Query 028699
Match_columns 205
No_of_seqs 81 out of 83
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 15:36:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028699.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028699hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04852 DUF640: Protein of un 100.0 1.2E-75 2.6E-80 470.5 11.7 123 32-154 10-132 (132)
2 PF08821 CGGC: CGGC domain; I 91.3 0.35 7.7E-06 37.6 4.3 55 63-127 41-98 (107)
3 PF02899 Phage_int_SAM_1: Phag 88.8 0.66 1.4E-05 31.4 3.5 40 44-84 21-60 (84)
4 cd00798 INT_XerDC XerD and Xer 86.6 2.9 6.2E-05 32.4 6.3 69 44-139 21-91 (284)
5 cd00799 INT_Cre Cre recombinas 85.5 8.5 0.00019 31.1 8.8 77 44-152 6-82 (287)
6 TIGR02225 recomb_XerD tyrosine 82.8 5 0.00011 31.4 6.2 70 43-140 19-90 (291)
7 PRK00283 xerD site-specific ty 82.3 4 8.6E-05 32.6 5.6 67 45-139 30-98 (299)
8 COG1080 PtsA Phosphoenolpyruva 78.8 2.8 6.1E-05 41.6 4.3 42 110-151 305-368 (574)
9 TIGR02224 recomb_XerC tyrosine 72.8 15 0.00032 29.0 6.2 69 46-140 22-92 (295)
10 PF10865 DUF2703: Domain of un 63.7 2.6 5.6E-05 33.9 0.3 43 73-135 2-44 (120)
11 TIGR01418 PEP_synth phosphoeno 61.2 13 0.00029 37.3 4.7 42 117-158 547-618 (782)
12 PRK10529 DNA-binding transcrip 57.9 8.5 0.00018 29.4 2.2 19 115-133 191-209 (225)
13 cd01185 INT_Tn4399 Tn4399 and 56.4 46 0.00099 27.0 6.3 33 48-80 44-78 (299)
14 PF02896 PEP-utilizers_C: PEP- 56.1 15 0.00033 33.0 3.8 40 113-152 58-120 (293)
15 PF00539 Tat: Transactivating 53.6 3.2 6.9E-05 31.1 -0.7 17 156-172 45-61 (68)
16 PRK10816 DNA-binding transcrip 50.9 11 0.00025 28.7 1.9 23 109-131 175-205 (223)
17 PF05528 Coronavirus_5: Corona 50.8 2.7 5.8E-05 32.5 -1.5 19 134-152 4-25 (82)
18 PRK11061 fused phosphoenolpyru 48.0 16 0.00034 36.6 2.9 36 115-150 475-531 (748)
19 PF13495 Phage_int_SAM_4: Phag 47.6 21 0.00045 24.3 2.6 53 47-129 24-77 (85)
20 TIGR01417 PTS_I_fam phosphoeno 47.4 21 0.00044 34.7 3.4 36 115-150 308-365 (565)
21 PRK00236 xerC site-specific ty 46.9 98 0.0021 24.3 6.6 36 46-82 32-67 (297)
22 PF00486 Trans_reg_C: Transcri 45.2 22 0.00047 23.8 2.4 21 114-134 44-64 (77)
23 COG4974 XerD Site-specific rec 44.4 23 0.0005 32.8 3.1 38 46-85 31-69 (300)
24 PF13276 HTH_21: HTH-like doma 42.8 41 0.00089 22.4 3.4 29 117-150 4-32 (60)
25 PF06252 DUF1018: Protein of u 41.1 1.5E+02 0.0032 22.7 6.7 88 48-149 2-89 (119)
26 PF14768 RPA_interact_C: Repli 40.7 26 0.00056 25.8 2.4 35 104-138 18-56 (82)
27 cd00801 INT_P4 Bacteriophage P 40.5 49 0.0011 27.1 4.2 26 114-140 135-163 (357)
28 smart00259 ZnF_A20 A20-like zi 40.2 15 0.00033 22.7 0.9 16 91-106 7-22 (26)
29 smart00862 Trans_reg_C Transcr 39.7 31 0.00068 22.9 2.5 19 114-132 45-63 (78)
30 PRK09279 pyruvate phosphate di 39.6 27 0.00059 36.1 3.1 36 123-158 636-685 (879)
31 PF00140 Sigma70_r1_2: Sigma-7 36.3 29 0.00063 22.2 1.8 12 142-153 2-13 (37)
32 PRK06464 phosphoenolpyruvate s 35.3 48 0.001 33.6 4.0 15 135-149 597-612 (795)
33 cd08793 Death_IRAK4 Death doma 35.0 45 0.00097 26.5 3.0 63 48-132 23-85 (100)
34 cd04372 RhoGAP_chimaerin RhoGA 34.8 47 0.001 27.2 3.2 36 118-153 45-87 (194)
35 PF11709 Mit_ribos_Mrp51: Mito 34.7 58 0.0013 29.4 4.1 67 34-100 144-229 (312)
36 TIGR01828 pyru_phos_dikin pyru 33.9 23 0.0005 36.3 1.6 25 134-158 652-679 (856)
37 PRK11177 phosphoenolpyruvate-p 32.3 39 0.00085 33.1 2.8 36 115-150 309-366 (575)
38 PF01213 CAP_N: Adenylate cycl 31.9 59 0.0013 29.8 3.7 53 109-167 156-213 (312)
39 cd04396 RhoGAP_fSAC7_BAG7 RhoG 31.8 2E+02 0.0044 24.3 6.7 37 117-153 60-103 (225)
40 PF09107 SelB-wing_3: Elongati 31.3 25 0.00053 24.3 0.9 20 68-87 22-41 (50)
41 PRK10701 DNA-binding transcrip 31.1 39 0.00084 26.3 2.1 16 115-130 201-216 (240)
42 smart00243 GAS2 Growth-Arrest- 31.0 34 0.00073 26.1 1.7 14 48-61 55-68 (73)
43 KOG2675 Adenylate cyclase-asso 30.9 81 0.0018 31.2 4.6 25 135-159 180-204 (480)
44 cd00383 trans_reg_C Effector d 29.5 47 0.001 22.8 2.1 20 114-133 62-81 (95)
45 PF08544 GHMP_kinases_C: GHMP 29.3 7.2 0.00016 26.5 -2.0 72 45-128 6-84 (85)
46 PF09336 Vps4_C: Vps4 C termin 29.2 48 0.001 23.5 2.1 31 49-84 32-62 (62)
47 PRK11235 bifunctional antitoxi 29.0 1.4E+02 0.0031 22.5 4.8 38 118-165 11-48 (80)
48 PF03801 Ndc80_HEC: HEC/Ndc80p 28.7 1.1E+02 0.0025 24.9 4.5 46 35-80 28-79 (157)
49 COG0745 OmpR Response regulato 28.1 46 0.001 28.3 2.2 27 108-134 178-212 (229)
50 PTZ00398 phosphoenolpyruvate c 27.8 1.1E+02 0.0024 32.3 5.2 43 113-155 264-337 (974)
51 PF09674 DUF2400: Protein of u 27.3 55 0.0012 28.9 2.6 52 110-161 24-94 (232)
52 PRK09468 ompR osmolarity respo 26.9 50 0.0011 25.6 2.1 17 115-131 201-217 (239)
53 TIGR02249 integrase_gron integ 26.7 1.2E+02 0.0026 25.1 4.3 33 46-82 23-55 (315)
54 cd04388 RhoGAP_p85 RhoGAP_p85: 26.7 84 0.0018 26.9 3.5 34 120-153 45-82 (200)
55 PRK05084 xerS site-specific ty 26.7 1.2E+02 0.0026 25.7 4.5 68 46-129 42-119 (357)
56 PF10520 Kua-UEV1_localn: Kua- 26.5 31 0.00067 29.4 0.9 24 112-135 17-41 (178)
57 cd01187 INT_SG4 INT_SG4, DNA b 26.2 3E+02 0.0064 22.5 6.5 59 48-139 25-86 (299)
58 PF09958 DUF2192: Uncharacteri 26.2 57 0.0012 29.3 2.5 21 115-135 27-47 (231)
59 PF07535 zf-DBF: DBF zinc fing 26.1 34 0.00074 23.8 0.9 12 113-124 37-48 (49)
60 PF00179 UQ_con: Ubiquitin-con 25.5 1.6E+02 0.0034 22.5 4.6 45 112-159 90-137 (140)
61 PRK11173 two-component respons 25.4 55 0.0012 25.5 2.1 19 115-133 200-218 (237)
62 PF06947 DUF1290: Protein of u 25.2 62 0.0013 25.5 2.3 17 114-130 16-32 (88)
63 TIGR02384 RelB_DinJ addiction 24.6 2E+02 0.0044 21.3 4.8 39 118-166 12-50 (83)
64 PLN02837 threonine-tRNA ligase 24.4 30 0.00066 33.6 0.6 15 110-124 489-503 (614)
65 cd01355 AcnX Putative Aconitas 24.4 75 0.0016 30.2 3.1 54 70-135 48-108 (389)
66 PF01663 Phosphodiest: Type I 24.4 59 0.0013 27.0 2.2 27 109-135 208-234 (365)
67 KOG1452 Predicted Rho GTPase-a 24.1 40 0.00086 32.6 1.2 30 122-152 233-270 (442)
68 cd04379 RhoGAP_SYD1 RhoGAP_SYD 24.1 95 0.0021 26.2 3.4 39 114-153 44-89 (207)
69 PF07700 HNOB: Heme NO binding 24.0 23 0.0005 28.3 -0.3 36 47-82 65-103 (171)
70 COG4865 Glutamate mutase epsil 23.7 51 0.0011 32.2 1.9 22 119-140 196-217 (485)
71 cd00778 ProRS_core_arch_euk Pr 23.6 38 0.00082 29.0 0.9 17 109-125 244-260 (261)
72 cd08782 Death_DAPK1 Death doma 23.4 43 0.00092 24.9 1.1 28 106-133 47-75 (82)
73 PF10780 MRP_L53: 39S ribosoma 23.4 35 0.00077 23.7 0.6 25 137-162 2-28 (51)
74 cd04399 RhoGAP_fRGD2 RhoGAP_fR 23.2 93 0.002 26.2 3.2 35 118-153 51-94 (212)
75 cd08802 Death_UNC5B Death doma 22.9 50 0.0011 25.3 1.4 17 117-133 60-76 (84)
76 cd04383 RhoGAP_srGAP RhoGAP_sr 22.6 99 0.0022 25.4 3.2 35 118-153 47-88 (188)
77 cd04377 RhoGAP_myosin_IX RhoGA 22.5 2E+02 0.0044 23.3 4.9 61 73-153 19-83 (186)
78 cd04390 RhoGAP_ARHGAP22_24_25 22.1 1.4E+02 0.0031 24.3 4.0 37 117-153 50-90 (199)
79 PF06480 FtsH_ext: FtsH Extrac 22.1 1.1E+02 0.0024 21.1 2.9 26 113-138 84-109 (110)
80 cd04436 DEP_fRgd2 DEP (Disheve 21.9 57 0.0012 25.2 1.5 41 50-90 33-77 (84)
81 cd08799 Death_UNC5C Death doma 21.9 48 0.001 25.3 1.1 17 117-133 60-76 (84)
82 cd04384 RhoGAP_CdGAP RhoGAP_Cd 21.9 1.4E+02 0.003 24.7 3.9 38 114-153 43-88 (195)
83 cd08177 MAR Maleylacetate redu 21.7 53 0.0011 28.9 1.5 93 60-153 102-197 (337)
84 cd08800 Death_UNC5A Death doma 21.6 48 0.001 25.6 1.0 17 117-133 60-76 (84)
85 PF00618 RasGEF_N: RasGEF N-te 21.6 55 0.0012 23.5 1.3 13 113-125 4-16 (104)
86 PF12067 Sox_C_TAD: Sox C-term 21.5 50 0.0011 28.7 1.3 16 46-61 140-155 (197)
87 PF10774 DUF4226: Domain of un 21.2 1.5E+02 0.0032 23.7 3.7 34 115-149 48-81 (112)
88 cd04406 RhoGAP_myosin_IXA RhoG 20.7 1E+02 0.0022 25.3 2.9 36 118-153 44-83 (186)
89 PF02187 GAS2: Growth-Arrest-S 20.5 19 0.00042 27.1 -1.2 13 49-61 56-68 (73)
90 PRK13977 myosin-cross-reactive 20.5 1.1E+02 0.0023 30.5 3.4 100 48-165 161-270 (576)
91 PF12055 DUF3536: Domain of un 20.3 80 0.0017 29.0 2.3 42 108-154 8-49 (285)
No 1
>PF04852 DUF640: Protein of unknown function (DUF640); InterPro: IPR006936 This conserved region is found in plant proteins including the resistance protein-like protein (O49468 from SWISSPROT).
