Query 025620
Match_columns 250
No_of_seqs 147 out of 436
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 07:42:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025620.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025620hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3077 Uncharacterized conser 100.0 1.2E-71 2.6E-76 494.7 21.4 248 1-249 1-256 (260)
2 PF03556 Cullin_binding: Culli 100.0 2.9E-45 6.4E-50 293.8 10.8 116 127-242 1-117 (117)
3 PF14555 UBA_4: UBA-like domai 99.4 4.6E-13 1E-17 89.2 4.4 41 9-49 1-41 (43)
4 smart00804 TAP_C C-terminal do 97.6 9.4E-05 2E-09 53.3 4.3 45 3-47 7-51 (63)
5 PF03943 TAP_C: TAP C-terminal 97.5 8.9E-05 1.9E-09 51.2 2.6 39 10-48 2-40 (51)
6 KOG1364 Predicted ubiquitin re 97.0 0.00071 1.5E-08 63.3 3.8 44 5-48 3-47 (356)
7 PF00627 UBA: UBA/TS-N domain; 96.6 0.0041 8.8E-08 39.7 4.1 33 9-42 3-35 (37)
8 smart00165 UBA Ubiquitin assoc 95.4 0.029 6.2E-07 35.3 3.9 35 9-44 2-36 (37)
9 cd00194 UBA Ubiquitin Associat 95.2 0.036 7.9E-07 35.0 4.0 36 9-45 2-37 (38)
10 PTZ00184 calmodulin; Provision 93.9 2.5 5.4E-05 33.1 13.4 67 56-122 10-76 (149)
11 KOG3077 Uncharacterized conser 93.9 0.13 2.8E-06 46.8 5.7 83 147-231 80-162 (260)
12 cd00051 EFh EF-hand, calcium b 93.8 0.35 7.6E-06 31.4 6.6 61 59-119 2-62 (63)
13 KOG2086 Protein tyrosine phosp 93.2 0.028 6.1E-07 53.4 0.3 41 7-47 3-43 (380)
14 cd05031 S-100A10_like S-100A10 92.9 0.41 9E-06 36.2 6.3 68 57-124 8-82 (94)
15 PF13833 EF-hand_8: EF-hand do 92.6 0.44 9.6E-06 31.9 5.5 50 72-121 3-53 (54)
16 PTZ00183 centrin; Provisional 91.9 5.3 0.00012 31.8 13.2 66 56-121 16-81 (158)
17 cd00052 EH Eps15 homology doma 91.5 0.77 1.7E-05 31.5 5.9 62 60-123 2-63 (67)
18 PTZ00183 centrin; Provisional 91.2 1.3 2.8E-05 35.4 7.8 66 56-121 89-154 (158)
19 cd05029 S-100A6 S-100A6: S-100 90.9 1.5 3.2E-05 33.2 7.4 67 57-123 10-81 (88)
20 TIGR00264 alpha-NAC-related pr 90.1 0.45 9.8E-06 38.3 4.1 34 9-42 79-112 (116)
21 PF13499 EF-hand_7: EF-hand do 90.0 1.5 3.3E-05 30.2 6.4 62 58-119 1-66 (66)
22 PRK06369 nac nascent polypepti 89.9 0.48 1E-05 38.1 4.0 34 9-42 77-110 (115)
23 smart00027 EH Eps15 homology d 89.6 1.3 2.9E-05 33.4 6.2 65 56-122 9-73 (96)
24 PTZ00184 calmodulin; Provision 88.4 2.3 5E-05 33.3 7.1 69 56-124 46-115 (149)
25 TIGR01446 DnaD_dom DnaD and ph 88.2 1.3 2.7E-05 31.8 5.0 56 73-131 15-72 (73)
26 cd05030 calgranulins Calgranul 88.1 1.9 4.1E-05 32.3 6.1 67 57-123 8-81 (88)
27 KOG4351 Uncharacterized conser 87.7 0.18 3.9E-06 45.1 0.3 45 5-49 20-67 (244)
28 cd00213 S-100 S-100: S-100 dom 86.7 3.3 7.1E-05 30.5 6.7 66 57-122 8-80 (88)
29 cd05026 S-100Z S-100Z: S-100Z 86.5 4.3 9.3E-05 30.7 7.3 67 57-123 10-83 (93)
30 cd05022 S-100A13 S-100A13: S-1 85.1 5.6 0.00012 30.2 7.3 66 57-122 8-76 (89)
31 cd05023 S-100A11 S-100A11: S-1 83.7 6.8 0.00015 29.6 7.2 68 56-123 8-82 (89)
32 PF09279 EF-hand_like: Phospho 83.5 2.6 5.6E-05 30.9 4.7 64 58-122 1-70 (83)
33 KOG0027 Calmodulin and related 81.9 9.9 0.00021 30.9 8.1 70 56-125 7-76 (151)
34 KOG2756 Predicted Mg2+-depende 81.0 1.1 2.5E-05 41.3 2.3 40 9-48 26-65 (349)
35 COG1308 EGD2 Transcription fac 79.7 2.9 6.2E-05 34.0 4.0 34 10-43 86-119 (122)
36 cd05025 S-100A1 S-100A1: S-100 78.4 15 0.00032 27.4 7.4 68 56-123 8-82 (92)
37 smart00546 CUE Domain that may 77.7 2.9 6.3E-05 27.1 2.9 38 10-47 4-42 (43)
38 PF05517 p25-alpha: p25-alpha 76.7 9.4 0.0002 31.8 6.5 76 59-134 1-88 (154)
39 cd05027 S-100B S-100B: S-100B 76.7 16 0.00036 27.4 7.2 66 57-122 8-80 (88)
40 COG5126 FRQ1 Ca2+-binding prot 76.1 13 0.00029 31.5 7.3 69 53-121 88-156 (160)
41 KOG0027 Calmodulin and related 75.9 19 0.0004 29.3 8.0 83 54-136 41-129 (151)
42 PF02845 CUE: CUE domain; Int 75.9 5.5 0.00012 25.7 3.9 38 9-46 2-40 (42)
43 KOG0036 Predicted mitochondria 73.6 38 0.00082 33.2 10.3 88 56-143 13-117 (463)
44 KOG0028 Ca2+-binding protein ( 72.9 40 0.00086 28.9 9.2 103 56-158 32-136 (172)
45 KOG0036 Predicted mitochondria 72.6 11 0.00024 36.8 6.5 80 56-138 81-160 (463)
46 COG5126 FRQ1 Ca2+-binding prot 72.6 37 0.00081 28.8 9.1 84 55-139 15-103 (160)
47 CHL00098 tsf elongation factor 71.8 5.3 0.00012 35.0 3.9 39 10-48 3-41 (200)
48 PRK12332 tsf elongation factor 71.2 5.6 0.00012 34.8 3.9 40 9-48 5-44 (198)
49 TIGR00116 tsf translation elon 69.9 5.9 0.00013 36.7 3.9 39 9-47 5-43 (290)
50 PRK09377 tsf elongation factor 67.9 6.8 0.00015 36.3 3.9 41 8-48 5-45 (290)
51 PF08671 SinI: Anti-repressor 67.9 7.8 0.00017 23.9 2.9 28 188-215 3-30 (30)
52 PF00036 EF-hand_1: EF hand; 67.2 4.3 9.2E-05 24.4 1.7 18 105-122 12-29 (29)
53 PF13833 EF-hand_8: EF-hand do 63.6 12 0.00026 24.7 3.6 32 107-138 2-35 (54)
54 PF14658 EF-hand_9: EF-hand do 62.9 30 0.00065 25.1 5.7 50 72-121 13-64 (66)
55 PF13405 EF-hand_6: EF-hand do 62.8 15 0.00033 21.7 3.6 30 58-87 1-31 (31)
56 PF06972 DUF1296: Protein of u 62.6 20 0.00043 25.6 4.5 44 5-48 2-46 (60)
57 KOG2643 Ca2+ binding protein, 61.9 33 0.00071 33.8 7.4 94 71-176 300-399 (489)
58 cd03567 VHS_GGA VHS domain fam 61.9 74 0.0016 26.1 8.6 45 108-152 75-129 (139)
59 PRK10391 oriC-binding nucleoid 60.9 24 0.00051 26.0 4.8 40 111-152 2-41 (71)
60 PF12096 DUF3572: Protein of u 59.6 42 0.00092 25.7 6.3 59 7-94 19-77 (88)
61 smart00027 EH Eps15 homology d 59.0 30 0.00065 25.9 5.5 88 87-175 3-91 (96)
62 PF09107 SelB-wing_3: Elongati 58.8 12 0.00027 25.5 2.9 22 11-32 12-33 (50)
63 KOG0030 Myosin essential light 58.8 40 0.00087 28.3 6.4 68 55-122 9-78 (152)
64 PLN02964 phosphatidylserine de 55.5 58 0.0012 33.6 8.3 78 57-138 143-225 (644)
65 KOG0028 Ca2+-binding protein ( 53.9 62 0.0013 27.8 6.9 67 55-121 104-170 (172)
66 KOG1071 Mitochondrial translat 53.8 17 0.00036 34.3 3.8 36 7-42 45-80 (340)
67 PRK05441 murQ N-acetylmuramic 52.6 17 0.00038 33.5 3.8 36 12-47 239-274 (299)
68 TIGR00274 N-acetylmuramic acid 51.2 18 0.00039 33.3 3.7 36 12-47 234-269 (291)
69 PF03765 CRAL_TRIO_N: CRAL/TRI 50.7 16 0.00035 24.6 2.5 25 20-44 28-52 (55)
70 PF13443 HTH_26: Cro/C1-type H 49.7 9.7 0.00021 26.0 1.3 35 55-93 23-57 (63)
71 KOG4380 Carnitine deficiency a 48.4 49 0.0011 29.1 5.6 85 18-108 71-165 (244)
72 cd00171 Sec7 Sec7 domain; Doma 48.1 1.7E+02 0.0036 25.0 9.0 68 56-123 82-163 (185)
73 PF13499 EF-hand_7: EF-hand do 47.2 52 0.0011 22.3 4.8 41 101-141 8-49 (66)
74 PRK12570 N-acetylmuramic acid- 46.5 24 0.00052 32.6 3.7 36 12-47 235-270 (296)
75 TIGR00084 ruvA Holliday juncti 45.3 50 0.0011 28.5 5.3 40 3-42 62-102 (191)
76 KOG3911 Nucleolar protein NOP5 45.3 2.4E+02 0.0053 27.0 10.1 120 93-215 26-197 (378)
77 KOG4199 Uncharacterized conser 45.2 1.1E+02 0.0024 29.6 7.9 149 10-162 81-242 (461)
78 COG2922 Smg Uncharacterized pr 44.4 17 0.00037 30.4 2.1 35 59-93 5-40 (157)
79 PF07261 DnaB_2: Replication i 44.2 4.3 9.4E-05 29.0 -1.3 58 73-133 15-74 (77)
80 cd00052 EH Eps15 homology doma 44.2 62 0.0013 21.6 4.7 34 103-137 9-42 (67)
81 PLN02230 phosphoinositide phos 43.8 62 0.0013 33.1 6.4 68 53-121 25-102 (598)
82 PF05042 Caleosin: Caleosin re 43.3 85 0.0019 27.1 6.3 62 54-115 93-160 (174)
83 PHA01083 hypothetical protein 43.0 25 0.00053 29.6 2.9 52 73-128 43-97 (149)
84 PF04659 Arch_fla_DE: Archaeal 42.2 60 0.0013 25.4 4.8 52 187-238 21-86 (99)
85 PRK10945 gene expression modul 41.5 57 0.0012 24.1 4.2 39 111-152 7-45 (72)
86 PF10075 PCI_Csn8: COP9 signal 40.7 19 0.0004 29.2 1.8 37 12-48 100-136 (143)
87 cd00252 SPARC_EC SPARC_EC; ext 40.2 1.5E+02 0.0033 23.5 7.0 61 55-119 46-106 (116)
88 PRK02264 N(5),N(10)-methenylte 39.3 6.3 0.00014 36.9 -1.3 72 23-97 85-167 (317)
89 PF06535 RGM_N: Repulsive guid 39.1 8.7 0.00019 32.7 -0.4 19 215-233 111-129 (161)
90 COG2103 Predicted sugar phosph 38.9 39 0.00085 31.3 3.7 37 11-47 236-272 (298)
91 PLN02223 phosphoinositide phos 38.8 66 0.0014 32.5 5.6 68 53-121 12-92 (537)
92 COG0264 Tsf Translation elonga 37.9 43 0.00093 31.2 3.9 40 9-48 6-45 (296)
93 smart00222 Sec7 Sec7 domain. D 37.0 2.6E+02 0.0057 23.7 9.9 38 9-46 3-43 (187)
94 cd01109 HTH_YyaN Helix-Turn-He 36.8 1.8E+02 0.0039 22.4 6.9 66 12-98 3-68 (113)
95 PF07848 PaaX: PaaX-like prote 36.3 34 0.00074 24.9 2.4 38 57-94 4-41 (70)
96 PRK03980 flap endonuclease-1; 36.2 64 0.0014 29.8 4.8 75 10-93 177-269 (292)
97 PF09036 Bcr-Abl_Oligo: Bcr-Ab 36.0 99 0.0021 23.1 4.8 42 113-155 5-62 (79)
98 PF06992 Phage_lambda_P: Repli 35.1 1.3E+02 0.0027 27.2 6.3 30 111-140 66-95 (233)
99 smart00862 Trans_reg_C Transcr 35.0 80 0.0017 21.9 4.2 53 90-143 6-60 (78)
100 cd04752 Commd4 COMM_Domain con 34.5 1.4E+02 0.0031 25.2 6.4 54 73-126 21-76 (174)
101 PF07531 TAFH: NHR1 homology t 34.2 65 0.0014 25.1 3.8 64 78-147 12-83 (96)
102 PRK00116 ruvA Holliday junctio 33.2 1E+02 0.0022 26.5 5.4 62 5-68 65-130 (192)
103 TIGR03120 one_C_mch methenylte 33.1 7.3 0.00016 36.4 -1.9 73 23-97 83-166 (312)
104 PF03793 PASTA: PASTA domain; 33.0 30 0.00066 23.6 1.7 23 17-39 5-27 (63)
105 PF12763 EF-hand_4: Cytoskelet 32.6 1.1E+02 0.0023 23.9 4.9 63 56-122 9-72 (104)
106 cd00545 MCH Methenyltetrahydro 31.7 7.7 0.00017 36.3 -2.0 70 26-97 84-166 (312)
107 PF01023 S_100: S-100/ICaBP ty 31.2 75 0.0016 20.9 3.3 28 57-84 6-35 (44)
108 PF12244 DUF3606: Protein of u 30.4 1.1E+02 0.0023 21.3 4.1 42 3-45 14-55 (57)
109 PRK13749 transcriptional regul 28.4 2.3E+02 0.0049 22.8 6.2 69 11-100 5-73 (121)
110 COG3710 CadC DNA-binding winge 28.2 60 0.0013 26.9 2.9 69 86-157 28-102 (148)
111 PLN02964 phosphatidylserine de 28.1 2.5E+02 0.0055 29.0 7.9 63 59-121 181-243 (644)
112 PF00486 Trans_reg_C: Transcri 27.6 1E+02 0.0022 21.3 3.8 50 93-143 9-59 (77)
113 KOG1575 Voltage-gated shaker-l 27.5 1.8E+02 0.0039 27.7 6.3 56 74-143 258-314 (336)
114 PF14327 CSTF2_hinge: Hinge do 27.4 58 0.0013 24.4 2.5 32 9-41 32-63 (84)
115 PF01314 AFOR_C: Aldehyde ferr 27.3 33 0.00071 32.7 1.4 35 80-115 117-151 (382)
116 PLN02222 phosphoinositide phos 27.1 1.5E+02 0.0032 30.4 5.9 64 55-121 23-90 (581)
117 KOG4070 Putative signal transd 26.7 88 0.0019 26.7 3.6 71 52-122 7-86 (180)
118 PLN02228 Phosphoinositide phos 26.7 2.2E+02 0.0048 29.0 7.1 67 53-121 20-92 (567)
119 cd05022 S-100A13 S-100A13: S-1 26.6 2.5E+02 0.0054 21.1 5.9 68 93-160 7-79 (89)
120 PF14229 DUF4332: Domain of un 26.2 1.3E+02 0.0027 24.0 4.4 61 77-141 30-92 (122)
121 PHA00680 hypothetical protein 26.1 2.5E+02 0.0054 22.3 5.9 73 81-153 59-136 (143)
122 cd04769 HTH_MerR2 Helix-Turn-H 25.7 2.5E+02 0.0053 21.8 6.0 65 12-98 3-67 (116)
123 PF13720 Acetyltransf_11: Udp 25.4 2.5E+02 0.0054 20.8 5.6 36 165-203 47-82 (83)
124 TIGR03674 fen_arch flap struct 24.0 1.6E+02 0.0035 27.6 5.4 78 10-93 224-316 (338)
125 PF13624 SurA_N_3: SurA N-term 23.9 76 0.0017 25.4 2.8 60 74-134 84-144 (154)
126 smart00549 TAFH TAF homology. 23.3 1.6E+02 0.0035 22.8 4.2 63 79-146 12-81 (92)
127 PLN02952 phosphoinositide phos 23.2 2.4E+02 0.0053 28.9 6.7 68 53-121 34-110 (599)
128 KOG2873 Ubiquinol cytochrome c 23.0 1.9E+02 0.004 26.8 5.3 49 147-197 201-252 (284)
129 PF01726 LexA_DNA_bind: LexA D 23.0 74 0.0016 22.6 2.2 24 1-24 1-27 (65)
130 PF04444 Dioxygenase_N: Catech 22.8 97 0.0021 22.8 2.9 45 186-240 11-56 (74)
131 cd00383 trans_reg_C Effector d 22.7 1.5E+02 0.0033 21.3 4.0 56 87-143 21-77 (95)
132 COG0667 Tas Predicted oxidored 22.6 2.1E+02 0.0046 26.4 5.8 59 77-150 245-304 (316)
133 PF12174 RST: RCD1-SRO-TAF4 (R 22.3 63 0.0014 23.6 1.8 30 107-138 39-68 (70)
134 COG2147 RPL19A Ribosomal prote 21.8 2E+02 0.0042 24.3 4.7 29 126-154 98-127 (150)
135 PF08716 nsp7: nsp7 replicase; 21.7 2.4E+02 0.0051 21.5 4.7 43 117-159 15-62 (83)
136 cd03022 DsbA_HCCA_Iso DsbA fam 21.7 1E+02 0.0023 25.2 3.3 38 55-92 102-139 (192)
137 PF14788 EF-hand_10: EF hand; 21.4 2.8E+02 0.0062 19.1 4.8 48 74-121 2-49 (51)
138 TIGR02051 MerR Hg(II)-responsi 21.0 3.5E+02 0.0076 21.3 6.1 65 12-97 2-66 (124)
139 PF11772 EpuA: DNA-directed RN 20.5 74 0.0016 21.5 1.7 16 200-215 30-45 (47)
140 PF12238 MSA-2c: Merozoite sur 20.4 1.5E+02 0.0033 26.2 4.1 53 39-92 65-119 (205)
141 cd07311 terB_like_1 tellurium 20.4 3.2E+02 0.0069 22.7 5.9 91 3-96 39-130 (150)
142 PF07647 SAM_2: SAM domain (St 20.2 2.5E+02 0.0053 19.0 4.5 57 74-136 4-61 (66)
143 PF13551 HTH_29: Winged helix- 20.1 3.6E+02 0.0078 19.8 8.1 81 11-94 14-103 (112)
No 1
>KOG3077 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.2e-71 Score=494.69 Aligned_cols=248 Identities=53% Similarity=0.968 Sum_probs=235.9
Q ss_pred CCCCCcchHHHHHHHHhhhCCCHHHHHHHHHhCCCCchhh-hhhhhccCCC------CCcCCHHHHHHHHHHhcCCCC-C
Q 025620 1 MHKLSRSNRDKLQQFVSITGASEKAALQALKASDWHLEGA-FDVFYSQPQS------KSLTDTRHLEELYNRYKDPYL-D 72 (250)
Q Consensus 1 m~~l~~~q~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A-~~~f~~~~~~------~~~~~~~~l~~lF~~Y~~~~~-d 72 (250)
|++|+..++.++++|+.+|++++.+++.+|++++|++.+| .+.||.++.. ..+.+.+.+.++|.+|++|.. +
T Consensus 1 mnklk~~~~d~~~~~~~~~~~~~~~s~~~~~~~dw~~~~~~~~s~~~~~~~~~~~~~~~~~s~~~l~~~f~~y~d~~d~~ 80 (260)
T KOG3077|consen 1 MNKLKSSQKDKFEQFMSFTASRKKTSLSCLAACDWNLKYAFNDSYYTNPQSLREESVQARVSEKRLEELFNQYKDPDDDN 80 (260)
T ss_pred CCccchhHHHHHHhhcccccccchhhhhhhcccccccchhcccchhcchhHHHHhhhhccccHHHHHHHHHHhcCccccc
Confidence 8899999999999999999999999999999999999999 6777777643 235788999999999999966 5
Q ss_pred ccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHHcCCCCHHHHHHHHHHHHHHccchHHHHHHHH
Q 025620 73 MILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSLGIDSLDKFRERISFMRAELKDEQKFREIYN 152 (250)
Q Consensus 73 ~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~~~si~~lk~~l~~L~~~l~~~~~Fk~~Y~ 152 (250)
.|++||+.+||+||||+|+|+++|||||+|+|++||+|||++|+.||.++||+|+++|+.+|+.++..+++.+.|+.+|+
T Consensus 81 ~i~~dgi~~fc~dlg~~p~~i~~LvlAwkl~A~~m~~Fsr~ef~~g~~~l~~dS~d~lq~~l~~l~~~l~d~~~Fk~iY~ 160 (260)
T KOG3077|consen 81 LIGPDGIEKFCEDLGVEPEDISVLVLAWKLGAATMCEFSREEFLKGMTALGCDSIDKLQQRLDFLRSVLKDLEKFKSIYR 160 (260)
T ss_pred ccChHHHHHHHHHhCCCchhHHHHHHHHHhccchhhhhhHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHccHHHhhHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998888999999
Q ss_pred HHHHhhhhcCCccccHHHHHHHHHhhcCCCCchhHHHHHHHHHhhcCCCCCHhhHHHHHHHHhhhCCCCCCCCcCCCchh
Q 025620 153 FAFAWAKEKGQKSLALDTAIGMWQLLFAEKQWPLVDHWCQFLQAKHNKAISRDTWSQLLEFARTVDPALSNYDAEGAWPY 232 (250)
Q Consensus 153 f~F~~~~~~~qk~l~~d~Ai~~W~lll~~~~~~~l~~w~~Fl~~~~~k~IskD~W~~~l~F~~~~~~~ls~YDe~~AWP~ 232 (250)
|+|+|++++|||+|++++||.||.+||+.+ +|+|++|++||+..+.+.|+||||||+|+|.+++++++|||||+||||+
T Consensus 161 faf~fa~e~~qk~Ld~~~ai~~w~ll~~~~-~pll~~w~~FL~~~~~~~~~KDtW~~~l~Fs~~i~~dlSnYDeegAWP~ 239 (260)
T KOG3077|consen 161 FAFNFAKEPGQKSLDLETAISLWKLLFGQT-PPLLDQWIQFLKDSPNRAISKDTWNLLLDFSKTIDPDLSNYDEEGAWPV 239 (260)
T ss_pred hhhhhccCcCcCcCCHHHHHHHHHHHhCCC-CchHHHHHHHHHhCcCcccCcccHHHHHHHHHhcCccccCccccccchH
Confidence 999999999999999999999999999766 9999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHhhcCCcC
Q 025620 233 LIDEFVEYLTENGIVQN 249 (250)
Q Consensus 233 liDeFVe~~r~~~~~~~ 249 (250)
||||||||+|+++.+.+
T Consensus 240 liDeFVe~~r~~~~~~~ 256 (260)
T KOG3077|consen 240 LIDEFVEYLRDKQSNSK 256 (260)
T ss_pred HHHHHHHHHHHhccCCC
Confidence 99999999999987654
No 2
>PF03556 Cullin_binding: Cullin binding; InterPro: IPR005176 The eukaryotic defective in cullin neddylation (DCN) protein family, may contribute to neddylation of cullin components of SCF-type E3 ubiquitin ligase complexes. These multi-protein complexes are required for polyubiquitination and subsequent degradation of target proteins by the 26S proteasome []. Proteins in the DCN family include: Yeast DCN1. Vertebrate DCN1-like protein 1. Vertebrate DCN1-like protein 2. Vertebrate DCN1-like protein 4. This entry represents a domain found within DCN family proteins. Its function is unknown but it has been suggested that it has the features of a basic helix-loop-helix leucine zipper (bHLH-ZIP) domain [].It is often found in association with a UBA-like domain (IPR009060 from INTERPRO).; PDB: 3TDI_A 2IS9_A 3O6B_E 3O2P_A 3BQ3_A 3TDZ_A 3TDU_B.
Probab=100.00 E-value=2.9e-45 Score=293.82 Aligned_cols=116 Identities=53% Similarity=1.042 Sum_probs=105.2
Q ss_pred HHHHHHHHHHHHHHcc-chHHHHHHHHHHHHhhhhcCCccccHHHHHHHHHhhcCCCCchhHHHHHHHHHhhcCCCCCHh
Q 025620 127 LDKFRERISFMRAELK-DEQKFREIYNFAFAWAKEKGQKSLALDTAIGMWQLLFAEKQWPLVDHWCQFLQAKHNKAISRD 205 (250)
Q Consensus 127 i~~lk~~l~~L~~~l~-~~~~Fk~~Y~f~F~~~~~~~qk~l~~d~Ai~~W~lll~~~~~~~l~~w~~Fl~~~~~k~IskD 205 (250)
|++||++|++|+++|. ++..|++||+|||+|+|++|||+|++|+||+||++||+++.++++++|++||+++++|+||||
T Consensus 1 I~~lk~~l~~l~~~l~~d~~~F~~~Y~f~F~~~~~~~qr~l~~e~Ai~~W~llf~~~~~~~l~~w~~Fl~~~~~k~IskD 80 (117)
T PF03556_consen 1 IDKLKQKLPELRKELRSDPEYFKKFYRFTFDFAREEGQRSLPLETAIAYWRLLFSGRFFPLLDSWIEFLEEKYKKAISKD 80 (117)
T ss_dssp HHHHHHCHHHHHHHCCHSHHHHHHHHHHHHHHHS-TT-SSEEHHHHHHHHHHHTTTTSSCCHHHHHHHHHHCT-SEEEHH
T ss_pred CHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHhCCcccCCCCHHHHHHHHHHHcCCCCcHHHHHHHHHHHHcCCcCcChh
Confidence 6899999999999997 677799999999999999999999999999999999998878999999999999999999999
Q ss_pred hHHHHHHHHhhhCCCCCCCCcCCCchhhHHHHHHHHH
Q 025620 206 TWSQLLEFARTVDPALSNYDAEGAWPYLIDEFVEYLT 242 (250)
Q Consensus 206 ~W~~~l~F~~~~~~~ls~YDe~~AWP~liDeFVe~~r 242 (250)
||+|+++|++++++++++|||+||||+||||||||+|
T Consensus 81 ~W~~~l~F~~~~~~dls~Yde~~AWP~liDeFVe~~r 117 (117)
T PF03556_consen 81 TWNQFLDFFKTVDEDLSNYDEEGAWPSLIDEFVEWLR 117 (117)
T ss_dssp HHHHHHHHHHH-HCCHCC--TTSSS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCccccCCCCCCCCcHHHHHHHHHhC
Confidence 9999999999999999999999999999999999997
No 3
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=99.38 E-value=4.6e-13 Score=89.19 Aligned_cols=41 Identities=41% Similarity=0.793 Sum_probs=36.3
Q ss_pred HHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhccCC
Q 025620 9 RDKLQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQPQ 49 (250)
Q Consensus 9 ~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~~ 49 (250)
+++|++||+|||+++.+|++||+.++|||+.||+.||+++.
