Query 032126
Match_columns 147
No_of_seqs 104 out of 142
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 09:56:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032126.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032126hhsearch_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 3.9E-54 8.4E-59 344.5 12.1 116 8-133 60-176 (176)
2 COG5162 Transcription initiati 100.0 4.5E-43 9.7E-48 282.5 10.8 110 16-133 70-197 (197)
3 PF03540 TFIID_30kDa: Transcri 100.0 5.5E-31 1.2E-35 175.7 6.4 51 33-91 1-51 (51)
4 PF07524 Bromo_TP: Bromodomain 97.8 0.0001 2.2E-09 50.8 7.1 67 38-127 10-76 (77)
5 smart00576 BTP Bromodomain tra 97.8 9.7E-05 2.1E-09 51.4 7.0 67 38-127 10-76 (77)
6 PF00808 CBFD_NFYB_HMF: Histon 96.7 0.014 3.1E-07 38.8 7.4 64 34-119 2-65 (65)
7 smart00803 TAF TATA box bindin 96.7 0.01 2.2E-07 40.8 6.8 64 34-120 2-65 (65)
8 PF02969 TAF: TATA box binding 96.5 0.012 2.5E-07 41.1 6.2 65 33-120 2-66 (66)
9 cd07979 TAF9 TATA Binding Prot 96.2 0.022 4.7E-07 43.0 6.7 64 38-124 5-68 (117)
10 PLN00035 histone H4; Provision 95.8 0.042 9.2E-07 41.5 6.8 75 28-125 23-97 (103)
11 cd00076 H4 Histone H4, one of 95.7 0.06 1.3E-06 39.2 6.8 74 28-124 7-80 (85)
12 COG2036 HHT1 Histones H3 and H 95.5 0.065 1.4E-06 39.6 6.7 84 20-126 5-88 (91)
13 cd08050 TAF6 TATA Binding Prot 95.5 0.054 1.2E-06 47.0 7.1 67 36-125 1-67 (343)
14 PTZ00015 histone H4; Provision 95.3 0.11 2.4E-06 39.1 7.4 74 29-125 25-98 (102)
15 PF03847 TFIID_20kDa: Transcri 94.8 0.17 3.8E-06 35.2 6.8 45 53-120 19-63 (68)
16 PF02291 TFIID-31kDa: Transcri 94.5 0.18 3.9E-06 39.1 6.8 62 38-122 16-77 (129)
17 cd07981 TAF12 TATA Binding Pro 93.0 0.57 1.2E-05 32.3 6.6 52 50-124 18-70 (72)
18 KOG1142 Transcription initiati 91.4 0.53 1.1E-05 40.8 5.9 81 14-136 153-233 (258)
19 PF05236 TAF4: Transcription i 91.4 0.24 5.2E-06 41.2 3.6 57 31-95 40-100 (264)
20 cd08045 TAF4 TATA Binding Prot 89.6 1 2.2E-05 36.5 5.8 47 40-94 54-100 (212)
21 KOG3334 Transcription initiati 85.1 4.1 9E-05 32.8 6.7 63 39-124 18-80 (148)
22 KOG4336 TBP-associated transcr 80.2 4.3 9.3E-05 36.3 5.5 77 35-135 6-84 (323)
23 KOG2549 Transcription initiati 77.2 13 0.00028 35.6 8.0 85 31-138 8-98 (576)
24 PF00125 Histone: Core histone 75.8 15 0.00033 24.3 6.1 68 34-120 5-73 (75)
25 smart00417 H4 Histone H4. 69.6 12 0.00026 26.7 4.6 54 28-89 7-60 (74)
26 PF10281 Ish1: Putative stress 67.9 5.4 0.00012 24.3 2.2 21 110-130 4-24 (38)
27 COG5095 TAF6 Transcription ini 66.0 35 0.00077 31.4 7.9 60 41-123 12-71 (450)
28 PF12949 HeH: HeH/LEM domain; 60.7 4.8 0.0001 25.0 1.1 18 109-126 3-20 (35)
29 COG5094 TAF9 Transcription ini 59.9 52 0.0011 26.4 7.0 44 65-121 38-81 (145)
30 COG5208 HAP5 CCAAT-binding fac 59.6 13 0.00029 32.3 3.9 40 67-121 135-174 (286)
31 KOG0482 DNA replication licens 55.5 80 0.0017 31.0 8.6 39 6-44 545-583 (721)
32 PHA02554 13 neck protein; Prov 54.4 19 0.00042 32.1 4.1 81 31-136 3-83 (311)
33 smart00513 SAP Putative DNA-bi 50.4 15 0.00032 21.8 2.0 19 109-127 3-21 (35)
34 KOG2406 MADS box transcription 48.9 9.3 0.0002 36.7 1.4 68 22-89 159-254 (635)
35 PF02037 SAP: SAP domain; Int 48.9 14 0.00031 22.2 1.7 19 109-127 3-21 (35)
36 KOG2389 Predicted bromodomain 48.5 62 0.0013 29.5 6.4 52 30-89 25-76 (353)
37 PF04239 DUF421: Protein of un 47.0 10 0.00023 27.5 1.1 19 106-124 23-41 (99)
38 PRK13710 plasmid maintenance p 42.8 12 0.00026 26.5 0.9 22 107-128 4-26 (72)
39 KOG0869 CCAAT-binding factor, 42.1 29 0.00062 28.6 3.0 37 73-124 65-101 (168)
40 PF09415 CENP-X: CENP-S associ 41.9 1.2E+02 0.0026 21.2 6.2 66 36-120 1-66 (72)
41 PF01842 ACT: ACT domain; Int 40.8 19 0.00041 22.1 1.5 23 112-134 14-36 (66)
42 PF01316 Arg_repressor: Argini 40.1 21 0.00046 24.9 1.8 20 108-127 18-37 (70)
43 PF15374 CCDC71L: Coiled-coil 40.1 19 0.00042 32.8 1.9 28 9-36 29-58 (376)
44 PF05873 Mt_ATP-synt_D: ATP sy 39.4 9.9 0.00021 30.2 0.0 33 107-139 128-160 (161)
45 KOG3449 60S acidic ribosomal p 39.4 24 0.00051 27.4 2.1 39 39-85 22-60 (112)
46 PF11848 DUF3368: Domain of un 39.1 37 0.0008 21.6 2.6 29 20-48 20-48 (48)
47 cd04377 RhoGAP_myosin_IX RhoGA 37.4 40 0.00087 26.4 3.2 41 14-56 67-107 (186)
48 cd04381 RhoGap_RalBP1 RhoGap_R 35.3 59 0.0013 25.4 3.8 42 13-56 70-111 (182)
49 cd04374 RhoGAP_Graf RhoGAP_Gra 35.3 47 0.001 26.9 3.3 40 15-56 87-126 (203)
50 PF00123 Hormone_2: Peptide ho 33.9 39 0.00084 20.1 2.0 17 64-80 11-27 (28)
51 KOG3467 Histone H4 [Chromatin 33.8 97 0.0021 23.6 4.5 74 30-126 25-98 (103)
52 PF03793 PASTA: PASTA domain; 33.5 23 0.0005 22.5 1.0 30 110-139 9-38 (63)
53 cd04395 RhoGAP_ARHGAP21 RhoGAP 33.0 60 0.0013 25.6 3.5 37 18-56 77-113 (196)
54 cd04402 RhoGAP_ARHGAP20 RhoGAP 32.8 51 0.0011 25.9 3.1 42 13-56 65-106 (192)
55 cd04902 ACT_3PGDH-xct C-termin 32.6 31 0.00068 21.7 1.6 19 111-129 12-30 (73)
56 PRK13916 plasmid segregation p 31.3 67 0.0014 24.3 3.3 41 16-56 15-56 (97)
57 KOG1488 Translational represso 31.1 43 0.00094 31.6 2.7 46 39-88 376-421 (503)
58 PF05931 AgrD: Staphylococcal 30.8 28 0.00061 22.9 1.1 12 32-43 33-44 (45)
59 cd04869 ACT_GcvR_2 ACT domains 30.7 38 0.00083 22.1 1.8 25 111-135 12-36 (81)
60 smart00428 H3 Histone H3. 29.7 1.6E+02 0.0035 22.2 5.2 44 67-125 61-104 (105)
61 PF14914 LRRC37AB_C: LRRC37A/B 29.2 41 0.0009 27.4 2.0 36 31-78 19-58 (154)
62 cd04870 ACT_PSP_1 CT domains f 29.1 42 0.0009 22.3 1.8 17 112-128 13-29 (75)
63 PRK03341 arginine repressor; P 28.9 41 0.00088 27.1 1.9 21 107-127 27-47 (168)
64 PF12767 SAGA-Tad1: Transcript 28.8 95 0.0021 25.6 4.2 38 41-86 213-250 (252)
65 KOG0870 DNA polymerase epsilon 28.8 1.4E+02 0.003 24.8 5.0 69 35-125 11-81 (172)
66 cd04387 RhoGAP_Bcr RhoGAP_Bcr: 28.0 67 0.0015 25.7 3.1 37 18-56 74-110 (196)
67 PRK00441 argR arginine repress 27.5 34 0.00073 26.8 1.2 22 108-129 17-38 (149)
68 COG0599 Uncharacterized homolo 27.2 44 0.00095 24.6 1.7 46 19-72 15-63 (124)
69 cd04879 ACT_3PGDH-like ACT_3PG 26.6 46 0.001 20.1 1.5 19 111-129 12-30 (71)
70 cd04873 ACT_UUR-ACR-like ACT d 26.5 49 0.0011 20.5 1.6 17 111-127 13-29 (70)
71 smart00540 LEM in nuclear memb 26.5 55 0.0012 21.2 1.9 18 109-126 5-22 (44)
72 cd04393 RhoGAP_FAM13A1a RhoGAP 26.2 1.3E+02 0.0027 23.6 4.3 33 13-47 71-103 (189)
73 PRK05066 arginine repressor; P 26.0 47 0.001 26.3 1.8 21 107-127 21-42 (156)
74 cd04386 RhoGAP_nadrin RhoGAP_n 25.9 89 0.0019 24.7 3.4 41 14-56 74-114 (203)
75 PF08887 GAD-like: GAD-like do 25.8 61 0.0013 24.3 2.3 23 28-51 25-47 (109)
76 cd04407 RhoGAP_myosin_IXB RhoG 25.6 84 0.0018 24.8 3.2 40 15-56 68-107 (186)
77 cd04403 RhoGAP_ARHGAP27_15_12_ 25.5 75 0.0016 24.9 2.9 37 18-56 74-110 (187)
78 cd04372 RhoGAP_chimaerin RhoGA 25.4 91 0.002 24.6 3.3 37 18-56 75-111 (194)
79 COG1438 ArgR Arginine represso 25.3 46 0.001 26.6 1.6 20 109-128 20-39 (150)
80 cd04384 RhoGAP_CdGAP RhoGAP_Cd 24.8 86 0.0019 25.0 3.1 41 14-56 72-112 (195)
81 PF02906 Fe_hyd_lg_C: Iron onl 24.8 65 0.0014 27.1 2.5 25 105-129 150-174 (285)
82 TIGR02512 Fe_only_hydrog hydro 24.7 58 0.0013 28.4 2.3 24 105-128 236-259 (374)
83 COG3830 ACT domain-containing 24.0 53 0.0011 24.5 1.6 16 112-127 17-32 (90)
84 PF08862 DUF1829: Domain of un 23.7 54 0.0012 23.5 1.6 15 112-126 68-82 (88)
85 KOG1657 CCAAT-binding factor, 23.6 1.2E+02 0.0025 25.8 3.8 42 67-123 100-141 (236)
86 cd04383 RhoGAP_srGAP RhoGAP_sr 23.5 1E+02 0.0022 24.4 3.3 37 18-56 76-112 (188)
87 cd04882 ACT_Bt0572_2 C-termina 23.4 65 0.0014 19.7 1.8 16 112-127 13-28 (65)
88 TIGR02928 orc1/cdc6 family rep 23.3 2E+02 0.0044 23.8 5.2 16 108-123 260-275 (365)
89 PRK07758 hypothetical protein; 23.3 59 0.0013 24.5 1.8 17 111-127 79-95 (95)
90 cd04376 RhoGAP_ARHGAP6 RhoGAP_ 23.2 1.9E+02 0.0041 23.3 4.8 40 14-56 61-100 (206)
91 PRK15451 tRNA cmo(5)U34 methyl 23.0 72 0.0016 25.7 2.4 36 18-53 192-227 (247)
92 PF04552 Sigma54_DBD: Sigma-54 22.7 37 0.0008 27.0 0.7 24 105-128 117-140 (160)
93 cd04398 RhoGAP_fRGD1 RhoGAP_fR 22.3 1.2E+02 0.0026 23.5 3.4 40 15-56 74-113 (192)
94 PF07967 zf-C3HC: C3HC zinc fi 22.0 42 0.00092 25.1 0.8 46 21-68 4-54 (133)
95 cd04908 ACT_Bt0572_1 N-termina 21.9 64 0.0014 20.7 1.6 17 111-127 14-30 (66)
96 COG2323 Predicted membrane pro 21.8 52 0.0011 27.8 1.4 20 106-125 109-128 (224)
97 smart00070 GLUCA Glucagon like 21.2 1E+02 0.0023 18.1 2.2 17 63-79 10-26 (27)
98 PF08367 M16C_assoc: Peptidase 21.0 1.4E+02 0.0031 24.3 3.7 48 39-95 179-226 (248)
99 cd04875 ACT_F4HF-DF N-terminal 20.9 74 0.0016 20.8 1.8 22 112-133 13-34 (74)
100 cd04883 ACT_AcuB C-terminal AC 20.7 71 0.0015 20.2 1.6 19 111-129 14-32 (72)
101 COG2815 Uncharacterized protei 20.6 1.1E+02 0.0024 26.8 3.2 32 108-139 168-199 (303)
102 cd04889 ACT_PDH-BS-like C-term 20.6 81 0.0017 19.3 1.8 18 111-128 11-28 (56)
103 COG3724 AstB Succinylarginine 20.4 1.1E+02 0.0025 28.3 3.3 59 41-118 70-135 (442)
104 cd04406 RhoGAP_myosin_IXA RhoG 20.4 1.3E+02 0.0028 23.8 3.3 41 14-56 67-107 (186)
105 smart00546 CUE Domain that may 20.2 1.1E+02 0.0024 18.5 2.3 25 24-48 5-29 (43)
106 cd04903 ACT_LSD C-terminal ACT 20.2 84 0.0018 19.1 1.8 18 111-128 12-29 (71)
107 PF09570 RE_SinI: SinI restric 20.1 93 0.002 26.7 2.6 51 32-91 74-128 (221)
108 COG3681 L-cysteine desulfidase 20.1 2.7E+02 0.0059 25.9 5.6 70 18-95 181-254 (433)
No 1
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=100.00 E-value=3.9e-54 Score=344.48 Aligned_cols=116 Identities=54% Similarity=0.825 Sum_probs=108.0
Q ss_pred CCCCCCCCCCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHH
Q 032126 8 QQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQC 87 (147)
Q Consensus 8 ~~~~~~~~~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~ 87 (147)
+.+....+.+|..|.|||.+|+||+|+|||+||+|||+++||+|+|||| +|||||||||||||||+||||||
T Consensus 60 ~~~~~~~~~~d~~l~efl~qLddYtP~IPDavt~~yL~~aGf~~~D~rv--------~RLvsLaAQKfvSDIa~DA~Q~~ 131 (176)
T KOG3423|consen 60 ANGELNPTTKDTHLEEFLAQLDDYTPTIPDAVTDHYLKKAGFQTSDPRV--------KRLVSLAAQKFVSDIANDALQHS 131 (176)
T ss_pred ccCCcCCCCcchHHHHHHHHHhcCCCCCcHHHHHHHHHhcCCCcCcHHH--------HHHHHHHHHHHHHHHHHHHHHHh
Confidence 4556667789999999999999999999999999999999999999999 99999999999999999999999
Q ss_pred HHhhh-hhhhchhcccccccceeeeHHHHHHHHHHhCcccCCCCccc
Q 032126 88 KARQA-AVVKDKRDKQQKDKRLILTMEDLSKALREYGVNVKHQEYFA 133 (147)
Q Consensus 88 kiR~~-~~~~~k~~~~~kd~r~vLTmEDLs~AL~EyGInvkrP~Yy~ 133 (147)
|||++ +.+++| +++||+|+|||||||++||+||||||+||+||+
T Consensus 132 k~r~~~~~~~~k--~~~kdkK~tLtmeDL~~AL~EyGinv~rP~y~~ 176 (176)
T KOG3423|consen 132 KIRTKTAIGKDK--KQAKDKKYTLTMEDLSPALAEYGINVKRPDYFT 176 (176)
T ss_pred hhcccccccccc--ccccccceeeeHHHHHHHHHHhCcccCCCCCCC
Confidence 99995 455554 678999999999999999999999999999995
No 2
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=100.00 E-value=4.5e-43 Score=282.48 Aligned_cols=110 Identities=39% Similarity=0.687 Sum_probs=98.4
Q ss_pred CCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 032126 16 DDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVV 95 (147)
Q Consensus 16 ~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~ 95 (147)
.+|++|+|||++||+|+|+|||+||+|||.++||.|+|+|| +||+||+|||||||||.|||||+|||+..+.
