Query psy13513
Match_columns 71
No_of_seqs 101 out of 153
Neff 4.6
Searched_HMMs 46136
Date Fri Aug 16 21:18:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13513.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13513hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04719 TAFII28: hTAFII28-lik 100.0 5.1E-36 1.1E-40 191.4 5.5 63 9-71 1-64 (90)
2 KOG3219|consensus 100.0 1.8E-34 4E-39 205.0 5.1 70 2-71 83-152 (195)
3 cd08048 TAF11 TATA Binding Pro 100.0 9.1E-30 2E-34 160.7 5.9 56 16-71 1-56 (85)
4 COG5251 TAF40 Transcription in 99.9 1.5E-28 3.2E-33 173.8 4.7 68 3-70 87-154 (199)
5 PF00808 CBFD_NFYB_HMF: Histon 95.3 0.023 5.1E-07 32.9 3.0 40 31-70 2-42 (65)
6 smart00803 TAF TATA box bindin 91.1 0.47 1E-05 28.2 3.8 41 30-70 1-41 (65)
7 PF13443 HTH_26: Cro/C1-type H 88.2 0.51 1.1E-05 26.4 2.3 53 17-70 7-59 (63)
8 cd00076 H4 Histone H4, one of 86.1 1.7 3.7E-05 27.4 4.0 41 30-70 12-52 (85)
9 smart00417 H4 Histone H4. 84.0 2.4 5.3E-05 26.1 3.9 40 31-70 13-52 (74)
10 PF02268 TFIIA_gamma_N: Transc 81.9 0.7 1.5E-05 26.7 0.8 35 23-57 2-36 (49)
11 COG2036 HHT1 Histones H3 and H 81.5 2.6 5.6E-05 27.0 3.4 51 18-68 6-56 (91)
12 PTZ00015 histone H4; Provision 77.2 5.6 0.00012 25.9 4.1 41 30-70 29-69 (102)
13 COG5123 TOA2 Transcription ini 75.2 4.1 8.9E-05 27.2 3.1 32 24-55 5-36 (113)
14 KOG3463|consensus 74.7 5.3 0.00012 26.6 3.5 34 23-56 3-36 (109)
15 PLN00035 histone H4; Provision 73.7 5.9 0.00013 25.9 3.5 40 31-70 29-68 (103)
16 COG3492 Uncharacterized protei 71.3 11 0.00024 24.8 4.4 42 13-62 3-45 (104)
17 PF08802 CytB6-F_Fe-S: Cytochr 68.8 3.1 6.6E-05 23.1 1.1 28 38-65 9-36 (39)
18 PF00125 Histone: Core histone 68.0 11 0.00023 21.8 3.5 41 30-70 4-49 (75)
19 PF08971 GlgS: Glycogen synthe 56.5 8 0.00017 23.7 1.5 20 10-29 31-54 (66)
20 PF12174 RST: RCD1-SRO-TAF4 (R 56.4 42 0.00092 20.2 4.7 38 9-46 15-56 (70)
21 COG5247 BUR6 Class 2 transcrip 54.9 23 0.0005 23.7 3.6 41 25-69 17-62 (113)
22 cd00074 H2A Histone 2A; H2A is 53.8 21 0.00045 23.5 3.3 40 31-70 20-60 (115)
23 cd03423 SirA SirA (also known 53.7 7.5 0.00016 22.6 1.0 27 44-70 4-30 (69)
24 COG0425 SirA Predicted redox p 52.9 7.2 0.00016 23.8 0.9 27 44-70 10-36 (78)
25 cd07981 TAF12 TATA Binding Pro 52.4 41 0.00089 19.9 4.2 39 32-70 2-41 (72)
26 PRK02922 glycogen synthesis pr 52.2 23 0.00049 21.8 3.0 23 10-32 32-58 (67)
27 PF07235 DUF1427: Protein of u 51.1 15 0.00032 23.8 2.2 29 41-69 16-44 (90)
28 cd00291 SirA_YedF_YeeD SirA, Y 49.7 9.4 0.0002 21.4 1.0 27 44-70 4-30 (69)
29 cd03421 SirA_like_N SirA_like_ 49.1 10 0.00023 21.5 1.2 26 44-70 4-29 (67)
30 PF07946 DUF1682: Protein of u 48.8 23 0.00051 26.4 3.2 24 3-26 289-312 (321)
31 PF02969 TAF: TATA box binding 48.5 29 0.00062 20.8 3.0 40 30-70 2-42 (66)
32 KOG0870|consensus 48.4 36 0.00078 24.3 3.9 38 31-68 10-50 (172)
33 KOG3467|consensus 46.9 41 0.00089 22.0 3.8 39 31-69 29-67 (103)
34 PF07813 LTXXQ: LTXXQ motif fa 46.7 42 0.00091 19.6 3.6 22 5-26 77-98 (100)
35 PF02978 SRP_SPB: Signal pepti 46.1 42 0.00091 21.4 3.7 25 3-27 47-71 (104)
36 PF08880 QLQ: QLQ; InterPro: 44.8 50 0.0011 17.7 3.5 13 46-58 24-36 (37)
37 COG4317 Uncharacterized protei 44.4 30 0.00065 22.4 2.8 30 40-69 16-45 (93)
38 PF01206 TusA: Sulfurtransfera 43.8 15 0.00033 20.8 1.3 27 44-70 5-31 (70)
39 PF09415 CENP-X: CENP-S associ 41.4 14 0.00031 22.4 0.9 37 33-69 1-40 (72)
40 PF13495 Phage_int_SAM_4: Phag 40.5 70 0.0015 18.1 3.9 30 13-42 38-69 (85)
41 cd04385 RhoGAP_ARAP RhoGAP_ARA 40.1 42 0.00091 22.8 3.2 43 26-69 36-84 (184)
42 PF08411 Exonuc_X-T_C: Exonucl 39.0 40 0.00086 24.7 3.1 23 14-36 207-229 (269)
43 KOG4054|consensus 38.3 39 0.00085 24.3 2.9 35 26-68 26-60 (183)
44 PF15540 Toxin_62: Putative to 38.1 15 0.00032 24.6 0.7 17 22-38 25-41 (113)
45 PRK10445 endonuclease VIII; Pr 38.0 33 0.00072 24.9 2.6 44 13-68 132-175 (263)
46 PF09336 Vps4_C: Vps4 C termin 37.3 44 0.00095 19.5 2.6 21 9-29 39-59 (62)
47 cd04378 RhoGAP_GMIP_PARG1 RhoG 36.0 54 0.0012 22.6 3.3 44 26-70 37-84 (203)
48 PHA02567 rnh RnaseH; Provision 35.0 79 0.0017 24.2 4.3 50 15-64 241-298 (304)
49 PF08367 M16C_assoc: Peptidase 33.6 52 0.0011 23.2 3.0 24 2-25 12-35 (248)
50 PF02260 FATC: FATC domain; I 33.5 66 0.0014 16.7 2.6 22 35-66 7-28 (33)
51 cd04377 RhoGAP_myosin_IX RhoGA 33.3 65 0.0014 21.8 3.3 44 25-69 35-82 (186)
52 cd03422 YedF YedF is a bacteri 32.2 26 0.00056 20.3 1.0 27 44-70 4-30 (69)
53 PRK13291 metal-dependent hydro 32.1 45 0.00098 22.6 2.3 39 7-47 118-156 (173)
54 PF10501 Ribosomal_L50: Riboso 31.8 74 0.0016 20.2 3.2 37 26-62 34-74 (112)
55 PF10260 SAYSvFN: Uncharacteri 31.6 24 0.00052 21.7 0.8 14 10-23 55-68 (71)
56 PF12397 U3snoRNP10: U3 small 31.4 1.3E+02 0.0029 18.7 4.3 37 28-64 36-73 (121)
57 TIGR00988 hip integration host 30.7 1.3E+02 0.0027 18.1 4.1 30 17-46 2-31 (94)
58 cd03420 SirA_RHOD_Pry_redox Si 30.2 30 0.00065 20.0 1.0 27 44-70 4-30 (69)
59 cd04406 RhoGAP_myosin_IXA RhoG 29.9 77 0.0017 21.7 3.2 44 25-69 35-82 (186)
60 TIGR03510 XapX XapX domain. Th 29.6 82 0.0018 18.0 2.8 27 43-69 17-44 (49)
61 PF06466 PCAF_N: PCAF (P300/CB 29.5 88 0.0019 23.5 3.6 38 31-68 140-180 (252)
62 COG4738 Predicted transcriptio 29.5 57 0.0012 22.2 2.4 24 16-39 9-32 (124)
63 PF08593 MUG2_C: Meiotically u 29.4 33 0.00072 20.1 1.1 12 13-24 44-55 (58)
64 COG2074 2-phosphoglycerate kin 29.3 93 0.002 24.0 3.8 27 5-31 58-84 (299)
65 PF11304 DUF3106: Protein of u 29.2 1.3E+02 0.0029 19.1 4.0 6 15-20 58-63 (107)
66 PRK11779 sbcB exonuclease I; P 29.1 57 0.0012 26.1 2.7 30 14-43 415-444 (476)
67 smart00414 H2A Histone 2A. 28.5 82 0.0018 20.4 3.0 40 31-70 9-49 (106)
68 cd04389 RhoGAP_KIAA1688 RhoGAP 27.8 1E+02 0.0022 21.1 3.5 44 26-70 43-89 (187)
69 cd04373 RhoGAP_p190 RhoGAP_p19 26.4 1E+02 0.0023 20.9 3.4 45 25-70 35-84 (185)
70 PF12763 EF-hand_4: Cytoskelet 26.3 1.1E+02 0.0025 19.4 3.4 63 2-66 5-78 (104)
71 PF08025 Antimicrobial_3: Spid 26.3 68 0.0015 17.4 1.9 14 53-66 6-19 (37)
72 COG5262 HTA1 Histone H2A [Chro 26.2 75 0.0016 21.8 2.6 42 29-70 24-66 (132)
73 KOG0844|consensus 25.9 46 0.001 26.4 1.7 25 17-45 177-201 (408)
74 PF06309 Torsin: Torsin; Inte 25.8 17 0.00036 24.5 -0.7 24 47-70 48-74 (127)
75 cd04394 RhoGAP-ARHGAP11A RhoGA 24.7 1.2E+02 0.0025 21.0 3.4 45 25-70 39-85 (202)
76 PF05678 VQ: VQ motif; InterP 24.5 96 0.0021 16.1 2.3 18 33-50 11-28 (31)
77 PRK00199 ihfB integration host 24.3 1.7E+02 0.0037 17.6 4.1 30 17-46 2-31 (94)
78 PF12719 Cnd3: Nuclear condens 24.3 1.2E+02 0.0026 21.9 3.5 35 35-69 113-147 (298)
79 PF02937 COX6C: Cytochrome c o 24.2 25 0.00054 21.5 -0.1 38 30-67 2-41 (73)
80 cd04404 RhoGAP-p50rhoGAP RhoGA 24.1 1.3E+02 0.0027 20.4 3.4 44 25-69 43-90 (195)
81 TIGR01568 A_thal_3678 uncharac 23.8 1.8E+02 0.0039 17.6 4.6 44 23-66 10-63 (66)
82 cd04397 RhoGAP_fLRG1 RhoGAP_fL 23.8 1.1E+02 0.0024 21.3 3.1 45 25-70 47-96 (213)
83 PF08281 Sigma70_r4_2: Sigma-7 23.7 1.3E+02 0.0028 15.9 3.6 36 6-41 1-36 (54)
84 cd01193 INT_IntI IntI (E2) int 23.7 1.9E+02 0.0041 18.8 4.1 30 12-41 6-37 (242)
85 PF04844 Ovate: Transcriptiona 23.5 1.7E+02 0.0037 17.2 4.2 43 24-66 5-56 (59)
86 PF09574 DUF2374: Protein of 23.5 1.5E+02 0.0032 16.7 3.0 28 36-65 3-30 (42)
87 PTZ00475 RESA-like protein; Pr 23.1 64 0.0014 24.6 1.9 35 34-68 90-124 (282)
88 PF15061 DUF4538: Domain of un 22.9 91 0.002 18.6 2.2 23 15-37 30-52 (58)
89 PF02758 PYRIN: PAAD/DAPIN/Pyr 22.8 1.7E+02 0.0036 17.5 3.4 22 7-28 3-24 (83)
90 cd04384 RhoGAP_CdGAP RhoGAP_Cd 22.7 1.1E+02 0.0023 21.1 2.9 44 25-69 37-87 (195)
91 PF02284 COX5A: Cytochrome c o 22.7 2.4E+02 0.0052 18.7 5.0 38 18-55 9-48 (108)
92 PF14400 Transglut_i_TM: Inact 22.6 1.3E+02 0.0027 21.1 3.2 35 25-60 127-161 (165)
93 COG1036 Archaeal flavoproteins 22.4 7.1 0.00015 28.2 -3.1 47 19-65 84-130 (187)
94 KOG0871|consensus 22.3 74 0.0016 22.4 2.0 19 30-48 11-29 (156)
95 PF09339 HTH_IclR: IclR helix- 22.1 1.2E+02 0.0026 16.2 2.5 22 25-46 23-44 (52)
96 COG5126 FRQ1 Ca2+-binding prot 22.1 2.7E+02 0.006 19.3 4.8 42 11-53 9-57 (160)
97 PF14308 DnaJ-X: X-domain of D 22.1 1.8E+02 0.004 20.1 4.0 31 35-65 148-183 (204)
98 COG5150 Class 2 transcription 22.0 76 0.0016 22.1 2.0 19 30-48 10-28 (148)
99 cd04376 RhoGAP_ARHGAP6 RhoGAP_ 21.9 1.4E+02 0.0029 20.9 3.3 43 26-69 30-76 (206)
100 PF15478 LKAAEAR: Family of un 21.9 65 0.0014 22.3 1.6 16 13-28 13-28 (137)
101 PF03661 UPF0121: Uncharacteri 21.8 1.1E+02 0.0025 22.0 3.0 35 22-57 195-233 (247)
102 PF14281 PDDEXK_4: PD-(D/E)XK 21.7 74 0.0016 20.8 1.9 19 14-32 97-115 (179)
103 PF08621 RPAP1_N: RPAP1-like, 21.7 1.7E+02 0.0036 16.5 3.7 31 12-42 11-41 (49)
104 KOG0006|consensus 21.6 58 0.0013 26.0 1.5 14 15-28 292-305 (446)
105 cd04374 RhoGAP_Graf RhoGAP_Gra 21.3 1.4E+02 0.0031 20.8 3.3 43 26-69 49-101 (203)
106 PHA02586 68 prohead core prote 21.3 2.9E+02 0.0063 19.1 5.3 55 3-60 5-59 (140)
107 PF09883 DUF2110: Uncharacteri 21.3 1.6E+02 0.0034 21.9 3.6 31 13-43 141-179 (225)
108 PF14069 SpoVIF: Stage VI spor 21.1 1.8E+02 0.0039 18.1 3.4 22 32-53 48-69 (79)
109 PF08774 VRR_NUC: VRR-NUC doma 20.9 1E+02 0.0023 18.5 2.3 19 14-32 73-91 (100)
110 COG1384 LysS Lysyl-tRNA synthe 20.7 3.2E+02 0.0069 22.7 5.5 52 19-70 466-518 (521)
111 COG3633 SstT Na+/serine sympor 20.6 1.4E+02 0.0031 23.7 3.4 41 24-68 8-52 (407)
112 PF02687 FtsX: FtsX-like perme 20.5 1.7E+02 0.0037 16.9 3.2 28 15-42 21-48 (121)
113 PF04718 ATP-synt_G: Mitochond 20.4 1.2E+02 0.0027 19.2 2.7 18 52-69 76-93 (103)
114 PF14165 YtzH: YtzH-like prote 20.3 1.5E+02 0.0032 19.0 2.9 48 7-58 5-53 (87)
115 PF08627 CRT-like: CRT-like; 20.3 1.5E+02 0.0032 20.3 3.1 37 30-66 32-69 (130)
116 PF01978 TrmB: Sugar-specific 20.1 87 0.0019 17.5 1.7 39 4-45 9-47 (68)
117 cd00315 Cyt_C5_DNA_methylase C 20.0 83 0.0018 22.7 2.0 45 13-58 225-270 (275)
No 1
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=100.00 E-value=5.1e-36 Score=191.44 Aligned_cols=63 Identities=71% Similarity=1.056 Sum_probs=46.2
Q ss_pred HHHHhhCCCHHHHHHHHHHHhcCCChHHHHHHHHHHhC-CCCChhHHHHHHHhhHhHhhhhccC
Q psy13513 9 MQVLVSNFTEDQLDRYEMYRRAAFPKAAIKRLIQTISG-GSVSQNVVIAMSGIAKVFVGEIVEQ 71 (71)
Q Consensus 9 ~~~L~~~~~~eQ~~Rye~fRRs~f~K~~ikkli~~~~~-~sv~~nv~i~v~g~aKvFVGEiVEe 71 (71)
|++|+++||+||++|||+||||+|||++||||+|+++| |+||+|++|||+|+||+|||||||+
T Consensus 1 ~~~L~~~f~~eQ~~Rye~fRRs~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~ 64 (90)
T PF04719_consen 1 MQLLLSNFDEEQLDRYEAFRRSSFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEE 64 (90)
T ss_dssp ---------HHHHHHHHHHHH----HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHH
T ss_pred ChHHHHcCCHHHHHHHHHHHHccCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999 9999999999999999999999985
No 2
>KOG3219|consensus
Probab=100.00 E-value=1.8e-34 Score=204.98 Aligned_cols=70 Identities=64% Similarity=1.047 Sum_probs=68.2
Q ss_pred cHHHHHHHHHHhhCCCHHHHHHHHHHHhcCCChHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhhccC
Q psy13513 2 EEEEREKMQVLVSNFTEDQLDRYEMYRRAAFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEIVEQ 71 (71)
Q Consensus 2 ~eee~~~~~~L~~~~~~eQ~~Rye~fRRs~f~K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEiVEe 71 (71)
+++|+++|+.|+++||+||++|||+||||+|||++||||+++++|++|++|++|||+|+||||||||||+
T Consensus 83 ~~ee~~r~q~L~s~fseEQl~RYEvfRrs~f~Ka~iKkL~~~itg~~v~~nv~Ia~~GiaKvFVGEvVEe 152 (195)
T KOG3219|consen 83 DAEEAQRMQTLLSNFSEEQLSRYEVFRRSAFPKAQIKKLMSSITGQSVSENVAIAMAGIAKVFVGEVVEE 152 (195)
T ss_pred CHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhCCccCcceeeeecchhhHhHHHHHHH
Confidence 5788899999999999999999999999999999999999999999999999999999999999999995
No 3
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) 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 11 (TAF11) 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 eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=99.96 E-value=9.1e-30 Score=160.67 Aligned_cols=56 Identities=75% Similarity=1.187 Sum_probs=55.0
Q ss_pred CCHHHHHHHHHHHhcCCChHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhhccC
Q psy13513 16 FTEDQLDRYEMYRRAAFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEIVEQ 71 (71)
Q Consensus 16 ~~~eQ~~Rye~fRRs~f~K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEiVEe 71 (71)
||+||++|||.||||+|+|++|||++++++||+||+|++|+|+|+||+|||||||+
T Consensus 1 f~~eQ~~Rye~~Rra~f~k~~iKr~~~~~~~~~v~~~v~i~v~glaKvFVGeivE~ 56 (85)
T cd08048 1 FSEEQMNRYEMFRRSSFPKAAIKRLIQSVTGQSVSQNVVIAVAGIAKVFVGEIVEE 56 (85)
T ss_pred CCHHHHHHHHHHHHhhccHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHHHHHHH
Confidence 79999999999999999999999999999999999999999999999999999985
No 4
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=99.95 E-value=1.5e-28 Score=173.85 Aligned_cols=68 Identities=41% Similarity=0.765 Sum_probs=65.4
Q ss_pred HHHHHHHHHHhhCCCHHHHHHHHHHHhcCCChHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 3 EEEREKMQVLVSNFTEDQLDRYEMYRRAAFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 3 eee~~~~~~L~~~~~~eQ~~Rye~fRRs~f~K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
..+.++.++|+.+||+||++|||.|||++|||++||||+++++||+|++|++|+++|++|||||||||
T Consensus 87 ~~~~~r~k~l~~~~deeq~~RyEvFrrt~lnKt~VKKlastV~nQtVspNi~I~l~g~~KVfvGEiIE 154 (199)
T COG5251 87 LAQDERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKKLASTVANQTVSPNIRIFLQGVGKVFVGEIIE 154 (199)
T ss_pred HhHHHHHHHHHhhcCHHHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCCeeeeeechhHHHHHHHHH
Confidence 45667889999999999999999999999999999999999999999999999999999999999997
No 5
>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=95.32 E-value=0.023 Score=32.93 Aligned_cols=40 Identities=25% Similarity=0.399 Sum_probs=33.2
Q ss_pred CCChHHHHHHHHHHhC-CCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 31 AFPKAAIKRLIQTISG-GSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 31 ~f~K~~ikkli~~~~~-~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
.||.+.|||++...-+ ..++.....+++=.+-+|+.+|..
