Query 016243
Match_columns 392
No_of_seqs 279 out of 1362
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 05:06:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016243.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016243hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1546 Metacaspase involved i 100.0 6.1E-70 1.3E-74 519.9 25.5 319 1-377 1-360 (362)
2 PF00656 Peptidase_C14: Caspas 100.0 6.5E-33 1.4E-37 261.3 16.1 218 82-317 1-230 (248)
3 cd00032 CASc Caspase, interleu 99.8 1.1E-17 2.4E-22 159.6 22.6 205 79-320 7-220 (243)
4 smart00115 CASc Caspase, inter 99.8 4.6E-17 1E-21 155.3 23.7 204 79-320 6-216 (241)
5 PF01650 Peptidase_C13: Peptid 99.5 3.3E-13 7.1E-18 129.9 15.2 192 82-320 1-236 (256)
6 COG4249 Uncharacterized protei 99.5 1.1E-13 2.3E-18 139.6 10.0 159 136-320 113-286 (380)
7 TIGR01053 LSD1 zinc finger dom 99.0 2.2E-10 4.8E-15 74.6 2.6 31 4-34 1-31 (31)
8 PF06943 zf-LSD1: LSD1 zinc fi 98.8 2.2E-09 4.7E-14 66.1 1.9 25 7-31 1-25 (25)
9 PF14538 Raptor_N: Raptor N-te 98.3 6.6E-06 1.4E-10 73.5 10.0 106 102-229 43-151 (154)
10 KOG1349 Gpi-anchor transamidas 98.2 2.1E-05 4.6E-10 74.6 11.5 189 79-315 26-262 (309)
11 KOG1348 Asparaginyl peptidases 97.9 0.0002 4.3E-09 71.1 13.4 131 77-229 41-213 (477)
12 COG5206 GPI8 Glycosylphosphati 97.8 0.00042 9.2E-09 66.3 12.7 189 78-314 25-261 (382)
13 COG4249 Uncharacterized protei 97.7 1.1E-05 2.5E-10 81.8 2.0 211 80-338 2-221 (380)
14 PF12770 CHAT: CHAT domain 97.2 0.0048 1E-07 59.4 12.1 180 85-320 82-270 (287)
15 KOG1517 Guanine nucleotide bin 96.8 0.0072 1.6E-07 67.2 10.0 168 102-298 139-312 (1387)
16 PF13719 zinc_ribbon_5: zinc-r 95.1 0.014 3E-07 39.6 1.8 31 3-33 1-36 (37)
17 PF13717 zinc_ribbon_4: zinc-r 93.8 0.05 1.1E-06 36.7 2.3 29 3-31 1-34 (36)
18 PF10122 Mu-like_Com: Mu-like 92.5 0.097 2.1E-06 37.9 2.2 36 1-36 1-38 (51)
19 TIGR02098 MJ0042_CXXC MJ0042 f 92.0 0.1 2.2E-06 35.2 1.7 32 3-34 1-37 (38)
20 PRK00398 rpoP DNA-directed RNA 90.5 0.21 4.6E-06 35.3 2.2 30 2-31 1-30 (46)
21 PF04810 zf-Sec23_Sec24: Sec23 82.0 0.94 2E-05 31.1 1.7 32 4-35 2-37 (40)
22 COG2051 RPS27A Ribosomal prote 76.2 1.8 3.9E-05 33.2 1.8 30 3-32 18-48 (67)
23 COG4995 Uncharacterized protei 75.9 10 0.00022 39.4 7.7 181 80-318 211-398 (420)
24 KOG1985 Vesicle coat complex C 74.1 3.6 7.8E-05 45.6 4.1 33 4-36 218-254 (887)
25 PRK00415 rps27e 30S ribosomal 69.3 3.2 6.9E-05 31.2 1.7 29 3-31 10-39 (59)
26 COG1996 RPC10 DNA-directed RNA 68.2 2.5 5.4E-05 30.6 0.9 33 3-35 5-37 (49)
27 PF01667 Ribosomal_S27e: Ribos 67.6 3.6 7.7E-05 30.5 1.6 30 3-32 6-36 (55)
28 COG1791 Uncharacterized conser 67.0 22 0.00047 32.5 6.8 58 105-170 52-109 (181)
29 PF12070 DUF3550: Protein of u 65.9 39 0.00084 36.0 9.5 37 135-171 292-328 (513)
30 PF11331 DUF3133: Protein of u 65.7 3.3 7.2E-05 29.5 1.1 32 4-35 6-44 (46)
31 PF09788 Tmemb_55A: Transmembr 64.4 4.2 9E-05 39.2 1.9 33 3-35 156-190 (256)
32 PF03415 Peptidase_C11: Clostr 61.6 23 0.0005 36.4 6.9 81 137-227 78-160 (397)
33 PF01364 Peptidase_C25: Peptid 61.3 9.2 0.0002 38.7 3.9 127 137-319 226-353 (378)
34 PF09082 DUF1922: Domain of un 59.1 4.8 0.0001 31.1 1.0 32 4-37 3-34 (68)
35 PF09297 zf-NADH-PPase: NADH p 58.6 8 0.00017 25.0 1.9 28 4-31 3-30 (32)
36 KOG1984 Vesicle coat complex C 58.2 6 0.00013 44.2 1.9 36 3-38 337-376 (1007)
37 PF03604 DNA_RNApol_7kD: DNA d 57.8 5.6 0.00012 26.1 1.0 24 6-30 2-25 (32)
38 COG0648 Nfo Endonuclease IV [D 57.5 26 0.00056 34.5 6.1 63 137-225 118-180 (280)
39 smart00659 RPOLCX RNA polymera 57.5 8.5 0.00018 27.1 2.0 27 5-32 3-29 (44)
40 PTZ00083 40S ribosomal protein 54.1 8.9 0.00019 30.9 1.8 29 3-31 34-63 (85)
41 PLN00209 ribosomal protein S27 52.6 9.6 0.00021 30.7 1.8 29 3-31 35-64 (86)
42 KOG1321 Protoheme ferro-lyase 52.1 40 0.00088 33.8 6.3 60 105-171 175-240 (395)
43 PF14803 Nudix_N_2: Nudix N-te 48.3 13 0.00028 24.8 1.6 27 6-32 2-32 (34)
44 TIGR01206 lysW lysine biosynth 47.6 16 0.00035 26.9 2.2 32 4-35 2-35 (54)
45 smart00661 RPOL9 RNA polymeras 46.3 22 0.00048 25.1 2.8 30 6-35 2-33 (52)
46 PF09827 CRISPR_Cas2: CRISPR a 41.7 59 0.0013 25.0 4.8 52 102-163 13-66 (78)
47 COG2379 GckA Putative glycerat 40.4 1.6E+02 0.0035 30.5 8.7 81 79-171 35-127 (422)
48 PF13660 DUF4147: Domain of un 40.1 57 0.0012 31.3 5.3 37 134-170 92-130 (238)
49 COG5028 Vesicle coat complex C 39.2 15 0.00033 40.7 1.3 34 4-37 199-236 (861)
50 PF06258 Mito_fiss_Elm1: Mitoc 38.6 1.4E+02 0.003 29.8 7.9 75 78-167 144-218 (311)
51 PRK10886 DnaA initiator-associ 38.5 1.9E+02 0.0041 26.8 8.4 71 80-169 40-122 (196)
52 PF02150 RNA_POL_M_15KD: RNA p 37.7 7.8 0.00017 25.9 -0.7 30 5-35 2-33 (35)
53 PF00130 C1_1: Phorbol esters/ 36.4 35 0.00076 24.1 2.5 32 3-35 10-41 (53)
54 PF02698 DUF218: DUF218 domain 36.1 1.1E+02 0.0024 26.3 6.2 44 101-151 52-95 (155)
55 COG4416 Com Mu-like prophage p 36.0 11 0.00024 27.7 -0.1 36 1-37 1-39 (60)
56 PLN00162 transport protein sec 35.7 25 0.00053 39.4 2.4 34 3-36 52-89 (761)
57 COG2830 Uncharacterized protei 34.9 35 0.00075 31.2 2.7 19 153-171 7-25 (214)
58 smart00109 C1 Protein kinase C 34.8 25 0.00054 24.0 1.5 30 3-34 10-39 (49)
59 cd00029 C1 Protein kinase C co 34.6 26 0.00056 24.1 1.6 30 4-34 11-40 (50)
60 PF10264 Stork_head: Winged he 34.5 1.2E+02 0.0025 24.3 5.3 44 105-169 32-75 (80)
61 PF03811 Zn_Tnp_IS1: InsA N-te 33.4 39 0.00084 22.7 2.1 26 4-29 5-36 (36)
62 COG1350 Predicted alternative 32.9 32 0.0007 34.8 2.4 34 138-171 384-419 (432)
63 PF13453 zf-TFIIB: Transcripti 31.5 36 0.00078 23.1 1.8 27 6-32 1-29 (41)
64 PRK11827 hypothetical protein; 31.2 39 0.00084 25.5 2.0 34 3-36 7-40 (60)
65 TIGR01979 sufS cysteine desulf 30.6 2.1E+02 0.0044 28.7 8.0 56 104-168 63-120 (403)
66 PRK06107 aspartate aminotransf 30.4 2.2E+02 0.0047 28.7 8.1 50 100-161 71-122 (402)
67 PRK08361 aspartate aminotransf 29.9 2.6E+02 0.0056 28.0 8.5 50 106-167 77-128 (391)
68 TIGR03402 FeS_nifS cysteine de 29.7 2E+02 0.0044 28.5 7.7 57 102-167 41-97 (379)
69 PF08357 SEFIR: SEFIR domain; 29.6 65 0.0014 27.7 3.6 51 102-164 15-67 (150)
70 PF12760 Zn_Tnp_IS1595: Transp 29.5 42 0.00092 23.4 1.9 26 5-30 19-45 (46)
71 cd02340 ZZ_NBR1_like Zinc fing 29.4 45 0.00098 23.1 2.0 22 5-30 1-22 (43)
72 PRK13130 H/ACA RNA-protein com 29.3 51 0.0011 24.5 2.4 27 4-36 5-31 (56)
73 PF03568 Peptidase_C50: Peptid 28.7 95 0.0021 31.7 5.1 52 95-169 269-320 (383)
74 PLN02994 1-aminocyclopropane-1 28.5 1E+02 0.0022 27.4 4.6 51 99-161 92-146 (153)
75 cd00615 Orn_deC_like Ornithine 28.3 3.6E+02 0.0078 25.9 9.0 118 96-231 52-173 (294)
76 PRK11088 rrmA 23S rRNA methylt 28.3 40 0.00086 32.4 2.2 29 4-34 2-30 (272)
77 PF07754 DUF1610: Domain of un 28.2 55 0.0012 20.1 2.0 22 7-29 1-23 (24)
78 PTZ00377 alanine aminotransfer 27.8 1.6E+02 0.0035 30.7 6.8 46 105-161 121-168 (481)
79 COG5178 PRP8 U5 snRNP spliceos 27.8 50 0.0011 38.6 3.0 12 68-79 22-33 (2365)
80 PF01878 EVE: EVE domain; Int 27.8 48 0.001 28.6 2.4 17 149-165 36-52 (143)
81 PRK00241 nudC NADH pyrophospha 27.6 46 0.00099 32.2 2.4 32 3-34 98-129 (256)
82 COG1198 PriA Primosomal protei 27.5 38 0.00083 37.8 2.1 28 4-31 444-471 (730)
83 PLN02450 1-aminocyclopropane-1 27.4 2.4E+02 0.0052 29.5 8.0 50 105-166 92-148 (468)
84 COG1645 Uncharacterized Zn-fin 26.8 44 0.00096 29.2 1.9 30 5-36 29-59 (131)
85 PRK14873 primosome assembly pr 26.7 39 0.00084 37.3 2.0 27 4-30 392-418 (665)
86 KOG1924 RhoA GTPase effector D 26.6 88 0.0019 35.1 4.5 39 34-76 550-588 (1102)
87 cd06259 YdcF-like YdcF-like. Y 26.3 1.6E+02 0.0035 25.1 5.6 59 81-152 35-93 (150)
88 TIGR00595 priA primosomal prot 26.2 43 0.00094 35.6 2.2 29 4-32 222-250 (505)
89 KOG3425 Uncharacterized conser 25.8 74 0.0016 27.5 3.1 25 142-166 11-35 (128)
90 smart00834 CxxC_CXXC_SSSS Puta 25.7 32 0.00069 22.9 0.7 26 5-30 6-34 (41)
91 PLN02651 cysteine desulfurase 25.6 2.8E+02 0.0062 27.4 7.9 55 105-168 45-100 (364)
92 PF04135 Nop10p: Nucleolar RNA 25.5 44 0.00096 24.6 1.5 29 1-36 1-31 (53)
93 COG2816 NPY1 NTP pyrophosphohy 25.5 46 0.001 32.7 2.0 110 4-146 111-220 (279)
94 PRK05942 aspartate aminotransf 25.3 3.5E+02 0.0076 27.1 8.6 46 106-162 80-127 (394)
95 KOG4684 Uncharacterized conser 25.1 20 0.00044 33.8 -0.5 34 3-36 169-203 (275)
96 PF13768 VWA_3: von Willebrand 24.9 2E+02 0.0044 24.5 5.9 46 122-169 2-47 (155)
97 cd06502 TA_like Low-specificit 24.7 5.5E+02 0.012 24.6 9.6 52 103-168 32-83 (338)
98 PRK09814 beta-1,6-galactofuran 24.4 1.6E+02 0.0035 28.9 5.8 55 105-166 21-75 (333)
99 cd06446 Trp-synth_B Tryptophan 24.4 2E+02 0.0044 29.0 6.5 33 139-171 330-362 (365)
100 TIGR00758 UDG_fam4 uracil-DNA 24.3 3.8E+02 0.0081 24.0 7.7 71 80-152 20-95 (173)
101 PF12773 DZR: Double zinc ribb 24.2 35 0.00077 23.9 0.7 27 4-31 12-38 (50)
102 PF13248 zf-ribbon_3: zinc-rib 24.1 49 0.0011 20.3 1.3 23 3-29 1-23 (26)
103 PRK00809 hypothetical protein; 24.0 69 0.0015 28.3 2.7 19 149-167 31-50 (144)
104 PF10058 DUF2296: Predicted in 24.0 49 0.0011 24.3 1.5 27 5-31 23-53 (54)
105 PRK00432 30S ribosomal protein 23.6 61 0.0013 23.4 1.9 25 6-31 22-46 (50)
106 PF00266 Aminotran_5: Aminotra 23.5 3.8E+02 0.0082 26.5 8.3 56 106-170 46-102 (371)
107 PF08541 ACP_syn_III_C: 3-Oxoa 23.4 1.2E+02 0.0026 23.6 3.8 56 111-170 26-83 (90)
108 PRK02948 cysteine desulfurase; 23.3 3E+02 0.0065 27.3 7.6 54 105-167 45-99 (381)
109 KOG0256 1-aminocyclopropane-1- 23.2 4.6E+02 0.01 27.5 8.7 34 196-231 243-276 (471)
110 TIGR00100 hypA hydrogenase nic 23.2 44 0.00096 28.2 1.3 28 3-32 69-96 (115)
111 COG1326 Uncharacterized archae 23.2 65 0.0014 30.0 2.4 34 1-35 1-43 (201)
112 COG0079 HisC Histidinol-phosph 23.1 5.8E+02 0.013 25.8 9.6 48 104-163 58-106 (356)
113 PF01485 IBR: IBR domain; Int 23.1 52 0.0011 23.7 1.5 30 5-34 19-52 (64)
114 PRK06260 threonine synthase; V 22.9 2.1E+02 0.0045 29.2 6.4 35 137-171 335-371 (397)
115 PRK05638 threonine synthase; V 22.8 2.6E+02 0.0056 29.0 7.2 39 137-175 323-363 (442)
116 PF14353 CpXC: CpXC protein 22.8 76 0.0016 26.9 2.7 32 4-35 1-51 (128)
117 PF07282 OrfB_Zn_ribbon: Putat 22.5 64 0.0014 24.2 2.0 26 6-31 30-55 (69)
118 PLN03026 histidinol-phosphate 22.3 2E+02 0.0043 28.9 6.1 46 105-162 88-133 (380)
119 PRK14012 cysteine desulfurase; 22.2 3.1E+02 0.0067 27.6 7.5 54 105-167 51-105 (404)
120 COG2194 Predicted membrane-ass 22.0 1E+02 0.0022 33.3 4.0 26 144-170 433-458 (555)
121 PRK00420 hypothetical protein; 22.0 73 0.0016 27.1 2.3 30 5-35 24-53 (112)
122 PRK06108 aspartate aminotransf 21.7 4.7E+02 0.01 25.7 8.6 55 100-166 62-118 (382)
123 PRK05580 primosome assembly pr 21.5 59 0.0013 35.9 2.2 28 4-31 390-417 (679)
124 TIGR00263 trpB tryptophan synt 21.3 2E+02 0.0044 29.3 5.9 34 137-170 344-377 (385)
125 KOG2907 RNA polymerase I trans 21.2 37 0.00081 28.8 0.4 34 3-36 6-39 (116)
126 cd02345 ZZ_dah Zinc finger, ZZ 21.0 66 0.0014 22.9 1.6 24 5-32 1-25 (49)
127 cd02338 ZZ_PCMF_like Zinc fing 21.0 64 0.0014 23.0 1.6 24 5-32 1-25 (49)
128 PRK07591 threonine synthase; V 21.0 2.5E+02 0.0054 29.0 6.5 35 137-171 358-394 (421)
129 KOG4146 Ubiquitin-like protein 20.8 4.9E+02 0.011 21.5 6.7 63 141-224 37-100 (101)
130 PF08271 TF_Zn_Ribbon: TFIIB z 20.8 76 0.0016 21.7 1.9 28 6-33 2-30 (43)
131 PRK12380 hydrogenase nickel in 20.4 53 0.0012 27.7 1.2 27 3-31 69-95 (113)
132 PRK13355 bifunctional HTH-doma 20.3 4.6E+02 0.0099 27.6 8.5 43 107-161 193-237 (517)
133 KOG4044 Mitochondrial associat 20.2 61 0.0013 29.7 1.6 23 210-232 126-148 (201)
No 1
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.1e-70 Score=519.88 Aligned_cols=319 Identities=45% Similarity=0.789 Sum_probs=268.1
Q ss_pred CCCcccCCCCCCccccCCCCceeeccccCceecccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 016243 1 MLMLVDCSKCRTTLQLPPGAQSIRCAICQAITHIADPRSGPPPPSSSSSSSYQPGHVPPSAVAPSPYNHAPPGQPPHAQG 80 (392)
Q Consensus 1 ~~~~~~C~~C~~~l~~p~~a~~vrC~~C~~vt~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (392)
+.+.++|+ |++++|+||||+. ||+.||+||.+..++..|||..+ ++ +.|+|+ |+.++|...+
T Consensus 1 ~~~~~~~~-~~~p~~~pp~ar~-q~~~~~~~~~~~~~~~~ppP~~~----~~---------~~PpPq---~~~~~~~~~g 62 (362)
T KOG1546|consen 1 PNNLVGCN-CQRPMAPPPGARY-QCAGCHAVTQIAQPRIQPPPQPS----SY---------PNPPPQ---PPYQYPQMAG 62 (362)
T ss_pred CCccccCC-CCCCCCCCCCCcc-cccccceeeeecccCcCCCCCCC----CC---------CCCCCC---CCCCCccccc
Confidence 35789998 9999999999999 99999999999987776665432 11 111121 2345677889
Q ss_pred ceEEEEEEeCCCCCCCCCcchHHHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEE
Q 016243 81 RKRALIVGVSYRHTNHELKGCINDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLL 160 (392)
Q Consensus 81 ~k~ALlIGI~Y~~~~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~ll 160 (392)
||+||||||||.++..+|+||+|||.+|+++|.++|||+.++|++|||++.++.++||++||++||+||++.+++||+||
T Consensus 63 krrAvLiGINY~gTk~ELrGCINDv~~M~~~Lv~rfGFs~ddI~~LtDt~~s~~~~PT~~Nir~Al~wLV~~aq~gD~Lv 142 (362)
T KOG1546|consen 63 KRRAVLIGINYPGTKNELRGCINDVHRMRKLLVERFGFSEDDILMLTDTDESPVRIPTGKNIRRALRWLVESAQPGDSLV 142 (362)
T ss_pred cceEEEEeecCCCcHHHHhhhHHHHHHHHHHHHHhhCCChhheEEEecCCCcccccCcHHHHHHHHHHHHhcCCCCCEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCccccCCCCCCCCCCcceeEEeccCCCCCcccHHHHHHhhcCcCCCCCeEEEEEeCCCCCCCCCCcchhccc---
Q 016243 161 FHFSGHGSQQRNYNGEEVDGYDETLCPVDFETQGMIVDDEINTTLVRPLPRGARLHAIIDACHSGTVLDLPFLCRMD--- 237 (392)
Q Consensus 161 fYFSGHG~~~~d~~gde~dG~de~Lvp~D~~~~g~i~d~eL~~~L~~~l~~g~~l~vIlD~C~SG~~~~~p~~~~~~--- 237 (392)
|||||||.+.++.+|||.||+||+|+|.|++.+|.|.|||+++.||++|++|+++++|+|+||||+++|+|++++++
T Consensus 143 fHYSGHGtr~~~~~gDe~dG~DE~I~P~D~~t~G~iIdDe~~r~lV~plp~G~~lt~I~DSCHSGgliDlp~i~~~~~~i 222 (362)
T KOG1546|consen 143 FHYSGHGTRQPDTNGDEVDGYDETIVPCDHNTQGPIIDDEIFRILVRPLPKGCKLTAISDSCHSGGLIDLPEIERTKGVI 222 (362)
T ss_pred EEecCCCCcCCCCCCCCCCCCcceeecccccccccccchHHHHHHHhccCCCceEEEEeecccCCCcccchhheeccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccCccccccCCCCCCccccc-------------------------------------CCCCEEEEEecCCCCcccccccC
Q 016243 238 RQGKYIWEDHRPRSGMWKGT-------------------------------------SGGEAISFSGCDDNQTSADTSAL 280 (392)
Q Consensus 238 r~g~~~~e~~~p~~~~~k~~-------------------------------------~~g~~i~~SAc~~~q~A~e~~~~ 280 (392)
|.+.+.||++++..+.++++ +..++|+||+|+++|+|+|....
T Consensus 223 r~~~l~~e~~~d~l~~~tG~~~ge~~~i~~~l~d~f~~dts~~~~~~~~~~~~~~~~~~d~~illSgcqadqtSad~~~~ 302 (362)
T KOG1546|consen 223 RNRNLPWEDHRDLLKAQTGTDGGEVGKIRGCLDDIFGEDTSPLPNGTIGDLGRQLKDSHDNGILLSGCQADQTSADASTY 302 (362)
T ss_pred ccCccchHHhHHHHHhhcCCCCceeeeeecchhhhhcccCCCCCCcchhhhhhhcccCCCCceEEecccccccccccccC
Confidence 88888888766432222221 12456888888888888887766
Q ss_pred CCCCCCChhHHHHHHHHHcCCC-CCHHHHHHHHHHHHhccCCCCCcccCCcccccceeeeccCCCCCCCcccceEEeecc
Q 016243 281 SKITSTGAMTYSFIQAIERGHG-ATYGSMLNSMRSTIRNTDSGSELSGAGGLVTSLVTMLLTGGSLSGGFRQVFMFVMFA 359 (392)
Q Consensus 281 g~~~~~G~FT~~Ll~aL~~~~~-iT~~~L~~~vr~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~p~l~~~~ 359 (392)
| ...|+|++++.+.|.++++ ++..+|.-..+..+++.. +.|+|+|.
T Consensus 303 G--~~~gAms~Aiq~i~~~n~g~~~~~~lvl~~~~~~~~~g----------------------------~sQ~P~L~--- 349 (362)
T KOG1546|consen 303 G--HLYGAMSNAIQEILTENKGRITNKLLVLRARGALKKQG----------------------------FSQEPGLY--- 349 (362)
T ss_pred C--cchhHHHHHHHHHHhcCcccchhHHHHHHHhhhhhccC----------------------------cccCcccc---
Confidence 5 3478888888888877654 455555544444443322 57999999
Q ss_pred ccccCCCCCccccccchh
Q 016243 360 NCYGYGLSSSLFDRFVSR 377 (392)
Q Consensus 360 ~~~~~~~~~~~~d~~~~~ 377 (392)
+++.||.+..-
T Consensus 350 -------csd~~~~~~~~ 360 (362)
T KOG1546|consen 350 -------CSDPFDVAPFI 360 (362)
T ss_pred -------CCcccccccee
Confidence 99999987653
No 2
>PF00656 Peptidase_C14: Caspase domain; InterPro: IPR011600 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of sequences represent the p20 (20kDa) and p10 (10kDa) subunits of caspases, which together form the catalytic domain of the caspase and are derived from the p45 (45 kDa) precursor (IPR002398 from INTERPRO) []. Caspases (Cysteine-dependent ASPartyl-specific proteASE) are cysteine peptidases that belong to the MEROPS peptidase family C14 (caspase family, clan CD) based on the architecture of their catalytic dyad or triad []. Caspases are tightly regulated proteins that require zymogen activation to become active, and once active can be regulated by caspase inhibitors. Activated caspases act as cysteine proteases, using the sulphydryl group of a cysteine side chain for catalysing peptide bond cleavage at aspartyl residues in their substrates. The catalytic cysteine and histidine residues are on the p20 subunit after cleavage of the p45 precursor. Caspases are mainly involved in mediating cell death (apoptosis) [, , ]. They have two main roles within the apoptosis cascade: as initiators that trigger the cell death process, and as effectors of the process itself. Caspase-mediated apoptosis follows two main pathways, one extrinsic and the other intrinsic or mitochondrial-mediated. The extrinsic pathway involves the stimulation of various TNF (tumour necrosis factor) cell surface receptors on cells targeted to die by various TNF cytokines that are produced by cells such as cytotoxic T cells. The activated receptor transmits the signal to the cytoplasm by recruiting FADD, which forms a death-inducing signalling complex (DISC) with caspase-8. The subsequent activation of caspase-8 initiates the apoptosis cascade involving caspases 3, 4, 6, 7, 9 and 10. The intrinsic pathway arises from signals that originate within the cell as a consequence of cellular stress or DNA damage. The stimulation or inhibition of different Bcl-2 family receptors results in the leakage of cytochrome c from the mitochondria, and the formation of an apoptosome composed of cytochrome c, Apaf1 and caspase-9. The subsequent activation of caspase-9 initiates the apoptosis cascade involving caspases 3 and 7, among others. At the end of the cascade, caspases act on a variety of signal transduction proteins, cytoskeletal and nuclear proteins, chromatin-modifying proteins, DNA repair proteins and endonucleases that destroy the cell by disintegrating its contents, including its DNA. The different caspases have different domain architectures depending upon where they fit into the apoptosis cascades, however they all carry the catalytic p10 and p20 subunits. Caspases can have roles other than in apoptosis, such as caspase-1 (interleukin-1 beta convertase) (3.4.22.36 from EC), which is involved in the inflammatory process. The activation of apoptosis can sometimes lead to caspase-1 activation, providing a link between apoptosis and inflammation, such as during the targeting of infected cells. Caspases may also be involved in cell differentiation [].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 1M72_C 2NN3_C 3V4L_A 3IBF_B 2QLF_D 2QLB_C 3IBC_B 2QL9_A 3R5K_B 3H1P_A ....