T Consensus 70 ~Kdktlee~l~~mDsy~PliPd~v~DYyl~k~Gf~~~D~rv--------KkLl~L~aqKFvsDiA~dayqYsrIr~~~sn 141 (197)
T COG5162 70 MKDKTLEELLQNMDSYTPLIPDSVTDYYLEKAGFVTSDQRV--------KKLLSLLAQKFVSDIAVDAYQYSRIRQGSSN 141 (197)
T ss_pred hhHHHHHHHHHhcccCCCCccHHHHHHHHHhcCceeccHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 68999999999999999999999999999999999999999 9999999999999999999999999994332
Q ss_pred hc------hh------------cccccccceeeeHHHHHHHHHHhCcccCCCCccc
Q 032126 96 KD------KR------------DKQQKDKRLILTMEDLSKALREYGVNVKHQEYFA 133 (147)
Q Consensus 96 ~~------k~------------~~~~kd~r~vLTmEDLs~AL~EyGInvkrP~Yy~ 133 (147)
.. ++ +++...+|.|||+.||++||.||||||+||+||+
T Consensus 142 a~~t~~~a~~f~~gg~~~i~~~~~~~dr~K~vltv~DLs~Al~EyGini~RPdfyr 197 (197)
T COG5162 142 AKATAQKAKRFAKGGASGIGSSGRRGDRKKPVLTVVDLSKALEEYGINISRPDFYR 197 (197)
T ss_pred chhhHHHHHHHHhcccccccccccccccCCceeeehHHHHHHHHhccccCCccccC
Confidence 21 10 1123448999999999999999999999999995
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=5.5e-31 Score=175.65 Aligned_cols=51 Identities=55% Similarity=0.952 Sum_probs=50.2
Q ss_pred CCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 032126 33 PTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQ 91 (147)
Q Consensus 33 P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~ 91 (147)
|+|||+||+|||+++||+|+|+|| +|||||||||||+||++|||||||+|+
T Consensus 1 P~IPD~v~~~yL~~~G~~~~D~rv--------~RLvSLaaQKFisdI~~dA~q~~k~r~ 51 (51)
T PF03540_consen 1 PTIPDEVTDYYLERSGFQTSDPRV--------KRLVSLAAQKFISDIANDAMQYCKIRT 51 (51)
T ss_pred CCCCHHHHHHHHHHCCCCCCCHhH--------HHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 999999999999999999999999 999999999999999999999999995
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=97.83 E-value=0.0001 Score=50.76 Aligned_cols=67 Identities=21% Similarity=0.361 Sum_probs=58.2
Q ss_pred HHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHH
Q 032126 38 ELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSK 117 (147)
Q Consensus 38 ~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~ 117 (147)
.++...|+.+||++..+-. .-.++-.+++||..|+..+.+|+.. .+|..-+..|+..
T Consensus 10 ~~va~il~~~GF~~~~~~a--------l~~Ltdi~~~yl~~l~~~~~~~ae~---------------~gRt~~~~~Dv~~ 66 (77)
T PF07524_consen 10 RSVAQILKHAGFDSASPSA--------LDTLTDILQRYLQELGRTAKRYAEH---------------AGRTEPNLQDVEQ 66 (77)
T ss_pred HHHHHHHHHcCccccCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------cCCCCCCHHHHHH
Confidence 3677899999999999999 9999999999999999999999842 1245567999999
Q ss_pred HHHHhCcccC
Q 032126 118 ALREYGVNVK 127 (147)
Q Consensus 118 AL~EyGInvk 127 (147)
||.|.||+|.
T Consensus 67 al~~~gi~v~ 76 (77)
T PF07524_consen 67 ALEEMGISVN 76 (77)
T ss_pred HHHHhCCCCC
Confidence 9999999985
No 5
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=97.82 E-value=9.7e-05 Score=51.37 Aligned_cols=67 Identities=19% Similarity=0.261 Sum_probs=58.3
Q ss_pred HHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHH
Q 032126 38 ELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSK 117 (147)
Q Consensus 38 ~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~ 117 (147)
-++..+|+.+||+...|.. .-.+.=..++|+..|+..+.+|+..- +|...+.+|+..
T Consensus 10 ~~Vaqil~~~Gf~~~~~sa--------le~ltdi~~~yl~~l~~~~~~~a~~a---------------gR~~~~~~Dv~~ 66 (77)
T smart00576 10 IAVAQILESAGFDSFQESA--------LETLTDILQSYIQELGRTAHSYAELA---------------GRTEPNLGDVVL 66 (77)
T ss_pred HHHHHHHHHcCccccCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHc---------------CCCCCCHHHHHH
Confidence 4678899999999999999 99999999999999999999998531 134567999999
Q ss_pred HHHHhCcccC
Q 032126 118 ALREYGVNVK 127 (147)
Q Consensus 118 AL~EyGInvk 127 (147)
||.+.||++.
T Consensus 67 Al~~~gi~~~ 76 (77)
T smart00576 67 ALENLGISVG 76 (77)
T ss_pred HHHHhCcccC
Confidence 9999999874
No 6
>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=96.68 E-value=0.014 Score=38.76 Aligned_cols=64 Identities=25% Similarity=0.356 Sum_probs=44.8
Q ss_pred CCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHH
Q 032126 34 TIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTME 113 (147)
Q Consensus 34 ~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmE 113 (147)
.+|-+-+.-+++.. ..+.+| ..-=.-+|+.|++.||..++.+|.+.|+- ++|-+++-+
T Consensus 2 ~lP~a~vkri~k~~---~~~~~v----s~ea~~~i~~a~e~Fi~~l~~~A~~~a~~---------------~~rkti~~~ 59 (65)
T PF00808_consen 2 SLPLARVKRIMKSD---PDVMRV----SKEAVEAIAKAAEEFIQYLAKEANEIAQR---------------DKRKTITYE 59 (65)
T ss_dssp SS-HHHHHHHHHHT---STTSEE-----HHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------TTSSEE-HH
T ss_pred CCChHHHHHHhccC---CCccch----hHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------cCCCccCHH
Confidence 36778888888876 223333 11114589999999999999999998851 222389999
Q ss_pred HHHHHH
Q 032126 114 DLSKAL 119 (147)
Q Consensus 114 DLs~AL 119 (147)
|+..||
T Consensus 60 Dv~~Av 65 (65)
T PF00808_consen 60 DVAKAV 65 (65)
T ss_dssp HHHHHH
T ss_pred HHHHHC
Confidence 999986
No 7
>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=96.68 E-value=0.01 Score=40.79 Aligned_cols=64 Identities=25% Similarity=0.335 Sum_probs=53.3
Q ss_pred CCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHH
Q 032126 34 TIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTME 113 (147)
Q Consensus 34 ~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmE 113 (147)
.||-+-+.-+.++.|++--..-+ ...++=....|+.+|+.+|..|.+. -+|-+||.+
T Consensus 2 ~~p~~~i~ria~~~Gi~ris~~a--------~~~l~~~~e~rl~~i~~~A~k~~~h---------------akRktlt~~ 58 (65)
T smart00803 2 WLPKETIKDVAESLGIGNLSDEA--------AKLLAEDVEYRIKEIVQEALKFMRH---------------SKRTTLTTS 58 (65)
T ss_pred CCCHHHHHHHHHHCCCccccHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------hCCCeecHH
Confidence 47888899999999999644448 8899999999999999999999742 134579999
Q ss_pred HHHHHHH
Q 032126 114 DLSKALR 120 (147)
Q Consensus 114 DLs~AL~ 120 (147)
|+..||+
T Consensus 59 DI~~Alk 65 (65)
T smart00803 59 DIDSALR 65 (65)
T ss_pred HHHHHhC
Confidence 9999984
No 8
>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=96.49 E-value=0.012 Score=41.05 Aligned_cols=65 Identities=23% Similarity=0.280 Sum_probs=47.3
Q ss_pred CCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeH
Q 032126 33 PTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTM 112 (147)
Q Consensus 33 P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTm 112 (147)
+.+|-+-+.-+-+..|+..-+.-+ .+++|--++--|.+|+++|.+|.+. -+|..||.
T Consensus 2 s~~~~esvk~iAes~Gi~~l~de~--------a~~La~dveyrlreiiq~a~kfm~h---------------skR~~Lt~ 58 (66)
T PF02969_consen 2 SVFSQESVKDIAESLGISNLSDEA--------AKALAEDVEYRLREIIQEALKFMRH---------------SKRTKLTT 58 (66)
T ss_dssp ----HHHHHHHHHHTT---B-HHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------TT-SSB-H
T ss_pred CcCCHHHHHHHHHHcCCCCCCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------hCCCCCCH
Confidence 467889999999999998777778 8899999999999999999999642 13567999
Q ss_pred HHHHHHHH
Q 032126 113 EDLSKALR 120 (147)
Q Consensus 113 EDLs~AL~ 120 (147)
+|+..||+
T Consensus 59 ~Di~~ALr 66 (66)
T PF02969_consen 59 DDINSALR 66 (66)
T ss_dssp HHHHHHH-
T ss_pred HHHHHHhC
Confidence 99999995
No 9
>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=96.20 E-value=0.022 Score=43.03 Aligned_cols=64 Identities=14% Similarity=0.178 Sum_probs=55.9
Q ss_pred HHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHH
Q 032126 38 ELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSK 117 (147)
Q Consensus 38 ~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~ 117 (147)
.++.-+|+..|.+.-++++ +..+.=-+.+++.+|+.||..|++.- +|-+++.||+..
