Query 032526
Match_columns 139
No_of_seqs 105 out of 143
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 02:34:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032526.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032526hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3423 Transcription initiati 100.0 7.1E-56 1.5E-60 350.6 12.8 116 8-125 60-176 (176)
2 COG5162 Transcription initiati 100.0 1.9E-44 4.1E-49 286.9 11.7 110 16-125 70-197 (197)
3 PF03540 TFIID_30kDa: Transcri 100.0 4.5E-32 9.8E-37 178.8 7.1 51 33-83 1-51 (51)
4 PF07524 Bromo_TP: Bromodomain 98.1 3.4E-05 7.4E-10 52.7 7.9 67 38-119 10-76 (77)
5 smart00576 BTP Bromodomain tra 98.0 4.1E-05 8.8E-10 52.8 8.0 67 38-119 10-76 (77)
6 smart00803 TAF TATA box bindin 97.1 0.004 8.8E-08 42.3 7.9 64 34-112 2-65 (65)
7 PF02969 TAF: TATA box binding 97.0 0.0051 1.1E-07 42.4 7.4 65 33-112 2-66 (66)
8 PF03847 TFIID_20kDa: Transcri 97.0 0.0067 1.5E-07 41.8 8.0 50 52-116 18-68 (68)
9 PF00808 CBFD_NFYB_HMF: Histon 97.0 0.0068 1.5E-07 40.0 7.5 63 34-111 2-65 (65)
10 cd07981 TAF12 TATA Binding Pro 96.7 0.016 3.4E-07 39.8 8.1 54 50-118 18-72 (72)
11 cd07979 TAF9 TATA Binding Prot 96.7 0.012 2.5E-07 44.1 7.8 64 38-116 5-68 (117)
12 PLN00035 histone H4; Provision 96.5 0.02 4.4E-07 42.7 7.9 75 28-117 23-97 (103)
13 cd00076 H4 Histone H4, one of 96.4 0.027 5.8E-07 40.5 8.0 74 28-116 7-80 (85)
14 COG2036 HHT1 Histones H3 and H 96.3 0.025 5.3E-07 41.3 7.4 80 20-118 5-88 (91)
15 cd08050 TAF6 TATA Binding Prot 96.1 0.033 7.1E-07 47.9 8.3 67 36-117 1-67 (343)
16 PTZ00015 histone H4; Provision 96.1 0.059 1.3E-06 40.1 8.5 74 29-117 25-98 (102)
17 KOG1142 Transcription initiati 95.3 0.046 9.9E-07 46.6 5.8 63 50-128 171-233 (258)
18 PF02291 TFIID-31kDa: Transcri 95.2 0.13 2.9E-06 39.4 7.7 62 38-114 16-77 (129)
19 PF05236 TAF4: Transcription i 93.5 0.087 1.9E-06 43.5 3.7 57 31-87 40-100 (264)
20 cd08045 TAF4 TATA Binding Prot 93.2 0.39 8.5E-06 38.5 6.8 47 40-86 54-100 (212)
21 KOG3334 Transcription initiati 89.9 2 4.3E-05 34.2 7.4 63 39-116 18-80 (148)
22 KOG4336 TBP-associated transcr 87.4 2.1 4.6E-05 37.7 6.6 77 35-127 6-84 (323)
23 smart00417 H4 Histone H4. 83.3 4.8 0.0001 28.3 5.7 53 28-80 7-59 (74)
24 KOG2549 Transcription initiati 81.3 11 0.00024 35.6 8.8 87 30-131 7-99 (576)
25 PF00125 Histone: Core histone 72.7 19 0.00042 23.6 5.9 64 34-112 5-73 (75)
26 COG5095 TAF6 Transcription ini 68.4 38 0.00082 30.8 8.4 67 41-122 12-84 (450)
27 PF10281 Ish1: Putative stress 66.8 5.7 0.00012 23.9 2.2 22 101-122 3-24 (38)
28 KOG3449 60S acidic ribosomal p 64.4 7.9 0.00017 29.6 3.0 37 40-76 23-59 (112)
29 KOG2389 Predicted bromodomain 63.8 30 0.00065 31.0 6.9 53 29-81 24-76 (353)
30 COG5094 TAF9 Transcription ini 62.5 58 0.0012 25.8 7.5 61 40-113 20-81 (145)
31 PF12949 HeH: HeH/LEM domain; 62.2 4.1 8.8E-05 25.0 0.9 18 101-118 3-20 (35)
32 COG5208 HAP5 CCAAT-binding fac 61.8 13 0.00027 32.0 4.1 40 59-113 135-174 (286)
33 cd04381 RhoGap_RalBP1 RhoGap_R 57.3 27 0.00058 27.1 5.0 47 14-62 71-117 (182)
34 cd04377 RhoGAP_myosin_IX RhoGA 56.1 22 0.00047 27.7 4.3 44 17-62 70-113 (186)
35 cd04374 RhoGAP_Graf RhoGAP_Gra 54.2 25 0.00053 28.2 4.4 44 17-62 89-132 (203)
36 smart00513 SAP Putative DNA-bi 53.1 13 0.00028 21.8 2.0 19 101-119 3-21 (35)
37 COG0599 Uncharacterized homolo 51.2 17 0.00037 26.5 2.9 47 18-64 14-63 (124)
38 PF02037 SAP: SAP domain; Int 50.7 13 0.00029 22.0 1.8 19 101-119 3-21 (35)
39 cd04395 RhoGAP_ARHGAP21 RhoGAP 50.1 36 0.00077 26.6 4.6 43 19-63 78-120 (196)
40 PF12767 SAGA-Tad1: Transcript 49.1 43 0.00093 27.5 5.1 38 41-78 213-250 (252)
41 KOG0869 CCAAT-binding factor, 48.3 22 0.00047 28.9 3.2 66 35-116 33-101 (168)
42 PF02269 TFIID-18kDa: Transcri 45.5 31 0.00068 24.6 3.4 57 50-121 18-74 (93)
43 PF08367 M16C_assoc: Peptidase 45.3 43 0.00094 27.1 4.6 48 39-87 179-226 (248)
44 PF04239 DUF421: Protein of un 45.1 13 0.00027 26.7 1.3 19 98-116 23-41 (99)
45 cd04386 RhoGAP_nadrin RhoGAP_n 44.0 47 0.001 26.1 4.5 43 15-59 75-117 (203)
46 cd04387 RhoGAP_Bcr RhoGAP_Bcr: 43.8 41 0.00088 26.7 4.1 37 18-56 74-110 (196)
47 cd04403 RhoGAP_ARHGAP27_15_12_ 43.4 40 0.00086 26.2 4.0 44 18-63 74-117 (187)
48 cd04402 RhoGAP_ARHGAP20 RhoGAP 43.4 50 0.0011 25.7 4.6 43 14-58 66-108 (192)
49 PF01842 ACT: ACT domain; Int 43.0 18 0.00039 22.1 1.6 23 104-126 14-36 (66)
50 cd04393 RhoGAP_FAM13A1a RhoGAP 42.6 78 0.0017 24.6 5.5 45 14-60 72-117 (189)
51 cd04407 RhoGAP_myosin_IXB RhoG 42.3 48 0.001 26.0 4.3 40 18-59 71-110 (186)
52 PF11848 DUF3368: Domain of un 42.1 33 0.00072 21.5 2.8 29 20-48 20-48 (48)
53 PF10815 ComZ: ComZ; InterPro 41.2 71 0.0015 21.7 4.3 48 23-80 5-52 (56)
54 PF01316 Arg_repressor: Argini 40.9 21 0.00046 24.6 1.8 20 100-119 18-37 (70)
55 cd04372 RhoGAP_chimaerin RhoGA 40.9 55 0.0012 25.6 4.4 42 18-61 75-116 (194)
56 cd04384 RhoGAP_CdGAP RhoGAP_Cd 40.1 52 0.0011 26.0 4.2 43 15-59 73-115 (195)
57 PF15374 CCDC71L: Coiled-coil 39.9 19 0.00041 32.5 1.8 27 10-36 30-58 (376)
58 PF00123 Hormone_2: Peptide ho 39.8 25 0.00053 20.6 1.7 15 59-73 14-28 (28)
59 KOG1488 Translational represso 39.3 42 0.00091 31.3 4.0 42 38-80 375-421 (503)
60 cd04383 RhoGAP_srGAP RhoGAP_sr 39.0 60 0.0013 25.4 4.4 42 18-61 76-117 (188)
61 PF09415 CENP-X: CENP-S associ 38.9 1.1E+02 0.0024 21.2 5.2 61 36-111 1-65 (72)
62 cd04376 RhoGAP_ARHGAP6 RhoGAP_ 37.4 1.2E+02 0.0026 24.2 5.9 40 17-59 64-103 (206)
63 PF05873 Mt_ATP-synt_D: ATP sy 37.3 11 0.00024 29.6 0.0 33 99-131 128-160 (161)
64 PF03793 PASTA: PASTA domain; 37.1 20 0.00044 22.6 1.2 31 102-132 9-39 (63)
65 cd04406 RhoGAP_myosin_IXA RhoG 35.0 77 0.0017 24.8 4.4 44 17-62 70-113 (186)
66 cd07978 TAF13 The TATA Binding 34.3 1.8E+02 0.0038 20.9 8.2 31 50-80 19-49 (92)
67 cd04398 RhoGAP_fRGD1 RhoGAP_fR 34.0 89 0.0019 24.1 4.6 44 17-62 76-119 (192)
68 cd04869 ACT_GcvR_2 ACT domains 33.8 28 0.0006 22.6 1.5 25 103-127 12-36 (81)
69 cd04382 RhoGAP_MgcRacGAP RhoGA 33.6 79 0.0017 25.0 4.3 42 16-59 71-112 (193)
70 cd04870 ACT_PSP_1 CT domains f 33.5 33 0.00071 22.6 1.8 18 104-121 13-30 (75)
71 cd04385 RhoGAP_ARAP RhoGAP_ARA 33.3 83 0.0018 24.4 4.3 42 18-61 73-114 (184)
72 cd04435 DEP_fRom2 DEP (Disheve 33.2 63 0.0014 23.5 3.3 23 52-74 45-69 (82)
73 KOG0482 DNA replication licens 33.2 62 0.0014 31.3 4.2 38 7-44 546-583 (721)
74 cd04902 ACT_3PGDH-xct C-termin 32.8 33 0.00072 21.4 1.7 19 103-121 12-30 (73)
75 cd04375 RhoGAP_DLC1 RhoGAP_DLC 32.4 77 0.0017 25.6 4.1 45 15-61 73-117 (220)
76 KOG3467 Histone H4 [Chromatin 32.2 2.2E+02 0.0047 21.3 7.5 76 28-118 23-98 (103)
77 smart00428 H3 Histone H3. 31.9 1.5E+02 0.0033 22.1 5.3 45 58-117 60-104 (105)
78 cd05832 Ribosomal_L12p Ribosom 30.7 1.2E+02 0.0025 22.8 4.5 51 23-75 7-57 (106)
79 KOG1657 CCAAT-binding factor, 30.6 87 0.0019 26.3 4.2 83 18-115 50-141 (236)
80 KOG0870 DNA polymerase epsilon 29.4 1.4E+02 0.0031 24.4 5.1 67 35-117 11-81 (172)
81 COG0576 GrpE Molecular chapero 29.2 1.5E+02 0.0031 23.9 5.2 92 19-121 43-141 (193)
82 smart00324 RhoGAP GTPase-activ 29.0 1.2E+02 0.0026 22.5 4.4 37 18-56 60-96 (174)
83 PRK03341 arginine repressor; P 28.6 42 0.00091 26.7 2.0 21 99-119 27-47 (168)
84 cd04404 RhoGAP-p50rhoGAP RhoGA 28.5 1.2E+02 0.0026 23.5 4.5 39 18-59 79-117 (195)
85 cd06102 citrate_synt_like_2 Ci 28.4 1.8E+02 0.0039 24.8 5.9 45 22-68 154-207 (282)
86 cd04873 ACT_UUR-ACR-like ACT d 28.3 45 0.00098 20.5 1.7 18 103-120 13-30 (70)
87 COG3830 ACT domain-containing 28.3 41 0.00088 24.7 1.7 17 104-120 17-33 (90)
88 PF05931 AgrD: Staphylococcal 28.3 33 0.00072 22.2 1.1 12 32-43 33-44 (45)
89 PF02906 Fe_hyd_lg_C: Iron onl 28.0 55 0.0012 27.3 2.6 26 97-122 150-175 (285)
90 cd04879 ACT_3PGDH-like ACT_3PG 27.5 45 0.00097 20.0 1.6 19 103-121 12-30 (71)
91 PRK14088 dnaA chromosomal repl 27.5 4.4E+02 0.0096 23.4 8.6 33 16-48 263-296 (440)
92 smart00540 LEM in nuclear memb 26.4 57 0.0012 20.8 1.9 18 101-118 5-22 (44)
93 PRK00441 argR arginine repress 26.2 38 0.00082 26.2 1.3 22 100-121 17-38 (149)
94 PHA02554 13 neck protein; Prov 26.1 84 0.0018 27.8 3.5 81 31-128 3-83 (311)
95 PF08887 GAD-like: GAD-like do 26.0 59 0.0013 24.1 2.2 22 28-50 25-46 (109)
96 TIGR02512 Fe_only_hydrog hydro 25.9 55 0.0012 28.3 2.4 24 97-120 236-259 (374)
97 COG1438 ArgR Arginine represso 25.7 47 0.001 26.3 1.7 20 101-120 20-39 (150)
98 cd04373 RhoGAP_p190 RhoGAP_p19 25.2 1.1E+02 0.0023 23.9 3.7 43 17-61 71-113 (185)
99 PHA02517 putative transposase 25.2 1.1E+02 0.0023 24.6 3.8 47 17-63 27-74 (277)
100 COG5099 RNA-binding protein of 25.1 99 0.0022 30.3 4.1 41 38-79 635-681 (777)
101 PRK05066 arginine repressor; P 25.1 52 0.0011 25.8 1.9 20 100-119 22-42 (156)
102 PF08862 DUF1829: Domain of un 25.0 50 0.0011 23.4 1.6 15 104-118 68-82 (88)
103 TIGR01527 arch_NMN_Atrans nico 24.9 96 0.0021 24.3 3.4 41 15-59 123-163 (165)
104 cd06100 CCL_ACL-C Citryl-CoA l 24.6 1.2E+02 0.0025 24.5 3.9 36 34-69 103-147 (227)
105 PF00620 RhoGAP: RhoGAP domain 24.5 1.3E+02 0.0028 21.6 3.8 36 18-55 57-92 (151)
106 PF04552 Sigma54_DBD: Sigma-54 24.3 34 0.00073 26.9 0.7 24 97-120 117-140 (160)
107 PRK13916 plasmid segregation p 24.2 96 0.0021 23.1 3.0 38 17-54 16-54 (97)
108 smart00070 GLUCA Glucagon like 24.2 75 0.0016 18.4 2.0 13 59-71 14-26 (27)
109 cd04875 ACT_F4HF-DF N-terminal 24.0 61 0.0013 21.0 1.8 23 104-126 13-35 (74)
110 cd04882 ACT_Bt0572_2 C-termina 23.8 64 0.0014 19.6 1.8 16 104-119 13-28 (65)
111 PRK07758 hypothetical protein; 23.4 60 0.0013 24.1 1.8 17 103-119 79-95 (95)
112 PF09957 DUF2191: Uncharacteri 23.4 1.8E+02 0.0038 18.5 3.8 31 34-68 6-36 (47)
113 cd04391 RhoGAP_ARHGAP18 RhoGAP 23.2 1.8E+02 0.0038 23.2 4.6 40 17-58 79-118 (216)
114 PF11753 DUF3310: Protein of u 23.1 96 0.0021 20.5 2.6 50 42-112 7-56 (60)
115 COG0228 RpsP Ribosomal protein 22.9 1.4E+02 0.003 21.9 3.6 39 24-64 32-78 (87)
116 TIGR00764 lon_rel lon-related 22.7 6.4E+02 0.014 23.6 9.0 58 42-114 320-391 (608)
117 cd04883 ACT_AcuB C-terminal AC 22.4 65 0.0014 20.2 1.7 19 103-121 14-32 (72)
118 cd04908 ACT_Bt0572_1 N-termina 22.2 65 0.0014 20.5 1.6 17 103-119 14-30 (66)
119 PRK00194 hypothetical protein; 22.2 68 0.0015 21.5 1.8 19 104-122 17-35 (90)
120 cd04871 ACT_PSP_2 ACT domains 21.9 65 0.0014 22.2 1.7 16 104-119 14-29 (84)
121 PF09570 RE_SinI: SinI restric 21.5 1.5E+02 0.0033 25.1 4.0 51 32-83 74-128 (221)
122 cd04400 RhoGAP_fBEM3 RhoGAP_fB 21.2 1.8E+02 0.0039 22.5 4.3 42 15-58 79-121 (190)
123 KOG0506 Glutaminase (contains 21.2 68 0.0015 30.5 2.1 22 41-62 109-130 (622)
124 TIGR03685 L21P_arch 50S riboso 21.1 2.5E+02 0.0054 20.7 4.7 51 24-76 8-58 (105)
125 smart00546 CUE Domain that may 21.1 99 0.0021 18.5 2.2 25 24-48 5-29 (43)
126 cd04909 ACT_PDH-BS C-terminal 21.0 75 0.0016 19.9 1.8 19 103-121 14-32 (69)
127 PRK15451 tRNA cmo(5)U34 methyl 21.0 1.4E+02 0.0029 23.9 3.6 40 18-57 192-231 (247)
128 smart00311 PWI PWI, domain in 20.9 1.6E+02 0.0034 19.9 3.4 35 37-71 26-64 (74)
129 COG2815 Uncharacterized protei 20.9 1.1E+02 0.0024 26.5 3.2 33 100-132 168-200 (303)
130 PF13865 FoP_duplication: C-te 20.8 78 0.0017 21.7 1.9 18 97-114 35-52 (74)
131 cd04903 ACT_LSD C-terminal ACT 20.6 83 0.0018 18.9 1.8 18 103-120 12-29 (71)
132 PTZ00373 60S Acidic ribosomal 20.5 1.4E+02 0.0029 22.6 3.3 53 24-77 10-62 (112)
133 cd04889 ACT_PDH-BS-like C-term 20.5 84 0.0018 19.1 1.8 18 103-120 11-28 (56)
134 PTZ00454 26S protease regulato 20.4 2.8E+02 0.0062 24.5 5.8 27 98-124 370-397 (398)
135 TIGR02928 orc1/cdc6 family rep 20.4 3.4E+02 0.0074 22.3 6.0 16 100-115 260-275 (365)
136 cd00159 RhoGAP RhoGAP: GTPase- 20.3 2.1E+02 0.0046 20.6 4.2 40 17-58 55-94 (169)
137 TIGR03241 arg_catab_astB succi 20.1 1.8E+02 0.004 26.9 4.5 66 42-111 69-134 (443)
138 PF15127 DUF4565: Protein of u 20.1 1.1E+02 0.0023 22.7 2.6 28 52-79 46-73 (91)
No 1
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=100.00 E-value=7.1e-56 Score=350.56 Aligned_cols=116 Identities=54% Similarity=0.825 Sum_probs=107.7
Q ss_pred CCCCCCCCCCchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-hh
Q 032526 8 QQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQA-AV 86 (139)
Q Consensus 8 ~~~~~~~~~~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~-~~ 86 (139)
+.+......++.+|.|||.+|+||+|+|||+||+|||+++||+|+||||+|||||||||||||||+|||||||||++ +.