T Consensus 2 ~lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~ 42 (65)
T PF00808_consen 2 SLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAK 42 (65)
T ss_dssp SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHH
T ss_pred CCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHH
Confidence 6999999999999843 469999999999999999998864
No 6
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=91.10 E-value=0.47 Score=28.24 Aligned_cols=41 Identities=22% Similarity=0.342 Sum_probs=35.9
Q ss_pred cCCChHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 30 AAFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 30 s~f~K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
+.+|++.|+++..+.=-..+++.++-.++...+.|+.+|+.
T Consensus 1 ~~~p~~~i~ria~~~Gi~ris~~a~~~l~~~~e~rl~~i~~ 41 (65)
T smart00803 1 SWLPKETIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQ 41 (65)
T ss_pred CCCCHHHHHHHHHHCCCccccHHHHHHHHHHHHHHHHHHHH
Confidence 35899999999997655679999999999999999999875
No 7
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=88.21 E-value=0.51 Score=26.35 Aligned_cols=53 Identities=11% Similarity=0.258 Sum_probs=31.8
Q ss_pred CHHHHHHHHHHHhcCCChHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 17 TEDQLDRYEMYRRAAFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 17 ~~eQ~~Rye~fRRs~f~K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
.+-.+..++..++++++++.+.++++.-. .+++-.....+|..-.+=++||++
T Consensus 7 ~~~~it~~~La~~~gis~~tl~~~~~~~~-~~~~~~~l~~ia~~l~~~~~el~~ 59 (63)
T PF13443_consen 7 AERGITQKDLARKTGISRSTLSRILNGKP-SNPSLDTLEKIAKALNCSPEELFE 59 (63)
T ss_dssp HHTT--HHHHHHHHT--HHHHHHHHTTT------HHHHHHHHHHHT--HHHCTE
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHhccc-ccccHHHHHHHHHHcCCCHHHHhh
Confidence 34566788889999999999999998331 256666666666666666777764
No 8
>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=86.08 E-value=1.7 Score=27.42 Aligned_cols=41 Identities=20% Similarity=0.317 Sum_probs=35.1
Q ss_pred cCCChHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 30 AAFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 30 s~f~K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
+.+||+.|+||...---.-+|..+.-.+.++.+.|.-+|+.
T Consensus 12 ~gi~k~~I~RLarr~GvkRIS~d~y~e~~~~l~~~l~~I~~ 52 (85)
T cd00076 12 KGITKPAIRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIR 52 (85)
T ss_pred ccCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHH
Confidence 46999999999997666679988989999999999988764
No 9
>smart00417 H4 Histone H4.
Probab=84.03 E-value=2.4 Score=26.12 Aligned_cols=40 Identities=23% Similarity=0.282 Sum_probs=34.0
Q ss_pred CCChHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 31 AFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 31 ~f~K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
++||+.|+||...-=-.-+|..+.-.+.++.|.|.-+|+.
T Consensus 13 gI~k~~IrRLaRr~GvkRIS~~~y~elr~vle~~l~~I~r 52 (74)
T smart00417 13 GITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVR 52 (74)
T ss_pred CCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHH
Confidence 6999999999996544578888889999999999988764
No 10
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=81.86 E-value=0.7 Score=26.68 Aligned_cols=35 Identities=26% Similarity=0.495 Sum_probs=24.3
Q ss_pred HHHHHHhcCCChHHHHHHHHHHhCCCCChhHHHHH
Q psy13513 23 RYEMYRRAAFPKAAIKRLIQTISGGSVSQNVVIAM 57 (71)
Q Consensus 23 Rye~fRRs~f~K~~ikkli~~~~~~sv~~nv~i~v 57 (71)
-|+-||+|++-.+=..-|=.-+..+.+++.++.-|
T Consensus 2 ~yelYR~stlG~aL~dtLDeli~~~~I~p~La~kV 36 (49)
T PF02268_consen 2 YYELYRRSTLGIALTDTLDELIQEGKITPQLAMKV 36 (49)
T ss_dssp --CGGGCSHHHHHHHHHHHHHHHTTSS-HHHHHHH
T ss_pred cHHHHHcchHHHHHHHHHHHHHHcCCCCHHHHHHH
Confidence 48999999987776666666677888888776544
No 11
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=81.49 E-value=2.6 Score=27.00 Aligned_cols=51 Identities=20% Similarity=0.408 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHhcCCChHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhh
Q psy13513 18 EDQLDRYEMYRRAAFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEI 68 (71)
Q Consensus 18 ~eQ~~Rye~fRRs~f~K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEi 68 (71)
.-+..||..+-.-.||++.|+||+....-.-|+....-.+.-...-|.=+|
T Consensus 6 ~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~~Rvs~~A~~~l~~~~e~~~~~i 56 (91)
T COG2036 6 LKEIRRYQRSTDLLLPKAPVRRILRKAGAERVSSSAIEELQEALEEYLEEI 56 (91)
T ss_pred HHHHHhhhhhhhhhcCchHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999999999998888787777666666666555444
No 12
>PTZ00015 histone H4; Provisional
Probab=77.20 E-value=5.6 Score=25.94 Aligned_cols=41 Identities=24% Similarity=0.400 Sum_probs=35.4
Q ss_pred cCCChHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 30 AAFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 30 s~f~K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
..++|+.|+||+...=-.-|+..+.-.+..+.+.|+-+|+.
T Consensus 29 ~gI~k~~IrRLarr~GvkRIS~d~y~e~r~vle~~l~~I~r 69 (102)
T PTZ00015 29 RGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVR 69 (102)
T ss_pred cCCCHHHHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHH
Confidence 46999999999997766689999988999999999988864
No 13
>COG5123 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=75.17 E-value=4.1 Score=27.20 Aligned_cols=32 Identities=38% Similarity=0.591 Sum_probs=20.9
Q ss_pred HHHHHhcCCChHHHHHHHHHHhCCCCChhHHH
Q psy13513 24 YEMYRRAAFPKAAIKRLIQTISGGSVSQNVVI 55 (71)
Q Consensus 24 ye~fRRs~f~K~~ikkli~~~~~~sv~~nv~i 55 (71)
||-||||..-|.-.+-|=.-+...-+++|.+.
T Consensus 5 YElYRrs~ig~~L~dalD~lis~g~isp~lam 36 (113)
T COG5123 5 YELYRRSMIGKVLEDALDELISAGVISPNLAM 36 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCcCHHHHH
Confidence 99999999877654444344444556666654
No 14
>KOG3463|consensus
Probab=74.70 E-value=5.3 Score=26.63 Aligned_cols=34 Identities=29% Similarity=0.497 Sum_probs=24.7
Q ss_pred HHHHHHhcCCChHHHHHHHHHHhCCCCChhHHHH
Q psy13513 23 RYEMYRRAAFPKAAIKRLIQTISGGSVSQNVVIA 56 (71)
Q Consensus 23 Rye~fRRs~f~K~~ikkli~~~~~~sv~~nv~i~ 56 (71)
=||-|||+.+-++--+-|=.-+..+.++++++.-
T Consensus 3 ~YelYR~ttlG~~L~~tLDe~v~~g~itp~la~~ 36 (109)
T KOG3463|consen 3 YYELYRRTTLGNALQKTLDELVSDGVITPSLAKK 36 (109)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHcCCCCHHHHHH
Confidence 4999999999877555555556667788777653
No 15
>PLN00035 histone H4; Provisional
Probab=73.70 E-value=5.9 Score=25.94 Aligned_cols=40 Identities=23% Similarity=0.375 Sum_probs=33.9
Q ss_pred CCChHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 31 AFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 31 ~f~K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
.+|++.|+||...-=-.-|+..+.-.+..+.+.|.-+|+.
T Consensus 29 ~ipk~~IrRLARr~GvkRIS~~ay~elr~vle~~l~~I~~ 68 (103)
T PLN00035 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIR 68 (103)
T ss_pred cCCHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHH
Confidence 3999999999997766689999988899999988877763
No 16
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.26 E-value=11 Score=24.78 Aligned_cols=42 Identities=31% Similarity=0.594 Sum_probs=29.7
Q ss_pred hhCCCHHHHHHHHHHHhcCCChHHHHHHHHHHhCCCCChhH-HHHHHHhhH
Q psy13513 13 VSNFTEDQLDRYEMYRRAAFPKAAIKRLIQTISGGSVSQNV-VIAMSGIAK 62 (71)
Q Consensus 13 ~~~~~~eQ~~Rye~fRRs~f~K~~ikkli~~~~~~sv~~nv-~i~v~g~aK 62 (71)
+.+||++|.+|+|+ ++.|+|+.+.--.+=-+|+ ..-++||-.
T Consensus 3 ~~~ls~~q~~~leA--------AaFRrLv~HL~~rsdvQNIDLMnLAgFCR 45 (104)
T COG3492 3 MQELSEEQRDRLEA--------AAFRRLVEHLQERSDVQNIDLMNLAGFCR 45 (104)
T ss_pred hHhcCHHHHHHHHH--------HHHHHHHHHHHHhcccchhHHHHHHHHHH
Confidence 46789999999986 5667888877766655666 344566544
No 17
>PF08802 CytB6-F_Fe-S: Cytochrome B6-F complex Fe-S subunit ; InterPro: IPR014909 The cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The cytochrome b6-f complex has 4 large subunits, these are: cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are: PetG, PetL, PetM and PetN. The complex functions as a dimer. This protein corresponds to the alpha helical transmembrane domain of the cytochrome b6-f complex Rieske iron-sulphur subunit. ; GO: 0009496 plastoquinol-plastocyanin reductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process, 0042651 thylakoid membrane; PDB: 1Q90_R 1VF5_D 2E75_D 2E74_D 2E76_D 2D2C_Q 2ZT9_D.
Probab=68.79 E-value=3.1 Score=23.07 Aligned_cols=28 Identities=25% Similarity=0.373 Sum_probs=25.0
Q ss_pred HHHHHHHhCCCCChhHHHHHHHhhHhHh
Q psy13513 38 KRLIQTISGGSVSQNVVIAMSGIAKVFV 65 (71)
Q Consensus 38 kkli~~~~~~sv~~nv~i~v~g~aKvFV 65 (71)
|.++|-+++.++.-+.+-++-.++|.||
T Consensus 9 R~lmN~ll~Gava~~a~~~lyP~~~ffv 36 (39)
T PF08802_consen 9 RQLMNLLLGGAVAVPAGGMLYPYVKFFV 36 (39)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHhhHHHHHHHHhhhheeEec
Confidence 7899999999999888888889999886
No 18
>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=68.03 E-value=11 Score=21.81 Aligned_cols=41 Identities=24% Similarity=0.441 Sum_probs=35.2
Q ss_pred cCCChHHHHHHHHHHhC-----CCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 30 AAFPKAAIKRLIQTISG-----GSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 30 s~f~K~~ikkli~~~~~-----~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
...+|..++|+...+.. ..++.....++.++...|+.+|.|
T Consensus 4 ~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~ 49 (75)
T PF00125_consen 4 RLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILE 49 (75)
T ss_dssp HSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHH
T ss_pred cccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhh
Confidence 35678899999998886 488999999999999999998876
No 19
>PF08971 GlgS: Glycogen synthesis protein; InterPro: IPR015065 Members of this protein are involved in glycogen synthesis in Enterobacteria. The structure of the polypeptide chain comprises a bundle of two parallel amphipathic helices, alpha-1 and alpha-3, and a short hydrophobic helix alpha-2 sandwiched between them []. ; GO: 0005978 glycogen biosynthetic process; PDB: 1RRZ_A.
Probab=56.49 E-value=8 Score=23.71 Aligned_cols=20 Identities=35% Similarity=0.763 Sum_probs=14.9
Q ss_pred HHHhhCCCHHHH----HHHHHHHh
Q psy13513 10 QVLVSNFTEDQL----DRYEMYRR 29 (71)
Q Consensus 10 ~~L~~~~~~eQ~----~Rye~fRR 29 (71)
.-+.++||+||. +||+.||.