Probab=100.00 E-value=6.5e-33 Score=261.27 Aligned_cols=218 Identities=33% Similarity=0.499 Sum_probs=160.2
Q ss_pred eEEEEEEeCCCCCCCCCcchHHHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEE
Q 016243 82 KRALIVGVSYRHTNHELKGCINDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLF 161 (392)
Q Consensus 82 k~ALlIGI~Y~~~~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llf 161 (392)
|+||||||+||+...+|+|++|||+.|+++| +++||++++| |.++ ||+++|+++|++|++..+++|.++|
T Consensus 1 ~~AliIg~~~y~~~~~L~~~~~D~~~~~~~L-~~~gf~~~~~--l~~~-------~t~~~i~~~l~~l~~~~~~~D~~~~ 70 (248)
T PF00656_consen 1 KRALIIGVNYYQNPPPLPGAVNDAEAMAEAL-EKLGFDVENI--LIDN-------ATRANILKALRELLQRAQPGDSVVF 70 (248)
T ss_dssp EEEEEEEESSTSSTCHCTTHHHHHHHHHHHH-HHTTEEEEEE--EEES-------SSHHHHHHHHHHHHTSGGTCSEEEE
T ss_pred CEEEEEEeeCCCCCCCCCCHHHHHHHHHHHH-HHcCCceeec--cccc-------hHHHHHHHHHhhhhccCCCCCeeEE
Confidence 7999999997776799999999999999999 6789998777 4433 9999999999999999999999999
Q ss_pred EEecCccccCCCCCCCCCCcceeEEeccCCCCCcccHHHHHHhhcCcCCCCCeEEEEEeCCCCCCCCCCcchhcccccCc
Q 016243 162 HFSGHGSQQRNYNGEEVDGYDETLCPVDFETQGMIVDDEINTTLVRPLPRGARLHAIIDACHSGTVLDLPFLCRMDRQGK 241 (392)
Q Consensus 162 YFSGHG~~~~d~~gde~dG~de~Lvp~D~~~~g~i~d~eL~~~L~~~l~~g~~l~vIlD~C~SG~~~~~p~~~~~~r~g~ 241 (392)
||||||.+.++..+++..+++++++|.|.. .+.++++..++.+.++...+ ++||||||||.+.+........+...
T Consensus 71 yfsGHG~~~~~~~~~~~~~~d~~~~~~d~~---~~~~~~l~~~~~~~~~~~~k-~~ilD~C~sg~~~~~~~~~~~~~~~~ 146 (248)
T PF00656_consen 71 YFSGHGIQVDGEGGDEDSGYDGYLLPLDAN---LILDDELRDLLCKSLPKKPK-LFILDCCRSGGFIDGLSSSSGESSKR 146 (248)
T ss_dssp EEESEEETETTCCSTEEEETSSEEEEHHHH---EEHHHHTSTTTTGGGTTS-E-EEEEESESSSBTBCEEEEEESSSTSS
T ss_pred EEeccccccCCccCcccccccceeeecchh---hhHHHHHhhhhhhhccCCcc-EEeeccccCCccCCcccccccccccc
Confidence 999999887765444556778899998854 56777777776554665567 89999999999877533211111000
Q ss_pred c---ccccCCCC-CCcccccCCCCEEEEEecCCCCcccccccCCCCCCCChhHHHHHHHHHcC--------CCCCHHHHH
Q 016243 242 Y---IWEDHRPR-SGMWKGTSGGEAISFSGCDDNQTSADTSALSKITSTGAMTYSFIQAIERG--------HGATYGSML 309 (392)
Q Consensus 242 ~---~~e~~~p~-~~~~k~~~~g~~i~~SAc~~~q~A~e~~~~g~~~~~G~FT~~Ll~aL~~~--------~~iT~~~L~ 309 (392)
. ......+. ..........+.++++||.++|+|+|... ..+|+||++|+++|++. ..+++.+|+
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~as~~~~~s~e~~~----~~~g~ft~~L~~~L~~~~~~~~~~~~~~~l~~~~ 222 (248)
T PF00656_consen 147 EERKLSSSIPPEDPNRSDVPSPSGFIVLSASRPGQTSYEDSP----GSGGLFTYALLEALKGNAADDPNQSWDELLEELL 222 (248)
T ss_dssp -EECHCCCCCCSSCCSEEEETTTSEEEEESSSTTBCEEEECT----TTEEHHHHHHHHHHHHHTTTSTTCCTTSBHHHHH
T ss_pred ccccccccccccccccccccCCCCcEEEEeccccceeecccC----ccCHHHHHHHHHHHHhhcccccchhHHHHHHHHH
Confidence 0 00000000 01111223456889999999999999831 47899999999999752 136777888
Q ss_pred HHHHHHHh
Q 016243 310 NSMRSTIR 317 (392)
Q Consensus 310 ~~vr~~v~ 317 (392)
.++.+.+.
T Consensus 223 ~~v~~~~~ 230 (248)
T PF00656_consen 223 TEVNQKVA 230 (248)
T ss_dssp HHHHHHHH
T ss_pred HHHHhHCC
Confidence 88877776
No 3
>cd00032 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
Probab=99.80 E-value=1.1e-17 Score=159.58 Aligned_cols=205 Identities=14% Similarity=0.106 Sum_probs=145.0
Q ss_pred CCceEEEEEEeC-CCCCCCCCcchHHHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHH-hCCCC
Q 016243 79 QGRKRALIVGVS-YRHTNHELKGCINDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQ-GCQPG 156 (392)
Q Consensus 79 ~~~k~ALlIGI~-Y~~~~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~-~~~~g 156 (392)
.++++|||||+. |.....+++|+.+|++.|+++|+ .+||. |.+..| +|+++|+++|+++.+ +.+..
T Consensus 7 ~~~g~aLII~n~~f~~~~~~r~g~~~D~~~l~~~f~-~lgF~---V~~~~n--------lt~~~~~~~l~~f~~~~~~~~ 74 (243)
T cd00032 7 KRRGLALIINNENFDKGLKDRDGTDVDAENLTKLFE-SLGYE---VEVKNN--------LTAEEILEELKEFASPDHSDS 74 (243)
T ss_pred CCCCEEEEEechhcCCCCCCCCChHHHHHHHHHHHH-HCCCE---EEEeCC--------CCHHHHHHHHHHHHhccCCCC
Confidence 478999999999 65436789999999999999998 58995 777766 899999999999985 78899
Q ss_pred CEEEEEEecCccccCCCCCCCCCCcceeEEeccCCCCCcccHHHHHHhhcC-c---CCCCCeEEEEEeCCCCCCCCCCcc
Q 016243 157 DSLLFHFSGHGSQQRNYNGEEVDGYDETLCPVDFETQGMIVDDEINTTLVR-P---LPRGARLHAIIDACHSGTVLDLPF 232 (392)
Q Consensus 157 D~llfYFSGHG~~~~d~~gde~dG~de~Lvp~D~~~~g~i~d~eL~~~L~~-~---l~~g~~l~vIlD~C~SG~~~~~p~ 232 (392)
|.++|||+|||.+ .+|++.|. ..+.-++|.+.+.. . |....| ++|||||+.........
T Consensus 75 d~~v~~~~sHG~~-------------~~l~~~D~---~~v~l~~i~~~f~~~~~~sl~~kPK-l~~iqACRg~~~~~~~~ 137 (243)
T cd00032 75 DSFVCVILSHGEE-------------GGIYGTDG---DVVPIDEITSLFNGDNCPSLAGKPK-LFFIQACRGDELDLGVE 137 (243)
T ss_pred CeeEEEECCCCCC-------------CEEEEecC---cEEEHHHHHHhhccCCCccccCCCc-EEEEECCCCCcCCCcee
Confidence 9999999999975 18999995 24555777776641 1 222234 69999999765533210
Q ss_pred hhcccccCccc--cccCCCCCCcccccCCCCEEEEEecCCCCcccccccCCCCCCCChhHHHHHHHHHcC-CCCCHHHHH
Q 016243 233 LCRMDRQGKYI--WEDHRPRSGMWKGTSGGEAISFSGCDDNQTSADTSALSKITSTGAMTYSFIQAIERG-HGATYGSML 309 (392)
Q Consensus 233 ~~~~~r~g~~~--~e~~~p~~~~~k~~~~g~~i~~SAc~~~q~A~e~~~~g~~~~~G~FT~~Ll~aL~~~-~~iT~~~L~ 309 (392)
. ...+... -+......+...-....+.++..|+.++..|++.. ..+|+|+.+|++.|... +.....+|+
T Consensus 138 -~--~~~~~~~~~~~~~~~~~~~~~~p~~~d~lv~ysT~pG~~a~r~~-----~~gS~fi~~l~~~l~~~~~~~~l~~il 209 (243)
T cd00032 138 -V--DSGADEPPDVETEAEDDAVQTIPVEADFLVAYSTVPGYVSWRNT-----KKGSWFIQSLCQVLRKYAHSLDLLDIL 209 (243)
T ss_pred -c--cCccccccccccccccccccCCCCcccEEEEecCCCCeEeecCC-----CCCCEeHHHHHHHHHHhCCCCcHHHHH
Confidence 0 0000000 00000000111111223455555688999998875 36899999999999874 358899999
Q ss_pred HHHHHHHhccC
Q 016243 310 NSMRSTIRNTD 320 (392)
Q Consensus 310 ~~vr~~v~~~~ 320 (392)
..|++.|....
T Consensus 210 ~~V~~~V~~~~ 220 (243)
T cd00032 210 TKVNRKVAEKF 220 (243)
T ss_pred HHHHHHHhhhh
Confidence 99999998876
No 4
>smart00115 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
Probab=99.78 E-value=4.6e-17 Score=155.27 Aligned_cols=204 Identities=14% Similarity=0.098 Sum_probs=143.8
Q ss_pred CCceEEEEEEeCCCCCCCCCcchHHHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHh--CCCC
Q 016243 79 QGRKRALIVGVSYRHTNHELKGCINDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQG--CQPG 156 (392)
Q Consensus 79 ~~~k~ALlIGI~Y~~~~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~--~~~g 156 (392)
.++++|||||+..+....+++|+.+||+.|+++|+ .+||. |.+..| +|+++|+++|+++.++ .+..
T Consensus 6 ~p~g~alII~n~~f~~~~~r~g~~~D~~~l~~~f~-~lgF~---V~~~~d--------lt~~em~~~l~~~~~~~~~~~~ 73 (241)
T smart00115 6 KPRGLALIINNENFHSLPRRNGTDVDAENLTELFQ-SLGYE---VHVKNN--------LTAEEMLEELKEFAERPEHSDS 73 (241)
T ss_pred CCCcEEEEEECccCCCCcCCCCcHHHHHHHHHHHH-HCCCE---EEEecC--------CCHHHHHHHHHHHHhccccCCC
Confidence 46899999999933346899999999999999998 58996 777776 8999999999999874 5589
Q ss_pred CEEEEEEecCccccCCCCCCCCCCcceeEEeccCCCCCcccHHHHHHhhcC----cCCCCCeEEEEEeCCCCCCCCCCcc
Q 016243 157 DSLLFHFSGHGSQQRNYNGEEVDGYDETLCPVDFETQGMIVDDEINTTLVR----PLPRGARLHAIIDACHSGTVLDLPF 232 (392)
Q Consensus 157 D~llfYFSGHG~~~~d~~gde~dG~de~Lvp~D~~~~g~i~d~eL~~~L~~----~l~~g~~l~vIlD~C~SG~~~~~p~ 232 (392)
|.++|||+|||.. .+|++.|.. .+.-++|.+.+.. .|....| ++|||||+....... .
T Consensus 74 d~~v~~~~sHG~~-------------~~l~~~D~~---~v~l~~i~~~f~~~~c~~L~~kPK-lffiqACRg~~~~~g-~ 135 (241)
T smart00115 74 DSFVCVLLSHGEE-------------GGIYGTDHS---PLPLDEIFSLFNGDNCPSLAGKPK-LFFIQACRGDELDGG-V 135 (241)
T ss_pred CEEEEEEcCCCCC-------------CeEEEecCC---EEEHHHHHHhccccCChhhcCCCc-EEEEeCCCCCCCCCC-e
Confidence 9999999999953 289999943 4566778777631 1222244 699999986533221 1
Q ss_pred hhcccccCccccccCCCCCCcccccCCCCEEEEEecCCCCcccccccCCCCCCCChhHHHHHHHHHcC-CCCCHHHHHHH
Q 016243 233 LCRMDRQGKYIWEDHRPRSGMWKGTSGGEAISFSGCDDNQTSADTSALSKITSTGAMTYSFIQAIERG-HGATYGSMLNS 311 (392)
Q Consensus 233 ~~~~~r~g~~~~e~~~p~~~~~k~~~~g~~i~~SAc~~~q~A~e~~~~g~~~~~G~FT~~Ll~aL~~~-~~iT~~~L~~~ 311 (392)
.. +.....-+......+..+-....+.++..|+.++..|++.. ..+++|+.+|++.|+.. +..+..+|+..
T Consensus 136 ~~---~~~~~~~~~~~~~~~~~~~p~~~D~li~ysT~pG~va~r~~-----~~gS~fi~~L~~~l~~~~~~~~l~~ilt~ 207 (241)
T smart00115 136 PV---EDDVDDPPTEFEDDAIYKIPVEADFLAAYSTTPGYVSWRNP-----TRGSWFIQSLCQVLKEYARSLDLLDILTE 207 (241)
T ss_pred ec---ccccccccccccccccccCCCcCcEEEEEeCCCCeEeecCC-----CCCchHHHHHHHHHHHcCCCCCHHHHHHH
Confidence 00 00000000000001111112233455556788999998875 36799999999999873 46899999999
Q ss_pred HHHHHhccC
Q 016243 312 MRSTIRNTD 320 (392)
Q Consensus 312 vr~~v~~~~ 320 (392)
|++.|....
T Consensus 208 V~~~V~~~~ 216 (241)
T smart00115 208 VNRKVAVKF 216 (241)
T ss_pred HHHHHhhhh
Confidence 999998876
No 5
>PF01650 Peptidase_C13: Peptidase C13 family; InterPro: IPR001096 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C13 (legumain family, clan CD). A type example is legumain from Canavalia ensiformis (Jack bean, Horse bean). The blood fluke parasite Schistosoma mansoni has two cysteine proteases in its digestive tract, one a cathepsin B-like protease, the other termed hemoglobinase [, ]. The latter has been hard to purify, free of cathepsin B, and expressed forms in Escherichia coli prove to be inactive, suggesting that hemoglobinase may act in association with cathepsin B [, ]. Plant vacuolar processing enzyme and legumain from legumes [] have been shown to have sequence and functional similarity to hemoglobinase. The catalytic residues of the family are currently unknown, but sequence alignments reveal one totally conserved cysteine and two totally conserved histidines.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis
Probab=99.51 E-value=3.3e-13 Score=129.87 Aligned_cols=192 Identities=16% Similarity=0.228 Sum_probs=131.0
Q ss_pred eEEEEEEeC-CCCCCCCCcchHHHHHHHHHHHHhccCCCCCceEEccCCCC-----CC----------------------
Q 016243 82 KRALIVGVS-YRHTNHELKGCINDARCMKYMLTNRFKFPESSIVMLTEEDP-----DP---------------------- 133 (392)
Q Consensus 82 k~ALlIGI~-Y~~~~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~-----~~---------------------- 133 (392)
+|||||.=+ +.. +.+- ..|+-.|.++|++ +||++++|+++..++. +|
T Consensus 1 ~wAvlvagS~~~~---NYRh-~ad~~~~Y~~l~~-~G~~~~~Iil~~~dd~a~~~~Np~~g~i~~~~~~~n~y~~~~iDY 75 (256)
T PF01650_consen 1 NWAVLVAGSNGWF---NYRH-QADVCHAYQLLKR-NGIPDENIILMMYDDIACNPRNPFPGKIFNDPDGTNVYKGVEIDY 75 (256)
T ss_pred CEEEEEeccCCce---eeeE-ehHHHHHHHHHHH-cCCCCceEEEEecCCccchhhCCCCceEEeCCCcccccCCccccc
Confidence 589999877 321 2222 4899999999996 8999999987765441 11
Q ss_pred -CCCccHHHHHHHHHHHH-------HhCCCCCEEEEEEecCccccCCCCCCCCCCcceeEEeccCCCCCcccHHHHHHhh
Q 016243 134 -LKRPTKYNMRMALYWLI-------QGCQPGDSLLFHFSGHGSQQRNYNGEEVDGYDETLCPVDFETQGMIVDDEINTTL 205 (392)
Q Consensus 134 -~~~pT~~nI~~al~~L~-------~~~~~gD~llfYFSGHG~~~~d~~gde~dG~de~Lvp~D~~~~g~i~d~eL~~~L 205 (392)
-...|.+++++.|.--. -+..++|.|||||+|||... .|.-. ....|+..+|.++|
T Consensus 76 ~g~~v~~~~fl~vL~G~~~~~~~kvl~s~~~D~vfiy~~~HG~~~-------------~l~~~---~~~~l~~~~L~~~L 139 (256)
T PF01650_consen 76 RGEDVTPENFLNVLTGDKSVPSGKVLNSTENDNVFIYFTGHGGPG-------------FLKFP---DGEELTADDLADAL 139 (256)
T ss_pred cccccCHHHHHHHhcCCCCCCccccccCCCCCeEEEEEeccCCCC-------------cccCC---CcccccHHHHHHHH
Confidence 12456677776664111 15679999999999999863 22111 12468889999988
Q ss_pred cCcCCCC---CeEEEEEeCCCCCCCCCCcchhcccccCccccccCCCCCCcccccCCCCEEEEEecCCCCccccccc--C
Q 016243 206 VRPLPRG---ARLHAIIDACHSGTVLDLPFLCRMDRQGKYIWEDHRPRSGMWKGTSGGEAISFSGCDDNQTSADTSA--L 280 (392)
Q Consensus 206 ~~~l~~g---~~l~vIlD~C~SG~~~~~p~~~~~~r~g~~~~e~~~p~~~~~k~~~~g~~i~~SAc~~~q~A~e~~~--~ 280 (392)
. .+... .++++++|+|+||++.+. .. ...++++++|+..+|.|+-... .
T Consensus 140 ~-~m~~~~~y~~lv~~veaC~SGs~~~~-L~------------------------~~~nv~~iTAa~~~e~Sy~~~~~~~ 193 (256)
T PF01650_consen 140 D-KMHEKKRYKKLVFVVEACYSGSFFEG-LL------------------------KSPNVYVITAANADESSYGCYCSDD 193 (256)
T ss_pred H-HHHhhCCcceEEEEEecccccchhhc-cC------------------------CCCCEEEEecCCccccccccccccc
Confidence 4 33322 358999999999999864 10 1135788899999998875521 1
Q ss_pred C-CCCCCChhHHHHHHHHHcCC--CCCHHHHHHHHHHHHhccC
Q 016243 281 S-KITSTGAMTYSFIQAIERGH--GATYGSMLNSMRSTIRNTD 320 (392)
Q Consensus 281 g-~~~~~G~FT~~Ll~aL~~~~--~iT~~~L~~~vr~~v~~~~ 320 (392)
. +.--...|++.+++-+...+ ..|+.++|+++++.+....
T Consensus 194 ~~~~~l~d~fs~~~m~~~~~~~~~~~Tl~~~f~~v~~~~~~sh 236 (256)
T PF01650_consen 194 SIGTYLGDAFSYNWMEDSDSHPLSEETLDDQFEYVKRKTTGSH 236 (256)
T ss_pred ccccEeHHHHHHHhhhhhccCCccccCHHHHHHHHHHhcccch
Confidence 1 01113478888888887754 3799999999999986554
No 6
>COG4249 Uncharacterized protein containing caspase domain [General function prediction only]
Probab=99.48 E-value=1.1e-13 Score=139.56 Aligned_cols=159 Identities=21% Similarity=0.324 Sum_probs=111.5
Q ss_pred CccHHHHHHHHHHHHHhCCCCCEEEEEEecCccccCCCCCCCCCCcceeEEeccCCC-------CCcccHHHHHHhhcCc
Q 016243 136 RPTKYNMRMALYWLIQGCQPGDSLLFHFSGHGSQQRNYNGEEVDGYDETLCPVDFET-------QGMIVDDEINTTLVRP 208 (392)
Q Consensus 136 ~pT~~nI~~al~~L~~~~~~gD~llfYFSGHG~~~~d~~gde~dG~de~Lvp~D~~~-------~g~i~d~eL~~~L~~~ 208 (392)
.|++.+|+..|..+...+.+.|..+|||||||.... .+| ..|||+.|++. ++.+....+..++.
T Consensus 113 ~p~~~~V~~~~lD~~~~~~~~d~~~~~fsG~g~~~~-~d~------~~~lia~~t~p~~~a~~~~~~~s~~~~~~~~~-- 183 (380)
T COG4249 113 LPARTKVRRVLLDAARDNPPADTILFFFSGHGATPG-ADG------RAYLIAFDTRPGAVAYDGEGGISPYSVAQALH-- 183 (380)
T ss_pred CCchhHHHHHHHHHhhcCchhhhhhheeeccccccC-CCC------ceeEEeecCChhhhcccCCCcccHHHHHHHHH--
Confidence 678999999999999999999999999999999863 222 23999999874 24566666655442
Q ss_pred CCCCCeEEEEEeCCCCCCCCCCcchhcccccCccccccCCCCCCcccccCCCCEEEEEecCCCCcccccccCCCCCCCCh
Q 016243 209 LPRGARLHAIIDACHSGTVLDLPFLCRMDRQGKYIWEDHRPRSGMWKGTSGGEAISFSGCDDNQTSADTSALSKITSTGA 288 (392)
Q Consensus 209 l~~g~~l~vIlD~C~SG~~~~~p~~~~~~r~g~~~~e~~~p~~~~~k~~~~g~~i~~SAc~~~q~A~e~~~~g~~~~~G~ 288 (392)
+....+.++++|+||+|.+...-. .....|+... . ...-....+.+|.+.|.++|.+.+ .+|+
T Consensus 184 ~~~~~~ql~~~d~~~~~~~~~~~~------~~~~p~l~~s----~---~~~~~~~~~~~~ap~~~~~e~~~~----g~gv 246 (380)
T COG4249 184 LSEPGNQLVDLDACVRGDVFKATA------GQQRPWLAQS----L---AREFGFGILDSCAPDQQSAEAPEL----GHGV 246 (380)
T ss_pred hccCCceeehhhhhcchhhhcccc------cccchHhhhh----h---hcceeeeeccCCCCCccccccccc----cCce
Confidence 233356689999999998875311 1112233211 0 112245667789999999999876 4999
Q ss_pred hHHHHHHHHHcC---C-----CCCHHHHHHHHHHHHhccC
Q 016243 289 MTYSFIQAIERG---H-----GATYGSMLNSMRSTIRNTD 320 (392)
Q Consensus 289 FT~~Ll~aL~~~---~-----~iT~~~L~~~vr~~v~~~~ 320 (392)
||+++++++.+. . .++...++.+...++.+..
