Query 037966
Match_columns 205
No_of_seqs 79 out of 81
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 06:12:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037966.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037966hhsearch_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 7.9E-76 1.7E-80 471.5 11.8 123 49-171 10-132 (132)
2 PF08821 CGGC: CGGC domain; I 91.0 0.41 8.9E-06 37.3 4.3 67 68-144 29-98 (107)
3 PF02899 Phage_int_SAM_1: Phag 90.0 0.53 1.1E-05 31.8 3.8 40 61-101 21-60 (84)
4 cd00798 INT_XerDC XerD and Xer 86.8 2.6 5.6E-05 32.6 6.2 69 61-156 21-91 (284)
5 cd00799 INT_Cre Cre recombinas 85.5 7.5 0.00016 31.5 8.4 77 61-169 6-82 (287)
6 TIGR02225 recomb_XerD tyrosine 83.3 4.7 0.0001 31.6 6.2 70 60-157 19-90 (291)
7 PRK00283 xerD site-specific ty 81.9 3.9 8.4E-05 32.6 5.4 68 62-157 30-99 (299)
8 COG1080 PtsA Phosphoenolpyruva 80.5 2 4.4E-05 42.5 4.0 41 127-167 305-367 (574)
9 TIGR02224 recomb_XerC tyrosine 70.5 21 0.00047 28.1 6.6 69 63-157 22-92 (295)
10 TIGR01418 PEP_synth phosphoeno 61.9 12 0.00027 37.5 4.6 42 134-175 547-618 (782)
11 PF00539 Tat: Transactivating 61.4 4.2 9.2E-05 30.4 1.0 19 172-190 44-62 (68)
12 cd01185 INT_Tn4399 Tn4399 and 60.1 40 0.00087 27.4 6.5 33 65-97 44-78 (299)
13 PF10865 DUF2703: Domain of un 59.5 3.4 7.3E-05 33.2 0.2 43 90-152 2-44 (120)
14 PRK11061 fused phosphoenolpyru 55.1 17 0.00036 36.4 4.2 35 132-166 475-530 (748)
15 PRK10529 DNA-binding transcrip 54.1 11 0.00024 28.8 2.2 18 132-149 191-208 (225)
16 PF02896 PEP-utilizers_C: PEP- 53.6 16 0.00034 32.9 3.5 40 130-169 58-120 (293)
17 PF05528 Coronavirus_5: Corona 52.9 2.4 5.1E-05 32.8 -1.5 19 151-169 4-25 (82)
18 PF13495 Phage_int_SAM_4: Phag 50.8 23 0.0005 24.1 3.2 53 64-146 24-77 (85)
19 PRK00236 xerC site-specific ty 49.3 79 0.0017 24.8 6.4 38 62-100 31-68 (297)
20 PRK10816 DNA-binding transcrip 45.3 16 0.00035 27.9 2.0 23 126-148 175-205 (223)
21 TIGR01417 PTS_I_fam phosphoeno 44.7 21 0.00046 34.6 3.1 36 132-167 308-365 (565)
22 COG4974 XerD Site-specific rec 44.4 22 0.00048 32.9 3.0 38 63-102 31-69 (300)
23 PF00486 Trans_reg_C: Transcri 42.7 25 0.00055 23.4 2.4 21 131-151 44-64 (77)
24 cd00801 INT_P4 Bacteriophage P 42.5 49 0.0011 27.2 4.5 26 131-157 135-163 (357)
25 PF06252 DUF1018: Protein of u 41.4 1.5E+02 0.0033 22.6 6.8 87 65-166 2-89 (119)
26 PRK09279 pyruvate phosphate di 39.7 26 0.00056 36.2 3.0 36 140-175 636-685 (879)
27 PF13276 HTH_21: HTH-like doma 38.3 54 0.0012 21.9 3.5 29 134-167 4-32 (60)
28 smart00259 ZnF_A20 A20-like zi 37.9 17 0.00037 22.4 0.9 16 108-123 7-22 (26)
29 smart00862 Trans_reg_C Transcr 37.7 36 0.00077 22.6 2.5 19 131-149 45-63 (78)
30 PRK06464 phosphoenolpyruvate s 36.3 44 0.00095 33.9 3.9 15 152-166 597-612 (795)
31 PF14768 RPA_interact_C: Repli 36.1 34 0.00074 25.1 2.4 35 121-155 18-56 (82)
32 PF00140 Sigma70_r1_2: Sigma-7 35.8 30 0.00065 22.1 1.8 13 159-171 2-14 (37)
33 cd04372 RhoGAP_chimaerin RhoGA 34.9 47 0.001 27.2 3.3 36 135-170 45-87 (194)
34 TIGR01828 pyru_phos_dikin pyru 34.6 22 0.00047 36.5 1.5 25 151-175 652-679 (856)
35 cd08793 Death_IRAK4 Death doma 33.8 42 0.00092 26.6 2.7 64 64-149 22-85 (100)
36 smart00243 GAS2 Growth-Arrest- 31.4 32 0.00069 26.3 1.6 14 65-78 55-68 (73)
37 PF09107 SelB-wing_3: Elongati 31.3 25 0.00055 24.2 1.0 21 84-104 21-41 (50)
38 PF11709 Mit_ribos_Mrp51: Mito 31.3 61 0.0013 29.3 3.6 69 49-117 142-229 (312)
39 PRK11177 phosphoenolpyruvate-p 30.7 39 0.00086 33.0 2.5 36 132-167 309-366 (575)
40 PF09336 Vps4_C: Vps4 C termin 30.6 42 0.00091 23.8 2.0 31 66-101 32-62 (62)
41 cd04396 RhoGAP_fSAC7_BAG7 RhoG 30.1 1.9E+02 0.0041 24.5 6.2 37 134-170 60-103 (225)
42 PF07700 HNOB: Heme NO binding 29.2 24 0.00052 28.2 0.7 36 64-99 65-103 (171)
43 PF08544 GHMP_kinases_C: GHMP 28.7 11 0.00023 25.7 -1.2 72 62-145 6-84 (85)
44 PRK05084 xerS site-specific ty 28.4 1.2E+02 0.0026 25.7 4.8 68 63-146 42-119 (357)
45 PF09958 DUF2192: Uncharacteri 27.3 54 0.0012 29.5 2.6 21 132-152 27-47 (231)
46 cd00383 trans_reg_C Effector d 26.6 58 0.0012 22.4 2.1 20 131-150 62-81 (95)
47 cd01355 AcnX Putative Aconitas 26.4 68 0.0015 30.4 3.2 53 88-152 49-108 (389)
48 KOG1452 Predicted Rho GTPase-a 26.0 35 0.00077 33.0 1.3 31 139-170 233-271 (442)
49 PTZ00398 phosphoenolpyruvate c 26.0 1.2E+02 0.0026 32.0 5.1 43 130-172 264-337 (974)
50 KOG4405 GDP dissociation inhib 25.4 29 0.00063 34.5 0.6 80 67-150 223-331 (547)
51 cd04388 RhoGAP_p85 RhoGAP_p85: 25.3 75 0.0016 27.1 3.0 34 137-170 45-82 (200)
52 PF00179 UQ_con: Ubiquitin-con 25.2 1.5E+02 0.0032 22.7 4.3 45 129-176 90-137 (140)
53 COG0745 OmpR Response regulato 25.1 57 0.0012 27.7 2.3 27 125-151 178-212 (229)
54 PF12067 Sox_C_TAD: Sox C-term 25.1 39 0.00084 29.4 1.3 17 62-78 139-155 (197)
55 PF09674 DUF2400: Protein of u 24.6 66 0.0014 28.4 2.6 25 127-151 24-48 (232)
56 cd04399 RhoGAP_fRGD2 RhoGAP_fR 24.1 87 0.0019 26.4 3.1 35 135-170 51-94 (212)
57 PRK11235 bifunctional antitoxi 24.0 1.8E+02 0.0038 22.0 4.5 37 135-181 11-47 (80)
58 PF06480 FtsH_ext: FtsH Extrac 23.9 1E+02 0.0022 21.3 3.0 26 130-155 84-109 (110)
59 TIGR02249 integrase_gron integ 23.9 1.9E+02 0.0042 23.9 5.1 33 63-99 23-55 (315)
60 PF06947 DUF1290: Protein of u 23.8 66 0.0014 25.3 2.2 17 131-147 16-32 (88)
61 cd04379 RhoGAP_SYD1 RhoGAP_SYD 23.7 98 0.0021 26.1 3.4 39 131-170 44-89 (207)
62 cd04436 DEP_fRgd2 DEP (Disheve 23.6 60 0.0013 25.1 1.9 40 67-106 33-76 (84)
63 PF02187 GAS2: Growth-Arrest-S 23.5 19 0.0004 27.3 -0.9 13 66-78 56-68 (73)
64 cd04383 RhoGAP_srGAP RhoGAP_sr 23.5 95 0.0021 25.5 3.2 35 135-170 47-88 (188)
65 PF03801 Ndc80_HEC: HEC/Ndc80p 23.4 1.3E+02 0.0029 24.5 4.0 45 53-97 29-79 (157)
66 PF10780 MRP_L53: 39S ribosoma 23.3 41 0.00089 23.4 0.9 25 154-179 2-28 (51)
67 PRK09468 ompR osmolarity respo 23.1 66 0.0014 24.9 2.1 17 132-148 201-217 (239)
68 cd01187 INT_SG4 INT_SG4, DNA b 23.0 3.2E+02 0.0069 22.3 6.1 29 65-97 25-53 (299)
69 PRK11173 two-component respons 23.0 67 0.0014 25.1 2.1 19 132-150 200-218 (237)
70 cd04390 RhoGAP_ARHGAP22_24_25 22.6 1.4E+02 0.003 24.4 4.0 37 134-170 50-90 (199)
71 PF03344 Daxx: Daxx Family; I 22.5 3.3E+02 0.0072 27.9 7.3 77 56-173 64-140 (713)
72 PF01663 Phosphodiest: Type I 22.4 66 0.0014 26.7 2.1 27 126-152 208-234 (365)
73 PF07535 zf-DBF: DBF zinc fing 22.3 43 0.00093 23.3 0.8 12 130-141 37-48 (49)
74 COG4865 Glutamate mutase epsil 22.1 58 0.0013 31.9 1.9 22 136-157 196-217 (485)
75 PF10520 Kua-UEV1_localn: Kua- 21.7 45 0.00097 28.5 1.0 24 129-152 17-41 (178)
76 TIGR02384 RelB_DinJ addiction 21.5 2.4E+02 0.0052 20.9 4.7 38 135-182 12-49 (83)
77 PF13099 DUF3944: Domain of un 21.4 49 0.0011 22.1 0.9 22 83-104 11-34 (35)
78 cd04406 RhoGAP_myosin_IXA RhoG 21.2 1E+02 0.0022 25.3 3.0 36 135-170 44-83 (186)
79 PF12055 DUF3536: Domain of un 20.9 75 0.0016 29.1 2.3 42 125-171 8-49 (285)
80 KOG4670 Uncharacterized conser 20.8 43 0.00094 33.8 0.8 59 61-119 468-544 (602)
81 cd01401 PncB_like Nicotinate p 20.6 2.1E+02 0.0045 27.0 5.1 69 65-154 234-305 (377)
82 PLN02837 threonine-tRNA ligase 20.5 41 0.00088 32.7 0.5 17 126-142 488-504 (614)
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=7.9e-76 Score=471.47 Aligned_cols=123 Identities=89% Similarity=1.517 Sum_probs=119.5
Q ss_pred CCCCCCCchHHHhhhhhhhHHHHHHHhcCCCCccccccchhhhHHHHhhcccCcccccccCCCCcCCCCCCCCCCCchhh
Q 037966 49 SSSTTTLSRYENQKRRDWNTFGQYLRNHRPPLSLERCSGAHVLEFLRYLDQFGKTKVHTQLCPFFGHPNPPAPCPCPLRQ 128 (205)
Q Consensus 49 ~~~~~~~SrYesQKRrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQ 128 (205)
.++++.+||||+|||||||||+|||+||+|||+|++|+++|||+||+|||||||||||.++|+|||+|+||+||+|||||
T Consensus 10 ~~~~~~~SrYesQKrrdwntf~qyL~n~rPP~~L~~csg~hVl~FL~~~d~~GkTkVh~~~C~~~g~~~~p~~C~CPlrq 89 (132)
T PF04852_consen 10 RSPQPAPSRYESQKRRDWNTFGQYLRNHRPPLSLSRCSGNHVLEFLRYLDQFGKTKVHGQGCPFFGHPSPPAPCPCPLRQ 89 (132)
T ss_pred CCCCCCCcccchhhhHHHHHHHHHHHccCCCcchhhcChHHHHHHHHHHhccCCeeecCCCCCCCCCCCCCCCCCCcHHH
Confidence 34556789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcchhHHHHHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHH
Q 037966 129 AWGSLDALIGRLRAAFEEHGGKPEANPFGARAVRLYLREVRDS 171 (205)
Q Consensus 129 AWGSLDALIGRLRAafEE~Gg~PE~NPF~araVRlYLReVRd~ 171 (205)
|||||||||||||||||||||+||+|||+++|||+|||||||+
T Consensus 90 AwGSlDalIGrLraafee~Gg~pe~NPf~~~~vr~yLr~vr~~ 132 (132)
T PF04852_consen 90 AWGSLDALIGRLRAAFEEHGGHPEANPFAARAVRLYLREVRDS 132 (132)
T ss_pred HhccHHHHHHHHHHHHHHhCCCCCCCchhhHHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999985
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=90.96 E-value=0.41 Score=37.29 Aligned_cols=67 Identities=22% Similarity=0.528 Sum_probs=49.7
Q ss_pred HHHHHHHhcCCCCcccccc---chhhhHHHHhhcccCcccccccCCCCcCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 037966 68 TFGQYLRNHRPPLSLERCS---GAHVLEFLRYLDQFGKTKVHTQLCPFFGHPNPPAPCPCPLRQAWGSLDALIGRLRAAF 144 (205)
Q Consensus 68 tf~qyL~n~rPPlsL~~cs---g~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAaf 144 (205)
.|.+|=.+..--+.+.+|. +..|+..++.+-..|-..||...|.+.+.+.+ +||. +|.|+-.|+++|
T Consensus 29 ~F~~y~~~~~elvgf~~CgGCpg~~~~~~~~~l~~~~~d~IHlssC~~~~~~~~----~CP~------~~~~~~~I~~~~ 98 (107)
T PF08821_consen 29 AFARYDDEDVELVGFFTCGGCPGRKLVRRIKKLKKNGADVIHLSSCMVKGNPHG----PCPH------IDEIKKIIEEKF 98 (107)
T ss_pred ccccCCCCCeEEEEEeeCCCCChhHHHHHHHHHHHCCCCEEEEcCCEecCCCCC----CCCC------HHHHHHHHHHHh
Confidence 3444443222234444554 58899999999999999999999999987654 6666 899999999888
No 3
>PF02899 Phage_int_SAM_1: Phage integrase, N-terminal SAM-like domain; InterPro: IPR004107 Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104 from INTERPRO).; GO: 0003677 DNA binding, 0015074 DNA integration; PDB: 1Z1G_B 1Z19_A 1Z1B_A 2OXO_A 1P7D_B 3NRW_A 1A0P_A.