T Consensus 60 ~~~~~~~~~~d~~l~efl~qLddYtP~IPDavt~~yL~~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~ 139 (176)
T KOG3423|consen 60 ANGELNPTTKDTHLEEFLAQLDDYTPTIPDAVTDHYLKKAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAI 139 (176)
T ss_pred ccCCcCCCCcchHHHHHHHHHhcCCCCCcHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccc
Confidence 44556677899999999999999999999999999999999999999999999999999999999999999999995 44
Q ss_pred hhhhhhccccccceeeeHHHHHHHHHHhCcccCCCCccc
Q 032526 87 VKDKRDKQQKDKRLILTMEDLSKALREYGVNVKHQEYFA 125 (139)
Q Consensus 87 ~~~k~~~~~kd~k~vLTmEDL~~AL~EyGInv~rP~Yy~ 125 (139)
++++ +++||+|+|||||||++||+||||||+||+||+
T Consensus 140 ~~~k--~~~kdkK~tLtmeDL~~AL~EyGinv~rP~y~~ 176 (176)
T KOG3423|consen 140 GKDK--KQAKDKKYTLTMEDLSPALAEYGINVKRPDYFT 176 (176)
T ss_pred cccc--ccccccceeeeHHHHHHHHHHhCcccCCCCCCC
Confidence 5544 678999999999999999999999999999995
No 2
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=100.00 E-value=1.9e-44 Score=286.94 Aligned_cols=110 Identities=39% Similarity=0.687 Sum_probs=97.9
Q ss_pred CCchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh------
Q 032526 16 DDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKD------ 89 (139)
Q Consensus 16 ~~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~------ 89 (139)
.+|++|+|||++||+|+|+|||+||+|||+++||.|.|+||+||+||+|||||||||.|||||+|||+..+...
T Consensus 70 ~Kdktlee~l~~mDsy~PliPd~v~DYyl~k~Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a 149 (197)
T COG5162 70 MKDKTLEELLQNMDSYTPLIPDSVTDYYLEKAGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKA 149 (197)
T ss_pred hhHHHHHHHHHhcccCCCCccHHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999433211
Q ss_pred hh------------hccccccceeeeHHHHHHHHHHhCcccCCCCccc
Q 032526 90 KR------------DKQQKDKRLILTMEDLSKALREYGVNVKHQEYFA 125 (139)
Q Consensus 90 k~------------~~~~kd~k~vLTmEDL~~AL~EyGInv~rP~Yy~ 125 (139)
++ ++....+|.|||+.||++||+||||||+||+||+
T Consensus 150 ~~f~~gg~~~i~~~~~~~dr~K~vltv~DLs~Al~EyGini~RPdfyr 197 (197)
T COG5162 150 KRFAKGGASGIGSSGRRGDRKKPVLTVVDLSKALEEYGINISRPDFYR 197 (197)
T ss_pred HHHHhcccccccccccccccCCceeeehHHHHHHHHhccccCCccccC
Confidence 10 1122337999999999999999999999999995
No 3
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=99.97 E-value=4.5e-32 Score=178.79 Aligned_cols=51 Identities=55% Similarity=0.952 Sum_probs=50.2
Q ss_pred CCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 032526 33 PTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQ 83 (139)
Q Consensus 33 P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~ 83 (139)
|+|||+||+|||+++||+|+|+||+|||||||||||+||++|||||||+|+
T Consensus 1 P~IPD~v~~~yL~~~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~r~ 51 (51)
T PF03540_consen 1 PTIPDEVTDYYLERSGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKIRT 51 (51)
T ss_pred CCCCHHHHHHHHHHCCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 999999999999999999999999999999999999999999999999995
No 4
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=98.05 E-value=3.4e-05 Score=52.72 Aligned_cols=67 Identities=21% Similarity=0.361 Sum_probs=58.8
Q ss_pred HHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHHHhCcc
Q 032526 38 ELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGVN 117 (139)
Q Consensus 38 ~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~EyGIn 117 (139)
.++...|..+||++..+-..-.++-.+++||..|...+..||.. .+|+.-+..|+..||.|.||+
T Consensus 10 ~~va~il~~~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~---------------~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 10 RSVAQILKHAGFDSASPSALDTLTDILQRYLQELGRTAKRYAEH---------------AGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------cCCCCCCHHHHHHHHHHhCCC
Confidence 46778999999999999999999999999999999999999842 234566799999999999999
Q ss_pred cC
Q 032526 118 VK 119 (139)
Q Consensus 118 v~ 119 (139)
|.
T Consensus 75 v~ 76 (77)
T PF07524_consen 75 VN 76 (77)
T ss_pred CC
Confidence 85
No 5
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.03 E-value=4.1e-05 Score=52.84 Aligned_cols=67 Identities=19% Similarity=0.261 Sum_probs=58.8
Q ss_pred HHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHHHhCcc
Q 032526 38 ELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGVN 117 (139)
Q Consensus 38 ~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~EyGIn 117 (139)
.++..+|..+||++..|...-.+.-..++|+..|+..+.+||..- +|...+.+|+..||.+.||+
T Consensus 10 ~~Vaqil~~~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~a---------------gR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 10 IAVAQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAELA---------------GRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc---------------CCCCCCHHHHHHHHHHhCcc
Confidence 467889999999999999999999999999999999999998531 13456799999999999998
Q ss_pred cC
Q 032526 118 VK 119 (139)
Q Consensus 118 v~ 119 (139)
+.
T Consensus 75 ~~ 76 (77)
T smart00576 75 VG 76 (77)
T ss_pred cC
Confidence 74
No 6
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=97.15 E-value=0.004 Score=42.31 Aligned_cols=64 Identities=25% Similarity=0.335 Sum_probs=54.8
Q ss_pred CCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHH
Q 032526 34 TIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR 112 (139)
Q Consensus 34 ~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~ 112 (139)
.||-+-+.-+.++.|++--..-+...++-...-|+..|+.+|..|.+. -+|-+||.+|+..||+
T Consensus 2 ~~p~~~i~ria~~~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~h---------------akRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRH---------------SKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------hCCCeecHHHHHHHhC
Confidence 478888999999999997666699999999999999999999999742 1345899999999984
No 7
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=97.01 E-value=0.0051 Score=42.38 Aligned_cols=65 Identities=23% Similarity=0.280 Sum_probs=48.3
Q ss_pred CCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHH
Q 032526 33 PTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR 112 (139)
Q Consensus 33 P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~ 112 (139)
+.+|-+-+.-+-+..|+..-+..+.++|+--++--|.+|+++|..+.+. -+|..||.+|+..||+
T Consensus 2 s~~~~esvk~iAes~Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~h---------------skR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 2 SVFSQESVKDIAESLGISNLSDEAAKALAEDVEYRLREIIQEALKFMRH---------------SKRTKLTTDDINSALR 66 (66)
T ss_dssp ----HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------TT-SSB-HHHHHHHH-
T ss_pred CcCCHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------hCCCCCCHHHHHHHhC
Confidence 4688899999999999988888899999999999999999999999642 2356799999999995
No 8
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=97.00 E-value=0.0067 Score=41.80 Aligned_cols=50 Identities=22% Similarity=0.323 Sum_probs=39.4
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHH-HhCc
Q 032526 52 PDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR-EYGV 116 (139)
Q Consensus 52 ~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~-EyGI 116 (139)
-|+-+..++.-.|..||.+|++.|++.||-|.+ -+|...|+.-.|+ +|+|
T Consensus 18 ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s---------------~tle~~Dv~~~Ler~~ni 68 (68)
T PF03847_consen 18 LDPDVEELLLELADDFVDDVVSFACRLAKHRKS---------------STLEVKDVQLHLERNWNI 68 (68)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----------------SEE-HHHHHHHHHHHS--
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC---------------CCCCHHHHHHHHHhhcCC
Confidence 388899999999999999999999999998743 2789999998887 5554
No 9
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=96.96 E-value=0.0068 Score=40.00 Aligned_cols=63 Identities=24% Similarity=0.355 Sum_probs=45.3
Q ss_pred CCCHHHHHHHHHhC-CCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHH
Q 032526 34 TIPDELVEHYLAKS-GFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKAL 111 (139)
Q Consensus 34 ~IPD~Vt~yyL~~a-Gf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL 111 (139)
.+|-+-+.-+++.. +..---..-.-+|+.|++-||..++.+|+++|.- ++|-+++-+|+..||
T Consensus 2 ~lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~---------------~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQR---------------DKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------TTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------cCCCccCHHHHHHHC
Confidence 36778888888887 2211224456789999999999999999998841 223389999999986
No 10
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=96.74 E-value=0.016 Score=39.75 Aligned_cols=54 Identities=22% Similarity=0.358 Sum_probs=46.1
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHH-HhCccc
Q 032526 50 QCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR-EYGVNV 118 (139)
Q Consensus 50 ~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~-EyGInv 118 (139)
..-|+-+..++.=.+..|+.+|+.+|..+||-|.. -++..+|+.-+|+ +|||.+
T Consensus 18 ~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~---------------~tv~~~Di~l~l~r~~~~~~ 72 (72)
T cd07981 18 EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKS---------------DTLEVKDVQLHLERNWNISI 72 (72)
T ss_pred CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC---------------CCCCHHHHHHHHHHhcCCCC
Confidence 56689999999999999999999999999987632 3599999999998 777753
No 11
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=96.70 E-value=0.012 Score=44.07 Aligned_cols=64 Identities=14% Similarity=0.178 Sum_probs=56.5
Q ss_pred HHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHHHhCc
Q 032526 38 ELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGV 116 (139)
Q Consensus 38 ~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~EyGI 116 (139)
.++.-+|+..|.+.-+++++..+.=-+.+++.+|+.||..|++.- +|-+++.||+.-|++.++-
T Consensus 5 ~~v~~iLk~~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA---------------~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 5 RVIAAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHA---------------GKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc---------------CCCCCCHHHHHHHHHHHhc
Confidence 478889999999999999999999999999999999999998531 2468999999999999886
No 12
>PLN00035 histone H4; Provisional
Probab=96.50 E-value=0.02 Score=42.69 Aligned_cols=75 Identities=17% Similarity=0.184 Sum_probs=61.3
Q ss_pred cccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHH
Q 032526 28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDL 107 (139)
Q Consensus 28 LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL 107 (139)
|-|+..-||-.-+.-++.++|..---.-++--+.-+...|+.+|+.||..|++-. +|-|+|.||+
T Consensus 23 ~~d~i~~ipk~~IrRLARr~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA---------------~RKTV~~~DV 87 (103)
T PLN00035 23 LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA---------------RRKTVTAMDV 87 (103)
T ss_pred HHhhhccCCHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc---------------CCCcCcHHHH
Confidence 3466666999999999999998865555677777788999999999999998631 2347899999
Q ss_pred HHHHHHhCcc
Q 032526 108 SKALREYGVN 117 (139)
Q Consensus 108 ~~AL~EyGIn 117 (139)
..||+..|-+
T Consensus 88 ~~Alkr~g~~ 97 (103)
T PLN00035 88 VYALKRQGRT 97 (103)
T ss_pred HHHHHHcCCc
Confidence 9999999863
No 13
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=96.44 E-value=0.027 Score=40.52 Aligned_cols=74 Identities=19% Similarity=0.214 Sum_probs=58.5
Q ss_pred cccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHH
Q 032526 28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDL 107 (139)
Q Consensus 28 LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL 107 (139)
|-|+..-||-.-+.-...++|..-=-.-+..-+.=+...|+.+|+.||..|++- .+|-|+|.+|+
T Consensus 7 ~~~~~~gi~k~~I~RLarr~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~H---------------a~RKTVt~~DV 71 (85)
T cd00076 7 LRDNIKGITKPAIRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEH---------------AKRKTVTAMDV 71 (85)
T ss_pred HHHhhccCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh---------------cCCCcCcHHHH
Confidence 446667799999999999999774333355566667789999999999999852 12347899999
Q ss_pred HHHHHHhCc
Q 032526 108 SKALREYGV 116 (139)
Q Consensus 108 ~~AL~EyGI 116 (139)
..||+..|-
T Consensus 72 ~~alkr~g~ 80 (85)
T cd00076 72 VYALKRQGR 80 (85)
T ss_pred HHHHHHCCC
Confidence 999999993
No 14
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=96.33 E-value=0.025 Score=41.32 Aligned_cols=80 Identities=25% Similarity=0.370 Sum_probs=65.3
Q ss_pred HHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHH----HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccc
Q 032526 20 ALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLI----RLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQ 95 (139)
Q Consensus 20 ~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~----RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~ 95 (139)
-+.++-.-+......||-.-++-++.++|-+ ||. -.+.=+.+-|+.+|+.+|..+|+
T Consensus 5 ~~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~~----Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~--------------- 65 (91)
T COG2036 5 GLKEIRRYQRSTDLLLPKAPVRRILRKAGAE----RVSSSAIEELQEALEEYLEEIAEDAVELAE--------------- 65 (91)
T ss_pred hHHHHHhhhhhhhhhcCchHHHHHHHHHhHH----HhhHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------
Confidence 3556666677788999999999999999987 664 44556777899999999999985
Q ss_pred cccceeeeHHHHHHHHHHhCccc
Q 032526 96 KDKRLILTMEDLSKALREYGVNV 118 (139)
Q Consensus 96 kd~k~vLTmEDL~~AL~EyGInv 118 (139)
..+|-|.+-||+..|+++.|..+
T Consensus 66 ha~RKTV~~~DI~la~~~~~~~~ 88 (91)
T COG2036 66 HAKRKTVKAEDIKLALKRLGRRI 88 (91)
T ss_pred HcCCCeecHHHHHHHHHHhcccc
Confidence 23466999999999999999765
No 15
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=96.11 E-value=0.033 Score=47.90 Aligned_cols=67 Identities=24% Similarity=0.290 Sum_probs=56.9
Q ss_pred CHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHHHhC
Q 032526 36 PDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYG 115 (139)
Q Consensus 36 PD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~EyG 115 (139)
|.+.+.-+++.+|.+.-+...++.++--...++..|+++|..++|. -+|.+||.||+..||+..+
T Consensus 1 ~~~~i~~ia~~~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~h---------------skR~~l~~~Di~~Al~~~n 65 (343)
T cd08050 1 PQESIKLIAESLGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRH---------------SKRRKLTTSDVNHALRLRN 65 (343)
T ss_pred ChhHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------hCCCcCCHHHHHHHHHHhC
Confidence 4466778899999999999999999999999999999999998742 1246899999999999755
Q ss_pred cc
Q 032526 116 VN 117 (139)
Q Consensus 116 In 117 (139)
+.
T Consensus 66 ~e 67 (343)
T cd08050 66 VE 67 (343)
T ss_pred CC
Confidence 54
No 16
>PTZ00015 histone H4; Provisional
Probab=96.09 E-value=0.059 Score=40.10 Aligned_cols=74 Identities=16% Similarity=0.173 Sum_probs=61.7
Q ss_pred ccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHH
Q 032526 29 MGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLS 108 (139)
Q Consensus 29 ddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~ 108 (139)
-|..+-||-+-+.-++.++|..---.-++.-+.-+...|+.+|+.||..|++-. +|-|.|.+|+.
T Consensus 25 r~~i~gI~k~~IrRLarr~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA---------------~RKTVt~~DV~ 89 (102)
T PTZ00015 25 RDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYA---------------RRKTVTAMDVV 89 (102)
T ss_pred hhcccCCCHHHHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc---------------CCCcccHHHHH
Confidence 578889999999999999999864444777777888999999999999998521 23478999999
Q ss_pred HHHHHhCcc
Q 032526 109 KALREYGVN 117 (139)
Q Consensus 109 ~AL~EyGIn 117 (139)
.||+..|-.
T Consensus 90 ~AlKr~g~~ 98 (102)
T PTZ00015 90 YALKRQGRT 98 (102)
T ss_pred HHHHhcCCC
Confidence 999999863
No 17
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=95.27 E-value=0.046 Score=46.63 Aligned_cols=63 Identities=17% Similarity=0.255 Sum_probs=44.3
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHHHhCcccCCCCccccCC
Q 032526 50 QCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGVNVKHQEYFADNP 128 (139)
Q Consensus 50 ~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~EyGInv~rP~Yy~d~~ 128 (139)
.--|+.|..||...|..||++|++-|+..||-|.+. +|-.-|+.-.| |.-.|+.=|.|=+|-.
T Consensus 171 ~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsd---------------tlEvrDIqLhL-Er~~Nm~iPgf~sd~~ 233 (258)
T KOG1142|consen 171 TKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSD---------------TVEVRDIQLHL-ERNFNMEIPGFSSDEK 233 (258)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC---------------ccchhheeeee-eccccccCCCcccccc
Confidence 334999999999999999999999999999887442 33444444444 3444555566655543
No 18
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=95.21 E-value=0.13 Score=39.41 Aligned_cols=62 Identities=15% Similarity=0.223 Sum_probs=45.9
Q ss_pred HHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHHHh
Q 032526 38 ELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREY 114 (139)
Q Consensus 38 ~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~Ey 114 (139)
.++..+|+..|++.-+|||.-.+==-+.+++++|..||..|+... +|..++++|+.-|..-+
T Consensus 16 ~~i~~iL~~~Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA---------------~~~~i~~~DVrLAi~~r 77 (129)
T PF02291_consen 16 RVIHLILKSMGVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHA---------------GRSTIDADDVRLAIQSR 77 (129)
T ss_dssp HHHHHHHHHTT---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHT---------------T-SSB-HHHHHHHHHHT
T ss_pred HHHHHHHHHcCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc---------------ccccCChHHHHHHHHHH
Confidence 477889999999888999987777777999999999999998642 12366799999888843
No 19
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=93.53 E-value=0.087 Score=43.49 Aligned_cols=57 Identities=16% Similarity=0.298 Sum_probs=30.9
Q ss_pred CCCCCCHHHHHHHHH----hCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 032526 31 YTPTIPDELVEHYLA----KSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVV 87 (139)
Q Consensus 31 Y~P~IPD~Vt~yyL~----~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~ 87 (139)
..|.+.-.+...+|. +.|....|+-|..|||+|+|-.|.+|+.++...|+.|.....
T Consensus 40 ~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~ 100 (264)
T PF05236_consen 40 EEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSK 100 (264)
T ss_dssp ----S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH-----------
T ss_pred cccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccC
Confidence 345555555555444 456666788899999999999999999999999999987643
No 20
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=93.15 E-value=0.39 Score=38.55 Aligned_cols=47 Identities=13% Similarity=0.251 Sum_probs=41.8
Q ss_pred HHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 032526 40 VEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAV 86 (139)
Q Consensus 40 t~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~ 86 (139)
+..++.+.|+..-|+.+..|||+|++-++.+|+.+....|+.|....
