 47 YESQKRRDWNTFLQYLKNHKPPLTL 71 (215)
Q Consensus 47 YesQKRRdWntF~qyL~n~rPPlsL 71 (215)
..++.|+.|+.|.++.+.+.+|++.
T Consensus 166 ~~n~~r~~~~~~~~l~~~~p~pitg 190 (377)
T TIGR03190 166 VCDENRRLLRELFDYRKEADPKVTG 190 (377)
T ss_pred HHHHHHHHHHHHHHHHccCCCCcCH
Confidence 4567899999999999888888873
No 53
>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=23.52 E-value=68 Score=24.97 Aligned_cols=41 Identities=22% Similarity=0.439 Sum_probs=32.0
Q ss_pred HHHHHHHHhcCCCcccccc--cchhHh--HHhhhhcccCceeeee
Q 028022 56 NTFLQYLKNHKPPLTLARC--SGAHVI--EFLKYLDQFGKTKVHI 96 (215)
Q Consensus 56 ntF~qyL~n~rPPlsL~~C--sg~hVl--eFLrylDqfGKTkVH~ 96 (215)
.++++||..++|=.++..+ -|.|++ .|||+.+..|.|-++-
T Consensus 33 ~~Iv~~L~~n~~~~s~~~aE~fGQdLv~~gfir~~g~vG~~F~nS 77 (84)
T cd04436 33 SEIVSWLQENMPEKDLDAAEAFGQDLLNQGFLRLVGGVGSTFVNS 77 (84)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHhCchHHHhcccCcceecC
Confidence 5789999999987777664 367775 4999999999887653
No 54
>PTZ00398 phosphoenolpyruvate carboxylase; Provisional
Probab=23.43 E-value=1.3e+02 Score=31.77 Aligned_cols=42 Identities=19% Similarity=0.365 Sum_probs=31.6
Q ss_pred cchhHHHHHHHHHHHHHhCC------------------CCCCCccch-------------hHHHHHHHHHHHH
Q 028022 119 WGSLDALIGRLRAAYEENGG------------------RPESNPFGA-------------RAVRIYLREVRES 160 (215)
Q Consensus 119 WGSLDALIGRLRAAfEE~Gg------------------~pE~NPF~a-------------raVRlYLReVRd~ 160 (215)
|-.+=.|..+|+.+++++|+ +=++|||.. .++++|+++|++.
T Consensus 264 ~~aiP~~~~~l~~al~~~~~~~~~~~~~~i~fGSWiGGDRDGNP~VTaevT~~~l~~~r~~al~~Y~~~l~~L 336 (974)
T PTZ00398 264 FDALPNFIRYIDNVLYEYNLDPLPPTKKLFTFSSWVGGDRDGNPFVTAEVTRQVVYFNRIRACELFIHMIEKL 336 (974)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCCCCceeccCCCCCCCCCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55566788899999988754 234999974 4778999998865
No 55
>cd04396 RhoGAP_fSAC7_BAG7 RhoGAP_fSAC7_BAG7: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal SAC7 and BAG7-like proteins. Both proteins are GTPase activating proteins of Rho1, but differ functionally in vivo: SAC7, but not BAG7, is involved in the control of Rho1-mediated activation of the PKC-MPK1 pathway. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=23.40 E-value=3e+02 Score=23.43 Aligned_cols=37 Identities=19% Similarity=0.289 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHhC---CCCCCCcc----chhHHHHHHHHHHH
Q 028022 123 DALIGRLRAAYEENG---GRPESNPF----GARAVRIYLREVRE 159 (215)
Q Consensus 123 DALIGRLRAAfEE~G---g~pE~NPF----~araVRlYLReVRd 159 (215)
-.-|.+|+..|++.. ...+-+.+ .+..++.|||+.-+
T Consensus 60 ~~~i~~L~~~~d~~~~~~~~~~~~~~~vh~va~lLK~fLReLPe 103 (225)
T cd04396 60 SKRIRELQLIFSTPPDYGKSFDWDGYTVHDAASVLRRYLNNLPE 103 (225)
T ss_pred HHHHHHHHHHHccCcccCCcCCccCCCHHHHHHHHHHHHHhCCC
Confidence 357889999998753 22222333 68899999998754
No 56
>PLN02837 threonine-tRNA ligase
Probab=23.32 E-value=38 Score=33.04 Aligned_cols=16 Identities=31% Similarity=0.524 Sum_probs=12.0
Q ss_pred hhhcchhHHHHHHHHH
Q 028022 116 KQAWGSLDALIGRLRA 131 (215)
Q Consensus 116 RQAWGSLDALIGRLRA 131 (215)
|-.|||+|.|||-|-.
