Query 022656
Match_columns 294
No_of_seqs 152 out of 286
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 05:11:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022656.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022656hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0796 Spliceosome subunit [R 100.0 9.5E-56 2.1E-60 412.4 17.2 181 4-189 53-234 (319)
2 PF03194 LUC7: LUC7 N_terminus 100.0 5.9E-52 1.3E-56 382.7 19.2 180 5-188 53-237 (254)
3 COG5200 LUC7 U1 snRNP componen 100.0 1.2E-35 2.5E-40 263.0 11.7 174 5-185 54-229 (258)
4 KOG0796 Spliceosome subunit [R 95.7 0.16 3.6E-06 48.7 11.8 114 34-150 74-192 (319)
5 KOG4676 Splicing factor, argin 93.6 0.047 1E-06 53.7 2.6 10 167-176 215-224 (479)
6 KOG2888 Putative RNA binding p 93.6 0.044 9.5E-07 53.0 2.3 30 98-127 120-149 (453)
7 COG5200 LUC7 U1 snRNP componen 91.8 1.9 4.1E-05 39.5 10.1 126 30-162 65-200 (258)
8 COG1579 Zn-ribbon protein, pos 91.5 0.69 1.5E-05 43.0 7.1 19 42-60 64-82 (239)
9 PRK02224 chromosome segregatio 91.1 4.8 0.0001 43.3 14.2 14 140-153 450-463 (880)
10 PHA02562 46 endonuclease subun 90.6 5.3 0.00011 40.5 13.3 15 140-154 283-297 (562)
11 smart00451 ZnF_U1 U1-like zinc 90.2 0.13 2.7E-06 32.7 0.8 27 142-171 4-30 (35)
12 COG0419 SbcC ATPase involved i 89.9 8.6 0.00019 41.9 15.0 24 141-165 457-480 (908)
13 PF04012 PspA_IM30: PspA/IM30 89.0 4.7 0.0001 36.2 10.4 82 40-127 26-107 (221)
14 PRK14143 heat shock protein Gr 87.6 2.5 5.5E-05 39.2 7.8 91 75-181 64-160 (238)
15 PRK01156 chromosome segregatio 86.9 5.8 0.00013 42.9 11.2 14 142-155 450-463 (895)
16 PRK06835 DNA replication prote 86.1 5.4 0.00012 38.6 9.5 67 79-149 37-106 (329)
17 KOG4368 Predicted RNA binding 86.1 1.7 3.7E-05 45.1 6.2 17 107-123 257-273 (757)
18 PRK14158 heat shock protein Gr 85.9 4.8 0.0001 36.3 8.4 95 72-182 34-132 (194)
19 PRK14144 heat shock protein Gr 85.2 4.2 9.1E-05 36.8 7.7 92 77-184 44-139 (199)
20 PRK15058 cytochrome b562; Prov 84.7 9.8 0.00021 32.2 9.2 42 78-119 78-122 (128)
21 PF04032 Rpr2: RNAse P Rpr2/Rp 83.4 3.6 7.9E-05 31.2 5.7 60 86-156 2-61 (85)
22 PF12171 zf-C2H2_jaz: Zinc-fin 83.3 0.41 8.8E-06 29.0 0.3 25 142-169 2-26 (27)
23 PF12874 zf-met: Zinc-finger o 82.3 0.43 9.3E-06 28.0 0.1 24 143-169 2-25 (25)
24 PRK14162 heat shock protein Gr 79.1 8.3 0.00018 34.8 7.2 94 75-184 36-134 (194)
25 PRK09720 cybC cytochrome b562; 79.0 7.5 0.00016 31.6 6.2 42 77-118 49-93 (100)
26 PRK14148 heat shock protein Gr 77.7 12 0.00026 33.8 7.8 91 78-184 40-135 (195)
27 PF07361 Cytochrom_B562: Cytoc 77.2 7.1 0.00015 31.5 5.7 41 79-119 54-97 (103)
28 TIGR02977 phageshock_pspA phag 77.0 30 0.00065 31.3 10.4 67 40-112 27-93 (219)
29 PF14282 FlxA: FlxA-like prote 77.0 9.7 0.00021 30.8 6.4 51 76-127 17-67 (106)
30 COG1675 TFA1 Transcription ini 76.6 8.6 0.00019 34.2 6.5 35 139-185 130-164 (176)
31 PRK14151 heat shock protein Gr 76.6 8.8 0.00019 34.0 6.5 94 75-184 17-116 (176)
32 PF13779 DUF4175: Domain of un 76.0 13 0.00028 40.4 8.8 35 84-118 537-571 (820)
33 PRK14163 heat shock protein Gr 74.7 16 0.00035 33.5 7.9 89 78-184 40-128 (214)
34 PRK10246 exonuclease subunit S 74.5 13 0.00029 41.2 8.7 11 140-150 502-512 (1047)
35 PF03962 Mnd1: Mnd1 family; I 74.2 64 0.0014 28.7 11.9 53 75-127 73-126 (188)
36 TIGR02302 aProt_lowcomp conser 74.1 11 0.00025 41.0 7.8 32 87-118 570-601 (851)
37 PRK03918 chromosome segregatio 73.7 40 0.00087 36.2 11.9 12 142-153 436-447 (880)
38 PRK14154 heat shock protein Gr 72.6 13 0.00029 33.9 6.8 89 79-183 53-147 (208)
39 PF13863 DUF4200: Domain of un 72.3 15 0.00033 29.8 6.6 51 41-97 50-100 (126)
40 PF02403 Seryl_tRNA_N: Seryl-t 71.9 11 0.00024 30.0 5.6 49 77-127 42-90 (108)