T Consensus 31 ~~I~gnM~ee~r~~F~~R~~~Yr~ 54 (66)
T PF08971_consen 31 DAITGNMSEEQREWFCERYAHYRQ 54 (66)
T ss_dssp HHHHHH--TTHHHHHHHHHHHHHH
T ss_pred HHHhccCCHHHHHHHHHHHHHHHH
Confidence 457789999995 69999997
No 20
>PF12174 RST: RCD1-SRO-TAF4 (RST) plant domain; InterPro: IPR022003 This domain is found in many plant proteins including SROs and RCD1s; it is required for interaction with multiple plant transcription factors.
Probab=56.41 E-value=42 Score=20.23 Aligned_cols=38 Identities=18% Similarity=0.500 Sum_probs=31.5
Q ss_pred HHHHhhCCCHHHHH----HHHHHHhcCCChHHHHHHHHHHhC
Q psy13513 9 MQVLVSNFTEDQLD----RYEMYRRAAFPKAAIKRLIQTISG 46 (71)
Q Consensus 9 ~~~L~~~~~~eQ~~----Rye~fRRs~f~K~~ikkli~~~~~ 46 (71)
+..|...+++++++ -|+.||+..++|...=|.+..+.|
T Consensus 15 ~~~l~~~l~~~~~~~l~~~Y~~~k~~kIsR~~fvr~lR~IVG 56 (70)
T PF12174_consen 15 FSALSKHLPPSKMDLLQKHYEEFKKKKISREEFVRKLRQIVG 56 (70)
T ss_pred HHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
Confidence 45677778877765 599999999999999888888887
No 21
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=54.91 E-value=23 Score=23.68 Aligned_cols=41 Identities=34% Similarity=0.536 Sum_probs=26.1
Q ss_pred HHHHhcCCChHHHHHHHHHHh-----CCCCChhHHHHHHHhhHhHhhhhc
Q psy13513 25 EMYRRAAFPKAAIKRLIQTIS-----GGSVSQNVVIAMSGIAKVFVGEIV 69 (71)
Q Consensus 25 e~fRRs~f~K~~ikkli~~~~-----~~sv~~nv~i~v~g~aKvFVGEiV 69 (71)
+.|-.++||-+.|||+||.=- ||++| +||-. ---+|+-+||
T Consensus 17 ~~~~ktrFP~ar~KkIMQ~deDiGKV~q~tP---VIask-alE~Fl~~iv 62 (113)
T COG5247 17 QKKKKTRFPIARLKKIMQLDEDIGKVGQSTP---VIASK-ALEMFLTEIV 62 (113)
T ss_pred hhhhhhcCCHHHHHHHHHhhhhhhhhhhcch---HHHHH-HHHHHHHHHH
Confidence 347789999999999998532 34443 33322 2246766665
No 22
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=53.83 E-value=21 Score=23.54 Aligned_cols=40 Identities=18% Similarity=0.382 Sum_probs=35.0
Q ss_pred CCChHHHHHHHHH-HhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 31 AFPKAAIKRLIQT-ISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 31 ~f~K~~ikkli~~-~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
.||-+.|.|++.. ....-|+....+.++++--.+..||.|
T Consensus 20 ~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIle 60 (115)
T cd00074 20 QFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLE 60 (115)
T ss_pred cCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHH
Confidence 3899999999987 667889999999999999999999876
No 23
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=53.73 E-value=7.5 Score=22.56 Aligned_cols=27 Identities=15% Similarity=0.203 Sum_probs=23.3
Q ss_pred HhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 44 ISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 44 ~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
+.|.++|.|+.-+-.++.++=.|+.++
T Consensus 4 ~~G~~CP~P~i~~k~~l~~l~~G~~l~ 30 (69)
T cd03423 4 TRGLRCPEPVMMLHKKVRKMKPGDTLL 30 (69)
T ss_pred ccCCcCCHHHHHHHHHHHcCCCCCEEE
Confidence 468899999999999999999998654
No 24
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=52.91 E-value=7.2 Score=23.76 Aligned_cols=27 Identities=33% Similarity=0.393 Sum_probs=24.3
Q ss_pred HhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 44 ISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 44 ~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
+.|..+|-|+..+-..++|+=.||++|
T Consensus 10 ~rG~~CP~Pv~~~kk~l~~m~~Ge~Le 36 (78)
T COG0425 10 LRGLRCPGPVVETKKALAKLKPGEILE 36 (78)
T ss_pred ccCCcCCccHHHHHHHHHcCCCCCEEE
Confidence 458999999999999999999999875
No 25
>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=52.43 E-value=41 Score=19.90 Aligned_cols=39 Identities=26% Similarity=0.416 Sum_probs=33.1
Q ss_pred CChHHHHHHHHHHhC-CCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 32 FPKAAIKRLIQTISG-GSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 32 f~K~~ikkli~~~~~-~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
++|..+..++.++.+ ..+++.+.-++.-++=-|+-++++
T Consensus 2 ~~k~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~ 41 (72)
T cd07981 2 LTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVE 41 (72)
T ss_pred CcHHHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHH
Confidence 578899999999875 578899999999999888887765
No 26
>PRK02922 glycogen synthesis protein GlgS; Provisional
Probab=52.17 E-value=23 Score=21.83 Aligned_cols=23 Identities=26% Similarity=0.504 Sum_probs=18.1
Q ss_pred HHHhhCCCHHHH----HHHHHHHhcCC
Q psy13513 10 QVLVSNFTEDQL----DRYEMYRRAAF 32 (71)
Q Consensus 10 ~~L~~~~~~eQ~----~Rye~fRRs~f 32 (71)
.-+-++||+||. +||..||.-..
T Consensus 32 d~V~gnmsee~r~~F~eRla~Yr~~~~ 58 (67)
T PRK02922 32 QAVTGNMDEEHRTWFCARYAWYCQQMM 58 (67)
T ss_pred HHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence 457789999996 68899987544
No 27
>PF07235 DUF1427: Protein of unknown function (DUF1427); InterPro: IPR009872 This family consists of several bacterial proteins of around 100 residues in length. The function of this family is unknown.
Probab=51.15 E-value=15 Score=23.77 Aligned_cols=29 Identities=24% Similarity=0.358 Sum_probs=23.2
Q ss_pred HHHHhCCCCChhHHHHHHHhhHhHhhhhc
Q psy13513 41 IQTISGGSVSQNVVIAMSGIAKVFVGEIV 69 (71)
Q Consensus 41 i~~~~~~sv~~nv~i~v~g~aKvFVGEiV 69 (71)
+-..++-..|.+.+||+.|+-=+|+||-+
T Consensus 16 iy~ll~v~sPAPP~iAl~GllGi~~Ge~~ 44 (90)
T PF07235_consen 16 IYSLLKVPSPAPPVIALVGLLGILLGEQA 44 (90)
T ss_pred HHHHhcCCCCCCcHhHHHHHHHHhcccch
Confidence 44556677888888899999999999853
No 28
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=49.72 E-value=9.4 Score=21.42 Aligned_cols=27 Identities=22% Similarity=0.349 Sum_probs=22.6
Q ss_pred HhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 44 ISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 44 ~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
+.|..+|.|+..+..++.++=.|+.++
T Consensus 4 ~rg~~CP~Pl~~~~~~l~~l~~g~~l~ 30 (69)
T cd00291 4 LRGLPCPLPVLKTKKALEKLKSGEVLE 30 (69)
T ss_pred ccCCcCCHHHHHHHHHHhcCCCCCEEE
Confidence 458899999999999999988887653
No 29
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=49.10 E-value=10 Score=21.52 Aligned_cols=26 Identities=19% Similarity=0.264 Sum_probs=21.4
Q ss_pred HhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 44 ISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 44 ~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
+.|.+.|.|+..+-.++ ++-.|+.++
T Consensus 4 ~rG~~CP~P~l~~k~al-~~~~g~~l~ 29 (67)
T cd03421 4 ARGLACPQPVIKTKKAL-ELEAGGEIE 29 (67)
T ss_pred cCCCCCCHHHHHHHHHH-hcCCCCEEE
Confidence 45889999999999999 888887653
No 30
>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function. One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.
Probab=48.84 E-value=23 Score=26.40 Aligned_cols=24 Identities=25% Similarity=0.471 Sum_probs=18.8
Q ss_pred HHHHHHHHHHhhCCCHHHHHHHHH
Q psy13513 3 EEEREKMQVLVSNFTEDQLDRYEM 26 (71)
Q Consensus 3 eee~~~~~~L~~~~~~eQ~~Rye~ 26 (71)
|.+++....+++.||+||..+||-
T Consensus 289 e~kr~e~~~~~~~lspeeQrK~ee 312 (321)
T PF07946_consen 289 EKKREERERKLSKLSPEEQRKYEE 312 (321)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHH
Confidence 344555568899999999999984
No 31
>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=48.52 E-value=29 Score=20.82 Aligned_cols=40 Identities=18% Similarity=0.300 Sum_probs=26.5
Q ss_pred cCCChHHHHHHHHHHhCC-CCChhHHHHHHHhhHhHhhhhcc
Q psy13513 30 AAFPKAAIKRLIQTISGG-SVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 30 s~f~K~~ikkli~~~~~~-sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
|-|++..||-+.. .+|. ++|+.++.+++-=.-.-+.|||+
T Consensus 2 s~~~~esvk~iAe-s~Gi~~l~de~a~~La~dveyrlreiiq 42 (66)
T PF02969_consen 2 SVFSQESVKDIAE-SLGISNLSDEAAKALAEDVEYRLREIIQ 42 (66)
T ss_dssp ----HHHHHHHHH-HTT---B-HHHHHHHHHHHHHHHHHHHH
T ss_pred CcCCHHHHHHHHH-HcCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4578888877666 4555 89999999999888888888775
No 32
>KOG0870|consensus
Probab=48.37 E-value=36 Score=24.33 Aligned_cols=38 Identities=32% Similarity=0.468 Sum_probs=30.6
Q ss_pred CCChHHHHHHHHHHhCC---CCChhHHHHHHHhhHhHhhhh
Q psy13513 31 AFPKAAIKRLIQTISGG---SVSQNVVIAMSGIAKVFVGEI 68 (71)
Q Consensus 31 ~f~K~~ikkli~~~~~~---sv~~nv~i~v~g~aKvFVGEi 68 (71)
.||++.|.||+..++.. +++.-...|++-=|-|||--+
T Consensus 10 ~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~L 50 (172)
T KOG0870|consen 10 NLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFL 50 (172)
T ss_pred hccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHH
Confidence 59999999999999965 466777778888888888543
No 33
>KOG3467|consensus
Probab=46.93 E-value=41 Score=22.02 Aligned_cols=39 Identities=26% Similarity=0.383 Sum_probs=23.8
Q ss_pred CCChHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhhc
Q psy13513 31 AFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEIV 69 (71)
Q Consensus 31 ~f~K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEiV 69 (71)
.+.|++||+|...--=..+.--+---..+.+|+|+-+.+
T Consensus 29 gitKpaIRRlARr~GVkRi~G~~yeE~~~~~k~fl~n~i 67 (103)
T KOG3467|consen 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVI 67 (103)
T ss_pred ccchHHHHHHHHhcCcchhchhhHHHHHHHHHHHHHHHH
Confidence 456999999986532223333344445677788876654
No 34
>PF07813 LTXXQ: LTXXQ motif family protein; InterPro: IPR012899 This five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (P32158 from SWISSPROT). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH []. Another member of this family, Spy (P77754 from SWISSPROT) is also a periplasmic protein that may be involved in the response to stress []. The homology between CpxP and Spy may indicate that these two proteins are functionally related []. The motif is found repeated twice in many members of this entry. ; GO: 0042597 periplasmic space; PDB: 3ITF_B 3QZC_B 3OEO_D 3O39_A.
Probab=46.69 E-value=42 Score=19.62 Aligned_cols=22 Identities=14% Similarity=0.338 Sum_probs=16.0
Q ss_pred HHHHHHHHhhCCCHHHHHHHHH
Q psy13513 5 EREKMQVLVSNFTEDQLDRYEM 26 (71)
Q Consensus 5 e~~~~~~L~~~~~~eQ~~Rye~ 26 (71)
..+...-+.+.|||||..+|..
T Consensus 77 ~~~~~~~~~~vLt~eQk~~~~~ 98 (100)
T PF07813_consen 77 RAKAQHALYAVLTPEQKEKFDQ 98 (100)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHH
T ss_pred HHHHHHHHHhcCCHHHHHHHHH
Confidence 3455667889999999998854
No 35
>PF02978 SRP_SPB: Signal peptide binding domain; InterPro: IPR004125 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the M domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 2FFH_B 3NDB_B 2V3C_C 1QZW_G 1QZX_B 3KL4_A 2JQE_A 1HQ1_A 1RY1_W 1MFQ_C ....
Probab=46.13 E-value=42 Score=21.41 Aligned_cols=25 Identities=16% Similarity=0.438 Sum_probs=19.8
Q ss_pred HHHHHHHHHHhhCCCHHHHHHHHHH
Q psy13513 3 EEEREKMQVLVSNFTEDQLDRYEMY 27 (71)
Q Consensus 3 eee~~~~~~L~~~~~~eQ~~Rye~f 27 (71)
+.+..++..++++||+++++--..+
T Consensus 47 ~~~lk~~~~Ii~SMT~~Er~~p~ll 71 (104)
T PF02978_consen 47 EKKLKRMEAIIDSMTPEERDNPKLL 71 (104)
T ss_dssp HHHHHHHHHHHTTSBHHHHHCGGGH
T ss_pred HHHHHHHHHHHHCcCHHHHhCcccc
Confidence 4456778899999999999766665
No 36
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=44.83 E-value=50 Score=17.69 Aligned_cols=13 Identities=15% Similarity=0.197 Sum_probs=10.9
Q ss_pred CCCCChhHHHHHH
Q psy13513 46 GGSVSQNVVIAMS 58 (71)
Q Consensus 46 ~~sv~~nv~i~v~ 58 (71)
|+.||+++..++.