T Consensus 5 ~~v~~iLk~~Gv~~~~~~v--------~~~Lle~~~ry~~~il~dA~~~a~hA---------------~r~tV~~eDV~l 61 (117)
T cd07979 5 RVIAAILKSMGITEYEPRV--------INQLLEFAYRYTTDVLDDAKVYSEHA---------------GKANIDADDVKL 61 (117)
T ss_pred HHHHHHHHHCCCCccCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHc---------------CCCCCCHHHHHH
Confidence 4788899999999999999 88888888999999999999998642 236899999999
Q ss_pred HHHHhCc
Q 032126 118 ALREYGV 124 (147)
Q Consensus 118 AL~EyGI 124 (147)
|++.++-
T Consensus 62 Ai~~r~~ 68 (117)
T cd07979 62 AIQSRVD 68 (117)
T ss_pred HHHHHhc
Confidence 9999986
No 10
>PLN00035 histone H4; Provisional
Probab=95.83 E-value=0.042 Score=41.48 Aligned_cols=75 Identities=17% Similarity=0.184 Sum_probs=57.9
Q ss_pred cCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccc
Q 032126 28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKR 107 (147)
Q Consensus 28 LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r 107 (147)
|-|...-||-.-+.-++.++|..---.-+ .--+.=+...|+.+|+.||..|++-. +|
T Consensus 23 ~~d~i~~ipk~~IrRLARr~GvkRIS~~a--------y~elr~vle~~l~~I~~dav~ya~HA---------------~R 79 (103)
T PLN00035 23 LRDNIQGITKPAIRRLARRGGVKRISGLI--------YEETRGVLKIFLENVIRDAVTYTEHA---------------RR 79 (103)
T ss_pred HHhhhccCCHHHHHHHHHHcCcccchHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhc---------------CC
Confidence 34666669999999999999976422224 44555677899999999999998631 23
Q ss_pred eeeeHHHHHHHHHHhCcc
Q 032126 108 LILTMEDLSKALREYGVN 125 (147)
Q Consensus 108 ~vLTmEDLs~AL~EyGIn 125 (147)
-|+|.+|+..||+..|-+
T Consensus 80 KTV~~~DV~~Alkr~g~~ 97 (103)
T PLN00035 80 KTVTAMDVVYALKRQGRT 97 (103)
T ss_pred CcCcHHHHHHHHHHcCCc
Confidence 478999999999999863
No 11
>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=95.66 E-value=0.06 Score=39.16 Aligned_cols=74 Identities=19% Similarity=0.212 Sum_probs=55.4
Q ss_pred cCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccc
Q 032126 28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKR 107 (147)
Q Consensus 28 LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r 107 (147)
|-|+..-||-.-+.-...++|..-=---+ .--+.=+...|+.+|+.||..|++-. +|
T Consensus 7 ~~~~~~gi~k~~I~RLarr~GvkRIS~d~--------y~e~~~~l~~~l~~I~~dav~ya~Ha---------------~R 63 (85)
T cd00076 7 LRDNIKGITKPAIRRLARRGGVKRISGGV--------YDEVRNVLKSYLEDVIRDAVTYTEHA---------------KR 63 (85)
T ss_pred HHHhhccCCHHHHHHHHHHcCcchhhHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhc---------------CC
Confidence 44666779999999999999965311113 33344456899999999999998621 23
Q ss_pred eeeeHHHHHHHHHHhCc
Q 032126 108 LILTMEDLSKALREYGV 124 (147)
Q Consensus 108 ~vLTmEDLs~AL~EyGI 124 (147)
-++|.+|+..||+..|-
T Consensus 64 KTVt~~DV~~alkr~g~ 80 (85)
T cd00076 64 KTVTAMDVVYALKRQGR 80 (85)
T ss_pred CcCcHHHHHHHHHHCCC
Confidence 46899999999999994
No 12
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=95.54 E-value=0.065 Score=39.57 Aligned_cols=84 Identities=25% Similarity=0.362 Sum_probs=64.8
Q ss_pred HHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchh
Q 032126 20 ALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKR 99 (147)
Q Consensus 20 ~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~ 99 (147)
-+.|+-.-+......||-.-++-++.++|-+ || ..-=+-.+.=+.+-|+.+|+.+|..+|+
T Consensus 5 ~~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~~----Rv----s~~A~~~l~~~~e~~~~~i~~~A~~~A~----------- 65 (91)
T COG2036 5 GLKEIRRYQRSTDLLLPKAPVRRILRKAGAE----RV----SSSAIEELQEALEEYLEEIAEDAVELAE----------- 65 (91)
T ss_pred hHHHHHhhhhhhhhhcCchHHHHHHHHHhHH----Hh----hHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------
Confidence 3566666777788999999999999999987 76 0000223444667899999999999985
Q ss_pred cccccccceeeeHHHHHHHHHHhCccc
Q 032126 100 DKQQKDKRLILTMEDLSKALREYGVNV 126 (147)
Q Consensus 100 ~~~~kd~r~vLTmEDLs~AL~EyGInv 126 (147)
..+|-|.+-+|+..|+++.|..+
T Consensus 66 ----ha~RKTV~~~DI~la~~~~~~~~ 88 (91)
T COG2036 66 ----HAKRKTVKAEDIKLALKRLGRRI 88 (91)
T ss_pred ----HcCCCeecHHHHHHHHHHhcccc
Confidence 33466999999999999999765
No 13
>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=95.50 E-value=0.054 Score=46.96 Aligned_cols=67 Identities=24% Similarity=0.290 Sum_probs=56.5
Q ss_pred cHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHH
Q 032126 36 PDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDL 115 (147)
Q Consensus 36 PD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDL 115 (147)
|.+.+.-+++.+|.+.-+... .+.++--.+.++..|+++|..+++. -+|.+||.||+
T Consensus 1 ~~~~i~~ia~~~Gi~~~~~~a--------~~~La~~~e~~~~~i~~~A~k~~~h---------------skR~~l~~~Di 57 (343)
T cd08050 1 PQESIKLIAESLGIDSLSDEV--------AQLLAEDVEYRLREIIQEAAKFMRH---------------SKRRKLTTSDV 57 (343)
T ss_pred ChhHHHHHHHHcCCCcCCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------hCCCcCCHHHH
Confidence 456677889999999888888 8999999999999999999999642 12468999999
Q ss_pred HHHHHHhCcc
Q 032126 116 SKALREYGVN 125 (147)
Q Consensus 116 s~AL~EyGIn 125 (147)
..||+..++.
T Consensus 58 ~~Al~~~n~e 67 (343)
T cd08050 58 NHALRLRNVE 67 (343)
T ss_pred HHHHHHhCCC
Confidence 9999986554
No 14
>PTZ00015 histone H4; Provisional
Probab=95.31 E-value=0.11 Score=39.10 Aligned_cols=74 Identities=16% Similarity=0.173 Sum_probs=59.5
Q ss_pred CCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccce
Q 032126 29 MGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRL 108 (147)
Q Consensus 29 ddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~ 108 (147)
-|..+-||-.-+.-++.++|..---.-+ .--+.-+...|+.+|+.||..|++-. +|-
T Consensus 25 r~~i~gI~k~~IrRLarr~GvkRIS~d~--------y~e~r~vle~~l~~I~rdav~~aeHA---------------~RK 81 (102)
T PTZ00015 25 RDNIRGITKGAIRRLARRGGVKRISGDI--------YEEVRGVLKAFLENVVRDSTAYTEYA---------------RRK 81 (102)
T ss_pred hhcccCCCHHHHHHHHHHcCCccchHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhc---------------CCC
Confidence 5788899999999999999997522225 55666678899999999999998531 234
Q ss_pred eeeHHHHHHHHHHhCcc
Q 032126 109 ILTMEDLSKALREYGVN 125 (147)
Q Consensus 109 vLTmEDLs~AL~EyGIn 125 (147)
|.|.+|+..||+..|-+
T Consensus 82 TVt~~DV~~AlKr~g~~ 98 (102)
T PTZ00015 82 TVTAMDVVYALKRQGRT 98 (102)
T ss_pred cccHHHHHHHHHhcCCC
Confidence 78999999999999864
No 15
>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=94.82 E-value=0.17 Score=35.18 Aligned_cols=45 Identities=24% Similarity=0.313 Sum_probs=37.0
Q ss_pred CcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHHHH
Q 032126 53 DVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR 120 (147)
Q Consensus 53 D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~AL~ 120 (147)
|+-+ ..++.-.|..||.+|++.|.+.||-|.+ -+|...|+.-.|+
T Consensus 19 d~~v--------ee~Ll~laddFv~~v~~~ac~lAKhR~s---------------~tle~~Dv~~~Le 63 (68)
T PF03847_consen 19 DPDV--------EELLLELADDFVDDVVSFACRLAKHRKS---------------STLEVKDVQLHLE 63 (68)
T ss_dssp -HHH--------HHHHHHHHHHHHHHHHHHHHHHHHHTT----------------SEE-HHHHHHHHH
T ss_pred CHHH--------HHHHHHHHHHHHHHHHHHHHHHHhccCC---------------CCCCHHHHHHHHH
Confidence 7778 8899999999999999999999998843 2788889888875
No 16
>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=94.47 E-value=0.18 Score=39.13 Aligned_cols=62 Identities=15% Similarity=0.223 Sum_probs=45.2
Q ss_pred HHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHH
Q 032126 38 ELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSK 117 (147)
Q Consensus 38 ~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~ 117 (147)
.++..+|+..|++--+||| .-.+-=-+.+++++|..||..|+.... |..++++|+..
T Consensus 16 ~~i~~iL~~~Gv~~yeprV--------v~qLLEfayRYt~~vL~DA~~ya~hA~---------------~~~i~~~DVrL 72 (129)
T PF02291_consen 16 RVIHLILKSMGVTEYEPRV--------VNQLLEFAYRYTSDVLEDAQVYADHAG---------------RSTIDADDVRL 72 (129)
T ss_dssp HHHHHHHHHTT---B-THH--------HHHHHHHHHHHHHHHHHHHHHHHHHTT----------------SSB-HHHHHH
T ss_pred HHHHHHHHHcCCcccCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhcc---------------cccCChHHHHH
Confidence 4778899999999889999 665555569999999999999986431 23667999999
Q ss_pred HHHHh
Q 032126 118 ALREY 122 (147)
Q Consensus 118 AL~Ey 122 (147)
|...+
T Consensus 73 Ai~~r 77 (129)
T PF02291_consen 73 AIQSR 77 (129)
T ss_dssp HHHHT
T ss_pred HHHHH
Confidence 98844
No 17
>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=93.04 E-value=0.57 Score=32.33 Aligned_cols=52 Identities=23% Similarity=0.337 Sum_probs=42.5
Q ss_pred CCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHHHH-HhCc
Q 032126 50 QCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR-EYGV 124 (147)
Q Consensus 50 ~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~AL~-EyGI 124 (147)
..-|+-+ ..++.=.+..|+.+|+.+|..+||-|. +-+++.+|+..+|+ +||+
T Consensus 18 ~~~~~da--------~~~l~~~~e~fv~~v~~~a~~lAkHr~---------------~~tv~~~Di~l~l~r~~~~ 70 (72)
T cd07981 18 EQLDPDV--------EELLLEIADDFVDDVVEDACRLAKHRK---------------SDTLEVKDVQLHLERNWNI 70 (72)
T ss_pred CCcCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHcC---------------CCCCCHHHHHHHHHHhcCC
Confidence 4557777 889999999999999999999998763 23599999999986 3444
No 18
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=91.44 E-value=0.53 Score=40.75 Aligned_cols=81 Identities=16% Similarity=0.232 Sum_probs=54.2
Q ss_pred CCCCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 032126 14 RHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAA 93 (147)
Q Consensus 14 ~~~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~ 93 (147)
+-.....|.||+.++|. =.--|+-| ..||.-.|..||++|++-|...||-|.+.
T Consensus 153 ~il~k~kl~dLvqqId~------------------~~~LD~dV--------edlLleiADdFV~sii~~sC~LAKHRKsd 206 (258)
T KOG1142|consen 153 PILSKRKLDDLVQQIDG------------------TTKLDDDV--------EDLLLEIADDFVSSIIHRSCKLAKHRKSD 206 (258)
T ss_pred ccccccchhHHHHhhcC------------------cccccHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhcccC
Confidence 33445566777776632 23348899 99999999999999999999999988532
Q ss_pred hhhchhcccccccceeeeHHHHHHHHHHhCcccCCCCccccCC
Q 032126 94 VVKDKRDKQQKDKRLILTMEDLSKALREYGVNVKHQEYFADNP 136 (147)
Q Consensus 94 ~~~~k~~~~~kd~r~vLTmEDLs~AL~EyGInvkrP~Yy~d~~ 136 (147)
+|-.-|+...| |.-.|+.=|.|=+|-.
T Consensus 207 ---------------tlEvrDIqLhL-Er~~Nm~iPgf~sd~~ 233 (258)
T KOG1142|consen 207 ---------------TVEVRDIQLHL-ERNFNMEIPGFSSDEK 233 (258)
T ss_pred ---------------ccchhheeeee-eccccccCCCcccccc
Confidence 23333443333 4556666676655543
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=91.35 E-value=0.24 Score=41.19 Aligned_cols=57 Identities=16% Similarity=0.298 Sum_probs=30.9
Q ss_pred CCCCCcHHHHHHHHHh----CCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 032126 31 YTPTIPDELVEHYLAK----SGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVV 95 (147)
Q Consensus 31 Y~P~IPD~Vt~yyL~~----aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~ 95 (147)
-.|.+.-.+...+|++ .|....|+-| ..|||+|+|-.|.+|+.++...|+.|+....
T Consensus 40 ~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~--------l~llS~A~e~rLr~lie~~~~~s~hR~~~~~ 100 (264)
T PF05236_consen 40 EEPFLNPSPLQKRIQKIAKKHGLKSVDEDV--------LELLSLATEERLRNLIEKAIVLSRHRRDSSK 100 (264)
T ss_dssp ----S-HHHHHHHHHHHHHCTT--EE-TCH--------HHHHHHHHHHHHHHHHHHHH-----------
T ss_pred cccccCHHHHHHHHHHHHHHcCCcCCCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhhhcccC
Confidence 3555555555555544 4655578889 9999999999999999999999999987653
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=89.65 E-value=1 Score=36.47 Aligned_cols=47 Identities=13% Similarity=0.251 Sum_probs=41.3
Q ss_pred HHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 032126 40 VEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAV 94 (147)
Q Consensus 40 t~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~ 94 (147)
+..++.+.|+...|+.+ ..|||+|++-++.+|+.+....|+.|....
T Consensus 54 ~~~i~~~~g~~~~~~d~--------~~lis~a~e~rlr~li~k~~~~s~hR~~~~ 100 (212)
T cd08045 54 IRKIAKKHGLKEVDEDV--------LDLISLALEERLRNLLEKLIEVSEHRVDSE 100 (212)
T ss_pred HHHHHHHcCCCCCCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 44566778888789999 999999999999999999999999998654
No 21
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=85.13 E-value=4.1 Score=32.83 Aligned_cols=63 Identities=19% Similarity=0.198 Sum_probs=49.0
Q ss_pred HHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHH
Q 032126 39 LVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKA 118 (147)
Q Consensus 39 Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~A 118 (147)
|+.-+|...|.+-=+||| +--+==-|-.++++|..||.-|++-- +|.+++.||+..|
T Consensus 18 ~i~~iL~s~GI~eyEprV--------i~qlLefa~rYtt~vL~DA~vys~HA---------------~ka~i~~eDVrlA 74 (148)
T KOG3334|consen 18 VIASILKSLGIQEYEPRV--------INQLLEFAYRYTTTVLDDAKVYSSHA---------------KKATIDAEDVRLA 74 (148)
T ss_pred HHHHHHHHcCccccChHH--------HHHHHHHHHHHHHHHHHHHHHHHHhc---------------cCCCCcHHHHHHH
Confidence 567788999999888888 65555567899999999999998531 1567888888888
Q ss_pred HHHhCc
Q 032126 119 LREYGV 124 (147)
Q Consensus 119 L~EyGI 124 (147)
..-.+.
T Consensus 75 ~~~~~~ 80 (148)
T KOG3334|consen 75 IQMRVD 80 (148)
T ss_pred HHHHhc
Confidence 776543
No 22
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=80.19 E-value=4.3 Score=36.28 Aligned_cols=77 Identities=25% Similarity=0.404 Sum_probs=58.8
Q ss_pred CcHHHHHHHHHhCCCCC-CCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHH
Q 032126 35 IPDELVEHYLAKSGFQC-PDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTME 113 (147)
Q Consensus 35 IPD~Vt~yyL~~aGf~~-~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmE 113 (147)
|=..|+.-.|...||+. ++.-+ --|+ .+-|+.|..|...+..||.. .+|+.-|.-
T Consensus 6 vl~~VV~~Ll~~~gfd~is~~al--------etlv-ell~~yi~eigrq~~n~cel---------------agRT~pT~~ 61 (323)
T KOG4336|consen 6 VLAPVVSNLLKTKGFDSISNAAL--------ETLV-ELLQSYIREIGRQLHNYCEL---------------AGRTIPTQG 61 (323)
T ss_pred HHHHHHHHHHHHhCchHHHHHHH--------HHHH-HHHHHHHHHHHHHHHHHHHH---------------hcccCCcHH
Confidence 45679999999999997 44444 4444 45689999999999999864 135778899
Q ss_pred HHHHHHHHhCcccCC-CCccccC
Q 032126 114 DLSKALREYGVNVKH-QEYFADN 135 (147)
Q Consensus 114 DLs~AL~EyGInvkr-P~Yy~d~ 135 (147)
||.-.|.+.||+|.- +.||.+.