Probab=90.01 E-value=0.53 Score=31.82 Aligned_cols=40 Identities=30% Similarity=0.487 Sum_probs=31.8
Q ss_pred hhhhhhhHHHHHHHhcCCCCccccccchhhhHHHHhhcccC
Q 037966 61 QKRRDWNTFGQYLRNHRPPLSLERCSGAHVLEFLRYLDQFG 101 (205)
Q Consensus 61 QKRrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfG 101 (205)
.-+++++.|.+||.+ ....++..++..||.+|+.++-+.|
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 446789999999999 6667788999999999999998766
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=86.85 E-value=2.6 Score=32.64 Aligned_cols=69 Identities=25% Similarity=0.265 Sum_probs=47.9
Q ss_pred hhhhhhhHHHHHHHhcCCCCccccccchhhhHHHHhhcccCcccccccCCCCcCCCCCCCCCCCchhhhcchhHHHHHHH
Q 037966 61 QKRRDWNTFGQYLRNHRPPLSLERCSGAHVLEFLRYLDQFGKTKVHTQLCPFFGHPNPPAPCPCPLRQAWGSLDALIGRL 140 (205)
Q Consensus 61 QKRrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRL 140 (205)
+-+..|+.|.+|+....... +..-+..||.+|+.++.+.| ....++...++-|
T Consensus 21 ~~~~~~~~~~~~~~~~~~~~-~~~l~~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~l 73 (284)
T cd00798 21 AYRRDLERFLEFLEERGILF-PADVTPDDIRRFLAELKDQG--------------------------LSARSIARKLSAL 73 (284)
T ss_pred HHHHHHHHHHHHHHHcCCCc-hhhCCHHHHHHHHHHhhhcC--------------------------CCHHHHHHHHHHH
Confidence 44567899999998754433 56677899999999887644 1235777778888
Q ss_pred HHHHHHhC--CCCCCCcc
Q 037966 141 RAAFEEHG--GKPEANPF 156 (205)
Q Consensus 141 RAafEE~G--g~PE~NPF 156 (205)
+++|.-.. +--+.||+
T Consensus 74 ~~~~~~~~~~~~~~~~p~ 91 (284)
T cd00798 74 RSFFKFLLREGLILANPA 91 (284)
T ss_pred HHHHHHHHHcCCccCChh
Confidence 88876322 33456777
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=85.45 E-value=7.5 Score=31.46 Aligned_cols=77 Identities=23% Similarity=0.304 Sum_probs=52.4
Q ss_pred hhhhhhhHHHHHHHhcCCCCccccccchhhhHHHHhhcccCcccccccCCCCcCCCCCCCCCCCchhhhcchhHHHHHHH
Q 037966 61 QKRRDWNTFGQYLRNHRPPLSLERCSGAHVLEFLRYLDQFGKTKVHTQLCPFFGHPNPPAPCPCPLRQAWGSLDALIGRL 140 (205)
Q Consensus 61 QKRrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRL 140 (205)
.-..+++.|.+|+..+- +....-+..+|.+|+.||.+. .+..++-..++.|
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 222223589999999988531 1456888899999
Q ss_pred HHHHHHhCCCCCCCcchhhHHHHHHHHHH
Q 037966 141 RAAFEEHGGKPEANPFGARAVRLYLREVR 169 (205)
Q Consensus 141 RAafEE~Gg~PE~NPF~araVRlYLReVR 169 (205)
+.+|+..+. .||+....++.-|+.++
T Consensus 57 ~~~~~~~~~---~~p~~~~~~~~~~~~~~ 82 (287)
T cd00799 57 SQLHRRSGL---PSPADSPLVRLVLRGIR 82 (287)
T ss_pred HHHHHHcCC---CCCccCHHHHHHHHHHH
Confidence 999985443 57876555555555554
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=83.26 E-value=4.7 Score=31.57 Aligned_cols=70 Identities=24% Similarity=0.411 Sum_probs=47.7
Q ss_pred HhhhhhhhHHHHHHHhcCCCCccccccchhhhHHHHhhcccCcccccccCCCCcCCCCCCCCCCCchhhhcchhHHHHHH
Q 037966 60 NQKRRDWNTFGQYLRNHRPPLSLERCSGAHVLEFLRYLDQFGKTKVHTQLCPFFGHPNPPAPCPCPLRQAWGSLDALIGR 139 (205)
Q Consensus 60 sQKRrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGR 139 (205)
.+-+..++.|.+|+.... ..+..-+..||.+|+.++.+.| .+.-+++..+..
T Consensus 19 ~~~~~~~~~~~~~~~~~~--~~~~~it~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~ 70 (291)
T TIGR02225 19 EAYRRDLEKFLEFLEERG--IDLEEVDRGDIVDFLAELKEAG--------------------------LSARSIARALSA 70 (291)
T ss_pred HHHHHHHHHHHHHHHhcC--CChHHCCHHHHHHHHHHhhcCC--------------------------CCHhHHHHHHHH
Confidence 445567788999988542 2455667899999999887644 122367888999
Q ss_pred HHHHHHHh--CCCCCCCcch
Q 037966 140 LRAAFEEH--GGKPEANPFG 157 (205)
Q Consensus 140 LRAafEE~--Gg~PE~NPF~ 157 (205)
|+++|+-. -+--+.|||.
T Consensus 71 l~~~~~~a~~~~~~~~np~~ 90 (291)
T TIGR02225 71 LRSFYRFLLREGIREDDPSA 90 (291)
T ss_pred HHHHHHHHHhcccccCCchh
Confidence 99998732 2334568863
No 7
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=81.86 E-value=3.9 Score=32.62 Aligned_cols=68 Identities=26% Similarity=0.288 Sum_probs=47.5
Q ss_pred hhhhhhHHHHHHHhcCCCCccccccchhhhHHHHhhcccCcccccccCCCCcCCCCCCCCCCCchhhhcchhHHHHHHHH
Q 037966 62 KRRDWNTFGQYLRNHRPPLSLERCSGAHVLEFLRYLDQFGKTKVHTQLCPFFGHPNPPAPCPCPLRQAWGSLDALIGRLR 141 (205)
Q Consensus 62 KRrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLR 141 (205)
-+++|+.|..||..+.- .+...+..||.+|+.++.+.| .+-.++...+..|+
T Consensus 30 ~~~~~~~~~~~~~~~~~--~~~~l~~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~l~ 81 (299)
T PRK00283 30 YRRDLELFAEWLAARGL--SLAEATRDDLQAFLAELAEGG--------------------------YKATSSARRLSALR 81 (299)
T ss_pred HHHHHHHHHHHHHhcCC--ChHHCCHHHHHHHHHHHHhCC--------------------------CCHHHHHHHHHHHH
Confidence 45688899999986532 566778999999999885532 23357778888888
Q ss_pred HHHHHhC--CCCCCCcch
Q 037966 142 AAFEEHG--GKPEANPFG 157 (205)
Q Consensus 142 AafEE~G--g~PE~NPF~ 157 (205)
++|+-.. +--+.|||.
T Consensus 82 ~~~~~a~~~~~i~~np~~ 99 (299)
T PRK00283 82 RFFQFLLREGLREDDPSA 99 (299)
T ss_pred HHHHHHHHcCCcccCchh
Confidence 8887331 234468863
No 8
>COG1080 PtsA Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]
Probab=80.55 E-value=2 Score=42.54 Aligned_cols=41 Identities=44% Similarity=0.698 Sum_probs=32.9
Q ss_pred hhhcchhHHHHHHHHHHHHHhCCC--------------------C-CCCcc-hhhHHHHHHHH
Q 037966 127 RQAWGSLDALIGRLRAAFEEHGGK--------------------P-EANPF-GARAVRLYLRE 167 (205)
Q Consensus 127 RQAWGSLDALIGRLRAafEE~Gg~--------------------P-E~NPF-~araVRlYLRe 167 (205)
|+.|=+.|..----++..|.+||+ | |.||| |-|+||+||..
T Consensus 305 r~~~P~EeEQ~~aY~~vlea~~g~pviiRTlDiGGDK~lpyl~lp~E~NPfLG~RaIRl~l~~ 367 (574)
T COG1080 305 RDALPDEEEQFEAYKAVLEAMGGKPVIIRTLDIGGDKPLPYLNLPKEENPFLGYRAIRLSLER 367 (574)
T ss_pred CCCCCChHHHHHHHHHHHHHcCCCceEEEecccCCCCcCCCCCCccccCchhhhHHHHHhhcc
Confidence 345556777777788888998887 3 79999 89999999964
No 9
>TIGR02224 recomb_XerC tyrosine recombinase XerC. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK.
Probab=70.50 E-value=21 Score=28.06 Aligned_cols=69 Identities=29% Similarity=0.347 Sum_probs=46.9
Q ss_pred hhhhhHHHHHHHhcCCCCccccccchhhhHHHHhhcccCcccccccCCCCcCCCCCCCCCCCchhhhcchhHHHHHHHHH
Q 037966 63 RRDWNTFGQYLRNHRPPLSLERCSGAHVLEFLRYLDQFGKTKVHTQLCPFFGHPNPPAPCPCPLRQAWGSLDALIGRLRA 142 (205)
Q Consensus 63 RrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRA 142 (205)
+.+++.|.+||......+.+..-+..||.+|+.++.+.|. +..++...+..||+
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~l~~~~i~~~~~~~~~~~~--------------------------~~~T~~~~~~~l~~ 75 (295)
T TIGR02224 22 RRDLKAFLEFLEEEGGLASLAEVTAADLRSFLAELHARGL--------------------------SRRSLARKLSALRS 75 (295)
T ss_pred HHHHHHHHHHHHhcCCCCccccCcHHHHHHHHHHhcccCC--------------------------CHHHHHHHHHHHHH
Confidence 3456678888888665677888889999999998766321 22456677778887
Q ss_pred HHHHhC--CCCCCCcch
Q 037966 143 AFEEHG--GKPEANPFG 157 (205)
Q Consensus 143 afEE~G--g~PE~NPF~ 157 (205)
+|.-.. +.-+.|||.
T Consensus 76 ~~~~a~~~~~~~~np~~ 92 (295)
T TIGR02224 76 FYRFLVRRGLIKANPAA 92 (295)
T ss_pred HHHHHHHcCccccChHh
Confidence 776421 223467763
No 10
>TIGR01418 PEP_synth phosphoenolpyruvate synthase. Also called pyruvate,water dikinase and PEP synthase. The member from Methanococcus jannaschii contains a large intein. This enzyme generates phosphoenolpyruvate (PEP) from pyruvate, hydrolyzing ATP to AMP and releasing inorganic phosphate in the process. The enzyme shows extensive homology to other enzymes that use PEP as substrate or product. This enzyme may provide PEP for gluconeogenesis, for PTS-type carbohydrate transport systems, or for other processes.