T Consensus 54 ~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~ 100 (212)
T cd08045 54 IRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSE 100 (212)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 45567788888889999999999999999999999999999997753
No 21
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=89.92 E-value=2 Score=34.20 Aligned_cols=63 Identities=19% Similarity=0.199 Sum_probs=49.7
Q ss_pred HHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHHHhCc
Q 032526 39 LVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGV 116 (139)
Q Consensus 39 Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~EyGI 116 (139)
|+.-+|...|.+-=+|||+--+==-|-.++++|..||.-|++- -+|.+++.||+.-|+.-.+-
T Consensus 18 ~i~~iL~s~GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~H---------------A~ka~i~~eDVrlA~~~~~~ 80 (148)
T KOG3334|consen 18 VIASILKSLGIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSH---------------AKKATIDAEDVRLAIQMRVD 80 (148)
T ss_pred HHHHHHHHcCccccChHHHHHHHHHHHHHHHHHHHHHHHHHHh---------------ccCCCCcHHHHHHHHHHHhc
Confidence 5677899999998888887666666789999999999999852 11568888998888875543
No 22
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=87.39 E-value=2.1 Score=37.71 Aligned_cols=77 Identities=25% Similarity=0.404 Sum_probs=58.8
Q ss_pred CCHHHHHHHHHhCCCCC-CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHHH
Q 032526 35 IPDELVEHYLAKSGFQC-PDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALRE 113 (139)
Q Consensus 35 IPD~Vt~yyL~~aGf~~-~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~E 113 (139)
|=..|+.-.|...||+. ++.-+--|+ .+-|+.|..|...+..||.. .+|+.-|.-||.-.|.+
T Consensus 6 vl~~VV~~Ll~~~gfd~is~~aletlv-ell~~yi~eigrq~~n~cel---------------agRT~pT~~Dv~l~Li~ 69 (323)
T KOG4336|consen 6 VLAPVVSNLLKTKGFDSISNAALETLV-ELLQSYIREIGRQLHNYCEL---------------AGRTIPTQGDVKLTLIE 69 (323)
T ss_pred HHHHHHHHHHHHhCchHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH---------------hcccCCcHHHHHHHHHH
Confidence 44579999999999997 455555555 44688999999999999854 23567789999999999
Q ss_pred hCcccCC-CCccccC
Q 032526 114 YGVNVKH-QEYFADN 127 (139)
Q Consensus 114 yGInv~r-P~Yy~d~ 127 (139)
.||+|.- +.||.+.
T Consensus 70 mnI~v~sL~~~~q~~ 84 (323)
T KOG4336|consen 70 MNIKVSSLYAYFQKQ 84 (323)
T ss_pred hCCChhhhHHHHHhc
Confidence 9999964 4455443
No 23
>smart00417 H4 Histone H4.
Probab=83.35 E-value=4.8 Score=28.32 Aligned_cols=53 Identities=13% Similarity=0.149 Sum_probs=41.9
Q ss_pred cccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032526 28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCK 80 (139)
Q Consensus 28 LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~k 80 (139)
|-|...-||-.-+.-.+.++|..=--.-++--+.=+...|+.+|+.||..|++
T Consensus 7 ~~d~i~gI~k~~IrRLaRr~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ 59 (74)
T smart00417 7 LRDNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTE 59 (74)
T ss_pred HHhhhcCCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34666679999999999999998433335555566678999999999999985
No 24
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=81.34 E-value=11 Score=35.65 Aligned_cols=87 Identities=25% Similarity=0.276 Sum_probs=66.9
Q ss_pred cCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHH
Q 032526 30 GYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSK 109 (139)
Q Consensus 30 dY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~ 109 (139)
.++-..|-+-++-.-+.-|..+=+....++++-=-.==|-+|++||.++= + +-+|.+||++|...
T Consensus 7 ~~~v~s~~Es~k~vAEslGi~nl~deaa~~La~dv~yrikEI~Q~aaKfm--~-------------hskR~kLtv~DV~~ 71 (576)
T KOG2549|consen 7 SPTVVSPKESVKVVAESLGITNLNDEAALLLAEDVEYRIKEIVQDAAKFM--V-------------HSKRTKLTVDDVDY 71 (576)
T ss_pred cccccCcHHHHHHHHHHhCccccCHHHHHHHHHHHHHHHHHHHHHHHHHh--h-------------cCCCCcCcHHHHHH
Confidence 34445568888888999999998888888888877777889998888762 2 34578999999999
Q ss_pred HHHH------hCcccCCCCccccCCCCC
Q 032526 110 ALRE------YGVNVKHQEYFADNPSTG 131 (139)
Q Consensus 110 AL~E------yGInv~rP~Yy~d~~~~~ 131 (139)
||+- ||+.-+++-=|+-.+..|
T Consensus 72 ALr~~nVep~yg~~s~~~i~fr~a~~~~ 99 (576)
T KOG2549|consen 72 ALRSLNVEPLYGFGAQEIIPFRKASGGG 99 (576)
T ss_pred HHhhcccccccCcccCceeeccccCCCC
Confidence 9984 788887666565554443
No 25
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=72.67 E-value=19 Score=23.62 Aligned_cols=64 Identities=19% Similarity=0.222 Sum_probs=44.2
Q ss_pred CCCHHHHHHHHHhCCCCCC-----ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHH
Q 032526 34 TIPDELVEHYLAKSGFQCP-----DVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLS 108 (139)
Q Consensus 34 ~IPD~Vt~yyL~~aGf~~~-----D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~ 108 (139)
.||-.-+...+.+.+-+.. .......+.-+.+-|+.+|+.+|..+++ ..+|.+||-+|+.
T Consensus 5 ~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~---------------~~kR~tI~~~DI~ 69 (75)
T PF00125_consen 5 LIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLAR---------------HAKRKTITPRDIQ 69 (75)
T ss_dssp SSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HTTBSEEGHHHHH
T ss_pred ccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHh---------------hcCCcEecHHHHH
Confidence 3555555555555544422 3455667777888899999999988874 2346789999999
Q ss_pred HHHH
Q 032526 109 KALR 112 (139)
Q Consensus 109 ~AL~ 112 (139)
.|+.
T Consensus 70 ~A~r 73 (75)
T PF00125_consen 70 LAVR 73 (75)
T ss_dssp HHHH
T ss_pred HHHh
Confidence 8875
No 26
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=68.36 E-value=38 Score=30.79 Aligned_cols=67 Identities=27% Similarity=0.349 Sum_probs=47.2
Q ss_pred HHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHHH------h
Q 032526 41 EHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALRE------Y 114 (139)
Q Consensus 41 ~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~E------y 114 (139)
.-.-+.-|...-|-...|.+|.--.==|-+|+++|..+- | ..||++||.+|++.||+- |
T Consensus 12 KdvAeslGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFm--v-------------hSKRtvLt~dDis~ALr~lNVePLy 76 (450)
T COG5095 12 KDVAESLGISNIDDDALRALAMDLEYRIKEVCQEASKFM--V-------------HSKRTVLTIDDISYALRSLNVEPLY 76 (450)
T ss_pred HHHHHHcCCcccccHHHHHHHHhHHHHHHHHHHHHHHHh--h-------------cccceeeeHHhHHHHHHhcCCCccc
Confidence 334456688776667778787777777777777766552 1 345899999999999996 5
Q ss_pred CcccCCCC
Q 032526 115 GVNVKHQE 122 (139)
Q Consensus 115 GInv~rP~ 122 (139)
|-+-.||-
T Consensus 77 Gyd~~r~l 84 (450)
T COG5095 77 GYDPSRPL 84 (450)
T ss_pred CCCCCcch
Confidence 55555553
No 27
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=66.79 E-value=5.7 Score=23.86 Aligned_cols=22 Identities=23% Similarity=0.302 Sum_probs=18.8
Q ss_pred eeeHHHHHHHHHHhCcccCCCC
Q 032526 101 ILTMEDLSKALREYGVNVKHQE 122 (139)
Q Consensus 101 vLTmEDL~~AL~EyGInv~rP~ 122 (139)
+-+.+||..-|.+|||.+.++.
T Consensus 3 tWs~~~L~~wL~~~gi~~~~~~ 24 (38)
T PF10281_consen 3 TWSDSDLKSWLKSHGIPVPKSA 24 (38)
T ss_pred CCCHHHHHHHHHHcCCCCCCCC
Confidence 3578999999999999988765
No 28
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=64.35 E-value=7.9 Score=29.56 Aligned_cols=37 Identities=16% Similarity=0.205 Sum_probs=33.8
Q ss_pred HHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHH
Q 032526 40 VEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDAL 76 (139)
Q Consensus 40 t~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~ 76 (139)
+..+|...|.++.+.||..+||...-|=|.||+....
T Consensus 23 ikkIl~sVG~E~d~e~i~~visel~GK~i~ElIA~G~ 59 (112)
T KOG3449|consen 23 IKKILESVGAEIDDERINLVLSELKGKDIEELIAAGR 59 (112)
T ss_pred HHHHHHHhCcccCHHHHHHHHHHhcCCCHHHHHHHhH
Confidence 6788999999999999999999999999999997543
No 29
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=63.83 E-value=30 Score=31.02 Aligned_cols=53 Identities=11% Similarity=0.190 Sum_probs=43.9
Q ss_pred ccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032526 29 MGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKA 81 (139)
Q Consensus 29 ddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~ki 81 (139)
.+|.=-+--..+..+++..|+.|.+--=-.+|...+|+||..++-.|.-|+.+
T Consensus 24 ~~ya~sla~~avaQIcqslg~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~ 76 (353)
T KOG2389|consen 24 AEYAFSLARVAVAQICQSLGYSSTQNSALETLTDVLQQYVQNLGKTAHRYSNL 76 (353)
T ss_pred HHHHHHHHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHHHHHHhhhhhhhhh
Confidence 34555566688999999999999776677777888999999999999999853
No 30
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=62.48 E-value=58 Score=25.77 Aligned_cols=61 Identities=23% Similarity=0.313 Sum_probs=37.8
Q ss_pred HHHHHHhCCCC-CCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHHH
Q 032526 40 VEHYLAKSGFQ-CPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALRE 113 (139)
Q Consensus 40 t~yyL~~aGf~-~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~E 113 (139)
+.-+|..-|++ |++.-...|+-. |+++-.||..||+-|++--. + ..-.+|.+||+--||+.
T Consensus 20 ihliL~Slgi~~ye~~VplQLl~F-AhRYTq~vl~Dalvya~htg-------r-----g~~a~l~veDvrLA~at 81 (145)
T COG5094 20 IHLILRSLGIEEYEPKVPLQLLEF-AHRYTQDVLEDALVYAKHTG-------R-----GHIATLGVEDVRLALAT 81 (145)
T ss_pred HHHHHHhcCchhhCccchHHHHHH-HHHHHHHHHHHHHHHHHhcC-------C-----CccCcccHHHHHHHHHH
Confidence 33344444443 233333444444 57899999999999986311 1 11245889999988873
No 31
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=62.23 E-value=4.1 Score=24.98 Aligned_cols=18 Identities=33% Similarity=0.538 Sum_probs=12.5
Q ss_pred eeeHHHHHHHHHHhCccc
Q 032526 101 ILTMEDLSKALREYGVNV 118 (139)
Q Consensus 101 vLTmEDL~~AL~EyGInv 118 (139)
.||+.+|-..|.|+||..
T Consensus 3 sltV~~Lk~iL~~~~I~~ 20 (35)
T PF12949_consen 3 SLTVAQLKRILDEHGIEF 20 (35)
T ss_dssp T--SHHHHHHHHHHT---
T ss_pred cCcHHHHHHHHHHcCCCC
Confidence 689999999999999964
No 32
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=61.80 E-value=13 Score=31.99 Aligned_cols=40 Identities=28% Similarity=0.427 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHHH
Q 032526 59 LVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALRE 113 (139)
Q Consensus 59 LiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~E 113 (139)
|.|.++.+||.++.--|.-+++ +.+|-+|.-.||.+|++.
T Consensus 135 lFak~~EiFI~ELTmRAW~~ae---------------~NkRRtLQksDia~Av~k 174 (286)
T COG5208 135 LFAKITEIFIEELTMRAWINAE---------------ENKRRTLQKSDIAAAVKK 174 (286)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh---------------HhhhhHHHHHHHHHHHHH
Confidence 5688999999999887776552 334568999999999874
No 33
>cd04381 RhoGap_RalBP1 RhoGap_RalBP1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in RalBP1 proteins, also known as RLIP, RLIP76 or cytocentrin. RalBP1 plays an important role in endocytosis during interphase. During mitosis, RalBP1 transiently associates with the centromere and has been shown to play an essential role in the proper assembly of the mitotic apparatus. RalBP1 is an effector of the Ral GTPase which itself is an effector of Ras. RalBP1 contains a RhoGAP domain, which shows weak activity towards Rac1 and Cdc42, but not towards Ral, and a Ral effector domain binding motif. 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 int
Probab=57.35 E-value=27 Score=27.13 Aligned_cols=47 Identities=19% Similarity=0.258 Sum_probs=34.5
Q ss_pred CCCCchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHH
Q 032526 14 RHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAV 62 (139)
Q Consensus 14 ~~~~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSL 62 (139)
.+.-..-|..||..|- .|+||.++.+.+.+-++-...+.|+..+-.+
T Consensus 71 ~h~va~lLK~fLReLP--~pLi~~~~~~~~~~~~~~~~~~~r~~~l~~l 117 (182)
T cd04381 71 PPTVASLLKQYLRELP--EPLLTKELMPRFEEACGRPTEAEREQELQRL 117 (182)
T ss_pred hHHHHHHHHHHHHhCC--CccCCHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence 3444566888999998 5999999999998888766556666544433
No 34
>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=56.06 E-value=22 Score=27.68 Aligned_cols=44 Identities=25% Similarity=0.334 Sum_probs=33.4
Q ss_pred CchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHH
Q 032526 17 DDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAV 62 (139)
Q Consensus 17 ~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSL 62 (139)
-..-|..||..|- .|+||.++.+.+++-++.+..+.|+..+-++
T Consensus 70 va~~LK~flr~Lp--epLi~~~~~~~~~~~~~~~~~~~~i~~l~~~ 113 (186)
T cd04377 70 ITSVLKQWLRELP--EPLMTFELYENFLRAMELEEKQERVRALYSV 113 (186)
T ss_pred HHHHHHHHHHcCC--CccCCHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence 3556788999887 4999999999999988876655566554433
No 35
>cd04374 RhoGAP_Graf RhoGAP_Graf: GTPase-activator protein (GAP) domain for Rho-like GTPases found in GRAF (GTPase regulator associated with focal adhesion kinase); Graf is a multi-domain protein, containing SH3 and PH domains, that binds focal adhesion kinase and influences cytoskeletal changes mediated by Rho proteins. Graf exhibits GAP activity toward RhoA and Cdc42, but only weakly activates Rac1. 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=54.16 E-value=25 Score=28.22 Aligned_cols=44 Identities=18% Similarity=0.288 Sum_probs=33.7
Q ss_pred CchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHH
Q 032526 17 DDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAV 62 (139)
Q Consensus 17 ~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSL 62 (139)
-..-|..||..|-+ |+||.++-+-++.-++-+..+.|+..|-.+
T Consensus 89 va~lLK~fLReLPe--PLi~~~~y~~~i~~~~~~~~~~ri~~l~~l 132 (203)
T cd04374 89 ITSALKTYLRNLPE--PLMTYELHNDFINAAKSENLESRVNAIHSL 132 (203)
T ss_pred HHHHHHHHHHcCCC--CcCCHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 34567888988875 999999999999887776667777655443
No 36
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=53.06 E-value=13 Score=21.76 Aligned_cols=19 Identities=21% Similarity=0.468 Sum_probs=16.7
Q ss_pred eeeHHHHHHHHHHhCcccC
Q 032526 101 ILTMEDLSKALREYGVNVK 119 (139)
Q Consensus 101 vLTmEDL~~AL~EyGInv~ 119 (139)
.||..+|...|+++|+.+.
T Consensus 3 ~l~~~~Lk~~l~~~gl~~~ 21 (35)
T smart00513 3 KLKVSELKDELKKRGLSTS 21 (35)
T ss_pred cCcHHHHHHHHHHcCCCCC
Confidence 5889999999999999763
No 37
>COG0599 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]
Probab=51.19 E-value=17 Score=26.54 Aligned_cols=47 Identities=21% Similarity=0.344 Sum_probs=34.6
Q ss_pred chHHHHHHHhcccCCCCCCHHHHHHHHH-hCCC-C-CCChHHHHHHHHHH
Q 032526 18 DAALTEFLSSLMGYTPTIPDELVEHYLA-KSGF-Q-CPDVRLIRLVAVAT 64 (139)
Q Consensus 18 d~~L~efL~~LddY~P~IPD~Vt~yyL~-~aGf-~-~~D~Rv~RLiSLAa 64 (139)
......+...++++.|..||-.+.+++- ..=+ . .=|+|.+.||+||.
T Consensus 14 ~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~Ld~ktr~Li~ia~ 63 (124)
T COG0599 14 AKVDKALAEGLEDFAPEFPELLEAFYAFGEIWFRKGALDAKTRELIAIAV 63 (124)
T ss_pred HHHHHHHHhhHHHHhHhhHHHHHHHHHhhhHHhcCCCCCHHHHHHHHHHH
Confidence 3456677888889999999999994443 2222 2 34899999999885
No 38
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=50.72 E-value=13 Score=22.01 Aligned_cols=19 Identities=32% Similarity=0.560 Sum_probs=15.8
Q ss_pred eeeHHHHHHHHHHhCcccC
Q 032526 101 ILTMEDLSKALREYGVNVK 119 (139)
Q Consensus 101 vLTmEDL~~AL~EyGInv~ 119 (139)
.||+.||...|+++|+.+.
T Consensus 3 ~l~v~eLk~~l~~~gL~~~ 21 (35)
T PF02037_consen 3 KLTVAELKEELKERGLSTS 21 (35)
T ss_dssp TSHHHHHHHHHHHTTS-ST
T ss_pred cCcHHHHHHHHHHCCCCCC
Confidence 4789999999999999764
No 39
>cd04395 RhoGAP_ARHGAP21 RhoGAP_ARHGAP21: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP21-like proteins. ArhGAP21 is a multi-domain protein, containing RhoGAP, PH and PDZ domains, and is believed to play a role in the organization of the cell-cell junction complex. It has been shown to function as a GAP of Cdc42 and RhoA, and to interact with alpha-catenin and Arf6. 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=50.09 E-value=36 Score=26.63 Aligned_cols=43 Identities=23% Similarity=0.386 Sum_probs=32.8
Q ss_pred hHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHH
Q 032526 19 AALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVA 63 (139)
Q Consensus 19 ~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLA 63 (139)
.-|..||..|- .|+||.++.+-+++.+..+..+.|+..+-.+.
T Consensus 78 ~llK~flr~Lp--~pli~~~~~~~~i~~~~~~~~~~~i~~l~~~i 120 (196)
T cd04395 78 SLLKSFFRKLP--EPLFTNELYPDFIEANRIEDPVERLKELRRLI 120 (196)
T ss_pred HHHHHHHHhCC--CccCCHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 56788999997 79999999999988776665566665554444
No 40
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=49.11 E-value=43 Score=27.45 Aligned_cols=38 Identities=13% Similarity=0.137 Sum_probs=33.6
Q ss_pred HHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHH
Q 032526 41 EHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQ 78 (139)
Q Consensus 41 ~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~ 78 (139)
...+...|++.-+...+.||.+|.+.|+-+|+..++..
T Consensus 213 ~~ia~e~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~ 250 (252)
T PF12767_consen 213 EQIAWEHGLGGVSDDCANLLNLALEVHLKNLIKSCLDL 250 (252)
T ss_pred HHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 44677899988999999999999999999999988764
No 41
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=48.30 E-value=22 Score=28.92 Aligned_cols=66 Identities=21% Similarity=0.350 Sum_probs=40.3
Q ss_pred CCHHHHHHHHHhCCCCCCC---hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHH
Q 032526 35 IPDELVEHYLAKSGFQCPD---VRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKAL 111 (139)
Q Consensus 35 IPD~Vt~yyL~~aGf~~~D---~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL 111 (139)
+|=+=+.-+|++. ++..- .--|--|-=..--|||=|...|-.-|. +++|=|.|=|||.-||
T Consensus 33 LPIANV~RIMK~~-lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~---------------~EkRKTIngdDllwAm 96 (168)
T KOG0869|consen 33 LPIANVSRIMKKA-LPANAKISKDAKETVQECVSEFISFVTGEASEKCQ---------------REKRKTINGDDLLWAM 96 (168)
T ss_pred ccHHHHHHHHHhc-CCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHH---------------HHhcCcccHHHHHHHH
Confidence 4445566666543 32210 111233333444688888888877772 4556689999999999
Q ss_pred HHhCc
Q 032526 112 REYGV 116 (139)
Q Consensus 112 ~EyGI 116 (139)
..-|.