T Consensus 62 Dv~l~Li~mnI~v~sL~~~~q~~ 84 (323)
T KOG4336|consen 62 DVKLTLIEMNIKVSSLYAYFQKQ 84 (323)
T ss_pred HHHHHHHHhCCChhhhHHHHHhc
Confidence 999999999999864 4455443
No 23
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=77.22 E-value=13 Score=35.59 Aligned_cols=85 Identities=25% Similarity=0.256 Sum_probs=63.2
Q ss_pred CCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceee
Q 032126 31 YTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLIL 110 (147)
Q Consensus 31 Y~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vL 110 (147)
++-..|.|-++-.-+.-|..+=+.-. .++++-=-.-=|-+|++||.++ ++ +-+|.+|
T Consensus 8 ~~v~s~~Es~k~vAEslGi~nl~dea--------a~~La~dv~yrikEI~Q~aaKf--m~-------------hskR~kL 64 (576)
T KOG2549|consen 8 PTVVSPKESVKVVAESLGITNLNDEA--------ALLLAEDVEYRIKEIVQDAAKF--MV-------------HSKRTKL 64 (576)
T ss_pred ccccCcHHHHHHHHHHhCccccCHHH--------HHHHHHHHHHHHHHHHHHHHHH--hh-------------cCCCCcC
Confidence 44455688888889999999866666 6777776667788888888887 22 4457899
Q ss_pred eHHHHHHHHHH------hCcccCCCCccccCCCC
Q 032126 111 TMEDLSKALRE------YGVNVKHQEYFADNPST 138 (147)
Q Consensus 111 TmEDLs~AL~E------yGInvkrP~Yy~d~~~~ 138 (147)
|.+|...||+- ||+.-..+-=|+-.+..
T Consensus 65 tv~DV~~ALr~~nVep~yg~~s~~~i~fr~a~~~ 98 (576)
T KOG2549|consen 65 TVDDVDYALRSLNVEPLYGFGAQEIIPFRKASGG 98 (576)
T ss_pred cHHHHHHHHhhcccccccCcccCceeeccccCCC
Confidence 99999999985 77777766555554444
No 24
>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=75.85 E-value=15 Score=24.34 Aligned_cols=68 Identities=19% Similarity=0.218 Sum_probs=44.6
Q ss_pred CCcHHHHHHHHHhCCCCCCC-cccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeH
Q 032126 34 TIPDELVEHYLAKSGFQCPD-VRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTM 112 (147)
Q Consensus 34 ~IPD~Vt~yyL~~aGf~~~D-~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTm 112 (147)
.||-.-+...+.+.+-+... .|+ ...-...+.-+.+-|+.+|..+|..++. ..+|.+||-
T Consensus 5 ~~~~~~~~r~~r~i~~~~~~~~ri----s~~a~~~L~~~~E~~~~~il~~A~~~a~---------------~~kR~tI~~ 65 (75)
T PF00125_consen 5 LIPKFPFSRLLREIGEEILSKYRI----SSEALVALQSVLEYLLVEILEEAGNLAR---------------HAKRKTITP 65 (75)
T ss_dssp SSSHHHHHHHHHHHHHTTSSSSEE----CHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HTTBSEEGH
T ss_pred ccCceEEeeeeehhhccccccccc----ccccchhhhhhhhhhhhhhhhHHHHHHh---------------hcCCcEecH
Confidence 45666666666666555433 354 2222455666778888888888888764 224678999
Q ss_pred HHHHHHHH
Q 032126 113 EDLSKALR 120 (147)
Q Consensus 113 EDLs~AL~ 120 (147)
+|+..|++
T Consensus 66 ~DI~~A~r 73 (75)
T PF00125_consen 66 RDIQLAVR 73 (75)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHh
Confidence 99998875
No 25
>smart00417 H4 Histone H4.
Probab=69.62 E-value=12 Score=26.67 Aligned_cols=54 Identities=13% Similarity=0.141 Sum_probs=39.3
Q ss_pred cCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 032126 28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKA 89 (147)
Q Consensus 28 LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~ki 89 (147)
|-|...-||-.-+.-.+.++|..==-.-+ .--+.=+...|+.+|+.||..|++-
T Consensus 7 ~~d~i~gI~k~~IrRLaRr~GvkRIS~~~--------y~elr~vle~~l~~I~rdav~~a~h 60 (74)
T smart00417 7 LRDNIQGITKPAIRRLARRGGVKRISGLI--------YDETRNVLKSFLENVVRDAVTYTEH 60 (74)
T ss_pred HHhhhcCCCHHHHHHHHHHcCcchhhHHH--------HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34566679999999999999986311113 3333445679999999999999863
No 26
>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=67.89 E-value=5.4 Score=24.28 Aligned_cols=21 Identities=24% Similarity=0.325 Sum_probs=18.5
Q ss_pred eeHHHHHHHHHHhCcccCCCC
Q 032126 110 LTMEDLSKALREYGVNVKHQE 130 (147)
Q Consensus 110 LTmEDLs~AL~EyGInvkrP~ 130 (147)
-+.+||..-|.+|||.+.++.
T Consensus 4 Ws~~~L~~wL~~~gi~~~~~~ 24 (38)
T PF10281_consen 4 WSDSDLKSWLKSHGIPVPKSA 24 (38)
T ss_pred CCHHHHHHHHHHcCCCCCCCC
Confidence 578999999999999988765
No 27
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=65.97 E-value=35 Score=31.40 Aligned_cols=60 Identities=27% Similarity=0.331 Sum_probs=40.1
Q ss_pred HHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHHHH
Q 032126 41 EHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR 120 (147)
Q Consensus 41 ~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~AL~ 120 (147)
.-.-+.-|...-|--. .|.+|.--.==|-+|+++|-.+- ...||++||.+|++.||+
T Consensus 12 KdvAeslGi~Ni~Dd~--------l~alamDlEYRI~ev~qea~KFm---------------vhSKRtvLt~dDis~ALr 68 (450)
T COG5095 12 KDVAESLGISNIDDDA--------LRALAMDLEYRIKEVCQEASKFM---------------VHSKRTVLTIDDISYALR 68 (450)
T ss_pred HHHHHHcCCcccccHH--------HHHHHHhHHHHHHHHHHHHHHHh---------------hcccceeeeHHhHHHHHH
Confidence 3344556776655555 56666666666667777666552 234689999999999999
Q ss_pred HhC
Q 032126 121 EYG 123 (147)
Q Consensus 121 EyG 123 (147)
-..
T Consensus 69 ~lN 71 (450)
T COG5095 69 SLN 71 (450)
T ss_pred hcC
Confidence 743
No 28
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=60.67 E-value=4.8 Score=25.02 Aligned_cols=18 Identities=33% Similarity=0.538 Sum_probs=12.5
Q ss_pred eeeHHHHHHHHHHhCccc
Q 032126 109 ILTMEDLSKALREYGVNV 126 (147)
Q Consensus 109 vLTmEDLs~AL~EyGInv 126 (147)
.||+.+|-..|.|+||..
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 589999999999999964
No 29
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=59.86 E-value=52 Score=26.40 Aligned_cols=44 Identities=25% Similarity=0.389 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHHHHH
Q 032126 65 IRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALRE 121 (147)
Q Consensus 65 ~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~AL~E 121 (147)
..|+-. |.++-.||..||+-|++--. ...-.+|.+||+-.||+.
T Consensus 38 lQLl~F-AhRYTq~vl~Dalvya~htg------------rg~~a~l~veDvrLA~at 81 (145)
T COG5094 38 LQLLEF-AHRYTQDVLEDALVYAKHTG------------RGHIATLGVEDVRLALAT 81 (145)
T ss_pred HHHHHH-HHHHHHHHHHHHHHHHHhcC------------CCccCcccHHHHHHHHHH
Confidence 344443 57889999999999987421 111245888998888864
No 30
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=59.63 E-value=13 Score=32.34 Aligned_cols=40 Identities=28% Similarity=0.427 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHHHHH
Q 032126 67 LVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALRE 121 (147)
Q Consensus 67 LvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~AL~E 121 (147)
|.|-++.+||.++.--|.-+++ +.+|-+|.-.||.+|++.
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 6788999999999988877653 334568888999999875
No 31
>KOG0482 consensus DNA replication licensing factor, MCM7 component [Replication, recombination and repair]
Probab=55.46 E-value=80 Score=30.97 Aligned_cols=39 Identities=18% Similarity=0.211 Sum_probs=30.8
Q ss_pred cCCCCCCCCCCCchHHHHHHHHcCCCCCCCcHHHHHHHH
Q 032126 6 NFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYL 44 (147)
Q Consensus 6 ~~~~~~~~~~~~d~~L~efl~~LddY~P~IPD~Vt~yyL 44 (147)
+.|....-..-+-..+++.++....|.|++|++|.+|+-
T Consensus 545 ~~qp~~~fepl~~~~mR~yI~~ak~~~P~vp~~l~dyi~ 583 (721)
T KOG0482|consen 545 EEQPPLDFEPLDPNLMRRYISLAKRKNPVVPEALADYIT 583 (721)
T ss_pred CCCCCccCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHH
Confidence 344444445566778899999999999999999999874
No 32
>PHA02554 13 neck protein; Provisional
Probab=54.42 E-value=19 Score=32.10 Aligned_cols=81 Identities=20% Similarity=0.232 Sum_probs=57.0
Q ss_pred CCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceee
Q 032126 31 YTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLIL 110 (147)
Q Consensus 31 Y~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vL 110 (147)
|.|.=|-++.+|+|+|-|.+.-++.| +.--|.|.+.+|+|+-.=..=... ..-=-+..|
T Consensus 3 ~~~~sp~eLkD~iLRrLGAPii~Iev---------------t~dQi~D~I~rALely~EYH~dG~------~k~y~~~~~ 61 (311)
T PHA02554 3 YNPNNPRELKDYILRRLGAPIINVEV---------------TEDQIYDCIQRALELYGEYHYDGV------NKGYLKFKV 61 (311)
T ss_pred CCCCCHHHHHHHHHHhcCCCeeEeec---------------CHHHHHHHHHHHHHHHHHHhccch------hceeEEEEc
Confidence 68889999999999999999988888 788899999999998643321100 111235667
Q ss_pred eHHHHHHHHHHhCcccCCCCccccCC
Q 032126 111 TMEDLSKALREYGVNVKHQEYFADNP 136 (147)
Q Consensus 111 TmEDLs~AL~EyGInvkrP~Yy~d~~ 136 (147)
|-||...- ++.++.+.-|+.+.
T Consensus 62 t~e~~~~g----~~d~~~~~vfavt~ 83 (311)
T PHA02554 62 TEEQARTG----VFDLSGSNVFAVTK 83 (311)
T ss_pred cHHHhccc----ceeccccccceeee
Confidence 75654432 56666666665543
No 33
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=50.35 E-value=15 Score=21.78 Aligned_cols=19 Identities=21% Similarity=0.468 Sum_probs=16.7
Q ss_pred eeeHHHHHHHHHHhCcccC
Q 032126 109 ILTMEDLSKALREYGVNVK 127 (147)
Q Consensus 109 vLTmEDLs~AL~EyGInvk 127 (147)
.||..+|...|+++|+.++
T Consensus 3 ~l~~~~Lk~~l~~~gl~~~ 21 (35)
T smart00513 3 KLKVSELKDELKKRGLSTS 21 (35)
T ss_pred cCcHHHHHHHHHHcCCCCC
Confidence 5789999999999999764
No 34
>KOG2406 consensus MADS box transcription factor [Transcription]
Probab=48.88 E-value=9.3 Score=36.67 Aligned_cols=68 Identities=21% Similarity=0.207 Sum_probs=45.9
Q ss_pred HHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCc---------------------cccccc-------ccchhHHHHHHHH
Q 032126 22 TEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDV---------------------RLNCCL-------CFCRIRLVAVATQ 73 (147)
Q Consensus 22 ~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~---------------------Rv~~~~-------~~~~~RLvSLAaQ 73 (147)
.+|+..|.+-+|++|.+|.--...-+-.-|++. |..|++ --++.||||.|.+
T Consensus 159 s~a~s~~~~~Ppt~~~al~fii~~g~~~raS~evqsai~~Rlk~ypeka~~s~hRa~~~vP~sivqvLkq~prLiSsAV~ 238 (635)
T KOG2406|consen 159 SEALSKMNRCPPTTREALIFIISSGSNLRASREVQSAISQRLKKYPEKAANSKHRAICTVPRSIVQVLKQNPRLISSAVN 238 (635)
T ss_pred ccchhhccCCCccHHHHHHHHHhcccchhhhHHHHHHHHHHHHhchhhHHHhhhhheeeccHHHHHHHhhCchHHHHHHH
Confidence 467888999999999999876666555555542 443443 4578899999999
Q ss_pred HHHHHHHHHHHHHHHH
Q 032126 74 KFVAEVATDALQQCKA 89 (147)
Q Consensus 74 KFisDIa~DA~q~~ki 89 (147)
.|---=..|--.+.++
T Consensus 239 aFy~RD~id~ka~r~m 254 (635)
T KOG2406|consen 239 AFYYRDPIDEKACRRM 254 (635)
T ss_pred HHHhcCchhHHHHHHH
Confidence 9975433333333333
No 35
>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=48.87 E-value=14 Score=22.18 Aligned_cols=19 Identities=32% Similarity=0.560 Sum_probs=15.7
Q ss_pred eeeHHHHHHHHHHhCcccC
Q 032126 109 ILTMEDLSKALREYGVNVK 127 (147)
Q Consensus 109 vLTmEDLs~AL~EyGInvk 127 (147)
.||+.||...|+++|+...
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 36
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=48.49 E-value=62 Score=29.47 Aligned_cols=52 Identities=12% Similarity=0.198 Sum_probs=42.2
Q ss_pred CCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 032126 30 GYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKA 89 (147)
Q Consensus 30 dY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~ki 89 (147)
+|.=-+--..+..+.+..|+.|.+.-- -.++...+|+||-.++..|.-|+.+
T Consensus 25 ~ya~sla~~avaQIcqslg~~~~~~sa--------le~Ltd~~~qyvQ~lgk~a~~~~n~ 76 (353)
T KOG2389|consen 25 EYAFSLARVAVAQICQSLGYSSTQNSA--------LETLTDVLQQYVQNLGKTAHRYSNL 76 (353)
T ss_pred HHHHHHHHHHHHHHHHhcCCcccccHH--------HHHHHHHHHHHHHHHHhhhhhhhhh
Confidence 444455567899999999999976555 5778888999999999999999863
No 37
>PF04239 DUF421: Protein of unknown function (DUF421); InterPro: IPR007353 This family of uncharacterised proteins is known as YDFR family; PDB: 3C6F_D.