Probab=61.94 E-value=12 Score=37.49 Aligned_cols=42 Identities=26% Similarity=0.305 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHhCCC-------------------------CCCCcc-hhhHHHHHH----HHHHHHHhhh
Q 037966 134 DALIGRLRAAFEEHGGK-------------------------PEANPF-GARAVRLYL----REVRDSQAKA 175 (205)
Q Consensus 134 DALIGRLRAafEE~Gg~-------------------------PE~NPF-~araVRlYL----ReVRd~QAkA 175 (205)
|.+.-.+|.+++.++++ .|.||| |.|.||+|| .++=+.|.+|
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 55566778888776544 378999 889999999 4466666554
No 11
>PF00539 Tat: Transactivating regulatory protein (Tat); InterPro: IPR001831 Like other lentiviruses, Human immunodeficiency virus 1 (HIV-1) encodes a trans-activating regulatory protein (Tat), which is essential for efficient transcription of the viral genome [, ]. Tat acts by binding to an RNA stem-loop structure, the trans-activating response element (TAR), found at the 5' ends of nascent HIV-1 transcripts. In binding to TAR, Tat alters the properties of the transcription complex, recruits a positive transcription elongation complex (P-TEFb) and hence increases the production of full-length viral RNA []. Tat protein also associates with RNA polymerase II complexes during early transcription elongation after the promoter clearance and before the synthesis of full-length TAR RNA transcript. This interaction of Tat with RNA polymerase II elongation complexes is P-TEFb-independent. There are two Tat binding sites on each transcription elongation complex; one is located on TAR RNA and the other one on RNA polymerase II near the exit site for nascent mRNA transcripts which suggests that two Tat molecules are involved in performing various functions during a single round of HIV-1 mRNA synthesis []. The minimum Tat sequence that can mediate specific TAR binding in vitro has been mapped to a basic domain of 10 amino acids, comprising mostly Arg and Lys residues. Regulatory activity, however, also requires the 47 N-terminal residues, which interact with components of the transcription complex and function as a transcriptional activation domain [, , ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 2W2H_D 1ZBN_B 1TVS_A 1TVT_A 3O6L_C 3O6M_C 3MI9_C 3MIA_C 1JFW_A 1TBC_A ....
Probab=61.41 E-value=4.2 Score=30.45 Aligned_cols=19 Identities=42% Similarity=0.688 Sum_probs=13.6
Q ss_pred HhhhcCCchhhhhcCCCCC
Q 037966 172 QAKARGISYEKKKRKRPPQ 190 (205)
Q Consensus 172 QAkARgi~y~kkkrkr~~~ 190 (205)
..|+-||.|.+|||||..+
T Consensus 44 l~KgLGI~Y~r~rrRrr~~ 62 (68)
T PF00539_consen 44 LQKGLGISYGRKRRRRRTP 62 (68)
T ss_dssp CCTSSSTSSSSSSCSCCCS
T ss_pred eeCCCcccccccccCcCCC
Confidence 3578899999776655443
No 12
>cd01185 INT_Tn4399 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the Bacteroides mobilizable transposon, Tn4399, integrase.
Probab=60.10 E-value=40 Score=27.38 Aligned_cols=33 Identities=15% Similarity=0.342 Sum_probs=26.3
Q ss_pred hhhHHHHHHHhcCC--CCccccccchhhhHHHHhh
Q 037966 65 DWNTFGQYLRNHRP--PLSLERCSGAHVLEFLRYL 97 (205)
Q Consensus 65 dWntf~qyL~n~rP--PlsL~~csg~hVleFLryl 97 (205)
..+.|..||....+ .+.+..-+..||.+|+.|+
T Consensus 44 ~~~~~~~~~~~~~~~~~~~l~~i~~~~i~~~~~~l 78 (299)
T cd01185 44 HLKNLREFIECTYKEIDIALLELTREFILEFKLFL 78 (299)
T ss_pred HHHHHHHHHHHhcCccCCCHHHccHHHHHHHHHHH
Confidence 46678888876554 6778888899999999998
No 13
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=59.47 E-value=3.4 Score=33.20 Aligned_cols=43 Identities=26% Similarity=0.303 Sum_probs=32.9
Q ss_pred hhHHHHhhcccCcccccccCCCCcCCCCCCCCCCCchhhhcchhHHHHHHHHHHHHHhCCCCC
Q 037966 90 VLEFLRYLDQFGKTKVHTQLCPFFGHPNPPAPCPCPLRQAWGSLDALIGRLRAAFEEHGGKPE 152 (205)
Q Consensus 90 VleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAafEE~Gg~PE 152 (205)
+|+|+ |||..|+| |... ...+.+|+..+-+|+.+|+..|..++
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 46786 56655776 4433 36678999999999999999998754
No 14
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=55.13 E-value=17 Score=36.40 Aligned_cols=35 Identities=26% Similarity=0.433 Sum_probs=29.2
Q ss_pred hhHHHHHHHHHHHHHhCCC--------------------CCCCcc-hhhHHHHHHH
Q 037966 132 SLDALIGRLRAAFEEHGGK--------------------PEANPF-GARAVRLYLR 166 (205)
Q Consensus 132 SLDALIGRLRAafEE~Gg~--------------------PE~NPF-~araVRlYLR 166 (205)
+.|......|.+.+.++++ +|.||| |.|+||+||+
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 4678888889888888765 589999 7899999984
No 15
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=54.07 E-value=11 Score=28.77 Aligned_cols=18 Identities=28% Similarity=0.471 Sum_probs=14.4
Q ss_pred hhHHHHHHHHHHHHHhCC
Q 037966 132 SLDALIGRLRAAFEEHGG 149 (205)
Q Consensus 132 SLDALIGRLRAafEE~Gg 149 (205)
+||.+|.|||.-+++.+.
T Consensus 191 ~~~~~i~rlR~kl~~~~~ 208 (225)
T PRK10529 191 YLRIYMGHLRQKLEQDPA 208 (225)
T ss_pred CHHHHHHHHHHHhccCCC
Confidence 589999999999976543
No 16
>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=53.55 E-value=16 Score=32.90 Aligned_cols=40 Identities=33% Similarity=0.324 Sum_probs=31.3
Q ss_pred cchhHHHHHHHHHHHHHhCCC----------------------CCCCcc-hhhHHHHHHHHHH
Q 037966 130 WGSLDALIGRLRAAFEEHGGK----------------------PEANPF-GARAVRLYLREVR 169 (205)
Q Consensus 130 WGSLDALIGRLRAafEE~Gg~----------------------PE~NPF-~araVRlYLReVR 169 (205)
+=+.|.+...++.+.+.++++ .|.||| |-|+||+||..-.
T Consensus 58 ~p~e~eq~~~y~~i~~~~~~~pV~iRtlD~g~dK~l~~~~~~~~E~NP~LG~RGiR~~l~~p~ 120 (293)
T PF02896_consen 58 PPSEEEQYEIYRKIAEAMGGKPVTIRTLDIGGDKPLPYLSREPKEENPALGLRGIRRSLAHPE 120 (293)
T ss_dssp HHHHHHHHHHHHHHHHHTTTSEEEEE---SBCCCGSCSSHHCH--SSGGGSSBTHHHHHHSHH
T ss_pred CchHHHHHHHHHHHHHHhccCcEEEEecCCCCCccCCcccccccccccccccccccccccchh
Confidence 446788899999999988876 569998 8899999997633
No 17
>PF05528 Coronavirus_5: Coronavirus gene 5 protein; InterPro: IPR008458 Infectious bronchitis virus, a member of Coronaviridae family, has a single-stranded positive-sense RNA genome, which is 27 kb in length. Gene 5 contains two (5a and 5b) open reading frames. The function of the 5a and 5b proteins is unknown [].
Probab=52.92 E-value=2.4 Score=32.84 Aligned_cols=19 Identities=53% Similarity=0.774 Sum_probs=15.0
Q ss_pred CCCCcc---hhhHHHHHHHHHH
Q 037966 151 PEANPF---GARAVRLYLREVR 169 (205)
Q Consensus 151 PE~NPF---~araVRlYLReVR 169 (205)
..+||| .||-+|+||||=-
T Consensus 4 ~k~NPfr~aiARKaRiyLr~Gl 25 (82)
T PF05528_consen 4 SKDNPFRGAIARKARIYLREGL 25 (82)
T ss_pred cccCchhhhhhhheeeeeecCC
Confidence 348999 5789999999743
No 18
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=50.77 E-value=23 Score=24.09 Aligned_cols=53 Identities=19% Similarity=0.373 Sum_probs=32.1
Q ss_pred hhhhHHHHHHHhcCCCCccccccchhhhHHHHhhc-ccCcccccccCCCCcCCCCCCCCCCCchhhhcchhHHHHHHHHH
Q 037966 64 RDWNTFGQYLRNHRPPLSLERCSGAHVLEFLRYLD-QFGKTKVHTQLCPFFGHPNPPAPCPCPLRQAWGSLDALIGRLRA 142 (205)
Q Consensus 64 rdWntf~qyL~n~rPPlsL~~csg~hVleFLrylD-qfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRA 142 (205)
...+.|.+|+.+. ++...+..||.+||.||- .-| .+..++...+.-||.
T Consensus 24 ~~l~~f~~~~~~~----~~~~it~~~i~~y~~~l~~~~~--------------------------~s~~T~~~~~~~l~~ 73 (85)
T PF13495_consen 24 YHLKRFLRFLGNK----PPDEITPEDIEQYLNYLQNERG--------------------------LSPSTINQYLSALRS 73 (85)
T ss_dssp HHHHHHHTTSSS------GGG--HHHHHHHHHHHHTTT-----------------------------HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcccC----ccchhHHHHHHHHHHHHHHhcC--------------------------CCHHHHHHHHHHHHH
Confidence 4455677777633 456678999999999987 322 345566666777777
Q ss_pred HHHH
Q 037966 143 AFEE 146 (205)
Q Consensus 143 afEE 146 (205)
.|+-
T Consensus 74 ff~~ 77 (85)
T PF13495_consen 74 FFRW 77 (85)
T ss_dssp HHHC
T ss_pred HHHH
Confidence 6653
No 19
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=49.29 E-value=79 Score=24.83 Aligned_cols=38 Identities=29% Similarity=0.352 Sum_probs=27.9
Q ss_pred hhhhhhHHHHHHHhcCCCCccccccchhhhHHHHhhccc
Q 037966 62 KRRDWNTFGQYLRNHRPPLSLERCSGAHVLEFLRYLDQF 100 (205)
Q Consensus 62 KRrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqf 100 (205)
-+.+|+.|..|+..... ..+..-...||.+||.++-+.
T Consensus 31 ~~~~~~~~~~~~~~~~~-~~~~~i~~~~i~~~~~~~~~~ 68 (297)
T PRK00236 31 YRRDLRAFLAFLEEHGI-SSLQDLDAADLRSFLARRRRQ 68 (297)
T ss_pred HHHHHHHHHHHHHHcCC-CchhhCCHHHHHHHHHHHHhc
Confidence 34577888888887543 556677889999999877543
No 20
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=45.30 E-value=16 Score=27.92 Aligned_cols=23 Identities=30% Similarity=0.570 Sum_probs=17.5
Q ss_pred hhhhcc--------hhHHHHHHHHHHHHHhC
Q 037966 126 LRQAWG--------SLDALIGRLRAAFEEHG 148 (205)
Q Consensus 126 lRQAWG--------SLDALIGRLRAafEE~G 148 (205)
+++.|| +||.+|.|||.-+++.+
T Consensus 175 ~~~~w~~~~~~~~~~v~~~i~rLR~kl~~~~ 205 (223)
T PRK10816 175 MLQLYPDAELRESHTIDVLMGRLRKKIQAQY 205 (223)
T ss_pred HHHhcCCCCCCCcCCHHHHHHHHHHHhccCC
Confidence 456676 78999999999887643
No 21
>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=44.68 E-value=21 Score=34.57 Aligned_cols=36 Identities=31% Similarity=0.517 Sum_probs=29.0
Q ss_pred hhHHHHHHHHHHHHHhCCC---------------------CCCCcc-hhhHHHHHHHH
Q 037966 132 SLDALIGRLRAAFEEHGGK---------------------PEANPF-GARAVRLYLRE 167 (205)
Q Consensus 132 SLDALIGRLRAafEE~Gg~---------------------PE~NPF-~araVRlYLRe 167 (205)
+.|...-..|.+.+.++++ .|.||| |-|++|+||..
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 4577777788888888766 379998 88999999974
No 22
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=44.42 E-value=22 Score=32.91 Aligned_cols=38 Identities=29% Similarity=0.527 Sum_probs=34.0
Q ss_pred hhhhhHHHHHHHhcCCCC-ccccccchhhhHHHHhhcccCc
Q 037966 63 RRDWNTFGQYLRNHRPPL-SLERCSGAHVLEFLRYLDQFGK 102 (205)
Q Consensus 63 RrdWntf~qyL~n~rPPl-sL~~csg~hVleFLrylDqfGK 102 (205)
|||-+.|.+||..+- + +|...+-.||.+||.++-++|.
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 689999999999876 5 6888899999999999999995
No 23
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=42.69 E-value=25 Score=23.42 Aligned_cols=21 Identities=52% Similarity=0.877 Sum_probs=18.1
Q ss_pred chhHHHHHHHHHHHHHhCCCC
Q 037966 131 GSLDALIGRLRAAFEEHGGKP 151 (205)
Q Consensus 131 GSLDALIGRLRAafEE~Gg~P 151 (205)
-+||.+|-|||..+++.|..+
T Consensus 44 ~~l~~~I~rLR~kL~~~~~~~ 64 (77)
T PF00486_consen 44 NSLDVHISRLRKKLEDAGGDP 64 (77)
T ss_dssp HHHHHHHHHHHHHHHSSTTSS
T ss_pred hhHHHHHHHHHHHHhhcCCCC
Confidence 489999999999999987543
No 24
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=42.48 E-value=49 Score=27.16 Aligned_cols=26 Identities=27% Similarity=0.324 Sum_probs=19.7
Q ss_pred chhHHHHHHHHHHHHH---hCCCCCCCcch
Q 037966 131 GSLDALIGRLRAAFEE---HGGKPEANPFG 157 (205)
Q Consensus 131 GSLDALIGRLRAafEE---~Gg~PE~NPF~ 157 (205)
-++...+..|+++|+- +|.-+ .|||.