T Consensus 24 ~~pVP~~l~~~I~ 36 (37)
T PF08880_consen 24 NQPVPPQLQQAIQ 36 (37)
T ss_pred CCCCCHHHHHhhh
Confidence 8899999888764
No 37
>COG4317 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.40 E-value=30 Score=22.39 Aligned_cols=30 Identities=23% Similarity=0.375 Sum_probs=23.6
Q ss_pred HHHHHhCCCCChhHHHHHHHhhHhHhhhhc
Q psy13513 40 LIQTISGGSVSQNVVIAMSGIAKVFVGEIV 69 (71)
Q Consensus 40 li~~~~~~sv~~nv~i~v~g~aKvFVGEiV 69 (71)
++-+.+.-..|.+.+||+-|+--++|||=+
T Consensus 16 iiyaLl~vrsPAPP~iAlvGllGilvGeq~ 45 (93)
T COG4317 16 IIYALLKVRSPAPPAIALVGLLGILVGEQI 45 (93)
T ss_pred HHHHHHhCCCCCCcHHHHHHHHHHHHHHHH
Confidence 344555667888899999999999999843
No 38
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=43.82 E-value=15 Score=20.81 Aligned_cols=27 Identities=22% Similarity=0.336 Sum_probs=21.0
Q ss_pred HhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 44 ISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 44 ~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
+.|..+|.++..+-..+.++=.|+.++
T Consensus 5 ~rg~~CP~Pll~~~~~l~~l~~G~~l~ 31 (70)
T PF01206_consen 5 LRGLSCPMPLLKAKKALKELPPGEVLE 31 (70)
T ss_dssp CSS-STTHHHHHHHHHHHTSGTT-EEE
T ss_pred CCCCCCCHHHHHHHHHHHhcCCCCEEE
Confidence 357899999999999999988887654
No 39
>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=41.37 E-value=14 Score=22.40 Aligned_cols=37 Identities=24% Similarity=0.370 Sum_probs=27.1
Q ss_pred ChHHHHHHHHHHh---CCCCChhHHHHHHHhhHhHhhhhc
Q psy13513 33 PKAAIKRLIQTIS---GGSVSQNVVIAMSGIAKVFVGEIV 69 (71)
Q Consensus 33 ~K~~ikkli~~~~---~~sv~~nv~i~v~g~aKvFVGEiV 69 (71)
|+..|.||+.... ...+++...-+++-+-++||-|-|
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv 40 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAV 40 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHH
Confidence 5777888887444 246778888899999999998865
No 40
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=40.50 E-value=70 Score=18.12 Aligned_cols=30 Identities=13% Similarity=0.399 Sum_probs=14.2
Q ss_pred hhCCCHHHHHHHHHHHh--cCCChHHHHHHHH
Q psy13513 13 VSNFTEDQLDRYEMYRR--AAFPKAAIKRLIQ 42 (71)
Q Consensus 13 ~~~~~~eQ~~Rye~fRR--s~f~K~~ikkli~ 42 (71)
+..+++++...|-.+-. .++..++++..++
T Consensus 38 ~~~it~~~i~~y~~~l~~~~~~s~~T~~~~~~ 69 (85)
T PF13495_consen 38 PDEITPEDIEQYLNYLQNERGLSPSTINQYLS 69 (85)
T ss_dssp GGG--HHHHHHHHHHHHTTT---HHHHHHHHH
T ss_pred cchhHHHHHHHHHHHHHHhcCCCHHHHHHHHH
Confidence 34556666666666655 4455555555444
No 41
>cd04385 RhoGAP_ARAP RhoGAP_ARAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in ARAPs. ARAPs (also known as centaurin deltas) contain, besides the RhoGAP domain, an Arf GAP, ankyrin repeat ras-associating, and PH domains. Since their ArfGAP activity is PIP3-dependent, ARAPs are considered integration points for phosphoinositide, Arf and Rho signaling. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=40.08 E-value=42 Score=22.80 Aligned_cols=43 Identities=16% Similarity=0.460 Sum_probs=29.0
Q ss_pred HHHhcCCChHHHHHHHHHHhCC----CC--ChhHHHHHHHhhHhHhhhhc
Q psy13513 26 MYRRAAFPKAAIKRLIQTISGG----SV--SQNVVIAMSGIAKVFVGEIV 69 (71)
Q Consensus 26 ~fRRs~f~K~~ikkli~~~~~~----sv--~~nv~i~v~g~aKvFVGEiV 69 (71)
-||.|+ +...|++|....-.. .+ +..-+-.+||+-|.|.-||=
T Consensus 36 IFR~sg-~~~~i~~L~~~~~~~~~~~~~~~~~~d~~~va~llK~yLreLP 84 (184)
T cd04385 36 IYRKNG-KNSSVKKLLEAFRKDARSVQLREGEYTVHDVADVLKRFLRDLP 84 (184)
T ss_pred eeeCCC-cHHHHHHHHHHHhcCCCcCCCCcccCCHHHHHHHHHHHHHhCC
Confidence 578887 677888888766421 11 22234467999999998874
No 42
>PF08411 Exonuc_X-T_C: Exonuclease C-terminal; InterPro: IPR013620 This bacterial domain is found at the C terminus of exodeoxyribonuclease I/Exonuclease I (IPR013520 from INTERPRO), which is a single-strand specific DNA nuclease affecting recombination and expression pathways. The exonuclease I protein in Escherichia coli is associated with DNA deoxyribophosphodiesterase (dRPase) []. ; GO: 0008852 exodeoxyribonuclease I activity, 0006281 DNA repair; PDB: 2QXF_A 3C94_A 3HL8_A 3C95_A 1FXX_A 3HP9_A.
Probab=38.99 E-value=40 Score=24.72 Aligned_cols=23 Identities=13% Similarity=0.420 Sum_probs=18.7
Q ss_pred hCCCHHHHHHHHHHHhcCCChHH
Q psy13513 14 SNFTEDQLDRYEMYRRAAFPKAA 36 (71)
Q Consensus 14 ~~~~~eQ~~Rye~fRRs~f~K~~ 36 (71)
+.||+++..|+..||+..|..+.
T Consensus 207 ~tL~~~E~~~W~~~~~~rL~~~~ 229 (269)
T PF08411_consen 207 ETLSEEEQQRWQEYCQQRLTDPD 229 (269)
T ss_dssp GG--HHHHHHHHHHHHHHS-HHH
T ss_pred hhCCHHHHHHHHHHHHHHccCCc
Confidence 67999999999999999999987
No 43
>KOG4054|consensus
Probab=38.25 E-value=39 Score=24.35 Aligned_cols=35 Identities=26% Similarity=0.359 Sum_probs=27.7
Q ss_pred HHHhcCCChHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhh
Q psy13513 26 MYRRAAFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEI 68 (71)
Q Consensus 26 ~fRRs~f~K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEi 68 (71)
.|--|...|+-+|++|= ...+|-+-++||+++|.+
T Consensus 26 hYq~s~~~Ks~lK~lif--------vh~lI~v~mlak~~l~hl 60 (183)
T KOG4054|consen 26 HYQMSVTLKSRLKKLIF--------VHALIWVLMLAKMSLGHL 60 (183)
T ss_pred HHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHhhhhh
Confidence 46668888999999985 236788889999998875
No 44
>PF15540 Toxin_62: Putative toxin 62
Probab=38.08 E-value=15 Score=24.63 Aligned_cols=17 Identities=29% Similarity=0.491 Sum_probs=13.7
Q ss_pred HHHHHHHhcCCChHHHH
Q psy13513 22 DRYEMYRRAAFPKAAIK 38 (71)
Q Consensus 22 ~Rye~fRRs~f~K~~ik 38 (71)
.=+|+|||..+||....
T Consensus 25 aldeAfrRTg~pk~~f~ 41 (113)
T PF15540_consen 25 ALDEAFRRTGVPKEQFT 41 (113)
T ss_pred HHHHHHHhhCCCccccc
Confidence 34799999999998653
No 45
>PRK10445 endonuclease VIII; Provisional
Probab=38.03 E-value=33 Score=24.90 Aligned_cols=44 Identities=20% Similarity=0.294 Sum_probs=28.4
Q ss_pred hhCCCHHHHHHHHHHHhcCCChHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhh
Q psy13513 13 VSNFTEDQLDRYEMYRRAAFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEI 68 (71)
Q Consensus 13 ~~~~~~eQ~~Rye~fRRs~f~K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEi 68 (71)
-..||.+.+ ++..+++.++|..||.+ .++|++ +||++=+|.-|+
T Consensus 132 ~~~~~~~~~--~~~l~~~~~~~~~IK~~---LLDQ~~-------vaGIGNiyadEi 175 (263)
T PRK10445 132 DPNLTPEQV--KERLLSPRFRNRQFSGL---LLDQAF-------LAGLGNYLRVEI 175 (263)
T ss_pred CCcCCHHHH--HHHHhcCccccccHHHH---HhcCCc-------cccccHHHHHHH
Confidence 345777764 56677776778788765 345543 457777776665
No 46
>PF09336 Vps4_C: Vps4 C terminal oligomerisation domain; InterPro: IPR015415 This domain is found at the C-terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation []. ; PDB: 1XWI_A 3EIH_C 2QPA_C 3EIE_A 2RKO_A 2QP9_X 3MHV_C 3CF3_C 3CF1_A 3CF2_A ....
Probab=37.27 E-value=44 Score=19.48 Aligned_cols=21 Identities=14% Similarity=0.542 Sum_probs=15.1
Q ss_pred HHHHhhCCCHHHHHHHHHHHh
Q psy13513 9 MQVLVSNFTEDQLDRYEMYRR 29 (71)
Q Consensus 9 ~~~L~~~~~~eQ~~Rye~fRR 29 (71)
++..-.+-++++++||+.|-+
T Consensus 39 l~~~kpSVs~~dl~~ye~w~~ 59 (62)
T PF09336_consen 39 LKKVKPSVSQEDLKKYEEWTK 59 (62)
T ss_dssp HHTCGGSS-HHHHHHHHHHHH
T ss_pred HHHcCCCCCHHHHHHHHHHHH
Confidence 344456788999999999864
No 47
>cd04378 RhoGAP_GMIP_PARG1 RhoGAP_GMIP_PARG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of GMIP (Gem interacting protein) and PARG1 (PTPL1-associated RhoGAP1). GMIP plays important roles in neurite growth and axonal guidance, and interacts with Gem, a member of the RGK subfamily of the Ras small GTPase superfamily, through the N-terminal half of the protein. GMIP contains a C-terminal RhoGAP domain. GMIP inhibits RhoA function, but is inactive towards Rac1 and Cdc41. PARG1 interacts with Rap2, also a member of the Ras small GTPase superfamily whose exact function is unknown, and shows strong preference for Rho. 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 ge
Probab=35.97 E-value=54 Score=22.60 Aligned_cols=44 Identities=25% Similarity=0.438 Sum_probs=31.0
Q ss_pred HHHhcCCChHHHHHHHHHHhC-CC---CChhHHHHHHHhhHhHhhhhcc
Q psy13513 26 MYRRAAFPKAAIKRLIQTISG-GS---VSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 26 ~fRRs~f~K~~ikkli~~~~~-~s---v~~nv~i~v~g~aKvFVGEiVE 70 (71)
-||.++ +++.|++|.+.+-. .. .++.-+-.+||+-|.|.-|+=|
T Consensus 37 IfR~sG-~~~~i~~l~~~~~~~~~~~~~~~~~~h~va~~LK~fLReLpe 84 (203)
T cd04378 37 IYRVSG-SKARVEKLCQAFENGKDLVELSELSPHDISSVLKLFLRQLPE 84 (203)
T ss_pred ceeCCC-cHHHHHHHHHHHhcCCCccccccCCHHHHHHHHHHHHHhCCC
Confidence 588888 58889999877643 22 1222355689999999988743
No 48
>PHA02567 rnh RnaseH; Provisional
Probab=35.03 E-value=79 Score=24.21 Aligned_cols=50 Identities=20% Similarity=0.379 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHhc----CCChHHHHHHHHHHhCCCCChhHHH----HHHHhhHhH
Q psy13513 15 NFTEDQLDRYEMYRRA----AFPKAAIKRLIQTISGGSVSQNVVI----AMSGIAKVF 64 (71)
Q Consensus 15 ~~~~eQ~~Rye~fRRs----~f~K~~ikkli~~~~~~sv~~nv~i----~v~g~aKvF 64 (71)
.|++||+.||.-=|+- -+|+..--+++....++.+|+.--| +=.|+.|++
T Consensus 241 ~~~~e~~~r~~~n~~l~d~~~ip~~i~~~i~~~~~~~~~~~~~k~~~yf~~~~l~~~~ 298 (304)
T PHA02567 241 LLTEEEYERYDENRELIDFDFIPDDIADKIIEAYNSYKPPPRGKIYSYFVKNGLSKLL 298 (304)
T ss_pred hcCHHHHHHhhccceeeccccCcHHHHHHHHHHHhcCCCCCccchHHHHHHhhHHHHH
Confidence 5899999999887764 3678877888888888877764322 335666654
No 49
>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=33.64 E-value=52 Score=23.24 Aligned_cols=24 Identities=29% Similarity=0.533 Sum_probs=18.5
Q ss_pred cHHHHHHHHHHhhCCCHHHHHHHH
Q psy13513 2 EEEEREKMQVLVSNFTEDQLDRYE 25 (71)
Q Consensus 2 ~eee~~~~~~L~~~~~~eQ~~Rye 25 (71)
+++++++++-+-++||+++.++-.
T Consensus 12 ~~~e~~~L~~~k~~Ls~~e~~~i~ 35 (248)
T PF08367_consen 12 EEEEKEKLAAYKASLSEEEKEKII 35 (248)
T ss_dssp HHHHHHHHHHHHHCS-HHHHHHHH
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHH
Confidence 577888889999999998877643
No 50
>PF02260 FATC: FATC domain; InterPro: IPR003152 The FATC domain is found at the C-terminal end of the PIK-related kinases. Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding; PDB: 2KIT_A 1W1N_A 2KIO_A.
Probab=33.52 E-value=66 Score=16.66 Aligned_cols=22 Identities=18% Similarity=0.507 Sum_probs=14.0
Q ss_pred HHHHHHHHHHhCCCCChhHHHHHHHhhHhHhh
Q psy13513 35 AAIKRLIQTISGGSVSQNVVIAMSGIAKVFVG 66 (71)
Q Consensus 35 ~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVG 66 (71)
..|.+||++ |+-..-++++|+|
T Consensus 7 ~qV~~LI~~----------At~~~nLa~my~G 28 (33)
T PF02260_consen 7 QQVDELISE----------ATDPENLARMYIG 28 (33)
T ss_dssp HHHHHHHHH----------HHHHHHHHHHCTS
T ss_pred HHHHHHHHH----------HcCHHHHHHHhcc
Confidence 456677763 4445667777776
No 51
>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=33.31 E-value=65 Score=21.85 Aligned_cols=44 Identities=23% Similarity=0.398 Sum_probs=30.1
Q ss_pred HHHHhcCCChHHHHHHHHHHhCC--CC--ChhHHHHHHHhhHhHhhhhc
Q psy13513 25 EMYRRAAFPKAAIKRLIQTISGG--SV--SQNVVIAMSGIAKVFVGEIV 69 (71)
Q Consensus 25 e~fRRs~f~K~~ikkli~~~~~~--sv--~~nv~i~v~g~aKvFVGEiV 69 (71)
..||.++ +...|+++.+.+-.. .+ .+--+-++||+-|-|..++=
T Consensus 35 GiFR~~g-~~~~i~~l~~~l~~~~~~~~~~~~~~~~va~~LK~flr~Lp 82 (186)
T cd04377 35 GIYRKSG-SANKIKELRQGLDTDPDSVNLEDYPIHVITSVLKQWLRELP 82 (186)
T ss_pred ceeeCCC-CHHHHHHHHHHHhCCCcccCcccCCHHHHHHHHHHHHHcCC
Confidence 4588887 567788888776433 22 22235678999999998874
No 52
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=32.22 E-value=26 Score=20.33 Aligned_cols=27 Identities=19% Similarity=0.404 Sum_probs=22.0
Q ss_pred HhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 44 ISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 44 ~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
+.|.++|.|+.-+-..+.++=.||+++
T Consensus 4 ~rG~~CP~Pvi~~kkal~~l~~G~~l~ 30 (69)
T cd03422 4 LRGEPCPYPAIATLEALPSLKPGEILE 30 (69)
T ss_pred cCCCcCCHHHHHHHHHHHcCCCCCEEE
Confidence 457889999999999998888888654
No 53
>PRK13291 metal-dependent hydrolase; Provisional
Probab=32.14 E-value=45 Score=22.57 Aligned_cols=39 Identities=15% Similarity=0.185 Sum_probs=24.0
Q ss_pred HHHHHHhhCCCHHHHHHHHHHHhcCCChHHHHHHHHHHhCC
Q psy13513 7 EKMQVLVSNFTEDQLDRYEMYRRAAFPKAAIKRLIQTISGG 47 (71)
Q Consensus 7 ~~~~~L~~~~~~eQ~~Rye~fRRs~f~K~~ikkli~~~~~~ 47 (71)
+.+..++.++++++++|.- ..+.+.+-.++-++..+.+.
T Consensus 118 ~~~i~ll~~l~~e~l~r~~--~~~~~~~~Tl~~~l~~~~~H 156 (173)
T PRK13291 118 KRWVALLESLTEEDLERTF--NHPDGGETTLDEAIGLYAWH 156 (173)
T ss_pred HHHHHHHHcCCHHHHHccc--CCCCCCeeeHHHHHHHHHHH
Confidence 3444677778888877763 33445565666666655544
No 54
>PF10501 Ribosomal_L50: Ribosomal subunit 39S; InterPro: IPR018305 This entry represents the L50 protein from the mitochondrial 39S ribosomal subunit. L50 appears to be a secondary RNA-binding protein []. The 39S ribosomal protein appears to be a subunit of one of the larger mitochondrial 66S or 70S units []. Under conditions of ethanol-stress in rats the larger subunit is largely dissociated into its smaller components [].; GO: 0005739 mitochondrion
Probab=31.75 E-value=74 Score=20.22 Aligned_cols=37 Identities=8% Similarity=0.275 Sum_probs=28.4
Q ss_pred HHHhcCCChHHHH----HHHHHHhCCCCChhHHHHHHHhhH
Q psy13513 26 MYRRAAFPKAAIK----RLIQTISGGSVSQNVVIAMSGIAK 62 (71)
Q Consensus 26 ~fRRs~f~K~~ik----kli~~~~~~sv~~nv~i~v~g~aK 62 (71)
.|....|....+| |-+++.+|..||+.....+..++.