T Consensus 97 ~tLGF 101 (168)
T KOG0869|consen 97 STLGF 101 (168)
T ss_pred HHcCc
Confidence 98886
No 42
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=45.47 E-value=31 Score=24.63 Aligned_cols=57 Identities=19% Similarity=0.279 Sum_probs=23.5
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHHHhCcccCCC
Q 032526 50 QCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGVNVKHQ 121 (139)
Q Consensus 50 ~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~EyGInv~rP 121 (139)
+.+.+..+.||-=....||.++++.|.++|..|.+ -.+++|||.-+|+---.-+.|=
T Consensus 18 ~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~---------------~~i~~eDl~F~lR~D~~Kl~Rl 74 (93)
T PF02269_consen 18 EEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGS---------------KKIKVEDLLFLLRKDPKKLARL 74 (93)
T ss_dssp SS--HHHHHHHHHHHHHHHHHHHHHHHC--------------------------------------------
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc---------------CcCcHHHHHHHHhcCHHHHHHH
Confidence 34678889999999999999999999998865421 2467777777776544444444
No 43
>PF08367 M16C_assoc: Peptidase M16C associated; InterPro: IPR013578 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 appears in eukaryotes as well as bacteria and tends to be found near the C terminus of metalloproteases and related sequences belonging to MEROPS peptidase family M16 (subfamily M16C, clan ME). These include: eupitrilysin, falcilysin, PreP peptidase, CYM1 peptidase and subfamily M16C non-peptidase homologues.; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 2FGE_B 3S5I_A 3S5H_A 3S5M_A 3S5K_A.
Probab=45.26 E-value=43 Score=27.07 Aligned_cols=48 Identities=15% Similarity=0.279 Sum_probs=37.4
Q ss_pred HHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 032526 39 LVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVV 87 (139)
Q Consensus 39 Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~ 87 (139)
+..-+|...-|+-.+ ||+.||.-....+-+.|+..++.|+..|..+.-
T Consensus 179 ll~eil~~~~f~d~~-rl~~ll~~~~s~~~~~i~~~Gh~~A~~ra~s~~ 226 (248)
T PF08367_consen 179 LLSEILTETDFDDKE-RLKELLKELKSDMESSIISSGHSYAMSRASSYL 226 (248)
T ss_dssp HHHHHHHCB-TT-HH-HHHHHHHHHHHHHHHHHHH-HHHHHHHHCCCTT
T ss_pred HHHHHHhccCCCcHH-HHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhcC
Confidence 456678888886333 999999999999999999999999998876543
No 44
>PF04239 DUF421: Protein of unknown function (DUF421); InterPro: IPR007353 This family of uncharacterised proteins is known as YDFR family; PDB: 3C6F_D.
Probab=45.14 E-value=13 Score=26.74 Aligned_cols=19 Identities=53% Similarity=0.704 Sum_probs=14.8
Q ss_pred cceeeeHHHHHHHHHHhCc
Q 032526 98 KRLILTMEDLSKALREYGV 116 (139)
Q Consensus 98 ~k~vLTmEDL~~AL~EyGI 116 (139)
+|.-||.+||..+|++.||
T Consensus 23 ~~~~it~~dl~~~LR~~gi 41 (99)
T PF04239_consen 23 RRARITEEDLLSALREQGI 41 (99)
T ss_dssp HHTT--HHHHHHHHHHTT-
T ss_pred hHcCCCHHHHHHHHHhhCC
Confidence 5778999999999999999
No 45
>cd04386 RhoGAP_nadrin RhoGAP_nadrin: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of Nadrin-like proteins. Nadrin, also named Rich-1, has been shown to be involved in the regulation of Ca2+-dependent exocytosis in neurons and recently has been implicated in tight junction maintenance in mammalian epithelium. 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=43.98 E-value=47 Score=26.11 Aligned_cols=43 Identities=26% Similarity=0.362 Sum_probs=31.2
Q ss_pred CCCchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHH
Q 032526 15 HDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (139)
Q Consensus 15 ~~~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RL 59 (139)
+.-..-|+.||..|- .|+||.++.+-+++-+.-...+.|+.-+
T Consensus 75 h~va~~lK~fLreLp--~pli~~~~~~~~~~~~~~~~~~~~~~~l 117 (203)
T cd04386 75 HAVASALKSYLRELP--DPLLTYNLYEDWVQAANKPDEDERLQAI 117 (203)
T ss_pred HHHHHHHHHHHHhCC--CccCCHHHHHHHHHHHccCCHHHHHHHH
Confidence 334556788999997 4999999999999887655444555444
No 46
>cd04387 RhoGAP_Bcr RhoGAP_Bcr: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of Bcr (breakpoint cluster region protein)-like proteins. Bcr is a multidomain protein with a variety of enzymatic functions. It contains a RhoGAP and a Rho GEF domain, a Ser/Thr kinase domain, an N-terminal oligomerization domain, and a C-terminal PDZ binding domain, in addition to PH and C2 domains. Bcr is a negative regulator of: i) RacGTPase, via the Rho GAP domain, ii) the Ras-Raf-MEK-ERK pathway, via phosphorylation of the Ras binding protein AF-6, and iii) the Wnt signaling pathway through binding beta-catenin. Bcr can form a complex with beta-catenin and Tcf1. The Wnt signaling pathway is involved in cell proliferation, differentiation, and cell renewal. Bcr was discovered as a fusion partner of Abl. The Bcr-Abl fusion is characteristic for a large majority of chronic myelogenous leukemias (CML). Small GTPases cluster into distinct families, and all act as molecular switch
Probab=43.82 E-value=41 Score=26.70 Aligned_cols=37 Identities=19% Similarity=0.312 Sum_probs=28.2
Q ss_pred chHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHH
Q 032526 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (139)
Q Consensus 18 d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (139)
..-|+.||..|-+ |+||.++.+.+++..+...+..|+
T Consensus 74 a~lLK~fLReLPe--PLip~~~y~~~~~~~~~~~~~~~~ 110 (196)
T cd04387 74 AGTLKLYFRELPE--PLFTDELYPNFAEGIALSDPVAKE 110 (196)
T ss_pred HHHHHHHHHhCCC--ccCCHHHHHHHHHHHHcCCHHHHH
Confidence 3567888888875 999999999999887765444443
No 47
>cd04403 RhoGAP_ARHGAP27_15_12_9 RhoGAP_ARHGAP27_15_12_9: GTPase-activator protein (GAP) domain for Rho-like GTPases found in ARHGAP27 (also called CAMGAP1), ARHGAP15, 12 and 9-like proteins; This subgroup of ARHGAPs are multidomain proteins that contain RhoGAP, PH, SH3 and WW domains. Most members that are studied show GAP activity towards Rac1, some additionally show activity towards Cdc42. 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=43.44 E-value=40 Score=26.22 Aligned_cols=44 Identities=20% Similarity=0.302 Sum_probs=32.5
Q ss_pred chHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHH
Q 032526 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVA 63 (139)
Q Consensus 18 d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLA 63 (139)
..-|..||..|-+ |+||.++.+.+++...-+..+.|+..+-.+.
T Consensus 74 a~lLK~fLReLPe--pLi~~~~~~~~~~~~~~~~~~~~i~~l~~ll 117 (187)
T cd04403 74 TGALKLFFRELPE--PLFPYSLFNDFVAAIKLSDYEQRVSAVKDLI 117 (187)
T ss_pred HHHHHHHHhcCCC--CcCCHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3568889999985 9999999999988766555556665554443
No 48
>cd04402 RhoGAP_ARHGAP20 RhoGAP_ARHGAP20: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP20-like proteins. ArhGAP20, also known as KIAA1391 and RA-RhoGAP, contains a RhoGAP, a RA, and a PH domain, and ANXL repeats. ArhGAP20 is activated by Rap1 and induces inactivation of Rho, which in turn leads to neurite outgrowth. 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=43.37 E-value=50 Score=25.75 Aligned_cols=43 Identities=14% Similarity=0.274 Sum_probs=31.1
Q ss_pred CCCCchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHH
Q 032526 14 RHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIR 58 (139)
Q Consensus 14 ~~~~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~R 58 (139)
.+.-..-|+.||..|-+ |+||.++.+-++.-.+....+.++..
T Consensus 66 ~~~va~~lK~flreLpe--pLi~~~~~~~~~~~~~~~~~~~~i~~ 108 (192)
T cd04402 66 VLLLASVLKDFLRNIPG--SLLSSDLYEEWMSALDQENEEEKIAE 108 (192)
T ss_pred HHHHHHHHHHHHHhCCC--ccCCHHHHHHHHHHHccCCHHHHHHH
Confidence 34445567889999984 99999999999887776544445443
No 49
>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [].; GO: 0016597 amino acid binding, 0008152 metabolic process; PDB: 3L76_B 2F06_B 3NRB_C 1Y7P_C 2QMX_A 2DT9_A 2ZHO_D 3K5P_A 3TVI_K 3C1M_C ....
Probab=43.00 E-value=18 Score=22.10 Aligned_cols=23 Identities=22% Similarity=0.459 Sum_probs=17.6
Q ss_pred HHHHHHHHHHhCcccCCCCcccc
Q 032526 104 MEDLSKALREYGVNVKHQEYFAD 126 (139)
Q Consensus 104 mEDL~~AL~EyGInv~rP~Yy~d 126 (139)
+-++...|+++||||..=.-+.+
T Consensus 14 l~~v~~~la~~~inI~~~~~~~~ 36 (66)
T PF01842_consen 14 LADVTEILADHGINIDSISQSSD 36 (66)
T ss_dssp HHHHHHHHHHTTEEEEEEEEEEE
T ss_pred HHHHHHHHHHcCCCHHHeEEEec
Confidence 57899999999999975444433
No 50
>cd04393 RhoGAP_FAM13A1a RhoGAP_FAM13A1a: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of FAM13A1, isoform a-like proteins. The function of FAM13A1a is unknown. 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 up several orders of magnitude.
Probab=42.60 E-value=78 Score=24.56 Aligned_cols=45 Identities=20% Similarity=0.040 Sum_probs=30.2
Q ss_pred CCCCchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCC-CCChHHHHHH
Q 032526 14 RHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQ-CPDVRLIRLV 60 (139)
Q Consensus 14 ~~~~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~-~~D~Rv~RLi 60 (139)
.+.-..-|..|+..|-+ |+||.++.+.+++-.+-. ..|.++.++-
T Consensus 72 ~~~va~~lK~flr~Lp~--pLi~~~~~~~l~~~~~~~~~~~~~~~~l~ 117 (189)
T cd04393 72 VCSAASLLRLFLQELPE--GLIPASLQIRLMQLYQDYNGEDEFGRKLR 117 (189)
T ss_pred HHHHHHHHHHHHHhCCC--ccCCHHHHHHHHHHHHHccChHHHHHHHH
Confidence 34445678889999985 999999988887643322 3455554443
No 51
>cd04407 RhoGAP_myosin_IXB RhoGAP_myosin_IXB: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in myosins IXB. Class IX myosins contain a characteristic head domain, a neck domain and a tail domain which contains a C6H2-zinc binding motif and a Rho-GAP domain. Class IX myosins are single-headed, processive myosins that are partly cytoplasmic, and partly associated with membranes and the actin cytoskeleton. Class IX myosins are implicated in the regulation of neuronal morphogenesis and function of sensory systems, like the inner ear. There are two major isoforms, myosin IXA and IXB with several splice variants, which are both expressed in developing neurons Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell prolifer
Probab=42.28 E-value=48 Score=25.98 Aligned_cols=40 Identities=15% Similarity=0.217 Sum_probs=29.9
Q ss_pred chHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHH
Q 032526 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (139)
Q Consensus 18 d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RL 59 (139)
..-|..||..|-+ |+||.++.+.++.-...+....|+..+
T Consensus 71 a~lLK~flReLPe--pLi~~~~~~~~~~~~~~~~~~~~~~~l 110 (186)
T cd04407 71 TGLLKQWLRELPE--PLMTFAQYNDFLRAVELPEKQEQLQAI 110 (186)
T ss_pred HHHHHHHHHhCCC--ccCCHHHHHHHHHHHHCCCHHHHHHHH
Confidence 4567889998887 999999999998877655444555433
No 52
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=42.13 E-value=33 Score=21.54 Aligned_cols=29 Identities=24% Similarity=0.363 Sum_probs=22.4
Q ss_pred HHHHHHHhcccCCCCCCHHHHHHHHHhCC
Q 032526 20 ALTEFLSSLMGYTPTIPDELVEHYLAKSG 48 (139)
Q Consensus 20 ~L~efL~~LddY~P~IPD~Vt~yyL~~aG 48 (139)
+++++++.|.+-.=-||+.+.+..|+++|
T Consensus 20 ~~~~~l~~l~~~g~~is~~l~~~~L~~~g 48 (48)
T PF11848_consen 20 EVKPLLDRLQQAGFRISPKLIEEILRRAG 48 (48)
T ss_pred hHHHHHHHHHHcCcccCHHHHHHHHHHcC
Confidence 56777778877777788888888888776
No 53
>PF10815 ComZ: ComZ; InterPro: IPR024558 ComZ, which contains a leucine zipper motif, negatively regulates transcription of the ComG operon [].
Probab=41.19 E-value=71 Score=21.75 Aligned_cols=48 Identities=27% Similarity=0.424 Sum_probs=36.8
Q ss_pred HHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032526 23 EFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCK 80 (139)
Q Consensus 23 efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~k 80 (139)
+|++--..| +|+ ....|.++|.+-+=..+--++.|- ..|.++||+..|
T Consensus 5 ~FmqIaMK~---lPE--ak~~L~k~GIeLsme~~qP~m~L~-----~~VM~eAYElG~ 52 (56)
T PF10815_consen 5 EFMQIAMKY---LPE--AKEELDKKGIELSMEMLQPLMQLL-----TKVMNEAYELGK 52 (56)
T ss_pred HHHHHHHHH---hHH--HHHHHHHcCccCCHHHHHHHHHHH-----HHHHHHHHHhhh
Confidence 455444455 455 678899999999988888888874 579999999764
No 54
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=40.92 E-value=21 Score=24.60 Aligned_cols=20 Identities=35% Similarity=0.473 Sum_probs=13.2
Q ss_pred eeeeHHHHHHHHHHhCcccC
Q 032526 100 LILTMEDLSKALREYGVNVK 119 (139)
Q Consensus 100 ~vLTmEDL~~AL~EyGInv~ 119 (139)
-+-|-+||...|+++||.|.
T Consensus 18 ~i~sQ~eL~~~L~~~Gi~vT 37 (70)
T PF01316_consen 18 EISSQEELVELLEEEGIEVT 37 (70)
T ss_dssp ---SHHHHHHHHHHTT-T--
T ss_pred CcCCHHHHHHHHHHcCCCcc
Confidence 47788999999999999875
No 55
>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=40.89 E-value=55 Score=25.58 Aligned_cols=42 Identities=21% Similarity=0.320 Sum_probs=31.3
Q ss_pred chHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHH
Q 032526 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVA 61 (139)
Q Consensus 18 d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiS 61 (139)
..-|..||..|-+ |+||.++.+.+++-+.....|.|+..+-.
T Consensus 75 a~lLK~flReLP~--pLi~~~~~~~~~~~~~~~~~~~~~~~l~~ 116 (194)
T cd04372 75 TGALKLYFRDLPI--PVITYDTYPKFIDAAKISNPDERLEAVHE 116 (194)
T ss_pred HHHHHHHHHhCCC--ccCCHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence 4456888988875 99999999999987766555666654443
No 56
>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=40.15 E-value=52 Score=25.97 Aligned_cols=43 Identities=16% Similarity=0.275 Sum_probs=31.8
Q ss_pred CCCchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHH
Q 032526 15 HDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (139)
Q Consensus 15 ~~~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RL 59 (139)
|.-..-|..||..|-+ |+||.++.+.+++-..-+..+.|+..|
T Consensus 73 h~va~lLK~flReLPe--PLi~~~~y~~~~~~~~~~~~~~~~~~l 115 (195)
T cd04384 73 HSVSSLCKLYFRELPN--PLLTYQLYEKFSEAVSAASDEERLEKI 115 (195)
T ss_pred HHHHHHHHHHHHhCCC--ccCCHHHHHHHHHHHhcCCHHHHHHHH
Confidence 3344567899999985 999999999988876665555565443
No 57
>PF15374 CCDC71L: Coiled-coil domain-containing protein 71L
Probab=39.85 E-value=19 Score=32.54 Aligned_cols=27 Identities=37% Similarity=0.527 Sum_probs=21.3
Q ss_pred CCCCCCCCchHHHHHHHhcc-c-CCCCCC
Q 032526 10 SSDGRHDDDAALTEFLSSLM-G-YTPTIP 36 (139)
Q Consensus 10 ~~~~~~~~d~~L~efL~~Ld-d-Y~P~IP 36 (139)
+..+-...+.+|.-||+.|. | |.|+|=
T Consensus 30 mS~dl~~te~qLv~Flq~Lr~eGfqP~IL 58 (376)
T PF15374_consen 30 MSKDLSDTEAQLVAFLQGLRHEGFQPTIL 58 (376)
T ss_pred cccccchhHHHHHHHHHHHhhcCCCceee
Confidence 44555677999999999994 3 999983
No 58
>PF00123 Hormone_2: Peptide hormone; InterPro: IPR000532 A number of polypeptidic hormones, mainly expressed in the intestine or the pancreas, belong to a group of structurally related peptides [, ]. Once such hormone, glucagon is widely distributed and produced in the alpha-cells of pancreatic islets []. It affects glucose metabolism in the liver [] by inhibiting glycogen synthesis, stimulating glycogenolysis and enchancing gluconeogenesis. It also increases mobilisation of glucose, free fatty acids and ketone bodies, which are metabolites produced in excess in diabetes mellitus. Glucagon is produced, like other peptide hormones, as part of a larger precursor (preproglucagon), which is cleaved to produce glucagon, glucagon-like protein I and glucagon-like protein II []. The structure of glucagon itself is fully conserved in all known mammalian species []. Other members of the structurally similar group include glicentin precursor, secretin, gastric inhibitory protein, vasoactive intestinal peptide (VIP), prealbumin, peptide HI-27 and growth hormone releasing factor.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1T5Q_A 2OBU_A 2QKH_B 2L70_A 2L71_A 2B4N_A 1GCN_A 1D0R_A 3IOL_B 2RRI_A ....