T Consensus 135 ~t~~~~~~~l~~~~~~a~~~g~i~-~nP~~ 163 (357)
T cd00801 135 ETARRVRQRLKQVFRYAIARGLIE-ANPAA 163 (357)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCcc-cCchH
Confidence 4788899999999984 44433 89985
No 25
>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=41.40 E-value=1.5e+02 Score=22.58 Aligned_cols=87 Identities=17% Similarity=0.221 Sum_probs=57.0
Q ss_pred hhhHHHHHHHhcCCCCccccccchhhhHHHHhhcccCcccccccCCCCcCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 037966 65 DWNTFGQYLRNHRPPLSLERCSGAHVLEFLRYLDQFGKTKVHTQLCPFFGHPNPPAPCPCPLRQAWGSLDALIGRLRAAF 144 (205)
Q Consensus 65 dWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAaf 144 (205)
|..++.++|.+..-=-|...++-....++|.++.+.|-. +..+.=.+-..|. . ...+.+.+++|..
T Consensus 2 ddd~YR~~L~~~~Gk~S~k~lt~~el~~vl~~l~~~G~k-~~~~~~~~~~~~~--~-----------~~~~q~~KI~aLw 67 (119)
T PF06252_consen 2 DDDTYRALLQRVTGKSSSKDLTEAELEKVLDELKRLGFK-PPKPARRPGRRPG--M-----------ATSAQLRKIRALW 67 (119)
T ss_pred CHHHHHHHHHHHhChhhHHHCCHHHHHHHHHHHHHccCc-CccccccCCCCCC--C-----------cchHHHHHHHHHH
Confidence 556788888888887788889999999999988888853 2111111111111 1 1788999999999
Q ss_pred HHhCCCCC-CCcchhhHHHHHHH
Q 037966 145 EEHGGKPE-ANPFGARAVRLYLR 166 (205)
Q Consensus 145 EE~Gg~PE-~NPF~araVRlYLR 166 (205)
.++|.... .|| ...++.-|++
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 26
>PRK09279 pyruvate phosphate dikinase; Provisional
Probab=39.72 E-value=26 Score=36.24 Aligned_cols=36 Identities=36% Similarity=0.472 Sum_probs=0.0
Q ss_pred HHHHHHHhCCC-----------CCCCcc-hhhHHHHHH--HHHHHHHhhh
Q 037966 140 LRAAFEEHGGK-----------PEANPF-GARAVRLYL--REVRDSQAKA 175 (205)
Q Consensus 140 LRAafEE~Gg~-----------PE~NPF-~araVRlYL--ReVRd~QAkA 175 (205)
++..-++.|+. -|.||| |.|.+|+|| .|+=++|.+|
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 27
>PF13276 HTH_21: HTH-like domain
Probab=38.30 E-value=54 Score=21.87 Aligned_cols=29 Identities=28% Similarity=0.434 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHhCCCCCCCcchhhHHHHHHHH
Q 037966 134 DALIGRLRAAFEEHGGKPEANPFGARAVRLYLRE 167 (205)
Q Consensus 134 DALIGRLRAafEE~Gg~PE~NPF~araVRlYLRe 167 (205)
|+|+-.++++|+++.+ =||.+-|..+|+.
T Consensus 4 ~~l~~~I~~i~~~~~~-----~yG~rri~~~L~~ 32 (60)
T PF13276_consen 4 EALRELIKEIFKESKP-----TYGYRRIWAELRR 32 (60)
T ss_pred HHHHHHHHHHHHHcCC-----CeehhHHHHHHhc
Confidence 6789999999999976 3788888888876
No 28
>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=37.91 E-value=17 Score=22.45 Aligned_cols=16 Identities=38% Similarity=0.918 Sum_probs=13.4
Q ss_pred cCCCCcCCCCCCCCCC
Q 037966 108 QLCPFFGHPNPPAPCP 123 (205)
Q Consensus 108 ~~C~ffG~p~ppapC~ 123 (205)
.+|.|||.|..-..|.
T Consensus 7 ~~CgF~G~~~t~~~Cs 22 (26)
T smart00259 7 PGCGFFGNPATEGLCS 22 (26)
T ss_pred CCCCCcCChhhcccCH
Confidence 6899999998777764
No 29
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=37.65 E-value=36 Score=22.58 Aligned_cols=19 Identities=42% Similarity=0.730 Sum_probs=17.1
Q ss_pred chhHHHHHHHHHHHHHhCC
Q 037966 131 GSLDALIGRLRAAFEEHGG 149 (205)
Q Consensus 131 GSLDALIGRLRAafEE~Gg 149 (205)
.+|+.+|-|||..+++.|+
T Consensus 45 ~~l~~~i~~LR~~l~~~~~ 63 (78)
T smart00862 45 NTLDVHISRLRKKLEDDGA 63 (78)
T ss_pred chHHHHHHHHHHHHhcCCC
Confidence 5799999999999999865
No 30
>PRK06464 phosphoenolpyruvate synthase; Validated
Probab=36.34 E-value=44 Score=33.88 Aligned_cols=15 Identities=47% Similarity=0.786 Sum_probs=13.7
Q ss_pred CCCcc-hhhHHHHHHH
Q 037966 152 EANPF-GARAVRLYLR 166 (205)
Q Consensus 152 E~NPF-~araVRlYLR 166 (205)
|.||| |.|.||+||.
T Consensus 597 E~NP~LG~RGiR~~l~ 612 (795)
T PRK06464 597 EENPMLGFRGASRYLS 612 (795)
T ss_pred CCCCccccchhhhccc
Confidence 78999 8899999996
No 31
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=36.08 E-value=34 Score=25.14 Aligned_cols=35 Identities=31% Similarity=0.544 Sum_probs=30.0
Q ss_pred CCCCchhhhcc----hhHHHHHHHHHHHHHhCCCCCCCc
Q 037966 121 PCPCPLRQAWG----SLDALIGRLRAAFEEHGGKPEANP 155 (205)
Q Consensus 121 pC~CPlRQAWG----SLDALIGRLRAafEE~Gg~PE~NP 155 (205)
-|+|-||..-+ ++|.|=-+|..+++||.-+...+|
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 47777988888 999999999999999987766666
No 32
>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=35.81 E-value=30 Score=22.14 Aligned_cols=13 Identities=38% Similarity=0.751 Sum_probs=10.6
Q ss_pred hHHHHHHHHHHHH
Q 037966 159 RAVRLYLREVRDS 171 (205)
Q Consensus 159 raVRlYLReVRd~ 171 (205)
-+|++||++|+..
T Consensus 2 D~l~~Yl~ei~~~ 14 (37)
T PF00140_consen 2 DSLRLYLKEIGRY 14 (37)
T ss_dssp HHHHHHHHHHHHS
T ss_pred cHHHHHHHHHcCC
Confidence 4799999999753
No 33
>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=34.90 E-value=47 Score=27.17 Aligned_cols=36 Identities=25% Similarity=0.458 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHhCCCCC---C---Cc-chhhHHHHHHHHHHH
Q 037966 135 ALIGRLRAAFEEHGGKPE---A---NP-FGARAVRLYLREVRD 170 (205)
Q Consensus 135 ALIGRLRAafEE~Gg~PE---~---NP-F~araVRlYLReVRd 170 (205)
.-|-+|+..|++.|...+ . ++ -.|..++.||||.-+
T Consensus 45 ~~i~~l~~~~d~~~~~~~~~~~~~~d~h~va~lLK~flReLP~ 87 (194)
T cd04372 45 EEIEDVKMAFDRDGEKADISATVYPDINVITGALKLYFRDLPI 87 (194)
T ss_pred HHHHHHHHHHcCCCCccCCcccccccHHHHHHHHHHHHHhCCC
Confidence 478889999998775432 1 22 368899999999754
No 34
>TIGR01828 pyru_phos_dikin pyruvate, phosphate dikinase. This model represents pyruvate,phosphate dikinase, also called pyruvate,orthophosphate dikinase. It is similar in sequence to other PEP-utilizing enzymes.
Probab=34.57 E-value=22 Score=36.51 Aligned_cols=25 Identities=40% Similarity=0.631 Sum_probs=19.3
Q ss_pred CCCCcc-hhhHHHHHH--HHHHHHHhhh
Q 037966 151 PEANPF-GARAVRLYL--REVRDSQAKA 175 (205)
Q Consensus 151 PE~NPF-~araVRlYL--ReVRd~QAkA 175 (205)
.|.||| +.|.||+|| .|+=++|.+|
T Consensus 652 ~E~NP~LG~RGiRl~l~~pei~~~QlrA 679 (856)
T TIGR01828 652 HEVNPMLGHRGCRLGITYPEIYEMQVRA 679 (856)
T ss_pred CCCCCccccchhhhccCChHHHHHHHHH
Confidence 499999 889999999 4555566554
No 35
>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=33.77 E-value=42 Score=26.59 Aligned_cols=64 Identities=23% Similarity=0.488 Sum_probs=43.6
Q ss_pred hhhhHHHHHHHhcCCCCccccccchhhhHHHHhhcccCcccccccCCCCcCCCCCCCCCCCchhhhcchhHHHHHHHHHH
Q 037966 64 RDWNTFGQYLRNHRPPLSLERCSGAHVLEFLRYLDQFGKTKVHTQLCPFFGHPNPPAPCPCPLRQAWGSLDALIGRLRAA 143 (205)
Q Consensus 64 rdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAa 143 (205)
.+|.++-.++.. |-.-.+.+--||-+|=.+.++ | .+| +|-|=..||+-++-||.|-..
T Consensus 22 ~~W~~LA~~i~~---~~~~~~y~~~ei~~ie~~~~~--------------g-~SP----T~~LL~dWgt~N~TV~~L~~l 79 (100)
T cd08793 22 EGWKKIAVAIKK---PSGDPRYSQFHIRRFEALVQQ--------------G-KSP----TCELLFDWGTTNCTVGDLVDL 79 (100)
T ss_pred ccHHHHHHHHhc---ccCCCCCCHHHHHHHHHHHHc--------------C-CCh----HHHHHHHHccCCCcHHHHHHH
Confidence 378888877755 223334544566666443333 2 222 455778999999999999999
Q ss_pred HHHhCC
Q 037966 144 FEEHGG 149 (205)
Q Consensus 144 fEE~Gg 149 (205)
|.+++-
T Consensus 80 L~k~~l 85 (100)
T cd08793 80 LIQNEF 85 (100)
T ss_pred HHHccc
Confidence 999884
No 36
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=31.36 E-value=32 Score=26.29 Aligned_cols=14 Identities=43% Similarity=1.075 Sum_probs=13.0
Q ss_pred hhhHHHHHHHhcCC
Q 037966 65 DWNTFGQYLRNHRP 78 (205)
Q Consensus 65 dWntf~qyL~n~rP 78 (205)
-|.||.+||..|.|
T Consensus 55 GW~tL~~fL~khDP 68 (73)
T smart00243 55 GWETLDEYLLKHDP 68 (73)
T ss_pred cHHHHHHHHHhCCC
Confidence 39999999999998
No 37
>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=31.31 E-value=25 Score=24.19 Aligned_cols=21 Identities=33% Similarity=0.456 Sum_probs=17.2
Q ss_pred cccchhhhHHHHhhcccCccc
Q 037966 84 RCSGAHVLEFLRYLDQFGKTK 104 (205)
Q Consensus 84 ~csg~hVleFLrylDqfGKTk 104 (205)
..|=+-++-+|.|+|+.|-|+
T Consensus 21 g~sRK~ai~lLE~lD~~g~T~ 41 (50)
T PF09107_consen 21 GLSRKYAIPLLEYLDREGITR 41 (50)
T ss_dssp TS-HHHHHHHHHHHHHTTSEE
T ss_pred CccHHHHHHHHHHHhccCCEE
Confidence 355677899999999999987
No 38
>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=31.26 E-value=61 Score=29.31 Aligned_cols=69 Identities=20% Similarity=0.224 Sum_probs=49.0
Q ss_pred CCCCCCCchHHHhhhhhhhHHHHHHHhcCCCCcc--ccccchhhhHHHHh-----------------hcccCcccccccC
Q 037966 49 SSSTTTLSRYENQKRRDWNTFGQYLRNHRPPLSL--ERCSGAHVLEFLRY-----------------LDQFGKTKVHTQL 109 (205)
Q Consensus 49 ~~~~~~~SrYesQKRrdWntf~qyL~n~rPPlsL--~~csg~hVleFLry-----------------lDqfGKTkVH~~~ 109 (205)
+.....-.+|-++=|..-.+|.+||+.+.|-... ..--...|.|||.. ....|..++|.-+
T Consensus 142 ~mt~~ef~~yL~kvr~~R~eF~~~L~~~~~e~~~~~~~~l~~~v~eFL~~~~~~~~~~~~~~~~~~~~~~~~~~~~hpsg 221 (312)
T PF11709_consen 142 GMTEGEFERYLKKVRPLRPEFKKWLREKHPESLTFDPSDLYDLVKEFLDLAPLKPPDVPDSKKSSSPYAEAGPPKTHPSG 221 (312)
T ss_pred CCCHHHHHHHHHHhHHHHHHHHHHHHHhChhhhccCHHHHHHHHHHHHhcccccCcccccchhccCcccccCCCccccCc
Confidence 3444556788888899999999999999986621 23345678899875 3346677788777
Q ss_pred CCCcCCCC
Q 037966 110 CPFFGHPN 117 (205)
Q Consensus 110 C~ffG~p~ 117 (205)
=--|.+++
T Consensus 222 GLSY~~~g 229 (312)
T PF11709_consen 222 GLSYNRTG 229 (312)
T ss_pred CcCcCCCc
Confidence 66666554
No 39
>PRK11177 phosphoenolpyruvate-protein phosphotransferase; Provisional
Probab=30.74 E-value=39 Score=33.02 Aligned_cols=36 Identities=31% Similarity=0.516 Sum_probs=29.5
Q ss_pred hhHHHHHHHHHHHHHhCCC---------------------CCCCcc-hhhHHHHHHHH
Q 037966 132 SLDALIGRLRAAFEEHGGK---------------------PEANPF-GARAVRLYLRE 167 (205)
Q Consensus 132 SLDALIGRLRAafEE~Gg~---------------------PE~NPF-~araVRlYLRe 167 (205)
+-|...--.|.+.+.++++ .|.||| |-|+||+||+.