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~~~ 41 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDDGE 41 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHSS-
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence 47899999999999999999999999999999999999864
No 4
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=97.60 E-value=9.4e-05 Score=53.29 Aligned_cols=45 Identities=24% Similarity=0.427 Sum_probs=41.8
Q ss_pred CCCcchHHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhcc
Q 025620 3 KLSRSNRDKLQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQ 47 (250)
Q Consensus 3 ~l~~~q~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~ 47 (250)
.+++.|.++|.+|+..||.+.+=++.+|+.++||++.|+..|-+-
T Consensus 7 ~~~~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~~l 51 (63)
T smart00804 7 TLSPEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFTEL 51 (63)
T ss_pred CCCHHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 467788999999999999999999999999999999999999874
No 5
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=97.47 E-value=8.9e-05 Score=51.16 Aligned_cols=39 Identities=26% Similarity=0.422 Sum_probs=34.9
Q ss_pred HHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhccC
Q 025620 10 DKLQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQP 48 (250)
Q Consensus 10 ~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~ 48 (250)
++|.+|+..||.+.+=|..||+.++||++.|+..|-...
T Consensus 2 ~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~~l~ 40 (51)
T PF03943_consen 2 EMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNFEELK 40 (51)
T ss_dssp HHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHHHCC
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 689999999999999999999999999999999998664
No 6
>KOG1364 consensus Predicted ubiquitin regulatory protein, contains UAS and UBX domains [Posttranslational modification, protein turnover, chaperones]
Probab=96.97 E-value=0.00071 Score=63.34 Aligned_cols=44 Identities=32% Similarity=0.583 Sum_probs=40.7
Q ss_pred CcchHHHHHHHHhhhC-CCHHHHHHHHHhCCCCchhhhhhhhccC
Q 025620 5 SRSNRDKLQQFVSITG-ASEKAALQALKASDWHLEGAFDVFYSQP 48 (250)
Q Consensus 5 ~~~q~~~i~~F~~iT~-~s~~~A~~~L~~~~w~le~A~~~f~~~~ 48 (250)
+.++.++|.+|+.||+ .+.+.|++||+..+|+++.|++-||++.
T Consensus 3 ~~~~~~lv~~fl~It~~~t~e~A~q~L~~~~~~le~ai~Lffe~~ 47 (356)
T KOG1364|consen 3 TGAQRALVSKFLAITVQQTVEIATQYLSAADWDLEAAINLFFEHG 47 (356)
T ss_pred cchHHHHHHHHHHHhccccHHHHHHHHHhcCCcHHHHHHHHHHhc
Confidence 4568899999999999 7799999999999999999999999875
No 7
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=96.58 E-value=0.0041 Score=39.67 Aligned_cols=33 Identities=36% Similarity=0.528 Sum_probs=30.3
Q ss_pred HHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhh
Q 025620 9 RDKLQQFVSITGASEKAALQALKASDWHLEGAFD 42 (250)
Q Consensus 9 ~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~ 42 (250)
++.|++.+++ |.++..|+..|+.+++|++.|++
T Consensus 3 ~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~ 35 (37)
T PF00627_consen 3 EEKVQQLMEM-GFSREQAREALRACNGNVERAVD 35 (37)
T ss_dssp HHHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHH
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHH
Confidence 5789999999 99999999999999999999986
No 8
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=95.40 E-value=0.029 Score=35.34 Aligned_cols=35 Identities=31% Similarity=0.527 Sum_probs=30.9
Q ss_pred HHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhh
Q 025620 9 RDKLQQFVSITGASEKAALQALKASDWHLEGAFDVF 44 (250)
Q Consensus 9 ~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f 44 (250)
++.|++++++ |.++..|+..|++++||++.|++-.
T Consensus 2 ~~~v~~L~~m-Gf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 2 EEKIDQLLEM-GFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 4678888888 9999999999999999999998743
No 9
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=95.24 E-value=0.036 Score=35.03 Aligned_cols=36 Identities=31% Similarity=0.490 Sum_probs=31.4
Q ss_pred HHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhh
Q 025620 9 RDKLQQFVSITGASEKAALQALKASDWHLEGAFDVFY 45 (250)
Q Consensus 9 ~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~ 45 (250)
++.|++++++ |.++..|+..|+.++||++.|++-.+
T Consensus 2 ~~~v~~L~~m-Gf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 2 EEKLEQLLEM-GFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 3578888885 99999999999999999999987654
No 10
>PTZ00184 calmodulin; Provisional
Probab=93.89 E-value=2.5 Score=33.13 Aligned_cols=67 Identities=10% Similarity=0.108 Sum_probs=53.1
Q ss_pred HHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHHc
Q 025620 56 TRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSL 122 (250)
Q Consensus 56 ~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l 122 (250)
.+.+.+.|..+-.+....|+.+-+..++..+|.+|.+..+-.+.-.+....-|.++.++|+..+...
T Consensus 10 ~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~~~~~~~~~~~~~~~~~d~~~~g~i~~~ef~~~l~~~ 76 (149)
T PTZ00184 10 IAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTLMARK 76 (149)
T ss_pred HHHHHHHHHHHcCCCCCcCCHHHHHHHHHHhCCCCCHHHHHHHHHhcCcCCCCcCcHHHHHHHHHHh
Confidence 3567778877643344689999999999999998887777777777777778999999999988763
No 11
>KOG3077 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.88 E-value=0.13 Score=46.84 Aligned_cols=83 Identities=14% Similarity=0.036 Sum_probs=66.1
Q ss_pred HHHHHHHHHHhhhhcCCccccHHHHHHHHHhhcCCCCchhHHHHHHHHHhhcCCCCCHhhHHHHHHHHhhhCCCCCCCCc
Q 025620 147 FREIYNFAFAWAKEKGQKSLALDTAIGMWQLLFAEKQWPLVDHWCQFLQAKHNKAISRDTWSQLLEFARTVDPALSNYDA 226 (250)
Q Consensus 147 Fk~~Y~f~F~~~~~~~qk~l~~d~Ai~~W~lll~~~~~~~l~~w~~Fl~~~~~k~IskD~W~~~l~F~~~~~~~ls~YDe 226 (250)
+.-.|...+.||.+-|....++.++|--|.+- ..+ ...+..|.-+-.-+.-...|-|+|.+.++|.+++-.|++.|+.
T Consensus 80 ~~i~~dgi~~fc~dlg~~p~~i~~LvlAwkl~-A~~-m~~Fsr~ef~~g~~~l~~dS~d~lq~~l~~l~~~l~d~~~Fk~ 157 (260)
T KOG3077|consen 80 NLIGPDGIEKFCEDLGVEPEDISVLVLAWKLG-AAT-MCEFSREEFLKGMTALGCDSIDKLQQRLDFLRSVLKDLEKFKS 157 (260)
T ss_pred cccChHHHHHHHHHhCCCchhHHHHHHHHHhc-cch-hhhhhHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHccHHHhhH
Confidence 88889999999999999999999999999988 555 6667676555444455789999999999999877557666665
Q ss_pred CCCch
Q 025620 227 EGAWP 231 (250)
Q Consensus 227 ~~AWP 231 (250)
-.+||
T Consensus 158 iY~fa 162 (260)
T KOG3077|consen 158 IYRFA 162 (260)
T ss_pred HHHhh
Confidence 54443
No 12
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=93.83 E-value=0.35 Score=31.42 Aligned_cols=61 Identities=11% Similarity=0.073 Sum_probs=50.2
Q ss_pred HHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHH
Q 025620 59 LEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGL 119 (250)
Q Consensus 59 l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~ 119 (250)
+..+|..|....++.|..+-+...+..+|..+.+..+-.+...+....-|.++-++|+..+
T Consensus 2 ~~~~f~~~d~~~~g~l~~~e~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ef~~~~ 62 (63)
T cd00051 2 LREAFRLFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLELM 62 (63)
T ss_pred HHHHHHHhCCCCCCcCcHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCCCCeEeHHHHHHHh
Confidence 5678888876556789999999999999988887777777777887778899999998754
No 13
>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]
Probab=93.16 E-value=0.028 Score=53.44 Aligned_cols=41 Identities=29% Similarity=0.330 Sum_probs=37.9
Q ss_pred chHHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhcc
Q 025620 7 SNRDKLQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQ 47 (250)
Q Consensus 7 ~q~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~ 47 (250)
...+.+++|+.+||.++..|++||...+|+++.|...++..
T Consensus 3 ~p~~~ls~f~~~t~~se~~~~~~l~s~~~d~~~a~~~~~~~ 43 (380)
T KOG2086|consen 3 IPLDSLSEFRAVTGPSESRARFYLESIYWDREAAHRSELEA 43 (380)
T ss_pred CchhHHHHHhccCCCCccccccccccCCCchhhhhhhhccc
Confidence 34578999999999999999999999999999999999975
No 14
>cd05031 S-100A10_like S-100A10_like: S-100A10 domain found in proteins similar to S100A10. S100A10 is a member of the S100 family of EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1_like group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. A unique feature of S100A10 is that it contains mutation in both of the calcium binding sites, making it calcium insensitive. S100A10 has been detected in brain, heart, gastrointestinal tract, kidney, liver, lung, spleen, testes, epidermis, aorta, and thymus. Structural data supports the homo- and hetero-dimeric as well as hetero-tetrameric nature of the protein. S100A10 has multiple binding partners in its calcium free state and is therefore involved in many diverse biological functions.
Probab=92.86 E-value=0.41 Score=36.15 Aligned_cols=68 Identities=13% Similarity=0.167 Sum_probs=54.2
Q ss_pred HHHHHHHHHhcC-CC-CCccchHHHHHHHhh-----cCCCCCchHHHHHHHhhcccccccccHHHHHHHHHHcCC
Q 025620 57 RHLEELYNRYKD-PY-LDMILVDGITLLCND-----LQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSLGI 124 (250)
Q Consensus 57 ~~l~~lF~~Y~~-~~-~d~i~~dG~~~~~ed-----Lgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~~ 124 (250)
..|...|..|-+ ++ ...|+.+-+..++.. +|..+....+--+.-.+....-|.|+.++|+..|..+++
T Consensus 8 ~~l~~~F~~~D~~dg~dG~Is~~El~~~l~~~~g~~lg~~~s~~ei~~~~~~~D~~~dg~I~f~eF~~l~~~~~~ 82 (94)
T cd05031 8 ESLILTFHRYAGKDGDKNTLSRKELKKLMEKELSEFLKNQKDPMAVDKIMKDLDQNRDGKVNFEEFVSLVAGLSI 82 (94)
T ss_pred HHHHHHHHHHhccCCCCCeECHHHHHHHHHHHhHHHhhccccHHHHHHHHHHhCCCCCCcCcHHHHHHHHHHHHH
Confidence 567888999976 43 468999999988876 677776666666666778888899999999999988764
No 15
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=92.57 E-value=0.44 Score=31.90 Aligned_cols=50 Identities=14% Similarity=0.041 Sum_probs=45.3
Q ss_pred CccchHHHHHHHhhcCCC-CCchHHHHHHHhhcccccccccHHHHHHHHHH
Q 025620 72 DMILVDGITLLCNDLQVD-PQDIVMLVVSWHMKAATMCEFSKQEFIGGLQS 121 (250)
Q Consensus 72 d~i~~dG~~~~~edLgv~-~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~ 121 (250)
+.|+.+-+...+..+|+. +.+-.+=.|...+-...=|.|+.+||+..|+.
T Consensus 3 G~i~~~~~~~~l~~~g~~~~s~~e~~~l~~~~D~~~~G~I~~~EF~~~~~~ 53 (54)
T PF13833_consen 3 GKITREEFRRALSKLGIKDLSEEEVDRLFREFDTDGDGYISFDEFISMMQR 53 (54)
T ss_dssp SEEEHHHHHHHHHHTTSSSSCHHHHHHHHHHHTTSSSSSEEHHHHHHHHHH
T ss_pred CEECHHHHHHHHHHhCCCCCCHHHHHHHHHhcccCCCCCCCHHHHHHHHHh
Confidence 478999999999889999 88888889999999999999999999999875
No 16
>PTZ00183 centrin; Provisional
Probab=91.95 E-value=5.3 Score=31.76 Aligned_cols=66 Identities=9% Similarity=0.152 Sum_probs=50.9
Q ss_pred HHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHH
Q 025620 56 TRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQS 121 (250)
Q Consensus 56 ~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~ 121 (250)
.+.+.++|..+-.+....|+.+-+..++..+|..+....+-.+.-.+....-|.|+.++|+..+..
T Consensus 16 ~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~~~~~~~~~~l~~~~d~~~~g~i~~~eF~~~~~~ 81 (158)
T PTZ00183 16 KKEIREAFDLFDTDGSGTIDPKELKVAMRSLGFEPKKEEIKQMIADVDKDGSGKIDFEEFLDIMTK 81 (158)
T ss_pred HHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCCCCcEeHHHHHHHHHH
Confidence 367788887765444468999999999999998776665555555667777899999999988765
No 17
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=91.49 E-value=0.77 Score=31.45 Aligned_cols=62 Identities=8% Similarity=0.058 Sum_probs=45.6
Q ss_pred HHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHHcC
Q 025620 60 EELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSLG 123 (250)
Q Consensus 60 ~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~ 123 (250)
.++|..+-.+....|+.+.+.+++..+|++.+.+. -+...+....-|.|+.++|+..|....
T Consensus 2 ~~~F~~~D~~~~G~i~~~el~~~l~~~g~~~~~~~--~i~~~~d~~~~g~i~~~ef~~~~~~~~ 63 (67)
T cd00052 2 DQIFRSLDPDGDGLISGDEARPFLGKSGLPRSVLA--QIWDLADTDKDGKLDKEEFAIAMHLIA 63 (67)
T ss_pred hHHHHHhCCCCCCcCcHHHHHHHHHHcCCCHHHHH--HHHHHhcCCCCCcCCHHHHHHHHHHHH
Confidence 45788875444568999999999999998444433 333456667789999999999987643
No 18
>PTZ00183 centrin; Provisional
Probab=91.24 E-value=1.3 Score=35.43 Aligned_cols=66 Identities=12% Similarity=0.123 Sum_probs=41.3
Q ss_pred HHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHH
Q 025620 56 TRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQS 121 (250)
Q Consensus 56 ~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~ 121 (250)
...+..+|..|-.++.+.|+.+.+..+|..+|..+.+-.+-.+...+.-..-|.|+.++|++.+..
T Consensus 89 ~~~l~~~F~~~D~~~~G~i~~~e~~~~l~~~~~~l~~~~~~~~~~~~d~~~~g~i~~~ef~~~~~~ 154 (158)
T PTZ00183 89 REEILKAFRLFDDDKTGKISLKNLKRVAKELGETITDEELQEMIDEADRNGDGEISEEEFYRIMKK 154 (158)
T ss_pred HHHHHHHHHHhCCCCCCcCcHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCCCCcCcHHHHHHHHhc
Confidence 356667776664334456777777777777776655555544555555555577777777776654
No 19
>cd05029 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interact
Probab=90.93 E-value=1.5 Score=33.17 Aligned_cols=67 Identities=15% Similarity=0.159 Sum_probs=52.7
Q ss_pred HHHHHHHHHhcCC-C-CCccchHHHHHHHhh---cCCCCCchHHHHHHHhhcccccccccHHHHHHHHHHcC
Q 025620 57 RHLEELYNRYKDP-Y-LDMILVDGITLLCND---LQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSLG 123 (250)
Q Consensus 57 ~~l~~lF~~Y~~~-~-~d~i~~dG~~~~~ed---Lgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~ 123 (250)
..|.++|.+|... + .+.|..+.+.+++.. +|..+.+-.+--+-..+....-|.|+-++|+.-+..+-
T Consensus 10 ~~~i~~F~~y~~~~~~~g~Is~~EL~~~l~~~~~lg~k~t~~ev~~m~~~~D~d~dG~Idf~EFv~lm~~l~ 81 (88)
T cd05029 10 GLLVAIFHKYSGREGDKNTLSKKELKELIQKELTIGSKLQDAEIAKLMEDLDRNKDQEVNFQEYVTFLGALA 81 (88)
T ss_pred HHHHHHHHHHHccCCCCCEECHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHH
Confidence 5678899999963 3 459999999999974 68777655565566677888889999999998887753
No 20
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=90.12 E-value=0.45 Score=38.29 Aligned_cols=34 Identities=21% Similarity=0.222 Sum_probs=30.7
Q ss_pred HHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhh
Q 025620 9 RDKLQQFVSITGASEKAALQALKASDWHLEGAFD 42 (250)
Q Consensus 9 ~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~ 42 (250)
.+.|.-.++=||+|++.|+..|+++|+|+-.|+-
T Consensus 79 ~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~ 112 (116)
T TIGR00264 79 EDDIELVMKQCNVSKEEARRALEECGGDLAEAIM 112 (116)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHH
Confidence 4557888999999999999999999999999985
No 21
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=90.03 E-value=1.5 Score=30.24 Aligned_cols=62 Identities=15% Similarity=0.128 Sum_probs=44.7
Q ss_pred HHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCc-hHHHH---HHHhhcccccccccHHHHHHHH
Q 025620 58 HLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQD-IVMLV---VSWHMKAATMCEFSKQEFIGGL 119 (250)
Q Consensus 58 ~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed-~~~Lv---La~~l~a~~~g~~tr~ef~~g~ 119 (250)
+|.++|+.|=.++.+.|+.+-+.+++..+|....+ ..--. +...+-...-|.|+.+||++.|
T Consensus 1 ~l~~~F~~~D~d~~G~i~~~el~~~~~~~~~~~~~~~~~~~~~~~~~~~D~d~dG~i~~~Ef~~~~ 66 (66)
T PF13499_consen 1 RLKEAFKKFDKDGDGYISKEELRRALKHLGRDMSDEESDEMIDQIFREFDTDGDGRISFDEFLNFM 66 (66)
T ss_dssp HHHHHHHHHSTTSSSEEEHHHHHHHHHHTTSHSTHHHHHHHHHHHHHHHTTTSSSSEEHHHHHHHH
T ss_pred CHHHHHHHHcCCccCCCCHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCCCCcCCCcHHHHhccC
Confidence 47789999877667799999999999999986522 21112 2334455667899999998754
No 22
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=89.88 E-value=0.48 Score=38.12 Aligned_cols=34 Identities=26% Similarity=0.323 Sum_probs=31.3
Q ss_pred HHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhh
Q 025620 9 RDKLQQFVSITGASEKAALQALKASDWHLEGAFD 42 (250)
Q Consensus 9 ~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~ 42 (250)
.+.|.-.++=||+|++.|+..|+.+++|+-.|+-
T Consensus 77 ~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~ 110 (115)
T PRK06369 77 EEDIELVAEQTGVSEEEARKALEEANGDLAEAIL 110 (115)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHH
Confidence 4568889999999999999999999999999985
No 23
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=89.58 E-value=1.3 Score=33.44 Aligned_cols=65 Identities=8% Similarity=0.030 Sum_probs=49.6
Q ss_pred HHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHHc
Q 025620 56 TRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSL 122 (250)
Q Consensus 56 ~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l 122 (250)
...+.+.|..+-.+....|+.+-+.+.+..+|++.+.+.-+. -.+....-|.|+.++|+..|..+
T Consensus 9 ~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~--~~~d~~~~g~I~~~eF~~~~~~~ 73 (96)
T smart00027 9 KAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIW--NLADIDNDGELDKDEFALAMHLI 73 (96)
T ss_pred HHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHH--HHhcCCCCCCcCHHHHHHHHHHH
Confidence 367788888876555568999999999999998766554332 23456677899999999988874
No 24
>PTZ00184 calmodulin; Provisional
Probab=88.40 E-value=2.3 Score=33.29 Aligned_cols=69 Identities=12% Similarity=-0.027 Sum_probs=29.8
Q ss_pred HHHHHHHHHHhcCCCCCccchHHHHHHHhhc-CCCCCchHHHHHHHhhcccccccccHHHHHHHHHHcCC
Q 025620 56 TRHLEELYNRYKDPYLDMILVDGITLLCNDL-QVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSLGI 124 (250)
Q Consensus 56 ~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edL-gv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~~ 124 (250)
...+.++|..+-.+..+.|+.+=...++... ...+....+-.+...+....-|.+++++|..+++.+|.
T Consensus 46 ~~~~~~~~~~~d~~~~g~i~~~ef~~~l~~~~~~~~~~~~~~~~F~~~D~~~~g~i~~~e~~~~l~~~~~ 115 (149)
T PTZ00184 46 EAELQDMINEVDADGNGTIDFPEFLTLMARKMKDTDSEEEIKEAFKVFDRDGNGFISAAELRHVMTNLGE 115 (149)
T ss_pred HHHHHHHHHhcCcCCCCcCcHHHHHHHHHHhccCCcHHHHHHHHHHhhCCCCCCeEeHHHHHHHHHHHCC
Confidence 3455555555544333455555444443322 11111111111222223334466666666666666554
No 25
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=88.18 E-value=1.3 Score=31.84 Aligned_cols=56 Identities=7% Similarity=0.213 Sum_probs=41.4
Q ss_pred ccchHHHHHHHhhcCCCCCchHHHHHHHhh--cccccccccHHHHHHHHHHcCCCCHHHHH
Q 025620 73 MILVDGITLLCNDLQVDPQDIVMLVVSWHM--KAATMCEFSKQEFIGGLQSLGIDSLDKFR 131 (250)
Q Consensus 73 ~i~~dG~~~~~edLgv~~ed~~~LvLa~~l--~a~~~g~~tr~ef~~g~~~l~~~si~~lk 131 (250)
....+-+..++++.|.+|+ ++...+-+.+ +.++++.+ +..+..|++-|+.|+++.+
T Consensus 15 ~~e~~~i~~~~~~~~~~~e-vI~~ai~~a~~~~~~~~~Yi--~~Il~~W~~~gi~T~e~~~ 72 (73)
T TIGR01446 15 PFEMEDLKYWLDEFGNSPE-LIKEALKEAVSNNKANYKYI--DAILNNWKNNGIKTVEDVE 72 (73)
T ss_pred HHHHHHHHHHHHHhCCCHH-HHHHHHHHHHHcCCCCHHHH--HHHHHHHHHcCCCCHHHHh
Confidence 4667788899999998755 6666666555 45556554 4677889999999999875
No 26
>cd05030 calgranulins Calgranulins: S-100 domain found in proteins belonging to the Calgranulin subgroup of the S100 family of EF-hand calcium-modulated proteins, including S100A8, S100A9, and S100A12 . Note that the S-100 hierarchy, to which this Calgranulin group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. These proteins are expressed mainly in granulocytes, and are involved in inflammation, allergy, and neuritogenesis, as well as in host-parasite response. Calgranulins are modulated not only by calcium, but also by other metals such as zinc and copper. Structural data suggested that calgranulins may exist in multiple structural forms, homodimers, as well as hetero-oligomers. For example, the S100A8/S100A9 complex called calprotectin plays important roles in the regulation of inflammatory processes, wound repair, and regulating zinc-dependent enzymes as well as microbial growth.
Probab=88.10 E-value=1.9 Score=32.35 Aligned_cols=67 Identities=12% Similarity=0.140 Sum_probs=48.4
Q ss_pred HHHHHHHHHhcCCC--CCccchHHHHHHHh-hcCCCCC----chHHHHHHHhhcccccccccHHHHHHHHHHcC
Q 025620 57 RHLEELYNRYKDPY--LDMILVDGITLLCN-DLQVDPQ----DIVMLVVSWHMKAATMCEFSKQEFIGGLQSLG 123 (250)
Q Consensus 57 ~~l~~lF~~Y~~~~--~d~i~~dG~~~~~e-dLgv~~e----d~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~ 123 (250)
..|...|.+|+..+ .+.|+.+-+..++. .+|-.+. +..+=-+...+....-|.|+-++|+..+..+.
T Consensus 8 ~~~~~~f~~y~~~~~~~~~Is~~El~~ll~~~~g~~~t~~~~~~~v~~i~~~~D~d~dG~I~f~eF~~~~~~~~ 81 (88)
T cd05030 8 ETIINVFHQYSVRKGHPDTLYKKEFKQLVEKELPNFLKKEKNQKAIDKIFEDLDTNQDGQLSFEEFLVLVIKVG 81 (88)
T ss_pred HHHHHHHHHHhccCCCcccCCHHHHHHHHHHHhhHhhccCCCHHHHHHHHHHcCCCCCCcCcHHHHHHHHHHHH
Confidence 46778999999763 46999999999997 4443232 33333444455667789999999999988763
No 27
>KOG4351 consensus Uncharacterized conserved protein [Function unknown]
Probab=87.72 E-value=0.18 Score=45.09 Aligned_cols=45 Identities=20% Similarity=0.407 Sum_probs=39.6
Q ss_pred CcchHHHHHHHHhhhCCC--H-HHHHHHHHhCCCCchhhhhhhhccCC
Q 025620 5 SRSNRDKLQQFVSITGAS--E-KAALQALKASDWHLEGAFDVFYSQPQ 49 (250)
Q Consensus 5 ~~~q~~~i~~F~~iT~~s--~-~~A~~~L~~~~w~le~A~~~f~~~~~ 49 (250)
+.++..+|.+|..++|.. + ..|++||+-.+|+|..|+..||+...