T Consensus 34 ~~~~~~l~D~~~KF~~lKrl~~~tGh~ipD~~L~~~~T~~d 74 (112)
T PF10501_consen 34 DWLDISLEDLQLKFAFLKRLQQLTGHRIPDSKLHSIHTVGD 74 (112)
T ss_pred cccccccCCHHHHHHHHHHHHHHHCCCCCcHHHHhcCCHHH
Confidence 3666678777666 778889999999988877766554
No 55
>PF10260 SAYSvFN: Uncharacterized conserved domain (SAYSvFN); InterPro: IPR019387 This domain of approximately 75 residues contains a highly conserved SATSv/iFN motif. The function is unknown but the domain is conserved from plants to humans.
Probab=31.64 E-value=24 Score=21.67 Aligned_cols=14 Identities=21% Similarity=0.499 Sum_probs=12.1
Q ss_pred HHHhhCCCHHHHHH
Q psy13513 10 QVLVSNFTEDQLDR 23 (71)
Q Consensus 10 ~~L~~~~~~eQ~~R 23 (71)
+-|..+|+.||++|
T Consensus 55 ~~i~Gtl~aE~~er 68 (71)
T PF10260_consen 55 ERIPGTLTAEQFER 68 (71)
T ss_pred cccCCCCCHHHHHH
Confidence 45788999999998
No 56
>PF12397 U3snoRNP10: U3 small nucleolar RNA-associated protein 10 ; InterPro: IPR022125 This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with PF08146 from PFAM. This family is the protein associated with U3 snoRNA which is involved in the processing of pre-rRNA.
Probab=31.37 E-value=1.3e+02 Score=18.67 Aligned_cols=37 Identities=11% Similarity=0.192 Sum_probs=27.4
Q ss_pred HhcCCChHHHHHHHHHHhCCCCChhH-HHHHHHhhHhH
Q psy13513 28 RRAAFPKAAIKRLIQTISGGSVSQNV-VIAMSGIAKVF 64 (71)
Q Consensus 28 RRs~f~K~~ikkli~~~~~~sv~~nv-~i~v~g~aKvF 64 (71)
.+..|++..+..++.+++...-+.+. .-++-+++.+|
T Consensus 36 ~k~~L~~~~l~~l~~~i~~~~~~~~~~~~~l~~L~~l~ 73 (121)
T PF12397_consen 36 SKVPLSDEVLNALMESILKNWTQETVQRQALICLIVLC 73 (121)
T ss_pred hhcCCcHHHHHHHHHHHHhccccchhHHHHHHHHHHHH
Confidence 57889999999999999977655555 55555565554
No 57
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=30.65 E-value=1.3e+02 Score=18.12 Aligned_cols=30 Identities=13% Similarity=0.232 Sum_probs=19.6
Q ss_pred CHHHHHHHHHHHhcCCChHHHHHHHHHHhC
Q psy13513 17 TEDQLDRYEMYRRAAFPKAAIKRLIQTISG 46 (71)
Q Consensus 17 ~~eQ~~Rye~fRRs~f~K~~ikkli~~~~~ 46 (71)
+..++-.+-+=+.+.+++..++.+++.++.
T Consensus 2 ~k~eli~~i~~~~~~~s~~~v~~vv~~~~~ 31 (94)
T TIGR00988 2 TKSELIERIATQQSHLPAKDVEDAVKTMLE 31 (94)
T ss_pred CHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 444443333323567999999999987763
No 58
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=30.15 E-value=30 Score=20.01 Aligned_cols=27 Identities=22% Similarity=0.207 Sum_probs=22.1
Q ss_pred HhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 44 ISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 44 ~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
+.|.++|.|+.-+-.++.++=.|+.++
T Consensus 4 ~rG~~CP~Pvl~~kkal~~l~~G~~l~ 30 (69)
T cd03420 4 ACGLQCPGPILKLKKEIDKLQDGEQLE 30 (69)
T ss_pred cCCCcCCHHHHHHHHHHHcCCCCCEEE
Confidence 457889999999999999888887653
No 59
>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=29.91 E-value=77 Score=21.67 Aligned_cols=44 Identities=20% Similarity=0.386 Sum_probs=31.0
Q ss_pred HHHHhcCCChHHHHHHHHHHhCC--CCC--hhHHHHHHHhhHhHhhhhc
Q psy13513 25 EMYRRAAFPKAAIKRLIQTISGG--SVS--QNVVIAMSGIAKVFVGEIV 69 (71)
Q Consensus 25 e~fRRs~f~K~~ikkli~~~~~~--sv~--~nv~i~v~g~aKvFVGEiV 69 (71)
..||-++ ++..|++|.+.+-.. .+. +.=+-++||+-|.|.-|+=
T Consensus 35 GIFR~sG-s~~~i~~l~~~~d~~~~~~~~~~~d~h~va~lLK~fLReLP 82 (186)
T cd04406 35 GIYRKSG-STNKIKELRQGLDTDANSVNLDDYNIHVIASVFKQWLRDLP 82 (186)
T ss_pred ceeeCCC-cHHHHHHHHHHHccCCCCCCcccCCHHHHHHHHHHHHHhCC
Confidence 5688887 788899998877532 121 2225578999999998873
No 60
>TIGR03510 XapX XapX domain. This model describes an uncharacterized small, hydrophobic protein of about 50 amino acids, found between the xapB and xapR genes of the E. coli xanthosine utilization system, and homologous regions in other small proteins, such as the N-terminal region of DUF1427 (Pfam model pfam07235). We name this domain XapX, as it comprises the full length of the protein encoded between the genes for the well-studied XapB and XapR proteins.
Probab=29.64 E-value=82 Score=18.05 Aligned_cols=27 Identities=19% Similarity=0.322 Sum_probs=21.1
Q ss_pred HHhCCCCChhHHHH-HHHhhHhHhhhhc
Q psy13513 43 TISGGSVSQNVVIA-MSGIAKVFVGEIV 69 (71)
Q Consensus 43 ~~~~~sv~~nv~i~-v~g~aKvFVGEiV 69 (71)
+.++-.+|.+.+++ +-|+-=+|+|+.+
T Consensus 17 ~~l~vp~PAPP~laGl~gi~gm~~G~~~ 44 (49)
T TIGR03510 17 SLLKVPSPAPPVLAGLVGLLGMLLGEQA 44 (49)
T ss_pred HHhCCCCCCCchHHHHHHHHHHHHhHHH
Confidence 44566778777777 9999999999864
No 61
>PF06466 PCAF_N: PCAF (P300/CBP-associated factor) N-terminal domain; InterPro: IPR009464 This region is spliced out of Q92830 from SWISSPROT isoform 2. It is predicted to be of a mixed alpha/beta fold - though predominantly helical.; GO: 0004402 histone acetyltransferase activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=29.52 E-value=88 Score=23.49 Aligned_cols=38 Identities=21% Similarity=0.319 Sum_probs=28.3
Q ss_pred CCChHHHHHHHHHHhC---CCCChhHHHHHHHhhHhHhhhh
Q psy13513 31 AFPKAAIKRLIQTISG---GSVSQNVVIAMSGIAKVFVGEI 68 (71)
Q Consensus 31 ~f~K~~ikkli~~~~~---~sv~~nv~i~v~g~aKvFVGEi 68 (71)
-|.|+.|-++|...+. .++++.=-.+|+-+||+|+-+|
T Consensus 140 PFE~PsI~k~V~nfv~~kf~~l~~~E~q~m~elakmFL~~l 180 (252)
T PF06466_consen 140 PFEKPSIEKAVTNFVLYKFSHLPQKEWQTMYELAKMFLHCL 180 (252)
T ss_pred CCCCccHHHHHHHHHHHHccCCCcHHHHHHHHHHHHHHHHH
Confidence 4778888888866553 4566666777899999998765
No 62
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=29.48 E-value=57 Score=22.19 Aligned_cols=24 Identities=21% Similarity=0.391 Sum_probs=15.6
Q ss_pred CCHHHHHHHHHHHhcCCChHHHHH
Q psy13513 16 FTEDQLDRYEMYRRAAFPKAAIKR 39 (71)
Q Consensus 16 ~~~eQ~~Rye~fRRs~f~K~~ikk 39 (71)
|++....=-+.+|..++||+.-.-
T Consensus 9 l~E~e~~~ie~L~~lgi~R~vA~t 32 (124)
T COG4738 9 LTEKEYEIIELLRILGIPRNVATT 32 (124)
T ss_pred cchhHHHHHHHHHHcCCCchHHHH
Confidence 666666666777777777764433
No 63
>PF08593 MUG2_C: Meiotically up-regulated glycoproteins C-terminal; InterPro: IPR013902 This entry represents a conserved domain found in certain meiotically up-regulated gene products (MUG) from fungi []. The actual function is not yet known. The proteins are likely to be cell-surface glycoproteins and may be situated close to telomeres, hence their being expressed during meiosis [].
Probab=29.42 E-value=33 Score=20.12 Aligned_cols=12 Identities=17% Similarity=0.512 Sum_probs=10.0
Q ss_pred hhCCCHHHHHHH
Q psy13513 13 VSNFTEDQLDRY 24 (71)
Q Consensus 13 ~~~~~~eQ~~Ry 24 (71)
++.||.+|..||
T Consensus 44 id~LS~~Q~s~f 55 (58)
T PF08593_consen 44 IDNLSKEQCSFF 55 (58)
T ss_pred hhhhCHHHHHHh
Confidence 567889999888
No 64
>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]
Probab=29.33 E-value=93 Score=24.01 Aligned_cols=27 Identities=30% Similarity=0.383 Sum_probs=22.5
Q ss_pred HHHHHHHHhhCCCHHHHHHHHHHHhcC
Q psy13513 5 EREKMQVLVSNFTEDQLDRYEMYRRAA 31 (71)
Q Consensus 5 e~~~~~~L~~~~~~eQ~~Rye~fRRs~ 31 (71)
=++-.+.|++.=++|-..||.-|||-.
T Consensus 58 ir~~~~~l~~k~~~e~a~rY~lwR~ir 84 (299)
T COG2074 58 IREVYQKLLEKGDPEVAKRYLLWRRIR 84 (299)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence 344568899999999999999999843
No 65
>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.
Probab=29.20 E-value=1.3e+02 Score=19.14 Aligned_cols=6 Identities=17% Similarity=0.451 Sum_probs=2.4
Q ss_pred CCCHHH
Q psy13513 15 NFTEDQ 20 (71)
Q Consensus 15 ~~~~eQ 20 (71)
+||++|
T Consensus 58 ~Lspeq 63 (107)
T PF11304_consen 58 ALSPEQ 63 (107)
T ss_pred hCCHHH
Confidence 344443
No 66
>PRK11779 sbcB exonuclease I; Provisional
Probab=29.13 E-value=57 Score=26.13 Aligned_cols=30 Identities=10% Similarity=0.281 Sum_probs=23.4
Q ss_pred hCCCHHHHHHHHHHHhcCCChHHHHHHHHH
Q psy13513 14 SNFTEDQLDRYEMYRRAAFPKAAIKRLIQT 43 (71)
Q Consensus 14 ~~~~~eQ~~Rye~fRRs~f~K~~ikkli~~ 43 (71)
+.|++++..|++.||+..|..+.+....+.
T Consensus 415 ~~L~~~e~~~w~~~~~~rl~~~~~~~~~~~ 444 (476)
T PRK11779 415 ETLDDEEQQRWLEHRRQRLTPERLQQYAAE 444 (476)
T ss_pred hhCCHHHHHHHHHHHHHHhccchHHHHHHH
Confidence 458999999999999999977554444443
No 67
>smart00414 H2A Histone 2A.
Probab=28.55 E-value=82 Score=20.40 Aligned_cols=40 Identities=20% Similarity=0.395 Sum_probs=33.9
Q ss_pred CCChHHHHHHHHHH-hCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 31 AFPKAAIKRLIQTI-SGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 31 ~f~K~~ikkli~~~-~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
.||=+-|.|++..- ....|+....+-++++--.++.||.|
T Consensus 9 ~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILe 49 (106)
T smart00414 9 QFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLE 49 (106)
T ss_pred cCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHH
Confidence 37888899999864 47789998999999999999999876
No 68
>cd04389 RhoGAP_KIAA1688 RhoGAP_KIAA1688: GTPase-activator protein (GAP) domain for Rho-like GTPases found in KIAA1688-like proteins; KIAA1688 is a protein of unknown function that contains a RhoGAP domain and a myosin tail homology 4 (MyTH4) 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 GTP hydrolysis by several orders of magnitude.
Probab=27.80 E-value=1e+02 Score=21.13 Aligned_cols=44 Identities=11% Similarity=0.169 Sum_probs=31.1
Q ss_pred HHHhcCCChHHHHHHHHHHhCCCCC--h-hHHHHHHHhhHhHhhhhcc
Q psy13513 26 MYRRAAFPKAAIKRLIQTISGGSVS--Q-NVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 26 ~fRRs~f~K~~ikkli~~~~~~sv~--~-nv~i~v~g~aKvFVGEiVE 70 (71)
.||.++ ++..|+++.+.+-...++ . .=+-.+||+=|.|.-|+-|
T Consensus 43 IFR~~G-~~~~i~~l~~~~d~~~~~~~~~~d~h~va~lLK~fLReLpe 89 (187)
T cd04389 43 IFRVPG-DIDEVNELKLRVDQWDYPLSGLEDPHVPASLLKLWLRELEE 89 (187)
T ss_pred eeeCCC-CHHHHHHHHHHHhcCCCCccccCCHHHHHHHHHHHHHhCCC
Confidence 466665 467888888877765554 1 1256689999999988754
No 69
>cd04373 RhoGAP_p190 RhoGAP_p190: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p190-like proteins. p190, also named RhoGAP5, plays a role in neuritogenesis and axon branch stability. p190 shows a preference for Rho, over Rac and Cdc42, and consists of an N-terminal GTPase domain and a C-terminal GAP domain. The central portion of p190 contains important regulatory phosphorylation sites. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=26.41 E-value=1e+02 Score=20.90 Aligned_cols=45 Identities=22% Similarity=0.372 Sum_probs=30.7
Q ss_pred HHHHhcCCChHHHHHHHHHHhC-CCCC----hhHHHHHHHhhHhHhhhhcc
Q psy13513 25 EMYRRAAFPKAAIKRLIQTISG-GSVS----QNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 25 e~fRRs~f~K~~ikkli~~~~~-~sv~----~nv~i~v~g~aKvFVGEiVE 70 (71)
..||-++ ++..++++.+.... ..+. +.-+-++||+-|.|.-|+-|
T Consensus 35 GIFR~~G-~~~~i~~l~~~~~~~~~~~~~~~~~~~~~va~~lK~fLreLPe 84 (185)
T cd04373 35 GIYRVSG-NKTHLDSLQKQFDQDHNLDLVSKDFTVNAVAGALKSFFSELPD 84 (185)
T ss_pred CeeecCC-cHHHHHHHHHHHhcCCCCCcccccCcHHHHHHHHHHHHhcCCc
Confidence 4588877 68888888876653 2221 11256789999999988743
No 70
>PF12763 EF-hand_4: Cytoskeletal-regulatory complex EF hand; PDB: 2QPT_A 2KSP_A 2KFG_A 2JQ6_A 2KFH_A 2KFF_A 1IQ3_A 3FIA_A 2KHN_A 2KGR_A ....