T Consensus 309 ~eeeq~~~y~~i~~~~~~~~v~iRtlDiGgDK~~~~~~~~~E~NP~LG~RgiR~~l~~ 366 (575)
T PRK11177 309 TEEEQFQAYKAVAEAMGSQAVIVRTMDIGGDKELPYMNLPKEENPFLGWRAIRIAMDR 366 (575)
T ss_pred CHHHHHHHHHHHHHHcCCCeEEEECcCCCcccccccCCCCCCCCcccccchhhhcCCC
Confidence 4677788888888888765 379999 77999999964
No 40
>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=30.60 E-value=42 Score=23.77 Aligned_cols=31 Identities=19% Similarity=0.485 Sum_probs=24.3
Q ss_pred hhHHHHHHHhcCCCCccccccchhhhHHHHhhcccC
Q 037966 66 WNTFGQYLRNHRPPLSLERCSGAHVLEFLRYLDQFG 101 (205)
Q Consensus 66 Wntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfG 101 (205)
-+.|.+=|++.+| +.+.+||..|..|-.+||
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 4557777777777 456889999999999998
No 41
>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=30.11 E-value=1.9e+02 Score=24.50 Aligned_cols=37 Identities=19% Similarity=0.298 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHhC---CCCCCCcc----hhhHHHHHHHHHHH
Q 037966 134 DALIGRLRAAFEEHG---GKPEANPF----GARAVRLYLREVRD 170 (205)
Q Consensus 134 DALIGRLRAafEE~G---g~PE~NPF----~araVRlYLReVRd 170 (205)
-+-|.+|+..|++.. ...+-+.+ .+..++.||||.-+
T Consensus 60 ~~~i~~L~~~~d~~~~~~~~~~~~~~~vh~va~lLK~fLReLPe 103 (225)
T cd04396 60 SKRIRELQLIFSTPPDYGKSFDWDGYTVHDAASVLRRYLNNLPE 103 (225)
T ss_pred HHHHHHHHHHHccCcccCCcCCccCCCHHHHHHHHHHHHHhCCC
Confidence 357889999998753 22222332 68899999999744
No 42
>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=29.20 E-value=24 Score=28.23 Aligned_cols=36 Identities=28% Similarity=0.448 Sum_probs=29.4
Q ss_pred hhhhHHHHHHHh---cCCCCccccccchhhhHHHHhhcc
Q 037966 64 RDWNTFGQYLRN---HRPPLSLERCSGAHVLEFLRYLDQ 99 (205)
Q Consensus 64 rdWntf~qyL~n---~rPPlsL~~csg~hVleFLrylDq 99 (205)
..|..|++|+-. ..-|-.+.++.+.++.+||.-+|.
T Consensus 65 ~~l~~fG~~~~~~~~~~~~~~~l~~~g~~~~~FL~~ld~ 103 (171)
T PF07700_consen 65 ELLEEFGEYFFDFLSESGYERLLRFLGRDLFDFLNNLDN 103 (171)
T ss_dssp HHHHHHHHHHHHHHHHHCCHHHHHCTCSSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhCcHHHHHhcCCCHHHHHHhHHH
Confidence 468889988876 455777889999999999998875
No 43
>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=28.67 E-value=11 Score=25.66 Aligned_cols=72 Identities=14% Similarity=0.218 Sum_probs=45.3
Q ss_pred hhhhhhHHHHHHHhcCC--CCccccccchhhhHHHHhhcccC--cccccc---cCCCCcCCCCCCCCCCCchhhhcchhH
Q 037966 62 KRRDWNTFGQYLRNHRP--PLSLERCSGAHVLEFLRYLDQFG--KTKVHT---QLCPFFGHPNPPAPCPCPLRQAWGSLD 134 (205)
Q Consensus 62 KRrdWntf~qyL~n~rP--PlsL~~csg~hVleFLrylDqfG--KTkVH~---~~C~ffG~p~ppapC~CPlRQAWGSLD 134 (205)
++.||..|.+.+.+..- +.....+...+|.+.+.++-+.| -+++-. -+|.|- |=.--...|
T Consensus 6 ~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~Ga~~~~~sGsG~G~~v~~------------l~~~~~~~~ 73 (85)
T PF08544_consen 6 AEGDLELLGELMNENQENEPENYREVLTPEIDELKEAAEENGALGAKMSGSGGGPTVFA------------LCKDEDDAE 73 (85)
T ss_dssp HTTCHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHTTESEEEEETTSSSSEEEE------------EESSHHHHH
T ss_pred HCcCHHHHHHHHHHhhhhcchHHHHHcCHHHHHHHHHHHHCCCCceecCCCCCCCeEEE------------EECCHHHHH
Confidence 56899999999995544 44456677788888888888888 333311 333322 111223566
Q ss_pred HHHHHHHHHHH
Q 037966 135 ALIGRLRAAFE 145 (205)
Q Consensus 135 ALIGRLRAafE 145 (205)
.++-+|++.|+
T Consensus 74 ~v~~~l~~~~~ 84 (85)
T PF08544_consen 74 RVAEALREHYK 84 (85)
T ss_dssp HHHHHHHHHTH
T ss_pred HHHHHHHHhCC
Confidence 67777777664
No 44
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed
Probab=28.39 E-value=1.2e+02 Score=25.73 Aligned_cols=68 Identities=18% Similarity=0.270 Sum_probs=43.4
Q ss_pred hhhhhHHHHHHHhcCC-----CC-----ccccccchhhhHHHHhhcccCcccccccCCCCcCCCCCCCCCCCchhhhcch
Q 037966 63 RRDWNTFGQYLRNHRP-----PL-----SLERCSGAHVLEFLRYLDQFGKTKVHTQLCPFFGHPNPPAPCPCPLRQAWGS 132 (205)
Q Consensus 63 RrdWntf~qyL~n~rP-----Pl-----sL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGS 132 (205)
+++...|.+||..+.. .. .|...+..||.+|+.|+.+.-. +.++.+ +...+..+
T Consensus 42 ~~~l~~f~~~l~~~~~~~~~~~~~~~~~~l~~lt~~~i~~f~~~l~~~~~---------~~~~~~-------~~~~s~~T 105 (357)
T PRK05084 42 LTEYRRFFNWLISEGLSDASKIKDIPLSTLENLTKKDVEAFILYLRERPL---------LNGHST-------KKGNSQTT 105 (357)
T ss_pred HHHHHHHHHHHHHcCCCCcCCcccCCHHHHHhhhHHHHHHHHHHHHhccc---------cccccc-------ccchhHHH
Confidence 3556778888876532 11 2456789999999999864210 000000 01246678
Q ss_pred hHHHHHHHHHHHHH
Q 037966 133 LDALIGRLRAAFEE 146 (205)
Q Consensus 133 LDALIGRLRAafEE 146 (205)
+...++-||++|.-
T Consensus 106 i~~~l~~l~~~~~~ 119 (357)
T PRK05084 106 INRTLSALKSLFKY 119 (357)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999999984
No 45
>PF09958 DUF2192: Uncharacterized protein conserved in archaea (DUF2192); InterPro: IPR018693 This family of various hypothetical archaeal proteins has no known function.
Probab=27.27 E-value=54 Score=29.50 Aligned_cols=21 Identities=33% Similarity=0.547 Sum_probs=18.3
Q ss_pred hhHHHHHHHHHHHHHhCCCCC
Q 037966 132 SLDALIGRLRAAFEEHGGKPE 152 (205)
Q Consensus 132 SLDALIGRLRAafEE~Gg~PE 152 (205)
+=+.||.-||..||++|..|=
T Consensus 27 ~R~~lv~~L~~~Y~~~gIeP~ 47 (231)
T PF09958_consen 27 DREELVELLREVYEENGIEPF 47 (231)
T ss_pred CHHHHHHHHHHHHHHcCCCcC
Confidence 558999999999999998763
No 46
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=26.56 E-value=58 Score=22.40 Aligned_cols=20 Identities=30% Similarity=0.509 Sum_probs=17.1
Q ss_pred chhHHHHHHHHHHHHHhCCC
Q 037966 131 GSLDALIGRLRAAFEEHGGK 150 (205)
Q Consensus 131 GSLDALIGRLRAafEE~Gg~ 150 (205)
.+|+.+|=|||..+.+.|+.
T Consensus 62 ~~l~~~I~rLRkkl~~~~~~ 81 (95)
T cd00383 62 RTVDVHISRLRKKLEDDPSN 81 (95)
T ss_pred ccHHHHHHHHHHHhccCCCC
Confidence 57999999999999987653
No 47
>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=26.44 E-value=68 Score=30.43 Aligned_cols=53 Identities=34% Similarity=0.491 Sum_probs=34.6
Q ss_pred hhhhHHHHhhcccC-cccccccCCCCcCCCCCCCCCCCchhhhcchh--HH----HHHHHHHHHHHhCCCCC
Q 037966 88 AHVLEFLRYLDQFG-KTKVHTQLCPFFGHPNPPAPCPCPLRQAWGSL--DA----LIGRLRAAFEEHGGKPE 152 (205)
Q Consensus 88 ~hVleFLrylDqfG-KTkVH~~~C~ffG~p~ppapC~CPlRQAWGSL--DA----LIGRLRAafEE~Gg~PE 152 (205)
.-=++||..|.+.| |-+|+ ..-.|-.+.++ |..+ |. .--||..||+++|.+|.
T Consensus 49 ~agl~f~e~l~~~gakv~Vp----------TTlNp~~~D~~--w~~~gvd~~f~~~q~~i~~ay~~mG~~~t 108 (389)
T cd01355 49 DAGLEFLERLADQGAKVAVP----------TTLNPISMDLH--WRELGVDEEFAEKQARLVKAYKAMGVDPT 108 (389)
T ss_pred hhhHHHHHHHHhCCCeEeec----------CccCCcccCcc--hhhcCCCHHHHHHHHHHHHHHHHcCCccc
Confidence 34479999886666 34333 23455666676 8755 22 34478899999998765
No 48
>KOG1452 consensus Predicted Rho GTPase-activating protein [Signal transduction mechanisms]
Probab=26.03 E-value=35 Score=32.95 Aligned_cols=31 Identities=32% Similarity=0.483 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCC--------CCCCcchhhHHHHHHHHHHH
Q 037966 139 RLRAAFEEHGGK--------PEANPFGARAVRLYLREVRD 170 (205)
Q Consensus 139 RLRAafEE~Gg~--------PE~NPF~araVRlYLReVRd 170 (205)
-||++||-||+. |+.|=. +..++.||||+=|
T Consensus 233 mLR~~fe~n~r~~el~~E~iPD~nvI-tg~~kD~lrElpE 271 (442)
T KOG1452|consen 233 MLRRDFEPNGRDFELGAESIPDYNVI-TGDSKDELRELPE 271 (442)
T ss_pred HHHHHhccCCcccccccccCCCccee-ecccHhHHHhCCC
Confidence 589999999975 344443 4589999999743
No 49
>PTZ00398 phosphoenolpyruvate carboxylase; Provisional
Probab=26.01 E-value=1.2e+02 Score=32.02 Aligned_cols=43 Identities=21% Similarity=0.358 Sum_probs=32.2
Q ss_pred cchhHHHHHHHHHHHHHhCC------------------CCCCCcch-------------hhHHHHHHHHHHHHH
Q 037966 130 WGSLDALIGRLRAAFEEHGG------------------KPEANPFG-------------ARAVRLYLREVRDSQ 172 (205)
Q Consensus 130 WGSLDALIGRLRAafEE~Gg------------------~PE~NPF~-------------araVRlYLReVRd~Q 172 (205)
|-.+=.|..+|+.+++++|+ .=++|||. ..|+++|++++++.-
T Consensus 264 ~~aiP~~~~~l~~al~~~~~~~~~~~~~~i~fGSWiGGDRDGNP~VTaevT~~~l~~~r~~al~~Y~~~l~~L~ 337 (974)
T PTZ00398 264 FDALPNFIRYIDNVLYEYNLDPLPPTKKLFTFSSWVGGDRDGNPFVTAEVTRQVVYFNRIRACELFIHMIEKLM 337 (974)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCCCCceeccCCCCCCCCCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566788899999988754 23499996 357889999998753
No 50
>KOG4405 consensus GDP dissociation inhibitor [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=25.36 E-value=29 Score=34.49 Aligned_cols=80 Identities=30% Similarity=0.551 Sum_probs=60.1
Q ss_pred hHHHHHHHhcCCCCccccc--------cch---------hhhHHHHhhcccCcccccccCCCCcCCCCCCCCCCCchhhh
Q 037966 67 NTFGQYLRNHRPPLSLERC--------SGA---------HVLEFLRYLDQFGKTKVHTQLCPFFGHPNPPAPCPCPLRQA 129 (205)
Q Consensus 67 ntf~qyL~n~rPPlsL~~c--------sg~---------hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQA 129 (205)
++|.+||+..+=+..|.+| +.. -...||..+.+||.|- --=|.||+-..| -|-|-+--.