Probab=39.79 E-value=25 Score=20.58 Aligned_cols=15 Identities=27% Similarity=0.364 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHH
Q 032526 59 LVAVATQKFVAEVAT 73 (139)
Q Consensus 59 LiSLAaQKFisDIa~ 73 (139)
|=.++|+|||..+.+
T Consensus 14 L~~~aak~fl~~L~~ 28 (28)
T PF00123_consen 14 LDQLAAKKFLQWLMN 28 (28)
T ss_dssp HHHHHHHHHHHHHCH
T ss_pred HHHHHHHHHHHHHhC
Confidence 457899999988753
No 59
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=39.29 E-value=42 Score=31.29 Aligned_cols=42 Identities=17% Similarity=0.286 Sum_probs=34.4
Q ss_pred HHHHHHHHhCCCCCCChHH-----HHHHHHHHHHHHHHHHHHHHHHHH
Q 032526 38 ELVEHYLAKSGFQCPDVRL-----IRLVAVATQKFVAEVATDALQQCK 80 (139)
Q Consensus 38 ~Vt~yyL~~aGf~~~D~Rv-----~RLiSLAaQKFisDIa~DA~q~~k 80 (139)
=|++|.++-.+. -.|.+| -.|++++.+||-|-|+.-|+.|+-
T Consensus 375 YVIQHVie~g~~-~~~~~I~~~l~~~ll~~Sq~KfASnVVEk~~~~a~ 421 (503)
T KOG1488|consen 375 YVIQHVIEHGSP-YRDTIIIKCLLGNLLSMSQHKFASNVVEKAFLFAP 421 (503)
T ss_pred HHHHHHHhcCCh-hhhhhHHHHHHhhHHHHHHHHHHHHHHHHHHhhCC
Confidence 388999988877 445555 468999999999999999999873
No 60
>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=38.99 E-value=60 Score=25.40 Aligned_cols=42 Identities=19% Similarity=0.362 Sum_probs=31.9
Q ss_pred chHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHH
Q 032526 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVA 61 (139)
Q Consensus 18 d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiS 61 (139)
..-|..||..|- .|+||.++.+.++.-++.+..+.|+..|-.
T Consensus 76 a~lLK~fLReLP--epLip~~~~~~~~~~~~~~~~~~~~~~l~~ 117 (188)
T cd04383 76 AGVLKLYFRGLE--NPLFPKERFEDLMSCVKLENPTERVHQIRE 117 (188)
T ss_pred HHHHHHHHHhCC--CccCCHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence 456778888887 699999999999988877655666554433
No 61
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=38.91 E-value=1.1e+02 Score=21.17 Aligned_cols=61 Identities=31% Similarity=0.445 Sum_probs=37.4
Q ss_pred CHHHHHHHHHhCCCCCCChHH----HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHH
Q 032526 36 PDELVEHYLAKSGFQCPDVRL----IRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKAL 111 (139)
Q Consensus 36 PD~Vt~yyL~~aGf~~~D~Rv----~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL 111 (139)
|.+++...|+ ..|.....|| .+|++=-..-||.+-+.-|.+-++.. .+. .+++.|||...+
T Consensus 1 p~~li~rll~-~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e-------------~~~-~~le~e~LEki~ 65 (72)
T PF09415_consen 1 PPELIARLLH-EHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAE-------------GDE-GFLEVEHLEKIL 65 (72)
T ss_dssp -CHHHHHHHC-TTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHT-------------T-S-SEE-HHHHHHHC
T ss_pred ChHHHHHHHH-HHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-------------CCC-CCCCHHHHHHHH
Confidence 6778888999 8898777666 45666556667776666555433211 011 189999998765
No 62
>cd04376 RhoGAP_ARHGAP6 RhoGAP_ARHGAP6: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP6-like proteins. ArhGAP6 shows GAP activity towards RhoA, but not towards Cdc42 and Rac1. ArhGAP6 is often deleted in microphthalmia with linear skin defects syndrome (MLS); MLS is a severe X-linked developmental disorder. 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=37.41 E-value=1.2e+02 Score=24.21 Aligned_cols=40 Identities=30% Similarity=0.525 Sum_probs=29.9
Q ss_pred CchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHH
Q 032526 17 DDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (139)
Q Consensus 17 ~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RL 59 (139)
-..-|..||..|- .|+||.++.+.++.-...+ .+.|+..|
T Consensus 64 va~lLK~fLReLP--ePLi~~~~y~~~i~~~~~~-~~~~~~~l 103 (206)
T cd04376 64 VAALLKEFFRDMP--DPLLPRELYTAFIGTALLE-PDEQLEAL 103 (206)
T ss_pred HHHHHHHHHHhCC--CccCCHHHHHHHHHHHcCC-HHHHHHHH
Confidence 3456788888886 5999999999999887765 45555444
No 63
>PF05873 Mt_ATP-synt_D: ATP synthase D chain, mitochondrial (ATP5H); InterPro: IPR008689 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit D from the F0 complex in F-ATPases found in mitochondria. The D subunit is part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D []. There is no homologue of subunit D in bacterial or chloroplast F-ATPase, whose peripheral stalks are composed of one copy of the delta subunit (homologous to OSCP), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o); PDB: 2CLY_E 2WSS_U.
Probab=37.26 E-value=11 Score=29.55 Aligned_cols=33 Identities=15% Similarity=0.393 Sum_probs=0.0
Q ss_pred ceeeeHHHHHHHHHHhCcccCCCCccccCCCCC
Q 032526 99 RLILTMEDLSKALREYGVNVKHQEYFADNPSTG 131 (139)
Q Consensus 99 k~vLTmEDL~~AL~EyGInv~rP~Yy~d~~~~~ 131 (139)
--.|||||+..|-=|--.++.||.|+=..+..+
T Consensus 128 ~e~mT~dd~~~a~Pe~~~d~~k~~~wPh~p~~~ 160 (161)
T PF05873_consen 128 FEQMTVDDYAAAFPEIALDINKPTFWPHTPEEQ 160 (161)
T ss_dssp ---------------------------------
T ss_pred hHhCCHHHHHHhCcccccccCCCCCCCCCcccc
Confidence 348999999999999999999999987666544
No 64
>PF03793 PASTA: PASTA domain; InterPro: IPR005543 The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (P71584 from SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan. PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [].; GO: 0008658 penicillin binding; PDB: 2ZC3_C 1QME_A 1RP5_B 2Z2M_C 2Z2L_F 2ZC4_C 1QMF_A 3M9G_A 3PY9_A 1K25_B ....
Probab=37.07 E-value=20 Score=22.58 Aligned_cols=31 Identities=23% Similarity=0.409 Sum_probs=23.6
Q ss_pred eeHHHHHHHHHHhCcccCCCCccccCCCCCC
Q 032526 102 LTMEDLSKALREYGVNVKHQEYFADNPSTGM 132 (139)
Q Consensus 102 LTmEDL~~AL~EyGInv~rP~Yy~d~~~~~~ 132 (139)
++.+|....|+++|+++..-.++.+....|.
T Consensus 9 ~~~~~a~~~l~~~g~~~~~~~~~~~~~~~g~ 39 (63)
T PF03793_consen 9 MTYDEAKSILEAAGLTVNVVEEYSDSVPKGT 39 (63)
T ss_dssp SBHHHHHHHHHHTT-EEEEEEEEESSSSTTS
T ss_pred CcHHHHHHHHHHCCCEEEEEEEecCCCCCCE
Confidence 6889999999999998777776666665553
No 65
>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=34.96 E-value=77 Score=24.82 Aligned_cols=44 Identities=23% Similarity=0.313 Sum_probs=33.1
Q ss_pred CchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHH
Q 032526 17 DDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAV 62 (139)
Q Consensus 17 ~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSL 62 (139)
-..-|+.||..|- .|+||.++.+-+++-.|.+....++..+.++
T Consensus 70 va~lLK~fLReLP--ePLi~~~~y~~~~~~~~~~~~~~~i~~~~~l 113 (186)
T cd04406 70 IASVFKQWLRDLP--NPLMTFELYEEFLRAMGLQERRETVRGVYSV 113 (186)
T ss_pred HHHHHHHHHHhCC--CccCCHHHHHHHHHHHhcccHHHHHHHHHHH
Confidence 3456788898887 6999999999999988876555566554443
No 66
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=34.26 E-value=1.8e+02 Score=20.92 Aligned_cols=31 Identities=16% Similarity=0.252 Sum_probs=27.4
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032526 50 QCPDVRLIRLVAVATQKFVAEVATDALQQCK 80 (139)
Q Consensus 50 ~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~k 80 (139)
+-+.+..++||-=...-||+++++.|.+.+.
T Consensus 19 ~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~ 49 (92)
T cd07978 19 QNPLPETVDLLEDIVVEYIIELCHKAAEVAQ 49 (92)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4577888999999999999999999999874
No 67
>cd04398 RhoGAP_fRGD1 RhoGAP_fRGD1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal RGD1-like proteins. Yeast Rgd1 is a GAP protein for Rho3 and Rho4 and plays a role in low-pH response. 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=33.97 E-value=89 Score=24.07 Aligned_cols=44 Identities=16% Similarity=0.224 Sum_probs=31.1
Q ss_pred CchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHH
Q 032526 17 DDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAV 62 (139)
Q Consensus 17 ~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSL 62 (139)
-..-|..||..|- .|+||.++.+.++..+..+....|+..+-.+
T Consensus 76 va~~LK~fLreLp--~pLi~~~~~~~~~~~~~~~~~~~~~~~l~~l 119 (192)
T cd04398 76 VASLLKLFFRELP--EPLLTKALSREFIEAAKIEDESRRRDALHGL 119 (192)
T ss_pred HHHHHHHHHHhCC--CccCCHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 3456788888886 6999999999998876655444455544443
No 68
>cd04869 ACT_GcvR_2 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the second of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR in
Probab=33.78 E-value=28 Score=22.62 Aligned_cols=25 Identities=8% Similarity=0.181 Sum_probs=21.1
Q ss_pred eHHHHHHHHHHhCcccCCCCccccC
Q 032526 103 TMEDLSKALREYGVNVKHQEYFADN 127 (139)
Q Consensus 103 TmEDL~~AL~EyGInv~rP~Yy~d~ 127 (139)
.+.+++..|.++|+||..=..+++.
T Consensus 12 iv~~it~~l~~~~~nI~~~~~~~~~ 36 (81)
T cd04869 12 IVHEVTQFLAQRNINIEDLSTETYS 36 (81)
T ss_pred HHHHHHHHHHHcCCCeEEeEeeeec
Confidence 3678999999999999988777765
No 69
>cd04382 RhoGAP_MgcRacGAP RhoGAP_MgcRacGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in MgcRacGAP proteins. MgcRacGAP plays an important dual role in cytokinesis: i) it is part of centralspindlin-complex, together with the mitotic kinesin MKLP1, which is critical for the structure of the central spindle by promoting microtuble bundling. ii) after phosphorylation by aurora B MgcRacGAP becomes an effective regulator of RhoA and plays an important role in the assembly of the contractile ring and the initiation of cytokinesis. MgcRacGAP-like proteins contain a N-terminal C1-like domain, and a C-terminal RhoGAP 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
Probab=33.58 E-value=79 Score=25.02 Aligned_cols=42 Identities=24% Similarity=0.222 Sum_probs=29.8
Q ss_pred CCchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHH
Q 032526 16 DDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (139)
Q Consensus 16 ~~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RL 59 (139)
.-..-|..||..|-+ |+||.+..+.+++-+.....+.++..+
T Consensus 71 ~vaslLK~fLReLPe--PLi~~~~y~~~~~~~~~~~~~~~~~~l 112 (193)
T cd04382 71 VICGCLKDFLRSLKE--PLITFALWKEFMEAAEILDEDNSRAAL 112 (193)
T ss_pred HHHHHHHHHHHhCCC--cCCCHHHHHHHHHHHHcCCHHHHHHHH
Confidence 334567888888875 999999999998876655444444443
No 70
>cd04870 ACT_PSP_1 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_1 CD includes the first of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=33.51 E-value=33 Score=22.56 Aligned_cols=18 Identities=22% Similarity=0.326 Sum_probs=15.3
Q ss_pred HHHHHHHHHHhCcccCCC
Q 032526 104 MEDLSKALREYGVNVKHQ 121 (139)
Q Consensus 104 mEDL~~AL~EyGInv~rP 121 (139)
+.+++.+|+++|+||..=
T Consensus 13 v~~vt~~la~~~~nI~dl 30 (75)
T cd04870 13 TSALTEVLAAHGVRILDV 30 (75)
T ss_pred HHHHHHHHHHCCCCEEec
Confidence 578999999999998643
No 71
>cd04385 RhoGAP_ARAP RhoGAP_ARAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in ARAPs. ARAPs (also known as centaurin deltas) contain, besides the RhoGAP domain, an Arf GAP, ankyrin repeat ras-associating, and PH domains. Since their ArfGAP activity is PIP3-dependent, ARAPs are considered integration points for phosphoinositide, Arf and Rho signaling. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=33.29 E-value=83 Score=24.43 Aligned_cols=42 Identities=24% Similarity=0.423 Sum_probs=30.3
Q ss_pred chHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHH
Q 032526 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVA 61 (139)
Q Consensus 18 d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiS 61 (139)
..-|..||..|- .|+||.++.+.++.-+.....+.|+..|-.
T Consensus 73 a~llK~yLreLP--~pLi~~~~~~~~~~~~~~~~~~~~i~~l~~ 114 (184)
T cd04385 73 ADVLKRFLRDLP--DPLLTSELHAEWIEAAELENKDERIARYKE 114 (184)
T ss_pred HHHHHHHHHhCC--CccCCHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 455788888887 799999999999887655544455544433
No 72
>cd04435 DEP_fRom2 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) Rom2-like proteins. Rom2-like proteins share a common domain architecture, containing, beside the RhoGEF domain, a DEP, a PH (pleckstrin homology) and a CNH domain. Rom2, a yeast GEF for Rho1 and Rho2, is involved in mediating stress response via the Ras-cAMP pathway and also plays a role in mediating resistance to sphingolipid disturbances.
Probab=33.21 E-value=63 Score=23.50 Aligned_cols=23 Identities=35% Similarity=0.510 Sum_probs=19.6
Q ss_pred CChHHHHHH--HHHHHHHHHHHHHH
Q 032526 52 PDVRLIRLV--AVATQKFVAEVATD 74 (139)
Q Consensus 52 ~D~Rv~RLi--SLAaQKFisDIa~D 74 (139)
+|.++.=|| ||=+|||.-||-=|
T Consensus 45 ~DRnlALllgRsLdaQkfFhdV~y~ 69 (82)
T cd04435 45 SDRNLALLLGRSLDAQKFFHDVTYD 69 (82)
T ss_pred ccHHHHHHHHHHHHHhHhhhhcccC
Confidence 899998888 57899999998654
No 73
>KOG0482 consensus DNA replication licensing factor, MCM7 component [Replication, recombination and repair]
Probab=33.19 E-value=62 Score=31.26 Aligned_cols=38 Identities=18% Similarity=0.209 Sum_probs=29.7
Q ss_pred CCCCCCCCCCCchHHHHHHHhcccCCCCCCHHHHHHHH
Q 032526 7 FQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYL 44 (139)
Q Consensus 7 ~~~~~~~~~~~d~~L~efL~~LddY~P~IPD~Vt~yyL 44 (139)
.|....-...+-..+++.+.....|.|++|++|.+|+-
T Consensus 546 ~qp~~~fepl~~~~mR~yI~~ak~~~P~vp~~l~dyi~ 583 (721)
T KOG0482|consen 546 EQPPLDFEPLDPNLMRRYISLAKRKNPVVPEALADYIT 583 (721)
T ss_pred CCCCccCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHH
Confidence 34443444456778899999999999999999999874
No 74
>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden
Probab=32.83 E-value=33 Score=21.44 Aligned_cols=19 Identities=21% Similarity=0.385 Sum_probs=15.6
Q ss_pred eHHHHHHHHHHhCcccCCC
Q 032526 103 TMEDLSKALREYGVNVKHQ 121 (139)
Q Consensus 103 TmEDL~~AL~EyGInv~rP 121 (139)
.+.++...|+++|+||..=
T Consensus 12 ~l~~i~~~l~~~~inI~~~ 30 (73)
T cd04902 12 VIGKVGTILGEAGINIAGM 30 (73)
T ss_pred HHHHHHHHHHHcCcChhhe
Confidence 4677899999999999653
No 75
>cd04375 RhoGAP_DLC1 RhoGAP_DLC1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of DLC1-like proteins. DLC1 shows in vitro GAP activity towards RhoA and CDC42. Beside its C-terminal GAP domain, DLC1 also contains a SAM (sterile alpha motif) and a START (StAR-related lipid transfer action) domain. DLC1 has tumor suppressor activity in cell culture. 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=32.37 E-value=77 Score=25.60 Aligned_cols=45 Identities=20% Similarity=0.319 Sum_probs=32.5
Q ss_pred CCCchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHH
Q 032526 15 HDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVA 61 (139)
Q Consensus 15 ~~~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiS 61 (139)
+.-...|..|+..|-+ |+||.++.+.+++-......+.|+..|-.
T Consensus 73 ~~va~lLK~flReLPe--PLlt~~l~~~fi~~~~~~~~~~~~~~l~~ 117 (220)
T cd04375 73 YDVADMLKQYFRDLPE--PLLTNKLSETFIAIFQYVPKEQRLEAVQC 117 (220)
T ss_pred HHHHHHHHHHHHhCCC--ccCCHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence 3345667889988875 99999999998876655555666655443
No 76
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=32.19 E-value=2.2e+02 Score=21.34 Aligned_cols=76 Identities=18% Similarity=0.201 Sum_probs=52.5
Q ss_pred cccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHH
Q 032526 28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDL 107 (139)
Q Consensus 28 LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL 107 (139)
|.|-..-|....+.-.-.++|+.-----+..=+-=++.-||.|++.+|..|.- .-+|-+.|--|+
T Consensus 23 LsDnIqgitKpaIRRlARr~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~---------------HAKRKTvT~~dv 87 (103)
T KOG3467|consen 23 LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTE---------------HAKRKTVTAMDV 87 (103)
T ss_pred HHhhccccchHHHHHHHHhcCcchhchhhHHHHHHHHHHHHHHHHHHHHHHHh---------------hhhhceeeHHHH
Confidence 33444455566677778888875333333344455788899999999998863 122347899999
Q ss_pred HHHHHHhCccc
Q 032526 108 SKALREYGVNV 118 (139)
Q Consensus 108 ~~AL~EyGInv 118 (139)
.-+|+..|+..
T Consensus 88 v~~LKR~G~~~ 98 (103)
T KOG3467|consen 88 VYALKRQGRTL 98 (103)
T ss_pred HHHHHHcCcee
Confidence 99999999863
No 77
>smart00428 H3 Histone H3.
Probab=31.91 E-value=1.5e+02 Score=22.07 Aligned_cols=45 Identities=18% Similarity=0.181 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHHHhCcc
Q 032526 58 RLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGVN 117 (139)
Q Consensus 58 RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~EyGIn 117 (139)
-.+.-|+..|+..+..||..++.. -+|.||+.+|+.-|..=.|.+
T Consensus 60 ~aLQeasE~ylv~lfeda~~~a~H---------------AkRvTl~~kDi~La~rir~~~ 104 (105)
T smart00428 60 MALQEAAEAYLVGLFEDTNLLAIH---------------AKRVTIMPKDIQLARRIRGER 104 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH---------------hCCccCcHhhHHHHHHHhccC
Confidence 455667888999999998876632 246899999998887666654
No 78
>cd05832 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera
Probab=30.66 E-value=1.2e+02 Score=22.77 Aligned_cols=51 Identities=24% Similarity=0.331 Sum_probs=41.3
Q ss_pred HHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHH
Q 032526 23 EFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDA 75 (139)
Q Consensus 23 efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA 75 (139)
-+|..+..- .|-.+-+..+|..+|.++.+.|++-|++...-|=|.+++..+
T Consensus 7 aLLL~~~G~--eITae~I~~IL~AAGveVd~~~~~ala~aL~gkdIeElIa~~ 57 (106)
T cd05832 7 ALLLHYAGK--EINEENLKKVLEAAGIEVDEARVKALVAALEEVNIDEAIKKA 57 (106)
T ss_pred HHHHHhcCC--CCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHHhc
Confidence 345455554 466788999999999999999999999998888888888654
No 79
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=30.57 E-value=87 Score=26.32 Aligned_cols=83 Identities=17% Similarity=0.179 Sum_probs=48.2
Q ss_pred chHHHHHHHhcc--------cCCCCCCHHHHHHHHHhCCC-CCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 032526 18 DAALTEFLSSLM--------GYTPTIPDELVEHYLAKSGF-QCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVK 88 (139)
Q Consensus 18 d~~L~efL~~Ld--------dY~P~IPD~Vt~yyL~~aGf-~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~ 88 (139)
...|..|+.... .+...+|=+=+..+|..-=- ..=-.-.-=|++-|++-||.++..-+..|.