Probab=100.00 E-value=1.2e-75 Score=470.50 Aligned_cols=123 Identities=84% Similarity=1.468 Sum_probs=119.5
Q ss_pred CCCCCCCchhHHhhhhhHHHHHHHHHhcCCCCCCCCCcchhHhHHHhhhcccCcccccCCCCCCCCCCCCCCCCCCchhh
Q 028699 32 SPSATTPSRYESQKRRDWNTFCQYLRNHRPPLSLPMCSGAHVLEFLRYLDQFGKTKVHNQNCPFFGLPNPPAPCPCPLRQ 111 (205)
Q Consensus 32 ~~~~~~~SrYesQKRrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQ 111 (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 34556889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcchhHHHHHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHH
Q 028699 112 AWGSLDALIGRLRAAYEEHGGRPEANPFGARAVRIFLREVRDF 154 (205)
Q Consensus 112 AWGSLDALIGRLRAafEE~Gg~pE~NPF~araVRlYLReVRd~ 154 (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=91.30 E-value=0.35 Score=37.64 Aligned_cols=55 Identities=22% Similarity=0.553 Sum_probs=44.9
Q ss_pred CCCCCCc---chhHhHHHhhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 028699 63 LSLPMCS---GAHVLEFLRYLDQFGKTKVHNQNCPFFGLPNPPAPCPCPLRQAWGSLDALIGRLRAAY 127 (205)
Q Consensus 63 lsL~~cs---g~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAaf 127 (205)
+.+.+|. +..|+..++.+-..|-..||...|.+.+.+.+ .||. +|.|+-.|+++|
T Consensus 41 vgf~~CgGCpg~~~~~~~~~l~~~~~d~IHlssC~~~~~~~~----~CP~------~~~~~~~I~~~~ 98 (107)
T PF08821_consen 41 VGFFTCGGCPGRKLVRRIKKLKKNGADVIHLSSCMVKGNPHG----PCPH------IDEIKKIIEEKF 98 (107)
T ss_pred EEEeeCCCCChhHHHHHHHHHHHCCCCEEEEcCCEecCCCCC----CCCC------HHHHHHHHHHHh
Confidence 3345555 58899999999999999999999999987553 6665 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=88.80 E-value=0.66 Score=31.37 Aligned_cols=40 Identities=28% Similarity=0.458 Sum_probs=31.7
Q ss_pred hhhhhHHHHHHHHHhcCCCCCCCCCcchhHhHHHhhhcccC
Q 028699 44 QKRRDWNTFCQYLRNHRPPLSLPMCSGAHVLEFLRYLDQFG 84 (205)
Q Consensus 44 QKRrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfG 84 (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 5667788899999999999998766
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=86.58 E-value=2.9 Score=32.40 Aligned_cols=69 Identities=23% Similarity=0.258 Sum_probs=48.1
Q ss_pred hhhhhHHHHHHHHHhcCCCCCCCCCcchhHhHHHhhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHH
Q 028699 44 QKRRDWNTFCQYLRNHRPPLSLPMCSGAHVLEFLRYLDQFGKTKVHNQNCPFFGLPNPPAPCPCPLRQAWGSLDALIGRL 123 (205)
Q Consensus 44 QKRrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRL 123 (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 34567899999998754332 56678899999999887644 1335777788888
Q ss_pred HHHHHHhC--CCCCCCcc
Q 028699 124 RAAYEEHG--GRPEANPF 139 (205)
Q Consensus 124 RAafEE~G--g~pE~NPF 139 (205)
+++|.-.. +--+.||+
T Consensus 74 ~~~~~~~~~~~~~~~~p~ 91 (284)
T cd00798 74 RSFFKFLLREGLILANPA 91 (284)
T ss_pred HHHHHHHHHcCCccCChh
Confidence 88887322 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=85.47 E-value=8.5 Score=31.15 Aligned_cols=77 Identities=22% Similarity=0.291 Sum_probs=53.1
Q ss_pred hhhhhHHHHHHHHHhcCCCCCCCCCcchhHhHHHhhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHH
Q 028699 44 QKRRDWNTFCQYLRNHRPPLSLPMCSGAHVLEFLRYLDQFGKTKVHNQNCPFFGLPNPPAPCPCPLRQAWGSLDALIGRL 123 (205)
Q Consensus 44 QKRrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRL 123 (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 34568889999998752 222234589999999988531 1457888999999
Q ss_pred HHHHHHhCCCCCCCcchhhHHHHHHHHHH
Q 028699 124 RAAYEEHGGRPEANPFGARAVRIFLREVR 152 (205)
Q Consensus 124 RAafEE~Gg~pE~NPF~araVRlYLReVR 152 (205)
+.+|+..+. .||+....++.-|+.++
T Consensus 57 ~~~~~~~~~---~~p~~~~~~~~~~~~~~ 82 (287)
T cd00799 57 SQLHRRSGL---PSPADSPLVRLVLRGIR 82 (287)
T ss_pred HHHHHHcCC---CCCccCHHHHHHHHHHH
Confidence 999985433 58877655666665554
No 6
>TIGR02225 recomb_XerD tyrosine recombinase XerD. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK.
Probab=82.78 E-value=5 Score=31.42 Aligned_cols=70 Identities=24% Similarity=0.402 Sum_probs=47.5
Q ss_pred HhhhhhHHHHHHHHHhcCCCCCCCCCcchhHhHHHhhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHH
Q 028699 43 SQKRRDWNTFCQYLRNHRPPLSLPMCSGAHVLEFLRYLDQFGKTKVHNQNCPFFGLPNPPAPCPCPLRQAWGSLDALIGR 122 (205)
Q Consensus 43 sQKRrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGR 122 (205)
.+-+..++.|..|+.... ..+..-+..||.+|+.++.+.| .+.-++...++.
T Consensus 19 ~~~~~~~~~~~~~~~~~~--~~~~~it~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~ 70 (291)
T TIGR02225 19 EAYRRDLEKFLEFLEERG--IDLEEVDRGDIVDFLAELKEAG--------------------------LSARSIARALSA 70 (291)
T ss_pred HHHHHHHHHHHHHHHhcC--CChHHCCHHHHHHHHHHhhcCC--------------------------CCHhHHHHHHHH
Confidence 445567788999998542 2455567899999999887644 122467888999
Q ss_pred HHHHHHHh--CCCCCCCcch
Q 028699 123 LRAAYEEH--GGRPEANPFG 140 (205)
Q Consensus 123 LRAafEE~--Gg~pE~NPF~ 140 (205)
|+++|+-. -+--+.|||.
T Consensus 71 l~~~~~~a~~~~~~~~np~~ 90 (291)
T TIGR02225 71 LRSFYRFLLREGIREDDPSA 90 (291)
T ss_pred HHHHHHHHHhcccccCCchh
Confidence 99988732 2334568863
No 7
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=82.28 E-value=4 Score=32.58 Aligned_cols=67 Identities=25% Similarity=0.270 Sum_probs=47.1
Q ss_pred hhhhHHHHHHHHHhcCCCCCCCCCcchhHhHHHhhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHH
Q 028699 45 KRRDWNTFCQYLRNHRPPLSLPMCSGAHVLEFLRYLDQFGKTKVHNQNCPFFGLPNPPAPCPCPLRQAWGSLDALIGRLR 124 (205)
Q Consensus 45 KRrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLR 124 (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 35688899999986532 566778999999999885432 23457778888888
Q ss_pred HHHHHhC--CCCCCCcc
Q 028699 125 AAYEEHG--GRPEANPF 139 (205)
Q Consensus 125 AafEE~G--g~pE~NPF 139 (205)
++|+-.. +--..|||
T Consensus 82 ~~~~~a~~~~~i~~np~ 98 (299)
T PRK00283 82 RFFQFLLREGLREDDPS 98 (299)
T ss_pred HHHHHHHHcCCcccCch
Confidence 8887331 23446776
No 8
>COG1080 PtsA Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]
Probab=78.76 E-value=2.8 Score=41.58 Aligned_cols=42 Identities=38% Similarity=0.631 Sum_probs=33.5
Q ss_pred hhhcchhHHHHHHHHHHHHHhCCCC---------------------CCCcc-hhhHHHHHHHHH
Q 028699 110 RQAWGSLDALIGRLRAAYEEHGGRP---------------------EANPF-GARAVRIFLREV 151 (205)
Q Consensus 110 RQAWGSLDALIGRLRAafEE~Gg~p---------------------E~NPF-~araVRlYLReV 151 (205)
|..|=+.|..----++..|.+||+| |.||| |-|+||+||..-
T Consensus 305 r~~~P~EeEQ~~aY~~vlea~~g~pviiRTlDiGGDK~lpyl~lp~E~NPfLG~RaIRl~l~~~ 368 (574)
T COG1080 305 RDALPDEEEQFEAYKAVLEAMGGKPVIIRTLDIGGDKPLPYLNLPKEENPFLGYRAIRLSLERP 368 (574)
T ss_pred CCCCCChHHHHHHHHHHHHHcCCCceEEEecccCCCCcCCCCCCccccCchhhhHHHHHhhccH
Confidence 3455567777777888889998883 79999 899999999643
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=72.77 E-value=15 Score=29.00 Aligned_cols=69 Identities=30% Similarity=0.363 Sum_probs=46.6
Q ss_pred hhhHHHHHHHHHhcCCCCCCCCCcchhHhHHHhhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHH
Q 028699 46 RRDWNTFCQYLRNHRPPLSLPMCSGAHVLEFLRYLDQFGKTKVHNQNCPFFGLPNPPAPCPCPLRQAWGSLDALIGRLRA 125 (205)
Q Consensus 46 RrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRA 125 (205)
+.+++.|.+||......+.+..-+..||.+|+.++.+.|. +..++...++.|++
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~l~~~~i~~~~~~~~~~~~--------------------------~~~T~~~~~~~l~~ 75 (295)
T TIGR02224 22 RRDLKAFLEFLEEEGGLASLAEVTAADLRSFLAELHARGL--------------------------SRRSLARKLSALRS 75 (295)
T ss_pred HHHHHHHHHHHHhcCCCCccccCcHHHHHHHHHHhcccCC--------------------------CHHHHHHHHHHHHH
Confidence 3456678888887665677888889999999998766321 22456677777887
Q ss_pred HHHHhC--CCCCCCcch
Q 028699 126 AYEEHG--GRPEANPFG 140 (205)
Q Consensus 126 afEE~G--g~pE~NPF~ 140 (205)
+|.-.. +.-+.|||.
T Consensus 76 ~~~~a~~~~~~~~np~~ 92 (295)
T TIGR02224 76 FYRFLVRRGLIKANPAA 92 (295)
T ss_pred HHHHHHHcCccccChHh
Confidence 776421 223467763
No 10
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=63.72 E-value=2.6 Score=33.87 Aligned_cols=43 Identities=28% Similarity=0.340 Sum_probs=32.9
Q ss_pred HhHHHhhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHHHHhCCCCC
Q 028699 73 VLEFLRYLDQFGKTKVHNQNCPFFGLPNPPAPCPCPLRQAWGSLDALIGRLRAAYEEHGGRPE 135 (205)
Q Consensus 73 VleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAafEE~Gg~pE 135 (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------CERCG-------------DTGETLREAVKELAPVLAPLGIEVR 44 (120)
T ss_pred eEEEE-EeecCCCc------CCchh-------------hHHHHHHHHHHHHHHHHHhCCcEEE
Confidence 46786 56655776 54433 5678999999999999999998754
No 11
>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=61.24 E-value=13 Score=37.27 Aligned_cols=42 Identities=21% Similarity=0.311 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHhCCC-------------------------CCCCcc-hhhHHHHHH----HHHHHHHHhh
Q 028699 117 DALIGRLRAAYEEHGGR-------------------------PEANPF-GARAVRIFL----REVRDFQAKA 158 (205)
Q Consensus 117 DALIGRLRAafEE~Gg~-------------------------pE~NPF-~araVRlYL----ReVRd~QAkA 158 (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 55566778888876544 378999 899999999 4466666554
No 12
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=57.88 E-value=8.5 Score=29.36 Aligned_cols=19 Identities=32% Similarity=0.494 Sum_probs=14.5
Q ss_pred hhHHHHHHHHHHHHHhCCC
Q 028699 115 SLDALIGRLRAAYEEHGGR 133 (205)
Q Consensus 115 SLDALIGRLRAafEE~Gg~ 133 (205)
+||.+|.|||.-+++.+..