T Consensus 20 t~dr~~Li~qf~~lm~~qm~P~~~aaF~Ld~knW~lqna~sv~~d~~t 67 (244)
T KOG4351|consen 20 TTDRPELIHQFQRLMNTQMNPMLSAAFVLDMKNWNLQNAGSVYWDQDT 67 (244)
T ss_pred CCCcHHHHHHHHHHhhhccCcccccceeeeccceeccccccEEEcCCC
Confidence 457889999999999875 5 67999999999999999999998753
No 28
>cd00213 S-100 S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents th
Probab=86.73 E-value=3.3 Score=30.49 Aligned_cols=66 Identities=12% Similarity=0.100 Sum_probs=48.5
Q ss_pred HHHHHHHHHhcC--CCCCccchHHHHHHHhh-cCCCC----CchHHHHHHHhhcccccccccHHHHHHHHHHc
Q 025620 57 RHLEELYNRYKD--PYLDMILVDGITLLCND-LQVDP----QDIVMLVVSWHMKAATMCEFSKQEFIGGLQSL 122 (250)
Q Consensus 57 ~~l~~lF~~Y~~--~~~d~i~~dG~~~~~ed-Lgv~~----ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l 122 (250)
+.+.++|..|-. ++.+.|+.+.+.+++.. +|..+ ....+=-+.-.+....-|.|+-++|+..+..+
T Consensus 8 ~~l~~~F~~~D~~~~~~G~Is~~el~~~l~~~~g~~~~~~~~~~ei~~i~~~~d~~~~g~I~f~eF~~~~~~~ 80 (88)
T cd00213 8 ETIIDVFHKYSGKEGDKDTLSKKELKELLETELPNFLKNQKDPEAVDKIMKDLDVNKDGKVDFQEFLVLIGKL 80 (88)
T ss_pred HHHHHHHHHHhhccCCCCcCcHHHHHHHHHHHhhhhccCCCCHHHHHHHHHHhccCCCCcCcHHHHHHHHHHH
Confidence 567778999976 45578999999999976 56433 23334334445577778999999999988875
No 29
>cd05026 S-100Z S-100Z: S-100Z domain found in proteins similar to S100Z. S100Z is a member of the S100 domain family within the EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100Z group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately.S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control. S100Z is normally expressed in various tissues, with its highest level of expression being in spleen and leukocytes. The function of S100Z remains unclear. Preliminary structural data suggests that S100Z is homodimer, however a heterodimer with S100P has been reported. S100Z is capable of binding calcium ions. When calcium binds to S110Z, the protein experiences a conformational change, which exposes hydrophobic surfac
Probab=86.55 E-value=4.3 Score=30.74 Aligned_cols=67 Identities=13% Similarity=0.153 Sum_probs=49.0
Q ss_pred HHHHHHHHHhcCCCCC--ccchHHHHHHHhh-c----CCCCCchHHHHHHHhhcccccccccHHHHHHHHHHcC
Q 025620 57 RHLEELYNRYKDPYLD--MILVDGITLLCND-L----QVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSLG 123 (250)
Q Consensus 57 ~~l~~lF~~Y~~~~~d--~i~~dG~~~~~ed-L----gv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~ 123 (250)
..|...|.+|.+.+.+ .|+.+-+.+++.. + +-.+.+-.+=-+...+....=|.|+-+||+.-+..+-
T Consensus 10 ~~~~~~F~~~dd~dgdg~~Is~~EL~~ll~~~~~~~~~~~~~~~~v~~i~~elD~n~dG~Idf~EF~~l~~~l~ 83 (93)
T cd05026 10 DTLIRIFHNYSGKEGDRYKLSKGELKELLQRELTDFLSSQKDPMLVDKIMNDLDSNKDNEVDFNEFVVLVAALT 83 (93)
T ss_pred HHHHHHHHHHHccCCCCCEECHHHHHHHHHHHhHHhcccccCHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHH
Confidence 4556669999976554 5999999999976 3 3333334455566666777789999999999888764
No 30
>cd05022 S-100A13 S-100A13: S-100A13 domain found in proteins similar to S100A13. S100A13 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A13 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100A13 is involved in the cellular export of interleukin-1 (IL-1) and of fibroblast growth factor-1 (FGF-1), which plays an important role in angiogenesis and tissue regeneration. Export is based on the CuII-dependent formation of multiprotein complexes containing the S100A13 protein. Assembly of these complexes occurs near the inner surface of the plasma membrane. Binding of two Ca(II) ions per monomer triggers key conformational changes leading to the creation of two identical and symmetrical Cu(II)-binding sites on the surface of the protein, close to the interface between the two monomers. These Cu
Probab=85.07 E-value=5.6 Score=30.23 Aligned_cols=66 Identities=12% Similarity=0.015 Sum_probs=50.3
Q ss_pred HHHHHHHHHhcC-CCCCccchHHHHHHHhh-cCCCCCc-hHHHHHHHhhcccccccccHHHHHHHHHHc
Q 025620 57 RHLEELYNRYKD-PYLDMILVDGITLLCND-LQVDPQD-IVMLVVSWHMKAATMCEFSKQEFIGGLQSL 122 (250)
Q Consensus 57 ~~l~~lF~~Y~~-~~~d~i~~dG~~~~~ed-Lgv~~ed-~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l 122 (250)
..|.+.|..|.. ++.+.|+.+.+..++.. ||--..+ ..+=-+.-.+....=|.|+-+||+.-+..+
T Consensus 8 ~~l~~~F~~fd~~~~~g~i~~~ELk~ll~~elg~~ls~~~~v~~mi~~~D~d~DG~I~F~EF~~l~~~l 76 (89)
T cd05022 8 ETLVSNFHKASVKGGKESLTASEFQELLTQQLPHLLKDVEGLEEKMKNLDVNQDSKLSFEEFWELIGEL 76 (89)
T ss_pred HHHHHHHHHHhCCCCCCeECHHHHHHHHHHHhhhhccCHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHH
Confidence 568889999987 66679999999999988 9844444 333334455667777999999999888775
No 31
>cd05023 S-100A11 S-100A11: S-100A11 domain found in proteins similar to S100A11. S100A11 is a member of the S-100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A11 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100 proteins have also been associated with a variety of pathological events, including neoplastic transformation and neurodegenerative diseases such as Alzheimer's, usually via over expression of the protein. S100A11 is expressed in smooth muscle and other tissues and involves in calcium-dependent membrane aggregation, which is important for cell vesiculation . As is the case for many other S100 proteins, S
Probab=83.71 E-value=6.8 Score=29.61 Aligned_cols=68 Identities=12% Similarity=0.080 Sum_probs=48.5
Q ss_pred HHHHHHHHHHhcCCCC--CccchHHHHHHHhhc-----CCCCCchHHHHHHHhhcccccccccHHHHHHHHHHcC
Q 025620 56 TRHLEELYNRYKDPYL--DMILVDGITLLCNDL-----QVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSLG 123 (250)
Q Consensus 56 ~~~l~~lF~~Y~~~~~--d~i~~dG~~~~~edL-----gv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~ 123 (250)
-..|.++|.+|.+.+. ..|+.+.+..+++.- +-..++..+--+.-.+....=|.|+-+||+.-+..+-
T Consensus 8 i~~l~~~F~~y~~~dg~~~~Ls~~Elk~ll~~e~~~~~~~~~~~~~~~~ll~~~D~d~DG~I~f~EF~~l~~~l~ 82 (89)
T cd05023 8 IESLIAVFQKYAGKDGDSYQLSKTEFLSFMNTELASFTKNQKDPGVLDRMMKKLDLNSDGQLDFQEFLNLIGGLA 82 (89)
T ss_pred HHHHHHHHHHHhccCCCcCeECHHHHHHHHHHhhhHhhcCCCCHHHHHHHHHHcCCCCCCcCcHHHHHHHHHHHH
Confidence 3678889999987644 379999999999875 2222323333444456677779999999998877753
No 32
>PF09279 EF-hand_like: Phosphoinositide-specific phospholipase C, efhand-like; InterPro: IPR015359 This domain is predominantly found in the enzyme phosphoinositol-specific phospholipase C. It adopts a structure consisting of a core of four alpha helices, in an EF like fold, and is required for functioning of the enzyme []. ; PDB: 3OHM_B 3QR0_A 2ZKM_X 2FJU_B 3QR1_D 1DJW_B 1DJI_B 1DJG_B 1QAS_B 2ISD_B ....
Probab=83.52 E-value=2.6 Score=30.87 Aligned_cols=64 Identities=11% Similarity=0.197 Sum_probs=44.7
Q ss_pred HHHHHHHHhcCCCCCccchHHHHHHHhhc----CCCCCchHHHHHHHhhc--ccccccccHHHHHHHHHHc
Q 025620 58 HLEELYNRYKDPYLDMILVDGITLLCNDL----QVDPQDIVMLVVSWHMK--AATMCEFSKQEFIGGLQSL 122 (250)
Q Consensus 58 ~l~~lF~~Y~~~~~d~i~~dG~~~~~edL----gv~~ed~~~LvLa~~l~--a~~~g~~tr~ef~~g~~~l 122 (250)
.|..+|.+|.. +...|+.+.+.+|+.+- .++++.+.-++--+.-. ...-+.+|.++|+.-|..-
T Consensus 1 ei~~if~~ys~-~~~~mt~~~f~~FL~~eQ~~~~~~~~~~~~li~~~~~~~~~~~~~~lt~~gF~~fL~S~ 70 (83)
T PF09279_consen 1 EIEEIFRKYSS-DKEYMTAEEFRRFLREEQGEPRLTDEQAKELIEKFEPDERNRQKGQLTLEGFTRFLFSD 70 (83)
T ss_dssp HHHHHHHHHCT-TSSSEEHHHHHHHHHHTSS-TTSSHHHHHHHHHHHHHHHHHHCTTEEEHHHHHHHHHST
T ss_pred CHHHHHHHHhC-CCCcCCHHHHHHHHHHHhccccCcHHHHHHHHHHHccchhhcccCCcCHHHHHHHHCCC
Confidence 47899999987 56799999999999643 33444455554443222 2346899999999887553
No 33
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=81.86 E-value=9.9 Score=30.95 Aligned_cols=70 Identities=14% Similarity=0.179 Sum_probs=61.2
Q ss_pred HHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHHcCCC
Q 025620 56 TRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSLGID 125 (250)
Q Consensus 56 ~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~~~ 125 (250)
...+.+.|..+-..+...|..+=+...+..||.+|....+-.+-..+....-|.|+.++|+.-|...+..
T Consensus 7 ~~el~~~F~~fD~d~~G~i~~~el~~~lr~lg~~~t~~el~~~~~~~D~dg~g~I~~~eF~~l~~~~~~~ 76 (151)
T KOG0027|consen 7 ILELKEAFQLFDKDGDGKISVEELGAVLRSLGQNPTEEELRDLIKEIDLDGDGTIDFEEFLDLMEKLGEE 76 (151)
T ss_pred HHHHHHHHHHHCCCCCCcccHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCCCCeEcHHHHHHHHHhhhcc
Confidence 4678888888865555789999999999999999999999999999999999999999999999987653
No 34
>KOG2756 consensus Predicted Mg2+-dependent phosphodiesterase TTRAP [Signal transduction mechanisms]
Probab=80.99 E-value=1.1 Score=41.33 Aligned_cols=40 Identities=23% Similarity=0.434 Sum_probs=36.7
Q ss_pred HHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhccC
Q 025620 9 RDKLQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQP 48 (250)
Q Consensus 9 ~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~ 48 (250)
++++-+|..+|.+.++.|+.+|..++|+++.|++.||...
T Consensus 26 ~~ll~efa~~~s~dea~aq~~l~~~dw~~~ral~~~~~se 65 (349)
T KOG2756|consen 26 RLLCVEFASVASCDAAVAQCFLAENDWEMERALNSYFEPE 65 (349)
T ss_pred HHHHHHHHHhhhhHHHhHHHHhhcchhHHHHHHHhhcCce
Confidence 4678899999999999999999999999999999999853
No 35
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=79.74 E-value=2.9 Score=33.99 Aligned_cols=34 Identities=21% Similarity=0.304 Sum_probs=30.0
Q ss_pred HHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhh
Q 025620 10 DKLQQFVSITGASEKAALQALKASDWHLEGAFDV 43 (250)
Q Consensus 10 ~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~ 43 (250)
+-|.=-++=||+|++.|+..|+.++.||-.||-.
T Consensus 86 eDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~ 119 (122)
T COG1308 86 EDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMK 119 (122)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHH
Confidence 3477778899999999999999999999999854
No 36
>cd05025 S-100A1 S-100A1: S-100A1 domain found in proteins similar to S100A1. S100A1 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. As is the case with many other members of S100 protein family, S100A1 is implicated in intracellular and extracellular regulatory activities, including interaction with myosin-associated twitchin kinase, actin-capping protein CapZ, sinapsin I, and tubulin. Structural data suggests that S100A1 proteins exist within cells as antiparallel homodimers, while heterodimers with S100A4 and S100B also has been reported. Upon binding calcium S100A1 changes conformation to expose a hydrophobic cleft which is the interaction site of S100A1 with its more that 20 known target proteins.
Probab=78.38 E-value=15 Score=27.36 Aligned_cols=68 Identities=12% Similarity=0.023 Sum_probs=48.9
Q ss_pred HHHHHHHHHHhc-CCCCC-ccchHHHHHHHhh-cCC----CCCchHHHHHHHhhcccccccccHHHHHHHHHHcC
Q 025620 56 TRHLEELYNRYK-DPYLD-MILVDGITLLCND-LQV----DPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSLG 123 (250)
Q Consensus 56 ~~~l~~lF~~Y~-~~~~d-~i~~dG~~~~~ed-Lgv----~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~ 123 (250)
...|.+.|..|- ..+.. .|+.+-+.+++.. +|. .|....+=-+...+....-|.|+-++|+.-+..+.
T Consensus 8 ~~~l~~~F~~fDd~dg~G~~Is~~El~~~l~~~lg~~~~~~~s~~~v~~i~~~~D~d~~G~I~f~eF~~l~~~~~ 82 (92)
T cd05025 8 METLINVFHAHSGKEGDKYKLSKKELKDLLQTELSDFLDAQKDADAVDKIMKELDENGDGEVDFQEFVVLVAALT 82 (92)
T ss_pred HHHHHHHHHHHhcccCCCCeECHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCCCCcCcHHHHHHHHHHHH
Confidence 356888999996 33444 5999999999975 553 44444444455556778889999999998877653
No 37
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=77.70 E-value=2.9 Score=27.12 Aligned_cols=38 Identities=13% Similarity=0.245 Sum_probs=30.2
Q ss_pred HHHHHHHhhh-CCCHHHHHHHHHhCCCCchhhhhhhhcc
Q 025620 10 DKLQQFVSIT-GASEKAALQALKASDWHLEGAFDVFYSQ 47 (250)
Q Consensus 10 ~~i~~F~~iT-~~s~~~A~~~L~~~~w~le~A~~~f~~~ 47 (250)
+.+.+.+++- +.++...+..|++++.|++.|++...+.
T Consensus 4 ~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~ 42 (43)
T smart00546 4 EALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLEG 42 (43)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 4555666554 5678999999999999999999987754
No 38
>PF05517 p25-alpha: p25-alpha ; InterPro: IPR008907 This family encodes a 25 kDa protein that is phosphorylated by a Ser/Thr-Pro kinase []. It has been described as a brain specific protein, but it is found in Tetrahymena thermophila.; PDB: 1WLM_A 1PUL_A 2JRF_A.
Probab=76.74 E-value=9.4 Score=31.83 Aligned_cols=76 Identities=18% Similarity=0.332 Sum_probs=52.0
Q ss_pred HHHHHHHhcC---CCCCccchHHHHHHHhhcCCCCC---chHHHHHHHhhcccccccccHHHHHHHHHHc----CCC--C
Q 025620 59 LEELYNRYKD---PYLDMILVDGITLLCNDLQVDPQ---DIVMLVVSWHMKAATMCEFSKQEFIGGLQSL----GID--S 126 (250)
Q Consensus 59 l~~lF~~Y~~---~~~d~i~~dG~~~~~edLgv~~e---d~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l----~~~--s 126 (250)
|+++|..|.. .....|+.....++|.|.||=.. ...+=++-.+++++.-..|+-++|+..+..+ +++ +
T Consensus 1 L~~~F~~f~~fG~~~~~~m~~~~F~Kl~kD~~i~d~k~t~tdvDiiF~Kvk~k~~~~I~f~~F~~aL~~lA~~~~~~~~~ 80 (154)
T PF05517_consen 1 LEAVFKAFASFGKKNGTEMDSKNFAKLCKDCGIIDKKLTSTDVDIIFSKVKAKGARKITFEQFLEALAELAEKKGKDKSS 80 (154)
T ss_dssp HHHHHHHHHCSSTSTSSEEEHHHHHHHHHHTSS--SSS-HHHHHHHHHHHT-SS-SEEEHHHHHHHHHHHHHHHSCCCTH
T ss_pred CHHHHHHHHHhcCCccccccHHHHHHHHHHcCCCCCCCchHHHHHHHHHhhcCCCcccCHHHHHHHHHHHHHHhhccccc
Confidence 6789999953 23458999999999999999332 2233344446677776679999999998875 332 5
Q ss_pred HHHHHHHH
Q 025620 127 LDKFRERI 134 (250)
Q Consensus 127 i~~lk~~l 134 (250)
.+++..+|
T Consensus 81 ~~~~~~kl 88 (154)
T PF05517_consen 81 AEELKEKL 88 (154)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 66666666
No 39
>cd05027 S-100B S-100B: S-100B domain found in proteins similar to S100B. S100B is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100B group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100B is most abundant in glial cells of the central nervous system, predominately in astrocytes. S100B is involved in signal transduction via the inhibition of protein phoshorylation, regulation of enzyme activity and by affecting the calcium homeostasis. Upon calcium binding the S100B homodimer changes conformation to expose a hydrophobic cleft, which represents the interaction site of S100B with its more than 20 known target proteins. These target proteins include several cellular architecture proteins such as tubulin and GFAP; S100B can inhibit polymerization of these oligomeric molecules. Furthermore, S100B i
Probab=76.66 E-value=16 Score=27.39 Aligned_cols=66 Identities=17% Similarity=0.124 Sum_probs=49.1
Q ss_pred HHHHHHHHHhcC-CCCC-ccchHHHHHHHhh-----cCCCCCchHHHHHHHhhcccccccccHHHHHHHHHHc
Q 025620 57 RHLEELYNRYKD-PYLD-MILVDGITLLCND-----LQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSL 122 (250)
Q Consensus 57 ~~l~~lF~~Y~~-~~~d-~i~~dG~~~~~ed-----Lgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l 122 (250)
..|.+.|..|.+ ++.. .|+.+-+..++.. +|-.++.-.+=-+--.+....-|.|+-++|+.-+..+
T Consensus 8 ~~l~~aF~~fD~~dgdG~~I~~~eL~~ll~~~~~~~lg~~~~~~~v~~~i~~~D~n~dG~v~f~eF~~li~~~ 80 (88)
T cd05027 8 VALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVAMV 80 (88)
T ss_pred HHHHHHHHHhcccCCCcCEECHHHHHHHHHHHhHHHhcCCCCHHHHHHHHHHhCCCCCCcCcHHHHHHHHHHH
Confidence 568889999974 3344 5999999999999 9976644433333445577778999999999876654
No 40
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=76.11 E-value=13 Score=31.46 Aligned_cols=69 Identities=12% Similarity=0.058 Sum_probs=52.0
Q ss_pred cCCHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHH
Q 025620 53 LTDTRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQS 121 (250)
Q Consensus 53 ~~~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~ 121 (250)
.....+|...|.-|=.+....|..+=+...+..||-...+-.+=-|...+.-..-|.|+.++|++.+..
T Consensus 88 ~~~~Eel~~aF~~fD~d~dG~Is~~eL~~vl~~lge~~~deev~~ll~~~d~d~dG~i~~~eF~~~~~~ 156 (160)
T COG5126 88 GDKEEELREAFKLFDKDHDGYISIGELRRVLKSLGERLSDEEVEKLLKEYDEDGDGEIDYEEFKKLIKD 156 (160)
T ss_pred CCcHHHHHHHHHHhCCCCCceecHHHHHHHHHhhcccCCHHHHHHHHHhcCCCCCceEeHHHHHHHHhc
Confidence 344678888888887766668888888888888888777666655555555566788888888887764
No 41
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=75.92 E-value=19 Score=29.31 Aligned_cols=83 Identities=18% Similarity=0.092 Sum_probs=63.4
Q ss_pred CCHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCc----hHHHHHHHh-hcccccccccHHHHHHHHHHcCCC-CH
Q 025620 54 TDTRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQD----IVMLVVSWH-MKAATMCEFSKQEFIGGLQSLGID-SL 127 (250)
Q Consensus 54 ~~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed----~~~LvLa~~-l~a~~~g~~tr~ef~~g~~~l~~~-si 127 (250)
+....+..+++++-.+++..|+.+-...++...+....+ ...+.=|+. +-...-|.||.+++..-|..+|-. |.
T Consensus 41 ~t~~el~~~~~~~D~dg~g~I~~~eF~~l~~~~~~~~~~~~~~~~el~eaF~~fD~d~~G~Is~~el~~~l~~lg~~~~~ 120 (151)
T KOG0027|consen 41 PTEEELRDLIKEIDLDGDGTIDFEEFLDLMEKLGEEKTDEEASSEELKEAFRVFDKDGDGFISASELKKVLTSLGEKLTD 120 (151)
T ss_pred CCHHHHHHHHHHhCCCCCCeEcHHHHHHHHHhhhcccccccccHHHHHHHHHHHccCCCCcCcHHHHHHHHHHhCCcCCH
Confidence 567899999999887666789999999999988886654 336666664 466678999999999999999854 44
Q ss_pred HHHHHHHHH
Q 025620 128 DKFRERISF 136 (250)
Q Consensus 128 ~~lk~~l~~ 136 (250)
+.++..+..
T Consensus 121 ~e~~~mi~~ 129 (151)
T KOG0027|consen 121 EECKEMIRE 129 (151)
T ss_pred HHHHHHHHh
Confidence 444444433
No 42
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=75.85 E-value=5.5 Score=25.71 Aligned_cols=38 Identities=18% Similarity=0.259 Sum_probs=30.9
Q ss_pred HHHHHHHHhhhC-CCHHHHHHHHHhCCCCchhhhhhhhc
Q 025620 9 RDKLQQFVSITG-ASEKAALQALKASDWHLEGAFDVFYS 46 (250)
Q Consensus 9 ~~~i~~F~~iT~-~s~~~A~~~L~~~~w~le~A~~~f~~ 46 (250)
.+.|++..++.- .++..-+..|++++++++.|++...+
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 456788888764 57899999999999999999998764
No 43
>KOG0036 consensus Predicted mitochondrial carrier protein [Nucleotide transport and metabolism]
Probab=73.57 E-value=38 Score=33.17 Aligned_cols=88 Identities=14% Similarity=0.080 Sum_probs=71.1
Q ss_pred HHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCC-CCchHHHHHHHhhcccccccccHHHHHHHHHHc------------
Q 025620 56 TRHLEELYNRYKDPYLDMILVDGITLLCNDLQVD-PQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSL------------ 122 (250)
Q Consensus 56 ~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~-~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l------------ 122 (250)
..++..+|+.+-......++.+-+++-++.|+.. |..-..=.|.-.+.+.+-|...-++|.+.+.+-
T Consensus 13 ~~r~~~lf~~lD~~~~g~~d~~~l~k~~~~l~~~~~~~~~~~~l~~~~d~~~dg~vDy~eF~~Y~~~~E~~l~~~F~~iD 92 (463)
T KOG0036|consen 13 DIRIRCLFKELDSKNDGQVDLDQLEKGLEKLDHPKPNYEAAKMLFSAMDANRDGRVDYSEFKRYLDNKELELYRIFQSID 92 (463)
T ss_pred HHHHHHHHHHhccCCCCceeHHHHHHHHHhcCCCCCchHHHHHHHHhcccCcCCcccHHHHHHHHHHhHHHHHHHHhhhc
Confidence 5788899999887666689999999999999998 777788888899999999999999999988762
Q ss_pred ----CCCCHHHHHHHHHHHHHHccc
Q 025620 123 ----GIDSLDKFRERISFMRAELKD 143 (250)
Q Consensus 123 ----~~~si~~lk~~l~~L~~~l~~ 143 (250)
|+-.+..|...|.++-.+|.+
T Consensus 93 ~~hdG~i~~~Ei~~~l~~~gi~l~d 117 (463)
T KOG0036|consen 93 LEHDGKIDPNEIWRYLKDLGIQLSD 117 (463)
T ss_pred cccCCccCHHHHHHHHHHhCCccCH
Confidence 334566677777766655533
No 44
>KOG0028 consensus Ca2+-binding protein (centrin/caltractin), EF-Hand superfamily protein [Cytoskeleton; Cell cycle control, cell division, chromosome partitioning]
Probab=72.94 E-value=40 Score=28.91 Aligned_cols=103 Identities=11% Similarity=0.194 Sum_probs=72.5
Q ss_pred HHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHHc-C-CCCHHHHHHH
Q 025620 56 TRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSL-G-IDSLDKFRER 133 (250)
Q Consensus 56 ~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l-~-~~si~~lk~~ 133 (250)
...|...|+-+-....+.|+.+++--=.-.||.+|..-.++-|.--...+.-|.|+-++|+..|... + -+|.+.++.+
T Consensus 32 ~q~i~e~f~lfd~~~~g~iD~~EL~vAmralGFE~~k~ei~kll~d~dk~~~g~i~fe~f~~~mt~k~~e~dt~eEi~~a 111 (172)
T KOG0028|consen 32 KQEIKEAFELFDPDMAGKIDVEELKVAMRALGFEPKKEEILKLLADVDKEGSGKITFEDFRRVMTVKLGERDTKEEIKKA 111 (172)
T ss_pred HhhHHHHHHhhccCCCCcccHHHHHHHHHHcCCCcchHHHHHHHHhhhhccCceechHHHHHHHHHHHhccCcHHHHHHH
Confidence 3667777776665455799999985556789999999988887777777778999999999997763 2 3688888887
Q ss_pred HHHHHHHccchHHHHHHHHHHHHhh
Q 025620 134 ISFMRAELKDEQKFREIYNFAFAWA 158 (250)
Q Consensus 134 l~~L~~~l~~~~~Fk~~Y~f~F~~~ 158 (250)
+...+..=.-.-.++.+-+-++.++
T Consensus 112 frl~D~D~~Gkis~~~lkrvakeLg 136 (172)
T KOG0028|consen 112 FRLFDDDKTGKISQRNLKRVAKELG 136 (172)
T ss_pred HHcccccCCCCcCHHHHHHHHHHhC
Confidence 7644322111112555555555554
No 45
>KOG0036 consensus Predicted mitochondrial carrier protein [Nucleotide transport and metabolism]
Probab=72.65 E-value=11 Score=36.76 Aligned_cols=80 Identities=15% Similarity=0.066 Sum_probs=56.9
Q ss_pred HHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHHcCCCCHHHHHHHHH
Q 025620 56 TRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSLGIDSLDKFRERIS 135 (250)
Q Consensus 56 ~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~~~si~~lk~~l~ 135 (250)
+.+|-..|.+-.-.....|++..|.++|.|+|+++.|-..--+-..+--..-+.|..+||.+-+.-.- .+.|+..+.
T Consensus 81 E~~l~~~F~~iD~~hdG~i~~~Ei~~~l~~~gi~l~de~~~k~~e~~d~~g~~~I~~~e~rd~~ll~p---~s~i~di~~ 157 (463)
T KOG0036|consen 81 ELELYRIFQSIDLEHDGKIDPNEIWRYLKDLGIQLSDEKAAKFFEHMDKDGKATIDLEEWRDHLLLYP---ESDLEDIYD 157 (463)
T ss_pred HHHHHHHHhhhccccCCccCHHHHHHHHHHhCCccCHHHHHHHHHHhccCCCeeeccHHHHhhhhcCC---hhHHHHHHH
Confidence 46666677655544445899999999999999999998777766777666677999999987655433 333444444
Q ss_pred HHH
Q 025620 136 FMR 138 (250)
Q Consensus 136 ~L~ 138 (250)
.++
T Consensus 158 ~W~ 160 (463)
T KOG0036|consen 158 FWR 160 (463)
T ss_pred hhh
Confidence 444
No 46
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=72.63 E-value=37 Score=28.79 Aligned_cols=84 Identities=13% Similarity=0.159 Sum_probs=63.6
Q ss_pred CHHHHHHHHHHhc---CCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHHcCC--CCHHH
Q 025620 55 DTRHLEELYNRYK---DPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSLGI--DSLDK 129 (250)
Q Consensus 55 ~~~~l~~lF~~Y~---~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~~--~si~~ 129 (250)
+...+.++.+.|+ -+....|+-+-+...+..||.+|.+..+.-|.-.+.+ .-|.++-.+|+..|...-+ ++-++
T Consensus 15 t~~qi~~lkeaF~l~D~d~~G~I~~~el~~ilr~lg~~~s~~ei~~l~~~~d~-~~~~idf~~Fl~~ms~~~~~~~~~Ee 93 (160)
T COG5126 15 TEEQIQELKEAFQLFDRDSDGLIDRNELGKILRSLGFNPSEAEINKLFEEIDA-GNETVDFPEFLTVMSVKLKRGDKEEE 93 (160)
T ss_pred CHHHHHHHHHHHHHhCcCCCCCCcHHHHHHHHHHcCCCCcHHHHHHHHHhccC-CCCccCHHHHHHHHHHHhccCCcHHH
Confidence 3445555544444 3334589999999999999999999998888888888 6679999999999988643 45677
Q ss_pred HHHHHHHHHH
Q 025620 130 FRERISFMRA 139 (250)
Q Consensus 130 lk~~l~~L~~ 139 (250)
|+.+..-.+.