T Consensus 247 ~t~al~~~l~~~~~~a~~~~~~~~~~~~~~~~~~~~~q~~ 286 (380)
T COG4249 247 FTDALLEGLRGGRAAAEDLDGLRSKDGLLAYDYAETAQLP 286 (380)
T ss_pred eehhhhhcccccchhcccccchhhhhhhhhhhhhHHhhcc
Confidence 999999999972 1 2556666777666666554
No 7
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=99.00 E-value=2.2e-10 Score=74.60 Aligned_cols=31 Identities=48% Similarity=0.992 Sum_probs=29.3
Q ss_pred cccCCCCCCccccCCCCceeeccccCceecc
Q 016243 4 LVDCSKCRTTLQLPPGAQSIRCAICQAITHI 34 (392)
Q Consensus 4 ~~~C~~C~~~l~~p~~a~~vrC~~C~~vt~v 34 (392)
+++|++|++.|+||+||++|||++|+.||.|
T Consensus 1 q~~C~~C~t~L~yP~gA~~vrCs~C~~vt~v 31 (31)
T TIGR01053 1 QVVCGGCRTLLMYPRGASSVRCALCQTVNLV 31 (31)
T ss_pred CcCcCCCCcEeecCCCCCeEECCCCCeEecC
Confidence 5799999999999999999999999999975
No 8
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=98.80 E-value=2.2e-09 Score=66.13 Aligned_cols=25 Identities=52% Similarity=1.144 Sum_probs=24.1
Q ss_pred CCCCCCccccCCCCceeeccccCce
Q 016243 7 CSKCRTTLQLPPGAQSIRCAICQAI 31 (392)
Q Consensus 7 C~~C~~~l~~p~~a~~vrC~~C~~v 31 (392)
|++|++.|+||+||++|||+.|+.|
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~V 25 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHTV 25 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCcC
Confidence 8999999999999999999999976
No 9
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=98.26 E-value=6.6e-06 Score=73.53 Aligned_cols=106 Identities=18% Similarity=0.251 Sum_probs=74.1
Q ss_pred HHHHHHHHHHHHhcc-CCCCC-ceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEecCccccCCCCCCCCC
Q 016243 102 INDARCMKYMLTNRF-KFPES-SIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFHFSGHGSQQRNYNGEEVD 179 (392)
Q Consensus 102 ~nDa~~m~~~L~~~~-Gf~~~-~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfYFSGHG~~~~d~~gde~d 179 (392)
.+-.+.+.+.|+..+ .+... ......| ||.+++++.+..+-+.++. +.++|||-|||+..+-.+|
T Consensus 43 ~~~~~~I~~~l~~qY~~~~~~~~~~~~~d--------pt~e~~~~~~~~~R~~a~~-~RvLFHYnGhGvP~Pt~~G---- 109 (154)
T PF14538_consen 43 SKASEEIGKNLQSQYESWQPRARYKQSLD--------PTVEDLKRLCQSLRRNAKD-ERVLFHYNGHGVPRPTENG---- 109 (154)
T ss_pred hhHHHHHHHHHHHHHHHhCccCcEEEecC--------CCHHHHHHHHHHHHhhCCC-ceEEEEECCCCCCCCCCCC----
Confidence 355556677777543 23322 3445555 9999999999999888775 8999999999999866554
Q ss_pred CcceeEEeccCCCC-CcccHHHHHHhhcCcCCCCCeEEEEEeCCCCCCCCC
Q 016243 180 GYDETLCPVDFETQ-GMIVDDEINTTLVRPLPRGARLHAIIDACHSGTVLD 229 (392)
Q Consensus 180 G~de~Lvp~D~~~~-g~i~d~eL~~~L~~~l~~g~~l~vIlD~C~SG~~~~ 229 (392)
|-++..+...+ -.++-.||.+|+. .-.++|+||..+|.+++
T Consensus 110 ---eIw~f~~~~tqyip~si~dL~~~lg------~Psi~V~DC~~AG~il~ 151 (154)
T PF14538_consen 110 ---EIWVFNKNYTQYIPLSIYDLQSWLG------SPSIYVFDCSNAGSILN 151 (154)
T ss_pred ---eEEEEcCCCCcceEEEHHHHHHhcC------CCEEEEEECCcHHHHHH
Confidence 34544332222 1467788988873 45689999999997764
No 10
>KOG1349 consensus Gpi-anchor transamidase [Posttranslational modification, protein turnover, chaperones]
Probab=98.16 E-value=2.1e-05 Score=74.61 Aligned_cols=189 Identities=17% Similarity=0.247 Sum_probs=120.2
Q ss_pred CCceEEEEEEeC--CCCCCCCCcchHHHHHHHHHHHHhccCCCCCceEE-ccCCCC----C-------------------
Q 016243 79 QGRKRALIVGVS--YRHTNHELKGCINDARCMKYMLTNRFKFPESSIVM-LTEEDP----D------------------- 132 (392)
Q Consensus 79 ~~~k~ALlIGI~--Y~~~~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~-Ltd~~~----~------------------- 132 (392)
+.+.||+||--+ +++. + -+..+-.|...++ +.|+|.++|++ |.|+.. +
T Consensus 26 htnNwAVLv~tSRfwfNY----R-H~aNvl~~YrsvK-rlGipDsqIilmladd~acn~RN~~pg~Vy~n~~~~~nlygd 99 (309)
T KOG1349|consen 26 HTNNWAVLVCTSRFWFNY----R-HVANVLSVYRSVK-RLGIPDSQIILMLADDMACNSRNPRPGTVYNNENHALNLYGD 99 (309)
T ss_pred ccCceEEEEecchhhhhH----H-HHHHHHHHHHHHH-HcCCCcccEEEEeccccccccCCCCCcceeccccccccccCC
Confidence 688999999988 3332 1 3566777888887 68999999765 444321 1
Q ss_pred ------CCCCccHHHHHHHHHHHHH---------hCCCCCEEEEEEecCccccCCCCCCCCCCcceeEEeccCCCCCccc
Q 016243 133 ------PLKRPTKYNMRMALYWLIQ---------GCQPGDSLLFHFSGHGSQQRNYNGEEVDGYDETLCPVDFETQGMIV 197 (392)
Q Consensus 133 ------~~~~pT~~nI~~al~~L~~---------~~~~gD~llfYFSGHG~~~~d~~gde~dG~de~Lvp~D~~~~g~i~ 197 (392)
.....|-+|+++.|..-.. -...+..++||..|||.- .+|=-.|++ .|+
T Consensus 100 ~vevdyrgyevtvEnflr~LTgR~~~~tprSKrlltDe~SNIlIYmtGHGgd-------------~FlKFqd~e---elt 163 (309)
T KOG1349|consen 100 DVEVDYRGYEVTVENFLRVLTGRHPNNTPRSKRLLTDEGSNILIYLTGHGGD-------------GFLKFQDAE---ELT 163 (309)
T ss_pred cceeecccchhHHHHHHHHHcCCCCCCCchhhhhcccCCCcEEEEEccCCCc-------------cceecccHH---Hhh
Confidence 1224677777777642111 123678899999999952 266566654 467
Q ss_pred HHHHHHhhcCcC-CCC-CeEEEEEeCCCCCCCCCCcchhcccccCccccccCCCCCCcccccCCCCEEEEEecCCCCccc
Q 016243 198 DDEINTTLVRPL-PRG-ARLHAIIDACHSGTVLDLPFLCRMDRQGKYIWEDHRPRSGMWKGTSGGEAISFSGCDDNQTSA 275 (392)
Q Consensus 198 d~eL~~~L~~~l-~~g-~~l~vIlD~C~SG~~~~~p~~~~~~r~g~~~~e~~~p~~~~~k~~~~g~~i~~SAc~~~q~A~ 275 (392)
.+||.+.|.+-. ++. .++++++|+|.+.++.+.- .++ +++.++++.-+|.|+
T Consensus 164 s~dLadai~qm~e~~Ryneil~miDTCQaasly~~~-------------------------~sP-NVLav~SS~~ge~Sy 217 (309)
T KOG1349|consen 164 SDDLADAIQQMWEKKRYNEILFMIDTCQAASLYERF-------------------------YSP-NVLAVASSLVGEPSY 217 (309)
T ss_pred hHHHHHHHHHHHHhhhhceEEEEeeccchHHHHHhh-------------------------cCC-CeEEEeecccCCccc
Confidence 778888774322 222 3589999999876554310 122 577888888888776
Q ss_pred ccccCCCC--CCCChhHHHHHHHHHcC-C--CCCHHHHHHHHHHH
Q 016243 276 DTSALSKI--TSTGAMTYSFIQAIERG-H--GATYGSMLNSMRST 315 (392)
Q Consensus 276 e~~~~g~~--~~~G~FT~~Ll~aL~~~-~--~iT~~~L~~~vr~~ 315 (392)
....-... .---=|||+.++-|++. + ..|..+|++..-.+
T Consensus 218 Sh~~d~~Igv~vIDrftyy~l~flek~~~~~~~~l~dl~~s~~~~ 262 (309)
T KOG1349|consen 218 SHHSDSDIGVYVIDRFTYYTLEFLEKGIGAKNRTLQDLFDSCPKR 262 (309)
T ss_pred ccCCCcccceeeeccchHHHHHHHHhcccchhhhHHHHHHhCChh
Confidence 44321110 11234999999999873 1 24678887765443
No 11
>KOG1348 consensus Asparaginyl peptidases [Posttranslational modification, protein turnover, chaperones]
Probab=97.91 E-value=0.0002 Score=71.13 Aligned_cols=131 Identities=20% Similarity=0.325 Sum_probs=88.5
Q ss_pred CCCCceEEEEEE-eC-CCCCCCCCcchHHHHHHHHHHHHhccCCCCCceEEccCCC-----CC-----------------
Q 016243 77 HAQGRKRALIVG-VS-YRHTNHELKGCINDARCMKYMLTNRFKFPESSIVMLTEED-----PD----------------- 132 (392)
Q Consensus 77 ~~~~~k~ALlIG-I~-Y~~~~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~-----~~----------------- 132 (392)
...+++|||||. -| |++-++ ..|+---.++|+ +.|.+++||+++.-++ .|
T Consensus 41 ddggt~waVLVAGSngyyNYRH-----QADvcHAYqiLr-kgGikeEnIvv~MYDDIA~~~~NPrpG~iiN~P~G~DvY~ 114 (477)
T KOG1348|consen 41 DDGGTRWAVLVAGSNGYYNYRH-----QADVCHAYQILR-KGGIKEENIVVMMYDDIANNEENPRPGVIINRPNGKDVYQ 114 (477)
T ss_pred ccCceeEEEEEecCCcccchhh-----hhhHHHHHHHHH-hcCCCchhEEEEEehhhhcCCCCCCCceeecCCCchhhhc
Confidence 344799999984 44 776432 467777788887 5699999988765432 11
Q ss_pred --C----CCCccHHHHHHHHHH---HHH-------hCCCCCEEEEEEecCccccCCCCCCCCCCcceeEEeccCCCCCcc
Q 016243 133 --P----LKRPTKYNMRMALYW---LIQ-------GCQPGDSLLFHFSGHGSQQRNYNGEEVDGYDETLCPVDFETQGMI 196 (392)
Q Consensus 133 --~----~~~pT~~nI~~al~~---L~~-------~~~~gD~llfYFSGHG~~~~d~~gde~dG~de~Lvp~D~~~~g~i 196 (392)
| -...|.+|+.+.|.- -++ ...|+|.+||||+-||... .|..-+ ...+
T Consensus 115 GvpkDYtg~~Vt~~Nf~aVllGd~savkGGsGKV~~SgpnDhiFiYytDHG~pG-------------vl~mP~---~~~l 178 (477)
T KOG1348|consen 115 GVPKDYTGEDVTPQNFLAVLLGDASAVKGGSGKVLKSGPNDHIFIYYTDHGGPG-------------VLGMPT---SPDL 178 (477)
T ss_pred CCCCcccCCcCCHHHHHHHHhcccccccCCCceeeccCCCceEEEEEecCCCCc-------------eEecCC---Ccch
Confidence 0 235788899888742 222 2469999999999999862 232222 1346
Q ss_pred cHHHHHHhhcCcCC--CCCeEEEEEeCCCCCCCCC
Q 016243 197 VDDEINTTLVRPLP--RGARLHAIIDACHSGTVLD 229 (392)
Q Consensus 197 ~d~eL~~~L~~~l~--~g~~l~vIlD~C~SG~~~~ 229 (392)
...+|++.|.+.-+ +=.++++-|.||-||++.+
T Consensus 179 ~akdlnevL~kmhk~k~Y~~mvfYlEACESGSmfe 213 (477)
T KOG1348|consen 179 YAKDLNEVLKKMHKSKTYKKMVFYLEACESGSMFE 213 (477)
T ss_pred hHHHHHHHHHHHHhccchheEEEEeeeccCcchhh
Confidence 66788888854322 2246889999999999986
No 12
>COG5206 GPI8 Glycosylphosphatidylinositol transamidase (GPIT), subunit GPI8 [Posttranslational modification, protein turnover, chaperones]
Probab=97.77 E-value=0.00042 Score=66.27 Aligned_cols=189 Identities=16% Similarity=0.289 Sum_probs=118.8
Q ss_pred CCCceEEEEEEeC--CCCCCCCCcchHHHHHHHHHHHHhccCCCCCceEEccCCCC--------------C---------
Q 016243 78 AQGRKRALIVGVS--YRHTNHELKGCINDARCMKYMLTNRFKFPESSIVMLTEEDP--------------D--------- 132 (392)
Q Consensus 78 ~~~~k~ALlIGI~--Y~~~~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~--------------~--------- 132 (392)
...+.||++|--+ +++- +- ...+-.|.+.++ +.|||.++|++...++. +
T Consensus 25 t~tnNwAvLlstSRfwfNY----RH-mANVl~~Yr~vk-rlGipDsQIilm~~dd~acnsRnlfpgsvf~N~Dra~dlyg 98 (382)
T COG5206 25 TNTNNWAVLLSTSRFWFNY----RH-MANVLVFYRVVK-RLGIPDSQIILMSYDDQACNSRNLFPGSVFNNSDRAGDLYG 98 (382)
T ss_pred ccCCceEEEEecccceeeh----hh-hhhHHHHHHHHH-HcCCCcceEEEEechhhhhhhcccCCcccccCcccccceeC
Confidence 4677999999988 3332 12 345667888887 68999998765543321 0
Q ss_pred -------CCCCccHHHHHHHHHHHHHh---------CCCCCEEEEEEecCccccCCCCCCCCCCcceeEEeccCCCCCcc
Q 016243 133 -------PLKRPTKYNMRMALYWLIQG---------CQPGDSLLFHFSGHGSQQRNYNGEEVDGYDETLCPVDFETQGMI 196 (392)
Q Consensus 133 -------~~~~pT~~nI~~al~~L~~~---------~~~gD~llfYFSGHG~~~~d~~gde~dG~de~Lvp~D~~~~g~i 196 (392)
.--.+|-+++.+.|.....+ ..+...+|||..|||.. .+|=-.|++ .+
T Consensus 99 e~~eidY~gyevTve~firLLt~r~~en~p~sKrlltdE~SNIfIYmtGHGgd-------------~FlKFqdae---em 162 (382)
T COG5206 99 EDSEIDYSGYEVTVEVFIRLLTARSGENHPKSKRLLTDESSNIFIYMTGHGGD-------------AFLKFQDAE---EM 162 (382)
T ss_pred cccccccccccchHHHHHHHHHhhccCCChhhhhhcccccCcEEEEEccCCCc-------------cceecccHH---Hh
Confidence 12368888887777544321 23556899999999953 255555544 35
Q ss_pred cHHHHHHhhcCcCC-CC-CeEEEEEeCCCCCCCCCCcchhcccccCccccccCCCCCCcccccCCCCEEEEEecCCCCcc
Q 016243 197 VDDEINTTLVRPLP-RG-ARLHAIIDACHSGTVLDLPFLCRMDRQGKYIWEDHRPRSGMWKGTSGGEAISFSGCDDNQTS 274 (392)
Q Consensus 197 ~d~eL~~~L~~~l~-~g-~~l~vIlD~C~SG~~~~~p~~~~~~r~g~~~~e~~~p~~~~~k~~~~g~~i~~SAc~~~q~A 274 (392)
+.++|.+.|.+.-. +. .++++++|+|...++.+.-+ ++ +++.+.++.-+|.|
T Consensus 163 tseDladai~ql~~~kRyNeIlfmiDTCQAnaly~k~y-------------------------sP-NvLavgsSeig~ss 216 (382)
T COG5206 163 TSEDLADAISQLAAKKRYNEILFMIDTCQANALYDKSY-------------------------SP-NVLAVGSSEIGQSS 216 (382)
T ss_pred hhHHHHHHHHHHHHhhhhceEEEEeeccccchhhhhcc-------------------------CC-ceEEEeccccCCcc
Confidence 56677777643222 12 35889999998765543211 12 56666777777766
Q ss_pred cccccCCC--CCCCChhHHHHHHHHHc---CCCCCHHHHHHHHHH
Q 016243 275 ADTSALSK--ITSTGAMTYSFIQAIER---GHGATYGSMLNSMRS 314 (392)
Q Consensus 275 ~e~~~~g~--~~~~G~FT~~Ll~aL~~---~~~iT~~~L~~~vr~ 314 (392)
+..-.-.. ..--.-|||++++-|++ +..+|..+|++....
T Consensus 217 yShhsd~~IgvaVIDrFty~~l~fle~id~~skltlqDL~~s~n~ 261 (382)
T COG5206 217 YSHHSDSLIGVAVIDRFTYFFLKFLEKIDIGSKLTLQDLLASLNK 261 (382)
T ss_pred ccccchhhhhHHHhhcchHHHHHHHhhcCcCCeeEHHHHHHhcCc
Confidence 54321110 11224599999999997 334899999987644
No 13
>COG4249 Uncharacterized protein containing caspase domain [General function prediction only]
Probab=97.75 E-value=1.1e-05 Score=81.78 Aligned_cols=211 Identities=23% Similarity=0.291 Sum_probs=142.2
Q ss_pred CceEEEEEEeC-CCCCCCCCcchHHHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCE
Q 016243 80 GRKRALIVGVS-YRHTNHELKGCINDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDS 158 (392)
Q Consensus 80 ~~k~ALlIGI~-Y~~~~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~ 158 (392)
.+|-||+||++ |+. ...|.++.||+..|+.+|+. .||++ ..-++ -.++.++..|+.+.+.++--|.
T Consensus 2 ~~r~alvigns~~~~-aa~l~np~~da~~~a~~L~~-iGfdv---y~~~d--------~~~~~~~~~L~~f~~da~ga~~ 68 (380)
T COG4249 2 ERRVALVIGNSTYYV-AAPLANPANDAGAMALWLTA-IGFDV---YLDTD--------LPKSGLRRALRYFAEDAEGADV 68 (380)
T ss_pred CcceEEEeecCcccc-cccCCCchhhHHHHHHHHHH-cCcee---ecccc--------cchHHHHhHHHHHHHHHHHHhH
Confidence 57899999999 554 68999999999999999984 79973 22233 3578899999999999999999
Q ss_pred EEEEEecCccccCCCCCCCCCCcceeEEeccCCCC-------CcccHHHHHHhhcCcCCCCCeE-EEEEeCCCCCCCCCC
Q 016243 159 LLFHFSGHGSQQRNYNGEEVDGYDETLCPVDFETQ-------GMIVDDEINTTLVRPLPRGARL-HAIIDACHSGTVLDL 230 (392)
Q Consensus 159 llfYFSGHG~~~~d~~gde~dG~de~Lvp~D~~~~-------g~i~d~eL~~~L~~~l~~g~~l-~vIlD~C~SG~~~~~ 230 (392)
+||||||||.|.... .||+|+|.... ..+.++++. .+++...+| .+|+|.|+.-...+.
T Consensus 69 al~~~aGhg~Q~~~~---------~~~~pv~~~~~~~~~~~~~~v~~~~~~----~~~p~~~~V~~~~lD~~~~~~~~d~ 135 (380)
T COG4249 69 ALIYYAGHGLQVDGT---------NYLLPVDADDVSPTFAVTEAVLIDCRL----IPLPARTKVRRVLLDAARDNPPADT 135 (380)
T ss_pred HHhhhccccccccCc---------cccccchhhhccccchhhhhhhhhhhc----ccCCchhHHHHHHHHHhhcCchhhh
Confidence 999999999997653 49999987632 122333332 223322333 589999998766443
Q ss_pred cchhcccccCccccccCCCCCCcccccCCCCEEEEEecCCCCcccccccCCCCCCCChhHHHHHHHHHcCCCCCHHHHHH
Q 016243 231 PFLCRMDRQGKYIWEDHRPRSGMWKGTSGGEAISFSGCDDNQTSADTSALSKITSTGAMTYSFIQAIERGHGATYGSMLN 310 (392)
Q Consensus 231 p~~~~~~r~g~~~~e~~~p~~~~~k~~~~g~~i~~SAc~~~q~A~e~~~~g~~~~~G~FT~~Ll~aL~~~~~iT~~~L~~ 310 (392)
...+- .| + ++..+..+..+++-+..+.++.+.+.. ..+++|+-.+...|.+. +.....+..
T Consensus 136 ~~~~f---sG------~----g~~~~~d~~~~lia~~t~p~~~a~~~~-----~~~s~~~~~~~~~~~~~-~~ql~~~d~ 196 (380)
T COG4249 136 ILFFF---SG------H----GATPGADGRAYLIAFDTRPGAVAYDGE-----GGISPYSVAQALHLSEP-GNQLVDLDA 196 (380)
T ss_pred hhhee---ec------c----ccccCCCCceeEEeecCChhhhcccCC-----CcccHHHHHHHHHhccC-Cceeehhhh
Confidence 22110 11 1 111111222244445566777777654 36889999999888875 345667888
Q ss_pred HHHHHHhccCCCCCcccCCcccccceee
Q 016243 311 SMRSTIRNTDSGSELSGAGGLVTSLVTM 338 (392)
Q Consensus 311 ~vr~~v~~~~~~~~~~~~~~~~~~~~~~ 338 (392)
.++..+.....+. +.|+..+++.+.
T Consensus 197 ~~~~~~~~~~~~~---~~p~l~~s~~~~ 221 (380)
T COG4249 197 CVRGDVFKATAGQ---QRPWLAQSLARE 221 (380)
T ss_pred hcchhhhcccccc---cchHhhhhhhcc
Confidence 8888777766432 267777776553
No 14
>PF12770 CHAT: CHAT domain
Probab=97.18 E-value=0.0048 Score=59.37 Aligned_cols=180 Identities=19% Similarity=0.259 Sum_probs=108.6
Q ss_pred EEEEeCCCCC-------CCCCcchHHHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCC
Q 016243 85 LIVGVSYRHT-------NHELKGCINDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGD 157 (392)
Q Consensus 85 LlIGI~Y~~~-------~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD 157 (392)
|+|+...... ..+|++....++.+++.+... +. .++...+ +|++++++.+ ...+
T Consensus 82 l~i~~p~~~~~~~~~~~~~~l~~~~~e~~~l~~~~~~~-~~-----~~~~~~~------at~~~l~~~l-------~~~~ 142 (287)
T PF12770_consen 82 LVIGNPDFGGSLIRGAALSPLPGAQREADALAELLGAG-GL-----RVLVGPE------ATKDALLEAL-------ERRG 142 (287)
T ss_pred EEEecCCCcccccccccccCchHHHHHHHHHHHHhccc-ce-----eEeeccC------CCHHHHHhhh-------ccCC
Confidence 7787763322 378999999999999988642 11 2333333 8999999987 2344
Q ss_pred EEEEEEecCccccCCCCCCCCCCcceeEEeccCCC--CCcccHHHHHHhhcCcCCCCCeEEEEEeCCCCCCCCCCcchhc
Q 016243 158 SLLFHFSGHGSQQRNYNGEEVDGYDETLCPVDFET--QGMIVDDEINTTLVRPLPRGARLHAIIDACHSGTVLDLPFLCR 235 (392)
Q Consensus 158 ~llfYFSGHG~~~~d~~gde~dG~de~Lvp~D~~~--~g~i~d~eL~~~L~~~l~~g~~l~vIlD~C~SG~~~~~p~~~~ 235 (392)
.=+|||+|||....+.. ....|+..|... .+.++..+|.. + .++. .+ +|||-+|+|+.......
T Consensus 143 ~~ilH~a~Hg~~~~~~~------~~~~l~l~~~~~~~~~~l~~~~l~~-l--~l~~-~~-lVvLsaC~s~~~~~~~~--- 208 (287)
T PF12770_consen 143 PDILHFAGHGTFDPDPP------DQSGLVLSDESGQEDGLLSAEELAQ-L--DLRG-PR-LVVLSACESASGDPSDG--- 208 (287)
T ss_pred CCEEEEEcccccCCCCC------CCCEEEEeccCCCCCcccCHHHHHh-h--cCCC-CC-EEEecCcCCcCCCCCCc---
Confidence 45999999999873221 123677665443 35788888887 3 1222 34 69999999994321100
Q ss_pred ccccCccccccCCCCCCcccccCCCCEEEEEecCCCCcccccccCCCCCCCChhHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 016243 236 MDRQGKYIWEDHRPRSGMWKGTSGGEAISFSGCDDNQTSADTSALSKITSTGAMTYSFIQAIERGHGATYGSMLNSMRST 315 (392)
Q Consensus 236 ~~r~g~~~~e~~~p~~~~~k~~~~g~~i~~SAc~~~q~A~e~~~~g~~~~~G~FT~~Ll~aL~~~~~iT~~~L~~~vr~~ 315 (392)
.+...+. ..+. ..+...| ++ . -++... .....|+..|.+.|..+ .+..+.+...+..
T Consensus 209 ---~~~~~l~------~~~l-~aG~~~V-i~-~-----~w~V~d----~~a~~f~~~fY~~L~~g--~~~~~Al~~Ar~~ 265 (287)
T PF12770_consen 209 ---DEVLGLA------RAFL-QAGAPAV-IG-M-----LWPVPD----QAAARFMRRFYRALLQG--QSVAEALRQARRA 265 (287)
T ss_pred ---hHHHHHH------HHHH-HcCCCEE-Ee-c-----ccCcch----HHHHHHHHHHHHhhhcC--CCHHHHHHHHHHH
Confidence 0000000 0000 1122233 33 1 122221 12457999999999884 5799999999999
Q ss_pred HhccC
Q 016243 316 IRNTD 320 (392)
Q Consensus 316 v~~~~ 320 (392)
+++..