T Consensus 191 ~~~~~i~rlR~kl~~~~~~ 209 (225)
T PRK10529 191 YLRIYMGHLRQKLEQDPAR 209 (225)
T ss_pred CHHHHHHHHHHHhccCCCC
Confidence 5899999999998765433
No 13
>cd01185 INT_Tn4399 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the Bacteroides mobilizable transposon, Tn4399, integrase.
Probab=56.39 E-value=46 Score=27.04 Aligned_cols=33 Identities=15% Similarity=0.310 Sum_probs=26.1
Q ss_pred hHHHHHHHHHhcCC--CCCCCCCcchhHhHHHhhh
Q 028699 48 DWNTFCQYLRNHRP--PLSLPMCSGAHVLEFLRYL 80 (205)
Q Consensus 48 dWntf~qyL~n~rP--PlsL~~csg~hVleFLryl 80 (205)
.++.|..||....+ .+.|..-+..||.+|+.|+
T Consensus 44 ~~~~~~~~~~~~~~~~~~~l~~i~~~~i~~~~~~l 78 (299)
T cd01185 44 HLKNLREFIECTYKEIDIALLELTREFILEFKLFL 78 (299)
T ss_pred HHHHHHHHHHHhcCccCCCHHHccHHHHHHHHHHH
Confidence 46668888876553 5678888899999999988
No 14
>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=56.13 E-value=15 Score=33.00 Aligned_cols=40 Identities=30% Similarity=0.311 Sum_probs=31.6
Q ss_pred cchhHHHHHHHHHHHHHhCCC----------------------CCCCcc-hhhHHHHHHHHHH
Q 028699 113 WGSLDALIGRLRAAYEEHGGR----------------------PEANPF-GARAVRIFLREVR 152 (205)
Q Consensus 113 WGSLDALIGRLRAafEE~Gg~----------------------pE~NPF-~araVRlYLReVR 152 (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 15
>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=53.64 E-value=3.2 Score=31.11 Aligned_cols=17 Identities=41% Similarity=0.802 Sum_probs=12.3
Q ss_pred HhhhCcchhhhhcCCCc
Q 028699 156 AKARGVSYDKKRKRPKQ 172 (205)
Q Consensus 156 AkARgi~y~kk~~~~~~ 172 (205)
.|+-||.|.+|||||..
T Consensus 45 ~KgLGI~Y~r~rrRrr~ 61 (68)
T PF00539_consen 45 QKGLGISYGRKRRRRRT 61 (68)
T ss_dssp CTSSSTSSSSSSCSCCC
T ss_pred eCCCcccccccccCcCC
Confidence 47889999987655443
No 16
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=50.89 E-value=11 Score=28.71 Aligned_cols=23 Identities=30% Similarity=0.546 Sum_probs=17.1
Q ss_pred hhhhcc--------hhHHHHHHHHHHHHHhC
Q 028699 109 LRQAWG--------SLDALIGRLRAAYEEHG 131 (205)
Q Consensus 109 lRQAWG--------SLDALIGRLRAafEE~G 131 (205)
+++.|| +||.+|.|||.-+++.+
T Consensus 175 ~~~~w~~~~~~~~~~v~~~i~rLR~kl~~~~ 205 (223)
T PRK10816 175 MLQLYPDAELRESHTIDVLMGRLRKKIQAQY 205 (223)
T ss_pred HHHhcCCCCCCCcCCHHHHHHHHHHHhccCC
Confidence 456676 68888999988887643
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=50.85 E-value=2.7 Score=32.55 Aligned_cols=19 Identities=53% Similarity=0.747 Sum_probs=15.0
Q ss_pred CCCCcc---hhhHHHHHHHHHH
Q 028699 134 PEANPF---GARAVRIFLREVR 152 (205)
Q Consensus 134 pE~NPF---~araVRlYLReVR 152 (205)
..+||| .||-+|+||||=-
T Consensus 4 ~k~NPfr~aiARKaRiyLr~Gl 25 (82)
T PF05528_consen 4 SKDNPFRGAIARKARIYLREGL 25 (82)
T ss_pred cccCchhhhhhhheeeeeecCC
Confidence 348999 5788999999743
No 18
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=47.98 E-value=16 Score=36.56 Aligned_cols=36 Identities=25% Similarity=0.422 Sum_probs=29.8
Q ss_pred hhHHHHHHHHHHHHHhCCC--------------------CCCCcc-hhhHHHHHHHH
Q 028699 115 SLDALIGRLRAAYEEHGGR--------------------PEANPF-GARAVRIFLRE 150 (205)
Q Consensus 115 SLDALIGRLRAafEE~Gg~--------------------pE~NPF-~araVRlYLRe 150 (205)
+-|......|.+.+.++++ +|.||| |.|+||+||+.
T Consensus 475 ~e~eQ~~~y~~~~~~~~~~pv~iRtlDiGgDK~~~~~~~~E~NP~lG~RgiR~~l~~ 531 (748)
T PRK11061 475 SEEEQVAQYQGMLQMFPDKPVTLRTLDIGADKQLPYMPISEENPCLGWRGIRITLDQ 531 (748)
T ss_pred CHHHHHHHHHHHHHHcCCCeEEEECCCCCcCCCCCCCCCCCCCcccccchhhccccC
Confidence 4678888889999888765 589999 78999999853
No 19
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=47.59 E-value=21 Score=24.29 Aligned_cols=53 Identities=17% Similarity=0.343 Sum_probs=31.9
Q ss_pred hhHHHHHHHHHhcCCCCCCCCCcchhHhHHHhhhc-ccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHH
Q 028699 47 RDWNTFCQYLRNHRPPLSLPMCSGAHVLEFLRYLD-QFGKTKVHNQNCPFFGLPNPPAPCPCPLRQAWGSLDALIGRLRA 125 (205)
Q Consensus 47 rdWntf~qyL~n~rPPlsL~~csg~hVleFLrylD-qfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRA 125 (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 3445566666522 566678999999999887 322 345566777777777
Q ss_pred HHHH
Q 028699 126 AYEE 129 (205)
Q Consensus 126 afEE 129 (205)
.|+-
T Consensus 74 ff~~ 77 (85)
T PF13495_consen 74 FFRW 77 (85)
T ss_dssp HHHC
T ss_pred HHHH
Confidence 7663
No 20
>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=47.37 E-value=21 Score=34.68 Aligned_cols=36 Identities=28% Similarity=0.480 Sum_probs=29.1
Q ss_pred hhHHHHHHHHHHHHHhCCC---------------------CCCCcc-hhhHHHHHHHH
Q 028699 115 SLDALIGRLRAAYEEHGGR---------------------PEANPF-GARAVRIFLRE 150 (205)
Q Consensus 115 SLDALIGRLRAafEE~Gg~---------------------pE~NPF-~araVRlYLRe 150 (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 89999999974
No 21
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=46.85 E-value=98 Score=24.32 Aligned_cols=36 Identities=31% Similarity=0.399 Sum_probs=27.1
Q ss_pred hhhHHHHHHHHHhcCCCCCCCCCcchhHhHHHhhhcc
Q 028699 46 RRDWNTFCQYLRNHRPPLSLPMCSGAHVLEFLRYLDQ 82 (205)
Q Consensus 46 RrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDq 82 (205)
+.+|+.|..|+..... ..+..-...||.+||.++-+
T Consensus 32 ~~~~~~~~~~~~~~~~-~~~~~i~~~~i~~~~~~~~~ 67 (297)
T PRK00236 32 RRDLRAFLAFLEEHGI-SSLQDLDAADLRSFLARRRR 67 (297)
T ss_pred HHHHHHHHHHHHHcCC-CchhhCCHHHHHHHHHHHHh
Confidence 4577888888887543 55667788999999987754
No 22
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=45.24 E-value=22 Score=23.78 Aligned_cols=21 Identities=52% Similarity=0.833 Sum_probs=18.1
Q ss_pred chhHHHHHHHHHHHHHhCCCC
Q 028699 114 GSLDALIGRLRAAYEEHGGRP 134 (205)
Q Consensus 114 GSLDALIGRLRAafEE~Gg~p 134 (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 489999999999999987554
No 23
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=44.41 E-value=23 Score=32.79 Aligned_cols=38 Identities=29% Similarity=0.496 Sum_probs=34.0
Q ss_pred hhhHHHHHHHHHhcCCCC-CCCCCcchhHhHHHhhhcccCc
Q 028699 46 RRDWNTFCQYLRNHRPPL-SLPMCSGAHVLEFLRYLDQFGK 85 (205)
Q Consensus 46 RrdWntf~qyL~n~rPPl-sL~~csg~hVleFLrylDqfGK 85 (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 24
>PF13276 HTH_21: HTH-like domain
Probab=42.76 E-value=41 Score=22.44 Aligned_cols=29 Identities=24% Similarity=0.403 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHhCCCCCCCcchhhHHHHHHHH
Q 028699 117 DALIGRLRAAYEEHGGRPEANPFGARAVRIFLRE 150 (205)
Q Consensus 117 DALIGRLRAafEE~Gg~pE~NPF~araVRlYLRe 150 (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 6789999999999977 3788888888876
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=41.11 E-value=1.5e+02 Score=22.68 Aligned_cols=88 Identities=17% Similarity=0.152 Sum_probs=57.5
Q ss_pred hHHHHHHHHHhcCCCCCCCCCcchhHhHHHhhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 028699 48 DWNTFCQYLRNHRPPLSLPMCSGAHVLEFLRYLDQFGKTKVHNQNCPFFGLPNPPAPCPCPLRQAWGSLDALIGRLRAAY 127 (205)
Q Consensus 48 dWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAaf 127 (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 456788888888887788888999988999888888853 2111111111111 1 1788999999999
Q ss_pred HHhCCCCCCCcchhhHHHHHHH
Q 028699 128 EEHGGRPEANPFGARAVRIFLR 149 (205)
Q Consensus 128 EE~Gg~pE~NPF~araVRlYLR 149 (205)
.++|....-+--...++.-|++
T Consensus 68 ~~~~~~~~v~~~s~~aL~~fvk 89 (119)
T PF06252_consen 68 KQLGKPGAVRDPSEAALDAFVK 89 (119)
T ss_pred HHhhccCCccchHHHHHHHHHH
Confidence 9999776522223344444443
No 26
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=40.66 E-value=26 Score=25.79 Aligned_cols=35 Identities=34% Similarity=0.551 Sum_probs=30.2
Q ss_pred CCCCchhhhcc----hhHHHHHHHHHHHHHhCCCCCCCc
Q 028699 104 PCPCPLRQAWG----SLDALIGRLRAAYEEHGGRPEANP 138 (205)
Q Consensus 104 pC~CPlRQAWG----SLDALIGRLRAafEE~Gg~pE~NP 138 (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 999999999999999987776666
No 27
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=40.51 E-value=49 Score=27.14 Aligned_cols=26 Identities=27% Similarity=0.349 Sum_probs=19.9
Q ss_pred chhHHHHHHHHHHHHH---hCCCCCCCcch
Q 028699 114 GSLDALIGRLRAAYEE---HGGRPEANPFG 140 (205)
Q Consensus 114 GSLDALIGRLRAafEE---~Gg~pE~NPF~ 140 (205)
.++...++.|+++|+- +|.- +.|||.
T Consensus 135 ~t~~~~~~~l~~~~~~a~~~g~i-~~nP~~ 163 (357)
T cd00801 135 ETARRVRQRLKQVFRYAIARGLI-EANPAA 163 (357)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCc-ccCchH
Confidence 4788999999999984 4443 489985
No 28
>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=40.23 E-value=15 Score=22.66 Aligned_cols=16 Identities=38% Similarity=0.930 Sum_probs=13.5
Q ss_pred CCCCCCCCCCCCCCCC
Q 028699 91 QNCPFFGLPNPPAPCP 106 (205)
Q Consensus 91 ~~C~ffG~p~ppapC~ 106 (205)
.+|.|||.+..-..|.
T Consensus 7 ~~CgF~G~~~t~~~Cs 22 (26)
T smart00259 7 PGCGFFGNPATEGLCS 22 (26)
T ss_pred CCCCCcCChhhcccCH
Confidence 6999999998777774
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=39.66 E-value=31 Score=22.86 Aligned_cols=19 Identities=42% Similarity=0.695 Sum_probs=17.1
Q ss_pred chhHHHHHHHHHHHHHhCC
Q 028699 114 GSLDALIGRLRAAYEEHGG 132 (205)
Q Consensus 114 GSLDALIGRLRAafEE~Gg 132 (205)
.+|+.+|-|||..+++.|+
T Consensus 45 ~~l~~~i~~LR~~l~~~~~ 63 (78)
T smart00862 45 NTLDVHISRLRKKLEDDGA 63 (78)
T ss_pred chHHHHHHHHHHHHhcCCC
Confidence 5799999999999999865
No 30
>PRK09279 pyruvate phosphate dikinase; Provisional
Probab=39.56 E-value=27 Score=36.12 Aligned_cols=36 Identities=33% Similarity=0.476 Sum_probs=0.0
Q ss_pred HHHHHHHhCCC-----------CCCCcc-hhhHHHHHH--HHHHHHHHhh
Q 028699 123 LRAAYEEHGGR-----------PEANPF-GARAVRIFL--REVRDFQAKA 158 (205)
Q Consensus 123 LRAafEE~Gg~-----------pE~NPF-~araVRlYL--ReVRd~QAkA 158 (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 31
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=36.31 E-value=29 Score=22.18 Aligned_cols=12 Identities=25% Similarity=0.758 Sum_probs=10.1
Q ss_pred hHHHHHHHHHHH
Q 028699 142 RAVRIFLREVRD 153 (205)
Q Consensus 142 raVRlYLReVRd 153 (205)
-+|++||++|+.