T Consensus 223 ~~F~EyL~~~rltp~lqs~vl~aIaM~~~~~~tt~eGm~at~~fl~slGrfgntp---fLfPlYGqGELp-QcFCRlcAV 298 (547)
T KOG4405|consen 223 RPFSEYLKTMRLTPKLQSIVLHAIAMLSESQLTTIEGMDATKNFLTSLGRFGNTP---FLFPLYGQGELP-QCFCRLCAV 298 (547)
T ss_pred CcHHHHHHhcCCChhhHHHHHHHHHhcCcccccHHHHHHHHHHHHHHhhccCCCc---ceeeccCCCcch-HHHHHHHHH
Confidence 3999999999988777644 211 2457999999999987 345678888764 477777777
Q ss_pred cch------------hHHHHHHHHHHHHHhCCC
Q 037966 130 WGS------------LDALIGRLRAAFEEHGGK 150 (205)
Q Consensus 130 WGS------------LDALIGRLRAafEE~Gg~ 150 (205)
.|+ ||.++++..|+.+.+|-+
T Consensus 299 fGgIYcLr~~Vq~ivldk~s~~~~~~l~s~g~r 331 (547)
T KOG4405|consen 299 FGGIYCLRRPVQAIVLDKESLDCKAILDSFGQR 331 (547)
T ss_pred hcceEEeccchhheeecccccchhhhHhhhcch
Confidence 775 577778888999999965
No 51
>cd04388 RhoGAP_p85 RhoGAP_p85: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in the p85 isoforms of the regulatory subunit of the class IA PI3K (phosphatidylinositol 3'-kinase). This domain is also called Bcr (breakpoint cluster region protein) homology (BH) domain. Class IA PI3Ks are heterodimers, containing a regulatory subunit (p85) and a catalytic subunit (p110) and are activated by growth factor receptor tyrosine kinases (RTKs); this activation is mediated by the p85 subunit. p85 isoforms, alpha and beta, contain a C-terminal p110-binding domain flanked by two SH2 domains, an N-terminal SH3 domain, and a RhoGAP domain flanked by two proline-rich regions. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell p
Probab=25.28 E-value=75 Score=27.13 Aligned_cols=34 Identities=18% Similarity=0.271 Sum_probs=24.3
Q ss_pred HHHHHHHHHHhCCCCC---CCcc-hhhHHHHHHHHHHH
Q 037966 137 IGRLRAAFEEHGGKPE---ANPF-GARAVRLYLREVRD 170 (205)
Q Consensus 137 IGRLRAafEE~Gg~PE---~NPF-~araVRlYLReVRd 170 (205)
+-.||.+||+.+...+ .++. .+.++|.||||.-|
T Consensus 45 ~~~lk~~~d~~~~~~d~~~~dv~~va~~LK~ylReLPe 82 (200)
T cd04388 45 LTELRQILDCDAASVDLEQFDVAALADALKRYLLDLPN 82 (200)
T ss_pred HHHHHHHHhcCCCCCCcccccHHHHHHHHHHHHHhCCC
Confidence 4568999998655443 2232 78999999998755
No 52
>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=25.16 E-value=1.5e+02 Score=22.70 Aligned_cols=45 Identities=20% Similarity=0.522 Sum_probs=36.0
Q ss_pred hcc---hhHHHHHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHhhhc
Q 037966 129 AWG---SLDALIGRLRAAFEEHGGKPEANPFGARAVRLYLREVRDSQAKAR 176 (205)
Q Consensus 129 AWG---SLDALIGRLRAafEE~Gg~PE~NPF~araVRlYLReVRd~QAkAR 176 (205)
-|- ++..+|-.|++.+.+- -..+|+-..|.++|..+-.+.+.+||
T Consensus 90 ~W~p~~~i~~il~~i~~ll~~p---~~~~~~n~~a~~~~~~~~~~f~~~~~ 137 (140)
T PF00179_consen 90 SWSPSYTIESILLSIQSLLSEP---NPEDPLNEEAAELYKNDREEFEKKAR 137 (140)
T ss_dssp TC-TTSHHHHHHHHHHHHHHST---CTTSTSSHHHHHHHHHCHHHHHHHHH
T ss_pred cCCcccccccHHHHHHHHHhCC---CCCCcchHHHHHHHHHCHHHHHHHHH
Confidence 376 8888888999999554 45788999999999998777777775
No 53
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=25.11 E-value=57 Score=27.70 Aligned_cols=27 Identities=37% Similarity=0.694 Sum_probs=21.7
Q ss_pred chhhhcc--------hhHHHHHHHHHHHHHhCCCC
Q 037966 125 PLRQAWG--------SLDALIGRLRAAFEEHGGKP 151 (205)
Q Consensus 125 PlRQAWG--------SLDALIGRLRAafEE~Gg~P 151 (205)
-+.+.|| +||..|.|||.-.++.+..+
T Consensus 178 L~~~vw~~~~~~~~rtvdvhI~rLR~Kl~~~~~~~ 212 (229)
T COG0745 178 LLEAVWGYDFEVDSRTVDVHISRLRKKLEKDPGAG 212 (229)
T ss_pred HHHHhcCCCCCCCccCHHHHHHHHHHHhccCCCCC
Confidence 3677787 49999999999999886543
No 54
>PF12067 Sox_C_TAD: Sox C-terminal transactivation domain; InterPro: IPR021934 The Sox family of high mobility group (HMG) box transcription factors that are homologous to the Y-chromosome encoded sex- determining factor SRY plays important roles in embryonic development. Sox18, together with Sox7 and -17, constitutes the subgroup F within this family. Bioinformatic analysis of the C-termini of subgroup F Sox family members from different species including humans, mice, rat, chicken and Xenopus revealed three conserved blocks including highly conserved residues. They were termed proline, charged, and serine according to the predominance of the respective amino acids. The charged block comprises a strong transactivating domain []. This entry covers the entire Sox C-terminal domain, and was previously annotated as DUF3547.
Probab=25.09 E-value=39 Score=29.42 Aligned_cols=17 Identities=35% Similarity=0.491 Sum_probs=12.4
Q ss_pred hhhhhhHHHHHHHhcCC
Q 037966 62 KRRDWNTFGQYLRNHRP 78 (205)
Q Consensus 62 KRrdWntf~qyL~n~rP 78 (205)
---|.++|.|||...+.
T Consensus 139 geVDR~EFdQYLn~~~~ 155 (197)
T PF12067_consen 139 GEVDRTEFDQYLNSSRC 155 (197)
T ss_pred hhhhHHHHHHHhccccC
Confidence 33478999999996443
No 55
>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=24.64 E-value=66 Score=28.36 Aligned_cols=25 Identities=24% Similarity=0.436 Sum_probs=23.3
Q ss_pred hhhcchhHHHHHHHHHHHHHhCCCC
Q 037966 127 RQAWGSLDALIGRLRAAFEEHGGKP 151 (205)
Q Consensus 127 RQAWGSLDALIGRLRAafEE~Gg~P 151 (205)
-.|||.+..+|-.|...|+.+|..|
T Consensus 24 ~lAyG~~~~I~~~~~~ll~~~~~~P 48 (232)
T PF09674_consen 24 LLAYGNRKQIIKKLERLLDLMGPSP 48 (232)
T ss_pred HHHccCHHHHHHHHHHHHHHhCCCH
Confidence 3699999999999999999999986
No 56
>cd04399 RhoGAP_fRGD2 RhoGAP_fRGD2: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal RGD2-like proteins. Yeast Rgd2 is a GAP protein for Cdc42 and Rho5. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=24.07 E-value=87 Score=26.38 Aligned_cols=35 Identities=31% Similarity=0.465 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHhCCCCC--------CCc-chhhHHHHHHHHHHH
Q 037966 135 ALIGRLRAAFEEHGGKPE--------ANP-FGARAVRLYLREVRD 170 (205)
Q Consensus 135 ALIGRLRAafEE~Gg~PE--------~NP-F~araVRlYLReVRd 170 (205)
+-|-.||.+|++ |..+. .++ -.+.++|+||||.-|
T Consensus 51 ~~i~~Lr~~~d~-~~~~~~~~~~~~~~dv~~va~~LK~ylReLPe 94 (212)
T cd04399 51 KETHQLRNLLNK-PKKPDKEVIILKKFEPSTVASVLKLYLLELPD 94 (212)
T ss_pred HHHHHHHHHHcC-CCCcchhhhccccCCHHHHHHHHHHHHHHCCC
Confidence 568899999997 43331 223 378899999999765
No 57
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=24.03 E-value=1.8e+02 Score=22.04 Aligned_cols=37 Identities=32% Similarity=0.486 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHhhhcCCchh
Q 037966 135 ALIGRLRAAFEEHGGKPEANPFGARAVRLYLREVRDSQAKARGISYE 181 (205)
Q Consensus 135 ALIGRLRAafEE~Gg~PE~NPF~araVRlYLReVRd~QAkARgi~y~ 181 (205)
.|--+.-++|+++|-.+ +.||++||+.| ++-+|||++
T Consensus 11 ~lK~~A~~vl~~lGls~------S~Ai~~fl~qi----~~~~~iPF~ 47 (80)
T PRK11235 11 ELKARAYAVLEKLGVTP------SEALRLLLQYV----AENGRLPFK 47 (80)
T ss_pred HHHHHHHHHHHHhCCCH------HHHHHHHHHHH----HHhCCCCCC
Confidence 44556678899999874 57999999887 344677776
No 58
>PF06480 FtsH_ext: FtsH Extracellular; InterPro: IPR011546 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain is found in the FtsH family of proteins that include FtsH a membrane-bound ATP-dependent protease universally conserved in prokaryotes []. The FtsH peptidases, which belong to MEROPS peptidase family M41 (clan MA(E)), efficiently degrade proteins that have a low thermodynamic stability - e.g. they lack robust unfoldase activity. This feature may be key and implies that this could be a criterion for degrading a protein. In Oenococcus oeni (Leuconostoc oenos) FtsH is involved in protection against environmental stress [], and shows increased expression under heat or osmotic stress. These two lines of evidence suggest that it is a fundamental prokaryotic self-protection mechanism that checks if proteins are correctly folded. The precise function of this N-terminal region is unclear. ; GO: 0004222 metalloendopeptidase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0016021 integral to membrane; PDB: 2LNA_A.
Probab=23.91 E-value=1e+02 Score=21.28 Aligned_cols=26 Identities=35% Similarity=0.289 Sum_probs=18.8
Q ss_pred cchhHHHHHHHHHHHHHhCCCCCCCc
Q 037966 130 WGSLDALIGRLRAAFEEHGGKPEANP 155 (205)
Q Consensus 130 WGSLDALIGRLRAafEE~Gg~PE~NP 155 (205)
++++|.+.-+|..+.+|+|..+++.|
T Consensus 84 ~~~~~~~~~~L~~~~~~~~v~~~~~~ 109 (110)
T PF06480_consen 84 IPSVDSFDEFLIEALVEKGVKYESVP 109 (110)
T ss_dssp -S-HHHHHHHHHHHHHHTT--TTT--
T ss_pred CCCCHHHHHHHHHHHHHCCCccceec
Confidence 45699999999999999999988765
No 59
>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=23.88 E-value=1.9e+02 Score=23.88 Aligned_cols=33 Identities=15% Similarity=0.073 Sum_probs=24.4
Q ss_pred hhhhhHHHHHHHhcCCCCccccccchhhhHHHHhhcc
Q 037966 63 RRDWNTFGQYLRNHRPPLSLERCSGAHVLEFLRYLDQ 99 (205)
Q Consensus 63 RrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDq 99 (205)
+..++.|.+|+.+ +.+..-+..||.+||.++-+
T Consensus 23 ~~~~~~~~~~~g~----~~~~~it~~~i~~~l~~l~~ 55 (315)
T TIGR02249 23 LHWIKRFIRFHNK----RHPSTMGDTEVEAFLSDLAV 55 (315)
T ss_pred HHHHHHHHHHhCC----CChHhcCHHHHHHHHHHHHh
Confidence 4577888888642 34556689999999999854
No 60
>PF06947 DUF1290: Protein of unknown function (DUF1290); InterPro: IPR009709 This family consists of several bacterial small basic proteins of around 100 residues in length. The function of this family is unknown.