T Consensus 266 l~~~~ 270 (287)
T PF12770_consen 266 LRRDS 270 (287)
T ss_pred HHhcC
Confidence 98876
No 15
>KOG1517 consensus Guanine nucleotide binding protein MIP1 [Cell cycle control, cell division, chromosome partitioning]
Probab=96.76 E-value=0.0072 Score=67.23 Aligned_cols=168 Identities=20% Similarity=0.222 Sum_probs=94.5
Q ss_pred HHHHHHHHHHHHhccC-CC-CCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEecCccccCCCCCCCCC
Q 016243 102 INDARCMKYMLTNRFK-FP-ESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFHFSGHGSQQRNYNGEEVD 179 (392)
Q Consensus 102 ~nDa~~m~~~L~~~~G-f~-~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfYFSGHG~~~~d~~gde~d 179 (392)
..-++.+-+-|...+- +. ...-.+-+| ||.+++++--..+-.. ..+|.++|||-|||+..+..+|+
T Consensus 139 ~KA~e~IG~nlq~qYE~wqprtRYK~~lD--------P~vddVrKlc~slRr~-ak~eRvLFHYNGHGVPkPT~nGE--- 206 (1387)
T KOG1517|consen 139 PKALEAIGKNLQRQYERWQPRTRYKVCLD--------PTVDDVRKLCTSLRRN-AKEERVLFHYNGHGVPKPTANGE--- 206 (1387)
T ss_pred hHHHHHHHHHHHHHHHhhChhhhhhhccC--------CcHHHHHHHHHHHhhh-cCCceEEEEecCCCCCCCCCCCc---
Confidence 3555666666664432 22 122233333 9999999866665444 45899999999999999988773
Q ss_pred CcceeEEeccCCCCC-cccHHHHHHhhcCcCCCCCeEEEEEeCCCCCCCCCC--cchhcccccCccccccCCCCCCcccc
Q 016243 180 GYDETLCPVDFETQG-MIVDDEINTTLVRPLPRGARLHAIIDACHSGTVLDL--PFLCRMDRQGKYIWEDHRPRSGMWKG 256 (392)
Q Consensus 180 G~de~Lvp~D~~~~g-~i~d~eL~~~L~~~l~~g~~l~vIlD~C~SG~~~~~--p~~~~~~r~g~~~~e~~~p~~~~~k~ 256 (392)
-||---.-++- .++--||..||. .-.+.|.||-..+.++-. +|.. .|++.. -++.....+...+
T Consensus 207 ----IWVFNK~fTQYIPlsi~dLqsWl~------aP~IyVydcssA~~Il~nf~~fae--~~~~~~-~~~~~~~~~~ps~ 273 (1387)
T KOG1517|consen 207 ----IWVFNKSFTQYIPLSIFDLQSWLG------APTIYVYDCSSAENILVNFNRFAE--QRDKMT-DADQANALAFPSG 273 (1387)
T ss_pred ----EEEEecCcceeecccHHHHHhhhc------CCeEEEEeccchHHHHHHHHHHHH--hhhccc-cccccccccCCCC
Confidence 44432111111 245567888884 223689998777755432 2211 121100 0000000011111
Q ss_pred c-CCCCEEEEEecCCCCcccccccCCCCCCCChhHHHHHHHHH
Q 016243 257 T-SGGEAISFSGCDDNQTSADTSALSKITSTGAMTYSFIQAIE 298 (392)
Q Consensus 257 ~-~~g~~i~~SAc~~~q~A~e~~~~g~~~~~G~FT~~Ll~aL~ 298 (392)
+ +-...|.++||..+|+---.+.+ ..-+||.+|.--|+
T Consensus 274 ~~~y~dCi~LAaC~~~e~LPms~~l----PADlFTsCLTTPI~ 312 (1387)
T KOG1517|consen 274 TSRYKDCIHLAACDAHETLPMSPEL----PADLFTSCLTTPIE 312 (1387)
T ss_pred CcchhhhheeccCCcccccCCCCCc----cHHHHhhhhcCchh
Confidence 1 12358999999999974433332 35799999876555
No 16
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=95.08 E-value=0.014 Score=39.62 Aligned_cols=31 Identities=29% Similarity=0.943 Sum_probs=25.5
Q ss_pred CcccCCCCCCccccCC-----CCceeeccccCceec
Q 016243 3 MLVDCSKCRTTLQLPP-----GAQSIRCAICQAITH 33 (392)
Q Consensus 3 ~~~~C~~C~~~l~~p~-----~a~~vrC~~C~~vt~ 33 (392)
|.+.|++|.+.+.+|. +.+.+||+.|+.+=.
T Consensus 1 M~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred CEEECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 6789999999887665 567899999997643
No 17
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=93.82 E-value=0.05 Score=36.67 Aligned_cols=29 Identities=28% Similarity=1.015 Sum_probs=24.1
Q ss_pred CcccCCCCCCccc-----cCCCCceeeccccCce
Q 016243 3 MLVDCSKCRTTLQ-----LPPGAQSIRCAICQAI 31 (392)
Q Consensus 3 ~~~~C~~C~~~l~-----~p~~a~~vrC~~C~~v 31 (392)
|.+.|.+|.+... +|++...+||..|+.+
T Consensus 1 M~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred CEEECCCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence 6789999999754 5567789999999865
No 18
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=92.50 E-value=0.097 Score=37.93 Aligned_cols=36 Identities=28% Similarity=0.652 Sum_probs=29.7
Q ss_pred CCCcccCCCCCCccccCCCCc--eeeccccCceecccC
Q 016243 1 MLMLVDCSKCRTTLQLPPGAQ--SIRCAICQAITHIAD 36 (392)
Q Consensus 1 ~~~~~~C~~C~~~l~~p~~a~--~vrC~~C~~vt~v~~ 36 (392)
|+..++|++|..-|.-.-++. .|+|.-|++++.|..
T Consensus 1 m~~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a 38 (51)
T PF10122_consen 1 MLKEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA 38 (51)
T ss_pred CCcceeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence 788899999999776643444 799999999999985
No 19
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=91.95 E-value=0.1 Score=35.23 Aligned_cols=32 Identities=22% Similarity=0.665 Sum_probs=25.2
Q ss_pred CcccCCCCCCccccCC-----CCceeeccccCceecc
Q 016243 3 MLVDCSKCRTTLQLPP-----GAQSIRCAICQAITHI 34 (392)
Q Consensus 3 ~~~~C~~C~~~l~~p~-----~a~~vrC~~C~~vt~v 34 (392)
|.+.|++|++...++. ....++|..|+.+-.+
T Consensus 1 M~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 1 MRIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred CEEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEEe
Confidence 5789999999888874 2347999999976543
No 20
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.52 E-value=0.21 Score=35.26 Aligned_cols=30 Identities=20% Similarity=0.581 Sum_probs=26.1
Q ss_pred CCcccCCCCCCccccCCCCceeeccccCce
Q 016243 2 LMLVDCSKCRTTLQLPPGAQSIRCAICQAI 31 (392)
Q Consensus 2 ~~~~~C~~C~~~l~~p~~a~~vrC~~C~~v 31 (392)
++...|++|++.+.+.+....++|..|+.-
T Consensus 1 ~~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 1 MAEYKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred CCEEECCCCCCEEEECCCCCceECCCCCCe
Confidence 356789999999999999889999999853
No 21
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=82.02 E-value=0.94 Score=31.10 Aligned_cols=32 Identities=28% Similarity=0.694 Sum_probs=19.9
Q ss_pred cccCCCCCCcc----ccCCCCceeeccccCceeccc
Q 016243 4 LVDCSKCRTTL----QLPPGAQSIRCAICQAITHIA 35 (392)
Q Consensus 4 ~~~C~~C~~~l----~~p~~a~~vrC~~C~~vt~v~ 35 (392)
.++|.+|++.| .+-.+.++-.|.+|+..+.+.
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~lp 37 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGTKNPLP 37 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--EEE--
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCCcCCCC
Confidence 57999999975 556678899999999988775
No 22
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=76.21 E-value=1.8 Score=33.18 Aligned_cols=30 Identities=20% Similarity=0.627 Sum_probs=25.1
Q ss_pred CcccCCCCCCc-cccCCCCceeeccccCcee
Q 016243 3 MLVDCSKCRTT-LQLPPGAQSIRCAICQAIT 32 (392)
Q Consensus 3 ~~~~C~~C~~~-l~~p~~a~~vrC~~C~~vt 32 (392)
+.|.|+.|+.. ..+..-++.|+|.+|..+-
T Consensus 18 l~VkCpdC~N~q~vFshast~V~C~~CG~~l 48 (67)
T COG2051 18 LRVKCPDCGNEQVVFSHASTVVTCLICGTTL 48 (67)
T ss_pred EEEECCCCCCEEEEeccCceEEEecccccEE
Confidence 46889999984 7888888999999998654
No 23
>COG4995 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.86 E-value=10 Score=39.35 Aligned_cols=181 Identities=16% Similarity=0.147 Sum_probs=95.5
Q ss_pred CceEEEEEEeCC-----CCCCCCCcchHHHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCC
Q 016243 80 GRKRALIVGVSY-----RHTNHELKGCINDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQ 154 (392)
Q Consensus 80 ~~k~ALlIGI~Y-----~~~~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~ 154 (392)
.+-++++-|.+- .....+|+++...|+.+++.+.. -.++.+++ =|.++....++..
T Consensus 211 ~~l~vl~~g~s~~~~~~~~~~~~Lp~~~~Ev~~Ia~~~~~--------~~~ll~q~------Ft~~~~~~~~~~~----- 271 (420)
T COG4995 211 QNLKVLAAGLSEPSGPARTGFDALPFAALEVETIAAIFPP--------QKLLLNQA------FTAANLAQEIDTK----- 271 (420)
T ss_pred cchhHHHhccCcccccccccccccchHHHHHHHHHHhhhh--------HHhhhccc------chhhHHhhhhhcC-----
Confidence 444556666652 22257999999999999988742 11333332 2444444444332
Q ss_pred CCCEEEEEEecCccccCCCCCCCCCCcceeEEeccCCCCCcccHHHHHHhhcCcCCCCCeEEEEEeCCCCCCC--CCCcc
Q 016243 155 PGDSLLFHFSGHGSQQRNYNGEEVDGYDETLCPVDFETQGMIVDDEINTTLVRPLPRGARLHAIIDACHSGTV--LDLPF 232 (392)
Q Consensus 155 ~gD~llfYFSGHG~~~~d~~gde~dG~de~Lvp~D~~~~g~i~d~eL~~~L~~~l~~g~~l~vIlD~C~SG~~--~~~p~ 232 (392)
+.=++||+.||.-.... ..+.+|+..|-..+....+..+.... .....+. ++||-||-.|.. .+..+
T Consensus 272 --~~~vvHlATHg~f~s~~------p~~S~l~~~~~~~~~~~~~~~~~~~~--~~~~~vd-LvVLSACqTa~g~gd~~a~ 340 (420)
T COG4995 272 --PYSVVHLATHGQFSSGN------PEDSFLLLWDGPINVTELDILLRNRN--NNLLPVE-LVVLSACQTALGEGDGRAY 340 (420)
T ss_pred --CCceEEEeccccccCCC------cccceeeecCCCCcccHHHHHHHhcc--cCCCCee-eEEEecchhccCCCCChhh
Confidence 34489999999876531 22458888886544222222221111 1112245 599999998874 21111
Q ss_pred hhcccccCccccccCCCCCCcccccCCCCEEEEEecCCCCcccccccCCCCCCCChhHHHHHHHHHcCCCCCHHHHHHHH
Q 016243 233 LCRMDRQGKYIWEDHRPRSGMWKGTSGGEAISFSGCDDNQTSADTSALSKITSTGAMTYSFIQAIERGHGATYGSMLNSM 312 (392)
Q Consensus 233 ~~~~~r~g~~~~e~~~p~~~~~k~~~~g~~i~~SAc~~~q~A~e~~~~g~~~~~G~FT~~Ll~aL~~~~~iT~~~L~~~v 312 (392)
+ | +.. .-+.+|.+..-+-++ +.|.. .+-++...|-+.|... .+|-.+-++..
T Consensus 341 l------G---Lag----~a~~aGa~s~laSLW--------~VdD~------sTa~LM~eFY~~L~~~-~~~kA~ALrqA 392 (420)
T COG4995 341 L------G---LAG----GAVYAGAKSALASLW--------SVDDE------STAALMTEFYRKLQQA-QLTKAEALRQA 392 (420)
T ss_pred h------h---HHH----HHHHhchhhhhheee--------eeCcH------HHHHHHHHHHHHHhhC-CCcHHHHHHHH
Confidence 0 0 000 000111111111111 22221 2345666777777764 47888888888
Q ss_pred HHHHhc
Q 016243 313 RSTIRN 318 (392)
Q Consensus 313 r~~v~~ 318 (392)
.-.+.+
T Consensus 393 Ql~L~~ 398 (420)
T COG4995 393 QLKLLE 398 (420)
T ss_pred HHHHHh
Confidence 888887
No 24
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=74.12 E-value=3.6 Score=45.55 Aligned_cols=33 Identities=27% Similarity=0.804 Sum_probs=27.7
Q ss_pred cccCCCCCCcc----ccCCCCceeeccccCceecccC
Q 016243 4 LVDCSKCRTTL----QLPPGAQSIRCAICQAITHIAD 36 (392)
Q Consensus 4 ~~~C~~C~~~l----~~p~~a~~vrC~~C~~vt~v~~ 36 (392)
.|+|.+||+++ .+...-+..||.+|..|+-|..
T Consensus 218 IvRCr~CRtYiNPFV~fid~gr~WrCNlC~~~NdvP~ 254 (887)
T KOG1985|consen 218 IVRCRRCRTYINPFVEFIDQGRRWRCNLCGRVNDVPD 254 (887)
T ss_pred eeeehhhhhhcCCeEEecCCCceeeechhhhhcCCcH
Confidence 58999999975 5555668999999999998885
No 25
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=69.30 E-value=3.2 Score=31.17 Aligned_cols=29 Identities=21% Similarity=0.699 Sum_probs=24.2
Q ss_pred CcccCCCCCCc-cccCCCCceeeccccCce
Q 016243 3 MLVDCSKCRTT-LQLPPGAQSIRCAICQAI 31 (392)
Q Consensus 3 ~~~~C~~C~~~-l~~p~~a~~vrC~~C~~v 31 (392)
+.|.|+.|... ..+..-.+.|+|..|..+
T Consensus 10 ~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~ 39 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHASTVVRCLVCGKT 39 (59)
T ss_pred EEEECCCCCCeEEEEecCCcEEECcccCCC
Confidence 56899999984 678888889999999843
No 26
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=68.18 E-value=2.5 Score=30.56 Aligned_cols=33 Identities=24% Similarity=0.646 Sum_probs=27.1
Q ss_pred CcccCCCCCCccccCCCCceeeccccCceeccc
Q 016243 3 MLVDCSKCRTTLQLPPGAQSIRCAICQAITHIA 35 (392)
Q Consensus 3 ~~~~C~~C~~~l~~p~~a~~vrC~~C~~vt~v~ 35 (392)
+.-.|..|++.+........+||..|..--.+-
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K 37 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGSRILVK 37 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCcEEEEe
Confidence 344699999999888899999999998665544
No 27
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=67.56 E-value=3.6 Score=30.50 Aligned_cols=30 Identities=20% Similarity=0.620 Sum_probs=20.4
Q ss_pred CcccCCCCCCc-cccCCCCceeeccccCcee
Q 016243 3 MLVDCSKCRTT-LQLPPGAQSIRCAICQAIT 32 (392)
Q Consensus 3 ~~~~C~~C~~~-l~~p~~a~~vrC~~C~~vt 32 (392)
|.|.|+.|... ..+..-.+.|.|..|..+-
T Consensus 6 m~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L 36 (55)
T PF01667_consen 6 MDVKCPGCYNIQTVFSHAQTVVKCVVCGTVL 36 (55)
T ss_dssp EEEE-TTT-SEEEEETT-SS-EE-SSSTSEE
T ss_pred EEEECCCCCCeeEEEecCCeEEEcccCCCEe
Confidence 67899999984 6788888999999998653
No 28
>COG1791 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=66.96 E-value=22 Score=32.46 Aligned_cols=58 Identities=12% Similarity=0.205 Sum_probs=44.0
Q ss_pred HHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEecCcccc
Q 016243 105 ARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFHFSGHGSQQ 170 (392)
Q Consensus 105 a~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfYFSGHG~~~ 170 (392)
-+..-+-|.+..||...+++.+.+.+ |.++++++.+.+ +-.-.+|.+-|+.+|||.-.
T Consensus 52 ~~~eid~l~~e~Gyk~~Dvvsv~~~~------pk~del~akF~~--EH~H~d~EvRy~vaG~GiF~ 109 (181)
T COG1791 52 YETEIDRLIRERGYKNRDVVSVSPSN------PKLDELRAKFLQ--EHLHTDDEVRYFVAGEGIFD 109 (181)
T ss_pred HHHHHHHHHHhhCCceeeEEEeCCCC------ccHHHHHHHHHH--HhccCCceEEEEEecceEEE
Confidence 33455566667899988888888876 899999988743 23447899999999999653
No 29
>PF12070 DUF3550: Protein of unknown function (DUF3550/UPF0682); InterPro: IPR022709 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 249 to 606 amino acids in length.
Probab=65.95 E-value=39 Score=36.04 Aligned_cols=37 Identities=24% Similarity=0.264 Sum_probs=33.1
Q ss_pred CCccHHHHHHHHHHHHHhCCCCCEEEEEEecCccccC
Q 016243 135 KRPTKYNMRMALYWLIQGCQPGDSLLFHFSGHGSQQR 171 (392)
Q Consensus 135 ~~pT~~nI~~al~~L~~~~~~gD~llfYFSGHG~~~~ 171 (392)
-.||-..++.-|....++.-++-.+++|.|.+|....
T Consensus 292 YrPT~sqll~~LAt~~kELP~n~~lLlYlSA~G~~~~ 328 (513)
T PF12070_consen 292 YRPTFSQLLAFLATAFKELPPNGALLLYLSADGCFST 328 (513)
T ss_pred ecCCHHHHHHHHHHHHHhcCCCceEEEEEeccCcccC
Confidence 3799999999999889999999999999999997554
No 30
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=65.67 E-value=3.3 Score=29.54 Aligned_cols=32 Identities=38% Similarity=0.784 Sum_probs=26.2
Q ss_pred cccCCCCCCccccCCCC-------ceeeccccCceeccc
Q 016243 4 LVDCSKCRTTLQLPPGA-------QSIRCAICQAITHIA 35 (392)
Q Consensus 4 ~~~C~~C~~~l~~p~~a-------~~vrC~~C~~vt~v~ 35 (392)
-|.|++|-.-|++|.+. +.+||.-|..|-.++
T Consensus 6 Fv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 6 FVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSFS 44 (46)
T ss_pred EeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEEe
Confidence 47899999999999754 469999999887654
No 31
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=64.38 E-value=4.2 Score=39.21 Aligned_cols=33 Identities=21% Similarity=0.537 Sum_probs=24.6
Q ss_pred CcccCCCCCCccccCCCC--ceeeccccCceeccc
Q 016243 3 MLVDCSKCRTTLQLPPGA--QSIRCAICQAITHIA 35 (392)
Q Consensus 3 ~~~~C~~C~~~l~~p~~a--~~vrC~~C~~vt~v~ 35 (392)
..+.|++|...++++.=. +--||..|++|+-|.
T Consensus 156 ~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG 190 (256)
T PF09788_consen 156 CRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVG 190 (256)
T ss_pred eeEECCCCCCcEeccCCCCCccccCCCCceecccc
Confidence 357899999887776433 446999999888776
No 32
>PF03415 Peptidase_C11: Clostripain family This family belongs to family C11 of the peptidase classification.; InterPro: IPR005077 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C11 (clostripain family, clan CD). ; PDB: 3UWS_A.
Probab=61.63 E-value=23 Score=36.43 Aligned_cols=81 Identities=17% Similarity=0.247 Sum_probs=42.4
Q ss_pred ccHHHHHHHHHHHHHhCCCCCEEEEEEecCccccCCCCCCCCCCcceeEEeccCCC-CCcccHHHHHHhhcCcCCCCCeE
Q 016243 137 PTKYNMRMALYWLIQGCQPGDSLLFHFSGHGSQQRNYNGEEVDGYDETLCPVDFET-QGMIVDDEINTTLVRPLPRGARL 215 (392)
Q Consensus 137 pT~~nI~~al~~L~~~~~~gD~llfYFSGHG~~~~d~~gde~dG~de~Lvp~D~~~-~g~i~d~eL~~~L~~~l~~g~~l 215 (392)
.+.+.+.+-|+|..+.. |-|.-.+-|.+||.-......... ..+ ..|-.. ...+.-.||.+.|. .+.++
T Consensus 78 ~dp~tL~~fi~~~~~~y-PA~~y~LIlw~HG~Gw~~~~~~~~----rg~-~~D~~~~~~~l~i~el~~aL~----~~~~~ 147 (397)
T PF03415_consen 78 GDPDTLSDFINWAKENY-PADRYGLILWDHGGGWLPASDSST----RGI-GFDETSGGDYLSIPELAEALE----GGPKF 147 (397)
T ss_dssp TSHHHHHHHHHHHHHHS--ECEEEEEEES-B-TT--TTGGG-------E-EEETTE---EE-HHHHHHHS------TT-E
T ss_pred CCHHHHHHHHHHHHHhC-CcccEEEEEEECCCCCCcCCCCCc----ceE-ecCCCChhhcccHHHHHHHHc----CCCCC
Confidence 44566666667776654 667888889999987633211000 112 223222 23566788988884 34565
Q ss_pred -EEEEeCCCCCCC
Q 016243 216 -HAIIDACHSGTV 227 (392)
Q Consensus 216 -~vIlD~C~SG~~ 227 (392)
++.+|+|.-|.+
T Consensus 148 d~I~FDaClM~~v 160 (397)
T PF03415_consen 148 DFIGFDACLMGSV 160 (397)
T ss_dssp EEEEEESTT--BH
T ss_pred cEEEECcccchhH
Confidence 789999998765
No 33
>PF01364 Peptidase_C25: Peptidase family C25 This family belongs to family C25 of the peptidase classification.; InterPro: IPR001769 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C25 (gingipain, clan CD). The protein fold of the peptidase domain for members of this entry resembles that of caspase 1, the type example for clan CD. This is a protein family found only in the bacteria. Porphyromonas gingivalis (Bacteroides gingivalis) a Gram-negative anaerobic bacterial species strongly associated with adult periodontitis. One of its distinguishing characteristics and putative virulence properties is the ability to agglutinate erythrocytes []. It is a highly proteolytic organism which metabolises small peptides and amino acids. Indirect evidence suggests that the proteases produced by this microorganism constitute an important virulence factor []. Protease-encoding genes have been shown to contain multiple copies of repeated nucleotide sequences. These conserved sequences have also been found in haemagglutinin genes [].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 1CVR_A.
Probab=61.35 E-value=9.2 Score=38.70 Aligned_cols=127 Identities=20% Similarity=0.259 Sum_probs=56.8
Q ss_pred ccHHHHHHHHHHHHHhCCCCCEEEEEEecCccccCCCCCCCCCCcceeEEeccCCCCCcccHHHHHHhhcCcCCCCCe-E
Q 016243 137 PTKYNMRMALYWLIQGCQPGDSLLFHFSGHGSQQRNYNGEEVDGYDETLCPVDFETQGMIVDDEINTTLVRPLPRGAR-L 215 (392)
Q Consensus 137 pT~~nI~~al~~L~~~~~~gD~llfYFSGHG~~~~d~~gde~dG~de~Lvp~D~~~~g~i~d~eL~~~L~~~l~~g~~-l 215 (392)
.++++|.++|++ | ..++.|.|||....= . ++-| ..+++.. +....+ -
T Consensus 226 ~~~~~i~~~ln~-------G-~~~v~y~GHG~~~~w--~------~~~~-----------~~~d~~~-----l~N~~~~p 273 (378)
T PF01364_consen 226 GTRDNIINALNQ-------G-AGFVNYFGHGSPTSW--A------DEDF-----------TSSDISN-----LNNKNKLP 273 (378)
T ss_dssp --HHHHHHHHHH----------SEEEEES-B-SSBB--T------TT-------------BTTTGGG--------TT---
T ss_pred chHHHHHHHHhC-------C-CeEEEEecCCchhhc--c------cCcc-----------cHhHHHH-----hcCCCCce
Confidence 578888888875 3 446677899987420 0 0111 1112221 222223 3
Q ss_pred EEEEeCCCCCCCCCCcchhcccccCccccccCCCCCCcccccCCCCEEEEEecCCCCcccccccCCCCCCCChhHHHHHH
Q 016243 216 HAIIDACHSGTVLDLPFLCRMDRQGKYIWEDHRPRSGMWKGTSGGEAISFSGCDDNQTSADTSALSKITSTGAMTYSFIQ 295 (392)
Q Consensus 216 ~vIlD~C~SG~~~~~p~~~~~~r~g~~~~e~~~p~~~~~k~~~~g~~i~~SAc~~~q~A~e~~~~g~~~~~G~FT~~Ll~ 295 (392)
+++.-+|..|.+......+ -++ .|- ....+|.+-.|++++.. +.. .+-.|...|.+
T Consensus 274 ~~~s~~C~~g~fd~~~~~s----l~E-~~v---------~~~~gGAia~ig~s~~~---~~~-------~~~~~~~~~~~ 329 (378)
T PF01364_consen 274 VVISAACYTGNFDDPDNPS----LGE-ALV---------LNPNGGAIAFIGSSRVS---YAS-------PNDRLNRGFYE 329 (378)
T ss_dssp EEEEESSSTT-TTSSS-------HHH-HHH---------TTEE-S-SEEEEESS-----SSH-------HHHHHHHHHTT
T ss_pred EEEEeECCCcCCCCCCCCc----HHH-Hhe---------ECCCCcEEEEEecceeE---ecc-------hHHHHHHHHHH
Confidence 7888999999885421100 000 111 01123334445544322 211 13467777777
Q ss_pred HHHcCCCCCHHHHHHHHHHHHhcc
Q 016243 296 AIERGHGATYGSMLNSMRSTIRNT 319 (392)
Q Consensus 296 aL~~~~~iT~~~L~~~vr~~v~~~ 319 (392)
.|-.....+.++++...+..+-..