T Consensus 2 D~l~~Yl~ei~~ 13 (37)
T PF00140_consen 2 DSLRLYLKEIGR 13 (37)
T ss_dssp HHHHHHHHHHHH
T ss_pred cHHHHHHHHHcC
Confidence 479999999975
No 32
>PRK06464 phosphoenolpyruvate synthase; Validated
Probab=35.31 E-value=48 Score=33.61 Aligned_cols=15 Identities=40% Similarity=0.722 Sum_probs=13.7
Q ss_pred CCCcc-hhhHHHHHHH
Q 028699 135 EANPF-GARAVRIFLR 149 (205)
Q Consensus 135 E~NPF-~araVRlYLR 149 (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 33
>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=35.00 E-value=45 Score=26.45 Aligned_cols=63 Identities=24% Similarity=0.492 Sum_probs=43.2
Q ss_pred hHHHHHHHHHhcCCCCCCCCCcchhHhHHHhhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 028699 48 DWNTFCQYLRNHRPPLSLPMCSGAHVLEFLRYLDQFGKTKVHNQNCPFFGLPNPPAPCPCPLRQAWGSLDALIGRLRAAY 127 (205)
Q Consensus 48 dWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAaf 127 (205)
+|.++-.++.. |-.-.+.+--||-+|=.+.++ | .+| +|-|=..||+-++-||.|-..|
T Consensus 23 ~W~~LA~~i~~---~~~~~~y~~~ei~~ie~~~~~--------------g-~SP----T~~LL~dWgt~N~TV~~L~~lL 80 (100)
T cd08793 23 GWKKIAVAIKK---PSGDPRYSQFHIRRFEALVQQ--------------G-KSP----TCELLFDWGTTNCTVGDLVDLL 80 (100)
T ss_pred cHHHHHHHHhc---ccCCCCCCHHHHHHHHHHHHc--------------C-CCh----HHHHHHHHccCCCcHHHHHHHH
Confidence 78888877755 223344544566666443333 3 222 4567789999999999999999
Q ss_pred HHhCC
Q 028699 128 EEHGG 132 (205)
Q Consensus 128 EE~Gg 132 (205)
.++|-
T Consensus 81 ~k~~l 85 (100)
T cd08793 81 IQNEF 85 (100)
T ss_pred HHccc
Confidence 99884
No 34
>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=34.75 E-value=47 Score=27.17 Aligned_cols=36 Identities=14% Similarity=0.400 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHhCCCCC---C---Cc-chhhHHHHHHHHHHH
Q 028699 118 ALIGRLRAAYEEHGGRPE---A---NP-FGARAVRIFLREVRD 153 (205)
Q Consensus 118 ALIGRLRAafEE~Gg~pE---~---NP-F~araVRlYLReVRd 153 (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 268889999999754
No 35
>PF11709 Mit_ribos_Mrp51: Mitochondrial ribosomal protein subunit ; InterPro: IPR016712 The function of mitochondrial ribosomal small-subunit protein MRP51 is not entirely clear, but deletion of the MRP51 gene completely blocks mitochondrial gene expression [].
Probab=34.68 E-value=58 Score=29.44 Aligned_cols=67 Identities=22% Similarity=0.235 Sum_probs=48.0
Q ss_pred CCCCCchhHHhhhhhHHHHHHHHHhcCCCCCC--CCCcchhHhHHHhh-----------------hcccCcccccCCCCC
Q 028699 34 SATTPSRYESQKRRDWNTFCQYLRNHRPPLSL--PMCSGAHVLEFLRY-----------------LDQFGKTKVHNQNCP 94 (205)
Q Consensus 34 ~~~~~SrYesQKRrdWntf~qyL~n~rPPlsL--~~csg~hVleFLry-----------------lDqfGKTkVH~~~C~ 94 (205)
....-.+|-++=|..-.+|.+||+.+.|-... ..--...|.|||.. ....|..++|.-+=-
T Consensus 144 t~~ef~~yL~kvr~~R~eF~~~L~~~~~e~~~~~~~~l~~~v~eFL~~~~~~~~~~~~~~~~~~~~~~~~~~~~hpsgGL 223 (312)
T PF11709_consen 144 TEGEFERYLKKVRPLRPEFKKWLREKHPESLTFDPSDLYDLVKEFLDLAPLKPPDVPDSKKSSSPYAEAGPPKTHPSGGL 223 (312)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHHHhChhhhccCHHHHHHHHHHHHhcccccCcccccchhccCcccccCCCccccCcCc
Confidence 33445678888899999999999999886621 23345678899875 335677788887777
Q ss_pred CCCCCC
Q 028699 95 FFGLPN 100 (205)
Q Consensus 95 ffG~p~ 100 (205)
.|.+++
T Consensus 224 SY~~~g 229 (312)
T PF11709_consen 224 SYNRTG 229 (312)
T ss_pred CcCCCc
Confidence 776654
No 36
>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=33.91 E-value=23 Score=36.28 Aligned_cols=25 Identities=36% Similarity=0.639 Sum_probs=19.2
Q ss_pred CCCCcc-hhhHHHHHH--HHHHHHHHhh
Q 028699 134 PEANPF-GARAVRIFL--REVRDFQAKA 158 (205)
Q Consensus 134 pE~NPF-~araVRlYL--ReVRd~QAkA 158 (205)
-|.||| |.|.||+|| .++=++|.+|
T Consensus 652 ~E~NP~LG~RGiRl~l~~pei~~~QlrA 679 (856)
T TIGR01828 652 HEVNPMLGHRGCRLGITYPEIYEMQVRA 679 (856)
T ss_pred CCCCCccccchhhhccCChHHHHHHHHH
Confidence 599999 889999999 4555555544
No 37
>PRK11177 phosphoenolpyruvate-protein phosphotransferase; Provisional
Probab=32.29 E-value=39 Score=33.05 Aligned_cols=36 Identities=33% Similarity=0.528 Sum_probs=29.7
Q ss_pred hhHHHHHHHHHHHHHhCCC---------------------CCCCcc-hhhHHHHHHHH
Q 028699 115 SLDALIGRLRAAYEEHGGR---------------------PEANPF-GARAVRIFLRE 150 (205)
Q Consensus 115 SLDALIGRLRAafEE~Gg~---------------------pE~NPF-~araVRlYLRe 150 (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 4677888888888888776 379999 77999999965
No 38
>PF01213 CAP_N: Adenylate cyclase associated (CAP) N terminal; InterPro: IPR013992 Cyclase-associated proteins (CAPs) are highly conserved actin-binding proteins present in a wide range of organisms including yeast, fly, plants, and mammals. CAPs are multifunctional proteins that contain several structural domains. CAP is involved in species-specific signalling pathways [, , , ]. In Drosophila, CAP functions in Hedgehog-mediated eye development and in establishing oocyte polarity. In Dictyostelium (slim mold), CAP is involved in microfilament reorganisation near the plasma membrane in a PIP2-regulated manner and is required to perpetuate the cAMP relay signal to organise fruitbody formation. In plants, CAP is involved in plant signalling pathways required for co-ordinated organ expansion. In yeast, CAP is involved in adenylate cyclase activation, as well as in vesicle trafficking and endocytosis. In both yeast and mammals, CAPs appear to be involved in recycling G-actin monomers from ADF/cofilins for subsequent rounds of filament assembly [, ]. In mammals, there are two different CAPs (CAP1 and CAP2) that share 64% amino acid identity. All CAPs appear to contain a C-terminal actin-binding domain that regulates actin remodelling in response to cellular signals and is required for normal cellular morphology, cell division, growth and locomotion in eukaryotes. CAP directly regulates actin filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localisation and the establishment of cell polarity. Actin exists both as globular (G) (monomeric) actin subunits and assembled into filamentous (F) actin. In cells, actin cycles between these two forms. Proteins that bind F-actin often regulate F-actin assembly and its interaction with other proteins, while proteins that interact with G-actin often control the availability of unpolymerised actin. CAPs bind G-actin. In addition to actin-binding, CAPs can have additional roles, and may act as bifunctional proteins. In Saccharomyces cerevisiae (Baker's yeast), CAP is a component of the adenylyl cyclase complex (Cyr1p) that serves as an effector of Ras during normal cell signalling. S. cerevisiae CAP functions to expose adenylate cyclase binding sites to Ras, thereby enabling adenylate cyclase to be activated by Ras regulatory signals. In Schizosaccharomyces pombe (Fission yeast), CAP is also required for adenylate cyclase activity, but not through the Ras pathway. In both organisms, the N-terminal domain is responsible for adenylate cyclase activation, but the S cerevisiae and S. pombe N-termini cannot complement one another. Yeast CAPs are unique among the CAP family of proteins, because they are the only ones to directly interact with and activate adenylate cyclase []. S. cerevisiae CAP has four major domains. In addition to the N-terminal adenylate cyclase-interacting domain, and the C-terminal actin-binding domain, it possesses two other domains: a proline-rich domain that interacts with Src homology 3 (SH3) domains of specific proteins, and a domain that is responsible for CAP oligomerisation to form multimeric complexes (although oligomerisation appears to involve the N- and C-terminal domains as well). The proline-rich domain interacts with profilin, a protein that catalyses nucleotide exchange on G-actin monomers and promotes addition to barbed ends of filamentous F-actin []. Since CAP can bind profilin via a proline-rich domain, and G-actin via a C-terminal domain, it has been suggested that a ternary G-actin/CAP/profilin complex could be formed. This entry represents the N-terminal domain of CAP proteins. This domain has an all-alpha structure consisting of six helices in a bundle with a left-handed twist and an up-and-down topology [].; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1TJF_B 1S0P_A.
Probab=31.90 E-value=59 Score=29.76 Aligned_cols=53 Identities=23% Similarity=0.354 Sum_probs=36.9
Q ss_pred hhhhcchhHHHHHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHHhh-----hCcchhhhh
Q 028699 109 LRQAWGSLDALIGRLRAAYEEHGGRPEANPFGARAVRIFLREVRDFQAKA-----RGVSYDKKR 167 (205)
Q Consensus 109 lRQAWGSLDALIGRLRAafEE~Gg~pE~NPF~araVRlYLReVRd~QAkA-----Rgi~y~kk~ 167 (205)
....|++-+-..-|+.--|.+ .||--...||.|+.-..+.|+=. -|+.+-+|-
T Consensus 156 V~e~~dsA~Fy~NRVLke~K~------kd~~hveWvks~~~l~~~L~~YVke~httGl~WN~~G 213 (312)
T PF01213_consen 156 VKEMKDSAQFYTNRVLKEYKE------KDPKHVEWVKSFKALLKELQAYVKEHHTTGLSWNPKG 213 (312)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT------T-HHHHHHHHHHHHHHHHHHHHHHHHSTTS----TTS
T ss_pred HHHHHHHHHHHHhHHHHHhhh------ccchhHHHHHHHHHHHHHHHHHHHHhCccCcccCCcc
Confidence 456677777788887777765 57888899999999999988753 478877665
No 39
>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=31.78 E-value=2e+02 Score=24.29 Aligned_cols=37 Identities=14% Similarity=0.252 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHhC---CCCCCCcc----hhhHHHHHHHHHHH
Q 028699 117 DALIGRLRAAYEEHG---GRPEANPF----GARAVRIFLREVRD 153 (205)
Q Consensus 117 DALIGRLRAafEE~G---g~pE~NPF----~araVRlYLReVRd 153 (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 22222222 68899999999744
No 40
>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=31.32 E-value=25 Score=24.27 Aligned_cols=20 Identities=35% Similarity=0.496 Sum_probs=16.8
Q ss_pred CcchhHhHHHhhhcccCccc
Q 028699 68 CSGAHVLEFLRYLDQFGKTK 87 (205)
Q Consensus 68 csg~hVleFLrylDqfGKTk 87 (205)
.|=+-++-+|.|+|+.|.|+
T Consensus 22 ~sRK~ai~lLE~lD~~g~T~ 41 (50)
T PF09107_consen 22 LSRKYAIPLLEYLDREGITR 41 (50)
T ss_dssp S-HHHHHHHHHHHHHTTSEE
T ss_pred ccHHHHHHHHHHHhccCCEE
Confidence 45677899999999999987
No 41
>PRK10701 DNA-binding transcriptional regulator RstA; Provisional
Probab=31.09 E-value=39 Score=26.35 Aligned_cols=16 Identities=38% Similarity=0.536 Sum_probs=10.8
Q ss_pred hhHHHHHHHHHHHHHh
Q 028699 115 SLDALIGRLRAAYEEH 130 (205)
Q Consensus 115 SLDALIGRLRAafEE~ 130 (205)
+||.+|.|||.-+++.