T Consensus 489 ~~~~G~~eRlia~Lie 504 (614)
T PLN02837 489 RAILGSLERFFGVLIE 504 (614)
T ss_pred cCCccCHHHHHHHHHH
Confidence 5679999998876543
No 57
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=23.09 E-value=1.9e+02 Score=22.00 Aligned_cols=38 Identities=32% Similarity=0.497 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHhCCCCCCCccchhHHHHHHHHHHHHHHhhhCCchhh
Q 028022 124 ALIGRLRAAYEENGGRPESNPFGARAVRIYLREVRESQAKARGIPYEK 171 (215)
Q Consensus 124 ALIGRLRAAfEE~Gg~pE~NPF~araVRlYLReVRd~QAKARgi~y~k 171 (215)
.|--+.-++|+++|-.+ ..|||+||+.| ++-+|||++.
T Consensus 11 ~lK~~A~~vl~~lGls~------S~Ai~~fl~qi----~~~~~iPF~~ 48 (80)
T PRK11235 11 ELKARAYAVLEKLGVTP------SEALRLLLQYV----AENGRLPFKT 48 (80)
T ss_pred HHHHHHHHHHHHhCCCH------HHHHHHHHHHH----HHhCCCCCCC
Confidence 44556678899999875 57899999876 4457888773
No 58
>smart00353 HLH helix loop helix domain.
Probab=22.97 E-value=1.1e+02 Score=19.60 Aligned_cols=24 Identities=29% Similarity=0.430 Sum_probs=20.6
Q ss_pred hhHhhhhhHHHHHHHHHhcCCCcc
Q 028022 47 YESQKRRDWNTFLQYLKNHKPPLT 70 (215)
Q Consensus 47 YesQKRRdWntF~qyL~n~rPPls 70 (215)
-|.+.|.++|+-.+=|+...|+..
T Consensus 3 ~Er~RR~~~n~~~~~L~~lip~~~ 26 (53)
T smart00353 3 RERRRRRKINEAFDELRSLLPTLP 26 (53)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCC
Confidence 477888999999999999999765
No 59
>cd08793 Death_IRAK4 Death domain of Interleukin-1 Receptor-Associated Kinase 4. Death Domain (DD) of Interleukin-1 Receptor-Associated Kinase 4 (IRAK4). IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. They are involved in signal transduction pathways involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB, and mitogen-activated protein kinases. IRAKs contain an N-terminal DD domain and a C-terminal kinase domain. IRAK4 is an active kinase that is also involved in T-cell receptor signaling pathways, implying that it may function in acquired immunity and not just in innate immunity. It is known as the master IRAK member because its absence strongly impairs TLR- and IL-1-mediated signaling and innate immune defenses, while the absence of other IRAK proteins only shows slight effects. IRAK4-deficient patients have impaired inflammatory responses and recurrent life-threatening infections. DDs are protein-protein int
Probab=22.78 E-value=92 Score=24.86 Aligned_cols=63 Identities=25% Similarity=0.433 Sum_probs=42.9
Q ss_pred hHHHHHHHHHhcCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 028022 54 DWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRAAY 133 (215)
Q Consensus 54 dWntF~qyL~n~rPPlsL~~Csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAAf 133 (215)
+|.++-.++.. |-.-.+.+--||-+|=++.++ | .+ .+|-|=..||+-++-||.|-..|
T Consensus 23 ~W~~LA~~i~~---~~~~~~y~~~ei~~ie~~~~~--------------g-~S----PT~~LL~dWgt~N~TV~~L~~lL 80 (100)
T cd08793 23 GWKKIAVAIKK---PSGDPRYSQFHIRRFEALVQQ--------------G-KS----PTCELLFDWGTTNCTVGDLVDLL 80 (100)
T ss_pred cHHHHHHHHhc---ccCCCCCCHHHHHHHHHHHHc--------------C-CC----hHHHHHHHHccCCCcHHHHHHHH
Confidence 78888766654 333344545567666554443 2 12 24557789999999999999999
Q ss_pred HHhCC
Q 028022 134 EENGG 138 (215)
Q Consensus 134 EE~Gg 138 (215)
.+++-
T Consensus 81 ~k~~l 85 (100)
T cd08793 81 IQNEF 85 (100)
T ss_pred HHccc
Confidence 99885
No 60
>PF09958 DUF2192: Uncharacterized protein conserved in archaea (DUF2192); InterPro: IPR018693 This family of various hypothetical archaeal proteins has no known function.