T Consensus 94 l~~aF~~fD~ 103 (160)
T COG5126 94 LREAFKLFDK 103 (160)
T ss_pred HHHHHHHhCC
Confidence 7777766553
No 47
>CHL00098 tsf elongation factor Ts
Probab=71.79 E-value=5.3 Score=35.05 Aligned_cols=39 Identities=18% Similarity=0.263 Sum_probs=34.6
Q ss_pred HHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhccC
Q 025620 10 DKLQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQP 48 (250)
Q Consensus 10 ~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~ 48 (250)
++|.+..+.||+.--.+...|..+++|++.|++--=.++
T Consensus 3 ~~ik~LR~~Tgag~~dck~AL~e~~gd~~~A~~~Lr~~g 41 (200)
T CHL00098 3 ELVKELRDKTGAGMMDCKKALQEANGDFEKALESLRQKG 41 (200)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 579999999999999999999999999999997655443
No 48
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=71.19 E-value=5.6 Score=34.80 Aligned_cols=40 Identities=18% Similarity=0.214 Sum_probs=35.6
Q ss_pred HHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhccC
Q 025620 9 RDKLQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQP 48 (250)
Q Consensus 9 ~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~ 48 (250)
.++|.+..+.||++--.+.+.|..+++|++.|++--=.++
T Consensus 5 a~~ik~LR~~tga~~~~ck~AL~~~~gd~~~A~~~lr~~g 44 (198)
T PRK12332 5 AKLVKELREKTGAGMMDCKKALEEANGDMEKAIEWLREKG 44 (198)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 4679999999999999999999999999999998665543
No 49
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=69.88 E-value=5.9 Score=36.73 Aligned_cols=39 Identities=18% Similarity=0.191 Sum_probs=35.0
Q ss_pred HHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhcc
Q 025620 9 RDKLQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQ 47 (250)
Q Consensus 9 ~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~ 47 (250)
.++|.+.++.||+.--.+.+.|..++||++.|++--=..
T Consensus 5 a~~IK~LRe~Tgagm~dCKkAL~e~~gDiekAi~~LRkk 43 (290)
T TIGR00116 5 AQLVKELRERTGAGMMDCKKALTEANGDFEKAIKNLRES 43 (290)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 467999999999999999999999999999999865544
No 50
>PRK09377 tsf elongation factor Ts; Provisional
Probab=67.93 E-value=6.8 Score=36.30 Aligned_cols=41 Identities=20% Similarity=0.214 Sum_probs=36.1
Q ss_pred hHHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhccC
Q 025620 8 NRDKLQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQP 48 (250)
Q Consensus 8 q~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~ 48 (250)
..++|.+.++.||+.--.+.+.|..+++|++.|++--=..+
T Consensus 5 s~~~IK~LR~~Tgagm~dCKkAL~e~~gD~ekAi~~Lrk~G 45 (290)
T PRK09377 5 TAALVKELRERTGAGMMDCKKALTEADGDIEKAIEWLRKKG 45 (290)
T ss_pred CHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHhc
Confidence 35789999999999999999999999999999998665443
No 51
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=67.91 E-value=7.8 Score=23.86 Aligned_cols=28 Identities=18% Similarity=0.667 Sum_probs=22.9
Q ss_pred HHHHHHHHhhcCCCCCHhhHHHHHHHHh
Q 025620 188 DHWCQFLQAKHNKAISRDTWSQLLEFAR 215 (250)
Q Consensus 188 ~~w~~Fl~~~~~k~IskD~W~~~l~F~~ 215 (250)
..|++.+.+...-+||++.-..||.|.+
T Consensus 3 ~EW~~Li~eA~~~Gls~eeir~FL~~~k 30 (30)
T PF08671_consen 3 EEWVELIKEAKESGLSKEEIREFLEFNK 30 (30)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence 4799999998889999999999998864
No 52
>PF00036 EF-hand_1: EF hand; InterPro: IPR018248 Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).; PDB: 1BJF_A 1XFW_R 1XFV_O 2K0J_A 2F3Z_A 3BYA_A 1XFU_Q 2R28_B 1ZOT_B 3G43_D ....
Probab=67.24 E-value=4.3 Score=24.39 Aligned_cols=18 Identities=17% Similarity=0.137 Sum_probs=12.2
Q ss_pred cccccccHHHHHHHHHHc
Q 025620 105 ATMCEFSKQEFIGGLQSL 122 (250)
Q Consensus 105 ~~~g~~tr~ef~~g~~~l 122 (250)
..=|.|+.+||+.+|++|
T Consensus 12 d~dG~I~~~Ef~~~~~~L 29 (29)
T PF00036_consen 12 DGDGKIDFEEFKEMMKKL 29 (29)
T ss_dssp TSSSEEEHHHHHHHHHHT
T ss_pred CCCCcCCHHHHHHHHHhC
Confidence 344777777777777654
No 53
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=63.64 E-value=12 Score=24.74 Aligned_cols=32 Identities=22% Similarity=0.311 Sum_probs=23.5
Q ss_pred cccccHHHHHHHHHHcCCC--CHHHHHHHHHHHH
Q 025620 107 MCEFSKQEFIGGLQSLGID--SLDKFRERISFMR 138 (250)
Q Consensus 107 ~g~~tr~ef~~g~~~l~~~--si~~lk~~l~~L~ 138 (250)
-|.||+++|...++.+|.. |.+.+...+..++
T Consensus 2 ~G~i~~~~~~~~l~~~g~~~~s~~e~~~l~~~~D 35 (54)
T PF13833_consen 2 DGKITREEFRRALSKLGIKDLSEEEVDRLFREFD 35 (54)
T ss_dssp SSEEEHHHHHHHHHHTTSSSSCHHHHHHHHHHHT
T ss_pred cCEECHHHHHHHHHHhCCCCCCHHHHHHHHHhcc
Confidence 3899999999999888866 4555555555544
No 54
>PF14658 EF-hand_9: EF-hand domain
Probab=62.87 E-value=30 Score=25.11 Aligned_cols=50 Identities=6% Similarity=0.090 Sum_probs=44.7
Q ss_pred CccchHHHHHHHhhcCC-CCCchHHHHHHHhhccccc-ccccHHHHHHHHHH
Q 025620 72 DMILVDGITLLCNDLQV-DPQDIVMLVVSWHMKAATM-CEFSKQEFIGGLQS 121 (250)
Q Consensus 72 d~i~~dG~~~~~edLgv-~~ed~~~LvLa~~l~a~~~-g~~tr~ef~~g~~~ 121 (250)
.+|-+.-+..|+..+|- +|++-.+=-|+-.+--..- |.+.++.|...|+.
T Consensus 13 G~V~v~~l~~~Lra~~~~~p~e~~Lq~l~~elDP~g~~~~v~~d~F~~iM~~ 64 (66)
T PF14658_consen 13 GRVPVSDLITYLRAVTGRSPEESELQDLINELDPEGRDGSVNFDTFLAIMRD 64 (66)
T ss_pred ceEeHHHHHHHHHHHcCCCCcHHHHHHHHHHhCCCCCCceEeHHHHHHHHHH
Confidence 57888999999999999 9999999899999877776 99999999999875
No 55
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=62.76 E-value=15 Score=21.71 Aligned_cols=30 Identities=13% Similarity=0.215 Sum_probs=19.3
Q ss_pred HHHHHHHHhcCCCCCccchHHHHHHHh-hcC
Q 025620 58 HLEELYNRYKDPYLDMILVDGITLLCN-DLQ 87 (250)
Q Consensus 58 ~l~~lF~~Y~~~~~d~i~~dG~~~~~e-dLg 87 (250)
++.++|..|=.++...|+.+=+...+. .||
T Consensus 1 ~l~~~F~~~D~d~dG~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 1 RLREAFKMFDKDGDGFIDFEELRAILRKSLG 31 (31)
T ss_dssp HHHHHHHHH-TTSSSEEEHHHHHHHHHHHTT
T ss_pred CHHHHHHHHCCCCCCcCcHHHHHHHHHHhcC
Confidence 356777777544445777777777777 565
No 56
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=62.57 E-value=20 Score=25.62 Aligned_cols=44 Identities=25% Similarity=0.320 Sum_probs=38.9
Q ss_pred CcchHHHHHHHHhhhCC-CHHHHHHHHHhCCCCchhhhhhhhccC
Q 025620 5 SRSNRDKLQQFVSITGA-SEKAALQALKASDWHLEGAFDVFYSQP 48 (250)
Q Consensus 5 ~~~q~~~i~~F~~iT~~-s~~~A~~~L~~~~w~le~A~~~f~~~~ 48 (250)
+++-+..|+...+|||+ |++.--..|..+|-|-+.|++.-..++
T Consensus 2 P~~~rk~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~qD 46 (60)
T PF06972_consen 2 PAASRKTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLSQD 46 (60)
T ss_pred ChHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHhcC
Confidence 45667889999999999 999999999999999999999888754
No 57
>KOG2643 consensus Ca2+ binding protein, contains EF-hand motifs [Inorganic ion transport and metabolism]
Probab=61.94 E-value=33 Score=33.78 Aligned_cols=94 Identities=15% Similarity=0.196 Sum_probs=66.6
Q ss_pred CCccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHHcCCCCHHHHHHHHHHHHHHccc------h
Q 025620 71 LDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSLGIDSLDKFRERISFMRAELKD------E 144 (250)
Q Consensus 71 ~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~~~si~~lk~~l~~L~~~l~~------~ 144 (250)
...+.+|-..+|.++|..+.-.++..-... ..-|.||..+|-.-+-.+-..+..+....+.+++.+..+ -
T Consensus 300 ~~kLs~deF~~F~e~Lq~Eil~lEF~~~~~----~~~g~Ise~DFA~~lL~~a~~n~~~k~~~lkrvk~kf~~~~~gISl 375 (489)
T KOG2643|consen 300 NGKLSIDEFLKFQENLQEEILELEFERFDK----GDSGAISEVDFAELLLAYAGVNSKKKHKYLKRVKEKFKDDGKGISL 375 (489)
T ss_pred CccccHHHHHHHHHHHHHHHHHHHHHHhCc----ccccccCHHHHHHHHHHHcccchHhHHHHHHHHHHhccCCCCCcCH
Confidence 347889999999999986554444433322 223999999999998887666666667777788777654 2
Q ss_pred HHHHHHHHHHHHhhhhcCCccccHHHHHHHHH
Q 025620 145 QKFREIYNFAFAWAKEKGQKSLALDTAIGMWQ 176 (250)
Q Consensus 145 ~~Fk~~Y~f~F~~~~~~~qk~l~~d~Ai~~W~ 176 (250)
++|+.|++|..+.+ +.++|+.+-.
T Consensus 376 ~Ef~~Ff~Fl~~l~--------dfd~Al~fy~ 399 (489)
T KOG2643|consen 376 QEFKAFFRFLNNLN--------DFDIALRFYH 399 (489)
T ss_pred HHHHHHHHHHhhhh--------HHHHHHHHHH
Confidence 35999999987766 4566655543
No 58
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=61.94 E-value=74 Score=26.13 Aligned_cols=45 Identities=29% Similarity=0.418 Sum_probs=27.8
Q ss_pred ccccHHHHHHHHHHcCC------CCHHHHHHHHHHH----HHHccchHHHHHHHH
Q 025620 108 CEFSKQEFIGGLQSLGI------DSLDKFRERISFM----RAELKDEQKFREIYN 152 (250)
Q Consensus 108 g~~tr~ef~~g~~~l~~------~si~~lk~~l~~L----~~~l~~~~~Fk~~Y~ 152 (250)
-+|...+|++.+.++-- .+....|.++-.| ...+.+.+.|+..|.
T Consensus 75 ~evas~~Fl~el~kl~~~k~~~~~~~~~Vk~kil~li~~W~~~f~~~p~~~~~Y~ 129 (139)
T cd03567 75 SEVGKFRFLNELIKLVSPKYLGSRTSEKVKTKIIELLYSWTLELPHEPKIKEAYD 129 (139)
T ss_pred HHHHhHHHHHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHHhcccchHHHHHH
Confidence 58899999998888642 2455666665544 444544444555554
No 59
>PRK10391 oriC-binding nucleoid-associated protein; Provisional
Probab=60.90 E-value=24 Score=26.01 Aligned_cols=40 Identities=20% Similarity=0.449 Sum_probs=32.5
Q ss_pred cHHHHHHHHHHcCCCCHHHHHHHHHHHHHHccchHHHHHHHH
Q 025620 111 SKQEFIGGLQSLGIDSLDKFRERISFMRAELKDEQKFREIYN 152 (250)
Q Consensus 111 tr~ef~~g~~~l~~~si~~lk~~l~~L~~~l~~~~~Fk~~Y~ 152 (250)
|+.+|+--+++ |+|++.|-+.+..++.+|.++.+...+|+
T Consensus 2 tk~eyLlkfRk--css~eTLEkv~e~~~y~L~~~~e~~~f~~ 41 (71)
T PRK10391 2 TVQDYLLKFRK--ISSLESLEKLFDHLNYTLTDDQEIINMYR 41 (71)
T ss_pred cHHHHHHHHHh--cCcHHHHHHHHHHhhcccCCHHHHHHHHH
Confidence 67788866655 99999999999999999988766666665
No 60
>PF12096 DUF3572: Protein of unknown function (DUF3572); InterPro: IPR021955 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 100 amino acids in length.
Probab=59.62 E-value=42 Score=25.74 Aligned_cols=59 Identities=17% Similarity=0.320 Sum_probs=39.5
Q ss_pred chHHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhccCCCCCcCCHHHHHHHHHHhcCCCCCccchHHHHHHHhhc
Q 025620 7 SNRDKLQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQPQSKSLTDTRHLEELYNRYKDPYLDMILVDGITLLCNDL 86 (250)
Q Consensus 7 ~q~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~~~~~~~~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edL 86 (250)
.+.+.+..|+..||+++..=+.-.. ++.=+-.+-|-+-.. ..=++.||+.+
T Consensus 19 ~d~e~l~rFLa~TG~~p~~LR~~a~-----------------------dp~FL~~VLdFl~~d------e~~l~af~~a~ 69 (88)
T PF12096_consen 19 GDPERLPRFLALTGLSPDDLRAAAG-----------------------DPAFLAAVLDFLLMD------EAWLLAFCDAA 69 (88)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHcc-----------------------ChHHHHHHHHHHHcc------hHHHHHHHHHc
Confidence 3567888999999999877654332 233344444444322 34578999999
Q ss_pred CCCCCchH
Q 025620 87 QVDPQDIV 94 (250)
Q Consensus 87 gv~~ed~~ 94 (250)
|++|+.+.
T Consensus 70 ~~~p~~v~ 77 (88)
T PF12096_consen 70 GIPPEAVA 77 (88)
T ss_pred CcChhHHH
Confidence 99998664
No 61
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=59.03 E-value=30 Score=25.89 Aligned_cols=88 Identities=7% Similarity=-0.021 Sum_probs=54.3
Q ss_pred CCCCCchHHHHHHHhh-cccccccccHHHHHHHHHHcCCCCHHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhhcCCcc
Q 025620 87 QVDPQDIVMLVVSWHM-KAATMCEFSKQEFIGGLQSLGIDSLDKFRERISFMRAELKDEQKFREIYNFAFAWAKEKGQKS 165 (250)
Q Consensus 87 gv~~ed~~~LvLa~~l-~a~~~g~~tr~ef~~g~~~l~~~si~~lk~~l~~L~~~l~~~~~Fk~~Y~f~F~~~~~~~qk~ 165 (250)
++++++...+--++.. -...-|.|+.+++...|+.+|+ +-+.++..+...+..-...-.|.+|+...-..++-...+-
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~-~~~ev~~i~~~~d~~~~g~I~~~eF~~~~~~~~~~~~g~~ 81 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGL-PQTLLAKIWNLADIDNDGELDKDEFALAMHLIYRKLNGYP 81 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCC-CHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHHHHHcCCC
Confidence 3455566666666554 4456799999999999999886 3445555444433221112237777777766666666666
Q ss_pred ccHHHHHHHH
Q 025620 166 LALDTAIGMW 175 (250)
Q Consensus 166 l~~d~Ai~~W 175 (250)
|+.++=-.+|
T Consensus 82 ~~~~~~~~~~ 91 (96)
T smart00027 82 IPASLPPSLI 91 (96)
T ss_pred CCccCCHhhc
Confidence 7666544443
No 62
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=58.85 E-value=12 Score=25.49 Aligned_cols=22 Identities=27% Similarity=0.398 Sum_probs=19.0
Q ss_pred HHHHHHhhhCCCHHHHHHHHHh
Q 025620 11 KLQQFVSITGASEKAALQALKA 32 (250)
Q Consensus 11 ~i~~F~~iT~~s~~~A~~~L~~ 32 (250)
.+.+|.+++|+|.+.|+.+|+-
T Consensus 12 tv~~~rd~lg~sRK~ai~lLE~ 33 (50)
T PF09107_consen 12 TVAEFRDLLGLSRKYAIPLLEY 33 (50)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHH
T ss_pred cHHHHHHHHCccHHHHHHHHHH
Confidence 4789999999999999999974
No 63
>KOG0030 consensus Myosin essential light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=58.85 E-value=40 Score=28.31 Aligned_cols=68 Identities=15% Similarity=0.127 Sum_probs=50.2
Q ss_pred CHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhhccc--ccccccHHHHHHHHHHc
Q 025620 55 DTRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAA--TMCEFSKQEFIGGLQSL 122 (250)
Q Consensus 55 ~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~--~~g~~tr~ef~~g~~~l 122 (250)
....+.++|+-|-......|+..-.---+..||.+|.+..++-..-..... ++-.++-++|+-.++.+
T Consensus 9 ~~~e~ke~F~lfD~~gD~ki~~~q~gdvlRalG~nPT~aeV~k~l~~~~~~~~~~~rl~FE~fLpm~q~v 78 (152)
T KOG0030|consen 9 QMEEFKEAFLLFDRTGDGKISGSQVGDVLRALGQNPTNAEVLKVLGQPKRREMNVKRLDFEEFLPMYQQV 78 (152)
T ss_pred hHHHHHHHHHHHhccCcccccHHHHHHHHHHhcCCCcHHHHHHHHcCcccchhhhhhhhHHHHHHHHHHH
Confidence 347788888877665556899888888899999999888777666666666 34467777777665553
No 64
>PLN02964 phosphatidylserine decarboxylase
Probab=55.54 E-value=58 Score=33.59 Aligned_cols=78 Identities=12% Similarity=0.057 Sum_probs=45.3
Q ss_pred HHHHHHHHHhcCCCCCccchHHHHHHHhhcC-CCCCchH---HHHHHHhhcccccccccHHHHHHHHHHcCC-CCHHHHH
Q 025620 57 RHLEELYNRYKDPYLDMILVDGITLLCNDLQ-VDPQDIV---MLVVSWHMKAATMCEFSKQEFIGGLQSLGI-DSLDKFR 131 (250)
Q Consensus 57 ~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLg-v~~ed~~---~LvLa~~l~a~~~g~~tr~ef~~g~~~l~~-~si~~lk 131 (250)
..+.+.|+.+-.+.+..| +-..+..|| .+|++.. +--+...+....-|.|+.+||+..+..++. .+-++++
T Consensus 143 ~elkeaF~lfD~dgdG~i----Lg~ilrslG~~~pte~e~~fi~~mf~~~D~DgdG~IdfdEFl~lL~~lg~~~seEEL~ 218 (644)
T PLN02964 143 ESACESFDLLDPSSSNKV----VGSIFVSCSIEDPVETERSFARRILAIVDYDEDGQLSFSEFSDLIKAFGNLVAANKKE 218 (644)
T ss_pred HHHHHHHHHHCCCCCCcC----HHHHHHHhCCCCCCHHHHHHHHHHHHHhCCCCCCeEcHHHHHHHHHHhccCCCHHHHH
Confidence 445555655543222233 556677888 5776654 222333345555688888888888887764 4555566
Q ss_pred HHHHHHH
Q 025620 132 ERISFMR 138 (250)
Q Consensus 132 ~~l~~L~ 138 (250)
.....++
T Consensus 219 eaFk~fD 225 (644)
T PLN02964 219 ELFKAAD 225 (644)
T ss_pred HHHHHhC
Confidence 6555544
No 65
>KOG0028 consensus Ca2+-binding protein (centrin/caltractin), EF-Hand superfamily protein [Cytoskeleton; Cell cycle control, cell division, chromosome partitioning]
Probab=53.92 E-value=62 Score=27.76 Aligned_cols=67 Identities=12% Similarity=0.174 Sum_probs=47.7
Q ss_pred CHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHH
Q 025620 55 DTRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQS 121 (250)
Q Consensus 55 ~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~ 121 (250)
+...|.+.|.-+-++....|.+.-+-+.+..||=++.|-.+--.-.-..--.-|+|+.++|...|+.
T Consensus 104 t~eEi~~afrl~D~D~~Gkis~~~lkrvakeLgenltD~El~eMIeEAd~d~dgevneeEF~~imk~ 170 (172)
T KOG0028|consen 104 TKEEIKKAFRLFDDDKTGKISQRNLKRVAKELGENLTDEELMEMIEEADRDGDGEVNEEEFIRIMKK 170 (172)
T ss_pred cHHHHHHHHHcccccCCCCcCHHHHHHHHHHhCccccHHHHHHHHHHhcccccccccHHHHHHHHhc
Confidence 4466667777666655567888888888888888887776665555555555678888888877764
No 66
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=53.77 E-value=17 Score=34.30 Aligned_cols=36 Identities=28% Similarity=0.198 Sum_probs=33.7
Q ss_pred chHHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhh
Q 025620 7 SNRDKLQQFVSITGASEKAALQALKASDWHLEGAFD 42 (250)
Q Consensus 7 ~q~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~ 42 (250)
.++++|.+..+=||++-....+-|+.++|||..|-.
T Consensus 45 ~~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~ 80 (340)
T KOG1071|consen 45 SSKALLKKLREKTGASMVNCKKALEECGGDLVLAEE 80 (340)
T ss_pred ccHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHH
Confidence 589999999999999999999999999999998864
No 67
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=52.59 E-value=17 Score=33.49 Aligned_cols=36 Identities=25% Similarity=0.267 Sum_probs=31.7
Q ss_pred HHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhcc
Q 025620 12 LQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQ 47 (250)
Q Consensus 12 i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~ 47 (250)
++=.+++||++.++|.+.|+++++++-.|+-.--.+
T Consensus 239 ~~i~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~~~~ 274 (299)
T PRK05441 239 VRIVMEATGVSREEAEAALEAADGSVKLAIVMILTG 274 (299)
T ss_pred HHHHHHHHCcCHHHHHHHHHHhCCCcHHHHHHHHhC
Confidence 455899999999999999999999999999876654
No 68
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=51.22 E-value=18 Score=33.30 Aligned_cols=36 Identities=22% Similarity=0.182 Sum_probs=31.2
Q ss_pred HHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhcc
Q 025620 12 LQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQ 47 (250)
Q Consensus 12 i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~ 47 (250)
++=.+++||++.++|...|.++++++-.||-.--.+
T Consensus 234 ~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~~~~~ 269 (291)
T TIGR00274 234 VRIVRQATDCNKELAEQTLLAADQNVKLAIVMILST 269 (291)
T ss_pred HHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHHHHhC
Confidence 455899999999999999999999999998866544
No 69
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=50.75 E-value=16 Score=24.62 Aligned_cols=25 Identities=24% Similarity=0.457 Sum_probs=19.9
Q ss_pred CCCHHHHHHHHHhCCCCchhhhhhh
Q 025620 20 GASEKAALQALKASDWHLEGAFDVF 44 (250)
Q Consensus 20 ~~s~~~A~~~L~~~~w~le~A~~~f 44 (250)
.++...-.+||.+.+||++.|...+
T Consensus 28 ~~~d~~llRFLRARkf~v~~A~~mL 52 (55)
T PF03765_consen 28 DHDDNFLLRFLRARKFDVEKAFKML 52 (55)
T ss_dssp S-SHHHHHHHHHHTTT-HHHHHHHH
T ss_pred CCCHHHHHHHHHHccCCHHHHHHHH
Confidence 3467889999999999999998754
No 70
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=49.69 E-value=9.7 Score=26.04 Aligned_cols=35 Identities=14% Similarity=0.272 Sum_probs=20.0
Q ss_pred CHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCch
Q 025620 55 DTRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDI 93 (250)
Q Consensus 55 ~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~ 93 (250)
+.+.+.+++. .....+..+-+.++|+.||++|+++
T Consensus 23 s~~tl~~~~~----~~~~~~~~~~l~~ia~~l~~~~~el 57 (63)
T PF13443_consen 23 SRSTLSRILN----GKPSNPSLDTLEKIAKALNCSPEEL 57 (63)
T ss_dssp -HHHHHHHHT----TT-----HHHHHHHHHHHT--HHHC
T ss_pred CHHHHHHHHh----cccccccHHHHHHHHHHcCCCHHHH
Confidence 4455555554 2224688999999999999999875
No 71
>KOG4380 consensus Carnitine deficiency associated protein [General function prediction only]
Probab=48.37 E-value=49 Score=29.15 Aligned_cols=85 Identities=16% Similarity=0.103 Sum_probs=46.9
Q ss_pred hhCCCHHHHHHHHHhCCCCchhhhhhhhccCCCCCcCCHHHHHHHHHHhcCC-CC----Cccc---hHHHHHHHhhcCCC
Q 025620 18 ITGASEKAALQALKASDWHLEGAFDVFYSQPQSKSLTDTRHLEELYNRYKDP-YL----DMIL---VDGITLLCNDLQVD 89 (250)
Q Consensus 18 iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~~~~~~~~~~~l~~lF~~Y~~~-~~----d~i~---~dG~~~~~edLgv~ 89 (250)
+.|+|...|+.|| |..|+..-|.+......--...-++.-+.-.+. +| |.-+ .+|.+.+|.-|||+
T Consensus 71 ~~~~~R~~AID~~------L~~AV~~~Y~~~~~~~~~~~~~~~K~~~~~~~~~~PL~~LD~~~P~F~~~~~AL~~iL~I~ 144 (244)
T KOG4380|consen 71 FKIQDRQEAIDWL------LGLAVRLEYGDNAEKYKDLVPDNSKTADNATKNAEPLINLDVNNPDFKAGVMALANLLQIQ 144 (244)
T ss_pred cccccHHHHHHHH------HHHHHHHHHHhcccchhhhhhhhHHHHHhhhcccCchhhcCCCCccHHHHHHHHHHHhccc
Confidence 4678888888765 788999999876442111111111222222211 11 1222 46999999999998
Q ss_pred C-CchHH-HHHHHhhcccccc
Q 025620 90 P-QDIVM-LVVSWHMKAATMC 108 (250)
Q Consensus 90 ~-ed~~~-LvLa~~l~a~~~g 108 (250)
- .|+.+ +--+-++=+++.|
T Consensus 145 ~H~D~~VmmKA~~i~i~E~L~ 165 (244)
T KOG4380|consen 145 RHDDYLVMLKAIRILVQERLT 165 (244)
T ss_pred cCCCHHHHHHHHHHHHHHHhh
Confidence 6 45533 3333344445544
No 72
>cd00171 Sec7 Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity.