T Consensus 201 ~i~~~i~rlR~kl~~~ 216 (240)
T PRK10701 201 SVDVAISRLRKKLLDN 216 (240)
T ss_pred CHHHHHHHHHHhcccC
Confidence 4677777777777643
No 42
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=30.97 E-value=34 Score=26.14 Aligned_cols=14 Identities=43% Similarity=0.997 Sum_probs=13.1
Q ss_pred hHHHHHHHHHhcCC
Q 028699 48 DWNTFCQYLRNHRP 61 (205)
Q Consensus 48 dWntf~qyL~n~rP 61 (205)
-|.||.+||..|.|
T Consensus 55 GW~tL~~fL~khDP 68 (73)
T smart00243 55 GWETLDEYLLKHDP 68 (73)
T ss_pred cHHHHHHHHHhCCC
Confidence 39999999999998
No 43
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=30.92 E-value=81 Score=31.19 Aligned_cols=25 Identities=24% Similarity=0.331 Sum_probs=22.0
Q ss_pred CCCcchhhHHHHHHHHHHHHHHhhh
Q 028699 135 EANPFGARAVRIFLREVRDFQAKAR 159 (205)
Q Consensus 135 E~NPF~araVRlYLReVRd~QAkAR 159 (205)
+.+|+.-..||-||...-+.|+-.|
T Consensus 180 ~~D~~hveWvKa~l~l~~eL~~YVk 204 (480)
T KOG2675|consen 180 EKDPRHVEWVKAYLALFLELQAYVK 204 (480)
T ss_pred cCChhHHHHHHHHHHHHHHHHHHHH
Confidence 4799999999999999999998655
No 44
>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=29.48 E-value=47 Score=22.84 Aligned_cols=20 Identities=30% Similarity=0.468 Sum_probs=17.2
Q ss_pred chhHHHHHHHHHHHHHhCCC
Q 028699 114 GSLDALIGRLRAAYEEHGGR 133 (205)
Q Consensus 114 GSLDALIGRLRAafEE~Gg~ 133 (205)
.+|+.+|-|||..+.+.|+.
T Consensus 62 ~~l~~~I~rLRkkl~~~~~~ 81 (95)
T cd00383 62 RTVDVHISRLRKKLEDDPSN 81 (95)
T ss_pred ccHHHHHHHHHHHhccCCCC
Confidence 57999999999999987653
No 45
>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=29.26 E-value=7.2 Score=26.50 Aligned_cols=72 Identities=14% Similarity=0.187 Sum_probs=44.8
Q ss_pred hhhhHHHHHHHHHhcCC--CCCCCCCcchhHhHHHhhhcccC--cccccC---CCCCCCCCCCCCCCCCCchhhhcchhH
Q 028699 45 KRRDWNTFCQYLRNHRP--PLSLPMCSGAHVLEFLRYLDQFG--KTKVHN---QNCPFFGLPNPPAPCPCPLRQAWGSLD 117 (205)
Q Consensus 45 KRrdWntf~qyL~n~rP--PlsL~~csg~hVleFLrylDqfG--KTkVH~---~~C~ffG~p~ppapC~CPlRQAWGSLD 117 (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 56899999999995543 44455667788888888888887 333321 333321 111223566
Q ss_pred HHHHHHHHHHH
Q 028699 118 ALIGRLRAAYE 128 (205)
Q Consensus 118 ALIGRLRAafE 128 (205)
.++-+|++.|+
T Consensus 74 ~v~~~l~~~~~ 84 (85)
T PF08544_consen 74 RVAEALREHYK 84 (85)
T ss_dssp HHHHHHHHHTH
T ss_pred HHHHHHHHhCC
Confidence 67777776664
No 46
>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=29.18 E-value=48 Score=23.48 Aligned_cols=31 Identities=19% Similarity=0.448 Sum_probs=24.4
Q ss_pred HHHHHHHHHhcCCCCCCCCCcchhHhHHHhhhcccC
Q 028699 49 WNTFCQYLRNHRPPLSLPMCSGAHVLEFLRYLDQFG 84 (205)
Q Consensus 49 Wntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfG 84 (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 556899999999999998
No 47
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=28.99 E-value=1.4e+02 Score=22.52 Aligned_cols=38 Identities=29% Similarity=0.447 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHHhhhCcchhh
Q 028699 118 ALIGRLRAAYEEHGGRPEANPFGARAVRIFLREVRDFQAKARGVSYDK 165 (205)
Q Consensus 118 ALIGRLRAafEE~Gg~pE~NPF~araVRlYLReVRd~QAkARgi~y~k 165 (205)
.|--+.-++|+++|-.+ +.||++||+.| ++.+|||++.
T Consensus 11 ~lK~~A~~vl~~lGls~------S~Ai~~fl~qi----~~~~~iPF~~ 48 (80)
T PRK11235 11 ELKARAYAVLEKLGVTP------SEALRLLLQYV----AENGRLPFKT 48 (80)
T ss_pred HHHHHHHHHHHHhCCCH------HHHHHHHHHHH----HHhCCCCCCC
Confidence 45556778999999874 67999999987 4558888874
No 48
>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=28.69 E-value=1.1e+02 Score=24.88 Aligned_cols=46 Identities=17% Similarity=0.292 Sum_probs=28.4
Q ss_pred CCCCchhHHhhhhhHHHHHHHHHhcCC------CCCCCCCcchhHhHHHhhh
Q 028699 35 ATTPSRYESQKRRDWNTFCQYLRNHRP------PLSLPMCSGAHVLEFLRYL 80 (205)
Q Consensus 35 ~~~~SrYesQKRrdWntf~qyL~n~rP------PlsL~~csg~hVleFLryl 80 (205)
.++|-+=++-+..-++++.+||..+-- +..|...+.+++++.+.+|
T Consensus 28 d~Rpl~Dk~~q~~~~~~I~~fL~~~~~~~~~is~k~l~~Pt~kdf~~I~~fL 79 (157)
T PF03801_consen 28 DPRPLSDKSYQQECIRKIYEFLSEHGFESHPISPKTLKSPTQKDFVEIFNFL 79 (157)
T ss_dssp --S-TT-HHHHHHHHHHHHHHHHHTT--SS---TTTTSS--HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHcCCCCccccccccCCCCHHHHHHHHHHH
Confidence 355555556667788999999987665 5666778888877665554
No 49
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=28.14 E-value=46 Score=28.27 Aligned_cols=27 Identities=37% Similarity=0.667 Sum_probs=21.6
Q ss_pred chhhhcc--------hhHHHHHHHHHHHHHhCCCC
Q 028699 108 PLRQAWG--------SLDALIGRLRAAYEEHGGRP 134 (205)
Q Consensus 108 PlRQAWG--------SLDALIGRLRAafEE~Gg~p 134 (205)
-+.+.|| +||..|+|||.-+++.++.+
T Consensus 178 L~~~vw~~~~~~~~rtvdvhI~rLR~Kl~~~~~~~ 212 (229)
T COG0745 178 LLEAVWGYDFEVDSRTVDVHISRLRKKLEKDPGAG 212 (229)
T ss_pred HHHHhcCCCCCCCccCHHHHHHHHHHHhccCCCCC
Confidence 3667777 49999999999999887643
No 50
>PTZ00398 phosphoenolpyruvate carboxylase; Provisional
Probab=27.81 E-value=1.1e+02 Score=32.25 Aligned_cols=43 Identities=21% Similarity=0.373 Sum_probs=32.1
Q ss_pred cchhHHHHHHHHHHHHHhCC------------------CCCCCcch-------------hhHHHHHHHHHHHHH
Q 028699 113 WGSLDALIGRLRAAYEEHGG------------------RPEANPFG-------------ARAVRIFLREVRDFQ 155 (205)
Q Consensus 113 WGSLDALIGRLRAafEE~Gg------------------~pE~NPF~-------------araVRlYLReVRd~Q 155 (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 357889999988753
No 51
>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=27.32 E-value=55 Score=28.85 Aligned_cols=52 Identities=15% Similarity=0.276 Sum_probs=38.8
Q ss_pred hhhcchhHHHHHHHHHHHHHhCCCCC--------------CCcc-----hhhHHHHHHHHHHHHHHhhhCc
Q 028699 110 RQAWGSLDALIGRLRAAYEEHGGRPE--------------ANPF-----GARAVRIFLREVRDFQAKARGV 161 (205)
Q Consensus 110 RQAWGSLDALIGRLRAafEE~Gg~pE--------------~NPF-----~araVRlYLReVRd~QAkARgi 161 (205)
-.|||.+..+|-.|..+|+.+|..|- -+-| ...-+..+|..++..-.+.-+|
T Consensus 24 ~lAyG~~~~I~~~~~~ll~~~~~~P~~~v~~~~~~~~~~~~~~~~yRf~~~~D~~~~~~~l~~i~~~~gsL 94 (232)
T PF09674_consen 24 LLAYGNRKQIIKKLERLLDLMGPSPYDFVLSGDEKDDRKDLEGFFYRFQNGEDMYAFFIALKRIYQEYGSL 94 (232)
T ss_pred HHHccCHHHHHHHHHHHHHHhCCCHHHHHHcCCHhhhHHHccCCCcCCCCHHHHHHHHHHHHHHHHccCCH
Confidence 36999999999999999999999862 2333 3445667777777766665555
No 52
>PRK09468 ompR osmolarity response regulator; Provisional
Probab=26.92 E-value=50 Score=25.60 Aligned_cols=17 Identities=47% Similarity=0.579 Sum_probs=13.0
Q ss_pred hhHHHHHHHHHHHHHhC
Q 028699 115 SLDALIGRLRAAYEEHG 131 (205)
Q Consensus 115 SLDALIGRLRAafEE~G 131 (205)
+||..|.|||.-++..+
T Consensus 201 ~l~~~i~~LR~kl~~~~ 217 (239)
T PRK09468 201 SIDVQISRLRRLIEEDP 217 (239)
T ss_pred CHHHHHHHHHHHhccCC
Confidence 68888888888886543
No 53
>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=26.72 E-value=1.2e+02 Score=25.13 Aligned_cols=33 Identities=15% Similarity=0.105 Sum_probs=24.2
Q ss_pred hhhHHHHHHHHHhcCCCCCCCCCcchhHhHHHhhhcc
Q 028699 46 RRDWNTFCQYLRNHRPPLSLPMCSGAHVLEFLRYLDQ 82 (205)
Q Consensus 46 RrdWntf~qyL~n~rPPlsL~~csg~hVleFLrylDq 82 (205)
...++.|.+|+.+ +.+..-+..||.+||.++-+
T Consensus 23 ~~~~~~~~~~~g~----~~~~~it~~~i~~~l~~l~~ 55 (315)
T TIGR02249 23 LHWIKRFIRFHNK----RHPSTMGDTEVEAFLSDLAV 55 (315)
T ss_pred HHHHHHHHHHhCC----CChHhcCHHHHHHHHHHHHh
Confidence 3577778888642 34566789999999999854
No 54
>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=26.72 E-value=84 Score=26.87 Aligned_cols=34 Identities=15% Similarity=0.231 Sum_probs=24.3
Q ss_pred HHHHHHHHHHhCCCCCC---Ccc-hhhHHHHHHHHHHH
Q 028699 120 IGRLRAAYEEHGGRPEA---NPF-GARAVRIFLREVRD 153 (205)
Q Consensus 120 IGRLRAafEE~Gg~pE~---NPF-~araVRlYLReVRd 153 (205)
+-.||.+||+.+...+- ++. .+.+++.|||+.-|
T Consensus 45 ~~~lk~~~d~~~~~~d~~~~dv~~va~~LK~ylReLPe 82 (200)
T cd04388 45 LTELRQILDCDAASVDLEQFDVAALADALKRYLLDLPN 82 (200)
T ss_pred HHHHHHHHhcCCCCCCcccccHHHHHHHHHHHHHhCCC
Confidence 45689999986554432 222 78999999998754
No 55
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed
Probab=26.68 E-value=1.2e+02 Score=25.70 Aligned_cols=68 Identities=13% Similarity=0.202 Sum_probs=43.2
Q ss_pred hhhHHHHHHHHHhcCC-----CC-----CCCCCcchhHhHHHhhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcch
Q 028699 46 RRDWNTFCQYLRNHRP-----PL-----SLPMCSGAHVLEFLRYLDQFGKTKVHNQNCPFFGLPNPPAPCPCPLRQAWGS 115 (205)
Q Consensus 46 RrdWntf~qyL~n~rP-----Pl-----sL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGS 115 (205)
+++...|.+||..+.. .. .|...+..||.+|+.|+.+.-.. + ++.+ +...+..|