Probab=22.47 E-value=75 Score=28.77 Aligned_cols=21 Identities=43% Similarity=0.618 Sum_probs=18.4
Q ss_pred hhHHHHHHHHHHHHHhCCCCC
Q 028022 121 SLDALIGRLRAAYEENGGRPE 141 (215)
Q Consensus 121 SLDALIGRLRAAfEE~Gg~pE 141 (215)
+=+.||.-||..|+++|..|=
T Consensus 27 ~R~~lv~~L~~~Y~~~gIeP~ 47 (231)
T PF09958_consen 27 DREELVELLREVYEENGIEPF 47 (231)
T ss_pred CHHHHHHHHHHHHHHcCCCcC
Confidence 458999999999999999864
No 61
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=22.47 E-value=76 Score=21.89 Aligned_cols=19 Identities=32% Similarity=0.518 Sum_probs=16.7
Q ss_pred chhHHHHHHHHHHHHHhCC
Q 028022 120 GSLDALIGRLRAAYEENGG 138 (215)
Q Consensus 120 GSLDALIGRLRAAfEE~Gg 138 (215)
.+|+.+|=|||..+.+.|+
T Consensus 62 ~~l~~~I~rLRkkl~~~~~ 80 (95)
T cd00383 62 RTVDVHISRLRKKLEDDPS 80 (95)
T ss_pred ccHHHHHHHHHHHhccCCC
Confidence 5799999999999998765
No 62
>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=22.43 E-value=51 Score=34.07 Aligned_cols=26 Identities=38% Similarity=0.561 Sum_probs=19.8
Q ss_pred CCCCCcc-chhHHHHHH--HHHHHHHHhh
Q 028022 139 RPESNPF-GARAVRIYL--REVRESQAKA 164 (215)
Q Consensus 139 ~pE~NPF-~araVRlYL--ReVRd~QAKA 164 (215)
..|.||| +.|.||+|| .++=+.|.+|
T Consensus 651 ~~E~NP~LG~RGiRl~l~~pei~~~QlrA 679 (856)
T TIGR01828 651 LHEVNPMLGHRGCRLGITYPEIYEMQVRA 679 (856)
T ss_pred CCCCCCccccchhhhccCChHHHHHHHHH
Confidence 3599999 579999999 4555666655
No 63
>KOG2731 consensus DNA alkylation damage repair protein [RNA processing and modification]
Probab=22.41 E-value=38 Score=32.65 Aligned_cols=38 Identities=29% Similarity=0.296 Sum_probs=33.8
Q ss_pred hhhhHHHHHHHHHhcCCCcccccccchhHhHHhhhhcccC
Q 028022 51 KRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFG 90 (215)
Q Consensus 51 KRRdWntF~qyL~n~rPPlsL~~Csg~hVleFLrylDqfG 90 (215)
+--+|+.+.+||+..|-=++|.+.+..| -||| |=||--
T Consensus 327 ~~~~~Q~~~ey~ks~r~nl~Irqv~~~d-~~f~-~~~~~d 364 (378)
T KOG2731|consen 327 SLGLHQDKAEYLKSSRVNLPIRQVSIGD-AEFL-YGDQRD 364 (378)
T ss_pred ccccchhHHHHHHhhhcCceeEEeccCc-cccc-cCchhh
Confidence 3458999999999999999999999999 9999 877654
No 64
>PRK10236 hypothetical protein; Provisional
Probab=22.13 E-value=64 Score=29.26 Aligned_cols=84 Identities=20% Similarity=0.373 Sum_probs=54.4
Q ss_pred cccccchhHhHHhhhh--cccCceeeeecCCCC--------CCCCCCCCCCCCchhhhcchhHHHHHHHHHHHHHhCCCC
Q 028022 71 LARCSGAHVIEFLKYL--DQFGKTKVHISGCPY--------FGHPNPPAPCACPLKQAWGSLDALIGRLRAAYEENGGRP 140 (215)
Q Consensus 71 L~~Csg~hVleFLryl--DqfGKTkVH~~~C~f--------fG~p~ppapC~CPlRQAWGSLDALIGRLRAAfEE~Gg~p 140 (215)
|..|+..|+.++..|| |.+||++--..-|.- + .+. .++-|- .|-++|| ..|+..