Probab=26.33 E-value=1.1e+02 Score=19.37 Aligned_cols=63 Identities=21% Similarity=0.417 Sum_probs=40.4
Q ss_pred cHHHHHHHHHHhhCCCH-------HHHHHHHHHHhcCCChHHHHHHHHHHhC---CCCC-hhHHHHHHHhhHhHhh
Q psy13513 2 EEEEREKMQVLVSNFTE-------DQLDRYEMYRRAAFPKAAIKRLIQTISG---GSVS-QNVVIAMSGIAKVFVG 66 (71)
Q Consensus 2 ~eee~~~~~~L~~~~~~-------eQ~~Rye~fRRs~f~K~~ikkli~~~~~---~sv~-~nv~i~v~g~aKvFVG 66 (71)
+++|+.+..-+...+++ ++.. +.|.+|+|+...+++|-+-.-. +..+ +-.+|||.=+...--|
T Consensus 5 s~~e~~~y~~~F~~l~~~~g~isg~~a~--~~f~~S~L~~~~L~~IW~LaD~~~dG~L~~~EF~iAm~Li~~~~~~ 78 (104)
T PF12763_consen 5 SPEEKQKYDQIFQSLDPQDGKISGDQAR--EFFMKSGLPRDVLAQIWNLADIDNDGKLDFEEFAIAMHLINRKLNG 78 (104)
T ss_dssp SCCHHHHHHHHHHCTSSSTTEEEHHHHH--HHHHHTTSSHHHHHHHHHHH-SSSSSEEEHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhcCCCCCeEeHHHHH--HHHHHcCCCHHHHHHHHhhhcCCCCCcCCHHHHHHHHHHHHHHhcC
Confidence 45677777777776664 3443 6899999999999988763321 2233 5677777655443333
No 71
>PF08025 Antimicrobial_3: Spider antimicrobial peptide; InterPro: IPR012522 This family includes antimicrobial peptides isolated from the crude venom of the wolf spider Oxyopes kitabensis (Wolf spider). These peptides, known as oxyopinins, are the largest linear cationic amphipathic peptides chemically characterised and exhibit disrupting activities towards biological membranes [].; GO: 0019836 hemolysis by symbiont of host erythrocytes, 0005576 extracellular region
Probab=26.26 E-value=68 Score=17.42 Aligned_cols=14 Identities=36% Similarity=0.496 Sum_probs=9.2
Q ss_pred HHHHHHHhhHhHhh
Q psy13513 53 VVIAMSGIAKVFVG 66 (71)
Q Consensus 53 v~i~v~g~aKvFVG 66 (71)
+.-++.++||+|-|
T Consensus 6 ~~kilrsiak~fkg 19 (37)
T PF08025_consen 6 FSKILRSIAKFFKG 19 (37)
T ss_pred HHHHHHHHHHHHHH
Confidence 34456778888755
No 72
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=26.22 E-value=75 Score=21.77 Aligned_cols=42 Identities=19% Similarity=0.347 Sum_probs=33.8
Q ss_pred hcCCChHHHHHHHH-HHhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 29 RAAFPKAAIKRLIQ-TISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 29 Rs~f~K~~ikkli~-~~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
-+.||=+.|||++. .-..+-|+....+.++++--....||.|
T Consensus 24 gl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEile 66 (132)
T COG5262 24 GLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILE 66 (132)
T ss_pred CccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHH
Confidence 35689999999999 4456788888888888888888888765
No 73
>KOG0844|consensus
Probab=25.93 E-value=46 Score=26.37 Aligned_cols=25 Identities=40% Similarity=0.708 Sum_probs=14.3
Q ss_pred CHHHHHHHHHHHhcCCChHHHHHHHHHHh
Q psy13513 17 TEDQLDRYEMYRRAAFPKAAIKRLIQTIS 45 (71)
Q Consensus 17 ~~eQ~~Rye~fRRs~f~K~~ikkli~~~~ 45 (71)
..+|+.|| |..|.|.+|-||=....
T Consensus 177 a~dqmRRY----RTAFTReQIaRLEKEFy 201 (408)
T KOG0844|consen 177 ADDQMRRY----RTAFTREQIARLEKEFY 201 (408)
T ss_pred ccHHHHHH----HhhhhHHHHHHHHHHHH
Confidence 45666666 45666666666654433
No 74
>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins. Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor
Probab=25.79 E-value=17 Score=24.50 Aligned_cols=24 Identities=21% Similarity=0.483 Sum_probs=16.7
Q ss_pred CCCChhHHHHH---HHhhHhHhhhhcc
Q psy13513 47 GSVSQNVVIAM---SGIAKVFVGEIVE 70 (71)
Q Consensus 47 ~sv~~nv~i~v---~g~aKvFVGEiVE 70 (71)
.+.+.|+++.. .|.+|-||+.||.
T Consensus 48 ~~p~KpLVlSfHG~tGtGKn~v~~liA 74 (127)
T PF06309_consen 48 PNPRKPLVLSFHGWTGTGKNFVSRLIA 74 (127)
T ss_pred CCCCCCEEEEeecCCCCcHHHHHHHHH
Confidence 34445655544 7889999999875
No 75
>cd04394 RhoGAP-ARHGAP11A RhoGAP-ARHGAP11A: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP11A-like proteins. The mouse homolog of human ArhGAP11A has been detected as a gene exclusively expressed in immature ganglion cells, potentially playing a role in retinal development. The exact function of ArhGAP11A is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=24.68 E-value=1.2e+02 Score=21.04 Aligned_cols=45 Identities=22% Similarity=0.434 Sum_probs=30.5
Q ss_pred HHHHhcCCChHHHHHHHHHHhCC-CCC-hhHHHHHHHhhHhHhhhhcc
Q psy13513 25 EMYRRAAFPKAAIKRLIQTISGG-SVS-QNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 25 e~fRRs~f~K~~ikkli~~~~~~-sv~-~nv~i~v~g~aKvFVGEiVE 70 (71)
.-||.|+ ++..|+.+...+-.. .+. ..-...+||+-|.|.-|+=|
T Consensus 39 GIFR~sG-~~~~i~~l~~~~d~~~~~~~~~~~~~vaslLK~flReLPe 85 (202)
T cd04394 39 GLFRKSG-SVVRQKELKAKLEGGEACLSSALPCDVAGLLKQFFRELPE 85 (202)
T ss_pred CeeeCCC-CHHHHHHHHHHHcCCCCCccccCHHHHHHHHHHHHhcCCC
Confidence 4688888 578888888876532 221 11234579999999988743
No 76
>PF05678 VQ: VQ motif; InterPro: IPR008889 This short motif is found in a variety of plant proteins. These proteins vary greatly in length and are mostly composed of low complexity regions. They all conserve a short motif FXhVQChTG, where X is any amino acid and h is a hydrophobic amino acid. The function of this motif is uncertain, however one protein in this family has been found to bind the SigA sigma factor Q9LDH1 from SWISSPROT. It would seem plausible that this motif is needed for this activity and that this whole family might be involved in modulating plastid sigma factors.
Probab=24.49 E-value=96 Score=16.06 Aligned_cols=18 Identities=17% Similarity=0.447 Sum_probs=14.2
Q ss_pred ChHHHHHHHHHHhCCCCC
Q psy13513 33 PKAAIKRLIQTISGGSVS 50 (71)
Q Consensus 33 ~K~~ikkli~~~~~~sv~ 50 (71)
+.+.-|.|+|..+|.+-+
T Consensus 11 d~~~Fr~lVQ~LTG~~~~ 28 (31)
T PF05678_consen 11 DPSNFRALVQRLTGAPSA 28 (31)
T ss_pred CHHHHHHHHHHhHCcCCC
Confidence 456779999999998654
No 77
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=24.27 E-value=1.7e+02 Score=17.59 Aligned_cols=30 Identities=13% Similarity=0.155 Sum_probs=20.0
Q ss_pred CHHHHHHHHHHHhcCCChHHHHHHHHHHhC
Q psy13513 17 TEDQLDRYEMYRRAAFPKAAIKRLIQTISG 46 (71)
Q Consensus 17 ~~eQ~~Rye~fRRs~f~K~~ikkli~~~~~ 46 (71)
+..++-++=+=+.+.++++.++++++.++.
T Consensus 2 tk~eli~~ia~~~~~~s~~~~~~vv~~~~~ 31 (94)
T PRK00199 2 TKSELIERLAARNPHLSAKDVENAVKEILE 31 (94)
T ss_pred CHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 344444433334578999999999987663
No 78
>PF12719 Cnd3: Nuclear condensing complex subunits, C-term domain
Probab=24.25 E-value=1.2e+02 Score=21.90 Aligned_cols=35 Identities=11% Similarity=0.307 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhhc
Q psy13513 35 AAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEIV 69 (71)
Q Consensus 35 ~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEiV 69 (71)
..+-++....+...-+.--++|+-|++|.|....+
T Consensus 113 ~~l~~~l~~~l~~~~~~~~~~a~EGl~KLlL~~~i 147 (298)
T PF12719_consen 113 KSLLKILTKFLDSENPELQAIAVEGLCKLLLSGRI 147 (298)
T ss_pred hHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhcCCC
Confidence 34555666666555556678999999999987665
No 79
>PF02937 COX6C: Cytochrome c oxidase subunit VIc; InterPro: IPR004204 Cytochrome c oxidase, a 13 subunit complex, 1.9.3.1 from EC is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit VIc.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3AG4_I 2DYS_V 3ASO_I 2EIK_V 2EIM_I 1OCC_V 1V54_V 1OCO_V 3ASN_V 2EIL_I ....
Probab=24.15 E-value=25 Score=21.53 Aligned_cols=38 Identities=16% Similarity=0.181 Sum_probs=16.6
Q ss_pred cCCChHHHHHHHHHHhCCCCC--hhHHHHHHHhhHhHhhh
Q psy13513 30 AAFPKAAIKRLIQTISGGSVS--QNVVIAMSGIAKVFVGE 67 (71)
Q Consensus 30 s~f~K~~ikkli~~~~~~sv~--~nv~i~v~g~aKvFVGE 67 (71)
+.++|+.+|-|...-+--++. =-++++++++-|.+|++
T Consensus 2 ~~l~KP~mrgll~~~l~~~i~~a~~ls~~~~~~~kf~v~~ 41 (73)
T PF02937_consen 2 SALAKPQMRGLLAKRLKRHIVVAFVLSLGVAAAYKFGVAE 41 (73)
T ss_dssp --------BSHHHHHHHHHHHHHHHHHHHHHHHHHHHTHH
T ss_pred CcccCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 567888888777655533322 23445556666777764
No 80
>cd04404 RhoGAP-p50rhoGAP RhoGAP-p50rhoGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p50RhoGAP-like proteins; p50RhoGAP, also known as RhoGAP-1, contains a C-terminal RhoGAP domain and an N-terminal Sec14 domain which binds phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3). It is ubiquitously expressed and preferentially active on Cdc42. This subgroup also contains closely related ARHGAP8. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=24.09 E-value=1.3e+02 Score=20.43 Aligned_cols=44 Identities=27% Similarity=0.326 Sum_probs=30.0
Q ss_pred HHHHhcCCChHHHHHHHHHHhC-CCCC--h-hHHHHHHHhhHhHhhhhc
Q psy13513 25 EMYRRAAFPKAAIKRLIQTISG-GSVS--Q-NVVIAMSGIAKVFVGEIV 69 (71)
Q Consensus 25 e~fRRs~f~K~~ikkli~~~~~-~sv~--~-nv~i~v~g~aKvFVGEiV 69 (71)
..||.++ +...++++.+.+.. ..+. + +=+.++|++-|-|.-++=
T Consensus 43 GIFR~~g-~~~~i~~l~~~~~~~~~~~~~~~~d~~~va~~LK~~lr~Lp 90 (195)
T cd04404 43 GIFRRSA-NTQVVKEVQQKYNMGEPVDFDQYEDVHLPAVILKTFLRELP 90 (195)
T ss_pred CeeeCCC-cHHHHHHHHHHHhCCCCCCcccccCHHHHHHHHHHHHHhCC
Confidence 3588876 67778888887763 3332 2 134567999999998863
No 81
>TIGR01568 A_thal_3678 uncharacterized plant-specific domain TIGR01568. This model describes an uncharacterized domain of about 70 residues found exclusively in plants, generally toward the C-terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana. Other regions of these proteins tend to consist largely of low-complexity sequence.
Probab=23.83 E-value=1.8e+02 Score=17.60 Aligned_cols=44 Identities=11% Similarity=0.229 Sum_probs=32.9
Q ss_pred HHHHHHhc--------CCC--hHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhh
Q psy13513 23 RYEMYRRA--------AFP--KAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVG 66 (71)
Q Consensus 23 Rye~fRRs--------~f~--K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVG 66 (71)
=|+-||+| .+. -..+..|+.-.+.-+.++.=.+++++++-++++
T Consensus 10 Py~DFr~SM~EMI~~~~i~~~w~~LeeLL~cYL~LN~~~~H~~Iv~AF~dl~~~ 63 (66)
T TIGR01568 10 PYEDFRRSMEEMIEERELEADWKELEELLACYLDLNPKKSHRFIVRAFVDILSA 63 (66)
T ss_pred hHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCchhhhHHHHHHHHHHHH
Confidence 36777776 342 378888999888888887777778888877765
No 82
>cd04397 RhoGAP_fLRG1 RhoGAP_fLRG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal LRG1-like proteins. Yeast Lrg1p is required for efficient cell fusion, and mother-daughter cell separation, possibly through acting as a RhoGAP specifically regulating 1,3-beta-glucan synthesis. 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=23.76 E-value=1.1e+02 Score=21.30 Aligned_cols=45 Identities=18% Similarity=0.392 Sum_probs=30.3
Q ss_pred HHHHhcCCChHHHHHHHHHHhCCC-----CChhHHHHHHHhhHhHhhhhcc
Q psy13513 25 EMYRRAAFPKAAIKRLIQTISGGS-----VSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 25 e~fRRs~f~K~~ikkli~~~~~~s-----v~~nv~i~v~g~aKvFVGEiVE 70 (71)
..||.++ ++..|+.+...+-... ....-+..+||+-|.|.-|+=|
T Consensus 47 GIFR~sG-~~~~i~~l~~~~d~~~~~~~d~~~~~~~~va~lLK~flReLPe 96 (213)
T cd04397 47 GVFRKNG-NIRRLKELTEEIDKNPTEVPDLSKENPVQLAALLKKFLRELPD 96 (213)
T ss_pred Ceeeecc-hHHHHHHHHHHHhcCCCcccccccCcHHHHHHHHHHHHHhCCC
Confidence 3577776 6788898887765321 1112245789999999988743
No 83
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=23.75 E-value=1.3e+02 Score=15.90 Aligned_cols=36 Identities=19% Similarity=0.289 Sum_probs=24.2
Q ss_pred HHHHHHHhhCCCHHHHHHHHHHHhcCCChHHHHHHH
Q psy13513 6 REKMQVLVSNFTEDQLDRYEMYRRAAFPKAAIKRLI 41 (71)
Q Consensus 6 ~~~~~~L~~~~~~eQ~~Rye~fRRs~f~K~~ikkli 41 (71)
++.+.-.++.|+++|..-+..+.--+++-..|-+.+
T Consensus 1 r~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIa~~l 36 (54)
T PF08281_consen 1 REALQQALAQLPERQREIFLLRYFQGMSYAEIAEIL 36 (54)
T ss_dssp HHHHHHHHHCS-HHHHHHHHHHHTS---HHHHHHHC
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCcCHHHHHHHH
Confidence 356677899999999999988888877766655443
No 84
>cd01193 INT_IntI IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and a secondary target called the attC (or 59-base element) present on various mobile gene cassettes. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.
Probab=23.66 E-value=1.9e+02 Score=18.81 Aligned_cols=30 Identities=3% Similarity=0.107 Sum_probs=22.5
Q ss_pred HhhCCCHHHHHHHHHHHh--cCCChHHHHHHH
Q psy13513 12 LVSNFTEDQLDRYEMYRR--AAFPKAAIKRLI 41 (71)
Q Consensus 12 L~~~~~~eQ~~Rye~fRR--s~f~K~~ikkli 41 (71)
.++.++++...+|-.|.+ .+.....+++.+
T Consensus 6 ~~~~it~~~i~~~~~~l~~~~~~s~~t~~~~~ 37 (242)
T cd01193 6 SPDELGEEDVRAFLTLLAVEGNVSASTQNQAL 37 (242)
T ss_pred ChhhCCHHHHHHHHHHHhhccccCHHHHHHHH
Confidence 467889999999999998 455666655544
No 85
>PF04844 Ovate: Transcriptional repressor, ovate; InterPro: IPR006458 This group of sequences contain an uncharacterised domain of about 70 residues found exclusively in plants, generally toward the C terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana (Mouse-ear cress). Other regions of these proteins tend to consist largely of low-complexity sequence. Function is not known.
Probab=23.54 E-value=1.7e+02 Score=17.24 Aligned_cols=43 Identities=14% Similarity=0.218 Sum_probs=32.9
Q ss_pred HHHHHhcC---------CChHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhh
Q psy13513 24 YEMYRRAA---------FPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVG 66 (71)
Q Consensus 24 ye~fRRs~---------f~K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVG 66 (71)
|+-||+|= .....++.|+.-.+.-+.+..=-+++++++.++++
T Consensus 5 ~~DFr~SM~EMI~~~~i~~~~~LeeLL~cYL~LN~~~~H~~Iv~aF~dv~~~ 56 (59)
T PF04844_consen 5 YEDFRESMVEMIEENGIRDWDDLEELLACYLSLNSPEHHKFIVEAFVDVWVE 56 (59)
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCChhhhhHHHHHHHHHHHH
Confidence 66677662 35577888998888888888777888999988875
No 86
>PF09574 DUF2374: Protein of unknown function (Duf2374); InterPro: IPR014175 This very small protein (about 46 amino acids) consists largely of a single predicted membrane-spanning region. It is found in Photobacterium profundum SS9 and in three species of Vibrio, always near periplasmic nitrate reductase genes, but far from the periplasmic nitrate reductase genes in Aeromonas hydrophila ATCC 7966.