T Consensus 42 ~~~l~~f~~~l~~~~~~~~~~~~~~~~~~l~~lt~~~i~~f~~~l~~~~~~------~---~~~~-------~~~~s~~T 105 (357)
T PRK05084 42 LTEYRRFFNWLISEGLSDASKIKDIPLSTLENLTKKDVEAFILYLRERPLL------N---GHST-------KKGNSQTT 105 (357)
T ss_pred HHHHHHHHHHHHHcCCCCcCCcccCCHHHHHhhhHHHHHHHHHHHHhcccc------c---cccc-------ccchhHHH
Confidence 3556778888876542 11 23467899999999998542110 0 0000 01246688
Q ss_pred hHHHHHHHHHHHHH
Q 028699 116 LDALIGRLRAAYEE 129 (205)
Q Consensus 116 LDALIGRLRAafEE 129 (205)
+...++-||++|.-
T Consensus 106 i~~~l~~l~~~~~~ 119 (357)
T PRK05084 106 INRTLSALKSLFKY 119 (357)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999999984
No 56
>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=26.46 E-value=31 Score=29.44 Aligned_cols=24 Identities=38% Similarity=0.815 Sum_probs=21.8
Q ss_pred hcchhHH-HHHHHHHHHHHhCCCCC
Q 028699 112 AWGSLDA-LIGRLRAAYEEHGGRPE 135 (205)
Q Consensus 112 AWGSLDA-LIGRLRAafEE~Gg~pE 135 (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 57
>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=26.23 E-value=3e+02 Score=22.46 Aligned_cols=59 Identities=12% Similarity=0.105 Sum_probs=37.1
Q ss_pred hHHHHHHHHHhcCCCCCCCCCcchhHhHHHhhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 028699 48 DWNTFCQYLRNHRPPLSLPMCSGAHVLEFLRYLDQFGKTKVHNQNCPFFGLPNPPAPCPCPLRQAWGSLDALIGRLRAAY 127 (205)
Q Consensus 48 dWntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAaf 127 (205)
.-+.|.+|+.++. +...+..||.+|+.++.. .+-.++...+.-||+.|
T Consensus 25 ~~~~f~~~~~~~~----~~~it~~~~~~~~~~~~~----------------------------~~~~t~~~~l~~l~~~~ 72 (299)
T cd01187 25 LLRDFVRFLERHG----AGFITTDLALRWAASPPS----------------------------AQPATWAGRLGVVRRFA 72 (299)
T ss_pred HHHHHHHHHHhCC----CCCCCHHHHHHHHhcCCC----------------------------CChHHHHHHHHHHHHHH
Confidence 4456888887654 567788888888765311 12245666777777777
Q ss_pred H---HhCCCCCCCcc
Q 028699 128 E---EHGGRPEANPF 139 (205)
Q Consensus 128 E---E~Gg~pE~NPF 139 (205)
. +.|. -+.||+
T Consensus 73 ~~~~~~~~-~~~~p~ 86 (299)
T cd01187 73 RHRRRADP-RTEVPP 86 (299)
T ss_pred HHHHhCCC-CccCCC
Confidence 7 2233 345776
No 58
>PF09958 DUF2192: Uncharacterized protein conserved in archaea (DUF2192); InterPro: IPR018693 This family of various hypothetical archaeal proteins has no known function.
Probab=26.21 E-value=57 Score=29.34 Aligned_cols=21 Identities=38% Similarity=0.577 Sum_probs=18.4
Q ss_pred hhHHHHHHHHHHHHHhCCCCC
Q 028699 115 SLDALIGRLRAAYEEHGGRPE 135 (205)
Q Consensus 115 SLDALIGRLRAafEE~Gg~pE 135 (205)
+=+.||.-||..|+++|..|=
T Consensus 27 ~R~~lv~~L~~~Y~~~gIeP~ 47 (231)
T PF09958_consen 27 DREELVELLREVYEENGIEPF 47 (231)
T ss_pred CHHHHHHHHHHHHHHcCCCcC
Confidence 558999999999999998864
No 59
>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=26.07 E-value=34 Score=23.83 Aligned_cols=12 Identities=42% Similarity=0.775 Sum_probs=10.5
Q ss_pred cchhHHHHHHHH
Q 028699 113 WGSLDALIGRLR 124 (205)
Q Consensus 113 WGSLDALIGRLR 124 (205)
|-.||.||.+|.
T Consensus 37 f~~lD~li~~l~ 48 (49)
T PF07535_consen 37 FKELDSLISQLQ 48 (49)
T ss_pred HHHHHHHHHHhc
Confidence 789999999885
No 60
>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=25.50 E-value=1.6e+02 Score=22.53 Aligned_cols=45 Identities=18% Similarity=0.551 Sum_probs=36.2
Q ss_pred hcc---hhHHHHHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHHhhh
Q 028699 112 AWG---SLDALIGRLRAAYEEHGGRPEANPFGARAVRIFLREVRDFQAKAR 159 (205)
Q Consensus 112 AWG---SLDALIGRLRAafEE~Gg~pE~NPF~araVRlYLReVRd~QAkAR 159 (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 377 8888888999999554 45788999999999998777777776
No 61
>PRK11173 two-component response regulator; Provisional
Probab=25.38 E-value=55 Score=25.52 Aligned_cols=19 Identities=26% Similarity=0.487 Sum_probs=16.0
Q ss_pred hhHHHHHHHHHHHHHhCCC
Q 028699 115 SLDALIGRLRAAYEEHGGR 133 (205)
Q Consensus 115 SLDALIGRLRAafEE~Gg~ 133 (205)
+||..|.|||.-+++.+..
T Consensus 200 ~~~~~i~rlR~kl~~~~~~ 218 (237)
T PRK11173 200 TVDVTIRRIRKHFESTPDT 218 (237)
T ss_pred cHHHHHHHHHHHhccCCCC
Confidence 8999999999999865543
No 62
>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=25.18 E-value=62 Score=25.49 Aligned_cols=17 Identities=35% Similarity=0.739 Sum_probs=15.2
Q ss_pred chhHHHHHHHHHHHHHh
Q 028699 114 GSLDALIGRLRAAYEEH 130 (205)
Q Consensus 114 GSLDALIGRLRAafEE~ 130 (205)
..||++.|-+||..|++
T Consensus 16 AaLDsvfGgiRA~le~~ 32 (88)
T PF06947_consen 16 AALDSVFGGIRASLEDK 32 (88)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 46999999999999975
No 63
>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=24.64 E-value=2e+02 Score=21.30 Aligned_cols=39 Identities=33% Similarity=0.647 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHHhhhCcchhhh
Q 028699 118 ALIGRLRAAYEEHGGRPEANPFGARAVRIFLREVRDFQAKARGVSYDKK 166 (205)
Q Consensus 118 ALIGRLRAafEE~Gg~pE~NPF~araVRlYLReVRd~QAkARgi~y~kk 166 (205)
.|--..-++|+++|..+ ..|||++|+.| ++-+|||++-+
T Consensus 12 ~lK~~a~~i~~~lGl~~------s~ai~~fl~qv----v~~~~lPF~~~ 50 (83)
T TIGR02384 12 ELKKEAYAVFEELGLTP------STAIRMFLKQV----IREQGLPFDLR 50 (83)
T ss_pred HHHHHHHHHHHHhCCCH------HHHHHHHHHHH----HHhCCCCCCcC
Confidence 34556678899999874 57999999976 45589999875
No 64
>PLN02837 threonine-tRNA ligase
Probab=24.44 E-value=30 Score=33.57 Aligned_cols=15 Identities=40% Similarity=0.603 Sum_probs=11.6
Q ss_pred hhhcchhHHHHHHHH
Q 028699 110 RQAWGSLDALIGRLR 124 (205)
Q Consensus 110 RQAWGSLDALIGRLR 124 (205)
|-.|||+|.|||-|-
T Consensus 489 ~~~~G~~eRlia~Li 503 (614)
T PLN02837 489 RAILGSLERFFGVLI 503 (614)
T ss_pred cCCccCHHHHHHHHH
Confidence 567999999887553
No 65
>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=24.43 E-value=75 Score=30.15 Aligned_cols=54 Identities=37% Similarity=0.535 Sum_probs=35.1
Q ss_pred chhHhHHHhhhcccC-cccccCCCCCCCCCCCCCCCCCCchhhhcchh--HH----HHHHHHHHHHHhCCCCC
Q 028699 70 GAHVLEFLRYLDQFG-KTKVHNQNCPFFGLPNPPAPCPCPLRQAWGSL--DA----LIGRLRAAYEEHGGRPE 135 (205)
Q Consensus 70 g~hVleFLrylDqfG-KTkVH~~~C~ffG~p~ppapC~CPlRQAWGSL--DA----LIGRLRAafEE~Gg~pE 135 (205)
|..=++||..|.+.| |-+|+ ..-.|-.+.++ |..+ |. .--||..||+++|..+.
T Consensus 48 G~agl~f~e~l~~~gakv~Vp----------TTlNp~~~D~~--w~~~gvd~~f~~~q~~i~~ay~~mG~~~t 108 (389)
T cd01355 48 GDAGLEFLERLADQGAKVAVP----------TTLNPISMDLH--WRELGVDEEFAEKQARLVKAYKAMGVDPT 108 (389)
T ss_pred chhhHHHHHHHHhCCCeEeec----------CccCCcccCcc--hhhcCCCHHHHHHHHHHHHHHHHcCCccc
Confidence 344579998886666 34443 23456666777 8755 32 34477899999998865
No 66
>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=24.38 E-value=59 Score=26.95 Aligned_cols=27 Identities=33% Similarity=0.553 Sum_probs=23.3
Q ss_pred hhhhcchhHHHHHHHHHHHHHhCCCCC
Q 028699 109 LRQAWGSLDALIGRLRAAYEEHGGRPE 135 (205)
Q Consensus 109 lRQAWGSLDALIGRLRAafEE~Gg~pE 135 (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 67
>KOG1452 consensus Predicted Rho GTPase-activating protein [Signal transduction mechanisms]
Probab=24.09 E-value=40 Score=32.64 Aligned_cols=30 Identities=30% Similarity=0.428 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCC--------CCCCcchhhHHHHHHHHHH
Q 028699 122 RLRAAYEEHGGR--------PEANPFGARAVRIFLREVR 152 (205)
Q Consensus 122 RLRAafEE~Gg~--------pE~NPF~araVRlYLReVR 152 (205)
-||++||-||+. |+.|=. +..++.||||+=
T Consensus 233 mLR~~fe~n~r~~el~~E~iPD~nvI-tg~~kD~lrElp 270 (442)
T KOG1452|consen 233 MLRRDFEPNGRDFELGAESIPDYNVI-TGDSKDELRELP 270 (442)
T ss_pred HHHHHhccCCcccccccccCCCccee-ecccHhHHHhCC
Confidence 589999999976 334433 458999999974
No 68
>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=24.05 E-value=95 Score=26.20 Aligned_cols=39 Identities=28% Similarity=0.348 Sum_probs=26.6
Q ss_pred chhHHHHHHHHHHHHHhCCCCCC------Ccc-hhhHHHHHHHHHHH
Q 028699 114 GSLDALIGRLRAAYEEHGGRPEA------NPF-GARAVRIFLREVRD 153 (205)
Q Consensus 114 GSLDALIGRLRAafEE~Gg~pE~------NPF-~araVRlYLReVRd 153 (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 3599999999986543221 222 58899999999544
No 69
>PF07700 HNOB: Heme NO binding; InterPro: IPR011644 This ligand-binding domain is found in soluble guanylate cyclases. In soluble guanylate cyclases this domain binds heme via a covalent linkage to histidine []. Soluble guanylate cyclases are nitric oxide-responsive signaling proteins.; GO: 0020037 heme binding; PDB: 3TFE_A 2O0C_B 3TFA_A 2O09_B 2O0G_B 3L6J_A 3TFG_B 3TF8_A 3TFF_A 3TF9_B ....