T Consensus 14 L~~cs~edL~~Lv~~Lt~d~dG~~R~te~lt~~~~yk~~~~~-~~~--------~~~yw~---~Ia~elq----~fGgnt 77 (237)
T PRK10236 14 LQHCSEEQLANFARLLTHNEKGKTRLSSVLMRNELFKSMEGH-PEQ--------HRRNWQ---LIAGELQ----HFGGDS 77 (237)
T ss_pred HHhCCHHHHHHHHHHHhcCCCCCEeehhhhcccHHHHhhccc-chh--------HHHHHH---HHHHHHH----HhcchH
Confidence 3569999999998888 999999866544422 2 122 455554 4444544 578877
Q ss_pred CCCccchhHHHHHHHHHHHHHHhhhCCchhhh
Q 028022 141 ESNPFGARAVRIYLREVRESQAKARGIPYEKK 172 (215)
Q Consensus 141 E~NPF~araVRlYLReVRd~QAKARgi~y~kk 172 (215)
-.|=|..+.| .|-.-+.| =.+--+|+|.|+
T Consensus 78 ~~n~lRG~Gv-~YreIL~D-Vc~~LKV~y~~~ 107 (237)
T PRK10236 78 IANKLRGHGK-LYRAILLD-VSKRLKLKADKE 107 (237)
T ss_pred HHHHHhcCCc-cHHHHHHH-HHHHcCCCCCCC
Confidence 7788887677 56433333 345578888774
No 65
>PRK13197 pyrrolidone-carboxylate peptidase; Provisional
Probab=22.07 E-value=2.4e+02 Score=24.27 Aligned_cols=83 Identities=22% Similarity=0.317 Sum_probs=50.4
Q ss_pred CCchhhHhhhhhHHHHHHHHHhcCCCcccccccchhHhHHhh-----hhcccCc-e---eeeecCCCCCCCCCCCCCCCC
Q 028022 43 PPSRYESQKRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLK-----YLDQFGK-T---KVHISGCPYFGHPNPPAPCAC 113 (215)
Q Consensus 43 ~~srYesQKRRdWntF~qyL~n~rPPlsL~~Csg~hVleFLr-----ylDqfGK-T---kVH~~~C~ffG~p~ppapC~C 113 (215)
.|..|.+. -+.....+.|++.--|..++.=-|.-||+|+- |+.+.+. + =||++..+--....+..| .+
T Consensus 108 gp~~~~t~--Lp~~~l~~~l~~~gip~~~S~dAG~YlCN~i~Y~sl~~~~~~~~~~~a~FIHvP~~~~~~~~~~~~p-~~ 184 (215)
T PRK13197 108 GPAAYFST--LPIKAMVKAIREAGIPASVSNTAGTFVCNHVMYGLLHLLDKKYPNIRAGFIHIPYLPEQAVNKPGTP-SM 184 (215)
T ss_pred CCceeEcC--CCHHHHHHHHHHcCCCceeccCCCceeehHHHHHHHHHHHhcCCCceeEEEEcCCchhhhhcCCCCC-Cc
Confidence 34556543 35677788888888899999988999999954 4454443 2 288876544321111111 12
Q ss_pred chhhhcchhHHHHHHHHHHHHH
Q 028022 114 PLKQAWGSLDALIGRLRAAYEE 135 (215)
Q Consensus 114 PlRQAWGSLDALIGRLRAAfEE 135 (215)
++|.++.-+|.+-++
T Consensus 185 -------~~~~~~~av~~~i~~ 199 (215)
T PRK13197 185 -------SLEDIVRGLELAIEA 199 (215)
T ss_pred -------cHHHHHHHHHHHHHH
Confidence 366666666665554
No 66
>PF02187 GAS2: Growth-Arrest-Specific Protein 2 Domain; InterPro: IPR003108 The growth-arrest-specific protein 2 domain is found associated with the spectrin repeat, calponin homology domain and EF hand in many proteins. It is found among others in the growth arrest-specific protein 2 [].; GO: 0007050 cell cycle arrest; PDB: 1V5R_A.
Probab=21.97 E-value=18 Score=27.51 Aligned_cols=13 Identities=46% Similarity=1.204 Sum_probs=11.4
Q ss_pred HHHHHHHHHhcCC
Q 028022 55 WNTFLQYLKNHKP 67 (215)
Q Consensus 55 WntF~qyL~n~rP 67 (215)
|.||.+||..|.|
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 9999999999987
No 67
>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=21.93 E-value=46 Score=23.36 Aligned_cols=12 Identities=42% Similarity=0.775 Sum_probs=10.5
Q ss_pred cchhHHHHHHHH
Q 028022 119 WGSLDALIGRLR 130 (215)
Q Consensus 119 WGSLDALIGRLR 130 (215)
|-.||.||.+|.