Probab=46.95 E-value=10 Score=27.46 Aligned_cols=19 Identities=53% Similarity=0.704 Sum_probs=14.7
Q ss_pred cceeeeHHHHHHHHHHhCc
Q 032126 106 KRLILTMEDLSKALREYGV 124 (147)
Q Consensus 106 ~r~vLTmEDLs~AL~EyGI 124 (147)
+|.-+|++||..+|++.||
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 5678999999999999999
No 38
>PRK13710 plasmid maintenance protein CcdA; Provisional
Probab=42.81 E-value=12 Score=26.45 Aligned_cols=22 Identities=27% Similarity=0.419 Sum_probs=17.1
Q ss_pred ceeeeH-HHHHHHHHHhCcccCC
Q 032126 107 RLILTM-EDLSKALREYGVNVKH 128 (147)
Q Consensus 107 r~vLTm-EDLs~AL~EyGInvkr 128 (147)
++.||+ .||...+++.|||+++
T Consensus 4 ~vnltld~dll~~ar~~giNlS~ 26 (72)
T PRK13710 4 RITVTVDSDSYQLLKAADVNISG 26 (72)
T ss_pred ceEeeECHHHHHHHHHcCCcHHH
Confidence 466665 4788888999999874
No 39
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=42.14 E-value=29 Score=28.61 Aligned_cols=37 Identities=30% Similarity=0.539 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHHHHHhCc
Q 032126 73 QKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGV 124 (147)
Q Consensus 73 QKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~AL~EyGI 124 (147)
-.|||=|...|-.-| ++++|=|+|=|||.-||..-|.
T Consensus 65 SEfISFvT~EAsekC---------------~~EkRKTIngdDllwAm~tLGF 101 (168)
T KOG0869|consen 65 SEFISFVTGEASEKC---------------QREKRKTINGDDLLWAMSTLGF 101 (168)
T ss_pred HHHHHHHhhHHHHHH---------------HHHhcCcccHHHHHHHHHHcCc
Confidence 457777777777766 2455668999999999998886
No 40
>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=41.91 E-value=1.2e+02 Score=21.23 Aligned_cols=66 Identities=29% Similarity=0.371 Sum_probs=40.1
Q ss_pred cHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHH
Q 032126 36 PDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDL 115 (147)
Q Consensus 36 PD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDL 115 (147)
|.+++...|+ ..|..+..|| +---.+|++=-..-||.+-+.-|.+.++.. .+. .+++.|||
T Consensus 1 p~~li~rll~-~~f~~~~tkI----s~dal~l~~eyl~iFV~EAv~Ra~~~a~~e-------------~~~-~~le~e~L 61 (72)
T PF09415_consen 1 PPELIARLLH-EHFKDDKTKI----SKDALKLSAEYLRIFVREAVARAAEQAEAE-------------GDE-GFLEVEHL 61 (72)
T ss_dssp -CHHHHHHHC-TTSSSTT-EE-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHT-------------T-S-SEE-HHHH
T ss_pred ChHHHHHHHH-HHhcCCCCCc----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-------------CCC-CCCCHHHH
Confidence 6788889999 8898888887 223345666556667776666665543211 000 18999999
Q ss_pred HHHHH
Q 032126 116 SKALR 120 (147)
Q Consensus 116 s~AL~ 120 (147)
.+.+.
T Consensus 62 Eki~p 66 (72)
T PF09415_consen 62 EKILP 66 (72)
T ss_dssp HHHCH
T ss_pred HHHHH
Confidence 88653
No 41
>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=40.81 E-value=19 Score=22.12 Aligned_cols=23 Identities=22% Similarity=0.459 Sum_probs=17.6
Q ss_pred HHHHHHHHHHhCcccCCCCcccc
Q 032126 112 MEDLSKALREYGVNVKHQEYFAD 134 (147)
Q Consensus 112 mEDLs~AL~EyGInvkrP~Yy~d 134 (147)
+-++...|.++||||..=.-+.+
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 56899999999999975444433
No 42
>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=40.12 E-value=21 Score=24.91 Aligned_cols=20 Identities=35% Similarity=0.473 Sum_probs=13.3
Q ss_pred eeeeHHHHHHHHHHhCcccC
Q 032126 108 LILTMEDLSKALREYGVNVK 127 (147)
Q Consensus 108 ~vLTmEDLs~AL~EyGInvk 127 (147)
-+-|-+||...|+++||.|.
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 43
>PF15374 CCDC71L: Coiled-coil domain-containing protein 71L
Probab=40.11 E-value=19 Score=32.85 Aligned_cols=28 Identities=39% Similarity=0.593 Sum_probs=22.4
Q ss_pred CCCCCCCCCchHHHHHHHHcC--CCCCCCc
Q 032126 9 QSSDGRHDDDAALTEFLSSLM--GYTPTIP 36 (147)
Q Consensus 9 ~~~~~~~~~d~~L~efl~~Ld--dY~P~IP 36 (147)
-++.+-.+.|.+|.-||+.|. +|.|+|=
T Consensus 29 PmS~dl~~te~qLv~Flq~Lr~eGfqP~IL 58 (376)
T PF15374_consen 29 PMSKDLSDTEAQLVAFLQGLRHEGFQPTIL 58 (376)
T ss_pred ccccccchhHHHHHHHHHHHhhcCCCceee
Confidence 455666778999999999994 4999983
No 44
>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=39.36 E-value=9.9 Score=30.15 Aligned_cols=33 Identities=15% Similarity=0.393 Sum_probs=0.0
Q ss_pred ceeeeHHHHHHHHHHhCcccCCCCccccCCCCC
Q 032126 107 RLILTMEDLSKALREYGVNVKHQEYFADNPSTG 139 (147)
Q Consensus 107 r~vLTmEDLs~AL~EyGInvkrP~Yy~d~~~~~ 139 (147)
--.|||||+..|-=|--.++.+|.|+-..|..+
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 348999999999999999999999997776654
No 45
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=39.36 E-value=24 Score=27.41 Aligned_cols=39 Identities=15% Similarity=0.175 Sum_probs=34.5
Q ss_pred HHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHH
Q 032126 39 LVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQ 85 (147)
Q Consensus 39 Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q 85 (147)
=+..+|...|.++.+.|| ..+||...-|=|.||+...-.
T Consensus 22 DikkIl~sVG~E~d~e~i--------~~visel~GK~i~ElIA~G~e 60 (112)
T KOG3449|consen 22 DIKKILESVGAEIDDERI--------NLVLSELKGKDIEELIAAGRE 60 (112)
T ss_pred HHHHHHHHhCcccCHHHH--------HHHHHHhcCCCHHHHHHHhHH
Confidence 367899999999999999 999999999999999876543
No 46
>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=39.08 E-value=37 Score=21.61 Aligned_cols=29 Identities=24% Similarity=0.363 Sum_probs=24.3
Q ss_pred HHHHHHHHcCCCCCCCcHHHHHHHHHhCC
Q 032126 20 ALTEFLSSLMGYTPTIPDELVEHYLAKSG 48 (147)
Q Consensus 20 ~L~efl~~LddY~P~IPD~Vt~yyL~~aG 48 (147)
+++++++.|.+-.=-||+.+.+..|+++|
T Consensus 20 ~~~~~l~~l~~~g~~is~~l~~~~L~~~g 48 (48)
T PF11848_consen 20 EVKPLLDRLQQAGFRISPKLIEEILRRAG 48 (48)
T ss_pred hHHHHHHHHHHcCcccCHHHHHHHHHHcC
Confidence 67778888887777899999999998887
No 47
>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=37.40 E-value=40 Score=26.40 Aligned_cols=41 Identities=24% Similarity=0.328 Sum_probs=31.8
Q ss_pred CCCCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 14 RHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 14 ~~~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
.|.-..-|..|+..|- .|+||.++.+.+++-.+.+..+.|+
T Consensus 67 ~~~va~~LK~flr~Lp--epLi~~~~~~~~~~~~~~~~~~~~i 107 (186)
T cd04377 67 IHVITSVLKQWLRELP--EPLMTFELYENFLRAMELEEKQERV 107 (186)
T ss_pred HHHHHHHHHHHHHcCC--CccCCHHHHHHHHHHHhcCCHHHHH
Confidence 3444566889999997 5999999999999988766555555
No 48
>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=35.31 E-value=59 Score=25.42 Aligned_cols=42 Identities=19% Similarity=0.265 Sum_probs=32.2
Q ss_pred CCCCCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 13 GRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 13 ~~~~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
+.|.-..-|..||..|- .|+||.++.+.+.+-.+-...+.|+
T Consensus 70 d~h~va~lLK~fLReLP--~pLi~~~~~~~~~~~~~~~~~~~r~ 111 (182)
T cd04381 70 EPPTVASLLKQYLRELP--EPLLTKELMPRFEEACGRPTEAERE 111 (182)
T ss_pred ChHHHHHHHHHHHHhCC--CccCCHHHHHHHHHHcCCCCHHHHH
Confidence 34444567889999998 5999999999998887765555565
No 49
>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=35.31 E-value=47 Score=26.87 Aligned_cols=40 Identities=20% Similarity=0.319 Sum_probs=31.3
Q ss_pred CCCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 15 HDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 15 ~~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
|.-...|..||..|-+ |+||.++-+-++.-++-+..+.|+
T Consensus 87 h~va~lLK~fLReLPe--PLi~~~~y~~~i~~~~~~~~~~ri 126 (203)
T cd04374 87 KTITSALKTYLRNLPE--PLMTYELHNDFINAAKSENLESRV 126 (203)
T ss_pred HHHHHHHHHHHHcCCC--CcCCHHHHHHHHHHHhCCCHHHHH
Confidence 3445567889999984 999999999999887766666666
No 50
>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=33.93 E-value=39 Score=20.07 Aligned_cols=17 Identities=24% Similarity=0.231 Sum_probs=13.7
Q ss_pred hhHHHHHHHHHHHHHHH
Q 032126 64 RIRLVAVATQKFVAEVA 80 (147)
Q Consensus 64 ~~RLvSLAaQKFisDIa 80 (147)
|+=|=.++|+|||..+.
T Consensus 11 s~~L~~~aak~fl~~L~ 27 (28)
T PF00123_consen 11 SKYLDQLAAKKFLQWLM 27 (28)
T ss_dssp HHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 45577899999998875
No 51
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=33.83 E-value=97 Score=23.57 Aligned_cols=74 Identities=20% Similarity=0.288 Sum_probs=47.7
Q ss_pred CCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhccccccccee
Q 032126 30 GYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLI 109 (147)
Q Consensus 30 dY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~v 109 (147)
|-..-|..--+.-.-.++|+. || .-+||--+ -=++.-||.|++.+|.-|.. .-+|-+
T Consensus 25 DnIqgitKpaIRRlARr~GVk----Ri-~G~~yeE~---~~~~k~fl~n~i~~A~~yt~---------------HAKRKT 81 (103)
T KOG3467|consen 25 DNIQGITKPAIRRLARRGGVK----RI-SGLIYEET---RGVLKVFLENVIRDAVTYTE---------------HAKRKT 81 (103)
T ss_pred hhccccchHHHHHHHHhcCcc----hh-chhhHHHH---HHHHHHHHHHHHHHHHHHHh---------------hhhhce
Confidence 333344455566677777763 33 11222222 23567899999999999863 122347
Q ss_pred eeHHHHHHHHHHhCccc
Q 032126 110 LTMEDLSKALREYGVNV 126 (147)
Q Consensus 110 LTmEDLs~AL~EyGInv 126 (147)
.|--|+.-+|+..|+..
T Consensus 82 vT~~dvv~~LKR~G~~~ 98 (103)
T KOG3467|consen 82 VTAMDVVYALKRQGRTL 98 (103)
T ss_pred eeHHHHHHHHHHcCcee
Confidence 89999999999999864
No 52
>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=33.49 E-value=23 Score=22.54 Aligned_cols=30 Identities=23% Similarity=0.429 Sum_probs=22.9
Q ss_pred eeHHHHHHHHHHhCcccCCCCccccCCCCC
Q 032126 110 LTMEDLSKALREYGVNVKHQEYFADNPSTG 139 (147)
Q Consensus 110 LTmEDLs~AL~EyGInvkrP~Yy~d~~~~~ 139 (147)
+|.+|....|+++|+++..-.++.+....|
T Consensus 9 ~~~~~a~~~l~~~g~~~~~~~~~~~~~~~g 38 (63)
T PF03793_consen 9 MTYDEAKSILEAAGLTVNVVEEYSDSVPKG 38 (63)
T ss_dssp SBHHHHHHHHHHTT-EEEEEEEEESSSSTT
T ss_pred CcHHHHHHHHHHCCCEEEEEEEecCCCCCC
Confidence 688999999999999877777666665555
No 53
>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=33.00 E-value=60 Score=25.55 Aligned_cols=37 Identities=24% Similarity=0.447 Sum_probs=29.2
Q ss_pred chHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 18 d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
..-|..||..|- .|+||.++.+-+++.+..+.++.|+
T Consensus 77 a~llK~flr~Lp--~pli~~~~~~~~i~~~~~~~~~~~i 113 (196)
T cd04395 77 SSLLKSFFRKLP--EPLFTNELYPDFIEANRIEDPVERL 113 (196)
T ss_pred HHHHHHHHHhCC--CccCCHHHHHHHHHHHcCCCHHHHH
Confidence 356788999997 8999999999998877655555665
No 54
>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=32.78 E-value=51 Score=25.93 Aligned_cols=42 Identities=12% Similarity=0.211 Sum_probs=31.0
Q ss_pred CCCCCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 13 GRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 13 ~~~~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
+.|.-..-|..||..|- .|+||.++.+-+++-.+....+.|+
T Consensus 65 ~~~~va~~lK~flreLp--epLi~~~~~~~~~~~~~~~~~~~~i 106 (192)
T cd04402 65 PVLLLASVLKDFLRNIP--GSLLSSDLYEEWMSALDQENEEEKI 106 (192)
T ss_pred CHHHHHHHHHHHHHhCC--CccCCHHHHHHHHHHHccCCHHHHH
Confidence 34445566788999998 5999999999998877665444444
No 55
>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=32.55 E-value=31 Score=21.71 Aligned_cols=19 Identities=21% Similarity=0.385 Sum_probs=15.7
Q ss_pred eHHHHHHHHHHhCcccCCC
Q 032126 111 TMEDLSKALREYGVNVKHQ 129 (147)
Q Consensus 111 TmEDLs~AL~EyGInvkrP 129 (147)
.+.++...|+++|+||..=
T Consensus 12 ~l~~i~~~l~~~~inI~~~ 30 (73)
T cd04902 12 VIGKVGTILGEAGINIAGM 30 (73)
T ss_pred HHHHHHHHHHHcCcChhhe
Confidence 4677899999999999653
No 56
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=31.34 E-value=67 Score=24.28 Aligned_cols=41 Identities=20% Similarity=0.287 Sum_probs=32.6
Q ss_pred CCchHHHHHHHHcC-CCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 16 DDDAALTEFLSSLM-GYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 16 ~~d~~L~efl~~Ld-dY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
.+-.+|=|||..|- +-.|+-=-+|.+.|.+..||.++=|.-
T Consensus 15 ~~~~~iF~FL~~~P~GT~~~~iR~~L~rYI~~~G~~~PiP~~ 56 (97)
T PRK13916 15 EDYPQIFDFLENVPRGTKTAHIREALRRYIEEIGENPPIPSK 56 (97)
T ss_pred cccHHHHHHHHHCCCCCccHHHHHHHHHHHHhcCCCCCCCcc
Confidence 34567889999995 467887788999999999999875543
No 57
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=31.06 E-value=43 Score=31.56 Aligned_cols=46 Identities=15% Similarity=0.248 Sum_probs=35.4
Q ss_pred HHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHH
Q 032126 39 LVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCK 88 (147)
Q Consensus 39 Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~k 88 (147)
|++|.++..+. -.|.+| ..--...|++++.+||-|-|+.-|+.|+-
T Consensus 376 VIQHVie~g~~-~~~~~I---~~~l~~~ll~~Sq~KfASnVVEk~~~~a~ 421 (503)
T KOG1488|consen 376 VIQHVIEHGSP-YRDTII---IKCLLGNLLSMSQHKFASNVVEKAFLFAP 421 (503)
T ss_pred HHHHHHhcCCh-hhhhhH---HHHHHhhHHHHHHHHHHHHHHHHHHhhCC
Confidence 78899988777 445555 22223679999999999999999999863
No 58
>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=30.85 E-value=28 Score=22.92 Aligned_cols=12 Identities=42% Similarity=0.924 Sum_probs=10.2
Q ss_pred CCCCcHHHHHHH
Q 032126 32 TPTIPDELVEHY 43 (147)
Q Consensus 32 ~P~IPD~Vt~yy 43 (147)
-|.||+|+|+-|
T Consensus 33 EpEVP~ELt~l~ 44 (45)
T PF05931_consen 33 EPEVPKELTKLY 44 (45)
T ss_pred CCcCcHHHHhhc
Confidence 589999999854
No 59
>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=30.65 E-value=38 Score=22.13 Aligned_cols=25 Identities=8% Similarity=0.181 Sum_probs=20.9
Q ss_pred eHHHHHHHHHHhCcccCCCCccccC
Q 032126 111 TMEDLSKALREYGVNVKHQEYFADN 135 (147)
Q Consensus 111 TmEDLs~AL~EyGInvkrP~Yy~d~ 135 (147)
.+.+++..|.++|+||..=..+.+.