T Consensus 330 ~l~~~~~~~lG~a~~~a~~~~~~~ 353 (378)
T PF01364_consen 330 ALFNSNMDTLGEALRQAKNYYLSN 353 (378)
T ss_dssp -STT----BHHHHHHHHHHHHHHH
T ss_pred HHhccCCCCHHHHHHHHHHHHHHh
Confidence 776654348999998888877654
No 34
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=59.10 E-value=4.8 Score=31.09 Aligned_cols=32 Identities=22% Similarity=0.662 Sum_probs=24.3
Q ss_pred cccCCCCCCccccCCCCceeeccccCceecccCC
Q 016243 4 LVDCSKCRTTLQLPPGAQSIRCAICQAITHIADP 37 (392)
Q Consensus 4 ~~~C~~C~~~l~~p~~a~~vrC~~C~~vt~v~~~ 37 (392)
..+| .|++.+-..-++..-+| +|.+..+|...
T Consensus 3 ifrC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~~ 34 (68)
T PF09082_consen 3 IFRC-DCGRYLYAKEGAKTKKC-VCGKTLKVKER 34 (68)
T ss_dssp EEEE-TTS--EEEETT-SEEEE-TTTEEEE--SS
T ss_pred EEEe-cCCCEEEecCCcceeEe-cCCCeeeeeeE
Confidence 4689 79999999999999999 99999999863
No 35
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=58.62 E-value=8 Score=24.99 Aligned_cols=28 Identities=25% Similarity=0.572 Sum_probs=18.9
Q ss_pred cccCCCCCCccccCCCCceeeccccCce
Q 016243 4 LVDCSKCRTTLQLPPGAQSIRCAICQAI 31 (392)
Q Consensus 4 ~~~C~~C~~~l~~p~~a~~vrC~~C~~v 31 (392)
+-.|+.|+.....-.+-.+-+|..|...
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CcccCcCCccccCCCCcCEeECCCCcCE
Confidence 4579999999988888899999999864
No 36
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=58.24 E-value=6 Score=44.21 Aligned_cols=36 Identities=22% Similarity=0.610 Sum_probs=30.6
Q ss_pred CcccCCCCCCc----cccCCCCceeeccccCceecccCCC
Q 016243 3 MLVDCSKCRTT----LQLPPGAQSIRCAICQAITHIADPR 38 (392)
Q Consensus 3 ~~~~C~~C~~~----l~~p~~a~~vrC~~C~~vt~v~~~~ 38 (392)
--|+|++|+.+ .++--+.++++|.+|+.++.|.+-+
T Consensus 337 gPvRC~RCkaYinPFmqF~~~gr~f~Cn~C~~~n~vp~~y 376 (1007)
T KOG1984|consen 337 GPVRCNRCKAYINPFMQFIDGGRKFICNFCGSKNQVPDDY 376 (1007)
T ss_pred CCcchhhhhhhcCcceEEecCCceEEecCCCccccCChhh
Confidence 46899999997 3677888999999999999998643
No 37
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=57.82 E-value=5.6 Score=26.13 Aligned_cols=24 Identities=38% Similarity=0.958 Sum_probs=18.7
Q ss_pred cCCCCCCccccCCCCceeeccccCc
Q 016243 6 DCSKCRTTLQLPPGAQSIRCAICQA 30 (392)
Q Consensus 6 ~C~~C~~~l~~p~~a~~vrC~~C~~ 30 (392)
.|+.|+....+.++. .|||..|..
T Consensus 2 ~C~~Cg~~~~~~~~~-~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELKPGD-PIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BSTSS-TSSBSSSS-
T ss_pred CCCcCCCeeEcCCCC-cEECCcCCC
Confidence 599999998888765 689999974
No 38
>COG0648 Nfo Endonuclease IV [DNA replication, recombination, and repair]
Probab=57.55 E-value=26 Score=34.49 Aligned_cols=63 Identities=24% Similarity=0.307 Sum_probs=39.8
Q ss_pred ccHHHHHHHHHHHHHhCCCCCEEEEEEecCccccCCCCCCCCCCcceeEEeccCCCCCcccHHHHHHhhcCcCCCCCeEE
Q 016243 137 PTKYNMRMALYWLIQGCQPGDSLLFHFSGHGSQQRNYNGEEVDGYDETLCPVDFETQGMIVDDEINTTLVRPLPRGARLH 216 (392)
Q Consensus 137 pT~~nI~~al~~L~~~~~~gD~llfYFSGHG~~~~d~~gde~dG~de~Lvp~D~~~~g~i~d~eL~~~L~~~l~~g~~l~ 216 (392)
-..++|..+|++++.. +....++.+.+|-|.-... ++ ++|.+.| +....-.++-
T Consensus 118 ~~l~~i~~~Ln~~~~~-~~v~i~~e~~agegs~~g~----------------~F--------~~L~eii-~~~~~~~~ig 171 (280)
T COG0648 118 EGLNRIAEALNELLEE-EGVIILLENTAGEGSGKGT----------------QF--------GELAEII-DLIEEKERIG 171 (280)
T ss_pred HHHHHHHHHHHHHhhc-cCCeEEEEEeccccCcccc----------------ch--------hhHHHHH-HhhcccCceE
Confidence 4567788888888775 4456777888888765431 11 3444444 2223334588
Q ss_pred EEEeCCCCC
Q 016243 217 AIIDACHSG 225 (392)
Q Consensus 217 vIlD~C~SG 225 (392)
+.||+||.-
T Consensus 172 vCiDtcH~~ 180 (280)
T COG0648 172 VCIDTCHAF 180 (280)
T ss_pred EEEEchhhh
Confidence 999999963
No 39
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=57.54 E-value=8.5 Score=27.08 Aligned_cols=27 Identities=19% Similarity=0.501 Sum_probs=21.4
Q ss_pred ccCCCCCCccccCCCCceeeccccCcee
Q 016243 5 VDCSKCRTTLQLPPGAQSIRCAICQAIT 32 (392)
Q Consensus 5 ~~C~~C~~~l~~p~~a~~vrC~~C~~vt 32 (392)
-.|+.|++.+.+. ....|||..|..-.
T Consensus 3 Y~C~~Cg~~~~~~-~~~~irC~~CG~rI 29 (44)
T smart00659 3 YICGECGRENEIK-SKDVVRCRECGYRI 29 (44)
T ss_pred EECCCCCCEeecC-CCCceECCCCCceE
Confidence 4799999988876 44679999998544
No 40
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=54.08 E-value=8.9 Score=30.87 Aligned_cols=29 Identities=24% Similarity=0.528 Sum_probs=23.0
Q ss_pred CcccCCCCCC-ccccCCCCceeeccccCce
Q 016243 3 MLVDCSKCRT-TLQLPPGAQSIRCAICQAI 31 (392)
Q Consensus 3 ~~~~C~~C~~-~l~~p~~a~~vrC~~C~~v 31 (392)
|-|.|++|.. ...+..-.+.|.|..|..+
T Consensus 34 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~ 63 (85)
T PTZ00083 34 MDVKCPGCSQITTVFSHAQTVVLCGGCSSQ 63 (85)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCE
Confidence 5678999988 4677788888999999744
No 41
>PLN00209 ribosomal protein S27; Provisional
Probab=52.56 E-value=9.6 Score=30.73 Aligned_cols=29 Identities=24% Similarity=0.574 Sum_probs=23.2
Q ss_pred CcccCCCCCCc-cccCCCCceeeccccCce
Q 016243 3 MLVDCSKCRTT-LQLPPGAQSIRCAICQAI 31 (392)
Q Consensus 3 ~~~~C~~C~~~-l~~p~~a~~vrC~~C~~v 31 (392)
+-|.|++|... ..+..-.+.|.|..|..+
T Consensus 35 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~ 64 (86)
T PLN00209 35 MDVKCQGCFNITTVFSHSQTVVVCGSCQTV 64 (86)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCE
Confidence 56889999884 677788888999999844
No 42
>KOG1321 consensus Protoheme ferro-lyase (ferrochelatase) [Coenzyme transport and metabolism]
Probab=52.07 E-value=40 Score=33.83 Aligned_cols=60 Identities=13% Similarity=0.104 Sum_probs=36.0
Q ss_pred HHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHh-C-----CCCCEEEEEEecCccccC
Q 016243 105 ARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQG-C-----QPGDSLLFHFSGHGSQQR 171 (392)
Q Consensus 105 a~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~-~-----~~gD~llfYFSGHG~~~~ 171 (392)
.+.+.+.+++ -|+..+--.-+.| +|||++-+.++|.++++. . ..-|.|+|+||.||....
T Consensus 175 ln~l~r~~r~-~~~~~~~~wsiId------rW~t~~glIkafA~~I~keL~~F~~~~r~~VVIlFSAHslPms 240 (395)
T KOG1321|consen 175 LNELWRQFRE-DGYERDIKWSIID------RWPTREGLIKAFAENIEKELQTFPEPVRDDVVILFSAHSLPMS 240 (395)
T ss_pred HHHHHHHHHh-cCcccCCceEeec------cccccchHHHHHHHHHHHHHHhcCCcccccEEEEEecCCCcHH
Confidence 4456666664 3554321112233 578888777777555432 1 134789999999998764
No 43
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=48.33 E-value=13 Score=24.78 Aligned_cols=27 Identities=30% Similarity=0.796 Sum_probs=15.2
Q ss_pred cCCCCCCcc--ccCCCCc--eeeccccCcee
Q 016243 6 DCSKCRTTL--QLPPGAQ--SIRCAICQAIT 32 (392)
Q Consensus 6 ~C~~C~~~l--~~p~~a~--~vrC~~C~~vt 32 (392)
.|++|+..| .+|.|.. ..-|..|+.|-
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCEE
Confidence 599999986 5576664 57799998774
No 44
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=47.59 E-value=16 Score=26.93 Aligned_cols=32 Identities=19% Similarity=0.502 Sum_probs=26.1
Q ss_pred cccCCCCCCccccCCCCc--eeeccccCceeccc
Q 016243 4 LVDCSKCRTTLQLPPGAQ--SIRCAICQAITHIA 35 (392)
Q Consensus 4 ~~~C~~C~~~l~~p~~a~--~vrC~~C~~vt~v~ 35 (392)
...|+.|+..+.+|.... -+.|..|.+.-.|.
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGaeleVv 35 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAELEVV 35 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCEEEEE
Confidence 458999999999987653 58999999776665
No 45
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=46.27 E-value=22 Score=25.07 Aligned_cols=30 Identities=27% Similarity=0.483 Sum_probs=22.1
Q ss_pred cCCCCCCccccCCCC--ceeeccccCceeccc
Q 016243 6 DCSKCRTTLQLPPGA--QSIRCAICQAITHIA 35 (392)
Q Consensus 6 ~C~~C~~~l~~p~~a--~~vrC~~C~~vt~v~ 35 (392)
-|+.|+..|..+... ....|..|.++-++.
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEECC
Confidence 499999966555443 378899999877665
No 46
>PF09827 CRISPR_Cas2: CRISPR associated protein Cas2; InterPro: IPR019199 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. Members of this family of bacterial proteins comprise various hypothetical proteins, as well as CRISPR (clustered regularly interspaced short palindromic repeats) associated proteins, conferring resistance to infection by certain bacteriophages. ; PDB: 3EXC_X 2I0X_A 3OQ2_B 3UI3_A 1ZPW_X 2I8E_A 2IVY_A.
Probab=41.70 E-value=59 Score=25.02 Aligned_cols=52 Identities=15% Similarity=0.049 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHhccCCCCC-ceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCC-CEEEEEE
Q 016243 102 INDARCMKYMLTNRFKFPES-SIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPG-DSLLFHF 163 (392)
Q Consensus 102 ~nDa~~m~~~L~~~~Gf~~~-~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~g-D~llfYF 163 (392)
.+....+++.|++ +|...+ +|... + .|..++...++.|.+...++ |.+.+|-
T Consensus 13 ~k~~~kv~k~L~~-~g~~iQ~SVf~~-~--------~~~~~~~~l~~~l~~~i~~~~d~i~i~~ 66 (78)
T PF09827_consen 13 NKRRNKVRKILKS-YGTRIQYSVFEG-N--------LTNAELRKLRRELEKLIDPDEDSIRIYP 66 (78)
T ss_dssp HHHHHHHHHHHHH-TTEEEETTEEEE-E--------E-HHHHHHHHHHHHHHSCTTTCEEEEEE
T ss_pred cHHHHHHHHHHHH-hCccccceEEEE-E--------cCHHHHHHHHHHHHhhCCCCCCEEEEEE
Confidence 3667889999985 674432 34333 2 45556655556666666677 8888874
No 47
>COG2379 GckA Putative glycerate kinase [Carbohydrate transport and metabolism]
Probab=40.42 E-value=1.6e+02 Score=30.48 Aligned_cols=81 Identities=19% Similarity=0.343 Sum_probs=48.9
Q ss_pred CCceEEEEEEeCCCCCCCCCcchHHHHHHHHHHHHh--------ccCC--CCCceEEccCCCCCCCCCccHHHHHHH--H
Q 016243 79 QGRKRALIVGVSYRHTNHELKGCINDARCMKYMLTN--------RFKF--PESSIVMLTEEDPDPLKRPTKYNMRMA--L 146 (392)
Q Consensus 79 ~~~k~ALlIGI~Y~~~~~~L~g~~nDa~~m~~~L~~--------~~Gf--~~~~I~~Ltd~~~~~~~~pT~~nI~~a--l 146 (392)
.++.++++||..- ++..=|..+++.+.. ++|+ +-++|.++--.+ ..|...-+..+ |
T Consensus 35 ~p~gr~~Vig~GK--------As~~MA~a~~~~~~~~~~GvVVt~~g~~~~~~~ieViea~H----PvPDe~s~~asrrl 102 (422)
T COG2379 35 PPKGRTIVIGAGK--------ASAEMARAFEEHWKGPLAGVVVTPYGYGGPCPRIEVIEAGH----PVPDEASLKASRRL 102 (422)
T ss_pred CCCCceEEEecch--------hHHHHHHHHHHHhccccCceEeccCccCCCCCceeEEeCCC----CCCCchhHHHHHHH
Confidence 4667889999652 344444455555521 2332 223455554433 34555555543 3
Q ss_pred HHHHHhCCCCCEEEEEEecCccccC
Q 016243 147 YWLIQGCQPGDSLLFHFSGHGSQQR 171 (392)
Q Consensus 147 ~~L~~~~~~gD~llfYFSGHG~~~~ 171 (392)
-+++.+.+++|.|+|.+||=|+..-
T Consensus 103 L~~v~~l~e~D~Vi~LISGGGSaL~ 127 (422)
T COG2379 103 LELVSGLTEDDLVIVLISGGGSALL 127 (422)
T ss_pred HHHhcCCCCCcEEEEEEeCCchhhc
Confidence 4456788899999999999998653
No 48
>PF13660 DUF4147: Domain of unknown function (DUF4147); PDB: 1X3L_A 2B8N_A.
Probab=40.07 E-value=57 Score=31.32 Aligned_cols=37 Identities=24% Similarity=0.282 Sum_probs=26.0
Q ss_pred CCCccHHHHHH--HHHHHHHhCCCCCEEEEEEecCcccc
Q 016243 134 LKRPTKYNMRM--ALYWLIQGCQPGDSLLFHFSGHGSQQ 170 (392)
Q Consensus 134 ~~~pT~~nI~~--al~~L~~~~~~gD~llfYFSGHG~~~ 170 (392)
+..|+...+.. ++.+++++++++|.|+|..||=|+-.
T Consensus 92 HP~Pd~~s~~aa~~il~~~~~~~~~dlvl~LiSGGgSAL 130 (238)
T PF13660_consen 92 HPLPDENSVRAARRILELARELTEDDLVLVLISGGGSAL 130 (238)
T ss_dssp SSS--HHHHHHHHHHHHHHCC--TTSEEEEEE-TTHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHhcCCCCCeEEEEecCChHHh
Confidence 45688888875 45678889999999999999999764
No 49
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=39.23 E-value=15 Score=40.65 Aligned_cols=34 Identities=26% Similarity=0.752 Sum_probs=28.4
Q ss_pred cccCCCCCCcc----ccCCCCceeeccccCceecccCC
Q 016243 4 LVDCSKCRTTL----QLPPGAQSIRCAICQAITHIADP 37 (392)
Q Consensus 4 ~~~C~~C~~~l----~~p~~a~~vrC~~C~~vt~v~~~ 37 (392)
.++|.+||.++ ++-.+-+..||.+|+.++.|+..
T Consensus 199 ivRCrrCrsYiNPfv~fi~~g~kw~CNiC~~kN~vp~~ 236 (861)
T COG5028 199 IVRCRRCRSYINPFVQFIEQGRKWRCNICRSKNDVPEG 236 (861)
T ss_pred chhhhhhHhhcCceEEEecCCcEEEEeeccccccCccc
Confidence 48999999974 56667789999999999999863
No 50
>PF06258 Mito_fiss_Elm1: Mitochondrial fission ELM1; InterPro: IPR009367 This family consists of several hypothetical eukaryotic and prokaryotic proteins. The function of this family is unknown.
Probab=38.55 E-value=1.4e+02 Score=29.77 Aligned_cols=75 Identities=17% Similarity=0.154 Sum_probs=44.1
Q ss_pred CCCceEEEEEEeCCCCCCCCCcchHHHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCC
Q 016243 78 AQGRKRALIVGVSYRHTNHELKGCINDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGD 157 (392)
Q Consensus 78 ~~~~k~ALlIGI~Y~~~~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD 157 (392)
...++.||+||=+ ...-.....|++.|.+.|.+...-....+.+.+.. =|-.++.++|+.+.+ ..+
T Consensus 144 l~~p~~avLIGG~----s~~~~~~~~~~~~l~~~l~~~~~~~~~~~~vttSR-------RTp~~~~~~L~~~~~---~~~ 209 (311)
T PF06258_consen 144 LPRPRVAVLIGGD----SKHYRWDEEDAERLLDQLAALAAAYGGSLLVTTSR-------RTPPEAEAALRELLK---DNP 209 (311)
T ss_pred CCCCeEEEEECcC----CCCcccCHHHHHHHHHHHHHHHHhCCCeEEEEcCC-------CCcHHHHHHHHHhhc---CCC
Confidence 3477899999843 11223456777777666664221111246566654 377888888877765 345
Q ss_pred EEEEEEecCc
Q 016243 158 SLLFHFSGHG 167 (392)
Q Consensus 158 ~llfYFSGHG 167 (392)
.++|| ++.|
T Consensus 210 ~~~~~-~~~~ 218 (311)
T PF06258_consen 210 GVYIW-DGTG 218 (311)
T ss_pred ceEEe-cCCC
Confidence 55455 6666
No 51
>PRK10886 DnaA initiator-associating protein DiaA; Provisional
Probab=38.47 E-value=1.9e+02 Score=26.78 Aligned_cols=71 Identities=18% Similarity=0.195 Sum_probs=41.2
Q ss_pred CceEEEEEEeCCCCCCCCCcchHHHHHHHHHHHHh-----ccCCCCCceEEccCCCCCCCCCccHH------HHHHHH-H
Q 016243 80 GRKRALIVGVSYRHTNHELKGCINDARCMKYMLTN-----RFKFPESSIVMLTEEDPDPLKRPTKY------NMRMAL-Y 147 (392)
Q Consensus 80 ~~k~ALlIGI~Y~~~~~~L~g~~nDa~~m~~~L~~-----~~Gf~~~~I~~Ltd~~~~~~~~pT~~------nI~~al-~ 147 (392)
..++.+++|+. +..-+|..+...|.. +.|++ ...+.++. .... .....+ +
T Consensus 40 ~~~rI~~~G~G---------gSa~~A~~~a~~l~~~~~~~r~gl~---a~~l~~d~------~~~ta~and~~~~~~f~~ 101 (196)
T PRK10886 40 NGNKILCCGNG---------TSAANAQHFAASMINRFETERPSLP---AIALNTDN------VVLTAIANDRLHDEVYAK 101 (196)
T ss_pred cCCEEEEEECc---------HHHHHHHHHHHHHhccccccCCCcc---eEEecCcH------HHHHHHhccccHHHHHHH
Confidence 55788999965 456688888877754 45665 44444331 1111 111222 4
Q ss_pred HHHHhCCCCCEEEEEEecCccc
Q 016243 148 WLIQGCQPGDSLLFHFSGHGSQ 169 (392)
Q Consensus 148 ~L~~~~~~gD~llfYFSGHG~~ 169 (392)
++....++||.+++ +|+-|..
T Consensus 102 ql~~~~~~gDvli~-iS~SG~s 122 (196)
T PRK10886 102 QVRALGHAGDVLLA-ISTRGNS 122 (196)
T ss_pred HHHHcCCCCCEEEE-EeCCCCC
Confidence 55566788988775 7766543
No 52
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 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. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=37.71 E-value=7.8 Score=25.85 Aligned_cols=30 Identities=23% Similarity=0.551 Sum_probs=18.9
Q ss_pred ccCCCCCCccccCCCCc--eeeccccCceeccc
Q 016243 5 VDCSKCRTTLQLPPGAQ--SIRCAICQAITHIA 35 (392)
Q Consensus 5 ~~C~~C~~~l~~p~~a~--~vrC~~C~~vt~v~ 35 (392)
.-|+.|+. |++|.... .+.|..|.++..+.
T Consensus 2 ~FCp~C~n-lL~p~~~~~~~~~C~~C~Y~~~~~ 33 (35)
T PF02150_consen 2 RFCPECGN-LLYPKEDKEKRVACRTCGYEEPIS 33 (35)
T ss_dssp -BETTTTS-BEEEEEETTTTEEESSSS-EEE-S
T ss_pred eeCCCCCc-cceEcCCCccCcCCCCCCCccCCC
Confidence 35899998 55555443 24799999887665
No 53
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=36.40 E-value=35 Score=24.10 Aligned_cols=32 Identities=25% Similarity=0.471 Sum_probs=23.9
Q ss_pred CcccCCCCCCccccCCCCceeeccccCceeccc
Q 016243 3 MLVDCSKCRTTLQLPPGAQSIRCAICQAITHIA 35 (392)
Q Consensus 3 ~~~~C~~C~~~l~~p~~a~~vrC~~C~~vt~v~ 35 (392)
....|..|+..++- .+-+.++|..|+.+-.-.
T Consensus 10 ~~~~C~~C~~~i~g-~~~~g~~C~~C~~~~H~~ 41 (53)
T PF00130_consen 10 KPTYCDVCGKFIWG-LGKQGYRCSWCGLVCHKK 41 (53)
T ss_dssp STEB-TTSSSBECS-SSSCEEEETTTT-EEETT
T ss_pred CCCCCcccCcccCC-CCCCeEEECCCCChHhhh
Confidence 45679999998855 788899999999776543
No 54
>PF02698 DUF218: DUF218 domain; InterPro: IPR003848 This domain of unknown function is found in several uncharacterised proteins.; PDB: 3CA8_A.
Probab=36.07 E-value=1.1e+02 Score=26.34 Aligned_cols=44 Identities=23% Similarity=0.257 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHH
Q 016243 101 CINDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQ 151 (392)
Q Consensus 101 ~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~ 151 (392)
....++.|+++|.+. |++.+.|.+..... =|.+|++...+.+.+
T Consensus 52 ~~~ea~~~~~~l~~~-gvp~~~I~~e~~s~------~T~ena~~~~~~~~~ 95 (155)
T PF02698_consen 52 GRSEAEAMRDYLIEL-GVPEERIILEPKST------NTYENARFSKRLLKE 95 (155)
T ss_dssp TS-HHHHHHHHHHHT----GGGEEEE----------SHHHHHHHHHHHHHT
T ss_pred CCCHHHHHHHHHHhc-ccchheeEccCCCC------CHHHHHHHHHHHHHh
Confidence 578999999999986 99988887654433 599999998877764
No 55
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=35.96 E-value=11 Score=27.72 Aligned_cols=36 Identities=22% Similarity=0.571 Sum_probs=26.9
Q ss_pred CCCcccCCCCCCccccCCCCc---eeeccccCceecccCC
Q 016243 1 MLMLVDCSKCRTTLQLPPGAQ---SIRCAICQAITHIADP 37 (392)
Q Consensus 1 ~~~~~~C~~C~~~l~~p~~a~---~vrC~~C~~vt~v~~~ 37 (392)
|+..++|..|.--|. ..+.. .++|.-|+.|+.+..+
T Consensus 1 ~~~tiRC~~CnKlLa-~a~~~~yle~KCPrCK~vN~~~~~ 39 (60)
T COG4416 1 MMQTIRCAKCNKLLA-EAEGQAYLEKKCPRCKEVNEFYIK 39 (60)
T ss_pred CceeeehHHHhHHHH-hcccceeeeecCCccceeeeeecc
Confidence 788899999988543 33333 5899999999877653
No 56
>PLN00162 transport protein sec23; Provisional
Probab=35.72 E-value=25 Score=39.45 Aligned_cols=34 Identities=24% Similarity=0.494 Sum_probs=28.2
Q ss_pred CcccCCCCCCcc----ccCCCCceeeccccCceecccC
Q 016243 3 MLVDCSKCRTTL----QLPPGAQSIRCAICQAITHIAD 36 (392)
Q Consensus 3 ~~~~C~~C~~~l----~~p~~a~~vrC~~C~~vt~v~~ 36 (392)
..++|.+|++.| .+-.+.+..+|.+|+..+.+..