T Consensus 37 f~~lD~li~~l~ 48 (49)
T PF07535_consen 37 FKELDSLISQLQ 48 (49)
T ss_pred HHHHHHHHHHhc
Confidence 778999999885
No 68
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=21.86 E-value=39 Score=27.24 Aligned_cols=35 Identities=20% Similarity=0.360 Sum_probs=24.6
Q ss_pred CCcccccccchhHhHHhhhhcccCcee-----eeecCCCCC
Q 028022 67 PPLTLARCSGAHVIEFLKYLDQFGKTK-----VHISGCPYF 102 (215)
Q Consensus 67 PPlsL~~Csg~hVleFLrylDqfGKTk-----VH~~~C~ff 102 (215)
.|++...++-.+..+|| |+-..=|-. +|.++|..|
T Consensus 27 RP~d~a~~sde~w~dY~-flR~NprG~~~E~W~H~~GCrr~ 66 (97)
T COG4311 27 RPADPADASDEEWGDYV-FLRDNPRGLHRERWRHTHGCRRW 66 (97)
T ss_pred CCCCcccCCHHHHhhhe-eeccCCCcchhHHhhhccchhhH
Confidence 37778888888888887 554433322 788999876
No 69
>KOG1452 consensus Predicted Rho GTPase-activating protein [Signal transduction mechanisms]
Probab=21.74 E-value=51 Score=32.11 Aligned_cols=30 Identities=33% Similarity=0.473 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCC--------CCCCccchhHHHHHHHHHH
Q 028022 128 RLRAAYEENGGR--------PESNPFGARAVRIYLREVR 158 (215)
Q Consensus 128 RLRAAfEE~Gg~--------pE~NPF~araVRlYLReVR 158 (215)
-||++||-||+. |+.|=. +..++.||||+=
T Consensus 233 mLR~~fe~n~r~~el~~E~iPD~nvI-tg~~kD~lrElp 270 (442)
T KOG1452|consen 233 MLRRDFEPNGRDFELGAESIPDYNVI-TGDSKDELRELP 270 (442)
T ss_pred HHHHHhccCCcccccccccCCCccee-ecccHhHHHhCC
Confidence 589999999985 445543 458999999974
No 70
>cd00778 ProRS_core_arch_euk Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from archaea, the cytoplasm of eukaryotes and some bacteria.
Probab=21.72 E-value=50 Score=28.36 Aligned_cols=17 Identities=29% Similarity=0.602 Sum_probs=12.3
Q ss_pred hhhhcchhHHHHHHHHH
Q 028022 115 LKQAWGSLDALIGRLRA 131 (215)
Q Consensus 115 lRQAWGSLDALIGRLRA 131 (215)
-+-.||+++.+||=|-+
T Consensus 244 h~~~~g~~~R~i~ali~ 260 (261)
T cd00778 244 HQTSWGISTRLIGAIIM 260 (261)
T ss_pred EEecccHHHHHHHHHHh
Confidence 45668988888886643
No 71
>COG4865 Glutamate mutase epsilon subunit [Amino acid transport and metabolism]
Probab=21.71 E-value=61 Score=31.90 Aligned_cols=22 Identities=45% Similarity=0.806 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHhCCCCCCCccc
Q 028022 125 LIGRLRAAYEENGGRPESNPFG 146 (215)
Q Consensus 125 LIGRLRAAfEE~Gg~pE~NPF~ 146 (215)
+|.||.-+|||||.+=...||+
T Consensus 196 YVDRL~G~YeE~Gi~INREpFg 217 (485)
T COG4865 196 YVDRLMGMYEEHGIRINREPFG 217 (485)
T ss_pred HHHHHHhHHHhcCeeeccccCC
Confidence 4556667999999986666665
No 72
>cd07287 PX_RPK118_like The phosphoinositide binding Phox Homology domain of RPK118-like proteins. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Members of this subfamily bear similarity to human RPK118, which contains an N-terminal PX domain, a Microtubule Interacting and Trafficking (MIT) domain, and a kinase domain. RPK118 binds sphingosine kinase, a key enzyme in the synthesis of sphingosine 1-phosphate (SPP), a lipid messenger involved in many cellular events. RPK118 may be involved in transmitting SPP-mediated signaling. It also binds the antioxidant peroxiredoxin-3 (PRDX3) and may be involved in the transport of PRDX3 from the cytoplasm to its site of function in the mitochondria. Members of this subfamily also show similarity to sorting nexin 15 (SNX15), which contains PX and MIT domains but does not contain a kinase doma
Probab=21.57 E-value=1e+02 Score=24.30 Aligned_cols=35 Identities=20% Similarity=0.294 Sum_probs=27.2
Q ss_pred chhhHhhhhhHHHHHHHHHhcCCCcccccccchhHhHHhh
Q 028022 45 SRYESQKRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLK 84 (215)
Q Consensus 45 srYesQKRRdWntF~qyL~n~rPPlsL~~Csg~hVleFLr 84 (215)
...-.+.|+--+.|.|++.||. .-|...++.+||.