T Consensus 12 iv~~it~~l~~~~~nI~~~~~~~~~ 36 (81)
T cd04869 12 IVHEVTQFLAQRNINIEDLSTETYS 36 (81)
T ss_pred HHHHHHHHHHHcCCCeEEeEeeeec
Confidence 3678999999999999887776665
No 60
>smart00428 H3 Histone H3.
Probab=29.74 E-value=1.6e+02 Score=22.19 Aligned_cols=44 Identities=18% Similarity=0.198 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHHHHHhCcc
Q 032126 67 LVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGVN 125 (147)
Q Consensus 67 LvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~AL~EyGIn 125 (147)
.+--|+..|+..+..||..++.. -+|+||+.+|+..|..=.|.+
T Consensus 61 aLQeasE~ylv~lfeda~~~a~H---------------AkRvTl~~kDi~La~rir~~~ 104 (105)
T smart00428 61 ALQEAAEAYLVGLFEDTNLLAIH---------------AKRVTIMPKDIQLARRIRGER 104 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH---------------hCCccCcHhhHHHHHHHhccC
Confidence 45557888999999998877632 246899999999888766654
No 61
>PF14914 LRRC37AB_C: LRRC37A/B like protein 1 C-terminal domain
Probab=29.17 E-value=41 Score=27.37 Aligned_cols=36 Identities=19% Similarity=0.518 Sum_probs=28.1
Q ss_pred CCCCCcHH----HHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHH
Q 032126 31 YTPTIPDE----LVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAE 78 (147)
Q Consensus 31 Y~P~IPD~----Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisD 78 (147)
-.|+||+. ++.|....--.+|+++++ -||+-|.||-
T Consensus 19 L~~LIPn~~vR~lIShVirtLkmDCse~~v------------qlaCAKLISr 58 (154)
T PF14914_consen 19 LQSLIPNNDVRRLISHVIRTLKMDCSEPHV------------QLACAKLISR 58 (154)
T ss_pred HHHhCCChHHHHHHHHHHHHHHhhcCCCcc------------cHHHHHHHHH
Confidence 47999996 677888888899999998 4556666654
No 62
>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=29.13 E-value=42 Score=22.27 Aligned_cols=17 Identities=24% Similarity=0.374 Sum_probs=14.9
Q ss_pred HHHHHHHHHHhCcccCC
Q 032126 112 MEDLSKALREYGVNVKH 128 (147)
Q Consensus 112 mEDLs~AL~EyGInvkr 128 (147)
+.+++.+|.++|+||-.
T Consensus 13 v~~vt~~la~~~~nI~d 29 (75)
T cd04870 13 TSALTEVLAAHGVRILD 29 (75)
T ss_pred HHHHHHHHHHCCCCEEe
Confidence 57899999999999864
No 63
>PRK03341 arginine repressor; Provisional
Probab=28.87 E-value=41 Score=27.06 Aligned_cols=21 Identities=19% Similarity=0.390 Sum_probs=17.6
Q ss_pred ceeeeHHHHHHHHHHhCcccC
Q 032126 107 RLILTMEDLSKALREYGVNVK 127 (147)
Q Consensus 107 r~vLTmEDLs~AL~EyGInvk 127 (147)
+-+-|.|||...|++.||+|.
T Consensus 27 ~~i~tQ~eL~~~L~~~Gi~vT 47 (168)
T PRK03341 27 QSVRSQAELAALLADEGIEVT 47 (168)
T ss_pred CCCccHHHHHHHHHHcCCccc
Confidence 447789999999999999874
No 64
>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=28.78 E-value=95 Score=25.65 Aligned_cols=38 Identities=13% Similarity=0.137 Sum_probs=32.9
Q ss_pred HHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHH
Q 032126 41 EHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQ 86 (147)
Q Consensus 41 ~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~ 86 (147)
...+...|++..+... ..||.+|.+.|+-+|+..++..
T Consensus 213 ~~ia~e~GL~gvs~~~--------a~ll~~ale~~LK~lI~s~l~~ 250 (252)
T PF12767_consen 213 EQIAWEHGLGGVSDDC--------ANLLNLALEVHLKNLIKSCLDL 250 (252)
T ss_pred HHHHHHcCCCCCCHHH--------HHHHHHHHHHHHHHHHHHHHhh
Confidence 4466788998888888 9999999999999999988764
No 65
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=28.76 E-value=1.4e+02 Score=24.76 Aligned_cols=69 Identities=20% Similarity=0.308 Sum_probs=43.1
Q ss_pred CcHHHHHHHHHhCCCCCCCcccccccccchhH--HHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeH
Q 032126 35 IPDELVEHYLAKSGFQCPDVRLNCCLCFCRIR--LVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTM 112 (147)
Q Consensus 35 IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~R--LvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTm 112 (147)
+|-+++--...+.==+| |..| ++-- -|+=||-=||.=+..-|-++|+ +.+|-+++-
T Consensus 11 lP~AiI~rlvke~l~E~-~vsi------sKeA~~Ai~raAtVFv~~Lts~s~e~A~---------------~q~rKt~sa 68 (172)
T KOG0870|consen 11 LPNAIITRLVKEVLPES-NVSI------SKEARLAIARAATVFVIFLTSVSNEIAK---------------DQKRKTISA 68 (172)
T ss_pred ccHHHHHHHHHHhCccc-cccc------cHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------hcccCcccH
Confidence 57777765555544444 3333 1111 3445666677777666666663 334568999
Q ss_pred HHHHHHHHHhCcc
Q 032126 113 EDLSKALREYGVN 125 (147)
Q Consensus 113 EDLs~AL~EyGIn 125 (147)
+|+-+||.|.|..
T Consensus 69 dDVl~aL~Eiefs 81 (172)
T KOG0870|consen 69 DDVLKALDEIEFS 81 (172)
T ss_pred HHHHHHHHHhchH
Confidence 9999999998753
No 66
>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=28.02 E-value=67 Score=25.71 Aligned_cols=37 Identities=19% Similarity=0.312 Sum_probs=28.3
Q ss_pred chHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 18 d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
..-|..|+..|-+ |+||.++.+.+++..+.+.+..|+
T Consensus 74 a~lLK~fLReLPe--PLip~~~y~~~~~~~~~~~~~~~~ 110 (196)
T cd04387 74 AGTLKLYFRELPE--PLFTDELYPNFAEGIALSDPVAKE 110 (196)
T ss_pred HHHHHHHHHhCCC--ccCCHHHHHHHHHHHHcCCHHHHH
Confidence 4578889998874 999999999999877665444443
No 67
>PRK00441 argR arginine repressor; Provisional
Probab=27.47 E-value=34 Score=26.76 Aligned_cols=22 Identities=32% Similarity=0.510 Sum_probs=18.4
Q ss_pred eeeeHHHHHHHHHHhCcccCCC
Q 032126 108 LILTMEDLSKALREYGVNVKHQ 129 (147)
Q Consensus 108 ~vLTmEDLs~AL~EyGInvkrP 129 (147)
-+.|.+||..+|++.|++|..+
T Consensus 17 ~~~~q~eL~~~L~~~G~~vSqa 38 (149)
T PRK00441 17 EIETQEELAEELKKMGFDVTQA 38 (149)
T ss_pred CCCcHHHHHHHHHhcCCCcCHH
Confidence 3668999999999999998643
No 68
>COG0599 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]
Probab=27.21 E-value=44 Score=24.61 Aligned_cols=46 Identities=20% Similarity=0.294 Sum_probs=33.5
Q ss_pred hHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCC---CCCcccccccccchhHHHHHHH
Q 032126 19 AALTEFLSSLMGYTPTIPDELVEHYLAKSGFQ---CPDVRLNCCLCFCRIRLVAVAT 72 (147)
Q Consensus 19 ~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~---~~D~Rv~~~~~~~~~RLvSLAa 72 (147)
.....+...++++.|..||-.+.+++-..-+. .=|+|. +.||+||.
T Consensus 15 ~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~Ld~kt--------r~Li~ia~ 63 (124)
T COG0599 15 KVDKALAEGLEDFAPEFPELLEAFYAFGEIWFRKGALDAKT--------RELIAIAV 63 (124)
T ss_pred HHHHHHHhhHHHHhHhhHHHHHHHHHhhhHHhcCCCCCHHH--------HHHHHHHH
Confidence 45566777888899999999999444322222 248899 99999885
No 69
>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=26.55 E-value=46 Score=20.10 Aligned_cols=19 Identities=21% Similarity=0.396 Sum_probs=16.0
Q ss_pred eHHHHHHHHHHhCcccCCC
Q 032126 111 TMEDLSKALREYGVNVKHQ 129 (147)
Q Consensus 111 TmEDLs~AL~EyGInvkrP 129 (147)
.+.++...|.++|+||..=
T Consensus 12 ~l~~i~~~l~~~~~nI~~~ 30 (71)
T cd04879 12 VIGKVGTILGEHGINIAAM 30 (71)
T ss_pred HHHHHHHHHHhcCCCeeeE
Confidence 4678999999999999643
No 70
>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=26.50 E-value=49 Score=20.48 Aligned_cols=17 Identities=24% Similarity=0.692 Sum_probs=15.0
Q ss_pred eHHHHHHHHHHhCcccC
Q 032126 111 TMEDLSKALREYGVNVK 127 (147)
Q Consensus 111 TmEDLs~AL~EyGInvk 127 (147)
.+.||..+|.++|++|.
T Consensus 13 ~l~~i~~~l~~~~~~I~ 29 (70)
T cd04873 13 LLADITRVLADLGLNIH 29 (70)
T ss_pred HHHHHHHHHHHCCCeEE
Confidence 36899999999999995
No 71
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=26.47 E-value=55 Score=21.20 Aligned_cols=18 Identities=28% Similarity=0.521 Sum_probs=16.1
Q ss_pred eeeHHHHHHHHHHhCccc
Q 032126 109 ILTMEDLSKALREYGVNV 126 (147)
Q Consensus 109 vLTmEDLs~AL~EyGInv 126 (147)
.|+-++|...|.+||+..
T Consensus 5 ~LSd~eL~~~L~~~G~~~ 22 (44)
T smart00540 5 RLSDAELRAELKQYGLPP 22 (44)
T ss_pred HcCHHHHHHHHHHcCCCC
Confidence 588899999999999975
No 72
>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=26.17 E-value=1.3e+02 Score=23.60 Aligned_cols=33 Identities=21% Similarity=0.178 Sum_probs=25.5
Q ss_pred CCCCCchHHHHHHHHcCCCCCCCcHHHHHHHHHhC
Q 032126 13 GRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKS 47 (147)
Q Consensus 13 ~~~~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~a 47 (147)
+.|.-..-|..|+..|-+ |+||.++.+.+++-.
T Consensus 71 d~~~va~~lK~flr~Lp~--pLi~~~~~~~l~~~~ 103 (189)
T cd04393 71 DVCSAASLLRLFLQELPE--GLIPASLQIRLMQLY 103 (189)
T ss_pred CHHHHHHHHHHHHHhCCC--ccCCHHHHHHHHHHH
Confidence 344455678899999984 999999998888643
No 73
>PRK05066 arginine repressor; Provisional
Probab=26.00 E-value=47 Score=26.28 Aligned_cols=21 Identities=19% Similarity=0.347 Sum_probs=16.9
Q ss_pred ceeeeHHHHHHHHHHhCcc-cC
Q 032126 107 RLILTMEDLSKALREYGVN-VK 127 (147)
Q Consensus 107 r~vLTmEDLs~AL~EyGIn-vk 127 (147)
.-+=|-|||...|+++||+ |.