Probab=23.82 E-value=66 Score=25.34 Aligned_cols=17 Identities=35% Similarity=0.778 Sum_probs=15.1
Q ss_pred chhHHHHHHHHHHHHHh
Q 037966 131 GSLDALIGRLRAAFEEH 147 (205)
Q Consensus 131 GSLDALIGRLRAafEE~ 147 (205)
..||++.|-+||..|++
T Consensus 16 AaLDsvfGgiRA~le~~ 32 (88)
T PF06947_consen 16 AALDSVFGGIRASLEDK 32 (88)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 46999999999999975
No 61
>cd04379 RhoGAP_SYD1 RhoGAP_SYD1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in SYD-1_like proteins. Syd-1, first identified and best studied in C.elegans, has been shown to play an important role in neuronal development by specifying axonal properties. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=23.69 E-value=98 Score=26.10 Aligned_cols=39 Identities=33% Similarity=0.387 Sum_probs=26.6
Q ss_pred chhHHHHHHHHHHHHHhCCCCCC------Ccc-hhhHHHHHHHHHHH
Q 037966 131 GSLDALIGRLRAAFEEHGGKPEA------NPF-GARAVRLYLREVRD 170 (205)
Q Consensus 131 GSLDALIGRLRAafEE~Gg~PE~------NPF-~araVRlYLReVRd 170 (205)
|+. +.|..||..|+..+...+- ++. .|..+|.||||.-|
T Consensus 44 Gs~-~~i~~L~~~~d~~~~~~~l~~~~~~dvh~vA~lLK~fLReLPe 89 (207)
T cd04379 44 GSA-AKKKELRDAFERNSAAVELSEELYPDINVITGVLKDYLRELPE 89 (207)
T ss_pred CcH-HHHHHHHHHHcCCCCcCCCChhhcccHHHHHHHHHHHHHhCCC
Confidence 444 3599999999986532221 222 58899999999544
No 62
>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=23.57 E-value=60 Score=25.10 Aligned_cols=40 Identities=28% Similarity=0.476 Sum_probs=30.2
Q ss_pred hHHHHHHHhcCCCCccccc--cchhhh--HHHHhhcccCccccc
Q 037966 67 NTFGQYLRNHRPPLSLERC--SGAHVL--EFLRYLDQFGKTKVH 106 (205)
Q Consensus 67 ntf~qyL~n~rPPlsL~~c--sg~hVl--eFLrylDqfGKTkVH 106 (205)
.++++||..++|=.++..+ -|.|++ .|||+.+..|.|-++
T Consensus 33 ~~Iv~~L~~n~~~~s~~~aE~fGQdLv~~gfir~~g~vG~~F~n 76 (84)
T cd04436 33 SEIVSWLQENMPEKDLDAAEAFGQDLLNQGFLRLVGGVGSTFVN 76 (84)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHhCchHHHhcccCcceec
Confidence 4688999998887666644 366775 499999999987664
No 63
>PF02187 GAS2: Growth-Arrest-Specific Protein 2 Domain; InterPro: IPR003108 The growth-arrest-specific protein 2 domain is found associated with the spectrin repeat, calponin homology domain and EF hand in many proteins. It is found among others in the growth arrest-specific protein 2 [].; GO: 0007050 cell cycle arrest; PDB: 1V5R_A.
Probab=23.48 E-value=19 Score=27.27 Aligned_cols=13 Identities=46% Similarity=1.214 Sum_probs=11.4
Q ss_pred hhHHHHHHHhcCC
Q 037966 66 WNTFGQYLRNHRP 78 (205)
Q Consensus 66 Wntf~qyL~n~rP 78 (205)
|.||.+||..|.|
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 9999999999887
No 64
>cd04383 RhoGAP_srGAP RhoGAP_srGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs contain an N-terminal FCH domain, a central RhoGAP domain and a C-terminal SH3 domain; this SH3 domain interacts with the intracellular proline-rich-tail of the Roundabout receptor (Robo). This interaction with Robo then activates the rhoGAP domain which in turn inhibits Cdc42 activity. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific group
Probab=23.47 E-value=95 Score=25.47 Aligned_cols=35 Identities=29% Similarity=0.578 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHhCCCC---CCCc----chhhHHHHHHHHHHH
Q 037966 135 ALIGRLRAAFEEHGGKP---EANP----FGARAVRLYLREVRD 170 (205)
Q Consensus 135 ALIGRLRAafEE~Gg~P---E~NP----F~araVRlYLReVRd 170 (205)
.-|.+||..|+. |..+ +.+. -.+..++.||||..|
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 4333 1122 268999999999754
No 65
>PF03801 Ndc80_HEC: HEC/Ndc80p family; InterPro: IPR005550 Members of this family are components of the mitotic spindle. It has been shown that Ndc80 from yeast is part of a complex called the Ndc80p complex []. This complex is thought to bind to the microtubules of the spindle.; PDB: 3IZ0_E 2VE7_B 2IGP_A.
Probab=23.39 E-value=1.3e+02 Score=24.47 Aligned_cols=45 Identities=13% Similarity=0.214 Sum_probs=26.4
Q ss_pred CCCchHHHhhhhhhhHHHHHHHhcCC------CCccccccchhhhHHHHhh
Q 037966 53 TTLSRYENQKRRDWNTFGQYLRNHRP------PLSLERCSGAHVLEFLRYL 97 (205)
Q Consensus 53 ~~~SrYesQKRrdWntf~qyL~n~rP------PlsL~~csg~hVleFLryl 97 (205)
++|-+=++=+..-++++.+||..+-- +..|...+.+++++.+.+|
T Consensus 29 ~Rpl~Dk~~q~~~~~~I~~fL~~~~~~~~~is~k~l~~Pt~kdf~~I~~fL 79 (157)
T PF03801_consen 29 PRPLSDKSYQQECIRKIYEFLSEHGFESHPISPKTLKSPTQKDFVEIFNFL 79 (157)
T ss_dssp -S-TT-HHHHHHHHHHHHHHHHHTT--SS---TTTTSS--HHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHcCCCCccccccccCCCCHHHHHHHHHHH
Confidence 44433344455668889999977665 5566678888877665554
No 66
>PF10780 MRP_L53: 39S ribosomal protein L53/MRP-L53; InterPro: IPR019716 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Mitochondrial ribosomal protein L53 (also known as L44) is part of the 39S ribosome [].
Probab=23.26 E-value=41 Score=23.35 Aligned_cols=25 Identities=48% Similarity=0.833 Sum_probs=17.8
Q ss_pred Ccc--hhhHHHHHHHHHHHHHhhhcCCc
Q 037966 154 NPF--GARAVRLYLREVRDSQAKARGIS 179 (205)
Q Consensus 154 NPF--~araVRlYLReVRd~QAkARgi~ 179 (205)
||| .++..|++|.-+ ..-+|++|+.
T Consensus 2 nPF~~~aksaR~FL~~i-p~s~k~~~tn 28 (51)
T PF10780_consen 2 NPFSPNAKSARLFLSLI-PPSAKARGTN 28 (51)
T ss_pred CCCCcccHHHHHHHHhc-CCccccccCC
Confidence 788 467899999988 4445555543
No 67
>PRK09468 ompR osmolarity response regulator; Provisional
Probab=23.05 E-value=66 Score=24.92 Aligned_cols=17 Identities=47% Similarity=0.612 Sum_probs=13.2
Q ss_pred hhHHHHHHHHHHHHHhC
Q 037966 132 SLDALIGRLRAAFEEHG 148 (205)
Q Consensus 132 SLDALIGRLRAafEE~G 148 (205)
+||..|.|||.-++..+
T Consensus 201 ~l~~~i~~LR~kl~~~~ 217 (239)
T PRK09468 201 SIDVQISRLRRLIEEDP 217 (239)
T ss_pred CHHHHHHHHHHHhccCC
Confidence 68888888888886543
No 68
>cd01187 INT_SG4 INT_SG4, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 4, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases for which not much biochemical characterization is available.
Probab=23.05 E-value=3.2e+02 Score=22.28 Aligned_cols=29 Identities=14% Similarity=0.113 Sum_probs=20.6
Q ss_pred hhhHHHHHHHhcCCCCccccccchhhhHHHHhh
Q 037966 65 DWNTFGQYLRNHRPPLSLERCSGAHVLEFLRYL 97 (205)
Q Consensus 65 dWntf~qyL~n~rPPlsL~~csg~hVleFLryl 97 (205)
.-+.|.+|+.++. +...+..||.+|+.++
T Consensus 25 ~~~~f~~~~~~~~----~~~it~~~~~~~~~~~ 53 (299)
T cd01187 25 LLRDFVRFLERHG----AGFITTDLALRWAASP 53 (299)
T ss_pred HHHHHHHHHHhCC----CCCCCHHHHHHHHhcC
Confidence 3456888887654 5677788888887653
No 69
>PRK11173 two-component response regulator; Provisional
Probab=22.95 E-value=67 Score=25.05 Aligned_cols=19 Identities=32% Similarity=0.525 Sum_probs=16.0
Q ss_pred hhHHHHHHHHHHHHHhCCC
Q 037966 132 SLDALIGRLRAAFEEHGGK 150 (205)
Q Consensus 132 SLDALIGRLRAafEE~Gg~ 150 (205)
+||..|.|||.-+++.+..
T Consensus 200 ~~~~~i~rlR~kl~~~~~~ 218 (237)
T PRK11173 200 TVDVTIRRIRKHFESTPDT 218 (237)
T ss_pred cHHHHHHHHHHHhccCCCC
Confidence 8999999999999865443
No 70
>cd04390 RhoGAP_ARHGAP22_24_25 RhoGAP_ARHGAP22_24_25: GTPase-activator protein (GAP) domain for Rho-like GTPases found in ARHGAP22, 24 and 25-like proteins; longer isoforms of these proteins contain an additional N-terminal pleckstrin homology (PH) domain. ARHGAP25 (KIA0053) has been identified as a GAP for Rac1 and Cdc42. Short isoforms (without the PH domain) of ARHGAP24, called RC-GAP72 and p73RhoGAP, and of ARHGAP22, called p68RacGAP, has been shown to be involved in angiogenesis and endothelial cell capillary formation. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the r
Probab=22.59 E-value=1.4e+02 Score=24.37 Aligned_cols=37 Identities=27% Similarity=0.500 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHhCC---CCCCCcc-hhhHHHHHHHHHHH
Q 037966 134 DALIGRLRAAFEEHGG---KPEANPF-GARAVRLYLREVRD 170 (205)
Q Consensus 134 DALIGRLRAafEE~Gg---~PE~NPF-~araVRlYLReVRd 170 (205)
.+.|.+||.+|+.... ..+.+|. .|..++.||||.-+
T Consensus 50 ~~~i~~l~~~~d~~~~~~~~~~~d~h~va~lLK~fLReLPe 90 (199)
T cd04390 50 ANLVKQLQDAFDAGERPSFDSDTDVHTVASLLKLYLRELPE 90 (199)
T ss_pred HHHHHHHHHHHhCCCCCCccccCCHHHHHHHHHHHHHhCCC
Confidence 4578999999975432 1234553 78899999998654
No 71
>PF03344 Daxx: Daxx Family; InterPro: IPR005012 Daxx is a ubiquitously expressed protein that functions, in part, as a transcriptional co-repressor through its interaction with a growing number of nuclear, DNA-associated proteins. Human Daxx contains four structural domains commonly found in transcriptional regulatory proteins: two predicted paired amphipathic helices, an acid-rich domain and a Ser/Pro/Thr (SPT)-rich domain. The post-translational modification status of the SPT-domain of hDaxx regulates its association with transcription factors such as Pax3 and ETS-1, effectively bringing hDaxx to sites of active transcription. Through its presence at the site of active transcription, hDaxx could then be able to associate with acetylated histones present in the nucleosomes and Dek that is associated with chromatin. Through its association with the SPT-domain of hDaxx, histone deacetylases may also be brought to the site of active transcription. As a consequence, nucleosomes in the vicinity of the site of active transcription will have the histone tails deacetylated, allowing the deactylated tail to bind to DNA, thereby leading to an inactive chromatin structure and transcriptional repression []. The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis as a component of nuclear promyelocytic leukemia protein (PML) oncogenic domains (PODS). Daxx associates with PODs through a direct interaction with PML, a critical component of PODs. The interaction is a dynamic, cell cycle regulated event and is dependent on the post-translational modification of PML by the small ubiquitin-related modifier SUMO-1. ; PDB: 2KZS_A 2KZU_A.
Probab=22.50 E-value=3.3e+02 Score=27.91 Aligned_cols=77 Identities=21% Similarity=0.241 Sum_probs=45.3
Q ss_pred chHHHhhhhhhhHHHHHHHhcCCCCccccccchhhhHHHHhhcccCcccccccCCCCcCCCCCCCCCCCchhhhcchhHH
Q 037966 56 SRYENQKRRDWNTFGQYLRNHRPPLSLERCSGAHVLEFLRYLDQFGKTKVHTQLCPFFGHPNPPAPCPCPLRQAWGSLDA 135 (205)
Q Consensus 56 SrYesQKRrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDA 135 (205)
.-||+|| ++..|..+-..+.- ....|++||+ +.|...++ .-++.-..=-
T Consensus 64 ~~~~~~~--lf~eFi~~C~~~~~-------d~~evv~~L~--------~~~~~~~~--------------~f~~S~~F~~ 112 (713)
T PF03344_consen 64 LSYENQK--LFEEFIELCLAQTS-------DMPEVVKFLK--------RRYEKAHP--------------EFLSSEEFRN 112 (713)
T ss_dssp H--HHHH--HHHHHHHHHHHHTT-------T-TTHHHHHH--------HHHHTC-C--------------CHHCSHHHHH
T ss_pred eeChHHH--HHHHHHHHhccccc-------CCHHHHHHHH--------HHHHhCCH--------------HHHhHHHHHH
Confidence 3456664 56666666554321 2346999997 33334443 3344445556
Q ss_pred HHHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHh
Q 037966 136 LIGRLRAAFEEHGGKPEANPFGARAVRLYLREVRDSQA 173 (205)
Q Consensus 136 LIGRLRAafEE~Gg~PE~NPF~araVRlYLReVRd~QA 173 (205)
+|++-++....+..+ |=+||++|-+.=.