T Consensus 82 ~~fIe~RR~~Le~fL~~i~~~p-----~l~~s~~~~~Fl~ 116 (118)
T cd07287 82 ESVIEERRQCAEDLLQFSANIP-----ALYNSSQLEDFFK 116 (118)
T ss_pred HHHHHHHHHHHHHHHHHHhcCc-----cccCChHHHHHhc
Confidence 3466677888999999998883 3367889999994
No 73
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=21.47 E-value=75 Score=27.13 Aligned_cols=29 Identities=34% Similarity=0.623 Sum_probs=22.5
Q ss_pred CCchhhhcc--------hhHHHHHHHHHHHHHhCCCC
Q 028022 112 ACPLKQAWG--------SLDALIGRLRAAYEENGGRP 140 (215)
Q Consensus 112 ~CPlRQAWG--------SLDALIGRLRAAfEE~Gg~p 140 (215)
.--+.+.|| +||..|.|||.-++..+..+
T Consensus 176 ~~L~~~vw~~~~~~~~rtvdvhI~rLR~Kl~~~~~~~ 212 (229)
T COG0745 176 EQLLEAVWGYDFEVDSRTVDVHISRLRKKLEKDPGAG 212 (229)
T ss_pred HHHHHHhcCCCCCCCccCHHHHHHHHHHHhccCCCCC
Confidence 344677887 49999999999998876543
No 74
>cd04407 RhoGAP_myosin_IXB RhoGAP_myosin_IXB: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in myosins IXB. Class IX myosins contain a characteristic head domain, a neck domain and a tail domain which contains a C6H2-zinc binding motif and a Rho-GAP domain. Class IX myosins are single-headed, processive myosins that are partly cytoplasmic, and partly associated with membranes and the actin cytoskeleton. Class IX myosins are implicated in the regulation of neuronal morphogenesis and function of sensory systems, like the inner ear. There are two major isoforms, myosin IXA and IXB with several splice variants, which are both expressed in developing neurons Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell prolifer
Probab=21.31 E-value=2.1e+02 Score=23.61 Aligned_cols=36 Identities=17% Similarity=0.162 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHhCCCC--C-CC-ccchhHHHHHHHHHHH
Q 028022 124 ALIGRLRAAYEENGGRP--E-SN-PFGARAVRIYLREVRE 159 (215)
Q Consensus 124 ALIGRLRAAfEE~Gg~p--E-~N-PF~araVRlYLReVRd 159 (215)
..|.+|+..|+..+..- + .+ .-.+..++.||||.-+
T Consensus 44 ~~i~~l~~~~~~~~~~~~~~~~d~h~va~lLK~flReLPe 83 (186)
T cd04407 44 NRMKELHQLLQADPENVKLENYPIHAITGLLKQWLRELPE 83 (186)
T ss_pred HHHHHHHHHHhcCCcccCcccCCHHHHHHHHHHHHHhCCC
Confidence 46889999998643221 1 11 2458889999998744
No 75
>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=21.27 E-value=1.2e+02 Score=27.42 Aligned_cols=38 Identities=32% Similarity=0.342 Sum_probs=30.0
Q ss_pred cchhHHHHHHHHHHHHHhCCC----------------------CCCCcc-chhHHHHHHHH
Q 028022 119 WGSLDALIGRLRAAYEENGGR----------------------PESNPF-GARAVRIYLRE 156 (215)
Q Consensus 119 WGSLDALIGRLRAAfEE~Gg~----------------------pE~NPF-~araVRlYLRe 156 (215)
+=+.|.+...++.+.+.++++ .|.||| |-|.||+||..