Probab=24.00 E-value=23 Score=28.34 Aligned_cols=36 Identities=22% Similarity=0.314 Sum_probs=28.7
Q ss_pred hhHHHHHHHHHh---cCCCCCCCCCcchhHhHHHhhhcc
Q 028699 47 RDWNTFCQYLRN---HRPPLSLPMCSGAHVLEFLRYLDQ 82 (205)
Q Consensus 47 rdWntf~qyL~n---~rPPlsL~~csg~hVleFLrylDq 82 (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 468888888876 445666778999999999998875
No 70
>COG4865 Glutamate mutase epsilon subunit [Amino acid transport and metabolism]
Probab=23.70 E-value=51 Score=32.22 Aligned_cols=22 Identities=50% Similarity=0.872 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHhCCCCCCCcch
Q 028699 119 LIGRLRAAYEEHGGRPEANPFG 140 (205)
Q Consensus 119 LIGRLRAafEE~Gg~pE~NPF~ 140 (205)
+|.||.-+|||||.+=...||+
T Consensus 196 YVDRL~G~YeE~Gi~INREpFg 217 (485)
T COG4865 196 YVDRLMGMYEEHGIRINREPFG 217 (485)
T ss_pred HHHHHHhHHHhcCeeeccccCC
Confidence 4566777999999887666665
No 71
>cd00778 ProRS_core_arch_euk Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from archaea, the cytoplasm of eukaryotes and some bacteria.
Probab=23.62 E-value=38 Score=28.98 Aligned_cols=17 Identities=29% Similarity=0.603 Sum_probs=12.1
Q ss_pred hhhhcchhHHHHHHHHH
Q 028699 109 LRQAWGSLDALIGRLRA 125 (205)
Q Consensus 109 lRQAWGSLDALIGRLRA 125 (205)
-+-.||+++.+||=|-+
T Consensus 244 h~~~~g~~~R~i~ali~ 260 (261)
T cd00778 244 HQTSWGISTRLIGAIIM 260 (261)
T ss_pred EEecccHHHHHHHHHHh
Confidence 44568988888886644
No 72
>cd08782 Death_DAPK1 Death domain found in death-associated protein kinase 1. Death domain (DD) found in death-associated protein kinase 1 (DAPK1). DAPK1 is composed of several functional domains, including a kinase domain, a CaM regulatory domain, ankyrin repeats, a cytoskeletal binding domain and a C-terminal DD. It plays important roles in a diverse range of signal transduction pathways including apoptosis, growth factor signalling, and autophagy. Loss of DAPK1 expression, usually because of DNA methylation, is implicated in many tumor types. DAPK1 is highly abundant in the brain and has also been associated with neurodegeneration. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as ad
Probab=23.36 E-value=43 Score=24.95 Aligned_cols=28 Identities=29% Similarity=0.420 Sum_probs=23.7
Q ss_pred CCchhhhcchhH-HHHHHHHHHHHHhCCC
Q 028699 106 PCPLRQAWGSLD-ALIGRLRAAYEEHGGR 133 (205)
Q Consensus 106 ~CPlRQAWGSLD-ALIGRLRAafEE~Gg~ 133 (205)
+|-+=+-|++-+ +-||.|..+.+|+|+.
T Consensus 47 T~~LL~~W~~~~~~tvg~L~~~L~~~gR~ 75 (82)
T cd08782 47 TDALLQEWATAPPSTIGTLIDKLRELGRE 75 (82)
T ss_pred HHHHHHHHhcCCcccHHHHHHHHHHcCcH
Confidence 455777899877 9999999999999974
No 73
>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=23.36 E-value=35 Score=23.68 Aligned_cols=25 Identities=48% Similarity=0.794 Sum_probs=17.4
Q ss_pred Ccc--hhhHHHHHHHHHHHHHHhhhCcc
Q 028699 137 NPF--GARAVRIFLREVRDFQAKARGVS 162 (205)
Q Consensus 137 NPF--~araVRlYLReVRd~QAkARgi~ 162 (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 74
>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=23.18 E-value=93 Score=26.20 Aligned_cols=35 Identities=23% Similarity=0.404 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHhCCCCC--------CCc-chhhHHHHHHHHHHH
Q 028699 118 ALIGRLRAAYEEHGGRPE--------ANP-FGARAVRIFLREVRD 153 (205)
Q Consensus 118 ALIGRLRAafEE~Gg~pE--------~NP-F~araVRlYLReVRd 153 (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 43332 223 378899999999765
No 75
>cd08802 Death_UNC5B Death domain found in Uncoordinated-5B. Death Domain (DD) found in Uncoordinated-5B (UNC5B). UNC5B is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5B signaling is involved in the netrin-1-induced proliferation and migration of renal proximal tubular cells. It is also required for vascular patterning during embryonic development, and its activation inhibits sprouting angiogenesis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activatio
Probab=22.94 E-value=50 Score=25.27 Aligned_cols=17 Identities=35% Similarity=0.438 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHhCCC
Q 028699 117 DALIGRLRAAYEEHGGR 133 (205)
Q Consensus 117 DALIGRLRAafEE~Gg~ 133 (205)
|+-||+|.++++|+|+.
T Consensus 60 ~~~v~~L~~~L~~mgR~ 76 (84)
T cd08802 60 DGDLNSLASALEEMGKS 76 (84)
T ss_pred cccHHHHHHHHHHcCcc
Confidence 45689999999999975
No 76
>cd04383 RhoGAP_srGAP RhoGAP_srGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs contain an N-terminal FCH domain, a central RhoGAP domain and a C-terminal SH3 domain; this SH3 domain interacts with the intracellular proline-rich-tail of the Roundabout receptor (Robo). This interaction with Robo then activates the rhoGAP domain which in turn inhibits Cdc42 activity. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific group
Probab=22.62 E-value=99 Score=25.36 Aligned_cols=35 Identities=20% Similarity=0.515 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHhCCCC---CCCc----chhhHHHHHHHHHHH
Q 028699 118 ALIGRLRAAYEEHGGRP---EANP----FGARAVRIFLREVRD 153 (205)
Q Consensus 118 ALIGRLRAafEE~Gg~p---E~NP----F~araVRlYLReVRd 153 (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 578999999986 4333 1122 268999999999754
No 77
>cd04377 RhoGAP_myosin_IX RhoGAP_myosin_IX: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in class IX myosins. Class IX myosins contain a characteristic head domain, a neck domain, a tail domain which contains a C6H2-zinc binding motif and a RhoGAP domain. Class IX myosins are single-headed, processive myosins that are partly cytoplasmic, and partly associated with membranes and the actin cytoskeleton. Class IX myosins are implicated in the regulation of neuronal morphogenesis and function of sensory systems, like the inner ear. There are two major isoforms, myosin IXA and IXB with several splice variants, which are both expressed in developing neurons. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell prolifer
Probab=22.50 E-value=2e+02 Score=23.32 Aligned_cols=61 Identities=16% Similarity=0.205 Sum_probs=38.7
Q ss_pred HhHHHhhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHHHHhCCC---CCCCcc-hhhHHHHHH
Q 028699 73 VLEFLRYLDQFGKTKVHNQNCPFFGLPNPPAPCPCPLRQAWGSLDALIGRLRAAYEEHGGR---PEANPF-GARAVRIFL 148 (205)
Q Consensus 73 VleFLrylDqfGKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLDALIGRLRAafEE~Gg~---pE~NPF-~araVRlYL 148 (205)
|...+.|+++.|-+..+. |+- .|+ ..-|.+|+..|++.... -+.+|. .+..++.||
T Consensus 19 l~~~~~~l~~~g~~~eGi----FR~---------------~g~-~~~i~~l~~~l~~~~~~~~~~~~~~~~va~~LK~fl 78 (186)
T cd04377 19 LEKLLEHIEMHGLYTEGI----YRK---------------SGS-ANKIKELRQGLDTDPDSVNLEDYPIHVITSVLKQWL 78 (186)
T ss_pred HHHHHHHHHHcCCCCCce----eeC---------------CCC-HHHHHHHHHHHhCCCcccCcccCCHHHHHHHHHHHH
Confidence 556678888888653322 222 133 35699999999874211 112444 789999999
Q ss_pred HHHHH
Q 028699 149 REVRD 153 (205)
Q Consensus 149 ReVRd 153 (205)
|+.-+
T Consensus 79 r~Lpe 83 (186)
T cd04377 79 RELPE 83 (186)
T ss_pred HcCCC
Confidence 98754
No 78
>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=22.13 E-value=1.4e+02 Score=24.31 Aligned_cols=37 Identities=19% Similarity=0.435 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHhCCC---CCCCcc-hhhHHHHHHHHHHH
Q 028699 117 DALIGRLRAAYEEHGGR---PEANPF-GARAVRIFLREVRD 153 (205)
Q Consensus 117 DALIGRLRAafEE~Gg~---pE~NPF-~araVRlYLReVRd 153 (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 45789999999753321 234553 78899999998754
No 79
>PF06480 FtsH_ext: FtsH Extracellular; InterPro: IPR011546 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain is found in the FtsH family of proteins that include FtsH a membrane-bound ATP-dependent protease universally conserved in prokaryotes []. The FtsH peptidases, which belong to MEROPS peptidase family M41 (clan MA(E)), efficiently degrade proteins that have a low thermodynamic stability - e.g. they lack robust unfoldase activity. This feature may be key and implies that this could be a criterion for degrading a protein. In Oenococcus oeni (Leuconostoc oenos) FtsH is involved in protection against environmental stress [], and shows increased expression under heat or osmotic stress. These two lines of evidence suggest that it is a fundamental prokaryotic self-protection mechanism that checks if proteins are correctly folded. The precise function of this N-terminal region is unclear. ; GO: 0004222 metalloendopeptidase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0016021 integral to membrane; PDB: 2LNA_A.
Probab=22.13 E-value=1.1e+02 Score=21.05 Aligned_cols=26 Identities=31% Similarity=0.257 Sum_probs=18.7
Q ss_pred cchhHHHHHHHHHHHHHhCCCCCCCc
Q 028699 113 WGSLDALIGRLRAAYEEHGGRPEANP 138 (205)
Q Consensus 113 WGSLDALIGRLRAafEE~Gg~pE~NP 138 (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 80
>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=21.93 E-value=57 Score=25.23 Aligned_cols=41 Identities=27% Similarity=0.470 Sum_probs=29.6
Q ss_pred HHHHHHHHhcCCCCCCCCC--cchhHh--HHHhhhcccCcccccC
Q 028699 50 NTFCQYLRNHRPPLSLPMC--SGAHVL--EFLRYLDQFGKTKVHN 90 (205)
Q Consensus 50 ntf~qyL~n~rPPlsL~~c--sg~hVl--eFLrylDqfGKTkVH~ 90 (205)
.++++||..+++=.++..| -|.|++ .|||+.+..|.|-++.
T Consensus 33 ~~Iv~~L~~n~~~~s~~~aE~fGQdLv~~gfir~~g~vG~~F~nS 77 (84)
T cd04436 33 SEIVSWLQENMPEKDLDAAEAFGQDLLNQGFLRLVGGVGSTFVNS 77 (84)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHhCchHHHhcccCcceecC
Confidence 4688888888886666444 366664 4899999999876643
No 81
>cd08799 Death_UNC5C Death domain found in Uncoordinated-5C. Death Domain (DD) found in Uncoordinated-5C (UNC5C). UNC5C is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5C plays a critical role in the development of spinal accesory motor neurons. Methylation of the UNC5C gene is associated with early stages of colorectal carcinogenesis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN.
Probab=21.91 E-value=48 Score=25.28 Aligned_cols=17 Identities=41% Similarity=0.552 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHhCCC
Q 028699 117 DALIGRLRAAYEEHGGR 133 (205)
Q Consensus 117 DALIGRLRAafEE~Gg~ 133 (205)
|+-||+|..+++|+|+.