T Consensus 113 ~l~~~~~~~~~~~~k----------~yv~i~~v~~~lk 140 (713)
T PF03344_consen 113 FLSRCLARIQNNPKK----------VYVHINEVCTELK 140 (713)
T ss_dssp HHHHHHHHHHH-CCC----------HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCe----------EEEEHHHHHHHHH
Confidence 778877777776655 8899999987643
No 72
>PF01663 Phosphodiest: Type I phosphodiesterase / nucleotide pyrophosphatase; InterPro: IPR002591 This family consists of phosphodiesterases, including human plasma-cell membrane glycoprotein PC-1 / alkaline phosphodiesterase I / nucleotide pyrophosphatase (nppase). These enzymes catalyse the cleavage of phosphodiester and phosphosulphate bonds in NAD, deoxynucleotides and nucleotide sugars []. Another member of this family is ATX an autotaxin, tumor cell motility-stimulating protein which exhibits type I phosphodiesterases activity []. The alignment encompasses the active site [, ]. Also present within this family is 60 kDa Ca2+-ATPase from Myroides odoratus []. This signature also hits a number of ethanolamine phosphate transferase involved in glycosylphosphatidylinositol-anchor biosynthesis.; GO: 0003824 catalytic activity; PDB: 2XRG_A 2XR9_A 3T02_A 3T01_A 3SZZ_A 3SZY_A 3T00_A 3NKM_A 3NKN_A 3NKR_A ....
Probab=22.35 E-value=66 Score=26.68 Aligned_cols=27 Identities=33% Similarity=0.578 Sum_probs=23.2
Q ss_pred hhhhcchhHHHHHHHHHHHHHhCCCCC
Q 037966 126 LRQAWGSLDALIGRLRAAFEEHGGKPE 152 (205)
Q Consensus 126 lRQAWGSLDALIGRLRAafEE~Gg~PE 152 (205)
.+++.-.+|..||+|.+++++.|...+
T Consensus 208 ~~~~~~~~D~~ig~l~~~l~~~~~~~~ 234 (365)
T PF01663_consen 208 IEDAYRRIDQAIGRLLEALDENGLLED 234 (365)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTT-TTT
T ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCc
Confidence 688999999999999999999976644
No 73
>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=22.35 E-value=43 Score=23.34 Aligned_cols=12 Identities=42% Similarity=0.775 Sum_probs=10.4
Q ss_pred cchhHHHHHHHH
Q 037966 130 WGSLDALIGRLR 141 (205)
Q Consensus 130 WGSLDALIGRLR 141 (205)
|-.||.||.+|.
T Consensus 37 f~~lD~li~~l~ 48 (49)
T PF07535_consen 37 FKELDSLISQLQ 48 (49)
T ss_pred HHHHHHHHHHhc
Confidence 778999999885
No 74
>COG4865 Glutamate mutase epsilon subunit [Amino acid transport and metabolism]
Probab=22.06 E-value=58 Score=31.86 Aligned_cols=22 Identities=41% Similarity=0.801 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHhCCCCCCCcch
Q 037966 136 LIGRLRAAFEEHGGKPEANPFG 157 (205)
Q Consensus 136 LIGRLRAafEE~Gg~PE~NPF~ 157 (205)
+|.||--+|||||.+=...||+
T Consensus 196 YVDRL~G~YeE~Gi~INREpFg 217 (485)
T COG4865 196 YVDRLMGMYEEHGIRINREPFG 217 (485)
T ss_pred HHHHHHhHHHhcCeeeccccCC
Confidence 4566677999999886666665
No 75
>PF10520 Kua-UEV1_localn: Kua-ubiquitin conjugating enzyme hybrid localisation domain; InterPro: IPR019547 This entry represents part of the transcript of the fusion of two genes, the UEV1. UEV1 is an enzymatically inactive variant of the E2 ubiquitin-conjugating enzymes that regulate non-canonical elongation of ubiquitin chains, and Kua, an otherwise unknown gene. UEV1A is a nuclear protein, whereas both Kua and Kua-UEV localise to cytoplasmic structures, indicating that the addition of a Kua domain to UEV confers new biological properties. UEV1-Kua carries the B domain with its characteristic double histidine motif, and it is probably this domain which determines the cytoplasmic localisation. It is postulated that this hybrid transcript could preferentially direct the variant polyubiquitination of substrates closely associated with the cytoplasmic face of the endoplasmic reticulum, possibly, although not necessarily, in conjunction with membrane-bound ubiquitin-conjugating enzymes [].
Probab=21.70 E-value=45 Score=28.50 Aligned_cols=24 Identities=42% Similarity=0.852 Sum_probs=21.7
Q ss_pred hcchhHH-HHHHHHHHHHHhCCCCC
Q 037966 129 AWGSLDA-LIGRLRAAFEEHGGKPE 152 (205)
Q Consensus 129 AWGSLDA-LIGRLRAafEE~Gg~PE 152 (205)
-|||+|- +||+.-++|.||-..|-
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 89999999999999875
No 76
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=21.45 E-value=2.4e+02 Score=20.91 Aligned_cols=38 Identities=32% Similarity=0.623 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHhhhcCCchhh
Q 037966 135 ALIGRLRAAFEEHGGKPEANPFGARAVRLYLREVRDSQAKARGISYEK 182 (205)
Q Consensus 135 ALIGRLRAafEE~Gg~PE~NPF~araVRlYLReVRd~QAkARgi~y~k 182 (205)
.|--+.-++|+++|..+ ..|||++|+.|- +-+|||++-
T Consensus 12 ~lK~~a~~i~~~lGl~~------s~ai~~fl~qvv----~~~~lPF~~ 49 (83)
T TIGR02384 12 ELKKEAYAVFEELGLTP------STAIRMFLKQVI----REQGLPFDL 49 (83)
T ss_pred HHHHHHHHHHHHhCCCH------HHHHHHHHHHHH----HhCCCCCCc
Confidence 34456677889999874 569999998764 447888764
No 77
>PF13099 DUF3944: Domain of unknown function (DUF3944)
Probab=21.38 E-value=49 Score=22.09 Aligned_cols=22 Identities=27% Similarity=0.582 Sum_probs=15.7
Q ss_pred ccccchhhhHHHHhh--cccCccc
Q 037966 83 ERCSGAHVLEFLRYL--DQFGKTK 104 (205)
Q Consensus 83 ~~csg~hVleFLryl--DqfGKTk 104 (205)
..|+..|+-++..+| |..|+++
T Consensus 11 ~~cs~edL~~L~~~Lt~dkdG~~R 34 (35)
T PF13099_consen 11 AECSNEDLKDLVDILTHDKDGKKR 34 (35)
T ss_pred HHCCHHHHHHHHHHHhcCCCCCcC
Confidence 468888877765554 7888764
No 78
>cd04406 RhoGAP_myosin_IXA RhoGAP_myosin_IXA: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in myosins IXA. 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 prolife
Probab=21.22 E-value=1e+02 Score=25.32 Aligned_cols=36 Identities=19% Similarity=0.293 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHhCCCCC---CCcc-hhhHHHHHHHHHHH
Q 037966 135 ALIGRLRAAFEEHGGKPE---ANPF-GARAVRLYLREVRD 170 (205)
Q Consensus 135 ALIGRLRAafEE~Gg~PE---~NPF-~araVRlYLReVRd 170 (205)
..|-.|+..|+..+.... .++. .+..++.||||.-|
T Consensus 44 ~~i~~l~~~~d~~~~~~~~~~~d~h~va~lLK~fLReLPe 83 (186)
T cd04406 44 NKIKELRQGLDTDANSVNLDDYNIHVIASVFKQWLRDLPN 83 (186)
T ss_pred HHHHHHHHHHccCCCCCCcccCCHHHHHHHHHHHHHhCCC
Confidence 458899999987543322 2333 78899999999754
No 79
>PF12055 DUF3536: Domain of unknown function (DUF3536); InterPro: IPR021923 This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is typically between 274 to 285 amino acids in length. This domain is found associated with PF03065 from PFAM.
Probab=20.89 E-value=75 Score=29.13 Aligned_cols=42 Identities=45% Similarity=0.708 Sum_probs=33.1
Q ss_pred chhhhcchhHHHHHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHH
Q 037966 125 PLRQAWGSLDALIGRLRAAFEEHGGKPEANPFGARAVRLYLREVRDS 171 (205)
Q Consensus 125 PlRQAWGSLDALIGRLRAafEE~Gg~PE~NPF~araVRlYLReVRd~ 171 (205)
|||.| ||.|-.+|...||+.|+.=-.+|..+|- -|.+-|-+.
T Consensus 8 PLR~A---ld~Lrd~l~~~fe~~~~~l~~Dpw~ar~--~Yi~Vil~~ 49 (285)
T PF12055_consen 8 PLREA---LDWLRDRLDELFEEEGGELFKDPWAARD--EYIEVILDR 49 (285)
T ss_pred HHHHH---HHHHHHHHHHHHHHHHHHhcCCHHHHHH--HHHHHHcCC
Confidence 56654 9999999999999999876678987764 677666554
No 80
>KOG4670 consensus Uncharacterized conserved membrane protein [Function unknown]
Probab=20.81 E-value=43 Score=33.77 Aligned_cols=59 Identities=25% Similarity=0.420 Sum_probs=41.1
Q ss_pred hhhhhhhH------------HHHHHHhcCCCCccccccchhhhHHHHhhcccCccc-----cc-ccCCCCcCCCCCC
Q 037966 61 QKRRDWNT------------FGQYLRNHRPPLSLERCSGAHVLEFLRYLDQFGKTK-----VH-TQLCPFFGHPNPP 119 (205)
Q Consensus 61 QKRrdWnt------------f~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTk-----VH-~~~C~ffG~p~pp 119 (205)
-|+|.|++ ||-||..|.+|..+--=.-.---.|++-+++.-++. || ...|.+-...+||
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 57777874 999999999998876321122345677888886654 44 4568877777773
No 81
>cd01401 PncB_like Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products. This subgroup is present in bacteria, archea and funghi.
Probab=20.61 E-value=2.1e+02 Score=27.00 Aligned_cols=69 Identities=25% Similarity=0.336 Sum_probs=45.5
Q ss_pred hhhHHHHHHHhcCCC--CccccccchhhhHHHHhhcc-cCcccccccCCCCcCCCCCCCCCCCchhhhcchhHHHHHHHH
Q 037966 65 DWNTFGQYLRNHRPP--LSLERCSGAHVLEFLRYLDQ-FGKTKVHTQLCPFFGHPNPPAPCPCPLRQAWGSLDALIGRLR 141 (205)
Q Consensus 65 dWntf~qyL~n~rPP--lsL~~csg~hVleFLrylDq-fGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLR 141 (205)
...-|..|.+....- +-|.-|-+. ..||+-.|. +++ .+.| +|+=.|.+-.|.-++|
T Consensus 234 e~~A~~~w~~~y~~~l~i~L~DTy~t--~~f~~~~~~~~~~--------~~~G-----------vR~DSGD~~~~~~k~r 292 (377)
T cd01401 234 QKAALERWVREYGGDLGIALTDTFGT--DAFLRDFDLYFAK--------LFDG-----------VRHDSGDPFEWGEKAI 292 (377)
T ss_pred HHHHHHHHHHHcCCCCeEEEEecCCC--HHHHHHHHHHhcc--------cCCE-----------EeeCCCCHHHHHHHHH
Confidence 334566666665543 344444443 456665554 332 2333 8999999999999999
Q ss_pred HHHHHhCCCCCCC
Q 037966 142 AAFEEHGGKPEAN 154 (205)
Q Consensus 142 AafEE~Gg~PE~N 154 (205)
+.|+++|..|..-
T Consensus 293 ~~~~~~Gi~p~~K 305 (377)
T cd01401 293 AHYEKLGIDPKTK 305 (377)
T ss_pred HHHHHcCCCCCCc
Confidence 9999999877643
No 82
>PLN02837 threonine-tRNA ligase
Probab=20.49 E-value=41 Score=32.74 Aligned_cols=17 Identities=35% Similarity=0.495 Sum_probs=12.4
Q ss_pred hhhhcchhHHHHHHHHH
Q 037966 126 LRQAWGSLDALIGRLRA 142 (205)
Q Consensus 126 lRQAWGSLDALIGRLRA 142 (205)
-|-.|||+|.|||-|-.
T Consensus 488 h~~~~G~~eRlia~Lie 504 (614)
T PLN02837 488 HRAILGSLERFFGVLIE 504 (614)
T ss_pred EcCCccCHHHHHHHHHH
Confidence 35679999998875533
Done!