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 346788899999999988876 569996 67999999975
No 76
>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=21.18 E-value=84 Score=27.84 Aligned_cols=52 Identities=13% Similarity=0.193 Sum_probs=36.3
Q ss_pred hhhcchhHHHHHHHHHHHHHhCCCCC--------------CCccch-----hHHHHHHHHHHHHHHhhhCC
Q 028022 116 KQAWGSLDALIGRLRAAYEENGGRPE--------------SNPFGA-----RAVRIYLREVRESQAKARGI 167 (215)
Q Consensus 116 RQAWGSLDALIGRLRAAfEE~Gg~pE--------------~NPF~a-----raVRlYLReVRd~QAKARgi 167 (215)
-.|||.+..+|-+|..+|+.+|..|- -+-|-+ .-+..+|..++..-.+--+|
T Consensus 24 ~lAyG~~~~I~~~~~~ll~~~~~~P~~~v~~~~~~~~~~~~~~~~yRf~~~~D~~~~~~~l~~i~~~~gsL 94 (232)
T PF09674_consen 24 LLAYGNRKQIIKKLERLLDLMGPSPYDFVLSGDEKDDRKDLEGFFYRFQNGEDMYAFFIALKRIYQEYGSL 94 (232)
T ss_pred HHHccCHHHHHHHHHHHHHHhCCCHHHHHHcCCHhhhHHHccCCCcCCCCHHHHHHHHHHHHHHHHccCCH
Confidence 36999999999999999999999862 244433 34556666666555543333
No 77
>PF00179 UQ_con: Ubiquitin-conjugating enzyme; InterPro: IPR000608 The post-translational attachment of ubiquitin (IPR000626 from INTERPRO) to proteins (ubiquitinylation) alters the function, location or trafficking of a protein, or targets it to the 26S proteasome for degradation [, , ]. Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade []. The E1 enzyme mediates an ATP-dependent transfer of a thioester-linked ubiquitin molecule to a cysteine residue on the E2 enzyme. The E2 enzyme (6.3.2.19 from EC) then either transfers the ubiquitin moiety directly to a substrate, or to an E3 ligase, which can also ubiquitinylate a substrate. There are several different E2 enzymes (over 30 in humans), which are broadly grouped into four classes, all of which have a core catalytic domain (containing the active site cysteine), and some of which have short N- and C-terminal amino acid extensions: class I enzymes consist of just the catalytic core domain (UBC), class II possess a UBC and a C-terminal extension, class III possess a UBC and an N-terminal extension, and class IV possess a UBC and both N- and C-terminal extensions. These extensions appear to be important for some subfamily function, including E2 localisation and protein-protein interactions []. In addition, there are proteins with an E2-like fold that are devoid of catalytic activity, but which appear to assist in poly-ubiquitin chain formation.; GO: 0016881 acid-amino acid ligase activity; PDB: 2AAK_A 3SY2_C 1FBV_C 3SQV_C 1C4Z_D 1JAT_B 2GMI_B 2H2Y_D 2R0J_A 3E95_B ....
Probab=21.09 E-value=2.1e+02 Score=21.91 Aligned_cols=45 Identities=20% Similarity=0.508 Sum_probs=36.0
Q ss_pred hcc---hhHHHHHHHHHHHHHhCCCCCCCccchhHHHHHHHHHHHHHHhhh
Q 028022 118 AWG---SLDALIGRLRAAYEENGGRPESNPFGARAVRIYLREVRESQAKAR 165 (215)
Q Consensus 118 AWG---SLDALIGRLRAAfEE~Gg~pE~NPF~araVRlYLReVRd~QAKAR 165 (215)
-|- ++..+|-.|+..+.+- -..+|+-..|.++|..+-.+.+.+||
T Consensus 90 ~W~p~~~i~~il~~i~~ll~~p---~~~~~~n~~a~~~~~~~~~~f~~~~~ 137 (140)
T PF00179_consen 90 SWSPSYTIESILLSIQSLLSEP---NPEDPLNEEAAELYKNDREEFEKKAR 137 (140)
T ss_dssp TC-TTSHHHHHHHHHHHHHHST---CTTSTSSHHHHHHHHHCHHHHHHHHH
T ss_pred cCCcccccccHHHHHHHHHhCC---CCCCcchHHHHHHHHHCHHHHHHHHH
Confidence 477 8888888999999554 45789999999999998777777775
No 78