T Consensus 50 ~~~l~~fw~~~~~e~e~~~d~~~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~T--------- 120 (236)
T KOG1657|consen 50 RQQLQSFWSKQAIEKEGQLDFKNHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHT--------- 120 (236)
T ss_pred hHHHHhhhhccccccccccchhhccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhh---------
Confidence 456777776552 24555555555444432100 000011234678899999999887655543
Q ss_pred hhhhccccccceeeeHHHHHHHHHHhC
Q 032526 89 DKRDKQQKDKRLILTMEDLSKALREYG 115 (139)
Q Consensus 89 ~k~~~~~kd~k~vLTmEDL~~AL~EyG 115 (139)
...+|-+|+-.||++|+....
T Consensus 121 ------ee~~rrtl~~sdia~av~~s~ 141 (236)
T KOG1657|consen 121 ------EENKRRTLQKSDIAAAVTQSE 141 (236)
T ss_pred ------cccccccchHHHHHHHhccCC
Confidence 244556777799999988643
No 80
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=29.41 E-value=1.4e+02 Score=24.38 Aligned_cols=67 Identities=21% Similarity=0.324 Sum_probs=42.8
Q ss_pred CCHHHHHHHHHhCCCCCCChHHHH----HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHH
Q 032526 35 IPDELVEHYLAKSGFQCPDVRLIR----LVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKA 110 (139)
Q Consensus 35 IPD~Vt~yyL~~aGf~~~D~Rv~R----LiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~A 110 (139)
+|-+++-....++==+| +..|-+ -|+=||-=||.=+..-|-++|+ +.+|-+|+-.|+-+|
T Consensus 11 lP~AiI~rlvke~l~E~-~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~---------------~q~rKt~sadDVl~a 74 (172)
T KOG0870|consen 11 LPNAIITRLVKEVLPES-NVSISKEARLAIARAATVFVIFLTSVSNEIAK---------------DQKRKTISADDVLKA 74 (172)
T ss_pred ccHHHHHHHHHHhCccc-cccccHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------hcccCcccHHHHHHH
Confidence 57777776555554444 333322 3555666677666666666663 334558999999999
Q ss_pred HHHhCcc
Q 032526 111 LREYGVN 117 (139)
Q Consensus 111 L~EyGIn 117 (139)
|.|.|-.
T Consensus 75 L~Eiefs 81 (172)
T KOG0870|consen 75 LDEIEFS 81 (172)
T ss_pred HHHhchH
Confidence 9998753
No 81
>COG0576 GrpE Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=29.23 E-value=1.5e+02 Score=23.93 Aligned_cols=92 Identities=22% Similarity=0.274 Sum_probs=57.1
Q ss_pred hHHHHHHHhcccCCCCCCHHHHHHHHHh-CCCCCC----ChHHHHHHHHHHHHHHHHHH--HHHHHHHHHHhhhhhhhhh
Q 032526 19 AALTEFLSSLMGYTPTIPDELVEHYLAK-SGFQCP----DVRLIRLVAVATQKFVAEVA--TDALQQCKARQAAVVKDKR 91 (139)
Q Consensus 19 ~~L~efL~~LddY~P~IPD~Vt~yyL~~-aGf~~~----D~Rv~RLiSLAaQKFisDIa--~DA~q~~kiR~~~~~~~k~ 91 (139)
..+.++-.++++ +.+.||+. +=|+.- -..+-....-|.+||+.|+. .|.+..+- .......+.
T Consensus 43 ~~i~~Le~q~~e--------~~~~~lr~~Ae~eN~rkR~~re~e~~~k~a~e~~~~dlLpviDnlerAl-~~~~~~~d~- 112 (193)
T COG0576 43 QEIAELEAQLEE--------LKDKYLRAQAEFENLRKRTEREREEAKKYAIEKFAKDLLPVIDNLERAL-EAAEDDKDP- 112 (193)
T ss_pred HHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-Hhcccccch-
Confidence 345566666666 66777754 344432 23344567889999999996 57777552 111110000
Q ss_pred hccccccceeeeHHHHHHHHHHhCcccCCC
Q 032526 92 DKQQKDKRLILTMEDLSKALREYGVNVKHQ 121 (139)
Q Consensus 92 ~~~~kd~k~vLTmEDL~~AL~EyGInv~rP 121 (139)
...=-..+-+|.+.|..+|..|||..=.|
T Consensus 113 -~~~l~~Gvem~~~~l~~~L~k~Gv~~i~~ 141 (193)
T COG0576 113 -EKALLEGVEMTLDQLLDALEKLGVEEIGP 141 (193)
T ss_pred -HHHHHHHHHHHHHHHHHHHHHCCCEEeCC
Confidence 00001348899999999999999988777
No 82
>smart00324 RhoGAP GTPase-activator protein for Rho-like GTPases. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases. etter domain limits and outliers.
Probab=28.97 E-value=1.2e+02 Score=22.46 Aligned_cols=37 Identities=32% Similarity=0.459 Sum_probs=27.1
Q ss_pred chHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHH
Q 032526 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (139)
Q Consensus 18 d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (139)
..-|..||..|. .|+||.+..+.++.-.+-...+.++
T Consensus 60 a~~lK~~Lr~Lp--~pli~~~~~~~~~~~~~~~~~~~~~ 96 (174)
T smart00324 60 AGLLKLFLRELP--EPLIPYELYEEFIEAAKVEDETERL 96 (174)
T ss_pred HHHHHHHHHhCC--CccCCHHHHHHHHHHHhCCCHHHHH
Confidence 455778888776 6999999999999877654333443
No 83
>PRK03341 arginine repressor; Provisional
Probab=28.64 E-value=42 Score=26.68 Aligned_cols=21 Identities=19% Similarity=0.390 Sum_probs=17.3
Q ss_pred ceeeeHHHHHHHHHHhCcccC
Q 032526 99 RLILTMEDLSKALREYGVNVK 119 (139)
Q Consensus 99 k~vLTmEDL~~AL~EyGInv~ 119 (139)
+-.-|.|||...|++.||+|.
T Consensus 27 ~~i~tQ~eL~~~L~~~Gi~vT 47 (168)
T PRK03341 27 QSVRSQAELAALLADEGIEVT 47 (168)
T ss_pred CCCccHHHHHHHHHHcCCccc
Confidence 346788999999999999874
No 84
>cd04404 RhoGAP-p50rhoGAP RhoGAP-p50rhoGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p50RhoGAP-like proteins; p50RhoGAP, also known as RhoGAP-1, contains a C-terminal RhoGAP domain and an N-terminal Sec14 domain which binds phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3). It is ubiquitously expressed and preferentially active on Cdc42. This subgroup also contains closely related ARHGAP8. 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=28.52 E-value=1.2e+02 Score=23.50 Aligned_cols=39 Identities=21% Similarity=0.312 Sum_probs=27.7
Q ss_pred chHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHH
Q 032526 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (139)
Q Consensus 18 d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RL 59 (139)
..-|..|+..|-+ |+||.++.+..+.-...+ .+.++..+
T Consensus 79 a~~LK~~lr~Lp~--pLi~~~~~~~l~~~~~~~-~~~~~~~~ 117 (195)
T cd04404 79 AVILKTFLRELPE--PLLTFDLYDDIVGFLNVD-KEERVERV 117 (195)
T ss_pred HHHHHHHHHhCCC--ccCCHHHHHHHHHHHcCC-HHHHHHHH
Confidence 4568889999985 999999988888765543 34444433
No 85
>cd06102 citrate_synt_like_2 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and
Probab=28.42 E-value=1.8e+02 Score=24.84 Aligned_cols=45 Identities=20% Similarity=0.183 Sum_probs=31.3
Q ss_pred HHHHHhcccCCCCCCHHHHHHHHHhC----CC-----CCCChHHHHHHHHHHHHHH
Q 032526 22 TEFLSSLMGYTPTIPDELVEHYLAKS----GF-----QCPDVRLIRLVAVATQKFV 68 (139)
Q Consensus 22 ~efL~~LddY~P~IPD~Vt~yyL~~a----Gf-----~~~D~Rv~RLiSLAaQKFi 68 (139)
.+++..+.+ +.=+++++..+|++. || ...|||.+.|..++-+-+.
T Consensus 154 ~~~l~e~~~--~~~~~~~v~~~l~~g~~ipGFGH~vy~~~DPRa~~L~~~~~~~~~ 207 (282)
T cd06102 154 EALLDEALR--AGDAEAAVRERLRRGEALPGFGHPLYPDGDPRAAALLAALRPLGP 207 (282)
T ss_pred HHHHHHhcC--CccHHHHHHHHHHcCCcccCCCCCCCCCCCccHHHHHHHHHHHhh
Confidence 344444433 334477777888875 88 4679999999999988654
No 86
>cd04873 ACT_UUR-ACR-like ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD. This ACT domain family, ACT_UUR_ACR-like, includes the two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the four ACT domains of a novel protein composed almost entirely of ACT domain repeats (the ACR protein) and like proteins. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. This CD also includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein and related domains, as well as, the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted t
Probab=28.34 E-value=45 Score=20.48 Aligned_cols=18 Identities=22% Similarity=0.661 Sum_probs=15.5
Q ss_pred eHHHHHHHHHHhCcccCC
Q 032526 103 TMEDLSKALREYGVNVKH 120 (139)
Q Consensus 103 TmEDL~~AL~EyGInv~r 120 (139)
.+.||..+|.++|++|..
T Consensus 13 ~l~~i~~~l~~~~~~I~~ 30 (70)
T cd04873 13 LLADITRVLADLGLNIHD 30 (70)
T ss_pred HHHHHHHHHHHCCCeEEE
Confidence 468999999999999953
No 87
>COG3830 ACT domain-containing protein [Signal transduction mechanisms]
Probab=28.30 E-value=41 Score=24.73 Aligned_cols=17 Identities=35% Similarity=0.552 Sum_probs=14.4
Q ss_pred HHHHHHHHHHhCcccCC
Q 032526 104 MEDLSKALREYGVNVKH 120 (139)
Q Consensus 104 mEDL~~AL~EyGInv~r 120 (139)
+-+++.+|+|+||||-.
T Consensus 17 va~is~vLAe~~vNIld 33 (90)
T COG3830 17 VAAVSRVLAEHGVNILD 33 (90)
T ss_pred hHHHHHHHHHcCCcEEE
Confidence 46899999999999853
No 88
>PF05931 AgrD: Staphylococcal AgrD protein; InterPro: IPR009229 This family consists of several AgrD proteins from many Staphylococcus species. The agr locus was initially described in Staphylococcus aureus as an element controlling the production of exoproteins implicated in virulence. Its pattern of action has been shown to be complex, upregulating certain extracellular toxins and enzymes expressed post-exponentially and repressing some exponential-phase surface components. AgrD encodes the precursor of the autoinducing peptide (AIP).The AIP derived from AgrD by the action of AgrB interacts with AgrC in the membrane to activate AgrA, which upregulates transcription both from promoter P2, amplifying the response, and from P3, initiating the production of a novel effector: RNAIII. In S. aureus, delta-hemolysin is the only translation product of RNA III and is not involved in the regulatory functions of the transcript, which is therefore the primary agent for modulating the expression of other operons controlled by agr [].
Probab=28.25 E-value=33 Score=22.21 Aligned_cols=12 Identities=42% Similarity=0.924 Sum_probs=10.2
Q ss_pred CCCCCHHHHHHH
Q 032526 32 TPTIPDELVEHY 43 (139)
Q Consensus 32 ~P~IPD~Vt~yy 43 (139)
-|.||.|+|+-|
T Consensus 33 EpEVP~ELt~l~ 44 (45)
T PF05931_consen 33 EPEVPKELTKLY 44 (45)
T ss_pred CCcCcHHHHhhc
Confidence 589999999865
No 89
>PF02906 Fe_hyd_lg_C: Iron only hydrogenase large subunit, C-terminal domain; InterPro: IPR004108 Proteins containing this domain may be involved in the mechanism of biological hydrogen activation and contain 4FE-4S clusters. They can use molecular hydrogen for the reduction of a variety of substances.; PDB: 3LX4_A 1HFE_L 1GX7_A 1E08_A 1C4C_A 1FEH_A 3C8Y_A 1C4A_A.
Probab=27.97 E-value=55 Score=27.26 Aligned_cols=26 Identities=35% Similarity=0.631 Sum_probs=20.2
Q ss_pred ccceeeeHHHHHHHHHHhCcccCCCC
Q 032526 97 DKRLILTMEDLSKALREYGVNVKHQE 122 (139)
Q Consensus 97 d~k~vLTmEDL~~AL~EyGInv~rP~ 122 (139)
+--.|||+++|..-|.+.||++.+-+
T Consensus 150 ~vD~VLT~~El~~~l~~~~i~~~~~~ 175 (285)
T PF02906_consen 150 DVDYVLTFEELAELLKEKGIDLAELE 175 (285)
T ss_dssp SSSEEEEHHHHHHHHHHTT--GGGSS
T ss_pred ccCEechHHHHHHHHHHcCCChhHCC
Confidence 34689999999999999999987643
No 90
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=27.54 E-value=45 Score=20.02 Aligned_cols=19 Identities=21% Similarity=0.396 Sum_probs=16.0
Q ss_pred eHHHHHHHHHHhCcccCCC
Q 032526 103 TMEDLSKALREYGVNVKHQ 121 (139)
Q Consensus 103 TmEDL~~AL~EyGInv~rP 121 (139)
.+.++...|+++|+||..=
T Consensus 12 ~l~~i~~~l~~~~~nI~~~ 30 (71)
T cd04879 12 VIGKVGTILGEHGINIAAM 30 (71)
T ss_pred HHHHHHHHHHhcCCCeeeE
Confidence 4678999999999999643
No 91
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=27.45 E-value=4.4e+02 Score=23.42 Aligned_cols=33 Identities=9% Similarity=0.216 Sum_probs=22.6
Q ss_pred CCchHHHHHHHhcc-cCCCCCCHHHHHHHHHhCC
Q 032526 16 DDDAALTEFLSSLM-GYTPTIPDELVEHYLAKSG 48 (139)
Q Consensus 16 ~~d~~L~efL~~Ld-dY~P~IPD~Vt~yyL~~aG 48 (139)
.+..+..++|.++- ...=.|||+|++|+....+
T Consensus 263 pd~e~r~~IL~~~~~~~~~~l~~ev~~~Ia~~~~ 296 (440)
T PRK14088 263 PDEETRKKIARKMLEIEHGELPEEVLNFVAENVD 296 (440)
T ss_pred CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHhccc
Confidence 34556666666653 3345589999999988864
No 92
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=26.44 E-value=57 Score=20.82 Aligned_cols=18 Identities=28% Similarity=0.521 Sum_probs=16.1
Q ss_pred eeeHHHHHHHHHHhCccc
Q 032526 101 ILTMEDLSKALREYGVNV 118 (139)
Q Consensus 101 vLTmEDL~~AL~EyGInv 118 (139)
.|+-++|..-|.+||+..
T Consensus 5 ~LSd~eL~~~L~~~G~~~ 22 (44)
T smart00540 5 RLSDAELRAELKQYGLPP 22 (44)
T ss_pred HcCHHHHHHHHHHcCCCC
Confidence 588899999999999975
No 93
>PRK00441 argR arginine repressor; Provisional
Probab=26.22 E-value=38 Score=26.22 Aligned_cols=22 Identities=32% Similarity=0.510 Sum_probs=18.4
Q ss_pred eeeeHHHHHHHHHHhCcccCCC
Q 032526 100 LILTMEDLSKALREYGVNVKHQ 121 (139)
Q Consensus 100 ~vLTmEDL~~AL~EyGInv~rP 121 (139)
-..|.+||..+|++.|++|..+
T Consensus 17 ~~~~q~eL~~~L~~~G~~vSqa 38 (149)
T PRK00441 17 EIETQEELAEELKKMGFDVTQA 38 (149)
T ss_pred CCCcHHHHHHHHHhcCCCcCHH
Confidence 3668999999999999998643
No 94
>PHA02554 13 neck protein; Provisional
Probab=26.09 E-value=84 Score=27.82 Aligned_cols=81 Identities=20% Similarity=0.222 Sum_probs=49.3
Q ss_pred CCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHH
Q 032526 31 YTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKA 110 (139)
Q Consensus 31 Y~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~A 110 (139)
|.|.=|-++.+|+|+|-|.+.-++.| +.--|.|.+.+|+|+-.=..- +. -..-=-+..||-||...
T Consensus 3 ~~~~sp~eLkD~iLRrLGAPii~Iev-------t~dQi~D~I~rALely~EYH~----dG--~~k~y~~~~~t~e~~~~- 68 (311)
T PHA02554 3 YNPNNPRELKDYILRRLGAPIINVEV-------TEDQIYDCIQRALELYGEYHY----DG--VNKGYLKFKVTEEQART- 68 (311)
T ss_pred CCCCCHHHHHHHHHHhcCCCeeEeec-------CHHHHHHHHHHHHHHHHHHhc----cc--hhceeEEEEccHHHhcc-
Confidence 57888999999999999998755554 345677888888876532211 00 00111356666555433
Q ss_pred HHHhCcccCCCCccccCC
Q 032526 111 LREYGVNVKHQEYFADNP 128 (139)
Q Consensus 111 L~EyGInv~rP~Yy~d~~ 128 (139)
=+|+++.++-|..+.
T Consensus 69 ---g~~d~~~~~vfavt~ 83 (311)
T PHA02554 69 ---GVFDLSGSNVFAVTK 83 (311)
T ss_pred ---cceeccccccceeee
Confidence 255566666555443
No 95
>PF08887 GAD-like: GAD-like domain; InterPro: IPR014983 This domain is functionally uncharacterised, but it appears to be distantly related to the GAD domain IPR004115 from INTERPRO.
Probab=25.98 E-value=59 Score=24.09 Aligned_cols=22 Identities=36% Similarity=0.649 Sum_probs=17.0
Q ss_pred cccCCCCCCHHHHHHHHHhCCCC
Q 032526 28 LMGYTPTIPDELVEHYLAKSGFQ 50 (139)
Q Consensus 28 LddY~P~IPD~Vt~yyL~~aGf~ 50 (139)
++.|...+|+++++| .+.-||-
T Consensus 25 I~kyk~~lP~~Ll~~-W~~~G~g 46 (109)
T PF08887_consen 25 IEKYKGKLPDELLEY-WKEYGFG 46 (109)
T ss_pred HHHhcCCCcHHHHHH-HHHcCCc
Confidence 367899999999986 4667774
No 96
>TIGR02512 Fe_only_hydrog hydrogenases, Fe-only. This model describes iron-only hydrogenases of anaerobic and microaerophilic bacteria and protozoa. This model is narrower, and covers a longer stretch of sequence, than Pfam model pfam02906. This family represents a division among families that belong to pfam02906, which also includes proteins such as nuclear prelamin A recognition factor in animals. Note that this family shows some heterogeneity in terms of periplasmic, cytosolic, or hydrogenosome location, NAD or NADP dependence, and overal protein protein length.