T Consensus 21 ~~I~tQeeL~~~L~~~Gi~~vT 42 (156)
T PRK05066 21 EKFGSQGEIVTALQEQGFDNIN 42 (156)
T ss_pred CCCCCHHHHHHHHHHCCCCeec
Confidence 3466889999999999998 53
No 74
>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=25.89 E-value=89 Score=24.73 Aligned_cols=41 Identities=27% Similarity=0.370 Sum_probs=30.5
Q ss_pred CCCCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 14 RHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 14 ~~~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
.|.-..-|..||..|- .|+||.++.+-+++-..-...+.|+
T Consensus 74 ~h~va~~lK~fLreLp--~pli~~~~~~~~~~~~~~~~~~~~~ 114 (203)
T cd04386 74 PHAVASALKSYLRELP--DPLLTYNLYEDWVQAANKPDEDERL 114 (203)
T ss_pred HHHHHHHHHHHHHhCC--CccCCHHHHHHHHHHHccCCHHHHH
Confidence 3444566788999997 5999999999999877655444454
No 75
>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=25.78 E-value=61 Score=24.31 Aligned_cols=23 Identities=35% Similarity=0.592 Sum_probs=17.8
Q ss_pred cCCCCCCCcHHHHHHHHHhCCCCC
Q 032126 28 LMGYTPTIPDELVEHYLAKSGFQC 51 (147)
Q Consensus 28 LddY~P~IPD~Vt~yyL~~aGf~~ 51 (147)
++.|...+|+++++| .+.-||-.
T Consensus 25 I~kyk~~lP~~Ll~~-W~~~G~g~ 47 (109)
T PF08887_consen 25 IEKYKGKLPDELLEY-WKEYGFGG 47 (109)
T ss_pred HHHhcCCCcHHHHHH-HHHcCCch
Confidence 467999999999986 56677754
No 76
>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=25.64 E-value=84 Score=24.83 Aligned_cols=40 Identities=18% Similarity=0.230 Sum_probs=29.6
Q ss_pred CCCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 15 HDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 15 ~~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
|.-..-|..|+..|-+ |+||.++.+-++.-...+....|+
T Consensus 68 h~va~lLK~flReLPe--pLi~~~~~~~~~~~~~~~~~~~~~ 107 (186)
T cd04407 68 HAITGLLKQWLRELPE--PLMTFAQYNDFLRAVELPEKQEQL 107 (186)
T ss_pred HHHHHHHHHHHHhCCC--ccCCHHHHHHHHHHHHCCCHHHHH
Confidence 3445567889999986 999999999998876554444444
No 77
>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=25.52 E-value=75 Score=24.90 Aligned_cols=37 Identities=24% Similarity=0.373 Sum_probs=28.6
Q ss_pred chHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 18 d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
...|..||..|-+ |+||.++.+.+++...-+..+.|+
T Consensus 74 a~lLK~fLReLPe--pLi~~~~~~~~~~~~~~~~~~~~i 110 (187)
T cd04403 74 TGALKLFFRELPE--PLFPYSLFNDFVAAIKLSDYEQRV 110 (187)
T ss_pred HHHHHHHHhcCCC--CcCCHHHHHHHHHHHHCCCHHHHH
Confidence 4578889999984 999999999998876554445555
No 78
>cd04372 RhoGAP_chimaerin RhoGAP_chimaerin: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of chimaerins. Chimaerins are a family of phorbolester- and diacylglycerol-responsive GAPs specific for the Rho-like GTPase Rac. Chimaerins exist in two alternative splice forms that each contain a C-terminal GAP domain, and a central C1 domain which binds phorbol esters, inducing a conformational change that activates the protein; one splice form is lacking the N-terminal Src homology-2 (SH2) domain. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GT
Probab=25.41 E-value=91 Score=24.57 Aligned_cols=37 Identities=24% Similarity=0.395 Sum_probs=28.8
Q ss_pred chHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 18 d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
..-|..||..|-+ |+||.++.+.+++-+.....|.|+
T Consensus 75 a~lLK~flReLP~--pLi~~~~~~~~~~~~~~~~~~~~~ 111 (194)
T cd04372 75 TGALKLYFRDLPI--PVITYDTYPKFIDAAKISNPDERL 111 (194)
T ss_pred HHHHHHHHHhCCC--ccCCHHHHHHHHHHHhcCCHHHHH
Confidence 4567889998874 999999999999877655555565
No 79
>COG1438 ArgR Arginine repressor [Transcription]
Probab=25.31 E-value=46 Score=26.64 Aligned_cols=20 Identities=40% Similarity=0.574 Sum_probs=16.7
Q ss_pred eeeHHHHHHHHHHhCcccCC
Q 032126 109 ILTMEDLSKALREYGVNVKH 128 (147)
Q Consensus 109 vLTmEDLs~AL~EyGInvkr 128 (147)
+-|-|+|...|+|+||.|..
T Consensus 20 i~TQ~Elv~~L~~~Gi~vTQ 39 (150)
T COG1438 20 ISTQEELVELLQEEGIEVTQ 39 (150)
T ss_pred CCCHHHHHHHHHHcCCeEeh
Confidence 66889999999999998753
No 80
>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=24.81 E-value=86 Score=24.95 Aligned_cols=41 Identities=17% Similarity=0.246 Sum_probs=30.7
Q ss_pred CCCCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 14 RHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 14 ~~~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
.|.-..-|..|+..|-+ |+||.++.+.+++-..-+..+.|+
T Consensus 72 ~h~va~lLK~flReLPe--PLi~~~~y~~~~~~~~~~~~~~~~ 112 (195)
T cd04384 72 IHSVSSLCKLYFRELPN--PLLTYQLYEKFSEAVSAASDEERL 112 (195)
T ss_pred HHHHHHHHHHHHHhCCC--ccCCHHHHHHHHHHHhcCCHHHHH
Confidence 34445567899999985 999999999998876655445555
No 81
>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=24.80 E-value=65 Score=27.05 Aligned_cols=25 Identities=32% Similarity=0.608 Sum_probs=19.8
Q ss_pred ccceeeeHHHHHHHHHHhCcccCCC
Q 032126 105 DKRLILTMEDLSKALREYGVNVKHQ 129 (147)
Q Consensus 105 d~r~vLTmEDLs~AL~EyGInvkrP 129 (147)
+--.|||+++|..-|++.||++..-
T Consensus 150 ~vD~VLT~~El~~~l~~~~i~~~~~ 174 (285)
T PF02906_consen 150 DVDYVLTFEELAELLKEKGIDLAEL 174 (285)
T ss_dssp SSSEEEEHHHHHHHHHHTT--GGGS
T ss_pred ccCEechHHHHHHHHHHcCCChhHC
Confidence 4468999999999999999997653
No 82
>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=24.66 E-value=58 Score=28.42 Aligned_cols=24 Identities=25% Similarity=0.553 Sum_probs=20.9
Q ss_pred ccceeeeHHHHHHHHHHhCcccCC
Q 032126 105 DKRLILTMEDLSKALREYGVNVKH 128 (147)
Q Consensus 105 d~r~vLTmEDLs~AL~EyGInvkr 128 (147)
+--.|||+++|..-|++.||++..
T Consensus 236 ~vD~vlT~~El~~~~~~~~i~~~~ 259 (374)
T TIGR02512 236 DVDAVLTTRELARMIKEAGIDFAK 259 (374)
T ss_pred cccEEeeHHHHHHHHHHcCCChhh
Confidence 455799999999999999999854
No 83
>COG3830 ACT domain-containing protein [Signal transduction mechanisms]
Probab=24.02 E-value=53 Score=24.48 Aligned_cols=16 Identities=38% Similarity=0.578 Sum_probs=14.0
Q ss_pred HHHHHHHHHHhCcccC
Q 032126 112 MEDLSKALREYGVNVK 127 (147)
Q Consensus 112 mEDLs~AL~EyGInvk 127 (147)
.-+++.+|+|+||||-
T Consensus 17 va~is~vLAe~~vNIl 32 (90)
T COG3830 17 VAAVSRVLAEHGVNIL 32 (90)
T ss_pred hHHHHHHHHHcCCcEE
Confidence 4689999999999984
No 84
>PF08862 DUF1829: Domain of unknown function DUF1829; InterPro: IPR014961 This short protein is usually associated with IPR014960 from INTERPRO.
Probab=23.69 E-value=54 Score=23.45 Aligned_cols=15 Identities=33% Similarity=0.612 Sum_probs=13.4
Q ss_pred HHHHHHHHHHhCccc
Q 032126 112 MEDLSKALREYGVNV 126 (147)
Q Consensus 112 mEDLs~AL~EyGInv 126 (147)
.+|+..||.+|||++
T Consensus 68 ~~~~~~a~~~y~I~~ 82 (88)
T PF08862_consen 68 SEDIINALEQYNIKP 82 (88)
T ss_pred CHHHHHHHHHCCCce
Confidence 489999999999985
No 85
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=23.63 E-value=1.2e+02 Score=25.85 Aligned_cols=42 Identities=24% Similarity=0.360 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHHHHHhC
Q 032126 67 LVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYG 123 (147)
Q Consensus 67 LvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~AL~EyG 123 (147)
|++=|++-||.++..-+..|. ...+|-+|+-.||++|+....
T Consensus 100 l~aka~E~Fi~elt~~sw~~T---------------ee~~rrtl~~sdia~av~~s~ 141 (236)
T KOG1657|consen 100 LFAKACELFITELTLRSWVHT---------------EENKRRTLQKSDIAAAVTQSE 141 (236)
T ss_pred HHHHHHHHHHHHHHHHhhhhh---------------cccccccchHHHHHHHhccCC
Confidence 778899999999887766553 244556777799999987653
No 86
>cd04383 RhoGAP_srGAP RhoGAP_srGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs contain an N-terminal FCH domain, a central RhoGAP domain and a C-terminal SH3 domain; this SH3 domain interacts with the intracellular proline-rich-tail of the Roundabout receptor (Robo). This interaction with Robo then activates the rhoGAP domain which in turn inhibits Cdc42 activity. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific group
Probab=23.51 E-value=1e+02 Score=24.37 Aligned_cols=37 Identities=22% Similarity=0.410 Sum_probs=29.8
Q ss_pred chHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 18 d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
..-|..||..|- .|+||.++.+.+++-++.+..+.|+
T Consensus 76 a~lLK~fLReLP--epLip~~~~~~~~~~~~~~~~~~~~ 112 (188)
T cd04383 76 AGVLKLYFRGLE--NPLFPKERFEDLMSCVKLENPTERV 112 (188)
T ss_pred HHHHHHHHHhCC--CccCCHHHHHHHHHHHhcCCHHHHH
Confidence 456788888887 7999999999999887766555565
No 87
>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=23.37 E-value=65 Score=19.73 Aligned_cols=16 Identities=25% Similarity=0.621 Sum_probs=14.1
Q ss_pred HHHHHHHHHHhCcccC
Q 032126 112 MEDLSKALREYGVNVK 127 (147)
Q Consensus 112 mEDLs~AL~EyGInvk 127 (147)
+.++...|.++|+||.
T Consensus 13 L~~i~~~l~~~~~nI~ 28 (65)
T cd04882 13 LHEILQILSEEGINIE 28 (65)
T ss_pred HHHHHHHHHHCCCChh
Confidence 5688999999999995
No 88
>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=23.30 E-value=2e+02 Score=23.83 Aligned_cols=16 Identities=19% Similarity=0.133 Sum_probs=11.1
Q ss_pred eeeeHHHHHHHHHHhC
Q 032126 108 LILTMEDLSKALREYG 123 (147)
Q Consensus 108 ~vLTmEDLs~AL~EyG 123 (147)
-.+|.+|+..|+.+..
T Consensus 260 ~~it~~~v~~a~~~~~ 275 (365)
T TIGR02928 260 ERVTEDHVEKAQEKIE 275 (365)
T ss_pred CCCCHHHHHHHHHHHH
Confidence 3577888887777653
No 89
>PRK07758 hypothetical protein; Provisional
Probab=23.29 E-value=59 Score=24.48 Aligned_cols=17 Identities=41% Similarity=0.636 Sum_probs=14.8
Q ss_pred eHHHHHHHHHHhCcccC
Q 032126 111 TMEDLSKALREYGVNVK 127 (147)
Q Consensus 111 TmEDLs~AL~EyGInvk 127 (147)
+++.|..+|.|+|++.+
T Consensus 79 SL~EIkekL~E~GLsfk 95 (95)
T PRK07758 79 SLPKLRKALEESGLSFK 95 (95)
T ss_pred HHHHHHHHHHHcCCCCC
Confidence 68899999999999764
No 90
>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=23.20 E-value=1.9e+02 Score=23.31 Aligned_cols=40 Identities=33% Similarity=0.591 Sum_probs=30.0
Q ss_pred CCCCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 14 RHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 14 ~~~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
.|.-..-|..||..|- .|+||.++.+.++.-...+ .+.|+
T Consensus 61 ~h~va~lLK~fLReLP--ePLi~~~~y~~~i~~~~~~-~~~~~ 100 (206)
T cd04376 61 VHDVAALLKEFFRDMP--DPLLPRELYTAFIGTALLE-PDEQL 100 (206)
T ss_pred HHHHHHHHHHHHHhCC--CccCCHHHHHHHHHHHcCC-HHHHH
Confidence 3344566788998887 5999999999999887765 34454
No 91
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=23.05 E-value=72 Score=25.72 Aligned_cols=36 Identities=22% Similarity=0.195 Sum_probs=28.3
Q ss_pred chHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCC
Q 032126 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPD 53 (147)
Q Consensus 18 d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D 53 (147)
..++.++...++..-+.++.+-....|+++||...+
T Consensus 192 ~~ei~~~~~~~~~~~~~~~~~~~~~~L~~aGF~~v~ 227 (247)
T PRK15451 192 ELEISQKRSMLENVMLTDSVETHKARLHKAGFEHSE 227 (247)
T ss_pred HHHHHHHHHHHHhhcccCCHHHHHHHHHHcCchhHH
Confidence 455666677777777778899999999999998644
No 92
>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=22.69 E-value=37 Score=26.98 Aligned_cols=24 Identities=25% Similarity=0.537 Sum_probs=15.2
Q ss_pred ccceeeeHHHHHHHHHHhCcccCC
Q 032126 105 DKRLILTMEDLSKALREYGVNVKH 128 (147)
Q Consensus 105 d~r~vLTmEDLs~AL~EyGInvkr 128 (147)
+++--|+=+.|+..|++.||+|.|
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 93
>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=22.33 E-value=1.2e+02 Score=23.53 Aligned_cols=40 Identities=18% Similarity=0.301 Sum_probs=29.2
Q ss_pred CCCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 15 HDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 15 ~~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
|.-..-|..||..|- .|+||.++.+.++..+..+.+..|+
T Consensus 74 ~~va~~LK~fLreLp--~pLi~~~~~~~~~~~~~~~~~~~~~ 113 (192)
T cd04398 74 HSVASLLKLFFRELP--EPLLTKALSREFIEAAKIEDESRRR 113 (192)
T ss_pred HHHHHHHHHHHHhCC--CccCCHHHHHHHHHHHhCCCHHHHH
Confidence 334556788998887 7999999999999876554334454
No 94
>PF07967 zf-C3HC: C3HC zinc finger-like ; InterPro: IPR012935 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) and other proteins. NIPA is thought to perform an antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signalling events []. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe protein containing this domain (O94506 from SWISSPROT) is involved in mRNA export from the nucleus []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=21.97 E-value=42 Score=25.12 Aligned_cols=46 Identities=26% Similarity=0.452 Sum_probs=35.6
Q ss_pred HHHHHHHcCCCCCC----CcHHHHHHHHHhCCCCCCCccc-ccccccchhHHH
Q 032126 21 LTEFLSSLMGYTPT----IPDELVEHYLAKSGFQCPDVRL-NCCLCFCRIRLV 68 (147)
Q Consensus 21 L~efl~~LddY~P~----IPD~Vt~yyL~~aGf~~~D~Rv-~~~~~~~~~RLv 68 (147)
-.+||..|.-|.+. =|..|...-+++-|+.|.|.-. .|. .|..+|+
T Consensus 4 r~~~l~RL~Tf~~~~W~~kp~~lspl~cA~~GW~~~~~d~l~C~--~C~~~l~ 54 (133)
T PF07967_consen 4 REDFLRRLETFKSLTWFPKPPWLSPLECARRGWICVSKDMLKCE--SCGARLC 54 (133)
T ss_pred HHHHHHHHHHcccccccCCCcccCHHHHHHcCCCcCCCCEEEeC--CCCCEEE
Confidence 46899999988874 5999999999999999988644 333 5555544
No 95
>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=21.90 E-value=64 Score=20.68 Aligned_cols=17 Identities=24% Similarity=0.599 Sum_probs=14.2
Q ss_pred eHHHHHHHHHHhCcccC
Q 032126 111 TMEDLSKALREYGVNVK 127 (147)
Q Consensus 111 TmEDLs~AL~EyGInvk 127 (147)
.+.++...|.+.||||.