Probab=23.53 E-value=1.5e+02 Score=16.68 Aligned_cols=28 Identities=32% Similarity=0.412 Sum_probs=19.8
Q ss_pred HHHHHHHHHhCCCCChhHHHHHHHhhHhHh
Q psy13513 36 AIKRLIQTISGGSVSQNVVIAMSGIAKVFV 65 (71)
Q Consensus 36 ~ikkli~~~~~~sv~~nv~i~v~g~aKvFV 65 (71)
.+..++.+++|-+-- .+|.++|++-|.|
T Consensus 3 tlEsviWhvLGY~Am--PvI~L~GF~~Vav 30 (42)
T PF09574_consen 3 TLESVIWHVLGYAAM--PVIILSGFAAVAV 30 (42)
T ss_pred hHHHHHHHHhccccc--hHHHHhhHHHHHH
Confidence 456788999997643 3566778776665
No 87
>PTZ00475 RESA-like protein; Provisional
Probab=23.12 E-value=64 Score=24.63 Aligned_cols=35 Identities=11% Similarity=0.256 Sum_probs=29.4
Q ss_pred hHHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhh
Q psy13513 34 KAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEI 68 (71)
Q Consensus 34 K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEi 68 (71)
.+-+++|+++..|.++=..+.-+-.-+|+.|+|+.
T Consensus 90 e~Eak~L~~ssFg~~iLesIGwiY~Nva~~ylge~ 124 (282)
T PTZ00475 90 ENEISMLLKSSFSNFILESIGWTYENVSNIFLEEK 124 (282)
T ss_pred HHHHHHHHhCcccHHHHHHhHHHHHHHHHHHHHHh
Confidence 45678888888888888888888899999999985
No 88
>PF15061 DUF4538: Domain of unknown function (DUF4538)
Probab=22.90 E-value=91 Score=18.58 Aligned_cols=23 Identities=9% Similarity=0.241 Sum_probs=19.2
Q ss_pred CCCHHHHHHHHHHHhcCCChHHH
Q psy13513 15 NFTEDQLDRYEMYRRAAFPKAAI 37 (71)
Q Consensus 15 ~~~~eQ~~Rye~fRRs~f~K~~i 37 (71)
-|++|.+.+-..+.|.++++..|
T Consensus 30 mm~~eeYk~~Q~~nR~gI~qedv 52 (58)
T PF15061_consen 30 MMNPEEYKKEQKINRAGIKQEDV 52 (58)
T ss_pred ccChHHHHHHHHHHHhcccHhhc
Confidence 36889999999999999887654
No 89
>PF02758 PYRIN: PAAD/DAPIN/Pyrin domain; InterPro: IPR004020 Pyrin domain was identified as putative protein-protein interaction domain at the N-terminal region of several proteins thought to function in apoptotic and inflammatory signalling pathways. Using secondary structure prediction and potential-based fold recognition methods, the PYRIN domain is predicted to be a member of the six-helix bundle death domain-fold superfamily that includes death domains (DDs), death effector domains (DEDs), and caspase recruitment domains (CARDs). Members of the death domain-fold superfamily are well established mediators of protein-protein interactions found in many proteins involved in apoptosis and inflammation, indicating further that the PYRIN domains serve a similar function. Comparison of a circular dichroism spectrum of the PYRIN domain of CARD7/DEFCAP/NAC/NALP1 with spectra of several proteins known to adopt the death domain-fold provides experimental support for the structure prediction [] It is found in interferon-inducible proteins, pyrin and myeloid cell nuclear differentiation antigen.; PDB: 2DO9_A 2YU0_A 2KN6_A 1UCP_A 2L6A_A 2KM6_A 1PN5_A 2DBG_A 3QF2_B 2HM2_Q.
Probab=22.81 E-value=1.7e+02 Score=17.49 Aligned_cols=22 Identities=9% Similarity=0.264 Sum_probs=16.6
Q ss_pred HHHHHHhhCCCHHHHHHHHHHH
Q psy13513 7 EKMQVLVSNFTEDQLDRYEMYR 28 (71)
Q Consensus 7 ~~~~~L~~~~~~eQ~~Rye~fR 28 (71)
..+.-.+.+++++|+.+|-.+=
T Consensus 3 ~~Ll~~Le~L~~~efk~FK~~L 24 (83)
T PF02758_consen 3 FLLLWYLEELSEEEFKRFKWLL 24 (83)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHhCCHHHHHHHHHHh
Confidence 3455678999999999998765
No 90
>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=22.75 E-value=1.1e+02 Score=21.14 Aligned_cols=44 Identities=18% Similarity=0.416 Sum_probs=30.4
Q ss_pred HHHHhcCCChHHHHHHHHHHhCCCCCh-------hHHHHHHHhhHhHhhhhc
Q psy13513 25 EMYRRAAFPKAAIKRLIQTISGGSVSQ-------NVVIAMSGIAKVFVGEIV 69 (71)
Q Consensus 25 e~fRRs~f~K~~ikkli~~~~~~sv~~-------nv~i~v~g~aKvFVGEiV 69 (71)
.-||.|+- ...|+++.+.+-....++ .=+=++||+-|.|.-|+=
T Consensus 37 GIFR~sG~-~~~i~~l~~~~d~~~~~~~~~~~~~~d~h~va~lLK~flReLP 87 (195)
T cd04384 37 GIYRLSGI-ASNIQRLRHEFDSEQIPDLTKDVYIQDIHSVSSLCKLYFRELP 87 (195)
T ss_pred CeeeCCCC-HHHHHHHHHHHcCCCCCCcccccccccHHHHHHHHHHHHHhCC
Confidence 56898885 577999888765433221 123467999999998873
No 91
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=22.70 E-value=2.4e+02 Score=18.73 Aligned_cols=38 Identities=24% Similarity=0.330 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHh-cCCChHHHHHHHHHHhCCC-CChhHHH
Q psy13513 18 EDQLDRYEMYRR-AAFPKAAIKRLIQTISGGS-VSQNVVI 55 (71)
Q Consensus 18 ~eQ~~Rye~fRR-s~f~K~~ikkli~~~~~~s-v~~nv~i 55 (71)
+|=-.||+.|=. ....-=-+||-+|...|.. ||++.+|
T Consensus 9 eeF~ary~~~F~~~~iD~we~rrglN~l~~~DlVP~P~ii 48 (108)
T PF02284_consen 9 EEFDARYEKYFNRPDIDGWELRRGLNNLFGYDLVPEPKII 48 (108)
T ss_dssp HHHHHHHHHHHH-TT--HHHHHHHHHHHTTSSB---HHHH
T ss_pred HHHHHHHHHHhCCccccHHHHHHHHHHHhccccCCChHHH
Confidence 344569998754 8888888999999999984 6655444
No 92
>PF14400 Transglut_i_TM: Inactive transglutaminase fused to 7 transmembrane helices
Probab=22.63 E-value=1.3e+02 Score=21.06 Aligned_cols=35 Identities=20% Similarity=0.261 Sum_probs=29.7
Q ss_pred HHHHhcCCChHHHHHHHHHHhCCCCChhHHHHHHHh
Q psy13513 25 EMYRRAAFPKAAIKRLIQTISGGSVSQNVVIAMSGI 60 (71)
Q Consensus 25 e~fRRs~f~K~~ikkli~~~~~~sv~~nv~i~v~g~ 60 (71)
+++.||+=+-+-.+.||..+.... ++|+.+.+.+.
T Consensus 127 ~a~~rSAd~~sfareLik~ln~~~-~qN~~LLl~~~ 161 (165)
T PF14400_consen 127 QARSRSADNESFARELIKRLNDPD-DQNAALLLSDN 161 (165)
T ss_pred HHHHhccChHHHHHHHHHHHcCCc-chhHHHHhccc
Confidence 478899988888999999988888 99999887654
No 93
>COG1036 Archaeal flavoproteins [Energy production and conversion]
Probab=22.35 E-value=7.1 Score=28.16 Aligned_cols=47 Identities=21% Similarity=0.302 Sum_probs=35.4
Q ss_pred HHHHHHHHHHhcCCChHHHHHHHHHHhCCCCChhHHHHHHHhhHhHh
Q psy13513 19 DQLDRYEMYRRAAFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFV 65 (71)
Q Consensus 19 eQ~~Rye~fRRs~f~K~~ikkli~~~~~~sv~~nv~i~v~g~aKvFV 65 (71)
-|+.||+.+==|--.-+++-|+...+...-|.+.++.|..|-..+|+
T Consensus 84 lqlGkYD~llvaPaTsNTvAKIa~GIADtLVTNAVaqa~Kg~VPvyi 130 (187)
T COG1036 84 LQLGKYDFLLVAPATSNTVAKIAYGIADTLVTNAVAQAGKGKVPVYI 130 (187)
T ss_pred eecccccEEEEcccccchHHHHHhhhHHHHHHHHHHHhcCCCCcEEE
Confidence 36677776666666667788888888888888888888887776664
No 94
>KOG0871|consensus
Probab=22.31 E-value=74 Score=22.44 Aligned_cols=19 Identities=21% Similarity=0.504 Sum_probs=16.3
Q ss_pred cCCChHHHHHHHHHHhCCC
Q psy13513 30 AAFPKAAIKRLIQTISGGS 48 (71)
Q Consensus 30 s~f~K~~ikkli~~~~~~s 48 (71)
.+|||++|-|+|..++.+.
T Consensus 11 ~sLPkAtv~KmIke~lP~d 29 (156)
T KOG0871|consen 11 LSLPKATVNKMIKEMLPKD 29 (156)
T ss_pred ccCcHHHHHHHHHHhCCcc
Confidence 4799999999999998753
No 95
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=22.13 E-value=1.2e+02 Score=16.23 Aligned_cols=22 Identities=36% Similarity=0.655 Sum_probs=17.0
Q ss_pred HHHHhcCCChHHHHHHHHHHhC
Q psy13513 25 EMYRRAAFPKAAIKRLIQTISG 46 (71)
Q Consensus 25 e~fRRs~f~K~~ikkli~~~~~ 46 (71)
|.-++.++||+.+-|+++....
T Consensus 23 eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 23 EIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHCcCHHHHHHHHHHHHH
Confidence 4567889999999999987653
No 96
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=22.10 E-value=2.7e+02 Score=19.26 Aligned_cols=42 Identities=14% Similarity=0.313 Sum_probs=30.4
Q ss_pred HHhhCCCHHHHHH-HHHHH------hcCCChHHHHHHHHHHhCCCCChhH
Q psy13513 11 VLVSNFTEDQLDR-YEMYR------RAAFPKAAIKRLIQTISGGSVSQNV 53 (71)
Q Consensus 11 ~L~~~~~~eQ~~R-ye~fR------Rs~f~K~~ikkli~~~~~~sv~~nv 53 (71)
..-.+||++|.++ |++|. ...++|.-+.+++. .+|+..|.+-
T Consensus 9 ~~~~~~t~~qi~~lkeaF~l~D~d~~G~I~~~el~~ilr-~lg~~~s~~e 57 (160)
T COG5126 9 LTFTQLTEEQIQELKEAFQLFDRDSDGLIDRNELGKILR-SLGFNPSEAE 57 (160)
T ss_pred hhcccCCHHHHHHHHHHHHHhCcCCCCCCcHHHHHHHHH-HcCCCCcHHH
Confidence 4557899999555 45654 46688999998888 7787777543
No 97
>PF14308 DnaJ-X: X-domain of DnaJ-containing
Probab=22.06 E-value=1.8e+02 Score=20.13 Aligned_cols=31 Identities=13% Similarity=0.273 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhC-CCCChhH----HHHHHHhhHhHh
Q psy13513 35 AAIKRLIQTISG-GSVSQNV----VIAMSGIAKVFV 65 (71)
Q Consensus 35 ~~ikkli~~~~~-~sv~~nv----~i~v~g~aKvFV 65 (71)
+++|.+++.++. .+||... |-|+.-++++|-
T Consensus 148 ~Tlr~Vc~~VL~D~~V~~~~r~~RA~aL~~LG~if~ 183 (204)
T PF14308_consen 148 STLREVCDKVLYDKGVDKETRLKRAEALKILGKIFQ 183 (204)
T ss_pred HHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 567788888884 7888766 556666666663
No 98
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=21.96 E-value=76 Score=22.06 Aligned_cols=19 Identities=21% Similarity=0.548 Sum_probs=16.6
Q ss_pred cCCChHHHHHHHHHHhCCC
Q psy13513 30 AAFPKAAIKRLIQTISGGS 48 (71)
Q Consensus 30 s~f~K~~ikkli~~~~~~s 48 (71)
-+|||++|.|.+.+++.+.
T Consensus 10 ~sLPKATVqKMvS~iLp~d 28 (148)
T COG5150 10 NSLPKATVQKMVSSILPKD 28 (148)
T ss_pred ccCcHHHHHHHHHHhcccc
Confidence 3699999999999999763
No 99
>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=21.91 E-value=1.4e+02 Score=20.88 Aligned_cols=43 Identities=16% Similarity=0.414 Sum_probs=29.5
Q ss_pred HHHhcCCChHHHHHHHHHHhCC-C--CCh-hHHHHHHHhhHhHhhhhc
Q psy13513 26 MYRRAAFPKAAIKRLIQTISGG-S--VSQ-NVVIAMSGIAKVFVGEIV 69 (71)
Q Consensus 26 ~fRRs~f~K~~ikkli~~~~~~-s--v~~-nv~i~v~g~aKvFVGEiV 69 (71)
.||-++ ++..|+++....-.. . .+. .=+-.+||+-|.|.-++=
T Consensus 30 IFR~~G-~~~~i~~l~~~~d~~~~~~~~~~~~~h~va~lLK~fLReLP 76 (206)
T cd04376 30 IFRVGS-SKKRVRQLREEFDRGIDVVLDENHSVHDVAALLKEFFRDMP 76 (206)
T ss_pred eeeCCC-CHHHHHHHHHHHhcCCCCCCcccCCHHHHHHHHHHHHHhCC
Confidence 477777 578889888776533 2 222 224567999999998874
No 100
>PF15478 LKAAEAR: Family of unknown function with LKAAEAR motif
Probab=21.90 E-value=65 Score=22.28 Aligned_cols=16 Identities=25% Similarity=0.538 Sum_probs=13.8
Q ss_pred hhCCCHHHHHHHHHHH
Q psy13513 13 VSNFTEDQLDRYEMYR 28 (71)
Q Consensus 13 ~~~~~~eQ~~Rye~fR 28 (71)
+..|++.|..||-.|=
T Consensus 13 L~kl~p~qR~ryl~ye 28 (137)
T PF15478_consen 13 LAKLSPQQRSRYLAYE 28 (137)
T ss_pred HHhcCHHHHHHHHHcc
Confidence 5678999999999984
No 101
>PF03661 UPF0121: Uncharacterised protein family (UPF0121); InterPro: IPR005344 Uncharacterised integral membrane protein family.; GO: 0016021 integral to membrane
Probab=21.76 E-value=1.1e+02 Score=22.00 Aligned_cols=35 Identities=20% Similarity=0.221 Sum_probs=22.9
Q ss_pred HHHHHHHhcCCChHHHHHHHH---HHh-CCCCChhHHHHH
Q psy13513 22 DRYEMYRRAAFPKAAIKRLIQ---TIS-GGSVSQNVVIAM 57 (71)
Q Consensus 22 ~Rye~fRRs~f~K~~ikkli~---~~~-~~sv~~nv~i~v 57 (71)
-||+. +|+.+.|...+++-. ..+ .+++|+-+.-+.
T Consensus 195 lRY~~-~~s~y~r~~f~~l~~~id~~v~hp~~P~~v~~~~ 233 (247)
T PF03661_consen 195 LRYAS-SRSPYTRSAFAQLRVRIDGLVSHPSCPPFVRQVY 233 (247)
T ss_pred HHHhC-CCCcHHHHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence 48876 577788887776654 344 457887665543
No 102
>PF14281 PDDEXK_4: PD-(D/E)XK nuclease superfamily
Probab=21.71 E-value=74 Score=20.83 Aligned_cols=19 Identities=32% Similarity=0.588 Sum_probs=14.0
Q ss_pred hCCCHHHHHHHHHHHhcCC
Q psy13513 14 SNFTEDQLDRYEMYRRAAF 32 (71)
Q Consensus 14 ~~~~~eQ~~Rye~fRRs~f 32 (71)
+...++|+.||..+=....