Probab=48.12 E-value=1.7e+02 Score=24.96 Aligned_cols=68 Identities=16% Similarity=0.247 Sum_probs=37.5
Q ss_pred HHHHHHHHHHhcCCCC----CccchHHHHHHHhh---cCC-CCCchHHHHHHHhh-----cccccc-cccHHHHHHHHHH
Q 025620 56 TRHLEELYNRYKDPYL----DMILVDGITLLCND---LQV-DPQDIVMLVVSWHM-----KAATMC-EFSKQEFIGGLQS 121 (250)
Q Consensus 56 ~~~l~~lF~~Y~~~~~----d~i~~dG~~~~~ed---Lgv-~~ed~~~LvLa~~l-----~a~~~g-~~tr~ef~~g~~~ 121 (250)
...|..++.+++-|++ |+|-..=..+||++ ... +++.+-+|+-|-+| ..+.+. .+|+++|++..+.
T Consensus 82 ~~ALR~~l~~f~lpgE~Q~Idrile~Fs~~y~~~Np~~~~~~~d~v~~l~~sllmLnTdlHn~~~~~kmt~~~Fi~~~~~ 161 (185)
T cd00171 82 DEALRKFLQSFRLPGEAQKIDRLLEKFSERYCECNPGIFSSSADAAYTLAYSIIMLNTDLHNPNVKKKMTLEDFIKNLRG 161 (185)
T ss_pred HHHHHHHHHhccCCchHHHHHHHHHHHHHHHHHHCCCCCCCChhHHHHHHHHHHHHhHHhcCcccCCCCCHHHHHHHHhc
Confidence 4566666666665533 12211112255543 222 55655555555544 555544 8899999988876
Q ss_pred cC
Q 025620 122 LG 123 (250)
Q Consensus 122 l~ 123 (250)
..
T Consensus 162 ~~ 163 (185)
T cd00171 162 IN 163 (185)
T ss_pred cc
Confidence 54
No 73
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=47.23 E-value=52 Score=22.28 Aligned_cols=41 Identities=24% Similarity=0.211 Sum_probs=29.8
Q ss_pred hhcccccccccHHHHHHHHHHcCCCC-HHHHHHHHHHHHHHc
Q 025620 101 HMKAATMCEFSKQEFIGGLQSLGIDS-LDKFRERISFMRAEL 141 (250)
Q Consensus 101 ~l~a~~~g~~tr~ef~~g~~~l~~~s-i~~lk~~l~~L~~~l 141 (250)
.+-...-|.|+++|+...++.++... -..++..+..+-+.+
T Consensus 8 ~~D~d~~G~i~~~el~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (66)
T PF13499_consen 8 KFDKDGDGYISKEELRRALKHLGRDMSDEESDEMIDQIFREF 49 (66)
T ss_dssp HHSTTSSSEEEHHHHHHHHHHTTSHSTHHHHHHHHHHHHHHH
T ss_pred HHcCCccCCCCHHHHHHHHHHhcccccHHHHHHHHHHHHHHh
Confidence 44566679999999999999998754 455566655555554
No 74
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=46.49 E-value=24 Score=32.56 Aligned_cols=36 Identities=28% Similarity=0.290 Sum_probs=31.5
Q ss_pred HHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhcc
Q 025620 12 LQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQ 47 (250)
Q Consensus 12 i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~ 47 (250)
++=.+++||+++++|...|.++++++-.||-..-.+
T Consensus 235 ~~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~~~~~ 270 (296)
T PRK12570 235 VRIVMQATGCSEDEAKELLKESDNDVKLAILMILTG 270 (296)
T ss_pred HHHHHHHHCcCHHHHHHHHHHhCCccHHHHHHHHhC
Confidence 555899999999999999999999999999876554
No 75
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=45.33 E-value=50 Score=28.52 Aligned_cols=40 Identities=18% Similarity=0.234 Sum_probs=33.4
Q ss_pred CCCcchHHHHHHHHhhhCCCHHHHHHHHHhCCC-Cchhhhh
Q 025620 3 KLSRSNRDKLQQFVSITGASEKAALQALKASDW-HLEGAFD 42 (250)
Q Consensus 3 ~l~~~q~~~i~~F~~iT~~s~~~A~~~L~~~~w-~le~A~~ 42 (250)
.++..+++.-..++++.|.-++.|...|...+- ++..||.
T Consensus 62 F~~~~Er~lF~~L~~V~GIGpK~Al~iL~~~~~~el~~aI~ 102 (191)
T TIGR00084 62 FNTLEERELFKELIKVNGVGPKLALAILSNMSPEEFVYAIE 102 (191)
T ss_pred CCCHHHHHHHHHHhCCCCCCHHHHHHHHhcCCHHHHHHHHH
Confidence 467888999999999999999999999997665 5555665
No 76
>KOG3911 consensus Nucleolar protein NOP52/RRP1 [RNA processing and modification]
Probab=45.27 E-value=2.4e+02 Score=26.98 Aligned_cols=120 Identities=15% Similarity=0.219 Sum_probs=74.6
Q ss_pred hHHHHHHHhhccccccc-ccHHHHHHHHHHcC-C----CC-H--HHHHHHHHHHHHHc----------------------
Q 025620 93 IVMLVVSWHMKAATMCE-FSKQEFIGGLQSLG-I----DS-L--DKFRERISFMRAEL---------------------- 141 (250)
Q Consensus 93 ~~~LvLa~~l~a~~~g~-~tr~ef~~g~~~l~-~----~s-i--~~lk~~l~~L~~~l---------------------- 141 (250)
-++=+|=-.+.+.+.-+ |++.+|+.-|+.|. | |- + +.|-..|..|....
T Consensus 26 rAlr~Lrkyi~ak~~k~~F~~~dflklWKGLfY~MWmqDkPllQeeLa~~laqLv~~f~~~~a~i~F~~~FwktM~rEW~ 105 (378)
T KOG3911|consen 26 RALRKLRKYISAKTQKEGFDQDDFLKLWKGLFYCMWMQDKPLLQEELADTLAQLVHIFTSTEAQILFVSAFWKTMCREWF 105 (378)
T ss_pred HHHHHHHHHHHHHhhccCCCHHHHHHHHHhhHHHHhhcCCchHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHhhhhc
Confidence 34555666666666654 99999999999975 3 11 0 12223333332211
Q ss_pred -----cchHH---HHHHHHHHHHhhhhcCCccccHHHHHHHHHhhcC-----CC-------CchhHHHHHHHHHhhcCCC
Q 025620 142 -----KDEQK---FREIYNFAFAWAKEKGQKSLALDTAIGMWQLLFA-----EK-------QWPLVDHWCQFLQAKHNKA 201 (250)
Q Consensus 142 -----~~~~~---Fk~~Y~f~F~~~~~~~qk~l~~d~Ai~~W~lll~-----~~-------~~~~l~~w~~Fl~~~~~k~ 201 (250)
+-+.. -+.+-+++|.+.+..+-.. +.--+||+.+.. .. .+.+++-|++=|....+..
T Consensus 106 gIDr~RlDKflmLiRrvlr~~l~~Lk~~~W~~---~li~e~~~~~q~~~~~~~s~~np~Gi~fHf~dI~ldEL~kv~~~e 182 (378)
T KOG3911|consen 106 GIDRLRLDKFLMLIRRVLRASLRVLKERNWEK---DLIDEYLKVLQEWVLSPDSQSNPNGIKFHFADILLDELDKVGGEE 182 (378)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHcCchH---HHHHHHHHHHHHhhcCCCCCCCCCccchhHHHHHHHHHHHhcCCc
Confidence 12222 2677778888887665443 333466666653 11 1346899999998889999
Q ss_pred CCHhhHHHHHH-HHh
Q 025620 202 ISRDTWSQLLE-FAR 215 (250)
Q Consensus 202 IskD~W~~~l~-F~~ 215 (250)
++.|+|+++++ |++
T Consensus 183 ~~~~q~~~~~d~~~~ 197 (378)
T KOG3911|consen 183 LTADQNLLFIDPFCR 197 (378)
T ss_pred chhhhhhcccCHHHH
Confidence 99999999875 444
No 77
>KOG4199 consensus Uncharacterized conserved protein [Function unknown]
Probab=45.23 E-value=1.1e+02 Score=29.58 Aligned_cols=149 Identities=19% Similarity=0.263 Sum_probs=89.5
Q ss_pred HHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhccCCCCCcCCHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCC-
Q 025620 10 DKLQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQPQSKSLTDTRHLEELYNRYKDPYLDMILVDGITLLCNDLQV- 88 (250)
Q Consensus 10 ~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~~~~~~~~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv- 88 (250)
+.+.+|.. .|....|..+|..-+-.+..-+...-...++.-++-.+.|+.+ .+.-+..||-.+.+|+.-...-|..
T Consensus 81 ~ll~~l~d--~ck~~~A~r~la~~~ga~~~~it~~~la~~~~~~~l~ksL~al-~~lt~~qpdl~da~g~~vvv~lL~~~ 157 (461)
T KOG4199|consen 81 ELLEQLAD--ECKKSLAHRVLAGKNGAHDALITLLELAESPNESVLKKSLEAI-NSLTHKQPDLFDAEAMAVVLKLLALK 157 (461)
T ss_pred HHHHHHHH--HHhhhHHHHHHhccCCCcchhhhHHHHhhCCchhHHHHHHHHH-HHhhcCCcchhccccHHHHHHHHhcc
Confidence 45667774 6667778888888887887777666532111112222333333 2233456788888888777765554
Q ss_pred -CCCchHHHHHHHhhcccccccccHHHHHHH-----HH-HcCCCCH-HHHHHHHHHHHHHccchHH----HHHHHHHHHH
Q 025620 89 -DPQDIVMLVVSWHMKAATMCEFSKQEFIGG-----LQ-SLGIDSL-DKFRERISFMRAELKDEQK----FREIYNFAFA 156 (250)
Q Consensus 89 -~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g-----~~-~l~~~si-~~lk~~l~~L~~~l~~~~~----Fk~~Y~f~F~ 156 (250)
+-+|+..+.+.|.-+|-.|-+..|..|++- +. .+.-.+- .-.|.....++.-+. |.+ |-..|.|+=.
T Consensus 158 ~~~~dlt~~~~~~v~~Ac~~hE~nrQ~~m~~~il~Li~~~l~~~gk~~~VRel~~a~r~l~~-dDDiRV~fg~ah~hAr~ 236 (461)
T KOG4199|consen 158 VESEEVTLLTLQWLQKACIMHEVNRQLFMELKILELILQVLNREGKTRTVRELYDAIRALLT-DDDIRVVFGQAHGHART 236 (461)
T ss_pred cchHHHHHHHHHHHHHHHHHhHHHHHHHHHhhHHHHHHHHHcccCccHHHHHHHHHHHHhcC-CCceeeecchhhHHHHH
Confidence 557788889999999999999999999873 11 1111111 223333344444433 333 5666666666
Q ss_pred hhhhcC
Q 025620 157 WAKEKG 162 (250)
Q Consensus 157 ~~~~~~ 162 (250)
++++.+
T Consensus 237 ia~e~~ 242 (461)
T KOG4199|consen 237 IAKEGI 242 (461)
T ss_pred HHHhhh
Confidence 665553
No 78
>COG2922 Smg Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.41 E-value=17 Score=30.45 Aligned_cols=35 Identities=23% Similarity=0.243 Sum_probs=30.7
Q ss_pred HHHHHHHhcCCCCC-ccchHHHHHHHhhcCCCCCch
Q 025620 59 LEELYNRYKDPYLD-MILVDGITLLCNDLQVDPQDI 93 (250)
Q Consensus 59 l~~lF~~Y~~~~~d-~i~~dG~~~~~edLgv~~ed~ 93 (250)
|-=||+.|.+.+.+ .++.|.+..-++|.|.+++|+
T Consensus 5 l~YLfE~y~h~ea~l~vd~d~L~~~L~~aGF~~~dI 40 (157)
T COG2922 5 LMYLFETYIHNEAELPVDQDSLENDLEDAGFDREDI 40 (157)
T ss_pred HHHHHHHHhccCCCCCcCHHHHHhHHHHcCCCHHHH
Confidence 45589999987765 789999999999999999987
No 79
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=44.21 E-value=4.3 Score=28.98 Aligned_cols=58 Identities=10% Similarity=0.269 Sum_probs=33.0
Q ss_pred ccchHHHHHHHhhcCCCCCchHHHHHHHhh--cccccccccHHHHHHHHHHcCCCCHHHHHHH
Q 025620 73 MILVDGITLLCNDLQVDPQDIVMLVVSWHM--KAATMCEFSKQEFIGGLQSLGIDSLDKFRER 133 (250)
Q Consensus 73 ~i~~dG~~~~~edLgv~~ed~~~LvLa~~l--~a~~~g~~tr~ef~~g~~~l~~~si~~lk~~ 133 (250)
....+=+.+++++.|.+|+ ++..++-+.+ +..++..+ +.-++.|...|+.|+++...+
T Consensus 15 ~~e~~~l~~~~~~~~~~~~-~v~~ai~~~~~~~~~~~~Yi--~~Il~~W~~~gi~t~e~~~~~ 74 (77)
T PF07261_consen 15 PSEIEKLEKWIDDYGFSPE-VVNEAIEYALENNKRSFNYI--EKILNNWKQKGIKTVEDAEEY 74 (77)
T ss_dssp HHHHHHHHHHHCCCHHHHH-HHHHHHHHHHHCT--SHHHH--HHHHHHHHHCT--SCCCCT--
T ss_pred HHHHHHHHHHHHHcCCCHH-HHHHHHHHHHHcCCCCHHHH--HHHHHHHHHcCCCCHHHHHHH
Confidence 4556667777777776665 5444444444 33343333 467788999999998766544
No 80
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=44.19 E-value=62 Score=21.61 Aligned_cols=34 Identities=12% Similarity=-0.048 Sum_probs=24.2
Q ss_pred cccccccccHHHHHHHHHHcCCCCHHHHHHHHHHH
Q 025620 103 KAATMCEFSKQEFIGGLQSLGIDSLDKFRERISFM 137 (250)
Q Consensus 103 ~a~~~g~~tr~ef~~g~~~l~~~si~~lk~~l~~L 137 (250)
....-|.|+.+++...+..+|. +.+.++..+..+
T Consensus 9 D~~~~G~i~~~el~~~l~~~g~-~~~~~~~i~~~~ 42 (67)
T cd00052 9 DPDGDGLISGDEARPFLGKSGL-PRSVLAQIWDLA 42 (67)
T ss_pred CCCCCCcCcHHHHHHHHHHcCC-CHHHHHHHHHHh
Confidence 3455689999999999999886 555555554443
No 81
>PLN02230 phosphoinositide phospholipase C 4
Probab=43.76 E-value=62 Score=33.10 Aligned_cols=68 Identities=13% Similarity=0.092 Sum_probs=45.6
Q ss_pred cCCHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCC-----CCchHHHHHHHhhcc-----cccccccHHHHHHHHHH
Q 025620 53 LTDTRHLEELYNRYKDPYLDMILVDGITLLCNDLQVD-----PQDIVMLVVSWHMKA-----ATMCEFSKQEFIGGLQS 121 (250)
Q Consensus 53 ~~~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~-----~ed~~~LvLa~~l~a-----~~~g~~tr~ef~~g~~~ 121 (250)
...+..|..+|.+|.... +.|+.+++.+|+.+-.=. +++..-++..+.-.- ..-+.+|.++|..-+..
T Consensus 25 ~~p~~ei~~lf~~~s~~~-~~mt~~~l~~FL~~~Q~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~F~~yL~s 102 (598)
T PLN02230 25 SGPVADVRDLFEKYADGD-AHMSPEQLQKLMAEEGGGEGETSLEEAERIVDEVLRRKHHIAKFTRRNLTLDDFNYYLFS 102 (598)
T ss_pred CCCcHHHHHHHHHHhCCC-CccCHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHhhccccccccccccCHHHHHHHHcC
Confidence 446789999999998654 689999999999887632 333334443221111 12245999999987754
No 82
>PF05042 Caleosin: Caleosin related protein; InterPro: IPR007736 This family contains plant proteins related to caleosin. Caleosins contain calcium-binding domains and have an oleosin-like association with lipid bodies. Caleosins are present at relatively low levels and are mainly bound to microsomal membrane fractions at the early stages of seed development. As the seeds mature, overall levels of caleosins increased dramatically and they were associated almost exclusively with storage lipid bodies []. The calcium binding domain is probably related to the calcium-binding EF-hands motif IPR002048 from INTERPRO.
Probab=43.29 E-value=85 Score=27.07 Aligned_cols=62 Identities=13% Similarity=0.175 Sum_probs=44.6
Q ss_pred CCHHHHHHHHHHhcCCCCCccchHHHHHHHhh--cCCCC----CchHHHHHHHhhcccccccccHHHH
Q 025620 54 TDTRHLEELYNRYKDPYLDMILVDGITLLCND--LQVDP----QDIVMLVVSWHMKAATMCEFSKQEF 115 (250)
Q Consensus 54 ~~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~ed--Lgv~~----ed~~~LvLa~~l~a~~~g~~tr~ef 115 (250)
-.+.+.+++|.+|+...+|.+...-+.++... .=.|| ....-..+.|.|-.+.-|..+||.-
T Consensus 93 Fvp~kFe~iF~kya~~~~d~LT~~E~~~m~~~nr~~~D~~GW~a~~~EW~~~y~L~~d~dG~l~Ke~i 160 (174)
T PF05042_consen 93 FVPQKFEEIFSKYAKTGPDALTLRELWRMLKGNRNANDPFGWFAAFFEWGALYILAKDKDGFLSKEDI 160 (174)
T ss_pred CCHHHHHHHHHHhCCCCCCCcCHHHHHHHHHhccccCCcchhhhhhhHHHHHHHHHcCcCCcEeHHHH
Confidence 34799999999999877888888888888765 22233 1234456677777778888877754
No 83
>PHA01083 hypothetical protein
Probab=43.04 E-value=25 Score=29.59 Aligned_cols=52 Identities=13% Similarity=0.167 Sum_probs=40.6
Q ss_pred ccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHH---cCCCCHH
Q 025620 73 MILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQS---LGIDSLD 128 (250)
Q Consensus 73 ~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~---l~~~si~ 128 (250)
.|+.+-+.++++-+|+||+.+...+.+..-+.|.. |.-|.+..++ +|..++.
T Consensus 43 ~i~de~A~~LAe~aGiDp~eall~i~aDraetp~~----kalWesIaKKlnglgl~~is 97 (149)
T PHA01083 43 YISDEEAIFLAESAGIDPEIALLGCHADRNENPRA----KAIWESIAKKQNGLGLRTIS 97 (149)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHHHHHhcCCHHH----HHHHHHHHHHHhccchhHHH
Confidence 58888999999999999999999999998888776 4446666655 4555554
No 84
>PF04659 Arch_fla_DE: Archaeal flagella protein ; InterPro: IPR006752 Archaeal flagella are unique motility structures, and the absence of bacterial structural motility genes in the complete genome sequences of flagellated archaeal species has always suggested that archaeal flagellar biogenesis is likely mediated by novel components. FlaD and FlaE, are present in the cell as membrane-associated proteins but are not major components of isolated flagellar filaments. Interestingly, flaD was found to encode two proteins, each translated from a separate ribosome binding site. This group of sequences contain the archaeal flaD and flaE proteins. The conserved region that defines these sequences is found in the N-teminal region of flaE but towards the C-terminal region of flaD [].; GO: 0001539 ciliary or flagellar motility
Probab=42.18 E-value=60 Score=25.37 Aligned_cols=52 Identities=23% Similarity=0.479 Sum_probs=39.1
Q ss_pred HHHHHHHHHhhcC--------------CCCCHhhHHHHHHHHhhhCCCCCCCCcCCCchhhHHHHH
Q 025620 187 VDHWCQFLQAKHN--------------KAISRDTWSQLLEFARTVDPALSNYDAEGAWPYLIDEFV 238 (250)
Q Consensus 187 l~~w~~Fl~~~~~--------------k~IskD~W~~~l~F~~~~~~~ls~YDe~~AWP~liDeFV 238 (250)
+=.|++||-++.+ .-||.+-=.++++|++.++.+-...+....|..-+||=+
T Consensus 21 ~~eWLefLve~~G~~~~~~~L~YY~~igWISe~V~~~L~~~~~G~~~~~~~~~~~~~~~Lt~~DH~ 86 (99)
T PF04659_consen 21 VFEWLEFLVERVGHNNAADALDYYESIGWISEEVREQLLKYLKGFKYDHDDFEWKPSWKLTIDDHI 86 (99)
T ss_pred HHHHHHHHHHHcccccHHHHHHHHHHcCCcCHHHHHHHHHHHhCCCCCccccccCCCCCCCHHHHH
Confidence 4589999977632 689999999999999977554444444778888888743
No 85
>PRK10945 gene expression modulator; Provisional
Probab=41.47 E-value=57 Score=24.14 Aligned_cols=39 Identities=21% Similarity=0.417 Sum_probs=31.0
Q ss_pred cHHHHHHHHHHcCCCCHHHHHHHHHHHHHHccchHHHHHHHH
Q 025620 111 SKQEFIGGLQSLGIDSLDKFRERISFMRAELKDEQKFREIYN 152 (250)
Q Consensus 111 tr~ef~~g~~~l~~~si~~lk~~l~~L~~~l~~~~~Fk~~Y~ 152 (250)
|+.+|+--+++ |.|.+.|-+.+..++..|.+ .++..||.
T Consensus 7 tk~dyL~~fRr--css~eTLEkvie~~~~~L~~-~E~~~f~~ 45 (72)
T PRK10945 7 TKTDYLMRLRR--CQTIDTLERVIEKNKYELSD-DELAVFYS 45 (72)
T ss_pred cHHHHHHHHHh--cCcHHHHHHHHHHhhccCCH-HHHHHHHH
Confidence 88999977666 99999999999999988866 34555554
No 86
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=40.68 E-value=19 Score=29.16 Aligned_cols=37 Identities=24% Similarity=0.489 Sum_probs=23.7
Q ss_pred HHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhccC
Q 025620 12 LQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQP 48 (250)
Q Consensus 12 i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~ 48 (250)
+..+.++.|.+++.+.+++++.||.++.+...+--+|
T Consensus 100 ~~~la~~Lg~~~~el~~~~~~~gW~~d~~~~~~~~~~ 136 (143)
T PF10075_consen 100 LSDLAEMLGLSEEELEKFIKSRGWTVDGDGVLFPPNP 136 (143)
T ss_dssp HHHHHHHTTS-HHHHHHHHHHHT-EE-----EE---H
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCEECCCccEEecCC
Confidence 5678889999999999999999999998776665443
No 87
>cd00252 SPARC_EC SPARC_EC; extracellular Ca2+ binding domain (containing 2 EF-hand motifs) of SPARC and related proteins (QR1, SC1/hevin, testican and tsc-36/FRP). SPARC (BM-40) is a multifunctional glycoprotein, a matricellular protein, that functions to regulate cell-matrix interactions; binds to such proteins as collagen and vitronectin and binds to endothelial cells thus inhibiting cellular proliferation. The EC domain interacts with a follistatin-like (FS) domain which appears to stabilize Ca2+ binding. The two EF-hands interact canonically but their conserved disulfide bonds confer a tight association between the EF-hand pair and an acid/amphiphilic N-terminal helix. Proposed active form involves a Ca2+ dependent symmetric homodimerization of EC-FS modules.
Probab=40.24 E-value=1.5e+02 Score=23.51 Aligned_cols=61 Identities=10% Similarity=0.067 Sum_probs=43.7
Q ss_pred CHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHH
Q 025620 55 DTRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGL 119 (250)
Q Consensus 55 ~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~ 119 (250)
...+|.-.|.++=.+....|+.+=+..++ +.+....+-.+...+-+..=|.||.+||..++
T Consensus 46 ~~~~l~w~F~~lD~d~DG~Ls~~EL~~~~----l~~~e~~~~~f~~~~D~n~Dg~IS~~Ef~~cl 106 (116)
T cd00252 46 CKDPVGWMFNQLDGNYDGKLSHHELAPIR----LDPNEHCIKPFFESCDLDKDGSISLDEWCYCF 106 (116)
T ss_pred HHHHHHHHHHHHCCCCCCcCCHHHHHHHH----ccchHHHHHHHHHHHCCCCCCCCCHHHHHHHH
Confidence 34678889999954444588888888776 44433444445555677788999999999988
No 88
>PRK02264 N(5),N(10)-methenyltetrahydromethanopterin cyclohydrolase; Provisional
Probab=39.28 E-value=6.3 Score=36.91 Aligned_cols=72 Identities=22% Similarity=0.368 Sum_probs=46.3
Q ss_pred HHHHHHHHHhCCCCchhhhhhhhccCCCCCcCCHHHHHHHHHH--hcCC--------CCCccchH-HHHHHHhhcCCCCC
Q 025620 23 EKAALQALKASDWHLEGAFDVFYSQPQSKSLTDTRHLEELYNR--YKDP--------YLDMILVD-GITLLCNDLQVDPQ 91 (250)
Q Consensus 23 ~~~A~~~L~~~~w~le~A~~~f~~~~~~~~~~~~~~l~~lF~~--Y~~~--------~~d~i~~d-G~~~~~edLgv~~e 91 (250)
+..|-=.=+.++|.|.. +.||.-.+++..+-..+ +.+|+. |+|. +.+.+-++ =+.+..++.||+||
T Consensus 85 P~iAcLgSQ~AGW~l~~--~~ffa~GSGPaRAla~k-e~l~~~l~Y~D~~~~avl~lE~~~lP~~~v~e~vA~~cgv~p~ 161 (317)
T PRK02264 85 PALACLGSQKAGWSLSV--GKFFALGSGPARALALK-EELYEELGYRDDADFAVLVLESDKLPPEEVAEKVAEECGVDPE 161 (317)
T ss_pred hHHHHHhccccCccccc--CCEeeecCcHHHHHhhh-hHHHHHhCCccccCeEEEEEecCCCCCHHHHHHHHHHcCCCHH
Confidence 44444444679999984 88998776644444344 788885 4443 12333333 45577899999999
Q ss_pred chHHHH
Q 025620 92 DIVMLV 97 (250)
Q Consensus 92 d~~~Lv 97 (250)
++.+|+
T Consensus 162 ~v~~lv 167 (317)
T PRK02264 162 NVYLLV 167 (317)
T ss_pred HEEEEE
Confidence 986554
No 89
>PF06535 RGM_N: Repulsive guidance molecule (RGM) N-terminus; InterPro: IPR010536 This entry represents the N-terminal region of several mammalian and one bird sequence from Gallus gallus (Chicken). All of the mammalian proteins are hypothetical and have no known function but Q8JG54 from SWISSPROT from the chicken is annotated as being a repulsive guidance molecule (RGM). RGM is a GPI-linked axon guidance molecule of the retinotectal system. RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons are able to receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM is likely to provide positional information for temporal axons invading the optic tectum in the stratum opticum [].