>cd04400 RhoGAP_fBEM3 RhoGAP_fBEM3: RhoGAP (GTPase-activator [GAP] protein for Rho-like small GTPases) domain of fungal BEM3-like proteins. Bem3 is a GAP protein of Cdc42, and is specifically involved in the control of the initial assembly of the septin ring in yeast bud formation. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=21.08 E-value=1.4e+02 Score=24.40 Aligned_cols=39 Identities=23% Similarity=0.349 Sum_probs=26.4
Q ss_pred chhHHHHHHHHHHHHHhCC---C--C--CCCccchhHHHHHHHHHHH
Q 028022 120 GSLDALIGRLRAAYEENGG---R--P--ESNPFGARAVRIYLREVRE 159 (215)
Q Consensus 120 GSLDALIGRLRAAfEE~Gg---~--p--E~NPF~araVRlYLReVRd 159 (215)
|+. ..|-+|+..|+..+. . + ....-.+..+|.||||.-+
T Consensus 49 G~~-~~i~~l~~~~~~~~~~~~~~~~~~~d~h~va~lLK~flreLP~ 94 (190)
T cd04400 49 GSA-SVIKQLKERFNTEYDVDLFSSSLYPDVHTVAGLLKLYLRELPT 94 (190)
T ss_pred CcH-HHHHHHHHHHcCCCCCCccccccccCHHHHHHHHHHHHHhCCc
Confidence 444 367899999987542 1 1 1233558999999999744
No 79
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=20.60 E-value=2.5e+02 Score=20.97 Aligned_cols=39 Identities=31% Similarity=0.675 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHhCCCCCCCccchhHHHHHHHHHHHHHHhhhCCchhhh
Q 028022 124 ALIGRLRAAYEENGGRPESNPFGARAVRIYLREVRESQAKARGIPYEKK 172 (215)
Q Consensus 124 ALIGRLRAAfEE~Gg~pE~NPF~araVRlYLReVRd~QAKARgi~y~kk 172 (215)
.|--+.-++|+++|..+ ..|||++|+.| .+-+|||++-+
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 34456677899999875 56999999876 44589998864
No 80
>PHA03019 hypothetical protein; Provisional
Probab=20.50 E-value=70 Score=24.76 Aligned_cols=21 Identities=38% Similarity=0.651 Sum_probs=17.7
Q ss_pred hhhHHHHHHHHHhcCCCcccc
Q 028022 52 RRDWNTFLQYLKNHKPPLTLA 72 (215)
Q Consensus 52 RRdWntF~qyL~n~rPPlsL~ 72 (215)
-+--|+|.+|++||.|-..|.
T Consensus 45 d~~in~~ld~~knh~~nidli 65 (77)
T PHA03019 45 DHCINKFLDFKKNHEPNIDLI 65 (77)
T ss_pred HHHHHHHHHHHHccCCCccee
Confidence 455799999999999988775
No 81
>PRK01381 Trp operon repressor; Provisional
Probab=20.23 E-value=1.4e+02 Score=23.76 Aligned_cols=28 Identities=21% Similarity=0.474 Sum_probs=21.6
Q ss_pred HhhhhhHHHHHHHHHhcCCCcccccccchhHhHHhh
Q 028022 49 SQKRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLK 84 (215)
Q Consensus 49 sQKRRdWntF~qyL~n~rPPlsL~~Csg~hVleFLr 84 (215)
.+.-.+|+.|.+.|.++.- ...+..||.
T Consensus 3 ~~~~~~W~~~v~ll~~a~~--------~~~~~~~l~ 30 (99)
T PRK01381 3 EQENQEWQRFVDLLKQAFE--------EDLHLPLLT 30 (99)
T ss_pred CcchhhHHHHHHHHHHhcc--------HHHHHHHHH
Confidence 3445789999999998765 677777875
No 82
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=20.17 E-value=1.5e+02 Score=30.02 Aligned_cols=35 Identities=26% Similarity=0.395 Sum_probs=28.6
Q ss_pred hhHHHHHHHHHHHHHhCCC--------------------CCCCcc-chhHHHHHHH
Q 028022 121 SLDALIGRLRAAYEENGGR--------------------PESNPF-GARAVRIYLR 155 (215)
Q Consensus 121 SLDALIGRLRAAfEE~Gg~--------------------pE~NPF-~araVRlYLR 155 (215)
+.|......|.+.+.++++ +|.||| |.|+||+||+
T Consensus 475 ~e~eQ~~~y~~~~~~~~~~pv~iRtlDiGgDK~~~~~~~~E~NP~lG~RgiR~~l~ 530 (748)
T PRK11061 475 SEEEQVAQYQGMLQMFPDKPVTLRTLDIGADKQLPYMPISEENPCLGWRGIRITLD 530 (748)
T ss_pred CHHHHHHHHHHHHHHcCCCeEEEECCCCCcCCCCCCCCCCCCCcccccchhhcccc
Confidence 4677888888888888765 589998 5699999984
Done!