T Consensus 52 ~pvRC~~CraylNPf~~~d~~~~~W~C~~C~~~N~~P~ 89 (761)
T PLN00162 52 DPLRCRTCRAVLNPYCRVDFQAKIWICPFCFQRNHFPP 89 (761)
T ss_pred CCCccCCCcCEECCceEEecCCCEEEccCCCCCCCCch
Confidence 468999999975 5556788999999998888764
No 57
>COG2830 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.85 E-value=35 Score=31.22 Aligned_cols=19 Identities=37% Similarity=0.877 Sum_probs=16.2
Q ss_pred CCCCCEEEEEEecCccccC
Q 016243 153 CQPGDSLLFHFSGHGSQQR 171 (392)
Q Consensus 153 ~~~gD~llfYFSGHG~~~~ 171 (392)
++.||.|++||+|-|+...
T Consensus 7 ~~qgd~LIvyFaGwgtpps 25 (214)
T COG2830 7 CKQGDHLIVYFAGWGTPPS 25 (214)
T ss_pred ecCCCEEEEEEecCCCCHH
Confidence 4679999999999998754
No 58
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=34.80 E-value=25 Score=23.97 Aligned_cols=30 Identities=27% Similarity=0.585 Sum_probs=22.7
Q ss_pred CcccCCCCCCccccCCCCceeeccccCceecc
Q 016243 3 MLVDCSKCRTTLQLPPGAQSIRCAICQAITHI 34 (392)
Q Consensus 3 ~~~~C~~C~~~l~~p~~a~~vrC~~C~~vt~v 34 (392)
....|..|+..++... +.++|..|+.+...
T Consensus 10 ~~~~C~~C~~~i~~~~--~~~~C~~C~~~~H~ 39 (49)
T smart00109 10 KPTKCCVCRKSIWGSF--QGLRCSWCKVKCHK 39 (49)
T ss_pred CCCCccccccccCcCC--CCcCCCCCCchHHH
Confidence 3457999999887644 68999999866543
No 59
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=34.65 E-value=26 Score=24.14 Aligned_cols=30 Identities=27% Similarity=0.500 Sum_probs=23.3
Q ss_pred cccCCCCCCccccCCCCceeeccccCceecc
Q 016243 4 LVDCSKCRTTLQLPPGAQSIRCAICQAITHI 34 (392)
Q Consensus 4 ~~~C~~C~~~l~~p~~a~~vrC~~C~~vt~v 34 (392)
...|..|+..++-. .....+|..|+.+..-
T Consensus 11 ~~~C~~C~~~i~~~-~~~~~~C~~C~~~~H~ 40 (50)
T cd00029 11 PTFCDVCRKSIWGL-FKQGLRCSWCKVKCHK 40 (50)
T ss_pred CCChhhcchhhhcc-ccceeEcCCCCCchhh
Confidence 45699999988764 6789999999866543
No 60
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=34.52 E-value=1.2e+02 Score=24.32 Aligned_cols=44 Identities=20% Similarity=0.265 Sum_probs=31.8
Q ss_pred HHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEecCccc
Q 016243 105 ARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFHFSGHGSQ 169 (392)
Q Consensus 105 a~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfYFSGHG~~ 169 (392)
.+.+.+.|.+. ||. | ..|+.+-|..+|..|++.- -||+.|+|..
T Consensus 32 ~E~l~~~L~~~--yp~--i-----------~~Ps~e~l~~~L~~Li~er------kIY~tg~GYf 75 (80)
T PF10264_consen 32 QETLREHLRKH--YPG--I-----------AIPSQEVLYNTLGTLIKER------KIYHTGEGYF 75 (80)
T ss_pred HHHHHHHHHHh--CCC--C-----------CCCCHHHHHHHHHHHHHcC------ceeeCCCceE
Confidence 45567777653 552 2 1289999999999998853 4899999964
No 61
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=33.40 E-value=39 Score=22.74 Aligned_cols=26 Identities=38% Similarity=0.841 Sum_probs=18.3
Q ss_pred cccCCCCCCcc-cc-----CCCCceeeccccC
Q 016243 4 LVDCSKCRTTL-QL-----PPGAQSIRCAICQ 29 (392)
Q Consensus 4 ~~~C~~C~~~l-~~-----p~~a~~vrC~~C~ 29 (392)
.|.|+.|.... .+ +.|.+.+||-.|+
T Consensus 5 ~v~CP~C~s~~~v~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPRCQSTEGVKKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCCCCCCCcceeCCCCCCCCEeEecCcCC
Confidence 36788888876 44 3456678888875
No 62
>COG1350 Predicted alternative tryptophan synthase beta-subunit (paralog of TrpB) [General function prediction only]
Probab=32.90 E-value=32 Score=34.80 Aligned_cols=34 Identities=21% Similarity=0.353 Sum_probs=22.1
Q ss_pred cHHHHHHHHHHHHHhCC--CCCEEEEEEecCccccC
Q 016243 138 TKYNMRMALYWLIQGCQ--PGDSLLFHFSGHGSQQR 171 (392)
Q Consensus 138 T~~nI~~al~~L~~~~~--~gD~llfYFSGHG~~~~ 171 (392)
|...|..+++.-.+.-+ ..-+++|-|||||...-
T Consensus 384 saHAi~~aid~A~~a~~~geekvI~fnlSGHGllDL 419 (432)
T COG1350 384 SAHAIKAAIDEALKAREEGEEKVILFNLSGHGLLDL 419 (432)
T ss_pred chhhHHHHHHHHHhccccCceeEEEEeccCccccch
Confidence 45566666655443222 33489999999998754
No 63
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=31.54 E-value=36 Score=23.15 Aligned_cols=27 Identities=26% Similarity=0.542 Sum_probs=18.1
Q ss_pred cCCCCCCccccC--CCCceeeccccCcee
Q 016243 6 DCSKCRTTLQLP--PGAQSIRCAICQAIT 32 (392)
Q Consensus 6 ~C~~C~~~l~~p--~~a~~vrC~~C~~vt 32 (392)
+|+.|++.|..- .+...-+|..|+.+=
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCeEE
Confidence 599999964211 345667899998653
No 64
>PRK11827 hypothetical protein; Provisional
Probab=31.19 E-value=39 Score=25.50 Aligned_cols=34 Identities=18% Similarity=0.392 Sum_probs=28.5
Q ss_pred CcccCCCCCCccccCCCCceeeccccCceecccC
Q 016243 3 MLVDCSKCRTTLQLPPGAQSIRCAICQAITHIAD 36 (392)
Q Consensus 3 ~~~~C~~C~~~l~~p~~a~~vrC~~C~~vt~v~~ 36 (392)
..+.|+.|+..|.+-......-|..|+-.=.|..
T Consensus 7 eILaCP~ckg~L~~~~~~~~Lic~~~~laYPI~d 40 (60)
T PRK11827 7 EIIACPVCNGKLWYNQEKQELICKLDNLAFPLRD 40 (60)
T ss_pred hheECCCCCCcCeEcCCCCeEECCccCeeccccC
Confidence 4678999999999988888888999987766664
No 65
>TIGR01979 sufS cysteine desulfurases, SufS subfamily. This model represents a subfamily of NifS-related cysteine desulfurases involved in FeS cluster formation needed for nitrogen fixation among other vital functions. Many cysteine desulfurases are also active as selenocysteine lyase and/or cysteine sulfinate desulfinase. This subfamily is associated with the six-gene SUF system described in E. coli and Erwinia as an FeS cluster formation system during oxidative stress. The active site Cys is this subfamily resembles GHHC with one or both His conserved.
Probab=30.62 E-value=2.1e+02 Score=28.69 Aligned_cols=56 Identities=14% Similarity=0.212 Sum_probs=35.3
Q ss_pred HHHHHHHHHHhccCCC-CCceEEccCCCCCCCCCccHHHHHHHHHHHHH-hCCCCCEEEEEEecCcc
Q 016243 104 DARCMKYMLTNRFKFP-ESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQ-GCQPGDSLLFHFSGHGS 168 (392)
Q Consensus 104 Da~~m~~~L~~~~Gf~-~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~-~~~~gD~llfYFSGHG~ 168 (392)
-.+.+++.+.+.+|.+ +++|.+ +.. +.+.+...+..+.. ..++||.|++.-..|..
T Consensus 63 ~~~~~r~~ia~~~~~~~~~~v~~-~~g--------~t~~l~~~~~~~~~~~~~~g~~vl~~~~~~~s 120 (403)
T TIGR01979 63 AYEAVREKVAKFINAASDEEIVF-TRG--------TTESINLVAYSWGDSNLKAGDEIVISEMEHHA 120 (403)
T ss_pred HHHHHHHHHHHHhCcCCCCeEEE-eCC--------HHHHHHHHHHHhhhhcCCCCCEEEECcchhhH
Confidence 3556777777778877 456654 432 34555555555532 35789999887776654
No 66
>PRK06107 aspartate aminotransferase; Provisional
Probab=30.35 E-value=2.2e+02 Score=28.74 Aligned_cols=50 Identities=18% Similarity=0.236 Sum_probs=29.7
Q ss_pred chHHHHHHHHHHHHhccCC--CCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEE
Q 016243 100 GCINDARCMKYMLTNRFKF--PESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLF 161 (392)
Q Consensus 100 g~~nDa~~m~~~L~~~~Gf--~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llf 161 (392)
|...=-+.++++|.+.+|. .+++|.+ +.. +...|...+..+ +++||.+++
T Consensus 71 G~~~lr~~ia~~l~~~~g~~~~~~~i~~-t~G--------~~~al~~~~~~~---~~~gd~vl~ 122 (402)
T PRK06107 71 GTPALRKAIIAKLERRNGLHYADNEITV-GGG--------AKQAIFLALMAT---LEAGDEVII 122 (402)
T ss_pred CCHHHHHHHHHHHHHhcCCCCChhhEEE-eCC--------HHHHHHHHHHHh---cCCCCEEEE
Confidence 4333335677888766675 5667654 432 345555555433 568998877
No 67
>PRK08361 aspartate aminotransferase; Provisional
Probab=29.89 E-value=2.6e+02 Score=28.02 Aligned_cols=50 Identities=8% Similarity=0.095 Sum_probs=29.0
Q ss_pred HHHHHHHHhccC--CCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEecCc
Q 016243 106 RCMKYMLTNRFK--FPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFHFSGHG 167 (392)
Q Consensus 106 ~~m~~~L~~~~G--f~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfYFSGHG 167 (392)
+.+++++.+.+| +++++|.+... +.+.|...+..+ +++||.|++---+|.
T Consensus 77 ~~ia~~~~~~~g~~~~~~~i~~t~G---------~~~al~~~~~~l---~~~g~~Vlv~~p~y~ 128 (391)
T PRK08361 77 EAIAEYYKKFYGVDVDVDNVIVTAG---------AYEATYLAFESL---LEEGDEVIIPDPAFV 128 (391)
T ss_pred HHHHHHHHHHhCCCCCcccEEEeCC---------hHHHHHHHHHHh---cCCCCEEEEcCCCCc
Confidence 356666655445 56677765433 244555555554 468998887444443
No 68
>TIGR03402 FeS_nifS cysteine desulfurase NifS. Members of this protein family are NifS, one of several related families of cysteine desulfurase involved in iron-sulfur (FeS) cluster biosynthesis. NifS is part of the NIF system, usually associated with other nif genes involved in nitrogenase expression and nitrogen fixation. The protein family is given a fairly broad interpretation here. It includes a clade nearly always found in extended nitrogen fixation genomic regions, plus a second clade more closely related to the first than to IscS and also part of NifS-like/NifU-like systems. This model does not extend to a more distantly clade found in the epsilon proteobacteria such as Helicobacter pylori, also named NifS in the literature, built instead in TIGR03403.
Probab=29.69 E-value=2e+02 Score=28.52 Aligned_cols=57 Identities=7% Similarity=-0.021 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEecCc
Q 016243 102 INDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFHFSGHG 167 (392)
Q Consensus 102 ~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfYFSGHG 167 (392)
..-.+.+++.+.+.+|.++++|.+ +.. +.+.+..++..+.....++|.+++.-..|.
T Consensus 41 ~~~~~~~r~~la~~~g~~~~~i~~-t~~--------~t~a~~~al~~~~~~~~~~~~vv~~~~~~~ 97 (379)
T TIGR03402 41 GKAVEEAREQVAKLLGAEPDEIIF-TSG--------GTESDNTAIKSALAAQPEKRHIITTAVEHP 97 (379)
T ss_pred HHHHHHHHHHHHHHhCCCCCeEEE-eCc--------HHHHHHHHHHHHHHhcCCCCeEEEcccccH
Confidence 344666778888778887766654 432 345555556555433345688877666664
No 69
>PF08357 SEFIR: SEFIR domain; InterPro: IPR013568 This domain is found in IL17 receptors (IL17Rs, e.g. Q60943 from SWISSPROT) and SEF proteins (e.g. Q8QHJ9 from SWISSPROT). The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (IPR000157 from INTERPRO), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways [].
Probab=29.58 E-value=65 Score=27.71 Aligned_cols=51 Identities=10% Similarity=0.104 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHH--HHHHHHHHHhCCCCCEEEEEEe
Q 016243 102 INDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNM--RMALYWLIQGCQPGDSLLFHFS 164 (392)
Q Consensus 102 ~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI--~~al~~L~~~~~~gD~llfYFS 164 (392)
.+=|.++++.|++.+|+++ ..|.- ...+| .....|+.++.+..|.|++-.|
T Consensus 15 ~~~V~~la~~L~~~~g~~V-----~lD~~-------~~~~i~~~g~~~W~~~~~~~ad~Vliv~S 67 (150)
T PF08357_consen 15 KEWVLALAEFLRQNCGIDV-----ILDQW-------ELNEIARQGPPRWMERQIREADKVLIVCS 67 (150)
T ss_pred HHHHHHHHHHHHhccCCce-----eecHH-------hhcccccCCHHHHHHHHHhcCCEEEEEec
Confidence 4668889999998779973 23321 11122 2367888888889999999998
No 70
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=29.54 E-value=42 Score=23.41 Aligned_cols=26 Identities=23% Similarity=0.581 Sum_probs=18.7
Q ss_pred ccCCCCCCccccCCCC-ceeeccccCc
Q 016243 5 VDCSKCRTTLQLPPGA-QSIRCAICQA 30 (392)
Q Consensus 5 ~~C~~C~~~l~~p~~a-~~vrC~~C~~ 30 (392)
+.|+.|+..-.+.... ...+|..|++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 5699999865444444 7899999874
No 71
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=29.37 E-value=45 Score=23.14 Aligned_cols=22 Identities=27% Similarity=0.747 Sum_probs=16.5
Q ss_pred ccCCCCCCccccCCCCceeeccccCc
Q 016243 5 VDCSKCRTTLQLPPGAQSIRCAICQA 30 (392)
Q Consensus 5 ~~C~~C~~~l~~p~~a~~vrC~~C~~ 30 (392)
|.|+.|++ |..-..++|..|..
T Consensus 1 v~Cd~C~~----~i~G~ry~C~~C~d 22 (43)
T cd02340 1 VICDGCQG----PIVGVRYKCLVCPD 22 (43)
T ss_pred CCCCCCCC----cCcCCeEECCCCCC
Confidence 57999998 32336899999974
No 72
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=29.33 E-value=51 Score=24.50 Aligned_cols=27 Identities=22% Similarity=0.518 Sum_probs=19.6
Q ss_pred cccCCCCCCccccCCCCceeeccccCceecccC
Q 016243 4 LVDCSKCRTTLQLPPGAQSIRCAICQAITHIAD 36 (392)
Q Consensus 4 ~~~C~~C~~~l~~p~~a~~vrC~~C~~vt~v~~ 36 (392)
...|+.|+++=+ .-+|..|...|.+.-
T Consensus 5 mr~C~~CgvYTL------k~~CP~CG~~t~~~~ 31 (56)
T PRK13130 5 IRKCPKCGVYTL------KEICPVCGGKTKNPH 31 (56)
T ss_pred ceECCCCCCEEc------cccCcCCCCCCCCCC
Confidence 446999998633 567999987777763
No 73
>PF03568 Peptidase_C50: Peptidase family C50; InterPro: IPR005314 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C50 (separase family, clan CD). The active site residues for members of this family and family C14 occur in the same order in the sequence: H,C. The separases are caspase-like proteases, which plays a central role in the chromosome segregation. In yeast they cleave the rad21 subunit of the cohesin complex at the onset of anaphase. During most of the cell cycle, separase is inactivated by the securin/cut2 protein, which probably covers its active site. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0005634 nucleus
Probab=28.70 E-value=95 Score=31.73 Aligned_cols=52 Identities=25% Similarity=0.335 Sum_probs=33.2
Q ss_pred CCCCcchHHHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEecCccc
Q 016243 95 NHELKGCINDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFHFSGHGSQ 169 (392)
Q Consensus 95 ~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfYFSGHG~~ 169 (392)
..+|+.+.+ .|..+|.+..++. -+++.. ||.+++..+|.. .| +|.|-|||.-
T Consensus 269 ~gDL~~T~~---~~~~~~~~~~~w~-----g~~g~~------P~~~e~~~~l~~-------~d--lf~Y~GHG~G 320 (383)
T PF03568_consen 269 SGDLKRTEK---RFEPFFKSWKGWK-----GIIGRA------PTEEEFLQALTS-------SD--LFLYCGHGSG 320 (383)
T ss_pred CCCHHHHHH---HHHHHHhcccCCC-----ceECCC------CCHHHHHHHHHh-------CC--eEEEecCCcH
Confidence 346666553 6777777654454 223333 999999888752 24 6668899974
No 74
>PLN02994 1-aminocyclopropane-1-carboxylate synthase
Probab=28.48 E-value=1e+02 Score=27.40 Aligned_cols=51 Identities=18% Similarity=0.374 Sum_probs=30.6
Q ss_pred cchHHHHHHHHHHHHhccC----CCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEE
Q 016243 99 KGCINDARCMKYMLTNRFK----FPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLF 161 (392)
Q Consensus 99 ~g~~nDa~~m~~~L~~~~G----f~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llf 161 (392)
.|...=-+++++++.+++| +++++|++... ....|...+.-| +.|||.+++
T Consensus 92 ~G~~~lR~AiA~~l~~~~g~~v~~~pd~Ivvt~G---------a~~al~~l~~~l---~dpGD~VlV 146 (153)
T PLN02994 92 HGLANFRKAIANFMAEARGGRVKFDADMIVLSAG---------ATAANEIIMFCI---ADPGDAFLV 146 (153)
T ss_pred CCcHHHHHHHHHHHHHHhCCCCccchhheEEcCC---------HHHHHHHHHHHH---cCCCCEEEE
Confidence 3445555678888887766 56677755433 233344433433 458998876
No 75
>cd00615 Orn_deC_like Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine decarboxylase (LDC). ODC is a dodecamer composed of six homodimers and catalyzes the decarboxylation of tryptophan. ADC catalyzes the decarboxylation of arginine and LDC catalyzes the decarboxylation of lysine. Members of this family are widely found in all three forms of life.
Probab=28.33 E-value=3.6e+02 Score=25.90 Aligned_cols=118 Identities=16% Similarity=0.213 Sum_probs=62.5
Q ss_pred CCCcchHHHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEecCccccCCCCC
Q 016243 96 HELKGCINDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFHFSGHGSQQRNYNG 175 (392)
Q Consensus 96 ~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfYFSGHG~~~~d~~g 175 (392)
.+|..+..-.+..++.+.+-+|-+ ++.++++. +...+...+..+ +++||.|++---.|.......
T Consensus 52 d~l~~~~g~i~~~~~~~A~~~ga~--~~~~~~~G--------st~a~~~~l~al---~~~gd~Vlv~~~~h~s~~~~~-- 116 (294)
T cd00615 52 DDLLDPTGPIKEAQELAARAFGAK--HTFFLVNG--------TSSSNKAVILAV---CGPGDKILIDRNCHKSVINGL-- 116 (294)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCC--CEEEEcCc--------HHHHHHHHHHHc---CCCCCEEEEeCCchHHHHHHH--
Confidence 455555555555656666556643 46666653 344444445444 569999999888886543211
Q ss_pred CCCCCcceeEEeccCCCC----CcccHHHHHHhhcCcCCCCCeEEEEEeCCCCCCCCCCc
Q 016243 176 EEVDGYDETLCPVDFETQ----GMIVDDEINTTLVRPLPRGARLHAIIDACHSGTVLDLP 231 (392)
Q Consensus 176 de~dG~de~Lvp~D~~~~----g~i~d~eL~~~L~~~l~~g~~l~vIlD~C~SG~~~~~p 231 (392)
...|..-.+++.+.... +.+..++|.+.|.+ - ...++++|--.-+.|...+..
T Consensus 117 -~~~g~~~~~v~~~~~~~~~~~~~i~~~~l~~~l~~-~-~~~k~v~l~~p~~~G~~~dl~ 173 (294)
T cd00615 117 -VLSGAVPVYLKPERNPYYGIAGGIPPETFKKALIE-H-PDAKAAVITNPTYYGICYNLR 173 (294)
T ss_pred -HHCCCEEEEecCccCcccCcCCCCCHHHHHHHHHh-C-CCceEEEEECCCCCCEecCHH
Confidence 01122223444433221 35677778777632 1 235655554434556655543
No 76
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=28.32 E-value=40 Score=32.42 Aligned_cols=29 Identities=21% Similarity=0.387 Sum_probs=22.7
Q ss_pred cccCCCCCCccccCCCCceeeccccCceecc
Q 016243 4 LVDCSKCRTTLQLPPGAQSIRCAICQAITHI 34 (392)
Q Consensus 4 ~~~C~~C~~~l~~p~~a~~vrC~~C~~vt~v 34 (392)
+..|+-|+..|.+ ..++.+|..+|..-..
T Consensus 2 ~~~CP~C~~~l~~--~~~~~~C~~~h~fd~a 30 (272)
T PRK11088 2 SYQCPLCHQPLTL--EENSWICPQNHQFDCA 30 (272)
T ss_pred cccCCCCCcchhc--CCCEEEcCCCCCCccc
Confidence 5689999999866 4578999999865433
No 77
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=28.17 E-value=55 Score=20.13 Aligned_cols=22 Identities=27% Similarity=0.801 Sum_probs=16.7
Q ss_pred CCCCCCccccCCC-CceeeccccC
Q 016243 7 CSKCRTTLQLPPG-AQSIRCAICQ 29 (392)
Q Consensus 7 C~~C~~~l~~p~~-a~~vrC~~C~ 29 (392)
|..|+..|. |.+ +..+.|..|.
T Consensus 1 C~sC~~~i~-~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIA-PREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCccc-CcccCceEeCCCCC
Confidence 677877554 666 7889999885
No 78
>PTZ00377 alanine aminotransferase; Provisional
Probab=27.84 E-value=1.6e+02 Score=30.70 Aligned_cols=46 Identities=20% Similarity=0.356 Sum_probs=28.1
Q ss_pred HHHHHHHHHhccC--CCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEE
Q 016243 105 ARCMKYMLTNRFK--FPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLF 161 (392)
Q Consensus 105 a~~m~~~L~~~~G--f~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llf 161 (392)
-+.+++++.++.| +++++|.+ |.. +.+.|...+..|+. .+||.|++
T Consensus 121 R~aia~~~~~~~g~~~~~~~I~i-t~G--------a~~al~~~~~~l~~--~~gD~Vlv 168 (481)
T PTZ00377 121 RKAVAAFIERRDGVPKDPSDIFL-TDG--------ASSGIKLLLQLLIG--DPSDGVMI 168 (481)
T ss_pred HHHHHHHHHHhcCCCCChhhEEE-cCC--------HHHHHHHHHHHhcc--CCCCEEEE
Confidence 3456777765556 45667754 442 45566666665532 48998887
No 79
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=27.84 E-value=50 Score=38.57 Aligned_cols=12 Identities=33% Similarity=0.844 Sum_probs=6.6
Q ss_pred CCCCCCCCCCCC
Q 016243 68 NHAPPGQPPHAQ 79 (392)
Q Consensus 68 ~~~~~~~~~~~~ 79 (392)
+++|||+||.+.
T Consensus 22 s~pppPppPg~~ 33 (2365)
T COG5178 22 SQPPPPPPPGVN 33 (2365)
T ss_pred CCCCCccCCCcc
Confidence 355555666654
No 80
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=27.76 E-value=48 Score=28.64 Aligned_cols=17 Identities=35% Similarity=0.745 Sum_probs=12.2
Q ss_pred HHHhCCCCCEEEEEEec
Q 016243 149 LIQGCQPGDSLLFHFSG 165 (392)
Q Consensus 149 L~~~~~~gD~llfYFSG 165 (392)
.+++.++||.++||=||
T Consensus 36 ~l~~mk~GD~vifY~s~ 52 (143)
T PF01878_consen 36 NLKRMKPGDKVIFYHSG 52 (143)
T ss_dssp HHHC--TT-EEEEEETS
T ss_pred hhhcCCCCCEEEEEEcC
Confidence 45588899999999999
No 81
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=27.63 E-value=46 Score=32.18 Aligned_cols=32 Identities=13% Similarity=0.240 Sum_probs=25.1
Q ss_pred CcccCCCCCCccccCCCCceeeccccCceecc
Q 016243 3 MLVDCSKCRTTLQLPPGAQSIRCAICQAITHI 34 (392)
Q Consensus 3 ~~~~C~~C~~~l~~p~~a~~vrC~~C~~vt~v 34 (392)
.+-.|+.|+..+..-.+-..-+|..|..+-..
T Consensus 98 ~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 98 SHRFCGYCGHPMHPSKTEWAMLCPHCRERYYP 129 (256)
T ss_pred cCccccccCCCCeecCCceeEECCCCCCEECC
Confidence 35679999999888777778889999854433
No 82
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=27.51 E-value=38 Score=37.76 Aligned_cols=28 Identities=25% Similarity=0.733 Sum_probs=24.4
Q ss_pred cccCCCCCCccccCCCCceeeccccCce
Q 016243 4 LVDCSKCRTTLQLPPGAQSIRCAICQAI 31 (392)
Q Consensus 4 ~~~C~~C~~~l~~p~~a~~vrC~~C~~v 31 (392)
...|.+|...|.+.......+|..|.+.