Probab=39.14 E-value=8.7 Score=32.67 Aligned_cols=19 Identities=37% Similarity=0.856 Sum_probs=13.6
Q ss_pred hhhCCCCCCCCcCCCchhh
Q 025620 215 RTVDPALSNYDAEGAWPYL 233 (250)
Q Consensus 215 ~~~~~~ls~YDe~~AWP~l 233 (250)
+++++++.-=-..||||.|
T Consensus 111 RTF~~~fqTC~v~GAWPLI 129 (161)
T PF06535_consen 111 RTFNDEFQTCKVEGAWPLI 129 (161)
T ss_pred hhccCCceeeeeecceeee
Confidence 4556666666689999954
No 90
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=38.90 E-value=39 Score=31.29 Aligned_cols=37 Identities=16% Similarity=0.183 Sum_probs=32.6
Q ss_pred HHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhcc
Q 025620 11 KLQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQ 47 (250)
Q Consensus 11 ~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~ 47 (250)
.++=.+++|||+.++|.+.|+.++-++-.||=.....
T Consensus 236 a~RIv~~aT~~~~~~A~~~L~~~~~~vK~AIvm~~~~ 272 (298)
T COG2103 236 AVRIVMEATGCSAEEAEALLEEAGGNVKLAIVMLLTG 272 (298)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCccHhHHHHHHhC
Confidence 4677899999999999999999999999998777655
No 91
>PLN02223 phosphoinositide phospholipase C
Probab=38.83 E-value=66 Score=32.48 Aligned_cols=68 Identities=6% Similarity=-0.073 Sum_probs=45.4
Q ss_pred cCCHHHHHHHHHHhcCCCCCccchHHHHHHHhhc-------CCCCCchHHHHHHHhh------cccccccccHHHHHHHH
Q 025620 53 LTDTRHLEELYNRYKDPYLDMILVDGITLLCNDL-------QVDPQDIVMLVVSWHM------KAATMCEFSKQEFIGGL 119 (250)
Q Consensus 53 ~~~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edL-------gv~~ed~~~LvLa~~l------~a~~~g~~tr~ef~~g~ 119 (250)
...+..+.++|++|.+ +.+.|+.+++.+|+.=| +...++...++=...- +...-+.++.++|..-+
T Consensus 12 ~~~p~~v~~~f~~~~~-~~~~m~~~~l~~fl~~l~~~q~e~~~~~~~a~~i~~~~~~~~~~~~~~~~~~~l~~~~f~~~L 90 (537)
T PLN02223 12 ANQPDLILNFFGNEFH-GYDDDMPELLPRFIELLDTEKDEDGAGLNAAEKIAAELKRRKCDILAFRNLRCLELDHLNEFL 90 (537)
T ss_pred CCCcHHHHHHHHHhhc-CCCCCCHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHhhcccchhhhhccccCHHHHHHHh
Confidence 4467899999999974 34689999999999433 5556666555444221 11222457888888877
Q ss_pred HH
Q 025620 120 QS 121 (250)
Q Consensus 120 ~~ 121 (250)
..
T Consensus 91 ~s 92 (537)
T PLN02223 91 FS 92 (537)
T ss_pred cC
Confidence 55
No 92
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=37.86 E-value=43 Score=31.21 Aligned_cols=40 Identities=18% Similarity=0.207 Sum_probs=35.4
Q ss_pred HHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhccC
Q 025620 9 RDKLQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQP 48 (250)
Q Consensus 9 ~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~ 48 (250)
-++|.+.++.||+.=-.+.+.|..++.|+|.|++--=..+
T Consensus 6 a~~VKeLRe~TgAGMmdCKkAL~E~~Gd~EkAie~LR~kG 45 (296)
T COG0264 6 AALVKELREKTGAGMMDCKKALEEANGDIEKAIEWLREKG 45 (296)
T ss_pred HHHHHHHHHHhCCcHHHHHHHHHHcCCCHHHHHHHHHHhc
Confidence 4679999999999999999999999999999998665543
No 93
>smart00222 Sec7 Sec7 domain. Domain named after the S. cerevisiae SEC7 gene product, which is required for proper protein transport through the Golgi. The domain facilitates guanine nucleotide exchange on the small GTPases, ARFs (ADP ribosylation factors).
Probab=37.00 E-value=2.6e+02 Score=23.73 Aligned_cols=38 Identities=13% Similarity=0.123 Sum_probs=26.6
Q ss_pred HHHHHHHHhhhCCCHHHHHHHHHhCCCCc---hhhhhhhhc
Q 025620 9 RDKLQQFVSITGASEKAALQALKASDWHL---EGAFDVFYS 46 (250)
Q Consensus 9 ~~~i~~F~~iT~~s~~~A~~~L~~~~w~l---e~A~~~f~~ 46 (250)
+..+.+++...+-++..++.||.+++--- ..+|..|+.
T Consensus 3 k~~~~~~~~~Fn~~p~~gi~~l~~~~~~~~~~~~~ia~fl~ 43 (187)
T smart00222 3 KKLLSEGSVKFNDKPKKGIDSLQEKGFLAKDDPQDVADFLS 43 (187)
T ss_pred hHHHHHHHHHHccCHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 45678888888888888888888877322 245555553
No 94
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=36.75 E-value=1.8e+02 Score=22.39 Aligned_cols=66 Identities=12% Similarity=-0.010 Sum_probs=39.2
Q ss_pred HHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhccCCCCCcCCHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCC
Q 025620 12 LQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQPQSKSLTDTRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQ 91 (250)
Q Consensus 12 i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~~~~~~~~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~e 91 (250)
|.++..++|+|..+-+.|=+ .+ -+.. +.+ .. + .|+.=+++.+..=..++.+.++|++++
T Consensus 3 i~e~a~~~gvs~~tlr~ye~-~g-ll~~--------~~r-~~-~---------gyR~Y~~~~l~~l~~I~~lr~~G~sL~ 61 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYEK-EG-LLPP--------VKR-DE-N---------GIRDFTEEDLEWLEFIKCLRNTGMSIK 61 (113)
T ss_pred HHHHHHHHCcCHHHHHHHHH-CC-CCCC--------CCc-CC-C---------CCccCCHHHHHHHHHHHHHHHcCCCHH
Confidence 78999999999998887743 33 1211 111 00 0 022111222333456788899999999
Q ss_pred chHHHHH
Q 025620 92 DIVMLVV 98 (250)
Q Consensus 92 d~~~LvL 98 (250)
++.-+.-
T Consensus 62 eI~~~l~ 68 (113)
T cd01109 62 DIKEYAE 68 (113)
T ss_pred HHHHHHH
Confidence 9876543
No 95
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=36.27 E-value=34 Score=24.86 Aligned_cols=38 Identities=18% Similarity=0.202 Sum_probs=29.3
Q ss_pred HHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchH
Q 025620 57 RHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIV 94 (250)
Q Consensus 57 ~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~ 94 (250)
+-|-.+|-.|--+.++.|..-+++.+++.+||++..+.
T Consensus 4 Sli~tl~Gdy~~~~g~~i~~~~Li~ll~~~Gv~e~avR 41 (70)
T PF07848_consen 4 SLIVTLLGDYLRPRGGWIWVASLIRLLAAFGVSESAVR 41 (70)
T ss_dssp HHHHHHHHHHCCTTTS-EEHHHHHHHHCCTT--HHHHH
T ss_pred eehHHHHHHHhccCCCceeHHHHHHHHHHcCCChHHHH
Confidence 45778888898877778999999999999999987653
No 96
>PRK03980 flap endonuclease-1; Provisional
Probab=36.21 E-value=64 Score=29.75 Aligned_cols=75 Identities=16% Similarity=0.280 Sum_probs=51.2
Q ss_pred HHHHHHHhhhCC---------CHHHHHHHHHhCCCCchhhhhhhhccCCCCCcCCHHHHHHHHHHhcCCCC--------C
Q 025620 10 DKLQQFVSITGA---------SEKAALQALKASDWHLEGAFDVFYSQPQSKSLTDTRHLEELYNRYKDPYL--------D 72 (250)
Q Consensus 10 ~~i~~F~~iT~~---------s~~~A~~~L~~~~w~le~A~~~f~~~~~~~~~~~~~~l~~lF~~Y~~~~~--------d 72 (250)
+.+-.|+-++|| -+++|.+++++++ +|+..++..-. ...+-..+.++|- +|+. .
T Consensus 177 ~q~id~~iL~G~Dy~~GI~GIG~ktA~kLi~~~~-sle~i~~~~~~-----~~~~~~~~r~~f~---~p~v~~~~~~~~~ 247 (292)
T PRK03980 177 EQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHG-DLEKVLEERGF-----EIENYDEIREFFL---NPPVTDDYELKWK 247 (292)
T ss_pred HHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHCC-CHHHHHHhccC-----CCCCHHHHHHHhc---CCCCCCCCCccCC
Confidence 445667777765 5899999999999 88888773221 1123355666653 3321 2
Q ss_pred ccchHHHHHHH-hhcCCCCCch
Q 025620 73 MILVDGITLLC-NDLQVDPQDI 93 (250)
Q Consensus 73 ~i~~dG~~~~~-edLgv~~ed~ 93 (250)
..+.||+.+|+ +..|.+++-+
T Consensus 248 ~pd~~~l~~fl~~e~~f~~~rv 269 (292)
T PRK03980 248 EPDKEGIIEFLVEEHDFSEERV 269 (292)
T ss_pred CCCHHHHHHHHhccCCCCHHHH
Confidence 68899999976 7899988755
No 97
>PF09036 Bcr-Abl_Oligo: Bcr-Abl oncoprotein oligomerisation domain; InterPro: IPR015123 This entry represents the oligomerisation domain of the breakpoint cluster region oncoprotein Bcr, and the Bcr/Abl (Abelson-leukemia-virus) fusion protein created by a reciprocal (9;22) fusion []. Brc displays serine/threonine protein kinase activity (2.7.11.1 from EC), acting as a GTPase-activating protein for RAC1 and CDC42. Brc promotes the exchange of RAC or CDC42-bound GDP by GTP, thereby activating them []. The Bcr/Abl fusion protein loses some of the regulatory function of Bcr with regards to small Rho-like GTPases with negative consequences on cell motility, in particular on the capacity to adhere to endothelial cells []. The Bcr, Bcr/Abl oncoprotein oligomerisation domain consists of a short N-terminal helix (alpha-1), a flexible loop and a long C-terminal helix (alpha-2). Together these form an N-shaped structure, with the loop allowing the two helices to assume a parallel orientation. The monomeric domains associate into a dimer through the formation of an antiparallel coiled coil between the alpha-2 helices and domain swapping of two alpha-1 helices, where one alpha-1 helix swings back and packs against the alpha-2 helix from the second monomer. Two dimers then associate into a tetramer. The oligomerisation domain is essential for the oncogenicity of the Bcr-Abl protein []. ; GO: 0004674 protein serine/threonine kinase activity, 0005096 GTPase activator activity, 0006468 protein phosphorylation, 0007165 signal transduction; PDB: 1K1F_C.
Probab=36.01 E-value=99 Score=23.09 Aligned_cols=42 Identities=17% Similarity=0.415 Sum_probs=23.3
Q ss_pred HHHHHHHHH---------cCCCCHHHHHHHH-------HHHHHHccchHHHHHHHHHHH
Q 025620 113 QEFIGGLQS---------LGIDSLDKFRERI-------SFMRAELKDEQKFREIYNFAF 155 (250)
Q Consensus 113 ~ef~~g~~~---------l~~~si~~lk~~l-------~~L~~~l~~~~~Fk~~Y~f~F 155 (250)
.+|++.|++ +.|.|+.+|-..| ..|.+++ +.+.|+-||--|-
T Consensus 5 ~~f~~~w~aqfp~~~~p~m~l~svgd~e~eLerCK~sirrLeqev-nkERFrmiYLQTl 62 (79)
T PF09036_consen 5 VGFAEAWRAQFPDSEPPVMELRSVGDIEQELERCKASIRRLEQEV-NKERFRMIYLQTL 62 (79)
T ss_dssp HHHHHHHHHHSTTS-------SSHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCccCCcHHHHHHhccHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Confidence 355555555 3466776665444 4455554 3345999997663
No 98
>PF06992 Phage_lambda_P: Replication protein P; InterPro: IPR009731 This family consists of several Bacteriophage lambda replication protein P like proteins. The bacteriophage lambda P protein promoters replication of the phage chromosome by recruiting a key component of the cellular replication machinery to the viral origin. Specifically, P protein delivers one or more molecules of Escherichia coli DnaB helicase to a nucleoprotein structure formed by the lambda O initiator at the lambda replication origin [].; GO: 0006270 DNA-dependent DNA replication initiation
Probab=35.10 E-value=1.3e+02 Score=27.25 Aligned_cols=30 Identities=23% Similarity=0.469 Sum_probs=26.5
Q ss_pred cHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 025620 111 SKQEFIGGLQSLGIDSLDKFRERISFMRAE 140 (250)
Q Consensus 111 tr~ef~~g~~~l~~~si~~lk~~l~~L~~~ 140 (250)
.|.+|+.++.+.||.|+++++.-|...|+.
T Consensus 66 aKr~Wi~~f~engI~t~eQv~~Gm~~aR~~ 95 (233)
T PF06992_consen 66 AKRQWIKAFAENGITTMEQVRAGMRRARAS 95 (233)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHHHHHhc
Confidence 488999999999999999999888887765
No 99
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=34.97 E-value=80 Score=21.88 Aligned_cols=53 Identities=13% Similarity=0.114 Sum_probs=37.8
Q ss_pred CCchHHHHHHHhhcccccccccHHHHHHH-HHHcC-CCCHHHHHHHHHHHHHHccc
Q 025620 90 PQDIVMLVVSWHMKAATMCEFSKQEFIGG-LQSLG-IDSLDKFRERISFMRAELKD 143 (250)
Q Consensus 90 ~ed~~~LvLa~~l~a~~~g~~tr~ef~~g-~~~l~-~~si~~lk~~l~~L~~~l~~ 143 (250)
+.....-+|++++..+.. .+|+++..+- |..-. ..+...++..|..||+.|.+
T Consensus 6 Lt~~e~~lL~~L~~~~~~-~vs~~~l~~~lw~~~~~~~~~~~l~~~i~~LR~~l~~ 60 (78)
T smart00862 6 LTPKEFRLLELLLRNPGR-VVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLED 60 (78)
T ss_pred cCHHHHHHHHHHHhCCCC-ccCHHHHHHHHcCCCCCCCccchHHHHHHHHHHHHhc
Confidence 344455678888877655 8999999986 54322 34567799999999988853
No 100
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=34.49 E-value=1.4e+02 Score=25.15 Aligned_cols=54 Identities=20% Similarity=0.316 Sum_probs=42.9
Q ss_pred ccchHHHHHHHhhcCCCCCch--HHHHHHHhhcccccccccHHHHHHHHHHcCCCC
Q 025620 73 MILVDGITLLCNDLQVDPQDI--VMLVVSWHMKAATMCEFSKQEFIGGLQSLGIDS 126 (250)
Q Consensus 73 ~i~~dG~~~~~edLgv~~ed~--~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~~~s 126 (250)
.++.+-+.++..|+|++..++ ++=+|.+++....--.++.+.|.+-+..+|.+.
T Consensus 21 ~~~~~~~~kl~~~~~~~~~~lk~~va~l~fiL~~A~k~n~~~~~l~~eL~~lglp~ 76 (174)
T cd04752 21 GIDYEKVLKLTADAKFESGDVKASIAVLSFILSSAAKYNVDGESLSSELQQLGLPK 76 (174)
T ss_pred cCCHHHHHHHHHHhCCCHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCH
Confidence 488999999999999999887 455677778433333599999999999998754
No 101
>PF07531 TAFH: NHR1 homology to TAF; InterPro: IPR003894 The TAF homology (TAFH) or Nervy homology region 1 (NHR1) domain is a domain of 95-100 amino acids present in eukaryotic proteins of the MTG/ETO family and whereof the core ~75-80 residues occur in TAF proteins. The transcription initiation TFIID complex is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). The TAFH/NHR1 domain is named after fruit fly TATA-box-associated factor 110 (TAF110), human TAF105 and TAF130, and the fruit fly protein Nervy, which is a homologue of human MTG8/ETO [, ]. The human eight twenty-one (ETO or MTG8) and related myeloid transforming gene products MTGR1 and MTG16 as well as the Nervy protein contain the NHR1-4 domains. The NHR1/TAFH domain occurs in the N-terminal part of these proteins, while a MYND-type zinc finger forms the NHR4 domain []. The TAFH/NHR1 domain can be involved in protein-protein interactions, e.g in MTG8/ETO with HSP90 and Gfi-1 []. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2P6V_A 2KNH_A 2PP4_A 2H7B_A.
Probab=34.22 E-value=65 Score=25.13 Aligned_cols=64 Identities=20% Similarity=0.274 Sum_probs=43.6
Q ss_pred HHHHHHhhcCCCCC---chHHHHHHHhhcccccccccHHHHHHHHHHcCC-----CCHHHHHHHHHHHHHHccchHHH
Q 025620 78 GITLLCNDLQVDPQ---DIVMLVVSWHMKAATMCEFSKQEFIGGLQSLGI-----DSLDKFRERISFMRAELKDEQKF 147 (250)
Q Consensus 78 G~~~~~edLgv~~e---d~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~~-----~si~~lk~~l~~L~~~l~~~~~F 147 (250)
-+++|+.+ .++|| .+..||.+-. -|.|+-|||...++..== .-++=||+.||.||+++.+...|
T Consensus 12 tLi~las~-~~spev~~~Vr~LV~~L~-----~~~i~~EeF~~~Lq~~lns~pqP~lvPFLK~~lp~Lr~~l~~~~~~ 83 (96)
T PF07531_consen 12 TLIQLASD-KQSPEVGENVRELVQNLV-----DGKIEAEEFTSKLQEELNSSPQPYLVPFLKKSLPALRQELPNCARF 83 (96)
T ss_dssp HHHHHHCC-SC-CCHHHHHHHHHHHHH-----TTSS-HHHHHHHHHHHCTSS--TTHHHHHHHHHHHHHHCHCHHHHH
T ss_pred HHHHHhcC-CCChHHHHHHHHHHHHHH-----cCCCCHHHHHHHHHHHhcCCCCcchHHHHHHhHHHHHHHHHHHHHH
Confidence 35677777 56664 3455555432 468999999999987422 33577999999999998776654
No 102
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=33.25 E-value=1e+02 Score=26.47 Aligned_cols=62 Identities=19% Similarity=0.241 Sum_probs=38.3
Q ss_pred CcchHHHHHHHHhhhCCCHHHHHHHHHhCCCC-chhhhhhhhccC---CCCCcCCHHHHHHHHHHhcC
Q 025620 5 SRSNRDKLQQFVSITGASEKAALQALKASDWH-LEGAFDVFYSQP---QSKSLTDTRHLEELYNRYKD 68 (250)
Q Consensus 5 ~~~q~~~i~~F~~iT~~s~~~A~~~L~~~~w~-le~A~~~f~~~~---~~~~~~~~~~l~~lF~~Y~~ 68 (250)
+...++....+.++-|.-+++|...|+..+-+ +..|+.. .++ ..-+...++..+++...+++
T Consensus 65 ~~~ek~~f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~--~d~~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 65 TKEERELFRLLISVSGVGPKLALAILSGLSPEELVQAIAN--GDVKALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHh--CCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 44556667788999999999999999987731 2222221 111 11233456666666666664
No 103
>TIGR03120 one_C_mch methenyltetrahydromethanopterin cyclohydrolase. Members of this protein family are the enzyme methenyltetrahydromethanopterin cyclohydrolase, a key enzyme for tetrahydromethanopterin (H4MPT)-linked C1 transfer metabolism.
Probab=33.09 E-value=7.3 Score=36.42 Aligned_cols=73 Identities=15% Similarity=0.297 Sum_probs=44.3
Q ss_pred HHHHHHHHHhCCCCchhhhhhhhccCCCCCcCCHHHHHHHHHHh--cCC--------CCCccchH-HHHHHHhhcCCCCC
Q 025620 23 EKAALQALKASDWHLEGAFDVFYSQPQSKSLTDTRHLEELYNRY--KDP--------YLDMILVD-GITLLCNDLQVDPQ 91 (250)
Q Consensus 23 ~~~A~~~L~~~~w~le~A~~~f~~~~~~~~~~~~~~l~~lF~~Y--~~~--------~~d~i~~d-G~~~~~edLgv~~e 91 (250)
+..|-=.=+.++|.|. .+.||.-.+++..+-..+=+++|+++ +|. +.+.+-++ =+.+..++.||+|+
T Consensus 83 P~iAcLgSQ~AGW~l~--~~~ffamGSGPaRAla~kpe~ly~~l~Y~d~~~~avl~lE~~~lP~~~v~~~vA~~cgv~p~ 160 (312)
T TIGR03120 83 PVIACLGSQKAGWQVK--VGKYFAMGSGPARALALKPKETYEEIGYEDDSDVAVIVLESDKLPDEEVAEYIADECGVDPE 160 (312)
T ss_pred HHHHHhhccccCcccc--cCCEeEecCchHHHhhcCcHHHHHHhCCcccCceEEEEEecCCCCCHHHHHHHHHHcCCCHH
Confidence 4334333466999998 88899876653322211115677765 443 12333333 45677899999999
Q ss_pred chHHHH
Q 025620 92 DIVMLV 97 (250)
Q Consensus 92 d~~~Lv 97 (250)
++.+|+
T Consensus 161 ~l~~lv 166 (312)
T TIGR03120 161 NLTLLV 166 (312)
T ss_pred HEEEEE
Confidence 986654
No 104
>PF03793 PASTA: PASTA domain; InterPro: IPR005543 The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (P71584 from SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan. PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [].; GO: 0008658 penicillin binding; PDB: 2ZC3_C 1QME_A 1RP5_B 2Z2M_C 2Z2L_F 2ZC4_C 1QMF_A 3M9G_A 3PY9_A 1K25_B ....
Probab=32.97 E-value=30 Score=23.57 Aligned_cols=23 Identities=17% Similarity=0.225 Sum_probs=18.7
Q ss_pred hhhCCCHHHHHHHHHhCCCCchh
Q 025620 17 SITGASEKAALQALKASDWHLEG 39 (250)
Q Consensus 17 ~iT~~s~~~A~~~L~~~~w~le~ 39 (250)
+++|.+...|...|++++|.+..
T Consensus 5 d~~g~~~~~a~~~l~~~g~~~~~ 27 (63)
T PF03793_consen 5 DLVGMTYDEAKSILEAAGLTVNV 27 (63)
T ss_dssp TTTTSBHHHHHHHHHHTT-EEEE
T ss_pred CcCCCcHHHHHHHHHHCCCEEEE
Confidence 57899999999999999995443
No 105
>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=32.58 E-value=1.1e+02 Score=23.91 Aligned_cols=63 Identities=10% Similarity=0.187 Sum_probs=47.4
Q ss_pred HHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhh-cccccccccHHHHHHHHHHc
Q 025620 56 TRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHM-KAATMCEFSKQEFIGGLQSL 122 (250)
Q Consensus 56 ~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l-~a~~~g~~tr~ef~~g~~~l 122 (250)
...-.++|+... +..+.|+.+.+..++..-|++.+.+.. -|-| -...-|..+++||+-+|+=.
T Consensus 9 ~~~y~~~F~~l~-~~~g~isg~~a~~~f~~S~L~~~~L~~---IW~LaD~~~dG~L~~~EF~iAm~Li 72 (104)
T PF12763_consen 9 KQKYDQIFQSLD-PQDGKISGDQAREFFMKSGLPRDVLAQ---IWNLADIDNDGKLDFEEFAIAMHLI 72 (104)
T ss_dssp HHHHHHHHHCTS-SSTTEEEHHHHHHHHHHTTSSHHHHHH---HHHHH-SSSSSEEEHHHHHHHHHHH
T ss_pred HHHHHHHHHhcC-CCCCeEeHHHHHHHHHHcCCCHHHHHH---HHhhhcCCCCCcCCHHHHHHHHHHH
Confidence 466778998764 455689999999999999998765432 2333 45677999999999998864
No 106
>cd00545 MCH Methenyltetrahydromethanopterin (methenyl-H4MPT) cyclohydrolase (MCH). MCH is a cytoplasmic enzyme that has been identified in methanogenic archaea, sulfate- reducing archaea, and methylotrophic bacteria. It catalyzes the reversible formation of N(5), N(10)-methenyltetrahydromethanopterin (methenyl-H4MPT+) from N(5)-formyltetrahydromethanopterin (formyl- H4MPT), in the third step of the reaction to reduce CO2 to CH4. The protein functions as a homodimer or homotrimer, depending on the organism.
Probab=31.67 E-value=7.7 Score=36.27 Aligned_cols=70 Identities=20% Similarity=0.378 Sum_probs=43.5
Q ss_pred HHHHH--HhCCCCchhhhhhhhccCCCCCcCCHHHHHHHHHHh--cCC--------CCCccch-HHHHHHHhhcCCCCCc
Q 025620 26 ALQAL--KASDWHLEGAFDVFYSQPQSKSLTDTRHLEELYNRY--KDP--------YLDMILV-DGITLLCNDLQVDPQD 92 (250)
Q Consensus 26 A~~~L--~~~~w~le~A~~~f~~~~~~~~~~~~~~l~~lF~~Y--~~~--------~~d~i~~-dG~~~~~edLgv~~ed 92 (250)
|+.+| +.++|.|. .+.||.-.+++..+-..+=+.+|+++ +|. +.+.+-+ +=+.+..++.||+|++
T Consensus 84 ~iAcLgSQ~AGW~l~--~~~ffamGSGPaRAla~kpe~ly~~l~Y~D~~~~avl~lE~~~lP~~~v~~~vA~~cgv~p~~ 161 (312)
T cd00545 84 VIACLGSQYAGWSLS--VGDFFALGSGPARALALKPEELYEEIGYRDDAEVAVLVLESDKLPPEEVAEKVAAECGVDPEN 161 (312)
T ss_pred HHHHhcccccCcccc--cCCEeEecCchHHHhhcCcHHHHHHhCCccccceEEEEEecCCCCCHHHHHHHHHHcCCCHHH
Confidence 44455 66999998 78899876653322211125677765 443 1233333 3456778999999999
Q ss_pred hHHHH
Q 025620 93 IVMLV 97 (250)
Q Consensus 93 ~~~Lv 97 (250)
+.+|+
T Consensus 162 l~~lv 166 (312)
T cd00545 162 VTLIV 166 (312)
T ss_pred EEEEE
Confidence 86654
No 107
>PF01023 S_100: S-100/ICaBP type calcium binding domain; InterPro: IPR013787 The calcium-binding domain found in S100 and CaBP-9k proteins is a subfamily of the EF-hand calcium-binding domain []. S100s are small dimeric acidic calcium and zinc-binding proteins abundant in the brain, with S100B playing an important role in modulating the proliferation and differentiation of neurons and glia cells []. S100 proteins have two different types of calcium-binding sites: a low affinity one with a special structure, and a 'normal' EF-hand type high-affinity site. Calbindin-D9k (CaBP-9k) also belong to this family of proteins, but it does not form dimers. CaBP-9k is a cytosolic protein expressed in a variety of tissues. Although its precise function is unknown, it appears to be under the control of the steroid hormones oestrogen and progesterone in the female reproductive system []. In the intestine, CaBP-9k may be involved in calcium absorption by mediating intracellular diffusion []. This entry represents a subdomain of the calcium-binding domain found in S100, CaBP-9k, and related proteins.; PDB: 2RGI_A 4DUQ_B 2KAY_B 2KAX_A 2CNP_A 1CNP_A 1A03_A 1JWD_B 2JTT_A 1XK4_B ....