T Consensus 60 ~~tv~~L~~~L~emgR~ 76 (84)
T cd08799 60 DGNLSRLAAVLEEMGRH 76 (84)
T ss_pred CCcHHHHHHHHHHcCCc
Confidence 56699999999999975
No 82
>cd04384 RhoGAP_CdGAP RhoGAP_CdGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of CdGAP-like proteins; CdGAP contains an N-terminal RhoGAP domain and a C-terminal proline-rich region, and it is active on both Cdc42 and Rac1 but not RhoA. CdGAP is recruited to focal adhesions via the interaction with the scaffold protein actopaxin (alpha-parvin). Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=21.87 E-value=1.4e+02 Score=24.71 Aligned_cols=38 Identities=21% Similarity=0.460 Sum_probs=26.6
Q ss_pred chhHHHHHHHHHHHHHhCCCCC-------CCcc-hhhHHHHHHHHHHH
Q 028699 114 GSLDALIGRLRAAYEEHGGRPE-------ANPF-GARAVRIFLREVRD 153 (205)
Q Consensus 114 GSLDALIGRLRAafEE~Gg~pE-------~NPF-~araVRlYLReVRd 153 (205)
|+. +-|.+||..|++.+ .++ .++. .|..++.||||.-|
T Consensus 43 G~~-~~i~~l~~~~d~~~-~~~~~~~~~~~d~h~va~lLK~flReLPe 88 (195)
T cd04384 43 GIA-SNIQRLRHEFDSEQ-IPDLTKDVYIQDIHSVSSLCKLYFRELPN 88 (195)
T ss_pred CCH-HHHHHHHHHHcCCC-CCCcccccccccHHHHHHHHHHHHHhCCC
Confidence 454 56999999998643 332 2333 78889999999754
No 83
>cd08177 MAR Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes. Maleylacetate reductases (MAR) play an important role in the degradation of aromatic compounds in aerobic microbes. In fungi and yeasts, the enzymes are involved in the catabolism of compounds such as phenol, tyrosine, benzoate, 4-hydroxybenzoate and resorcinol. In bacteria, the enzymes contribute to the degradation of resorcinol, 2,4-dihydroxybenzoate ([beta]-resorcylate) and 2,6-dihydroxybenzoate ([gamma]-resorcylate) via hydroxyquinol and maleylacetate. Maleylacetate reductases catalyze NADH- or NADPH-dependent reduction, at the carbon-carbon double bond, of maleylacetate or 2-chloromaleylacetate to 3-oxoadipate. In the case of 2-chloromaleylacetate, Maleylacetate reductases initially catalyses the NAD(P)H-dependent dechlorination to maleylacetate, which is then reduced to 3-oxoadipate. This enzyme is a homodimer. It is inhibited by thiol-blocking reagents such as p-
Probab=21.74 E-value=53 Score=28.94 Aligned_cols=93 Identities=16% Similarity=0.206 Sum_probs=59.4
Q ss_pred CCCCCCC-CCcchhHhHHHhhhcccCcccc-cCCCCCCCCCCCCCCCCCCchhhhc-chhHHHHHHHHHHHHHhCCCCCC
Q 028699 60 RPPLSLP-MCSGAHVLEFLRYLDQFGKTKV-HNQNCPFFGLPNPPAPCPCPLRQAW-GSLDALIGRLRAAYEEHGGRPEA 136 (205)
Q Consensus 60 rPPlsL~-~csg~hVleFLrylDqfGKTkV-H~~~C~ffG~p~ppapC~CPlRQAW-GSLDALIGRLRAafEE~Gg~pE~ 136 (205)
.|-+.++ +++|..+-.|-.+.|...|..+ |....+...--.|-.--.+|.++.. +.+|||+--+-+.+.. ...|.+
T Consensus 102 ~p~i~IPTtatgse~t~~avit~~g~K~~i~~~~~~P~~~i~Dp~l~~~~P~~~~~~~g~Dal~h~iE~~~s~-~~~~~s 180 (337)
T cd08177 102 LPIIAIPTTLSGSEMTPIAGVTENGVKTTGRDPEVLPRTVIYDPELTLTTPRRLWLSSGIRAIDHAVEALYAP-DANPIV 180 (337)
T ss_pred CCEEEEcCCchhhhhcCeEEEecCCceeEeeCccccCCEEEEChHHhcCCCHHHHHHHHHHHHHHHHHHHHcC-CCChHH
Confidence 4545554 3577778788777787545555 4344444444455666789999975 7899998777655433 234555
Q ss_pred CcchhhHHHHHHHHHHH
Q 028699 137 NPFGARAVRIFLREVRD 153 (205)
Q Consensus 137 NPF~araVRlYLReVRd 153 (205)
.-|+-.++++-++..+.
T Consensus 181 ~~~a~~ai~~i~~~l~~ 197 (337)
T cd08177 181 DLLAEEGIRALAEALPR 197 (337)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 55677788886665543
No 84
>cd08800 Death_UNC5A Death domain found in Uncoordinated-5A. Death Domain (DD) found in Uncoordinated-5A (UNC5A). UNC5A is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a critical role in neuronal development and differentiation, as well as axon-guidance. It also plays a role in regulating apoptosis in non-neuronal cells as a downstream target of p53. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathway
Probab=21.59 E-value=48 Score=25.59 Aligned_cols=17 Identities=24% Similarity=0.347 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHhCCC
Q 028699 117 DALIGRLRAAYEEHGGR 133 (205)
Q Consensus 117 DALIGRLRAafEE~Gg~ 133 (205)
|.-|+.|.++++|+|+.
T Consensus 60 ~g~l~~L~~~l~emGR~ 76 (84)
T cd08800 60 NGNLNQLAAVVAEIGKQ 76 (84)
T ss_pred CCcHHHHHHHHHHhCch
Confidence 44589999999999975
No 85
>PF00618 RasGEF_N: RasGEF N-terminal motif; InterPro: IPR000651 The crystal structure of the guanine nucleotide exchange factor (GEF) region of human Sos1 complexes with Ras has been solved []. The structure consists of two distinct alpha helical structural domains: the N-terminal domain which seems to have a purely structural role and the C-terminal domain which is sufficient for catalytic activity and contains all residues that interact with Ras. A main feature of the catalytic domain is the protrusion of a helical hairpin important for the nucleotide-exchange mechanism. The N-terminal domain is likely to be important for the stability and correct placement of the hairpin structure. This entry represents a domain found in several GEF for Ras-like small GTPases which lies N-terminal to the RasGef (Cdc25-like) domain. ; GO: 0005085 guanyl-nucleotide exchange factor activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3CF6_E 2BYV_E 1NVW_S 1BKD_S 1XDV_A 2II0_A 1NVU_S 1NVX_S 1NVV_S 1XD4_B ....
Probab=21.57 E-value=55 Score=23.46 Aligned_cols=13 Identities=46% Similarity=0.708 Sum_probs=8.0
Q ss_pred cchhHHHHHHHHH
Q 028699 113 WGSLDALIGRLRA 125 (205)
Q Consensus 113 WGSLDALIGRLRA 125 (205)
.||||+||.+|=.
T Consensus 4 ~gtl~~Li~~L~~ 16 (104)
T PF00618_consen 4 AGTLEKLIERLTS 16 (104)
T ss_dssp EE-HHHHHHHHCH
T ss_pred eeCHHHHHHHHhc
Confidence 4677777777754
No 86
>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=21.54 E-value=50 Score=28.74 Aligned_cols=16 Identities=38% Similarity=0.476 Sum_probs=11.9
Q ss_pred hhhHHHHHHHHHhcCC
Q 028699 46 RRDWNTFCQYLRNHRP 61 (205)
Q Consensus 46 RrdWntf~qyL~n~rP 61 (205)
-=|.++|.|||...+.
T Consensus 140 eVDR~EFdQYLn~~~~ 155 (197)
T PF12067_consen 140 EVDRTEFDQYLNSSRC 155 (197)
T ss_pred hhhHHHHHHHhccccC
Confidence 3478999999986443
No 87
>PF10774 DUF4226: Domain of unknown function (DUF4226); InterPro: IPR019710 This entry represents an uncharacterised family of proteins belonging to Mycobacteria. It was previously incorrectly annotated as Biofilm regulator BssS (also known as YliH).
Probab=21.22 E-value=1.5e+02 Score=23.72 Aligned_cols=34 Identities=35% Similarity=0.504 Sum_probs=29.5
Q ss_pred hhHHHHHHHHHHHHHhCCCCCCCcchhhHHHHHHH
Q 028699 115 SLDALIGRLRAAYEEHGGRPEANPFGARAVRIFLR 149 (205)
Q Consensus 115 SLDALIGRLRAafEE~Gg~pE~NPF~araVRlYLR 149 (205)
.||+||..++++....+. --.-|.|+|.+--||+
T Consensus 48 ~Ld~i~aeI~~Av~~~~~-aldTPaG~r~f~~fL~ 81 (112)
T PF10774_consen 48 RLDAIQAEIEAAVAAQAP-ALDTPAGAREFQRFLR 81 (112)
T ss_pred HHHHHHHHHHHHHHhccc-ccCCHHHHHHHHHHHH
Confidence 799999999999998886 4578999999888874
No 88
>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=20.75 E-value=1e+02 Score=25.31 Aligned_cols=36 Identities=19% Similarity=0.265 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHhCCCCC---CCcc-hhhHHHHHHHHHHH
Q 028699 118 ALIGRLRAAYEEHGGRPE---ANPF-GARAVRIFLREVRD 153 (205)
Q Consensus 118 ALIGRLRAafEE~Gg~pE---~NPF-~araVRlYLReVRd 153 (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 78899999999744
No 89
>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=20.53 E-value=19 Score=27.15 Aligned_cols=13 Identities=46% Similarity=1.158 Sum_probs=11.3
Q ss_pred HHHHHHHHHhcCC
Q 028699 49 WNTFCQYLRNHRP 61 (205)
Q Consensus 49 Wntf~qyL~n~rP 61 (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 90
>PRK13977 myosin-cross-reactive antigen; Provisional
Probab=20.51 E-value=1.1e+02 Score=30.54 Aligned_cols=100 Identities=16% Similarity=0.135 Sum_probs=59.0
Q ss_pred hHHHHHHHHHhcCCCCCCC-------CCcch-hHhHHHhhhccc--CcccccCCCCCCCCCCCCCCCCCCchhhhcchhH
Q 028699 48 DWNTFCQYLRNHRPPLSLP-------MCSGA-HVLEFLRYLDQF--GKTKVHNQNCPFFGLPNPPAPCPCPLRQAWGSLD 117 (205)
Q Consensus 48 dWntf~qyL~n~rPPlsL~-------~csg~-hVleFLrylDqf--GKTkVH~~~C~ffG~p~ppapC~CPlRQAWGSLD 117 (205)
|-.++.+|+..+....++. -.-.. -..||++|+-+| ---..+...|-.|...++ -|
T Consensus 161 d~~tI~d~f~~~Ff~t~Fw~~w~t~FaF~~whSA~E~rry~~rf~~~~~~l~~~s~l~ft~ynq--------------ye 226 (576)
T PRK13977 161 DDKTIEDWFSPEFFETNFWYYWRTMFAFEKWHSALEMRRYMHRFIHHIGGLPDLSGLKFTKYNQ--------------YE 226 (576)
T ss_pred CCcCHHHHHhhcCchhHHHHHHHHHHCCchhhHHHHHHHHHHHHHHhhccCCccccccCCCCCc--------------hh
Confidence 3455666666655533321 01111 156788888777 233356666666665552 49
Q ss_pred HHHHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHHhhhCcchhh
Q 028699 118 ALIGRLRAAYEEHGGRPEANPFGARAVRIFLREVRDFQAKARGVSYDK 165 (205)
Q Consensus 118 ALIGRLRAafEE~Gg~pE~NPF~araVRlYLReVRd~QAkARgi~y~k 165 (205)
+||.-|+...+++|+.=..| .++.+|. .+..+.+-++.||-+++
T Consensus 227 SLV~PL~~~Le~~GV~f~~~---t~VtdL~-~~~d~~~~~VtgI~~~~ 270 (576)
T PRK13977 227 SLVLPLIKYLEDHGVDFQYG---TKVTDID-FDITGGKKTATAIHLTR 270 (576)
T ss_pred HHHHHHHHHHHhCCCEEEeC---CEEEEEE-EcCCCCceEEEEEEEEe
Confidence 99999999999999874433 3333332 12223446788998865
No 91
>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=20.31 E-value=80 Score=28.96 Aligned_cols=42 Identities=38% Similarity=0.632 Sum_probs=33.7
Q ss_pred chhhhcchhHHHHHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHH
Q 028699 108 PLRQAWGSLDALIGRLRAAYEEHGGRPEANPFGARAVRIFLREVRDF 154 (205)
Q Consensus 108 PlRQAWGSLDALIGRLRAafEE~Gg~pE~NPF~araVRlYLReVRd~ 154 (205)
|||. .||.|-.+|..+||+.|+.=-.+|..+|- -|.+-|-+.
T Consensus 8 PLR~---Ald~Lrd~l~~~fe~~~~~l~~Dpw~ar~--~Yi~Vil~~ 49 (285)
T PF12055_consen 8 PLRE---ALDWLRDRLDELFEEEGGELFKDPWAARD--EYIEVILDR 49 (285)
T ss_pred HHHH---HHHHHHHHHHHHHHHHHHHhcCCHHHHHH--HHHHHHcCC
Confidence 5555 49999999999999999887788987764 777777554
Done!