T Consensus 444 v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~ 471 (730)
T COG1198 444 IAECPNCDSPLTLHKATGQLRCHYCGYQ 471 (730)
T ss_pred cccCCCCCcceEEecCCCeeEeCCCCCC
Confidence 3569999999999999999999999854
No 83
>PLN02450 1-aminocyclopropane-1-carboxylate synthase
Probab=27.36 E-value=2.4e+02 Score=29.45 Aligned_cols=50 Identities=18% Similarity=0.424 Sum_probs=30.0
Q ss_pred HHHHHHHHHhccC----CCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEE---EEecC
Q 016243 105 ARCMKYMLTNRFK----FPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLF---HFSGH 166 (392)
Q Consensus 105 a~~m~~~L~~~~G----f~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llf---YFSGH 166 (392)
-++++++|.+.+| +++++|.+ ++. +.+.|...+..| +.|||.|++ +|.++
T Consensus 92 R~aiA~~l~~~~~~~~~v~~~~Iii-t~G--------a~~al~~l~~~l---~~pGd~Vlv~~P~Y~~~ 148 (468)
T PLN02450 92 KNALAEFMSEIRGNKVTFDPNKLVL-TAG--------ATSANETLMFCL---AEPGDAFLLPTPYYPGF 148 (468)
T ss_pred HHHHHHHHHHhhCCCCCcChHHeEE-ccC--------hHHHHHHHHHHh---CCCCCEEEECCCCCCch
Confidence 3557777776555 46777754 432 244444444444 469999988 55554
No 84
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=26.81 E-value=44 Score=29.16 Aligned_cols=30 Identities=23% Similarity=0.553 Sum_probs=23.7
Q ss_pred ccCCCCCCccccCCCCceeeccccC-ceecccC
Q 016243 5 VDCSKCRTTLQLPPGAQSIRCAICQ-AITHIAD 36 (392)
Q Consensus 5 ~~C~~C~~~l~~p~~a~~vrC~~C~-~vt~v~~ 36 (392)
..|+.|+++|.= ..-.|-|++|. .++.+..
T Consensus 29 ~hCp~Cg~PLF~--KdG~v~CPvC~~~~~~v~~ 59 (131)
T COG1645 29 KHCPKCGTPLFR--KDGEVFCPVCGYREVVVEE 59 (131)
T ss_pred hhCcccCCccee--eCCeEECCCCCceEEEeec
Confidence 469999999755 77789999999 6666654
No 85
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.69 E-value=39 Score=37.31 Aligned_cols=27 Identities=30% Similarity=0.707 Sum_probs=23.4
Q ss_pred cccCCCCCCccccCCCCceeeccccCc
Q 016243 4 LVDCSKCRTTLQLPPGAQSIRCAICQA 30 (392)
Q Consensus 4 ~~~C~~C~~~l~~p~~a~~vrC~~C~~ 30 (392)
.+.|.+|...|.+..+....+|..|.+
T Consensus 392 ~~~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 392 PARCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred eeECCCCCCceeEecCCCeeECCCCcC
Confidence 467999999999988888899999984
No 86
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=26.58 E-value=88 Score=35.14 Aligned_cols=39 Identities=28% Similarity=0.566 Sum_probs=0.0
Q ss_pred ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 016243 34 IADPRSGPPPPSSSSSSSYQPGHVPPSAVAPSPYNHAPPGQPP 76 (392)
Q Consensus 34 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 76 (392)
+.+..+.|||+...+ +.++.||.|++|++-.-+||||||
T Consensus 550 lpggag~PPPPpplP----g~aG~PPpPppppg~~gppPPPpp 588 (1102)
T KOG1924|consen 550 LPGGAGPPPPPPPLP----GIAGGPPPPPPPPGGGGPPPPPPP 588 (1102)
T ss_pred CCCCCCCCccCCCCC----cccCCCCccCCCCCCCCCCCcCCC
No 87
>cd06259 YdcF-like YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been idenitified. The family also includes Escherichia coli sanA and Salmonella typhimurium sfiX, which are involved in vancomycin resistance; sfiX may also be involved in murein synthesis.
Probab=26.33 E-value=1.6e+02 Score=25.07 Aligned_cols=59 Identities=17% Similarity=0.190 Sum_probs=41.1
Q ss_pred ceEEEEEEeCCCCCCCCCcchHHHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHh
Q 016243 81 RKRALIVGVSYRHTNHELKGCINDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQG 152 (392)
Q Consensus 81 ~k~ALlIGI~Y~~~~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~ 152 (392)
..+.|+-|-.-.+ .....++.|+++|.+ .|.+.+.|.+..... =|.+|+....+++.+.
T Consensus 35 ~~~ii~sGg~~~~------~~~~ea~~m~~~l~~-~gv~~~~I~~e~~s~------~T~ena~~~~~~~~~~ 93 (150)
T cd06259 35 APKLIVSGGQGPG------EGYSEAEAMARYLIE-LGVPAEAILLEDRST------NTYENARFSAELLRER 93 (150)
T ss_pred CCEEEEcCCCCCC------CCCCHHHHHHHHHHH-cCCCHHHeeecCCCC------CHHHHHHHHHHHHHhc
Confidence 4556666644211 346789999999996 588877776654432 4999999998888664
No 88
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.18 E-value=43 Score=35.58 Aligned_cols=29 Identities=21% Similarity=0.586 Sum_probs=23.5
Q ss_pred cccCCCCCCccccCCCCceeeccccCcee
Q 016243 4 LVDCSKCRTTLQLPPGAQSIRCAICQAIT 32 (392)
Q Consensus 4 ~~~C~~C~~~l~~p~~a~~vrC~~C~~vt 32 (392)
.+.|.+|...|.+.......+|..|....
T Consensus 222 ~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~ 250 (505)
T TIGR00595 222 ILCCPNCDVSLTYHKKEGKLRCHYCGYQE 250 (505)
T ss_pred ccCCCCCCCceEEecCCCeEEcCCCcCcC
Confidence 35688888888888888899999997443
No 89
>KOG3425 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.82 E-value=74 Score=27.52 Aligned_cols=25 Identities=12% Similarity=0.214 Sum_probs=19.4
Q ss_pred HHHHHHHHHHhCCCCCEEEEEEecC
Q 016243 142 MRMALYWLIQGCQPGDSLLFHFSGH 166 (392)
Q Consensus 142 I~~al~~L~~~~~~gD~llfYFSGH 166 (392)
...+|++++++...|+.+|+||.|-
T Consensus 11 g~e~~~~~~~~~~n~~~ifvlF~gs 35 (128)
T KOG3425|consen 11 GYESFEETLKNVENGKTIFVLFLGS 35 (128)
T ss_pred hHHHHHHHHHHHhCCceEEEEEecc
Confidence 3456777777777889999999974
No 90
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=25.65 E-value=32 Score=22.90 Aligned_cols=26 Identities=19% Similarity=0.538 Sum_probs=18.9
Q ss_pred ccCCCCCCccccCCC---CceeeccccCc
Q 016243 5 VDCSKCRTTLQLPPG---AQSIRCAICQA 30 (392)
Q Consensus 5 ~~C~~C~~~l~~p~~---a~~vrC~~C~~ 30 (392)
..|..|+..+.+..+ ...++|..|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 369999997654443 45788999986
No 91
>PLN02651 cysteine desulfurase
Probab=25.64 E-value=2.8e+02 Score=27.38 Aligned_cols=55 Identities=7% Similarity=0.037 Sum_probs=33.0
Q ss_pred HHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHH-hCCCCCEEEEEEecCcc
Q 016243 105 ARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQ-GCQPGDSLLFHFSGHGS 168 (392)
Q Consensus 105 a~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~-~~~~gD~llfYFSGHG~ 168 (392)
.+.+++.|.+.+|.++++|.+ +.. . .+.+..++..+.. ..++||.+++--..|..
T Consensus 45 ~~~~r~~la~~~g~~~~~v~~-t~~-------~-t~a~~~~l~~~~~~~~~~g~~vl~~~~~h~s 100 (364)
T PLN02651 45 VEKARAQVAALIGADPKEIIF-TSG-------A-TESNNLAIKGVMHFYKDKKKHVITTQTEHKC 100 (364)
T ss_pred HHHHHHHHHHHhCCCCCeEEE-eCC-------H-HHHHHHHHHHHHHhccCCCCEEEEcccccHH
Confidence 556667777777877666654 442 2 3444444444433 23689988886667754
No 92
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=25.52 E-value=44 Score=24.56 Aligned_cols=29 Identities=31% Similarity=0.650 Sum_probs=20.9
Q ss_pred CCCcc-cCCCCCCc-cccCCCCceeeccccCceecccC
Q 016243 1 MLMLV-DCSKCRTT-LQLPPGAQSIRCAICQAITHIAD 36 (392)
Q Consensus 1 ~~~~~-~C~~C~~~-l~~p~~a~~vrC~~C~~vt~v~~ 36 (392)
|...+ .|.+|+.+ |. -+|..|...|.+.-
T Consensus 1 m~~~~r~c~~~~~YTLk-------~~cp~cG~~T~~ah 31 (53)
T PF04135_consen 1 MRYYIRKCPGCRVYTLK-------DKCPPCGGPTESAH 31 (53)
T ss_dssp -EEEEEECTTTCEEESS-------SBBTTTSSBSEESS
T ss_pred CCcccccCCCCCcEeCC-------CccCCCCCCCcCCc
Confidence 44455 89999974 32 26999999998884
No 93
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=25.50 E-value=46 Score=32.71 Aligned_cols=110 Identities=10% Similarity=0.124 Sum_probs=60.9
Q ss_pred cccCCCCCCccccCCCCceeeccccCceecccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceE
Q 016243 4 LVDCSKCRTTLQLPPGAQSIRCAICQAITHIADPRSGPPPPSSSSSSSYQPGHVPPSAVAPSPYNHAPPGQPPHAQGRKR 83 (392)
Q Consensus 4 ~~~C~~C~~~l~~p~~a~~vrC~~C~~vt~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~ 83 (392)
|--|++|++....-.+-...+|..|.....=+ ..|-+= .... .+..-. .+..++-.+..|
T Consensus 111 ~RFCg~CG~~~~~~~~g~~~~C~~cg~~~fPR---~dP~vI-v~v~--~~~~il--------------La~~~~h~~g~y 170 (279)
T COG2816 111 HRFCGRCGTKTYPREGGWARVCPKCGHEHFPR---IDPCVI-VAVI--RGDEIL--------------LARHPRHFPGMY 170 (279)
T ss_pred CcCCCCCCCcCccccCceeeeCCCCCCccCCC---CCCeEE-EEEe--cCCcee--------------ecCCCCCCCcce
Confidence 34599999999888899999999998544211 111100 0000 000000 000111225567
Q ss_pred EEEEEeCCCCCCCCCcchHHHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHH
Q 016243 84 ALIVGVSYRHTNHELKGCINDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMAL 146 (392)
Q Consensus 84 ALlIGI~Y~~~~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al 146 (392)
.+|-|-=-.+ -+... ...++++.+ -|....||..+..+ .+|=..-++-.+
T Consensus 171 S~LAGFVE~G------ETlE~-AV~REv~EE-~Gi~V~~vrY~~SQ-----PWPfP~SLMigf 220 (279)
T COG2816 171 SLLAGFVEPG------ETLEQ-AVAREVFEE-VGIKVKNVRYVGSQ-----PWPFPHSLMLGF 220 (279)
T ss_pred eeeeecccCC------ccHHH-HHHHHHHHh-hCeEEeeeeEEecc-----CCCCchhhhhhh
Confidence 7777744332 12232 236778876 59998899888765 366666655544
No 94
>PRK05942 aspartate aminotransferase; Provisional
Probab=25.27 E-value=3.5e+02 Score=27.10 Aligned_cols=46 Identities=15% Similarity=0.198 Sum_probs=26.9
Q ss_pred HHHHHHHHhccC--CCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEE
Q 016243 106 RCMKYMLTNRFK--FPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFH 162 (392)
Q Consensus 106 ~~m~~~L~~~~G--f~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfY 162 (392)
+.+++++..++| +.+++..+++.. +.+.|...+..+ +++||.|++-
T Consensus 80 ~aia~~~~~~~~~~~~~~~~i~vt~G--------~~~al~~~~~~~---~~~gd~Vlv~ 127 (394)
T PRK05942 80 QAITDWYHRRYGVELDPDSEALPLLG--------SKEGLTHLALAY---VNPGDVVLVP 127 (394)
T ss_pred HHHHHHHHHHHCCCcCCCCeEEEccC--------hHHHHHHHHHHh---CCCCCEEEEc
Confidence 456777766556 455554444542 344555555444 5699988864
No 95
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=25.08 E-value=20 Score=33.80 Aligned_cols=34 Identities=21% Similarity=0.565 Sum_probs=25.3
Q ss_pred CcccCCCCCCccccC-CCCceeeccccCceecccC
Q 016243 3 MLVDCSKCRTTLQLP-PGAQSIRCAICQAITHIAD 36 (392)
Q Consensus 3 ~~~~C~~C~~~l~~p-~~a~~vrC~~C~~vt~v~~ 36 (392)
-.|.|++|...+.+- --..--||..|++|..|..
T Consensus 169 cRV~CgHC~~tFLfnt~tnaLArCPHCrKvSsvGs 203 (275)
T KOG4684|consen 169 CRVKCGHCNETFLFNTLTNALARCPHCRKVSSVGS 203 (275)
T ss_pred eEEEecCccceeehhhHHHHHhcCCcccchhhhhh
Confidence 467899999875443 3346689999999887764
No 96
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=24.87 E-value=2e+02 Score=24.50 Aligned_cols=46 Identities=20% Similarity=0.247 Sum_probs=34.3
Q ss_pred ceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEecCccc
Q 016243 122 SIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFHFSGHGSQ 169 (392)
Q Consensus 122 ~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfYFSGHG~~ 169 (392)
+|.+|.|-. .+....++.++++|+.+++...++|.+-|+.-|+...
T Consensus 2 ~vvilvD~S--~Sm~g~~~~~k~al~~~l~~L~~~d~fnii~f~~~~~ 47 (155)
T PF13768_consen 2 DVVILVDTS--GSMSGEKELVKDALRAILRSLPPGDRFNIIAFGSSVR 47 (155)
T ss_pred eEEEEEeCC--CCCCCcHHHHHHHHHHHHHhCCCCCEEEEEEeCCEee
Confidence 567777753 2222333788889999999999999999999888654
No 97
>cd06502 TA_like Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a secondary glycine biosynthetic pathway.
Probab=24.72 E-value=5.5e+02 Score=24.62 Aligned_cols=52 Identities=19% Similarity=0.202 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEecCcc
Q 016243 103 NDARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFHFSGHGS 168 (392)
Q Consensus 103 nDa~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfYFSGHG~ 168 (392)
...+.+++.+.+.+| + +++.+..+ .| +.+..++..+ +++||.+++-=.+|..
T Consensus 32 ~~~~~l~~~~a~~~g-~-~~~~~~~~--------gt-~a~~~~~~~l---~~~gd~v~~~~~~~~~ 83 (338)
T cd06502 32 PTTAKLEARAAELFG-K-EAALFVPS--------GT-AANQLALAAH---TQPGGSVICHETAHIY 83 (338)
T ss_pred HHHHHHHHHHHHHhC-C-CeEEEecC--------ch-HHHHHHHHHh---cCCCCeEEEecCccee
Confidence 356777888887778 3 35555444 34 5566666655 4689999976666654
No 98
>PRK09814 beta-1,6-galactofuranosyltransferase; Provisional
Probab=24.37 E-value=1.6e+02 Score=28.88 Aligned_cols=55 Identities=18% Similarity=0.285 Sum_probs=34.4
Q ss_pred HHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEecC
Q 016243 105 ARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFHFSGH 166 (392)
Q Consensus 105 a~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfYFSGH 166 (392)
-.+|.+.|. +.||..-.+.. .... .-...++...+..++.+.++||.|+|++...
T Consensus 21 ~~d~~~~~~-~~g~~~~~~~~-~~~~-----~~~~~~~~~~~~~~~~~~~~~Dvv~~~~P~~ 75 (333)
T PRK09814 21 KNDVTKIAK-QLGFEELGIYF-YNIK-----RDSLSERSKRLDGILASLKPGDIVIFQFPTW 75 (333)
T ss_pred HHHHHHHHH-HCCCeEeEEEe-cccc-----cchHHHHHHHHHHHHhcCCCCCEEEEECCCC
Confidence 344667776 47997533322 2111 0124556667777888899999999988654
No 99
>cd06446 Trp-synth_B Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to glyceraldehyde 3-phosphate and indole at the active site of the alpha subunit. In the beta reaction, indole undergoes a PLP-dependent reaction with L-serine to form L-tryptophan at the active site of the beta subunit. Members of this CD, Trp-synth_B, are found in all three major phylogenetic divisions.
Probab=24.37 E-value=2e+02 Score=29.03 Aligned_cols=33 Identities=12% Similarity=0.121 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHhCCCCCEEEEEEecCccccC
Q 016243 139 KYNMRMALYWLIQGCQPGDSLLFHFSGHGSQQR 171 (392)
Q Consensus 139 ~~nI~~al~~L~~~~~~gD~llfYFSGHG~~~~ 171 (392)
-..-..++..+.++..+++.+++.|+|||....
T Consensus 330 sgaalAa~~~~~~~~~~~~~Vv~i~~g~G~k~~ 362 (365)
T cd06446 330 SSHAIAYAIKLAKKLGKEKVIVVNLSGRGDKDL 362 (365)
T ss_pred chHHHHHHHHHHHhcCCCCeEEEEeCCCCcccc
Confidence 333334444455554678899999999997643
No 100
>TIGR00758 UDG_fam4 uracil-DNA glycosylase, family 4. This well-conserved family of proteins is about 200 residues in length and homologous to the N-terminus of the DNA polymerase of phage SPO1 of Bacillus subtilis. The member from Thermus thermophilus HB8 is known to act as uracil-DNA glycosylase, an enzyme of DNA base excision repair. Its appearance as a domain of phage DNA polymerases could be consistent with uracil-DNA glycosylase activity.
Probab=24.28 E-value=3.8e+02 Score=23.98 Aligned_cols=71 Identities=13% Similarity=0.176 Sum_probs=44.6
Q ss_pred CceEEEEEEeC-C-CCCCCCCcchHHHHHHHHHHHHhccCCCCCceEEccCC---CCCCCCCccHHHHHHHHHHHHHh
Q 016243 80 GRKRALIVGVS-Y-RHTNHELKGCINDARCMKYMLTNRFKFPESSIVMLTEE---DPDPLKRPTKYNMRMALYWLIQG 152 (392)
Q Consensus 80 ~~k~ALlIGI~-Y-~~~~~~L~g~~nDa~~m~~~L~~~~Gf~~~~I~~Ltd~---~~~~~~~pT~~nI~~al~~L~~~ 152 (392)
.+-+.++||-. - ..........-...+.+.++|. ..|++.+++.+ ++- .+...+.||.++|.....+|.++
T Consensus 20 ~~A~im~VgeaPg~~e~~~g~pf~g~sG~~L~~~l~-~~gl~~~~vy~-t~~~kc~P~~~r~P~~~Ei~~c~~~l~~e 95 (173)
T TIGR00758 20 PDANIMFVGEAPGREEDRKGRPFVGRAGKLLDEMLA-AIGLSRENVYI-TNVVKCRPPNNRDPTPEEVEACAPYLVKQ 95 (173)
T ss_pred CCCCEEEEeCCCCccccccCCCCcChHHHHHHHHHH-HcCCCcccEEE-eccccccCCCCCCcCHHHHHHHHHHHHHH
Confidence 44578888876 2 2222233333456777888887 68998877644 332 12234579999999888777654
No 101
>PF12773 DZR: Double zinc ribbon
Probab=24.17 E-value=35 Score=23.90 Aligned_cols=27 Identities=33% Similarity=0.643 Sum_probs=20.5
Q ss_pred cccCCCCCCccccCCCCceeeccccCce
Q 016243 4 LVDCSKCRTTLQLPPGAQSIRCAICQAI 31 (392)
Q Consensus 4 ~~~C~~C~~~l~~p~~a~~vrC~~C~~v 31 (392)
...|.+|++.|. ......+.|..|.+.
T Consensus 12 ~~fC~~CG~~l~-~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCPHCGTPLP-PPDQSKKICPNCGAE 38 (50)
T ss_pred ccCChhhcCChh-hccCCCCCCcCCcCC
Confidence 356899999887 555667889999865
No 102
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=24.06 E-value=49 Score=20.29 Aligned_cols=23 Identities=30% Similarity=0.784 Sum_probs=14.7
Q ss_pred CcccCCCCCCccccCCCCceeeccccC
Q 016243 3 MLVDCSKCRTTLQLPPGAQSIRCAICQ 29 (392)
Q Consensus 3 ~~~~C~~C~~~l~~p~~a~~vrC~~C~ 29 (392)
|.+.|++|++ .++.+++ -|..|.
T Consensus 1 m~~~Cp~Cg~--~~~~~~~--fC~~CG 23 (26)
T PF13248_consen 1 MEMFCPNCGA--EIDPDAK--FCPNCG 23 (26)
T ss_pred CcCCCcccCC--cCCcccc--cChhhC
Confidence 4578999998 3455543 366664
No 103
>PRK00809 hypothetical protein; Provisional
Probab=24.00 E-value=69 Score=28.28 Aligned_cols=19 Identities=37% Similarity=0.616 Sum_probs=14.9
Q ss_pred HHHhCCCCCEEEEEEec-Cc
Q 016243 149 LIQGCQPGDSLLFHFSG-HG 167 (392)
Q Consensus 149 L~~~~~~gD~llfYFSG-HG 167 (392)
.+.+.++||.+|||-|+ +|
T Consensus 31 ~lr~Mk~GD~v~fYhs~~~~ 50 (144)
T PRK00809 31 TIEKVKPGDKLIIYVSQEYG 50 (144)
T ss_pred HHhhCCCCCEEEEEECCccC
Confidence 34457899999999997 55
No 104
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=23.99 E-value=49 Score=24.27 Aligned_cols=27 Identities=33% Similarity=0.648 Sum_probs=18.6
Q ss_pred ccCCCCCCc-cccCCCC---ceeeccccCce
Q 016243 5 VDCSKCRTT-LQLPPGA---QSIRCAICQAI 31 (392)
Q Consensus 5 ~~C~~C~~~-l~~p~~a---~~vrC~~C~~v 31 (392)
+.|++|+.. =++|... -.++|+.|+..
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred EECcccchhhcccccccCCceEEEcCCCCCc
Confidence 459999985 3454322 36999999864
No 105
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=23.56 E-value=61 Score=23.36 Aligned_cols=25 Identities=16% Similarity=0.426 Sum_probs=19.2
Q ss_pred cCCCCCCccccCCCCceeeccccCce
Q 016243 6 DCSKCRTTLQLPPGAQSIRCAICQAI 31 (392)
Q Consensus 6 ~C~~C~~~l~~p~~a~~vrC~~C~~v 31 (392)
.|++|+..++.+.. ....|..|+..
T Consensus 22 fCP~Cg~~~m~~~~-~r~~C~~Cgyt 46 (50)
T PRK00432 22 FCPRCGSGFMAEHL-DRWHCGKCGYT 46 (50)
T ss_pred cCcCCCcchheccC-CcEECCCcCCE
Confidence 69999988555554 68899999864
No 106
>PF00266 Aminotran_5: Aminotransferase class-V; InterPro: IPR000192 Aminotransferases share certain mechanistic features with other pyridoxal- phosphate dependent enzymes, such as the covalent binding of the pyridoxal- phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped [] into subfamilies. This entry represents the class V aminotransferases and the related, though functionally distinct, cysteine desulfurases.; GO: 0008152 metabolic process; PDB: 3FFR_A 1N2T_B 1ELQ_A 1N31_A 1ELU_B 1QZ9_A 1VJO_A 3ISL_B 1BJO_B 1BJN_B ....
Probab=23.48 E-value=3.8e+02 Score=26.46 Aligned_cols=56 Identities=20% Similarity=0.277 Sum_probs=39.4
Q ss_pred HHHHHHHHhccCCCC-CceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEecCcccc
Q 016243 106 RCMKYMLTNRFKFPE-SSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFHFSGHGSQQ 170 (392)
Q Consensus 106 ~~m~~~L~~~~Gf~~-~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfYFSGHG~~~ 170 (392)
+..++.+.+-+|.++ ++|. ++.. +...+...+..+....++||.+++.-.+|....
T Consensus 46 ~~~r~~la~~lg~~~~~~v~-~~~~--------~t~a~~~~~~~l~~~~~~g~~vl~~~~~~~s~~ 102 (371)
T PF00266_consen 46 EEAREALAKLLGAPPDEEVV-FTSN--------GTEALNAVASSLLNPLKPGDEVLVTSNEHPSNR 102 (371)
T ss_dssp HHHHHHHHHHHTSSTTEEEE-EESS--------HHHHHHHHHHHHHHHGTTTCEEEEEESSHHHHH
T ss_pred HHHHHHHHHhcCCccccccc-cccc--------cchhhhhhhhccccccccccccccccccccccc
Confidence 345566666678887 6664 4442 334777777777666789999999999998765
No 107
>PF08541 ACP_syn_III_C: 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal ; InterPro: IPR013747 This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III 2.3.1.41 from EC, the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria. ; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0008610 lipid biosynthetic process; PDB: 3IL3_A 1ZOW_C 3GWE_B 3GWA_B 1UB7_B 3LED_B 2EBD_A 1HNJ_A 2EFT_B 1HN9_B ....