Probab=31.21 E-value=75 Score=20.89 Aligned_cols=28 Identities=11% Similarity=0.263 Sum_probs=21.7
Q ss_pred HHHHHHHHHhcCC--CCCccchHHHHHHHh
Q 025620 57 RHLEELYNRYKDP--YLDMILVDGITLLCN 84 (250)
Q Consensus 57 ~~l~~lF~~Y~~~--~~d~i~~dG~~~~~e 84 (250)
..|..+|.+|+.. +.+.+.-..+-++++
T Consensus 6 ~~iI~vFhkYa~~~Gd~~~Lsk~Elk~Ll~ 35 (44)
T PF01023_consen 6 ETIIDVFHKYAGKEGDKDTLSKKELKELLE 35 (44)
T ss_dssp HHHHHHHHHHHTSSSSTTSEEHHHHHHHHH
T ss_pred HHHHHHHHHHhccCCCCCeEcHHHHHHHHH
Confidence 4678899999944 456888888887775
No 108
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=30.37 E-value=1.1e+02 Score=21.31 Aligned_cols=42 Identities=14% Similarity=0.256 Sum_probs=34.4
Q ss_pred CCCcchHHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhh
Q 025620 3 KLSRSNRDKLQQFVSITGASEKAALQALKASDWHLEGAFDVFY 45 (250)
Q Consensus 3 ~l~~~q~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~ 45 (250)
+++..+.-.|+-++.-.|+|+++.+...++.| +--.+|..|.
T Consensus 14 ~I~~~e~~ev~ywa~~~gvt~~~L~~AV~~vG-~~~~~V~~~L 55 (57)
T PF12244_consen 14 RIDLSEPYEVRYWAKRFGVTEEQLREAVRAVG-NSRAAVRAYL 55 (57)
T ss_pred hcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHC-cCHHHHHHHH
Confidence 45566778899999999999999999999999 5566666664
No 109
>PRK13749 transcriptional regulator MerD; Provisional
Probab=28.37 E-value=2.3e+02 Score=22.78 Aligned_cols=69 Identities=7% Similarity=-0.065 Sum_probs=41.1
Q ss_pred HHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhccCCCCCcCCHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCC
Q 025620 11 KLQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQPQSKSLTDTRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDP 90 (250)
Q Consensus 11 ~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~~~~~~~~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ 90 (250)
.|.++...||+|..+=+.|=+. | ....+.+..+. |+-=+++.+.-=.+++.|.++|+++
T Consensus 5 tIgelA~~~gvS~~tiR~YE~~-G---------Ll~p~~r~~~g-----------yR~Y~~~~l~rL~~I~~~r~~G~sL 63 (121)
T PRK13749 5 TVSRLALDAGVSVHIVRDYLLR-G---------LLRPVACTTGG-----------YGLFDDAALQRLCFVRAAFEAGIGL 63 (121)
T ss_pred cHHHHHHHHCCCHHHHHHHHHC-C---------CCCCCCcCCCC-----------CccCCHHHHHHHHHHHHHHHcCCCH
Confidence 3889999999998876655443 3 11111110011 1211112233336788899999999
Q ss_pred CchHHHHHHH
Q 025620 91 QDIVMLVVSW 100 (250)
Q Consensus 91 ed~~~LvLa~ 100 (250)
+++.-|+-++
T Consensus 64 ~eI~~ll~l~ 73 (121)
T PRK13749 64 DALARLCRAL 73 (121)
T ss_pred HHHHHHHhhh
Confidence 9997776665
No 110
>COG3710 CadC DNA-binding winged-HTH domains [Transcription]
Probab=28.18 E-value=60 Score=26.92 Aligned_cols=69 Identities=14% Similarity=0.139 Sum_probs=47.2
Q ss_pred cCCCCCchHHHHHHHhhcccccc-cccHHHHHH-HHHHcCCCCHHHHHHHHHHHHHHccchH---H-HHHHHHHHHHh
Q 025620 86 LQVDPQDIVMLVVSWHMKAATMC-EFSKQEFIG-GLQSLGIDSLDKFRERISFMRAELKDEQ---K-FREIYNFAFAW 157 (250)
Q Consensus 86 Lgv~~ed~~~LvLa~~l~a~~~g-~~tr~ef~~-g~~~l~~~si~~lk~~l~~L~~~l~~~~---~-Fk~~Y~f~F~~ 157 (250)
--|..+-.+.-||..+++ ..| .++|+++++ -|..-.+..- .|...|..||+.|.+.. . ++.|++=-|.|
T Consensus 28 ~~v~l~~~~~~lL~~L~e--~~geVvsk~eL~~~VW~~~~v~~~-~Ltq~I~~LRr~L~d~~~~~~~I~TvPrrGyk~ 102 (148)
T COG3710 28 EVVKLGPRELKLLSLLLE--RAGEVVSKDELLDAVWPGRIVTVN-TLTQAISALRRALRDIGDGHRLIATVPRRGYKF 102 (148)
T ss_pred eEEEecHHHHHHHHHHHh--ccCceecHHHHHHHhCCCceEccC-hHHHHHHHHHHHHhccCCcceEEEEeCCcceEE
Confidence 345556677888888888 444 899999999 5777655433 39999999999986533 2 45554433333
No 111
>PLN02964 phosphatidylserine decarboxylase
Probab=28.11 E-value=2.5e+02 Score=29.03 Aligned_cols=63 Identities=5% Similarity=-0.207 Sum_probs=47.6
Q ss_pred HHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHH
Q 025620 59 LEELYNRYKDPYLDMILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQS 121 (250)
Q Consensus 59 l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~ 121 (250)
+.++|..+-.++++.|+.+=+..++..+|-.+.+-.+.-+--.+.-..-|.||.+|+.+.|+.
T Consensus 181 i~~mf~~~D~DgdG~IdfdEFl~lL~~lg~~~seEEL~eaFk~fDkDgdG~Is~dEL~~vL~~ 243 (644)
T PLN02964 181 ARRILAIVDYDEDGQLSFSEFSDLIKAFGNLVAANKKEELFKAADLNGDGVVTIDELAALLAL 243 (644)
T ss_pred HHHHHHHhCCCCCCeEcHHHHHHHHHHhccCCCHHHHHHHHHHhCCCCCCcCCHHHHHHHHHh
Confidence 789999875444568999999999999985443334444444556666799999999999988
No 112
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=27.56 E-value=1e+02 Score=21.34 Aligned_cols=50 Identities=20% Similarity=0.181 Sum_probs=36.1
Q ss_pred hHHHHHHHhhcccccccccHHHHHHHHHHcCC-CCHHHHHHHHHHHHHHccc
Q 025620 93 IVMLVVSWHMKAATMCEFSKQEFIGGLQSLGI-DSLDKFRERISFMRAELKD 143 (250)
Q Consensus 93 ~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~~-~si~~lk~~l~~L~~~l~~ 143 (250)
.+.-+|+.++..+.- .+||++..+..-.-.. .+-..|+..|..||+.|..
T Consensus 9 ~e~~lL~~L~~~~~~-~vs~~~l~~~~w~~~~~~~~~~l~~~I~rLR~kL~~ 59 (77)
T PF00486_consen 9 KEFRLLELLLRNPGR-VVSREELIEALWGDEEDVSDNSLDVHISRLRKKLED 59 (77)
T ss_dssp HHHHHHHHHHHTTTS-EEEHHHHHHHHTSSSSTTCTHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHhCCCC-CCCHHHhCChhhhcccccchhhHHHHHHHHHHHHhh
Confidence 345566666655432 7999999986544444 6778899999999999854
No 113
>KOG1575 consensus Voltage-gated shaker-like K+ channel, subunit beta/KCNAB [Energy production and conversion]
Probab=27.46 E-value=1.8e+02 Score=27.66 Aligned_cols=56 Identities=11% Similarity=0.360 Sum_probs=43.7
Q ss_pred cchHHHHHHHhhcCCCCCchHHHHHHHhhcccc-cccccHHHHHHHHHHcCCCCHHHHHHHHHHHHHHccc
Q 025620 74 ILVDGITLLCNDLQVDPQDIVMLVVSWHMKAAT-MCEFSKQEFIGGLQSLGIDSLDKFRERISFMRAELKD 143 (250)
Q Consensus 74 i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~-~g~~tr~ef~~g~~~l~~~si~~lk~~l~~L~~~l~~ 143 (250)
.-.+.+.+..+..|+ .+..|.|||.+..+. +..| .|..++++|+.-|..|.-.|.+
T Consensus 258 ~~~~~~~~iA~k~g~---T~~qlALawv~~~~~v~~pI-----------pG~s~ve~l~eni~Al~~~Lt~ 314 (336)
T KOG1575|consen 258 PILEALSKIAEKHGC---TVPQLALAWVLSNGKVSSPI-----------PGASKIEQLKENIGALSVKLTP 314 (336)
T ss_pred HHHHHHHHHHHHcCC---CHHHHHHHHHHHhCCCEEec-----------CCCCcHHHHHHHHhhhhccCCH
Confidence 345667888899994 467799999997665 4566 7899999999999888777643
No 114
>PF14327 CSTF2_hinge: Hinge domain of cleavage stimulation factor subunit 2; PDB: 4EBA_G.
Probab=27.35 E-value=58 Score=24.37 Aligned_cols=32 Identities=22% Similarity=0.233 Sum_probs=22.6
Q ss_pred HHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhh
Q 025620 9 RDKLQQFVSITGASEKAALQALKASDWHLEGAF 41 (250)
Q Consensus 9 ~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~ 41 (250)
-+.+.++..+...+++.|+++|..|. .|-.|+
T Consensus 32 ~ell~~mK~l~~~~p~~ar~lL~~nP-qLa~Al 63 (84)
T PF14327_consen 32 YELLSQMKQLAQQNPEQARQLLQQNP-QLAYAL 63 (84)
T ss_dssp HHHHHHHHHHHC----HHHHHHHS-T-HHHHHH
T ss_pred HHHHHHHHHHHHhCHHHHHHHHHHCc-HHHHHH
Confidence 46689999999999999999999988 666654
No 115
>PF01314 AFOR_C: Aldehyde ferredoxin oxidoreductase, domains 2 & 3; InterPro: IPR001203 Enzymes of the aldehyde ferredoxin oxidoreductase (AOR) family [] contain a tungsten cofactor and an 4Fe4S cluster and catalyse the interconversion of aldehydes to carboxylates []. This family includes AOR, formaldehyde ferredoxin oxidoreductase (FOR), glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR), all isolated from hyperthermophilic archea []; carboxylic acid reductase found in clostridia []; and hydroxycarboxylate viologen oxidoreductase from Proteus vulgaris, the sole member of the AOR family containing molybdenum []. GAPOR may be involved in glycolysis [], but the functions of the other proteins are not yet clear. AOR has been proposed to be the primary enzyme responsible for oxidising the aldehydes that are produced by the 2-keto acid oxidoreductases []. This entry represents the C-terminal region of these enzymes, containing the alpha-helical structural domains 2 and 3 [, ].; GO: 0009055 electron carrier activity, 0016491 oxidoreductase activity, 0016625 oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor, 0051536 iron-sulfur cluster binding, 0055114 oxidation-reduction process; PDB: 1B25_C 1B4N_C 1AOR_B.
Probab=27.34 E-value=33 Score=32.73 Aligned_cols=35 Identities=20% Similarity=0.364 Sum_probs=29.5
Q ss_pred HHHHhhcCCCCCchHHHHHHHhhcccccccccHHHH
Q 025620 80 TLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEF 115 (250)
Q Consensus 80 ~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef 115 (250)
..+|.++|+|.-+... +|||.+.+-.-|.|++++.
T Consensus 117 ~~lcd~~GlDtis~G~-~ia~~me~~e~G~i~~~d~ 151 (382)
T PF01314_consen 117 NDLCDDYGLDTISAGN-TIAWAMELYEKGLITKEDT 151 (382)
T ss_dssp HHHHHHHTB-HHHHHH-HHHHHHHHHHTTSSSCHHH
T ss_pred HHHHHHhCCcHHHHHH-HHHHHHHHHHCCCCChhhc
Confidence 3789999999865554 8999999999999999887
No 116
>PLN02222 phosphoinositide phospholipase C 2
Probab=27.11 E-value=1.5e+02 Score=30.35 Aligned_cols=64 Identities=16% Similarity=0.237 Sum_probs=43.3
Q ss_pred CHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCC----CchHHHHHHHhhcccccccccHHHHHHHHHH
Q 025620 55 DTRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDP----QDIVMLVVSWHMKAATMCEFSKQEFIGGLQS 121 (250)
Q Consensus 55 ~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~----ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~ 121 (250)
-+..|..+|.+|.+ .+.|+.+.+.+|+.+-.=++ ++...|+=.+ -....-+.++.++|..-+..
T Consensus 23 ~~~ei~~if~~~~~--~~~mt~~~l~~FL~~~Q~~~~~~~~~~~~ii~~~-~~~~~~~~~~~~gF~~yL~s 90 (581)
T PLN02222 23 APREIKTIFEKYSE--NGVMTVDHLHRFLIDVQKQDKATREDAQSIINSA-SSLLHRNGLHLDAFFKYLFG 90 (581)
T ss_pred CcHHHHHHHHHhcC--CCCcCHHHHHHHHHHhcCCccCCHHHHHHHHHhh-hhhhhccCcCHHHHHHHhcC
Confidence 45799999999986 35899999999998866443 3333332222 12223456889999988765
No 117
>KOG4070 consensus Putative signal transduction protein p25 [General function prediction only; Signal transduction mechanisms]
Probab=26.73 E-value=88 Score=26.67 Aligned_cols=71 Identities=20% Similarity=0.255 Sum_probs=44.9
Q ss_pred CcCCHHHHHHHHHHhc---CCC--CCccchHHHHHHHhhcCCCC-CchHHH--HHHH-hhcccccccccHHHHHHHHHHc
Q 025620 52 SLTDTRHLEELYNRYK---DPY--LDMILVDGITLLCNDLQVDP-QDIVML--VVSW-HMKAATMCEFSKQEFIGGLQSL 122 (250)
Q Consensus 52 ~~~~~~~l~~lF~~Y~---~~~--~d~i~~dG~~~~~edLgv~~-ed~~~L--vLa~-~l~a~~~g~~tr~ef~~g~~~l 122 (250)
.++..+.+++-|.+|. |+. .-.|.-....++|.|.+|-- -.+... -+.+ ++++++.+.||-++|-..+..|
T Consensus 7 ~s~~~a~~~~~f~~Fa~fGd~~asg~em~gkn~~KlcKdc~V~DgK~vT~tdt~i~fsKvkg~~~~~~tf~~fkkal~el 86 (180)
T KOG4070|consen 7 ASPDMAGLEESFRAFAKFGDSKASGTEMNGKNWDKLCKDCKVIDGKSVTGTDTDIVFSKVKGKKARTITFEEFKKALEEL 86 (180)
T ss_pred cCcchhhHHHHHHHHHHcCCccccccccccccHHHHHhhcCcccCCcccccccceeeeeccccccccccHHHHHHHHHHH
Confidence 3455677888888887 331 23688888899999999833 333211 1222 6667777777777765555444
No 118
>PLN02228 Phosphoinositide phospholipase C
Probab=26.66 E-value=2.2e+02 Score=28.96 Aligned_cols=67 Identities=12% Similarity=0.124 Sum_probs=44.7
Q ss_pred cCCHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCC-Cch-HHHHHHHhhccc----ccccccHHHHHHHHHH
Q 025620 53 LTDTRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDP-QDI-VMLVVSWHMKAA----TMCEFSKQEFIGGLQS 121 (250)
Q Consensus 53 ~~~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~-ed~-~~LvLa~~l~a~----~~g~~tr~ef~~g~~~ 121 (250)
...+..|..+|.+|... +.|+.+++.+|+.+..=+. .+. .+.-|-..++.. .-|.++.++|..-+..
T Consensus 20 ~~~~~ei~~if~~~s~~--~~~t~~~~~~FL~~~Q~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~gF~~yl~s 92 (567)
T PLN02228 20 REPPVSIKRLFEAYSRN--GKMSFDELLRFVSEVQGERHAGLDYVQDIFHSVKHHNVFHHHGLVHLNAFYRYLFS 92 (567)
T ss_pred CCCcHHHHHHHHHhcCC--CccCHHHHHHHHHHhcCCccCCHHHHHHHHHHhccchhhcccCccCHHHHHHHhcC
Confidence 44679999999999864 4799999999998875332 111 122222333211 2367999999888754
No 119
>cd05022 S-100A13 S-100A13: S-100A13 domain found in proteins similar to S100A13. S100A13 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A13 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100A13 is involved in the cellular export of interleukin-1 (IL-1) and of fibroblast growth factor-1 (FGF-1), which plays an important role in angiogenesis and tissue regeneration. Export is based on the CuII-dependent formation of multiprotein complexes containing the S100A13 protein. Assembly of these complexes occurs near the inner surface of the plasma membrane. Binding of two Ca(II) ions per monomer triggers key conformational changes leading to the creation of two identical and symmetrical Cu(II)-binding sites on the surface of the protein, close to the interface between the two monomers. These Cu
Probab=26.57 E-value=2.5e+02 Score=21.11 Aligned_cols=68 Identities=19% Similarity=0.304 Sum_probs=42.3
Q ss_pred hHHHHHHHhhccc--ccccccHHHHHHHHHH-cC--CCCHHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhh
Q 025620 93 IVMLVVSWHMKAA--TMCEFSKQEFIGGLQS-LG--IDSLDKFRERISFMRAELKDEQKFREIYNFAFAWAKE 160 (250)
Q Consensus 93 ~~~LvLa~~l~a~--~~g~~tr~ef~~g~~~-l~--~~si~~lk~~l~~L~~~l~~~~~Fk~~Y~f~F~~~~~ 160 (250)
+..|+-++..=+. .-|.|+++|+..-++. +| ++..+.++..+..++..=...-.|.+|-+.....+..
T Consensus 7 i~~l~~~F~~fd~~~~~g~i~~~ELk~ll~~elg~~ls~~~~v~~mi~~~D~d~DG~I~F~EF~~l~~~l~~~ 79 (89)
T cd05022 7 IETLVSNFHKASVKGGKESLTASEFQELLTQQLPHLLKDVEGLEEKMKNLDVNQDSKLSFEEFWELIGELAKA 79 (89)
T ss_pred HHHHHHHHHHHhCCCCCCeECHHHHHHHHHHHhhhhccCHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHH
Confidence 4566667766555 6789999999999999 77 2222344444444332211122388888777776654
No 120
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=26.23 E-value=1.3e+02 Score=24.01 Aligned_cols=61 Identities=15% Similarity=0.273 Sum_probs=45.3
Q ss_pred HHHHHHHhhcCCCCCch-HHHHHHHhhcccccccccHHHHHHHHHHcCCCCHHHHHHHHH-HHHHHc
Q 025620 77 DGITLLCNDLQVDPQDI-VMLVVSWHMKAATMCEFSKQEFIGGLQSLGIDSLDKFRERIS-FMRAEL 141 (250)
Q Consensus 77 dG~~~~~edLgv~~ed~-~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~~~si~~lk~~l~-~L~~~l 141 (250)
.|=.++...+|+++..+ ....+|.++..+.||. .|..-+...|++|+++|...=| +|.+.+
T Consensus 30 ~~r~~La~~~~i~~~~l~~w~~~AdL~ri~gi~~----~~a~LL~~AGv~Tv~~LA~~~p~~L~~~l 92 (122)
T PF14229_consen 30 LGRKALAKKLGISERNLLKWVNQADLMRIPGIGP----QYAELLEHAGVDTVEELAQRNPQNLHQKL 92 (122)
T ss_pred HHHHHHHHhcCCCHHHHHHHHhHHHhhhcCCCCH----HHHHHHHHhCcCcHHHHHhCCHHHHHHHH
Confidence 34456999999999887 6667888888888874 5788889999999998875432 344433
No 121
>PHA00680 hypothetical protein
Probab=26.14 E-value=2.5e+02 Score=22.34 Aligned_cols=73 Identities=18% Similarity=0.342 Sum_probs=42.4
Q ss_pred HHHhhcCC-CCCchHHHHHHHhhcccccccccHHHHHHHHHHcCCCCHHHHHHHHH---HHHHHccchHH-HHHHHHH
Q 025620 81 LLCNDLQV-DPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSLGIDSLDKFRERIS---FMRAELKDEQK-FREIYNF 153 (250)
Q Consensus 81 ~~~edLgv-~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~~~si~~lk~~l~---~L~~~l~~~~~-Fk~~Y~f 153 (250)
-+|+-|.- +..|+..=.||..+.|--+|.-.-...++.+.....+..+.||..|. ..|.-+.+... |.++-..
T Consensus 59 vlcetldtldahdiepgalaqlcdamligpantaallnalaaadldapeslkaeldlakqfralvedagdvfsrlsel 136 (143)
T PHA00680 59 VLCETLDTLDAHDIEPGALAQLCDAMLIGPANTAALLNALAAADLDAPESLKAELDLAKQFRALVEDAGDVFSRLSEL 136 (143)
T ss_pred HHHHhhccchhhcCCchHHHHHhHHHhcCcccHHHHHHHHHhhccCChHHHHHHHhHHHHHHHHHHhHHHHHHHHHHH
Confidence 35555543 44555555555555555556556666677778888888888887774 23333333333 6555443
No 122
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.68 E-value=2.5e+02 Score=21.82 Aligned_cols=65 Identities=12% Similarity=0.067 Sum_probs=38.7
Q ss_pred HHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhccCCCCCcCCHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCC
Q 025620 12 LQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQPQSKSLTDTRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQ 91 (250)
Q Consensus 12 i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~~~~~~~~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~e 91 (250)
|.++.++||+|..+-+.|=+. | =+. |..... + |+.=+.+.+..=-+++.+.++|++++
T Consensus 3 ige~a~~~gvs~~tLryYe~~-G-Li~---------p~~~~~-~----------yR~Y~~~d~~~l~~I~~lr~~G~sl~ 60 (116)
T cd04769 3 IGELAQQTGVTIKAIRLYEEK-G-LLP---------SPKRSG-N----------YRVYDAQHVECLRFIKEARQLGFTLA 60 (116)
T ss_pred HHHHHHHHCcCHHHHHHHHHC-C-CCC---------CCCCCC-C----------ceeeCHHHHHHHHHHHHHHHcCCCHH
Confidence 789999999999988776554 2 110 111000 0 22111112333345788899999999
Q ss_pred chHHHHH
Q 025620 92 DIVMLVV 98 (250)
Q Consensus 92 d~~~LvL 98 (250)
++..+.=
T Consensus 61 eI~~~l~ 67 (116)
T cd04769 61 ELKAIFA 67 (116)
T ss_pred HHHHHHh
Confidence 9987653
No 123
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=25.36 E-value=2.5e+02 Score=20.84 Aligned_cols=36 Identities=19% Similarity=0.379 Sum_probs=25.3
Q ss_pred cccHHHHHHHHHhhcCCCCchhHHHHHHHHHhhcCCCCC
Q 025620 165 SLALDTAIGMWQLLFAEKQWPLVDHWCQFLQAKHNKAIS 203 (250)
Q Consensus 165 ~l~~d~Ai~~W~lll~~~~~~~l~~w~~Fl~~~~~k~Is 203 (250)
.+.++.|++-..-..++ .|.+...++|++++ +++|.
T Consensus 47 ~~~~~~a~~~l~~~~~~--~~~v~~~~~Fi~~S-~RGi~ 82 (83)
T PF13720_consen 47 GLTLEEALEELEEEYPD--SPEVREIVDFIRNS-KRGIC 82 (83)
T ss_dssp SS-HHHHHHHHHHHTTS--CHHHHHHHHHHHHT-SS-B-
T ss_pred CCCHHHHHHHHHHhccC--CHHHHHHHHHHHhC-CCCCc
Confidence 36888898887776665 49999999999854 36654
No 124
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=24.05 E-value=1.6e+02 Score=27.61 Aligned_cols=78 Identities=17% Similarity=0.247 Sum_probs=49.3
Q ss_pred HHHHHHHhhhCC---------CHHHHHHHHHhCCCCchhhhhhhhccCCCCCcCCHHHHHHHHHHhcCCCC-----Cccc
Q 025620 10 DKLQQFVSITGA---------SEKAALQALKASDWHLEGAFDVFYSQPQSKSLTDTRHLEELYNRYKDPYL-----DMIL 75 (250)
Q Consensus 10 ~~i~~F~~iT~~---------s~~~A~~~L~~~~w~le~A~~~f~~~~~~~~~~~~~~l~~lF~~Y~~~~~-----d~i~ 75 (250)
+.+-.|+-++|+ -+++|..+++.++ +++..++.. +.+ .. +...+.++|-.=.-.+. ...+
T Consensus 224 ~q~id~~iL~G~dyn~Gv~GIG~ktA~kli~~~g-sie~il~~~-~~~---~~-~~~~~~~~f~~~~v~~~~~~~~~~pd 297 (338)
T TIGR03674 224 EQLIDIAILVGTDYNEGVKGIGPKTALKLIKEHG-DLEKVLKAR-GED---IE-NYDEIREFFLNPPVTDDYELKWRKPD 297 (338)
T ss_pred HHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHcC-CHHHHHHhh-cCC---CC-CHHHHHHHhCCCCCCCCCCccCCCCC
Confidence 335555655554 5899999999998 887766541 111 11 22566666653221111 1577
Q ss_pred hHHHHH-HHhhcCCCCCch
Q 025620 76 VDGITL-LCNDLQVDPQDI 93 (250)
Q Consensus 76 ~dG~~~-~~edLgv~~ed~ 93 (250)
.+|+.+ +|+..|.+++-+
T Consensus 298 ~e~l~~fl~~e~~~~~~rv 316 (338)
T TIGR03674 298 KEGIIEFLCDEHDFSEDRV 316 (338)
T ss_pred HHHHHHHHhhcCCCCHHHH
Confidence 899999 789999998833
No 125
>PF13624 SurA_N_3: SurA N-terminal domain; PDB: 3NRK_A.