T Consensus 97 a~~~~~QL~rY~~~~~~~~ 115 (179)
T PF14281_consen 97 ASDQENQLERYYKYLKKRY 115 (179)
T ss_pred CCcCHHHHHHHHHHHHHhc
Confidence 4567889999998754444
No 103
>PF08621 RPAP1_N: RPAP1-like, N-terminal; InterPro: IPR013930 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans.
Probab=21.68 E-value=1.7e+02 Score=16.51 Aligned_cols=31 Identities=6% Similarity=0.096 Sum_probs=18.0
Q ss_pred HhhCCCHHHHHHHHHHHhcCCChHHHHHHHH
Q psy13513 12 LVSNFTEDQLDRYEMYRRAAFPKAAIKRLIQ 42 (71)
Q Consensus 12 L~~~~~~eQ~~Rye~fRRs~f~K~~ikkli~ 42 (71)
.+++||+++...=-.-=.++|+.+.|..|.+
T Consensus 11 rL~~MS~eEI~~er~eL~~~LdP~li~~L~~ 41 (49)
T PF08621_consen 11 RLASMSPEEIEEEREELLESLDPKLIEFLKK 41 (49)
T ss_pred HHHhCCHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence 4566666666555444555666666555554
No 104
>KOG0006|consensus
Probab=21.60 E-value=58 Score=26.04 Aligned_cols=14 Identities=36% Similarity=0.691 Sum_probs=11.6
Q ss_pred CCCHHHHHHHHHHH
Q psy13513 15 NFTEDQLDRYEMYR 28 (71)
Q Consensus 15 ~~~~eQ~~Rye~fR 28 (71)
-|.+||++||..|-
T Consensus 292 ilg~e~Y~rYQr~a 305 (446)
T KOG0006|consen 292 ILGEEQYNRYQRYA 305 (446)
T ss_pred ecchhHHHHHHHhh
Confidence 46899999998774
No 105
>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=21.28 E-value=1.4e+02 Score=20.82 Aligned_cols=43 Identities=12% Similarity=0.278 Sum_probs=28.5
Q ss_pred HHHhcCCChHHHHHHHHHHhCCC------C--C--hhHHHHHHHhhHhHhhhhc
Q psy13513 26 MYRRAAFPKAAIKRLIQTISGGS------V--S--QNVVIAMSGIAKVFVGEIV 69 (71)
Q Consensus 26 ~fRRs~f~K~~ikkli~~~~~~s------v--~--~nv~i~v~g~aKvFVGEiV 69 (71)
-||-|+= ++.|+++.+...++. + . ..=+-++||+-|.|.-|+=
T Consensus 49 IFR~sGs-~~~i~~l~~~~~d~~~~~~~~id~~~~~~d~h~va~lLK~fLReLP 101 (203)
T cd04374 49 LYRVVGV-NSKVQKLLSLGLDPKTSTPGDVDLDNSEWEIKTITSALKTYLRNLP 101 (203)
T ss_pred eeeCCCc-HHHHHHHHHHHhCcCCCCccccccccccccHHHHHHHHHHHHHcCC
Confidence 3777654 778899887765432 1 1 1114568999999998874
No 106
>PHA02586 68 prohead core protein; Provisional
Probab=21.26 E-value=2.9e+02 Score=19.15 Aligned_cols=55 Identities=24% Similarity=0.350 Sum_probs=40.4
Q ss_pred HHHHHHHHHHhhCCCHHHHHHHHHHHhcCCChHHHHHHHHHHhCCCCChhHHHHHHHh
Q psy13513 3 EEEREKMQVLVSNFTEDQLDRYEMYRRAAFPKAAIKRLIQTISGGSVSQNVVIAMSGI 60 (71)
Q Consensus 3 eee~~~~~~L~~~~~~eQ~~Rye~fRRs~f~K~~ikkli~~~~~~sv~~nv~i~v~g~ 60 (71)
+++-+-..-+++.+=++-.+|.+..--. |.+..|-.++.... .--+++++||.++
T Consensus 5 ~~~~~~~~~~vEa~~~ea~~R~d~l~~~-f~~dei~~vien~~--~dE~~~alAm~Si 59 (140)
T PHA02586 5 PEDYELVLELVEAVLPEAQGRVDILSEA-FAKDEINGVIENML--DDEPDLALAMLSI 59 (140)
T ss_pred hhhHHHHHHHHHHHhHHHHHHHHHHHHH-hhhhhHHHHHHccc--cccHHHHHHHHHH
Confidence 4455556677888888889999988777 88888888877655 3336788888664
No 107
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.26 E-value=1.6e+02 Score=21.95 Aligned_cols=31 Identities=16% Similarity=0.392 Sum_probs=23.9
Q ss_pred hhCCCHHHHHHHHHHHhcC--------CChHHHHHHHHH
Q psy13513 13 VSNFTEDQLDRYEMYRRAA--------FPKAAIKRLIQT 43 (71)
Q Consensus 13 ~~~~~~eQ~~Rye~fRRs~--------f~K~~ikkli~~ 43 (71)
-..|+++|.+|.--|-|+. -.++.+|+.+|.
T Consensus 141 ~~rltd~q~d~l~~W~~~~~drl~Vnsatr~ev~~alnr 179 (225)
T PF09883_consen 141 EARLTDEQVDRLYEWTRDGTDRLNVNSATRSEVRAALNR 179 (225)
T ss_pred ccccCHHHHHHHHHHhhCCCCeEEEecccHHHHHHHHHh
Confidence 3578999999999999983 446677776664
No 108
>PF14069 SpoVIF: Stage VI sporulation protein F
Probab=21.05 E-value=1.8e+02 Score=18.08 Aligned_cols=22 Identities=14% Similarity=0.330 Sum_probs=12.8
Q ss_pred CChHHHHHHHHHHhCCCCChhH
Q psy13513 32 FPKAAIKRLIQTISGGSVSQNV 53 (71)
Q Consensus 32 f~K~~ikkli~~~~~~sv~~nv 53 (71)
+++....+|++++.++.+|.|+
T Consensus 48 Vs~~~ed~IV~~I~~~~~p~d~ 69 (79)
T PF14069_consen 48 VSKEQEDQIVQAIINQKIPNDM 69 (79)
T ss_pred CCHHHHHHHHHHHHhCCCCcCH
Confidence 4555555666666666555554
No 109
>PF08774 VRR_NUC: VRR-NUC domain; InterPro: IPR014883 This entry contains proteins with the VRR-NUC domain. It is associated with members of the PD-(D/E)XK nuclease superfamily, which include the type III restriction modification enzymes, for example StyLTI: (P40815 from SWISSPROT).; GO: 0016788 hydrolase activity, acting on ester bonds
Probab=20.85 E-value=1e+02 Score=18.49 Aligned_cols=19 Identities=21% Similarity=0.410 Sum_probs=16.5
Q ss_pred hCCCHHHHHHHHHHHhcCC
Q psy13513 14 SNFTEDQLDRYEMYRRAAF 32 (71)
Q Consensus 14 ~~~~~eQ~~Rye~fRRs~f 32 (71)
+.++++|...++.+++.++
T Consensus 73 ~~ls~~Q~~~~~~l~~~G~ 91 (100)
T PF08774_consen 73 DRLSPNQKEWIDKLREAGF 91 (100)
T ss_pred CCcCHHHHHHHHHHHHCCC
Confidence 5789999999999998865
No 110
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=20.68 E-value=3.2e+02 Score=22.70 Aligned_cols=52 Identities=13% Similarity=0.139 Sum_probs=43.8
Q ss_pred HHHHHHHHHHhcCCCh-HHHHHHHHHHhCCCCChhHHHHHHHhhHhHhhhhcc
Q psy13513 19 DQLDRYEMYRRAAFPK-AAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEIVE 70 (71)
Q Consensus 19 eQ~~Rye~fRRs~f~K-~~ikkli~~~~~~sv~~nv~i~v~g~aKvFVGEiVE 70 (71)
-|..+|+.-|+.+... ..-+-+=+-++|++-.+-++-.++.+.|-||=.++.
T Consensus 466 ~~~~vy~~a~~~~~~~~~~F~~~Y~vliGk~~GPRlg~Fla~lg~dfv~~rir 518 (521)
T COG1384 466 LHNEVYEVAKKKGILPRAFFQALYRVLIGKERGPRLGSFLALLGVDFVIRRIR 518 (521)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCccHHHHHHHhChHHHHHHHH
Confidence 5788999999988766 666666677889999999999999999999877654
No 111
>COG3633 SstT Na+/serine symporter [Amino acid transport and metabolism]
Probab=20.55 E-value=1.4e+02 Score=23.73 Aligned_cols=41 Identities=20% Similarity=0.482 Sum_probs=27.6
Q ss_pred HHHHHhcCCChHHHHHHHH-HHhC---CCCChhHHHHHHHhhHhHhhhh
Q psy13513 24 YEMYRRAAFPKAAIKRLIQ-TISG---GSVSQNVVIAMSGIAKVFVGEI 68 (71)
Q Consensus 24 ye~fRRs~f~K~~ikkli~-~~~~---~sv~~nv~i~v~g~aKvFVGEi 68 (71)
|..|-|.++ ||++.- -++| ..++++.+.++.=++++|||-+
T Consensus 8 ~~~~~~gsL----v~qI~iGlvlGi~~a~~s~~~a~~vgllG~lFv~aL 52 (407)
T COG3633 8 FRLLARGSL----VKQILIGLVLGILLAIISPPAAEAVGLLGTLFVGAL 52 (407)
T ss_pred HHHHHhccH----HHHHHHHHHHHHHHHhcChhHHHHhhHHHHHHHHHH
Confidence 334445555 444432 2333 4788899999999999999965
No 112
>PF02687 FtsX: FtsX-like permease family; InterPro: IPR003838 This domain is found in predicted permeases and hypothetical transmembrane proteins. P57382 from SWISSPROT has been shown to transport lipids targeted to the outer membrane across the inner membrane. Both P57382 and O54500 from SWISSPROT have been shown to require ATP. This domain contains three transmembrane helices.; GO: 0016020 membrane
Probab=20.50 E-value=1.7e+02 Score=16.89 Aligned_cols=28 Identities=11% Similarity=0.208 Sum_probs=23.1
Q ss_pred CCCHHHHHHHHHHHhcCCChHHHHHHHH
Q psy13513 15 NFTEDQLDRYEMYRRAAFPKAAIKRLIQ 42 (71)
Q Consensus 15 ~~~~eQ~~Rye~fRRs~f~K~~ikkli~ 42 (71)
..-.++..+|..+|..+.+|..+++..-
T Consensus 21 ~~~~~~~~~~~il~~lG~s~~~i~~~~~ 48 (121)
T PF02687_consen 21 SSIRERRREIAILRALGASKRQIRKMFL 48 (121)
T ss_pred HHHHHHHHHHHHHHHcCCChhhhhHHHH
Confidence 3445788999999999999999888763
No 113
>PF04718 ATP-synt_G: Mitochondrial ATP synthase g subunit; InterPro: IPR006808 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 the G subunit found in the F0 complex of F-ATPases in mitochondria. The function of subunit G is currently unknown. There is no counterpart in chloroplast or bacterial F-ATPases identified so far []. 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)
Probab=20.45 E-value=1.2e+02 Score=19.24 Aligned_cols=18 Identities=33% Similarity=0.486 Sum_probs=15.0
Q ss_pred hHHHHHHHhhHhHhhhhc
Q psy13513 52 NVVIAMSGIAKVFVGEIV 69 (71)
Q Consensus 52 nv~i~v~g~aKvFVGEiV 69 (71)
+.++++-.++=.||||||
T Consensus 76 ~~l~~~Ev~~wF~vGEiI 93 (103)
T PF04718_consen 76 NGLVGAEVYGWFFVGEII 93 (103)
T ss_pred HHHHHHHHHHHHhhheee
Confidence 567777888889999997
No 114
>PF14165 YtzH: YtzH-like protein
Probab=20.31 E-value=1.5e+02 Score=19.01 Aligned_cols=48 Identities=15% Similarity=0.311 Sum_probs=34.5
Q ss_pred HHHHHHhhCCCHHHHHHHHHHHhcCCChHHHHHHHHHHh-CCCCChhHHHHHH
Q psy13513 7 EKMQVLVSNFTEDQLDRYEMYRRAAFPKAAIKRLIQTIS-GGSVSQNVVIAMS 58 (71)
Q Consensus 7 ~~~~~L~~~~~~eQ~~Rye~fRRs~f~K~~ikkli~~~~-~~sv~~nv~i~v~ 58 (71)
-++.+|-+-|++-|.|.|..--- =..|.||+++.. +..+++.+-.++-
T Consensus 5 hQl~LLkDIL~~hq~DccgTvsE----cEQieRLvksLm~n~~i~~~ik~~L~ 53 (87)
T PF14165_consen 5 HQLTLLKDILSNHQLDCCGTVSE----CEQIERLVKSLMANPNIDADIKQTLE 53 (87)
T ss_pred HHHHHHHHHHHhhhhhccCcHHH----HHHHHHHHHHHHcCCCcCHHHHHHHH
Confidence 46778888889999998865433 256889998877 4567777765543
No 115
>PF08627 CRT-like: CRT-like; InterPro: IPR013936 This region is found in proteins related to Plasmodium falciparum chloroquine resistance transporter (CRT).
Probab=20.29 E-value=1.5e+02 Score=20.34 Aligned_cols=37 Identities=19% Similarity=0.214 Sum_probs=25.5
Q ss_pred cCCChHHHHHHHHHHhCCCCC-hhHHHHHHHhhHhHhh
Q psy13513 30 AAFPKAAIKRLIQTISGGSVS-QNVVIAMSGIAKVFVG 66 (71)
Q Consensus 30 s~f~K~~ikkli~~~~~~sv~-~nv~i~v~g~aKvFVG 66 (71)
|..++..+.+.+...+.++.+ +|+-|.++.+.=++.|
T Consensus 32 ~~i~~~~~~~k~k~~~k~s~~ke~~~L~v~~vv~V~s~ 69 (130)
T PF08627_consen 32 SNIKQKSISEKIKDFLKQSYSKENFKLLVYVVVYVVSG 69 (130)
T ss_pred ccchHHHHHHHHHHHHHHhhhhcchHHHHHHHHHHHHH
Confidence 456677777777777777766 5777777666665554
No 116
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=20.07 E-value=87 Score=17.52 Aligned_cols=39 Identities=10% Similarity=0.233 Sum_probs=27.9
Q ss_pred HHHHHHHHHhhCCCHHHHHHHHHHHhcCCChHHHHHHHHHHh
Q psy13513 4 EEREKMQVLVSNFTEDQLDRYEMYRRAAFPKAAIKRLIQTIS 45 (71)
Q Consensus 4 ee~~~~~~L~~~~~~eQ~~Rye~fRRs~f~K~~ikkli~~~~ 45 (71)
.|.+-...|+ +...+.-.+.-+.++++++.+.+.++...
T Consensus 9 ~E~~vy~~Ll---~~~~~t~~eIa~~l~i~~~~v~~~L~~L~ 47 (68)
T PF01978_consen 9 NEAKVYLALL---KNGPATAEEIAEELGISRSTVYRALKSLE 47 (68)
T ss_dssp HHHHHHHHHH---HHCHEEHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3444444444 55566667778899999999999998765
No 117
>cd00315 Cyt_C5_DNA_methylase Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.
Probab=20.05 E-value=83 Score=22.67 Aligned_cols=45 Identities=18% Similarity=0.172 Sum_probs=31.1
Q ss_pred hhCCCHHHHHHHHHHHhcCCChHH-HHHHHHHHhCCCCChhHHHHHH
Q psy13513 13 VSNFTEDQLDRYEMYRRAAFPKAA-IKRLIQTISGGSVSQNVVIAMS 58 (71)
Q Consensus 13 ~~~~~~eQ~~Rye~fRRs~f~K~~-ikkli~~~~~~sv~~nv~i~v~ 58 (71)
...||..+..|...|-. .|.-.. -+.-....+|.+||.+++-+++
T Consensus 225 ~R~lT~rE~arlqgFPd-~f~f~g~~~~~~~~qiGNAVp~~~~~~I~ 270 (275)
T cd00315 225 IRRLTPRECARLQGFPD-DFEFPGKSVTQAYRQIGNSVPVPVAEAIA 270 (275)
T ss_pred CCCCCHHHHHHHcCCCC-CcEEcCCCHHHHHHhhcCCcCHHHHHHHH
Confidence 34677777777776654 444433 4555667889999999977654
Done!