Probab=25.94 E-value=55 Score=28.34 Aligned_cols=24 Identities=25% Similarity=0.553 Sum_probs=20.8
Q ss_pred ccceeeeHHHHHHHHHHhCcccCC
Q 032526 97 DKRLILTMEDLSKALREYGVNVKH 120 (139)
Q Consensus 97 d~k~vLTmEDL~~AL~EyGInv~r 120 (139)
+--.|||+++|..-|++.||++..
T Consensus 236 ~vD~vlT~~El~~~~~~~~i~~~~ 259 (374)
T TIGR02512 236 DVDAVLTTRELARMIKEAGIDFAK 259 (374)
T ss_pred cccEEeeHHHHHHHHHHcCCChhh
Confidence 445799999999999999999854
No 97
>COG1438 ArgR Arginine repressor [Transcription]
Probab=25.69 E-value=47 Score=26.28 Aligned_cols=20 Identities=40% Similarity=0.574 Sum_probs=16.6
Q ss_pred eeeHHHHHHHHHHhCcccCC
Q 032526 101 ILTMEDLSKALREYGVNVKH 120 (139)
Q Consensus 101 vLTmEDL~~AL~EyGInv~r 120 (139)
.-|-|+|...|+|+||.|..
T Consensus 20 i~TQ~Elv~~L~~~Gi~vTQ 39 (150)
T COG1438 20 ISTQEELVELLQEEGIEVTQ 39 (150)
T ss_pred CCCHHHHHHHHHHcCCeEeh
Confidence 56889999999999998753
No 98
>cd04373 RhoGAP_p190 RhoGAP_p190: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p190-like proteins. p190, also named RhoGAP5, plays a role in neuritogenesis and axon branch stability. p190 shows a preference for Rho, over Rac and Cdc42, and consists of an N-terminal GTPase domain and a C-terminal GAP domain. The central portion of p190 contains important regulatory phosphorylation sites. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=25.24 E-value=1.1e+02 Score=23.88 Aligned_cols=43 Identities=26% Similarity=0.305 Sum_probs=31.1
Q ss_pred CchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHH
Q 032526 17 DDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVA 61 (139)
Q Consensus 17 ~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiS 61 (139)
-..-|..||..|- .|+||-++.+.+++-.+-.....|+..+-.
T Consensus 71 va~~lK~fLreLP--ePlip~~~~~~~~~~~~~~~~~~~i~~l~~ 113 (185)
T cd04373 71 VAGALKSFFSELP--DPLIPYSMHLELVEAAKINDREQRLHALKE 113 (185)
T ss_pred HHHHHHHHHhcCC--chhccHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 3456788888887 799999999999887775544456555443
No 99
>PHA02517 putative transposase OrfB; Reviewed
Probab=25.22 E-value=1.1e+02 Score=24.59 Aligned_cols=47 Identities=15% Similarity=0.065 Sum_probs=37.0
Q ss_pred CchHHHHHHHhc-ccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHH
Q 032526 17 DDAALTEFLSSL-MGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVA 63 (139)
Q Consensus 17 ~d~~L~efL~~L-ddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLA 63 (139)
.+..|.+++..+ .+..|..--.-+...|.+-|+..+..+|.|++.-+
T Consensus 27 ~~~~l~~~I~~i~~~~~~~~G~r~I~~~L~~~g~~vs~~tV~Rim~~~ 74 (277)
T PHA02517 27 HDDWLKSEILRVYDENHQVYGVRKVWRQLNREGIRVARCTVGRLMKEL 74 (277)
T ss_pred hhHHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCcccCHHHHHHHHHHc
Confidence 466777777777 46677877777777889999999999999988654
No 100
>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]
Probab=25.14 E-value=99 Score=30.29 Aligned_cols=41 Identities=27% Similarity=0.368 Sum_probs=33.1
Q ss_pred HHHHHHHHhCCCCC-----CChHHH-HHHHHHHHHHHHHHHHHHHHHH
Q 032526 38 ELVEHYLAKSGFQC-----PDVRLI-RLVAVATQKFVAEVATDALQQC 79 (139)
Q Consensus 38 ~Vt~yyL~~aGf~~-----~D~Rv~-RLiSLAaQKFisDIa~DA~q~~ 79 (139)
-|++|+|.. |.++ .++.+. |++.|-++||=|-|+..+..||
T Consensus 635 yvvq~il~~-g~~~~k~~i~~~~l~~~v~elS~~kfaSnvVeK~i~~~ 681 (777)
T COG5099 635 YVVQHILDN-GAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIKYA 681 (777)
T ss_pred hhhhHHhhc-CCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 378888875 5544 356777 9999999999999999998876
No 101
>PRK05066 arginine repressor; Provisional
Probab=25.08 E-value=52 Score=25.78 Aligned_cols=20 Identities=20% Similarity=0.358 Sum_probs=16.3
Q ss_pred eeeeHHHHHHHHHHhCcc-cC
Q 032526 100 LILTMEDLSKALREYGVN-VK 119 (139)
Q Consensus 100 ~vLTmEDL~~AL~EyGIn-v~ 119 (139)
-+=|-|||...|+++||+ |.
T Consensus 22 ~I~tQeeL~~~L~~~Gi~~vT 42 (156)
T PRK05066 22 KFGSQGEIVTALQEQGFDNIN 42 (156)
T ss_pred CCCCHHHHHHHHHHCCCCeec
Confidence 466789999999999998 53
No 102
>PF08862 DUF1829: Domain of unknown function DUF1829; InterPro: IPR014961 This short protein is usually associated with IPR014960 from INTERPRO.
Probab=25.03 E-value=50 Score=23.35 Aligned_cols=15 Identities=33% Similarity=0.612 Sum_probs=13.4
Q ss_pred HHHHHHHHHHhCccc
Q 032526 104 MEDLSKALREYGVNV 118 (139)
Q Consensus 104 mEDL~~AL~EyGInv 118 (139)
.+|+..||.+|||++
T Consensus 68 ~~~~~~a~~~y~I~~ 82 (88)
T PF08862_consen 68 SEDIINALEQYNIKP 82 (88)
T ss_pred CHHHHHHHHHCCCce
Confidence 389999999999986
No 103
>TIGR01527 arch_NMN_Atrans nicotinamide-nucleotide adenylyltransferase. In some archaeal species, a lower-scoring paralog, uncharacterized with respect to activity, is also present. These score between trusted and noise cutoffs.
Probab=24.95 E-value=96 Score=24.26 Aligned_cols=41 Identities=10% Similarity=0.174 Sum_probs=33.9
Q ss_pred CCCchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHH
Q 032526 15 HDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (139)
Q Consensus 15 ~~~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RL 59 (139)
.-++..+++.|..=++|.-.+|.+|.+++-+-.|. .||++|
T Consensus 123 ~~S~T~IR~~i~~~~~W~~lVP~~v~~~i~~i~~~----~r~~~~ 163 (165)
T TIGR01527 123 EYSGTEIRRRMLNGEDWEHLVPKAVADVIKEIKGV----ERLRKI 163 (165)
T ss_pred cccHHHHHHHHHcCCChhhhCCHHHHHHHHHcCcH----HHHHHh
Confidence 45789999999877789999999999999888874 466654
No 104
>cd06100 CCL_ACL-C Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA). ACL catalyzes an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. In fungi, yeast, plants, and animals ACL is cytosolic and generates AcCoA for lipogenesis. ACL may be required for fruiting body maturation in the filamentous fungus Sordaria macrospore. In several groups of autotrophic prokaryotes and archaea, ACL carries out the citrate-cleavage reaction of the reductive tricarboxylic acid (rTCA) cycle. In the family Aquificaceae this latter reaction in the rTCA cycle is carried out via a two enzyme system the second enzyme of which is CCL; the first enzyme is citryl-CoA synthetase (CC
Probab=24.62 E-value=1.2e+02 Score=24.54 Aligned_cols=36 Identities=36% Similarity=0.502 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHhC----CC-----CCCChHHHHHHHHHHHHHHH
Q 032526 34 TIPDELVEHYLAKS----GF-----QCPDVRLIRLVAVATQKFVA 69 (139)
Q Consensus 34 ~IPD~Vt~yyL~~a----Gf-----~~~D~Rv~RLiSLAaQKFis 69 (139)
.-+.++++.++++. || .+.|||...|.+++-+....
T Consensus 103 ~~~~~~v~~~~~~~~~ipGfGH~v~~~~DPRa~~L~~~~~~~~~~ 147 (227)
T cd06100 103 AAAAEFVAEYRAAKKRIPGFGHPVHKNPDPRVPRLLELARELGPA 147 (227)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCCCCCCchHHHHHHHHHHhccC
Confidence 46777888888765 66 46899999999999886544
No 105
>PF00620 RhoGAP: RhoGAP domain; InterPro: IPR000198 Members of the Rho family of small G proteins transduce signals from plasma-membrane receptors and control cell adhesion, motility and shape by actin cytoskeleton formation. Like all other GTPases, Rho proteins act as molecular switches, with an active GTP-bound form and an inactive GDP-bound form. The active conformation is promoted by guanine-nucleotide exchange factors, and the inactive state by GTPase-activating proteins (GAPs) which stimulate the intrinsic GTPase activity of small G proteins. This entry is a Rho/Rac/Cdc42-like GAP domain, that is found in a wide variety of large, multi-functional proteins []. A number of structure are known for this family [, , ]. The domain is composed of seven alpha helices. This domain is also known as the breakpoint cluster region-homology (BH) domain.; GO: 0007165 signal transduction, 0005622 intracellular; PDB: 1RGP_A 1AM4_B 1GRN_B 2NGR_B 1OW3_A 1TX4_A 3BYI_B 1XA6_A 3FK2_B 1F7C_A ....
Probab=24.53 E-value=1.3e+02 Score=21.57 Aligned_cols=36 Identities=31% Similarity=0.477 Sum_probs=25.4
Q ss_pred chHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChH
Q 032526 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVR 55 (139)
Q Consensus 18 d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~R 55 (139)
..-|..||..|. .|+||+++.+-+++...-...+.+
T Consensus 57 a~~lK~~L~~lp--~pli~~~~~~~~~~~~~~~~~~~~ 92 (151)
T PF00620_consen 57 ASLLKRFLRELP--EPLIPSELYDKFIAASKSADEEEQ 92 (151)
T ss_dssp HHHHHHHHHHSS--STSTTHHHHHHHHHHHTSSSHHHH
T ss_pred cccceeeeeccc--cchhhhhHHHHHhhhhccchhhHH
Confidence 345677888886 599999999999875444443333
No 106
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=24.28 E-value=34 Score=26.93 Aligned_cols=24 Identities=25% Similarity=0.537 Sum_probs=15.3
Q ss_pred ccceeeeHHHHHHHHHHhCcccCC
Q 032526 97 DKRLILTMEDLSKALREYGVNVKH 120 (139)
Q Consensus 97 d~k~vLTmEDL~~AL~EyGInv~r 120 (139)
+++-.|+=+.|+..|++.||+|.|
T Consensus 117 d~~~PlSD~~i~~~L~~~gi~isR 140 (160)
T PF04552_consen 117 DKKKPLSDQEIAELLKEEGIKISR 140 (160)
T ss_dssp -TTS---HHHHHHHHTTTTS---H
T ss_pred CCCCCCCHHHHHHHHHHcCCCccH
Confidence 455689999999999999999976
No 107
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=24.16 E-value=96 Score=23.07 Aligned_cols=38 Identities=18% Similarity=0.239 Sum_probs=30.3
Q ss_pred CchHHHHHHHhccc-CCCCCCHHHHHHHHHhCCCCCCCh
Q 032526 17 DDAALTEFLSSLMG-YTPTIPDELVEHYLAKSGFQCPDV 54 (139)
Q Consensus 17 ~d~~L~efL~~Ldd-Y~P~IPD~Vt~yyL~~aGf~~~D~ 54 (139)
+-.+|-|||..|-+ -.|+-=-+|...|.+..||.++=|
T Consensus 16 ~~~~iF~FL~~~P~GT~~~~iR~~L~rYI~~~G~~~PiP 54 (97)
T PRK13916 16 DYPQIFDFLENVPRGTKTAHIREALRRYIEEIGENPPIP 54 (97)
T ss_pred ccHHHHHHHHHCCCCCccHHHHHHHHHHHHhcCCCCCCC
Confidence 34678899999965 567777888999999999987644
No 108
>smart00070 GLUCA Glucagon like hormones.
Probab=24.15 E-value=75 Score=18.36 Aligned_cols=13 Identities=31% Similarity=0.424 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHH
Q 032526 59 LVAVATQKFVAEV 71 (139)
Q Consensus 59 LiSLAaQKFisDI 71 (139)
|=.++|+|||..+
T Consensus 14 L~~~~ar~fl~~L 26 (27)
T smart00070 14 LDQLAAKKFLQWL 26 (27)
T ss_pred HHHHHHHHHHHHh
Confidence 4578999999865
No 109
>cd04875 ACT_F4HF-DF N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase). This CD includes the N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase) which catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Formyl-FH4 hydrolase generates the formate that is used by purT-encoded 5'-phosphoribosylglycinamide transformylase for step three of de novo purine nucleotide synthesis. Formyl-FH4 hydrolase, a hexamer which is activated by methionine and inhibited by glycine, is proposed to regulate the balance FH4 and C1-FH4 in response to changing growth conditions. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.96 E-value=61 Score=20.98 Aligned_cols=23 Identities=30% Similarity=0.416 Sum_probs=19.2
Q ss_pred HHHHHHHHHHhCcccCCCCcccc
Q 032526 104 MEDLSKALREYGVNVKHQEYFAD 126 (139)
Q Consensus 104 mEDL~~AL~EyGInv~rP~Yy~d 126 (139)
+.+++..|.++|+||..=.-+++
T Consensus 13 v~~it~~l~~~g~nI~~~~~~~~ 35 (74)
T cd04875 13 VAAVSGFLAEHGGNIVESDQFVD 35 (74)
T ss_pred HHHHHHHHHHcCCCEEeeeeeec
Confidence 57899999999999988766653
No 110
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.77 E-value=64 Score=19.58 Aligned_cols=16 Identities=25% Similarity=0.621 Sum_probs=14.1
Q ss_pred HHHHHHHHHHhCcccC
Q 032526 104 MEDLSKALREYGVNVK 119 (139)
Q Consensus 104 mEDL~~AL~EyGInv~ 119 (139)
+.++...|+++|+||.
T Consensus 13 L~~i~~~l~~~~~nI~ 28 (65)
T cd04882 13 LHEILQILSEEGINIE 28 (65)
T ss_pred HHHHHHHHHHCCCChh
Confidence 5688999999999995
No 111
>PRK07758 hypothetical protein; Provisional
Probab=23.44 E-value=60 Score=24.10 Aligned_cols=17 Identities=41% Similarity=0.636 Sum_probs=14.7
Q ss_pred eHHHHHHHHHHhCcccC
Q 032526 103 TMEDLSKALREYGVNVK 119 (139)
Q Consensus 103 TmEDL~~AL~EyGInv~ 119 (139)
+++.|..+|.|+|++.+
T Consensus 79 SL~EIkekL~E~GLsfk 95 (95)
T PRK07758 79 SLPKLRKALEESGLSFK 95 (95)
T ss_pred HHHHHHHHHHHcCCCCC
Confidence 58899999999999754
No 112
>PF09957 DUF2191: Uncharacterized protein conserved in bacteria (DUF2191); InterPro: IPR019239 This entry, found in various hypothetical prokaryotic proteins, has no known function.
Probab=23.43 E-value=1.8e+02 Score=18.45 Aligned_cols=31 Identities=23% Similarity=0.315 Sum_probs=22.2
Q ss_pred CCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHH
Q 032526 34 TIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFV 68 (139)
Q Consensus 34 ~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFi 68 (139)
.|||++.+--+.-+|+.+. +-+|..|-+.||
T Consensus 6 ~iDd~Ll~eA~~l~g~~tk----~~~V~~ALr~~i 36 (47)
T PF09957_consen 6 DIDDELLAEAMRLTGTKTK----KEAVNEALRELI 36 (47)
T ss_pred eeCHHHHHHHHHHhCCCCH----HHHHHHHHHHHH
Confidence 4899999999999997764 244555555554
No 113
>cd04391 RhoGAP_ARHGAP18 RhoGAP_ARHGAP18: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP18-like proteins. The function of ArhGAP18 is unknown. 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=23.23 E-value=1.8e+02 Score=23.18 Aligned_cols=40 Identities=18% Similarity=0.298 Sum_probs=29.4
Q ss_pred CchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHH
Q 032526 17 DDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIR 58 (139)
Q Consensus 17 ~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~R 58 (139)
-..-|+.||..|- .|+||.+..+.+++-.+.+..+.++..
T Consensus 79 va~lLK~flReLP--ePLi~~~~~~~~~~~~~~~~~~~~~~~ 118 (216)
T cd04391 79 AASLLKLFIRELP--QPLLTVEYLPAFYSVQGLPSKKDQLQA 118 (216)
T ss_pred HHHHHHHHHHhCC--CccCCHHHHHHHHHHHcCCCHHHHHHH
Confidence 3455677887776 699999999999988777655445443
No 114
>PF11753 DUF3310: Protein of unknwon function (DUF3310); InterPro: IPR021739 This entry is represented by Bacteriophage T7, Gp1.7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=23.14 E-value=96 Score=20.51 Aligned_cols=50 Identities=28% Similarity=0.456 Sum_probs=32.4
Q ss_pred HHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHHH
Q 032526 42 HYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR 112 (139)
Q Consensus 42 yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL~ 112 (139)
||- ..|++|-|.= ..+. .+.|+.=-...|+.|. .|.. .|+. .|||.+|..
T Consensus 7 HY~-~~~ie~id~~--~~~~--~~~~~~f~~gnaiKY~-~R~~----------~K~~-----~eDl~KA~~ 56 (60)
T PF11753_consen 7 HYK-SGGIECIDFI--EQFT--EEQFLGFCLGNAIKYL-WRAG----------KKNG-----IEDLKKAKW 56 (60)
T ss_pred ccC-CCCccHHHHH--HHhc--chhhhhHHHHHHHHHH-HHHc----------ccCc-----HHHHHHHHH
Confidence 555 6777766643 3333 6777777788888887 5532 1222 899999863
No 115
>COG0228 RpsP Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=22.87 E-value=1.4e+02 Score=21.86 Aligned_cols=39 Identities=31% Similarity=0.448 Sum_probs=29.4
Q ss_pred HHHhcccCCCCCCH--------HHHHHHHHhCCCCCCChHHHHHHHHHH
Q 032526 24 FLSSLMGYTPTIPD--------ELVEHYLAKSGFQCPDVRLIRLVAVAT 64 (139)
Q Consensus 24 fL~~LddY~P~IPD--------~Vt~yyL~~aGf~~~D~Rv~RLiSLAa 64 (139)
|++.|--|.|+++. +-+.|.|. .|-+.+| +|.+|++-+.