Probab=23.89 E-value=76 Score=25.37 Aligned_cols=60 Identities=17% Similarity=0.150 Sum_probs=23.1
Q ss_pred cchHHHHHHHhhcCCCCCchHHHH-HHHhhcccccccccHHHHHHHHHHcCCCCHHHHHHHH
Q 025620 74 ILVDGITLLCNDLQVDPQDIVMLV-VSWHMKAATMCEFSKQEFIGGLQSLGIDSLDKFRERI 134 (250)
Q Consensus 74 i~~dG~~~~~edLgv~~ed~~~Lv-La~~l~a~~~g~~tr~ef~~g~~~l~~~si~~lk~~l 134 (250)
|...=+.+.++++||.+.|-.+=- +........-|.++++.|.+.++..|.+ .+.++..|
T Consensus 84 I~~~ll~q~A~~~gi~vsd~ev~~~i~~~~~f~~~g~~~~~~f~~~L~~~g~t-~~~~~~~l 144 (154)
T PF13624_consen 84 IDQKLLLQEAKKLGISVSDAEVDDAIKQIPAFQENGKFDKEAFEEFLKQQGMT-EEEFKEEL 144 (154)
T ss_dssp HHHHHHHHHHHHTT----HHHHHHHHHH--HHHHH----HHHHHHHHH--------------
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHhhcc-ccccchhh
Confidence 333445578899999987754443 3331111123889999999999998874 45555444
No 126
>smart00549 TAFH TAF homology. Domain in Drosophila nervy, CBFA2T1, human TAF105, human TAF130, and Drosophila TAF110. Also known as nervy homology region 1 (NHR1).
Probab=23.33 E-value=1.6e+02 Score=22.82 Aligned_cols=63 Identities=19% Similarity=0.276 Sum_probs=42.6
Q ss_pred HHHHHhhcC-CCC-CchHHHHHHHhhcccccccccHHHHHHHHHHc-----CCCCHHHHHHHHHHHHHHccchHH
Q 025620 79 ITLLCNDLQ-VDP-QDIVMLVVSWHMKAATMCEFSKQEFIGGLQSL-----GIDSLDKFRERISFMRAELKDEQK 146 (250)
Q Consensus 79 ~~~~~edLg-v~~-ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l-----~~~si~~lk~~l~~L~~~l~~~~~ 146 (250)
+++|..+.+ -+. +.+..||++-. -|.++-|||...++.. +-.-++=||+.||-||+++.+...
T Consensus 12 Li~ls~~~~qpe~~~~Vr~LV~~L~-----~~~i~~EeF~~~Lq~~lns~~qP~lvPFLK~slp~Lr~~l~~~~~ 81 (92)
T smart00549 12 LIQLSNDISQPEVAERVRTLVLGLV-----NGTITAEEFTSRLQEALNSPLQPYLIPFLKNSLPLLRRELLHCAR 81 (92)
T ss_pred HHHHhcCCCcchHHHHHHHHHHHHH-----hCCCCHHHHHHHHHHHHcCCCCchhHHHHHHhhHHHHHHHHHHHH
Confidence 456666666 333 44666666533 3688999999988873 223466789999999998866544
No 127
>PLN02952 phosphoinositide phospholipase C
Probab=23.18 E-value=2.4e+02 Score=28.88 Aligned_cols=68 Identities=7% Similarity=0.005 Sum_probs=44.2
Q ss_pred cCCHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCC----CCCchHHHHHHHhh--c-cccc--ccccHHHHHHHHHH
Q 025620 53 LTDTRHLEELYNRYKDPYLDMILVDGITLLCNDLQV----DPQDIVMLVVSWHM--K-AATM--CEFSKQEFIGGLQS 121 (250)
Q Consensus 53 ~~~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv----~~ed~~~LvLa~~l--~-a~~~--g~~tr~ef~~g~~~ 121 (250)
...+..|..+|.+|...+ +.|+.+.+.+|+.+-.= ++++..-|+-.+.= + .... +.++.++|...+..
T Consensus 34 ~~~r~ei~~lf~~~~~~~-~~mt~~~l~~FL~~~Q~e~~~~~~~~~~i~~~~~~~~~~~~~~~~~~l~~~~F~~~l~s 110 (599)
T PLN02952 34 AEPPDDVKDVFCKFSVGG-GHMGADQLRRFLVLHQDELDCTLAEAQRIVEEVINRRHHVTRYTRHGLNLDDFFHFLLY 110 (599)
T ss_pred CCChHHHHHHHHHHhCCC-CccCHHHHHHHHHHhCCCcCCCHHHHHHHHHHHHhhccccccccccCcCHHHHHHHHcC
Confidence 346789999999998643 58999999999987553 33443333222110 1 1111 34889999988863
No 128
>KOG2873 consensus Ubiquinol cytochrome c reductase assembly protein CBP3 [Energy production and conversion]
Probab=23.05 E-value=1.9e+02 Score=26.83 Aligned_cols=49 Identities=20% Similarity=0.405 Sum_probs=35.5
Q ss_pred HHHHHHHHHHhhhhcCCccccHHHHHHHHHhhcCCCC---chhHHHHHHHHHhh
Q 025620 147 FREIYNFAFAWAKEKGQKSLALDTAIGMWQLLFAEKQ---WPLVDHWCQFLQAK 197 (250)
Q Consensus 147 Fk~~Y~f~F~~~~~~~qk~l~~d~Ai~~W~lll~~~~---~~~l~~w~~Fl~~~ 197 (250)
++.+|.=.|.| ++|-=+-+-..|+++|+.||.+++ ..+++.-.+|++.+
T Consensus 201 ~~qf~gaifaY--DeG~l~dD~vLA~alWRnlF~~r~~~D~~hle~vV~YvR~q 252 (284)
T KOG2873|consen 201 ERQFYGAIFAY--DEGFLSDDRVLATALWRNLFSGRGNVDLVHLEAVVRYVRSQ 252 (284)
T ss_pred HHHHHHHHHHh--cccccccchHHHHHHHHHHhCCCCCcCHHHHHHHHHHHHHH
Confidence 45566644444 355555555889999999999873 56899999998765
No 129
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=22.97 E-value=74 Score=22.64 Aligned_cols=24 Identities=13% Similarity=0.457 Sum_probs=11.2
Q ss_pred CCCCCcchHHH---HHHHHhhhCCCHH
Q 025620 1 MHKLSRSNRDK---LQQFVSITGASEK 24 (250)
Q Consensus 1 m~~l~~~q~~~---i~~F~~iT~~s~~ 24 (250)
|..|++.|++. |.+|+.-+|.++.
T Consensus 1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt 27 (65)
T PF01726_consen 1 MKELTERQKEVLEFIREYIEENGYPPT 27 (65)
T ss_dssp -----HHHHHHHHHHHHHHHHHSS---
T ss_pred CCCCCHHHHHHHHHHHHHHHHcCCCCC
Confidence 67788877765 4667777777653
No 130
>PF04444 Dioxygenase_N: Catechol dioxygenase N terminus; InterPro: IPR007535 This domain is the N-terminal region of catechol, chlorocatechol or hydroxyquinol 1,2-dioxygenase proteins. This region is always found adjacent to the dioxygenase domain (IPR000627 from INTERPRO). Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes (IPR000486 from INTERPRO) use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) []. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Enzymes that belong to the intradiol family include catechol 1,2-dioxygenase (1,2-CTD) (1.13.11.1 from EC); protocatechuate 3,4-dioxygenase (3,4-PCD) (1.13.11.3 from EC); and chlorocatechol 1,2-dioxygenase (1.13.11.1 from EC) [].; GO: 0005506 iron ion binding, 0018576 catechol 1,2-dioxygenase activity, 0009712 catechol-containing compound metabolic process, 0055114 oxidation-reduction process; PDB: 3O6R_B 1S9A_A 3O6J_A 3O5U_B 3O32_B 3HHY_A 3HHX_A 3HJS_A 3HJQ_A 3HKP_A ....
Probab=22.84 E-value=97 Score=22.82 Aligned_cols=45 Identities=24% Similarity=0.488 Sum_probs=35.0
Q ss_pred hHHHHHHHHHhhcCCCCCHhhHHHHHHHHhhhCCCCCCCCcCCCchhhHHHH-HHH
Q 025620 186 LVDHWCQFLQAKHNKAISRDTWSQLLEFARTVDPALSNYDAEGAWPYLIDEF-VEY 240 (250)
Q Consensus 186 ~l~~w~~Fl~~~~~k~IskD~W~~~l~F~~~~~~~ls~YDe~~AWP~liDeF-Ve~ 240 (250)
++..-.+|+.+. .||-|.|..-.+|+..+.. .+-||.|.|=| ++.
T Consensus 11 lv~~lh~~i~e~---~lT~~E~~~av~~L~~~G~-------~~E~~Ll~DvlGle~ 56 (74)
T PF04444_consen 11 LVRHLHDFIREV---DLTEDEWWAAVDFLNRVGQ-------RNEFILLSDVLGLEH 56 (74)
T ss_dssp HHHHHHHHHHHC---T--HHHHHHHHHHHHHHHH-------TTHHHHHHHHTTHHH
T ss_pred HHHHHHHHHHHh---CCCHHHHHHHHHHHHHhcC-------CCchhhhhhhhccch
Confidence 456667787664 5999999999999997765 77899999998 776
No 131
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=22.75 E-value=1.5e+02 Score=21.30 Aligned_cols=56 Identities=13% Similarity=0.115 Sum_probs=39.1
Q ss_pred CCCCCchHHHHHHHhhcccccccccHHHHHHHHHHcCC-CCHHHHHHHHHHHHHHccc
Q 025620 87 QVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQSLGI-DSLDKFRERISFMRAELKD 143 (250)
Q Consensus 87 gv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~l~~-~si~~lk~~l~~L~~~l~~ 143 (250)
-|.+..-+..+|+.++..+.. .+||++..+.+-.-.. .+-..++..|..||+.|..
T Consensus 21 ~v~Lt~~e~~lL~~L~~~~~~-~vs~~~l~~~lw~~~~~~~~~~l~~~I~rLRkkl~~ 77 (95)
T cd00383 21 PVELTPKEFELLELLARNPGR-VLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLED 77 (95)
T ss_pred EEEeCHHHHHHHHHHHhCCCC-cCCHHHHHHHhcCCCCCCCcccHHHHHHHHHHHhcc
Confidence 345555567777777776543 8999999987543332 3556788999999998853
No 132
>COG0667 Tas Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]
Probab=22.65 E-value=2.1e+02 Score=26.40 Aligned_cols=59 Identities=12% Similarity=0.375 Sum_probs=41.7
Q ss_pred HHHHHHHhhcCCCCCchHHHHHHHhhccccc-ccccHHHHHHHHHHcCCCCHHHHHHHHHHHHHHccchHHHHHH
Q 025620 77 DGITLLCNDLQVDPQDIVMLVVSWHMKAATM-CEFSKQEFIGGLQSLGIDSLDKFRERISFMRAELKDEQKFREI 150 (250)
Q Consensus 77 dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~-g~~tr~ef~~g~~~l~~~si~~lk~~l~~L~~~l~~~~~Fk~~ 150 (250)
+-+...++++|++ +..+.|||.+.-+.. ..| .|..++++|+.-+..+.-.|.+. .++.+
T Consensus 245 ~~l~~~a~~~g~t---~aq~ALawvl~~~~v~~~I-----------~Ga~~~~qL~en~~A~~~~L~~~-~~~~l 304 (316)
T COG0667 245 RALEELAKELGAT---PAQVALAWVLAQPGVTSPI-----------VGASKAEQLEENLAALDIKLSEE-ELAAL 304 (316)
T ss_pred HHHHHHHHHhCCC---HHHHHHHHHHhCCCCceEe-----------ecCCCHHHHHHHHHHhcCCCCHH-HHHHH
Confidence 3456777788887 678899999987664 455 68888888888888777665332 24444
No 133
>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=22.26 E-value=63 Score=23.57 Aligned_cols=30 Identities=23% Similarity=0.360 Sum_probs=19.3
Q ss_pred cccccHHHHHHHHHHcCCCCHHHHHHHHHHHH
Q 025620 107 MCEFSKQEFIGGLQSLGIDSLDKFRERISFMR 138 (250)
Q Consensus 107 ~g~~tr~ef~~g~~~l~~~si~~lk~~l~~L~ 138 (250)
-++|||++|++-++..=-| .-|+..|..++
T Consensus 39 ~~kIsR~~fvr~lR~IVGD--~lL~s~I~~lq 68 (70)
T PF12174_consen 39 KKKISREEFVRKLRQIVGD--QLLRSAIKSLQ 68 (70)
T ss_pred HCCCCHHHHHHHHHHHHHH--HHHHHHHHHhc
Confidence 5799999999998874212 12455554443
No 134
>COG2147 RPL19A Ribosomal protein L19E [Translation, ribosomal structure and biogenesis]
Probab=21.82 E-value=2e+02 Score=24.28 Aligned_cols=29 Identities=21% Similarity=0.520 Sum_probs=19.8
Q ss_pred CHHHHHHHHHHHHHHc-cchHHHHHHHHHH
Q 025620 126 SLDKFRERISFMRAEL-KDEQKFREIYNFA 154 (250)
Q Consensus 126 si~~lk~~l~~L~~~l-~~~~~Fk~~Y~f~ 154 (250)
+|-.|+..|.+|++.= -|+..|+.+|+.+
T Consensus 98 ~IRalR~~Lr~lrd~gkIdk~~YR~lY~~a 127 (150)
T COG2147 98 RIRALRRELRKLRDDGKIDKHTYRKLYRMA 127 (150)
T ss_pred HHHHHHHHHHHHHHcCCcCHHHHHHHHHHH
Confidence 3455888888888763 3556677777653
No 135
>PF08716 nsp7: nsp7 replicase; InterPro: IPR014828 Nsp7 (non structural protein 7) has been implicated in viral RNA replication and is predominantly alpha helical in structure []. It forms a hexadecameric supercomplex with Nsp8 that adopts a hollow cylinder-like structure []. The dimensions of the central channel and positive electrostatic properties of the cylinder imply that it confers processivity on RNA-dependent RNA polymerase []. ; GO: 0004197 cysteine-type endopeptidase activity, 0008242 omega peptidase activity, 0016740 transferase activity; PDB: 3UB0_C 2AHM_C 2KYS_A 1YSY_A.
Probab=21.70 E-value=2.4e+02 Score=21.47 Aligned_cols=43 Identities=26% Similarity=0.439 Sum_probs=33.8
Q ss_pred HHHHHcCCCCHHHHHHHHHHHHHHc---cchHH-HHHHHH-HHHHhhh
Q 025620 117 GGLQSLGIDSLDKFRERISFMRAEL---KDEQK-FREIYN-FAFAWAK 159 (250)
Q Consensus 117 ~g~~~l~~~si~~lk~~l~~L~~~l---~~~~~-Fk~~Y~-f~F~~~~ 159 (250)
+-++++|+.+-.++-+++-+|..++ .++++ |..++. .+|-+++
T Consensus 15 ~~L~~l~veanSk~w~~cV~LHN~Il~~~d~~eA~e~l~~LLa~lls~ 62 (83)
T PF08716_consen 15 GLLQKLNVEANSKLWAYCVQLHNEILLSSDPEEAFEKLLALLAFLLSK 62 (83)
T ss_dssp HHHHHTTGGGSHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHcCchhhhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhc
Confidence 4467899999999999999999996 45665 888877 5566655
No 136
>cd03022 DsbA_HCCA_Iso DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1,2-dihydroxynapthalene by a dioxygenase, into cis-o-hydroxybenzylidenepyruvate (cHBPA). This is the fourth reaction in a six-step pathway that converts napthalene into salicylate. HCCA isomerase is unique to bacteria that degrade polycyclic aromatic compounds. It is closely related to the eukaryotic protein, GSH transferase kappa (GSTK).
Probab=21.67 E-value=1e+02 Score=25.17 Aligned_cols=38 Identities=8% Similarity=0.089 Sum_probs=27.4
Q ss_pred CHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCCc
Q 025620 55 DTRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQD 92 (250)
Q Consensus 55 ~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~ed 92 (250)
...-+.++|..|-..+.|.-+.+.+.+.++++|++++.
T Consensus 102 ~~~~~~~lf~a~~~~~~~i~~~~~l~~~a~~~Gld~~~ 139 (192)
T cd03022 102 AEAFARAVFRALWGEGLDIADPAVLAAVAAAAGLDADE 139 (192)
T ss_pred HHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHcCCCHHH
Confidence 34666778888765555545567788999999998753
No 137
>PF14788 EF-hand_10: EF hand; PDB: 1DJW_B 1DJI_B 1DJG_B 1QAS_B 2ISD_B 1DJZ_B 1DJY_B 1DJX_B 1QAT_A 1DJH_A ....
Probab=21.45 E-value=2.8e+02 Score=19.06 Aligned_cols=48 Identities=8% Similarity=0.043 Sum_probs=31.4
Q ss_pred cchHHHHHHHhhcCCCCCchHHHHHHHhhcccccccccHHHHHHHHHH
Q 025620 74 ILVDGITLLCNDLQVDPQDIVMLVVSWHMKAATMCEFSKQEFIGGLQS 121 (250)
Q Consensus 74 i~~dG~~~~~edLgv~~ed~~~LvLa~~l~a~~~g~~tr~ef~~g~~~ 121 (250)
|...-+.+|+..++|++++--...|-..+--..-|....+||+.=.+.
T Consensus 2 msf~Evk~lLk~~NI~~~~~yA~~LFq~~D~s~~g~Le~~Ef~~Fy~~ 49 (51)
T PF14788_consen 2 MSFKEVKKLLKMMNIEMDDEYARQLFQECDKSQSGRLEGEEFEEFYKR 49 (51)
T ss_dssp BEHHHHHHHHHHTT----HHHHHHHHHHH-SSSSSEBEHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHccCcCHHHHHHHHHHhcccCCCCccHHHHHHHHHH
Confidence 444556788888888888877777777777666788888888765544
No 138
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=21.00 E-value=3.5e+02 Score=21.28 Aligned_cols=65 Identities=11% Similarity=0.098 Sum_probs=38.9
Q ss_pred HHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhccCCCCCcCCHHHHHHHHHHhcCCCCCccchHHHHHHHhhcCCCCC
Q 025620 12 LQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQPQSKSLTDTRHLEELYNRYKDPYLDMILVDGITLLCNDLQVDPQ 91 (250)
Q Consensus 12 i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~~~~~~~~~~~l~~lF~~Y~~~~~d~i~~dG~~~~~edLgv~~e 91 (250)
|.+|...||+|..+-+.| ++-+ =+. .+....+. |+.=+++.|..=.+++.+.++|++++
T Consensus 2 I~e~a~~~gvs~~tlR~Y-e~~G-Ll~--------~~~r~~~g-----------~R~Y~~~~l~~l~~I~~l~~~G~sl~ 60 (124)
T TIGR02051 2 IGELAKAAGVNVETIRYY-ERKG-LLP--------EPDRPEGG-----------YRRYPEETVKRLRFIKRAQELGFSLE 60 (124)
T ss_pred HHHHHHHHCcCHHHHHHH-HHCC-CCC--------CCccCCCC-----------CEeECHHHHHHHHHHHHHHHCCCCHH
Confidence 789999999999988777 3333 111 11110111 12111122333367888899999999
Q ss_pred chHHHH
Q 025620 92 DIVMLV 97 (250)
Q Consensus 92 d~~~Lv 97 (250)
++.-++
T Consensus 61 eI~~~l 66 (124)
T TIGR02051 61 EIGGLL 66 (124)
T ss_pred HHHHHH
Confidence 987755
No 139
>PF11772 EpuA: DNA-directed RNA polymerase subunit beta; InterPro: IPR024596 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry represents the short 60-residue long bacterial family that is the beta subunit of the DNA-directed RNA polymerase, likely to be 2.7.7.6 from EC It is membrane-bound and is referred to by the name EpuA.
Probab=20.49 E-value=74 Score=21.53 Aligned_cols=16 Identities=31% Similarity=0.802 Sum_probs=14.0
Q ss_pred CCCCHhhHHHHHHHHh
Q 025620 200 KAISRDTWSQLLEFAR 215 (250)
Q Consensus 200 k~IskD~W~~~l~F~~ 215 (250)
...+.|||+.+.+|+.
T Consensus 30 ~vf~~~tW~hi~d~~~ 45 (47)
T PF11772_consen 30 DVFSPDTWQHIIDFFT 45 (47)
T ss_pred HhCCHHHHHHHHHHHc
Confidence 5689999999999974
No 140
>PF12238 MSA-2c: Merozoite surface antigen 2c; InterPro: IPR021060 This family of proteins are restricted to the apicomplexan Babesia bovis. Proteins in this entry are typically between 263 and 318 amino acids in length and plasma membrane glycoproteins. These antigens present on the merozoite surface (MSA) and are involved in the parasite invasion of the bovine erythrocyte. MSA-2c has been suggested as a possible antigen for a vaccine candidate [].
Probab=20.41 E-value=1.5e+02 Score=26.18 Aligned_cols=53 Identities=13% Similarity=0.299 Sum_probs=34.2
Q ss_pred hhhhhhhc-cCCCCCcCCHHHHHHHHHHhcCCCCCcc-chHHHHHHHhhcCCCCCc
Q 025620 39 GAFDVFYS-QPQSKSLTDTRHLEELYNRYKDPYLDMI-LVDGITLLCNDLQVDPQD 92 (250)
Q Consensus 39 ~A~~~f~~-~~~~~~~~~~~~l~~lF~~Y~~~~~d~i-~~dG~~~~~edLgv~~ed 92 (250)
.|+++|.. +++.-......++++-|-+-.-.++..+ +.+|+.+||++- ++.++
T Consensus 65 ~~~n~fl~~~~~~~~~~~~~~~~~YyKkhIy~~d~~v~d~~~lv~~ck~F-l~~~s 119 (205)
T PF12238_consen 65 SHMNAFLNDWPPHMLEEGREKMTKYYKKHIYKEDSEVKDYNGLVKFCKDF-LDSES 119 (205)
T ss_pred HHHHHHHccCchhhhhccHHHHHHHHHHhccCcccccccHHHHHHHHHHH-hcccc
Confidence 35566665 2222234466888888887665444456 999999999986 34444
No 141
>cd07311 terB_like_1 tellurium resistance terB-like protein, subgroup 1. This family includes several uncharacterized bacterial proteins. The prototype of this CD is tellurite resistance protein from Nostoc punctiforme that belongs to COG3793. Its precise biological function and its mechanism responsible for tellurium resistance still remains rather poorly understood.
Probab=20.36 E-value=3.2e+02 Score=22.69 Aligned_cols=91 Identities=11% Similarity=0.046 Sum_probs=52.5
Q ss_pred CCCcchHHHHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhccCCCCCcCCHHHHHHHH-HHhcCCCCCccchHHHHH
Q 025620 3 KLSRSNRDKLQQFVSITGASEKAALQALKASDWHLEGAFDVFYSQPQSKSLTDTRHLEELY-NRYKDPYLDMILVDGITL 81 (250)
Q Consensus 3 ~l~~~q~~~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~~~~~~~~~~~~~l~~lF-~~Y~~~~~d~i~~dG~~~ 81 (250)
+.+..+.+.+++++.-.|.+++.....++. .-+.+++.+...-..........|..++ --|+|+.-+.-..+=+.+
T Consensus 39 ~Vse~Ei~~~~~~m~~~~L~~e~~~~aie~---~~~~~L~~~~~~~~~~~~~~~~ll~~~l~vA~ADG~l~~~E~~lL~~ 115 (150)
T cd07311 39 VISPEERDWAIGYAAARGGDADMVEELKEY---TADEDLEEVDFRSPNIKSSRRALLYDAIQVCAADGELSPGEVAAVRK 115 (150)
T ss_pred CCCHHHHHHHHHHHHHcCCCHHHHHHHHHh---CccccHHHHHHHHHhcchhHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence 356677778888887778888877777777 4555566554321111111122222222 223444334444556678
Q ss_pred HHhhcCCCCCchHHH
Q 025620 82 LCNDLQVDPQDIVML 96 (250)
Q Consensus 82 ~~edLgv~~ed~~~L 96 (250)
.|.-||+++.+..-+
T Consensus 116 iA~~LGis~~~~~~l 130 (150)
T cd07311 116 AASLLGISEDEVQKL 130 (150)
T ss_pred HHHHcCCCHHHHHHH
Confidence 999999998776544
No 142
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=20.19 E-value=2.5e+02 Score=19.03 Aligned_cols=57 Identities=12% Similarity=0.144 Sum_probs=35.8
Q ss_pred cchHHHHHHHhhcCCCCCchHHHHHHH-hhcccccccccHHHHHHHHHHcCCCCHHHHHHHHHH
Q 025620 74 ILVDGITLLCNDLQVDPQDIVMLVVSW-HMKAATMCEFSKQEFIGGLQSLGIDSLDKFRERISF 136 (250)
Q Consensus 74 i~~dG~~~~~edLgv~~ed~~~LvLa~-~l~a~~~g~~tr~ef~~g~~~l~~~si~~lk~~l~~ 136 (250)
-+++.+.+++..+|+ +...-..... .-|+..+-.+|.+.. +++|+.+...-+.-+..
T Consensus 4 w~~~~v~~WL~~~gl--~~y~~~f~~~~i~g~~~L~~l~~~~L----~~lGI~~~~~r~kll~~ 61 (66)
T PF07647_consen 4 WSPEDVAEWLKSLGL--EQYADNFRENGIDGLEDLLQLTEEDL----KELGITNLGHRRKLLSA 61 (66)
T ss_dssp HCHHHHHHHHHHTTC--GGGHHHHHHTTCSHHHHHTTSCHHHH----HHTTTTHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHCCc--HHHHHHHHHcCCcHHHHHhhCCHHHH----HHcCCCCHHHHHHHHHH
Confidence 356778888888888 3343333333 334366677887765 57898887765544443
No 143
>PF13551 HTH_29: Winged helix-turn helix
Probab=20.12 E-value=3.6e+02 Score=19.77 Aligned_cols=81 Identities=11% Similarity=0.202 Sum_probs=48.2
Q ss_pred HHHHHHhhhCCCHHHHHHHHHhCCCCchhhhhhhhc-cCC-CCC-c-CCHHHHHHHHHHhcCCCC---CccchHHHHHHH
Q 025620 11 KLQQFVSITGASEKAALQALKASDWHLEGAFDVFYS-QPQ-SKS-L-TDTRHLEELYNRYKDPYL---DMILVDGITLLC 83 (250)
Q Consensus 11 ~i~~F~~iT~~s~~~A~~~L~~~~w~le~A~~~f~~-~~~-~~~-~-~~~~~l~~lF~~Y~~~~~---d~i~~dG~~~~~ 83 (250)
.+.+.+..+|+|..+...+++++. +.-++.... .+. +++ . -++.....+-+-+..+.. ......-+...+
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~---~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l 90 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYR---EGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWL 90 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHH---cccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHH
Confidence 488999999999999999999976 223444444 332 222 2 355666666666664322 135556555532
Q ss_pred -h-hcCCCCCchH
Q 025620 84 -N-DLQVDPQDIV 94 (250)
Q Consensus 84 -e-dLgv~~ed~~ 94 (250)
+ ..|+.+....
T Consensus 91 ~~~~~~~~~s~~t 103 (112)
T PF13551_consen 91 IEEEFGIDVSPST 103 (112)
T ss_pred HHhccCccCCHHH
Confidence 2 3356554333
Done!