Probab=23.43 E-value=1.2e+02 Score=23.61 Aligned_cols=56 Identities=18% Similarity=0.198 Sum_probs=34.8
Q ss_pred HHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHH--hCCCCCEEEEEEecCcccc
Q 016243 111 MLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQ--GCQPGDSLLFHFSGHGSQQ 170 (392)
Q Consensus 111 ~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~--~~~~gD~llfYFSGHG~~~ 170 (392)
.+.+.+|++.+.+..-..+- -.--...+.-.|..+++ ..++||.+++.=.|-|...
T Consensus 26 ~~~~~lgi~~~~~~~~~~~~----Gn~~sa~~~~~L~~~~~~g~~~~Gd~vl~~~~G~G~~~ 83 (90)
T PF08541_consen 26 SIAKRLGIPPERFPDNLAEY----GNTGSASIPINLADALEEGRIKPGDRVLLVGFGAGFSW 83 (90)
T ss_dssp HHHHHHTS-GGGBE-THHHH-----B-GGGHHHHHHHHHHHTTSSCTTEEEEEEEEETTTEE
T ss_pred HHHHHcCCcHHHHHHHHhcc----CcchhhhHHHHHHHHHHcCCCCCCCEEEEEEEEhhhee
Confidence 34456788877654322110 01234556777888887 7899999999988888654
No 108
>PRK02948 cysteine desulfurase; Provisional
Probab=23.35 E-value=3e+02 Score=27.28 Aligned_cols=54 Identities=13% Similarity=0.074 Sum_probs=31.8
Q ss_pred HHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHh-CCCCCEEEEEEecCc
Q 016243 105 ARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQG-CQPGDSLLFHFSGHG 167 (392)
Q Consensus 105 a~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~-~~~gD~llfYFSGHG 167 (392)
.+.+++.|.+.+|.++++|.+ +.. +.+.+..++..+... .++||.+++--..|.
T Consensus 45 ~~~~r~~la~~~g~~~~~i~~-~~g--------~t~a~~~~~~~~~~~~~~~g~~vv~~~~~h~ 99 (381)
T PRK02948 45 LQVCRKTFAEMIGGEEQGIYF-TSG--------GTESNYLAIQSLLNALPQNKKHIITTPMEHA 99 (381)
T ss_pred HHHHHHHHHHHhCCCCCeEEE-eCc--------HHHHHHHHHHHHHHhccCCCCEEEECCcccH
Confidence 445667777777887777754 432 234444555555443 357888876444553
No 109
>KOG0256 consensus 1-aminocyclopropane-1-carboxylate synthase, and related proteins [Signal transduction mechanisms]
Probab=23.25 E-value=4.6e+02 Score=27.53 Aligned_cols=34 Identities=24% Similarity=0.342 Sum_probs=24.9
Q ss_pred ccHHHHHHhhcCcCCCCCeEEEEEeCCCCCCCCCCc
Q 016243 196 IVDDEINTTLVRPLPRGARLHAIIDACHSGTVLDLP 231 (392)
Q Consensus 196 i~d~eL~~~L~~~l~~g~~l~vIlD~C~SG~~~~~p 231 (392)
.+.++|..++. - ....++|+|+|==|+|++.+.+
T Consensus 243 ~~~e~L~~ll~-F-a~~kniHvI~DEIya~sVF~~~ 276 (471)
T KOG0256|consen 243 LSPEELISLLN-F-ASRKNIHVISDEIYAGSVFDKS 276 (471)
T ss_pred cCHHHHHHHHH-H-HhhcceEEEeehhhcccccCcc
Confidence 45567777653 2 2347899999999999998754
No 110
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=23.18 E-value=44 Score=28.23 Aligned_cols=28 Identities=25% Similarity=0.739 Sum_probs=19.5
Q ss_pred CcccCCCCCCccccCCCCceeeccccCcee
Q 016243 3 MLVDCSKCRTTLQLPPGAQSIRCAICQAIT 32 (392)
Q Consensus 3 ~~~~C~~C~~~l~~p~~a~~vrC~~C~~vt 32 (392)
...+|.+|+... +......+|+.|+...
T Consensus 69 ~~~~C~~Cg~~~--~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 69 VECECEDCSEEV--SPEIDLYRCPKCHGIM 96 (115)
T ss_pred cEEEcccCCCEE--ecCCcCccCcCCcCCC
Confidence 457899999644 4444568899998654
No 111
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=23.17 E-value=65 Score=30.02 Aligned_cols=34 Identities=18% Similarity=0.516 Sum_probs=22.9
Q ss_pred CCCcc--cCCCCCCccccCC-------CCceeeccccCceeccc
Q 016243 1 MLMLV--DCSKCRTTLQLPP-------GAQSIRCAICQAITHIA 35 (392)
Q Consensus 1 ~~~~~--~C~~C~~~l~~p~-------~a~~vrC~~C~~vt~v~ 35 (392)
|.+++ .|.+|+ ...++. ....+||.-|..|....
T Consensus 1 m~~~iy~~Cp~Cg-~eev~hEVik~~g~~~lvrC~eCG~V~~~~ 43 (201)
T COG1326 1 MTEEIYIECPSCG-SEEVSHEVIKERGREPLVRCEECGTVHPAI 43 (201)
T ss_pred CcceEEEECCCCC-cchhhHHHHHhcCCceEEEccCCCcEeece
Confidence 44444 599999 555532 22589999999888543
No 112
>COG0079 HisC Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]
Probab=23.11 E-value=5.8e+02 Score=25.76 Aligned_cols=48 Identities=17% Similarity=0.246 Sum_probs=32.0
Q ss_pred HHHHHHHHHHhccC-CCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEE
Q 016243 104 DARCMKYMLTNRFK-FPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFHF 163 (392)
Q Consensus 104 Da~~m~~~L~~~~G-f~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfYF 163 (392)
+...+++.+.+.+| .+.++|.+-.. .++++..+-.... .+||.+++-.
T Consensus 58 ~~~~l~~a~a~~~~~~~~~~V~~gnG----------sde~i~~l~~~~~--~~gd~vl~~~ 106 (356)
T COG0079 58 DYRELRAALAEYYGVVDPENVLVGNG----------SDELIELLVRAFV--EPGDTVLIPE 106 (356)
T ss_pred cHHHHHHHHHHHhCCCCcceEEEcCC----------hHHHHHHHHHHhh--cCCCEEEEcC
Confidence 67778888888888 77777655433 4566666544433 3889998863
No 113
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=23.08 E-value=52 Score=23.72 Aligned_cols=30 Identities=20% Similarity=0.498 Sum_probs=19.5
Q ss_pred ccCCC--CCCccccCCCCce--eeccccCceecc
Q 016243 5 VDCSK--CRTTLQLPPGAQS--IRCAICQAITHI 34 (392)
Q Consensus 5 ~~C~~--C~~~l~~p~~a~~--vrC~~C~~vt~v 34 (392)
..|++ |...+....+... ++|..|+...=.
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~ 52 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCF 52 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEECS
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcCcc
Confidence 47977 9999999988887 999999976633
No 114
>PRK06260 threonine synthase; Validated
Probab=22.85 E-value=2.1e+02 Score=29.25 Aligned_cols=35 Identities=14% Similarity=0.186 Sum_probs=27.0
Q ss_pred ccHHHHHHHHHHHHHh--CCCCCEEEEEEecCccccC
Q 016243 137 PTKYNMRMALYWLIQG--CQPGDSLLFHFSGHGSQQR 171 (392)
Q Consensus 137 pT~~nI~~al~~L~~~--~~~gD~llfYFSGHG~~~~ 171 (392)
|+-..-..++.++.+. ..+++.+++.++|||....
T Consensus 335 pssaaalAa~~~l~~~g~i~~~~~VV~i~tG~glK~~ 371 (397)
T PRK06260 335 PASAASVAGLIKLVEEGVIDKDERVVCITTGHLLKDP 371 (397)
T ss_pred chHHHHHHHHHHHHHcCCCCCCCeEEEEeCCCccCch
Confidence 6666667777777765 5688999999999998643
No 115
>PRK05638 threonine synthase; Validated
Probab=22.83 E-value=2.6e+02 Score=29.05 Aligned_cols=39 Identities=21% Similarity=0.229 Sum_probs=30.3
Q ss_pred ccHHHHHHHHHHHHHh--CCCCCEEEEEEecCccccCCCCC
Q 016243 137 PTKYNMRMALYWLIQG--CQPGDSLLFHFSGHGSQQRNYNG 175 (392)
Q Consensus 137 pT~~nI~~al~~L~~~--~~~gD~llfYFSGHG~~~~d~~g 175 (392)
|+-..-..++.++.+. ..+++.|++.++|||......-|
T Consensus 323 pssaaa~Aa~~~~~~~g~i~~~~~Vv~i~tG~g~k~~~~~~ 363 (442)
T PRK05638 323 LSSAVVMPALLKLGEEGYIEKGDKVVLVVTGSGLKGYGEGG 363 (442)
T ss_pred chHHHHHHHHHHHHHcCCCCCCCeEEEEeCCCCCCCCCCCc
Confidence 6677777777777765 57899999999999998764433
No 116
>PF14353 CpXC: CpXC protein
Probab=22.76 E-value=76 Score=26.92 Aligned_cols=32 Identities=16% Similarity=0.467 Sum_probs=22.4
Q ss_pred cccCCCCCCccccCC-------------------CCceeeccccCceeccc
Q 016243 4 LVDCSKCRTTLQLPP-------------------GAQSIRCAICQAITHIA 35 (392)
Q Consensus 4 ~~~C~~C~~~l~~p~-------------------~a~~vrC~~C~~vt~v~ 35 (392)
++.|++|+....+.. .--++.|..|++..++.
T Consensus 1 ~itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred CcCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecC
Confidence 478999998765441 11378999998777665
No 117
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=22.54 E-value=64 Score=24.15 Aligned_cols=26 Identities=15% Similarity=0.461 Sum_probs=15.6
Q ss_pred cCCCCCCccccCCCCceeeccccCce
Q 016243 6 DCSKCRTTLQLPPGAQSIRCAICQAI 31 (392)
Q Consensus 6 ~C~~C~~~l~~p~~a~~vrC~~C~~v 31 (392)
.|+.|+....-+...+.+.|..|+..
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCcccccccccccceEEcCCCCCE
Confidence 36666665554555566666666544
No 118
>PLN03026 histidinol-phosphate aminotransferase; Provisional
Probab=22.26 E-value=2e+02 Score=28.88 Aligned_cols=46 Identities=13% Similarity=0.234 Sum_probs=30.5
Q ss_pred HHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEE
Q 016243 105 ARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFH 162 (392)
Q Consensus 105 a~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfY 162 (392)
...+++.+.+.+|.++++|.+ +.. +.+.|...+..+ +++||.+++.
T Consensus 88 ~~~lr~~ia~~~~~~~~~I~~-t~G--------a~~~i~~~~~~~---~~~gd~Vlv~ 133 (380)
T PLN03026 88 SRRLRAALAEDSGLESENILV-GCG--------ADELIDLLMRCV---LDPGDKIIDC 133 (380)
T ss_pred HHHHHHHHHHHhCcChhhEEE-cCC--------HHHHHHHHHHHh---cCCCCEEEEc
Confidence 346888888888888888854 542 344554444444 4589988874
No 119
>PRK14012 cysteine desulfurase; Provisional
Probab=22.17 E-value=3.1e+02 Score=27.63 Aligned_cols=54 Identities=9% Similarity=0.066 Sum_probs=31.3
Q ss_pred HHHHHHHHHhccCCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHH-hCCCCCEEEEEEecCc
Q 016243 105 ARCMKYMLTNRFKFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQ-GCQPGDSLLFHFSGHG 167 (392)
Q Consensus 105 a~~m~~~L~~~~Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~-~~~~gD~llfYFSGHG 167 (392)
.+.+++.+.+.+|.++++|.+..+ . .+.+..++.-+.. ..++||.|++-=..|.
T Consensus 51 ~~~~r~~ia~~~g~~~~~v~~~~g--------~-t~al~~~l~~l~~~~~~~gd~Vi~~~~~~~ 105 (404)
T PRK14012 51 VDIARNQIADLIGADPREIVFTSG--------A-TESDNLAIKGAAHFYQKKGKHIITSKTEHK 105 (404)
T ss_pred HHHHHHHHHHHcCcCcCeEEEeCC--------H-HHHHHHHHHHHHHhhcCCCCEEEEecCccH
Confidence 556677777777877666654433 2 3344444443332 1368998887655553
No 120
>COG2194 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]
Probab=22.01 E-value=1e+02 Score=33.35 Aligned_cols=26 Identities=23% Similarity=0.286 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCCCCEEEEEEecCcccc
Q 016243 144 MALYWLIQGCQPGDSLLFHFSGHGSQQ 170 (392)
Q Consensus 144 ~al~~L~~~~~~gD~llfYFSGHG~~~ 170 (392)
..+-+++++-++ |.++||||=||...
T Consensus 433 ~~vi~~Lk~~~~-~~~liY~SDHGEsl 458 (555)
T COG2194 433 SKLIDQLKDKKD-NTSLIYFSDHGESL 458 (555)
T ss_pred HHHHHHHHhCCC-CeEEEEEcCccHhh
Confidence 333333343334 89999999999865
No 121
>PRK00420 hypothetical protein; Validated
Probab=21.97 E-value=73 Score=27.08 Aligned_cols=30 Identities=13% Similarity=0.305 Sum_probs=22.7
Q ss_pred ccCCCCCCccccCCCCceeeccccCceeccc
Q 016243 5 VDCSKCRTTLQLPPGAQSIRCAICQAITHIA 35 (392)
Q Consensus 5 ~~C~~C~~~l~~p~~a~~vrC~~C~~vt~v~ 35 (392)
-.|+-|+++|.=- ....+.|..|..+-.|.
T Consensus 24 ~~CP~Cg~pLf~l-k~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 24 KHCPVCGLPLFEL-KDGEVVCPVHGKVYIVK 53 (112)
T ss_pred CCCCCCCCcceec-CCCceECCCCCCeeeec
Confidence 5799999987532 44578999999876666
No 122
>PRK06108 aspartate aminotransferase; Provisional
Probab=21.73 E-value=4.7e+02 Score=25.75 Aligned_cols=55 Identities=16% Similarity=0.145 Sum_probs=31.9
Q ss_pred chHHHHHHHHHHHHhccC--CCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEecC
Q 016243 100 GCINDARCMKYMLTNRFK--FPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLFHFSGH 166 (392)
Q Consensus 100 g~~nDa~~m~~~L~~~~G--f~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llfYFSGH 166 (392)
|...=-+.++++|.+.+| .++++|.+ +.. +.+.+..++..+ +++||.+++---.|
T Consensus 62 G~~~lr~~la~~~~~~~~~~~~~~~i~~-t~g--------~~~al~~~~~~l---~~~gd~vl~~~p~y 118 (382)
T PRK06108 62 GIPELREALARYVSRLHGVATPPERIAV-TSS--------GVQALMLAAQAL---VGPGDEVVAVTPLW 118 (382)
T ss_pred CCHHHHHHHHHHHHHHhCCCcCcceEEE-eCC--------hHHHHHHHHHHh---cCCCCEEEEeCCCc
Confidence 333333556777766567 67777765 332 244555555555 45899888744333
No 123
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.53 E-value=59 Score=35.90 Aligned_cols=28 Identities=25% Similarity=0.651 Sum_probs=23.0
Q ss_pred cccCCCCCCccccCCCCceeeccccCce
Q 016243 4 LVDCSKCRTTLQLPPGAQSIRCAICQAI 31 (392)
Q Consensus 4 ~~~C~~C~~~l~~p~~a~~vrC~~C~~v 31 (392)
.+.|++|...|.+.......+|..|...
T Consensus 390 ~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 390 VAECPHCDASLTLHRFQRRLRCHHCGYQ 417 (679)
T ss_pred ccCCCCCCCceeEECCCCeEECCCCcCC
Confidence 3568888888888888888999999743
No 124
>TIGR00263 trpB tryptophan synthase, beta subunit. Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan. the beta chain contains the functional domain for or the synthesis of tryptophan from indole and serine. The enzyme requires pyridoxal-phosphate as a cofactor. The pyridoxal-P attachment site is contained within the conserved region [LIVM]-x-H-x-G-[STA]-H-K-x-N] [K is the pyridoxal-P attachment site] which is present between residues 90-100 of the model.
Probab=21.28 E-value=2e+02 Score=29.30 Aligned_cols=34 Identities=12% Similarity=0.137 Sum_probs=24.2
Q ss_pred ccHHHHHHHHHHHHHhCCCCCEEEEEEecCcccc
Q 016243 137 PTKYNMRMALYWLIQGCQPGDSLLFHFSGHGSQQ 170 (392)
Q Consensus 137 pT~~nI~~al~~L~~~~~~gD~llfYFSGHG~~~ 170 (392)
++-..-..++.++.+...+++.+++.++|||...
T Consensus 344 ~ssaaalaa~~~~~~~l~~~~~Vv~i~~g~G~~d 377 (385)
T TIGR00263 344 LESSHALAHLEKIAPTLPKDQIVVVNLSGRGDKD 377 (385)
T ss_pred hHHHHHHHHHHHHHHhCCCCCeEEEEeCCCCcCC
Confidence 3344444555556666778999999999999764
No 125
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=21.16 E-value=37 Score=28.81 Aligned_cols=34 Identities=24% Similarity=0.512 Sum_probs=28.6
Q ss_pred CcccCCCCCCccccCCCCceeeccccCceecccC
Q 016243 3 MLVDCSKCRTTLQLPPGAQSIRCAICQAITHIAD 36 (392)
Q Consensus 3 ~~~~C~~C~~~l~~p~~a~~vrC~~C~~vt~v~~ 36 (392)
-++-|+-|+.-|+.|.-...+-|..|+..-.|++
T Consensus 6 ~~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~~ 39 (116)
T KOG2907|consen 6 DLDFCSDCGSLLEEPSAQSTVLCIRCKIEYPVSQ 39 (116)
T ss_pred CcchhhhhhhhcccccccCceEeccccccCCHHH
Confidence 3567999999999999888899999997777664
No 126
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=21.04 E-value=66 Score=22.93 Aligned_cols=24 Identities=29% Similarity=0.935 Sum_probs=17.5
Q ss_pred ccCCCCCC-ccccCCCCceeeccccCcee
Q 016243 5 VDCSKCRT-TLQLPPGAQSIRCAICQAIT 32 (392)
Q Consensus 5 ~~C~~C~~-~l~~p~~a~~vrC~~C~~vt 32 (392)
+.|+.|+. .+. | ..++|+.|..+.
T Consensus 1 ~~C~~C~~~~i~---g-~R~~C~~C~dyd 25 (49)
T cd02345 1 LSCSACRKQDIS---G-IRFPCQVCRDYS 25 (49)
T ss_pred CcCCCCCCCCce---E-eeEECCCCCCcC
Confidence 46999988 444 4 567999997544
No 127
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=20.99 E-value=64 Score=22.96 Aligned_cols=24 Identities=29% Similarity=0.845 Sum_probs=17.4
Q ss_pred ccCCCCCC-ccccCCCCceeeccccCcee
Q 016243 5 VDCSKCRT-TLQLPPGAQSIRCAICQAIT 32 (392)
Q Consensus 5 ~~C~~C~~-~l~~p~~a~~vrC~~C~~vt 32 (392)
|.|..|+. .+. | ..++|..|..+.
T Consensus 1 i~C~~C~~~~i~---g-~R~~C~~C~d~d 25 (49)
T cd02338 1 VSCDGCGKSNFT---G-RRYKCLICYDYD 25 (49)
T ss_pred CCCCCCcCCCcE---E-eeEEeCCCCCCc
Confidence 57999994 454 3 789999996443
No 128
>PRK07591 threonine synthase; Validated
Probab=20.97 E-value=2.5e+02 Score=29.04 Aligned_cols=35 Identities=14% Similarity=0.185 Sum_probs=26.9
Q ss_pred ccHHHHHHHHHHHHH--hCCCCCEEEEEEecCccccC
Q 016243 137 PTKYNMRMALYWLIQ--GCQPGDSLLFHFSGHGSQQR 171 (392)
Q Consensus 137 pT~~nI~~al~~L~~--~~~~gD~llfYFSGHG~~~~ 171 (392)
|+-..-..++..+.+ ..++++.+++..+|||....
T Consensus 358 pssaaalAal~~l~~~g~i~~~~~VV~i~tG~G~kd~ 394 (421)
T PRK07591 358 TAGGVTVAVLKKLVEAGKIDPDEETVVYITGNGLKTL 394 (421)
T ss_pred chHHHHHHHHHHHHHhCCCCCCCeEEEEeCCCccCCH
Confidence 556666667777766 46789999999999998754
No 129
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=20.82 E-value=4.9e+02 Score=21.52 Aligned_cols=63 Identities=22% Similarity=0.283 Sum_probs=35.9
Q ss_pred HHHHHHHHHHH-hCCCCCEEEEEEecCccccCCCCCCCCCCcceeEEeccCCCCCcccHHHHHHhhcCcCCCCCeEEEEE
Q 016243 141 NMRMALYWLIQ-GCQPGDSLLFHFSGHGSQQRNYNGEEVDGYDETLCPVDFETQGMIVDDEINTTLVRPLPRGARLHAII 219 (392)
Q Consensus 141 nI~~al~~L~~-~~~~gD~llfYFSGHG~~~~d~~gde~dG~de~Lvp~D~~~~g~i~d~eL~~~L~~~l~~g~~l~vIl 219 (392)
.+.+.|.|+++ -+..-|. +|-=||+..++ .||..+- .|.||.+-..-++..|-++ +++
T Consensus 37 tvgdll~yi~~~~ie~r~~---lFi~~gsvrpG-----------ii~lINd------~DWEllekedy~ledgD~i-vfi 95 (101)
T KOG4146|consen 37 TVGDLLDYIFGKYIETRDS---LFIHHGSVRPG-----------IIVLIND------MDWELLEKEDYPLEDGDHI-VFI 95 (101)
T ss_pred cHHHHHHHHHHHHhcCCcc---eEeeCCcCcCc-----------EEEEEec------cchhhhcccccCcccCCEE-EEE
Confidence 34455555554 2333444 45567777653 6766531 4577776665567777665 555
Q ss_pred eCCCC
Q 016243 220 DACHS 224 (392)
Q Consensus 220 D~C~S 224 (392)
.+=|.
T Consensus 96 STlHG 100 (101)
T KOG4146|consen 96 STLHG 100 (101)
T ss_pred EeccC
Confidence 55554
No 130
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=20.76 E-value=76 Score=21.73 Aligned_cols=28 Identities=18% Similarity=0.650 Sum_probs=21.4
Q ss_pred cCCCCCCc-cccCCCCceeeccccCceec
Q 016243 6 DCSKCRTT-LQLPPGAQSIRCAICQAITH 33 (392)
Q Consensus 6 ~C~~C~~~-l~~p~~a~~vrC~~C~~vt~ 33 (392)
.|+.|+.. +..-.....+-|..|..|-.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGLVLE 30 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-BBEE
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCCEee
Confidence 69999996 46667777889999987763
No 131
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=20.38 E-value=53 Score=27.67 Aligned_cols=27 Identities=15% Similarity=0.426 Sum_probs=18.6
Q ss_pred CcccCCCCCCccccCCCCceeeccccCce
Q 016243 3 MLVDCSKCRTTLQLPPGAQSIRCAICQAI 31 (392)
Q Consensus 3 ~~~~C~~C~~~l~~p~~a~~vrC~~C~~v 31 (392)
...+|..|+.... ......+|+.|+..
T Consensus 69 ~~~~C~~Cg~~~~--~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 69 AQAWCWDCSQVVE--IHQHDAQCPHCHGE 95 (113)
T ss_pred cEEEcccCCCEEe--cCCcCccCcCCCCC
Confidence 4678999986443 33456679999854
No 132
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=20.31 E-value=4.6e+02 Score=27.62 Aligned_cols=43 Identities=12% Similarity=0.074 Sum_probs=26.0
Q ss_pred HHHHHHHhcc--CCCCCceEEccCCCCCCCCCccHHHHHHHHHHHHHhCCCCCEEEE
Q 016243 107 CMKYMLTNRF--KFPESSIVMLTEEDPDPLKRPTKYNMRMALYWLIQGCQPGDSLLF 161 (392)
Q Consensus 107 ~m~~~L~~~~--Gf~~~~I~~Ltd~~~~~~~~pT~~nI~~al~~L~~~~~~gD~llf 161 (392)
++++++..+. ++.+++|.+-.. +.+.|..++..| +.+||.|++
T Consensus 193 aia~~~~~~~~~~~~~~~I~it~G---------~~eal~~~~~~l---~~~Gd~Vli 237 (517)
T PRK13355 193 AIMQYAQLKGLPNVDVDDIYTGNG---------VSELINLSMSAL---LDDGDEVLI 237 (517)
T ss_pred HHHHHHHhcCCCCCChhHEEEeCc---------HHHHHHHHHHHh---CCCCCEEEE
Confidence 4455554443 366777754433 356666666666 468998886
No 133
>KOG4044 consensus Mitochondrial associated endoribonuclease MAR1 (isochorismatase superfamily) [General function prediction only]
Probab=20.16 E-value=61 Score=29.65 Aligned_cols=23 Identities=35% Similarity=0.598 Sum_probs=18.1
Q ss_pred CCCCeEEEEEeCCCCCCCCCCcc
Q 016243 210 PRGARLHAIIDACHSGTVLDLPF 232 (392)
Q Consensus 210 ~~g~~l~vIlD~C~SG~~~~~p~ 232 (392)
..|.+|+++.|||.|-...|-.+
T Consensus 126 ~rgl~VhvVaDacSSRs~~DR~~ 148 (201)
T KOG4044|consen 126 ERGLNVHVVADACSSRSNQDRDL 148 (201)
T ss_pred hCCceEEEEeehhccccchhHHH
Confidence 45789999999999987776443
Done!