T Consensus 32 ~IE~lG~ynP~~~~~~~v~l~~eri~~Wl~-~GAqpSd-tV~~ll~~~g 78 (87)
T COG0228 32 FIERLGTYNPLLGKEERVKLDEERILYWLS-QGAQPSD-TVRRLLKKAG 78 (87)
T ss_pred chhhhcccCCCCCccceEEEcHHHHHHHHH-cCCcccH-HHHHHHHHhh
Confidence 77889999997743 46778876 5777776 6888888763
No 116
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=22.73 E-value=6.4e+02 Score=23.65 Aligned_cols=58 Identities=17% Similarity=0.162 Sum_probs=34.4
Q ss_pred HHHHhCC-CC-CCChHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHH
Q 032526 42 HYLAKSG-FQ-CPDVRLIRLVAVATQ------------KFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDL 107 (139)
Q Consensus 42 yyL~~aG-f~-~~D~Rv~RLiSLAaQ------------KFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL 107 (139)
..+++.| +. .++.-|.+|+--++. +=+.+|+..|-.+++ .+.+.+.|.+|+
T Consensus 320 ~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~---------------~~~~~~I~~ehV 384 (608)
T TIGR00764 320 QEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAK---------------SSGKVYVTAEHV 384 (608)
T ss_pred HHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHH---------------hcCCceecHHHH
Confidence 3455665 33 367777777765552 445555555533332 123457999999
Q ss_pred HHHHHHh
Q 032526 108 SKALREY 114 (139)
Q Consensus 108 ~~AL~Ey 114 (139)
..|++..
T Consensus 385 ~~Ai~~~ 391 (608)
T TIGR00764 385 LKAKKLA 391 (608)
T ss_pred HHHHHHH
Confidence 9987744
No 117
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.43 E-value=65 Score=20.22 Aligned_cols=19 Identities=21% Similarity=0.515 Sum_probs=15.6
Q ss_pred eHHHHHHHHHHhCcccCCC
Q 032526 103 TMEDLSKALREYGVNVKHQ 121 (139)
Q Consensus 103 TmEDL~~AL~EyGInv~rP 121 (139)
.+..+...|.++||||..=
T Consensus 14 ~l~~i~~~l~~~~inI~~i 32 (72)
T cd04883 14 QLADIAAIFKDRGVNIVSV 32 (72)
T ss_pred HHHHHHHHHHHcCCCEEEE
Confidence 5677889999999999743
No 118
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=22.25 E-value=65 Score=20.46 Aligned_cols=17 Identities=24% Similarity=0.599 Sum_probs=14.2
Q ss_pred eHHHHHHHHHHhCcccC
Q 032526 103 TMEDLSKALREYGVNVK 119 (139)
Q Consensus 103 TmEDL~~AL~EyGInv~ 119 (139)
.+.++...|.+.||||.
T Consensus 14 ~La~v~~~l~~~~inI~ 30 (66)
T cd04908 14 RLAAVTEILSEAGINIR 30 (66)
T ss_pred hHHHHHHHHHHCCCCEE
Confidence 35678899999999995
No 119
>PRK00194 hypothetical protein; Validated
Probab=22.24 E-value=68 Score=21.51 Aligned_cols=19 Identities=26% Similarity=0.371 Sum_probs=15.6
Q ss_pred HHHHHHHHHHhCcccCCCC
Q 032526 104 MEDLSKALREYGVNVKHQE 122 (139)
Q Consensus 104 mEDL~~AL~EyGInv~rP~ 122 (139)
+.+++..|.++|+||..=.
T Consensus 17 va~vt~~la~~g~nI~~~~ 35 (90)
T PRK00194 17 IAGVSTVLAELNVNILDIS 35 (90)
T ss_pred HHHHHHHHHHcCCCEEehh
Confidence 5789999999999986543
No 120
>cd04871 ACT_PSP_2 ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_2 CD includes the second of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains
Probab=21.87 E-value=65 Score=22.17 Aligned_cols=16 Identities=13% Similarity=0.555 Sum_probs=13.2
Q ss_pred HHHHHHHHHHhCcccC
Q 032526 104 MEDLSKALREYGVNVK 119 (139)
Q Consensus 104 mEDL~~AL~EyGInv~ 119 (139)
+..++..|+++|+||-
T Consensus 14 ia~Vs~~lA~~~~NI~ 29 (84)
T cd04871 14 LAAVTRVVADQGLNID 29 (84)
T ss_pred HHHHHHHHHHcCCCHH
Confidence 4567889999999984
No 121
>PF09570 RE_SinI: SinI restriction endonuclease; InterPro: IPR019070 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the restriction endonuclease SinI, which recognises and cleaves the double-stranded sequence G^GWCC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=21.51 E-value=1.5e+02 Score=25.07 Aligned_cols=51 Identities=18% Similarity=0.258 Sum_probs=35.8
Q ss_pred CCCCCHHHHHHHHHhC-CCCC---CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 032526 32 TPTIPDELVEHYLAKS-GFQC---PDVRLIRLVAVATQKFVAEVATDALQQCKARQ 83 (139)
Q Consensus 32 ~P~IPD~Vt~yyL~~a-Gf~~---~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~ 83 (139)
+-||||++++-.|+.+ |+.. ...+.-..+|+|+.--+-+|... |-..++|.
T Consensus 74 p~TvpDE~vs~i~~~~~~~s~e~l~~i~~~HrlsM~aENivG~LLEr-YL~~~Le~ 128 (221)
T PF09570_consen 74 PTTVPDEMVSVIMNASFGYSQEDLELIKEGHRLSMAAENIVGALLER-YLAEVLEP 128 (221)
T ss_pred CCCCChHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhcc
Confidence 4589999999999954 5543 34555667899999988888763 33355554
No 122
>cd04400 RhoGAP_fBEM3 RhoGAP_fBEM3: RhoGAP (GTPase-activator [GAP] protein for Rho-like small GTPases) domain of fungal BEM3-like proteins. Bem3 is a GAP protein of Cdc42, and is specifically involved in the control of the initial assembly of the septin ring in yeast bud formation. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=21.23 E-value=1.8e+02 Score=22.52 Aligned_cols=42 Identities=19% Similarity=0.166 Sum_probs=29.1
Q ss_pred CCCchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCC-CChHHHH
Q 032526 15 HDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQC-PDVRLIR 58 (139)
Q Consensus 15 ~~~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~-~D~Rv~R 58 (139)
+.-...|+.|+..|- .|+||.++.+.+.+-.+-.. .+.|+..
T Consensus 79 h~va~lLK~flreLP--~PLi~~~~~~~~~~~~~~~~~~~~~~~~ 121 (190)
T cd04400 79 HTVAGLLKLYLRELP--TLILGGELHNDFKRLVEENHDRSQRALE 121 (190)
T ss_pred HHHHHHHHHHHHhCC--cccCCHHHHHHHHHHHhccCCHHHHHHH
Confidence 333566788888887 69999999998877665542 3344433
No 123
>KOG0506 consensus Glutaminase (contains ankyrin repeat) [Amino acid transport and metabolism]
Probab=21.17 E-value=68 Score=30.54 Aligned_cols=22 Identities=23% Similarity=0.326 Sum_probs=18.7
Q ss_pred HHHHHhCCCCCCChHHHHHHHH
Q 032526 41 EHYLAKSGFQCPDVRLIRLVAV 62 (139)
Q Consensus 41 ~yyL~~aGf~~~D~Rv~RLiSL 62 (139)
---|...|+.++||||+.+++-
T Consensus 109 iTALkstGLrtsDPRLk~mMd~ 130 (622)
T KOG0506|consen 109 ITALKSTGLRTSDPRLKDMMDE 130 (622)
T ss_pred HHHHHHcCCCcCCchHHHHHHH
Confidence 3468899999999999998764
No 124
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=21.10 E-value=2.5e+02 Score=20.73 Aligned_cols=51 Identities=24% Similarity=0.279 Sum_probs=40.4
Q ss_pred HHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHH
Q 032526 24 FLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDAL 76 (139)
Q Consensus 24 fL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~ 76 (139)
+|..+..- .|=.+-+..+|..+|++..+.++.-|++...-|=|.+++..+.
T Consensus 8 Lll~~~g~--~iT~e~I~~IL~AAGv~ve~~~~~~la~~L~gk~i~eli~~~~ 58 (105)
T TIGR03685 8 LLLHSAGK--EINEENLKAVLEAAGVEVDEARVKALVAALEGVNIEEAIKKAA 58 (105)
T ss_pred HHHHhcCC--CCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHHhhh
Confidence 44444444 4667889999999999999999999999888888888886554
No 125
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=21.07 E-value=99 Score=18.49 Aligned_cols=25 Identities=20% Similarity=0.373 Sum_probs=20.0
Q ss_pred HHHhcccCCCCCCHHHHHHHHHhCC
Q 032526 24 FLSSLMGYTPTIPDELVEHYLAKSG 48 (139)
Q Consensus 24 fL~~LddY~P~IPD~Vt~yyL~~aG 48 (139)
-+..|.+-=|-++.+++.+.|..++
T Consensus 5 ~v~~L~~mFP~l~~~~I~~~L~~~~ 29 (43)
T smart00546 5 ALHDLKDMFPNLDEEVIKAVLEANN 29 (43)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHcC
Confidence 3445556689999999999999876
No 126
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.02 E-value=75 Score=19.93 Aligned_cols=19 Identities=16% Similarity=0.508 Sum_probs=16.2
Q ss_pred eHHHHHHHHHHhCcccCCC
Q 032526 103 TMEDLSKALREYGVNVKHQ 121 (139)
Q Consensus 103 TmEDL~~AL~EyGInv~rP 121 (139)
.+.+|...|+++||||..=
T Consensus 14 ~L~~l~~~l~~~~i~i~~~ 32 (69)
T cd04909 14 VIAEVTQILGDAGISIKNI 32 (69)
T ss_pred HHHHHHHHHHHcCCCceee
Confidence 5678999999999999754
No 127
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=20.98 E-value=1.4e+02 Score=23.93 Aligned_cols=40 Identities=20% Similarity=0.179 Sum_probs=30.3
Q ss_pred chHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHH
Q 032526 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLI 57 (139)
Q Consensus 18 d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~ 57 (139)
..++.++...++..-+.++.+-....|+++||...+.--+
T Consensus 192 ~~ei~~~~~~~~~~~~~~~~~~~~~~L~~aGF~~v~~~~~ 231 (247)
T PRK15451 192 ELEISQKRSMLENVMLTDSVETHKARLHKAGFEHSELWFQ 231 (247)
T ss_pred HHHHHHHHHHHHhhcccCCHHHHHHHHHHcCchhHHHHHH
Confidence 4456666677777777788899999999999997655443
No 128
>smart00311 PWI PWI, domain in splicing factors.
Probab=20.93 E-value=1.6e+02 Score=19.90 Aligned_cols=35 Identities=26% Similarity=0.482 Sum_probs=22.1
Q ss_pred HHHHHHHHHhCCCC-CCChHHHHHHHH---HHHHHHHHH
Q 032526 37 DELVEHYLAKSGFQ-CPDVRLIRLVAV---ATQKFVAEV 71 (139)
Q Consensus 37 D~Vt~yyL~~aGf~-~~D~Rv~RLiSL---AaQKFisDI 71 (139)
|.|++|++....=. .+|+.+.+|-.. -|.+|+.++
T Consensus 26 ~~vvd~i~~~l~~~~~~~~l~~~L~~~~f~da~~Fv~~L 64 (74)
T smart00311 26 DTLVEFILSQIRQHKGPQAKLLQINLTGFEDAEEFVDKL 64 (74)
T ss_pred HHHHHHHHHHHHhCCChHHHHHHHHhhcchhHHHHHHHH
Confidence 34555555444322 567888777655 588888776
No 129
>COG2815 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.87 E-value=1.1e+02 Score=26.49 Aligned_cols=33 Identities=24% Similarity=0.474 Sum_probs=28.0
Q ss_pred eeeeHHHHHHHHHHhCcccCCCCccccCCCCCC
Q 032526 100 LILTMEDLSKALREYGVNVKHQEYFADNPSTGM 132 (139)
Q Consensus 100 ~vLTmEDL~~AL~EyGInv~rP~Yy~d~~~~~~ 132 (139)
.-+|.++....|+++|+++.-++||.+....|.
T Consensus 168 ~G~t~~~A~~~L~~~G~~~~~~~~~ss~~~~G~ 200 (303)
T COG2815 168 VGMTYDEASSNLKAAGLTVNSKEYVSSDRPEGE 200 (303)
T ss_pred ccccHHHHHHHHHHhCCCcccccccCCCCCCCe
Confidence 457889999999999999998888888776663
No 130
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=20.84 E-value=78 Score=21.74 Aligned_cols=18 Identities=33% Similarity=0.414 Sum_probs=15.9
Q ss_pred ccceeeeHHHHHHHHHHh
Q 032526 97 DKRLILTMEDLSKALREY 114 (139)
Q Consensus 97 d~k~vLTmEDL~~AL~Ey 114 (139)
.++...|.|||-+.|..|
T Consensus 35 ~~~~~kT~EeLDaELD~Y 52 (74)
T PF13865_consen 35 RKKPPKTAEELDAELDAY 52 (74)
T ss_pred CCCCCCCHHHHHHHHHHH
Confidence 348899999999999988
No 131
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.62 E-value=83 Score=18.94 Aligned_cols=18 Identities=11% Similarity=0.366 Sum_probs=15.5
Q ss_pred eHHHHHHHHHHhCcccCC
Q 032526 103 TMEDLSKALREYGVNVKH 120 (139)
Q Consensus 103 TmEDL~~AL~EyGInv~r 120 (139)
.+.++...|.++|+||..
T Consensus 12 ~l~~i~~~l~~~~~~I~~ 29 (71)
T cd04903 12 AIAKVTSVLADHEINIAF 29 (71)
T ss_pred hHHHHHHHHHHcCcCeee
Confidence 467899999999999863
No 132
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=20.53 E-value=1.4e+02 Score=22.59 Aligned_cols=53 Identities=15% Similarity=0.120 Sum_probs=40.8
Q ss_pred HHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHH
Q 032526 24 FLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQ 77 (139)
Q Consensus 24 fL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q 77 (139)
+|..|-...+ |--+=+..+|..+|.+..+.++..+++...-|=|.+++.....
T Consensus 10 lL~~lgG~~~-pTaddI~kIL~AaGveVd~~~~~l~~~~L~GKdI~ELIa~G~~ 62 (112)
T PTZ00373 10 LMCVLGGNEN-PTKKEVKNVLSAVNADVEDDVLDNFFKSLEGKTPHELIAAGMK 62 (112)
T ss_pred HHHHHcCCCC-CCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHH
Confidence 3444444321 2355678999999999999999999999999999999986544
No 133
>cd04889 ACT_PDH-BS-like C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate. Included in this CD is the C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Also included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem A
Probab=20.48 E-value=84 Score=19.06 Aligned_cols=18 Identities=28% Similarity=0.608 Sum_probs=14.9
Q ss_pred eHHHHHHHHHHhCcccCC
Q 032526 103 TMEDLSKALREYGVNVKH 120 (139)
Q Consensus 103 TmEDL~~AL~EyGInv~r 120 (139)
.+.++...|.+.||||..
T Consensus 11 ~l~~i~~~l~~~~inI~~ 28 (56)
T cd04889 11 RLAEVTEILAEAGINIKA 28 (56)
T ss_pred hHHHHHHHHHHcCCCEee
Confidence 367889999999999953
No 134
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=20.41 E-value=2.8e+02 Score=24.50 Aligned_cols=27 Identities=11% Similarity=0.374 Sum_probs=18.8
Q ss_pred cceeeeHHHHHHHHHHh-CcccCCCCcc
Q 032526 98 KRLILTMEDLSKALREY-GVNVKHQEYF 124 (139)
Q Consensus 98 ~k~vLTmEDL~~AL~Ey-GInv~rP~Yy 124 (139)
.+.++|++|+..|+..- .-+-....||
T Consensus 370 ~~~~i~~~df~~A~~~v~~~~~~~~~~~ 397 (398)
T PTZ00454 370 NRYVILPKDFEKGYKTVVRKTDRDYDFY 397 (398)
T ss_pred CCCccCHHHHHHHHHHHHhccccchhcc
Confidence 35699999999999972 2233445665
No 135
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=20.41 E-value=3.4e+02 Score=22.33 Aligned_cols=16 Identities=19% Similarity=0.133 Sum_probs=11.0
Q ss_pred eeeeHHHHHHHHHHhC
Q 032526 100 LILTMEDLSKALREYG 115 (139)
Q Consensus 100 ~vLTmEDL~~AL~EyG 115 (139)
-.+|.+|+..|+.+..
T Consensus 260 ~~it~~~v~~a~~~~~ 275 (365)
T TIGR02928 260 ERVTEDHVEKAQEKIE 275 (365)
T ss_pred CCCCHHHHHHHHHHHH
Confidence 3577888877777653
No 136
>cd00159 RhoGAP RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins 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. The RhoGAPs are one of the major classes of regulators of Rho G proteins.
Probab=20.28 E-value=2.1e+02 Score=20.55 Aligned_cols=40 Identities=23% Similarity=0.346 Sum_probs=28.6
Q ss_pred CchHHHHHHHhcccCCCCCCHHHHHHHHHhCCCCCCChHHHH
Q 032526 17 DDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIR 58 (139)
Q Consensus 17 ~d~~L~efL~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~R 58 (139)
-...|..|+..|. .|+||.++.+-++...+......++..
T Consensus 55 va~~lK~~l~~Lp--~pli~~~~~~~~~~~~~~~~~~~~~~~ 94 (169)
T cd00159 55 VASLLKLYLRELP--EPLIPFELYDEFIELAKIEDEEERIEA 94 (169)
T ss_pred HHHHHHHHHHcCC--CccCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 3456788888876 799999999988888776643334433
No 137
>TIGR03241 arg_catab_astB succinylarginine dihydrolase. Members of this family are succinylarginine dihydrolase (EC 3.5.3.23), the second of five enzymes in the arginine succinyltransferase (AST) pathway.
Probab=20.10 E-value=1.8e+02 Score=26.93 Aligned_cols=66 Identities=17% Similarity=0.257 Sum_probs=45.1
Q ss_pred HHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeeHHHHHHHH
Q 032526 42 HYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKAL 111 (139)
Q Consensus 42 yyL~~aGf~~~D~Rv~RLiSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~k~vLTmEDL~~AL 111 (139)
..|.+-||.-+|..|..-.+-.+-.+++-..+ -+-|=+.++..-..+....|+|+.+|.--|..-+
T Consensus 69 ~~Lr~LGFsGsD~~vl~~aak~aP~Ll~a~~S----ASsMWtANAATVsPSaDt~DgrvHfT~ANL~~k~ 134 (443)
T TIGR03241 69 PVLRRLGFSGSDEQVLAKAARQAPVLLSAVSS----ASSMWTANAATVSPSADTADGRVHFTVANLNNKF 134 (443)
T ss_pred HHHHHhCCCCcHHHHHHHHHhhCHHHHHHHhh----HHHHHHhhhcccCCCCcCCCCceeecchhhcccc
Confidence 47999999999999988887777777665443 2223333332222345678999999988776544
No 138
>PF15127 DUF4565: Protein of unknown function (DUF4565)
Probab=20.07 E-value=1.1e+02 Score=22.72 Aligned_cols=28 Identities=29% Similarity=0.348 Sum_probs=23.0
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032526 52 PDVRLIRLVAVATQKFVAEVATDALQQC 79 (139)
Q Consensus 52 ~D~Rv~RLiSLAaQKFisDIa~DA~q~~ 79 (139)
..+.+.-+|.==||+.-.+|++||+|.+
T Consensus 46 ~~~~a~~vvlEyA~rLSqEIl~dAlqQW 73 (91)
T PF15127_consen 46 PSPGASPVVLEYAHRLSQEILSDALQQW 73 (91)
T ss_pred CCCCCCchhHHHHHHHHHHHHHHHHHHH
Confidence 4555666677779999999999999987
Done!