T Consensus 14 ~La~v~~~l~~~~inI~ 30 (66)
T cd04908 14 RLAAVTEILSEAGINIR 30 (66)
T ss_pred hHHHHHHHHHHCCCCEE
Confidence 35678899999999995
No 96
>COG2323 Predicted membrane protein [Function unknown]
Probab=21.77 E-value=52 Score=27.76 Aligned_cols=20 Identities=40% Similarity=0.547 Sum_probs=18.4
Q ss_pred cceeeeHHHHHHHHHHhCcc
Q 032126 106 KRLILTMEDLSKALREYGVN 125 (147)
Q Consensus 106 ~r~vLTmEDLs~AL~EyGIn 125 (147)
+|.-||.+||...|++.||-
T Consensus 109 kk~rlt~ddL~~~LR~kgi~ 128 (224)
T COG2323 109 KKSRLTIDDLLMKLRQKGIF 128 (224)
T ss_pred HHhcCCHHHHHHHHHHcCCC
Confidence 68889999999999999984
No 97
>smart00070 GLUCA Glucagon like hormones.
Probab=21.24 E-value=1e+02 Score=18.08 Aligned_cols=17 Identities=24% Similarity=0.235 Sum_probs=13.4
Q ss_pred chhHHHHHHHHHHHHHH
Q 032126 63 CRIRLVAVATQKFVAEV 79 (147)
Q Consensus 63 ~~~RLvSLAaQKFisDI 79 (147)
.|+=|=.++|+|||..+
T Consensus 10 ysk~L~~~~ar~fl~~L 26 (27)
T smart00070 10 YSKYLDQLAAKKFLQWL 26 (27)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 45667789999999865
No 98
>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=20.97 E-value=1.4e+02 Score=24.28 Aligned_cols=48 Identities=15% Similarity=0.279 Sum_probs=36.9
Q ss_pred HHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 032126 39 LVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVV 95 (147)
Q Consensus 39 Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~ 95 (147)
+..-+|...-|+-.+ || +.||.=....+-+.|+..+.+|+..|..+.-
T Consensus 179 ll~eil~~~~f~d~~-rl--------~~ll~~~~s~~~~~i~~~Gh~~A~~ra~s~~ 226 (248)
T PF08367_consen 179 LLSEILTETDFDDKE-RL--------KELLKELKSDMESSIISSGHSYAMSRASSYL 226 (248)
T ss_dssp HHHHHHHCB-TT-HH-HH--------HHHHHHHHHHHHHHHHH-HHHHHHHHCCCTT
T ss_pred HHHHHHhccCCCcHH-HH--------HHHHHHHHHHHHHhhhhhHHHHHHHHHHhcC
Confidence 456677788885444 99 9999999999999999999999998876543
No 99
>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=20.95 E-value=74 Score=20.77 Aligned_cols=22 Identities=27% Similarity=0.363 Sum_probs=18.6
Q ss_pred HHHHHHHHHHhCcccCCCCccc
Q 032126 112 MEDLSKALREYGVNVKHQEYFA 133 (147)
Q Consensus 112 mEDLs~AL~EyGInvkrP~Yy~ 133 (147)
+.+++..|.++|+||..=.-++
T Consensus 13 v~~it~~l~~~g~nI~~~~~~~ 34 (74)
T cd04875 13 VAAVSGFLAEHGGNIVESDQFV 34 (74)
T ss_pred HHHHHHHHHHcCCCEEeeeeee
Confidence 5789999999999998766664
No 100
>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=20.72 E-value=71 Score=20.20 Aligned_cols=19 Identities=21% Similarity=0.515 Sum_probs=15.5
Q ss_pred eHHHHHHHHHHhCcccCCC
Q 032126 111 TMEDLSKALREYGVNVKHQ 129 (147)
Q Consensus 111 TmEDLs~AL~EyGInvkrP 129 (147)
.+..+...|.++||||..=
T Consensus 14 ~l~~i~~~l~~~~inI~~i 32 (72)
T cd04883 14 QLADIAAIFKDRGVNIVSV 32 (72)
T ss_pred HHHHHHHHHHHcCCCEEEE
Confidence 4677889999999999743
No 101
>COG2815 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.63 E-value=1.1e+02 Score=26.78 Aligned_cols=32 Identities=25% Similarity=0.509 Sum_probs=27.4
Q ss_pred eeeeHHHHHHHHHHhCcccCCCCccccCCCCC
Q 032126 108 LILTMEDLSKALREYGVNVKHQEYFADNPSTG 139 (147)
Q Consensus 108 ~vLTmEDLs~AL~EyGInvkrP~Yy~d~~~~~ 139 (147)
.-+|.++....|+++|+++.-++||.+....|
T Consensus 168 ~G~t~~~A~~~L~~~G~~~~~~~~~ss~~~~G 199 (303)
T COG2815 168 VGMTYDEASSNLKAAGLTVNSKEYVSSDRPEG 199 (303)
T ss_pred ccccHHHHHHHHHHhCCCcccccccCCCCCCC
Confidence 45788999999999999999888888776665
No 102
>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=20.58 E-value=81 Score=19.33 Aligned_cols=18 Identities=28% Similarity=0.608 Sum_probs=15.0
Q ss_pred eHHHHHHHHHHhCcccCC
Q 032126 111 TMEDLSKALREYGVNVKH 128 (147)
Q Consensus 111 TmEDLs~AL~EyGInvkr 128 (147)
.+.++...|.+.||||..
T Consensus 11 ~l~~i~~~l~~~~inI~~ 28 (56)
T cd04889 11 RLAEVTEILAEAGINIKA 28 (56)
T ss_pred hHHHHHHHHHHcCCCEee
Confidence 367889999999999953
No 103
>COG3724 AstB Succinylarginine dihydrolase [Amino acid transport and metabolism]
Probab=20.44 E-value=1.1e+02 Score=28.27 Aligned_cols=59 Identities=24% Similarity=0.239 Sum_probs=41.3
Q ss_pred HHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhc-------hhcccccccceeeeHH
Q 032126 41 EHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKD-------KRDKQQKDKRLILTME 113 (147)
Q Consensus 41 ~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~-------k~~~~~kd~r~vLTmE 113 (147)
-+.|.+-||..+|..| +++++.+|...-..-++++.+= ..+...-|.|+.||.-
T Consensus 70 ~~~LR~LGFsGsDe~V-------------------l~~var~ap~ll~a~sSAS~MWtANAATV~psaDtaDGrVH~t~A 130 (442)
T COG3724 70 IPVLRQLGFSGSDEQV-------------------LEKVARQAPHLLSAVSSASPMWTANAATVSPSADTADGRVHLTVA 130 (442)
T ss_pred hHHHHHhCCCCchHHH-------------------HHHHHHhChHHHHHhccccchhhhccccccCCccccCCeEEEeeh
Confidence 4679999999999999 6788888887754444333221 1123567899999987
Q ss_pred HHHHH
Q 032126 114 DLSKA 118 (147)
Q Consensus 114 DLs~A 118 (147)
-|-.-
T Consensus 131 NL~~k 135 (442)
T COG3724 131 NLNNK 135 (442)
T ss_pred hhcch
Confidence 77543
No 104
>cd04406 RhoGAP_myosin_IXA RhoGAP_myosin_IXA: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in myosins IXA. Class IX myosins contain a characteristic head domain, a neck domain and a tail domain which contains a C6H2-zinc binding motif and a Rho-GAP domain. Class IX myosins are single-headed, processive myosins that are partly cytoplasmic, and partly associated with membranes and the actin cytoskeleton. Class IX myosins are implicated in the regulation of neuronal morphogenesis and function of sensory systems, like the inner ear. There are two major isoforms, myosin IXA and IXB with several splice variants, which are both expressed in developing neurons. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell prolife
Probab=20.40 E-value=1.3e+02 Score=23.80 Aligned_cols=41 Identities=24% Similarity=0.327 Sum_probs=31.2
Q ss_pred CCCCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCccc
Q 032126 14 RHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (147)
Q Consensus 14 ~~~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv 56 (147)
.|.-..-|..||..|- .|+||.++.+-+++-.|.+-...++
T Consensus 67 ~h~va~lLK~fLReLP--ePLi~~~~y~~~~~~~~~~~~~~~i 107 (186)
T cd04406 67 IHVIASVFKQWLRDLP--NPLMTFELYEEFLRAMGLQERRETV 107 (186)
T ss_pred HHHHHHHHHHHHHhCC--CccCCHHHHHHHHHHHhcccHHHHH
Confidence 3344556788999887 7999999999999988765544555
No 105
>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=20.22 E-value=1.1e+02 Score=18.52 Aligned_cols=25 Identities=20% Similarity=0.373 Sum_probs=19.8
Q ss_pred HHHHcCCCCCCCcHHHHHHHHHhCC
Q 032126 24 FLSSLMGYTPTIPDELVEHYLAKSG 48 (147)
Q Consensus 24 fl~~LddY~P~IPD~Vt~yyL~~aG 48 (147)
-+..|.+-=|.++.+++.+.|..++
T Consensus 5 ~v~~L~~mFP~l~~~~I~~~L~~~~ 29 (43)
T smart00546 5 ALHDLKDMFPNLDEEVIKAVLEANN 29 (43)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHcC
Confidence 3445555689999999999999776
No 106
>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=20.17 E-value=84 Score=19.06 Aligned_cols=18 Identities=11% Similarity=0.366 Sum_probs=15.5
Q ss_pred eHHHHHHHHHHhCcccCC
Q 032126 111 TMEDLSKALREYGVNVKH 128 (147)
Q Consensus 111 TmEDLs~AL~EyGInvkr 128 (147)
.+.++...|.++|+|+..
T Consensus 12 ~l~~i~~~l~~~~~~I~~ 29 (71)
T cd04903 12 AIAKVTSVLADHEINIAF 29 (71)
T ss_pred hHHHHHHHHHHcCcCeee
Confidence 467899999999999863
No 107
>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=20.13 E-value=93 Score=26.67 Aligned_cols=51 Identities=20% Similarity=0.315 Sum_probs=32.7
Q ss_pred CCCCcHHHHHHHHHhC-CCCCCC---cccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 032126 32 TPTIPDELVEHYLAKS-GFQCPD---VRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQ 91 (147)
Q Consensus 32 ~P~IPD~Vt~yyL~~a-Gf~~~D---~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~ 91 (147)
+-||||+++.-.|+.+ |+...+ .+. -..+|+||.--|-+|... |-..++|.
T Consensus 74 p~TvpDE~vs~i~~~~~~~s~e~l~~i~~--------~HrlsM~aENivG~LLEr-YL~~~Le~ 128 (221)
T PF09570_consen 74 PTTVPDEMVSVIMNASFGYSQEDLELIKE--------GHRLSMAAENIVGALLER-YLAEVLEP 128 (221)
T ss_pred CCCCChHHHHHHHHHHhCCCHHHHHHHHH--------HHHHHHHHHHHHHHHHHH-HHHHHhcc
Confidence 3589999999999954 444323 334 556788888777776643 33344443
No 108
>COG3681 L-cysteine desulfidase [Amino acid transport and metabolism]
Probab=20.12 E-value=2.7e+02 Score=25.88 Aligned_cols=70 Identities=17% Similarity=0.192 Sum_probs=45.9
Q ss_pred chHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCC--CCcccccccccchhHHHHHHHHHHHH--HHHHHHHHHHHHhhhh
Q 032126 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQC--PDVRLNCCLCFCRIRLVAVATQKFVA--EVATDALQQCKARQAA 93 (147)
Q Consensus 18 d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~--~D~Rv~~~~~~~~~RLvSLAaQKFis--DIa~DA~q~~kiR~~~ 93 (147)
-.+|.||+. |.-.||-+++..+|+..-+.| +++-+.--...|-... -.+|++ +.+.|-..+.-+|+++
T Consensus 181 ~ltlk~i~d----~v~~ip~d~Ik~I~~~ir~N~als~egl~gk~g~~ig~~----l~d~ierg~l~~dl~n~~l~~tsa 252 (433)
T COG3681 181 RLTLKEILD----FVNEIPFDAIKFILDSIRLNCALSQEGLSGKWGLHIGAT----LEDQIERGLLAKDLSNSILIRTSA 252 (433)
T ss_pred hccHHHHHH----HHHhCCHHHHHHHHHHHHhcccccCccccCccccccchh----HHHHHhhhhHHHHHHHHHHHHHhh
Confidence 456788874 888999999999999877776 5774421112221221 257777 6667777777677765
Q ss_pred hh
Q 032126 94 VV 95 (147)
Q Consensus 94 ~~ 95 (147)
+.
T Consensus 253 as 254 (433)
T COG3681 253 AS 254 (433)
T ss_pred hh
Confidence 54
Done!