41 PRK11115 transcriptional regul 69.3 55 0.0012 29.2 10.1 81 77-165 125-207 (236)
42 PRK14147 heat shock protein Gr 69.2 15 0.00032 32.4 6.2 87 82-184 22-111 (172)
43 PF03194 LUC7: LUC7 N_terminus 68.3 10 0.00022 35.5 5.2 85 40-127 79-165 (254)
44 COG2093 DNA-directed RNA polym 67.8 1.7 3.6E-05 32.4 -0.1 26 140-165 17-52 (64)
45 KOG1847 mRNA splicing factor [ 67.8 5.4 0.00012 42.0 3.5 7 165-171 692-698 (878)
46 PRK14141 heat shock protein Gr 66.9 20 0.00044 32.7 6.8 86 83-184 36-132 (209)
47 PRK10698 phage shock protein P 66.2 74 0.0016 29.0 10.4 77 40-122 27-110 (222)
48 PRK14160 heat shock protein Gr 66.1 34 0.00073 31.3 8.0 44 139-182 106-151 (211)
49 PF11931 DUF3449: Domain of un 66.0 2 4.3E-05 38.9 0.0 28 140-169 100-127 (196)
50 COG1842 PspA Phage shock prote 65.7 77 0.0017 29.2 10.4 82 40-127 27-108 (225)
51 PRK14155 heat shock protein Gr 65.3 19 0.00041 32.8 6.2 88 81-184 16-111 (208)
52 KOG4368 Predicted RNA binding 64.9 11 0.00023 39.4 5.0 10 46-55 171-180 (757)
53 PF12325 TMF_TATA_bd: TATA ele 64.9 82 0.0018 26.3 10.8 70 36-127 15-84 (120)
54 COG3783 CybC Soluble cytochrom 64.8 51 0.0011 26.7 7.8 26 93-118 68-93 (100)
55 PRK14146 heat shock protein Gr 64.7 23 0.0005 32.4 6.7 46 139-184 99-149 (215)
56 PF10367 Vps39_2: Vacuolar sor 64.6 16 0.00034 28.4 5.0 13 141-153 78-90 (109)
57 PF02151 UVR: UvrB/uvrC motif; 64.2 24 0.00053 22.9 5.0 35 85-119 2-36 (36)
58 KOG3454 U1 snRNP-specific prot 63.1 11 0.00024 33.2 4.1 39 142-183 4-42 (165)
59 PF04645 DUF603: Protein of un 61.3 13 0.00028 33.0 4.2 71 79-158 106-177 (181)
60 PF04423 Rad50_zn_hook: Rad50 61.1 4.8 0.0001 28.4 1.2 12 143-154 22-33 (54)
61 PRK14139 heat shock protein Gr 60.7 39 0.00084 30.3 7.2 92 77-184 31-125 (185)
62 PF07295 DUF1451: Protein of u 60.2 75 0.0016 27.4 8.7 112 38-156 5-127 (146)
63 PRK10884 SH3 domain-containing 59.8 74 0.0016 28.9 9.0 54 42-97 91-144 (206)
64 PF01895 PhoU: PhoU domain; I 59.4 34 0.00074 24.8 5.8 82 80-165 1-82 (88)
65 KOG0835 Cyclin L [General func 59.4 9 0.00019 37.4 3.1 18 168-185 232-249 (367)
66 KOG4727 U1-like Zn-finger prot 59.2 3.5 7.5E-05 36.7 0.3 32 135-169 69-100 (193)
67 COG3058 FdhE Uncharacterized p 58.7 44 0.00096 32.0 7.5 17 33-49 97-113 (308)
68 PRK01156 chromosome segregatio 58.6 37 0.0008 36.8 8.0 16 140-155 451-466 (895)
69 TIGR02420 dksA RNA polymerase- 58.3 65 0.0014 26.0 7.6 14 139-152 78-91 (110)
70 PRK06266 transcription initiat 58.0 5.8 0.00013 35.1 1.5 34 140-185 135-168 (178)
71 PF00435 Spectrin: Spectrin re 57.8 74 0.0016 23.4 7.9 83 43-127 7-96 (105)
72 PRK14161 heat shock protein Gr 57.1 46 0.00099 29.6 7.0 88 79-182 20-114 (178)
73 KOG1847 mRNA splicing factor [ 57.1 14 0.00031 39.0 4.3 14 94-107 637-650 (878)
74 PF03962 Mnd1: Mnd1 family; I 56.8 53 0.0011 29.3 7.5 79 39-118 71-149 (188)
75 PF06220 zf-U1: U1 zinc finger 55.3 6.7 0.00014 26.1 1.1 32 142-174 4-35 (38)
76 PF12854 PPR_1: PPR repeat 54.2 16 0.00036 23.1 2.8 20 93-112 13-32 (34)
77 PRK03954 ribonuclease P protei 54.2 31 0.00067 28.9 5.1 66 84-161 19-85 (121)
78 TIGR00373 conserved hypothetic 53.7 6.9 0.00015 33.9 1.3 21 140-160 127-147 (158)
79 PRK14153 heat shock protein Gr 53.0 38 0.00083 30.6 5.9 89 80-184 35-128 (194)
80 PRK14150 heat shock protein Gr 52.9 40 0.00086 30.3 6.0 46 139-184 83-134 (193)
81 KOG0978 E3 ubiquitin ligase in 52.8 65 0.0014 34.5 8.4 20 137-156 674-693 (698)
82 PF10475 DUF2450: Protein of u 52.6 1.2E+02 0.0026 28.5 9.5 80 39-119 69-159 (291)
83 PF05191 ADK_lid: Adenylate ki 52.5 5.2 0.00011 26.4 0.2 16 137-152 17-32 (36)
84 PF10458 Val_tRNA-synt_C: Valy 52.5 58 0.0013 23.8 5.9 59 40-98 7-66 (66)
85 PRK14140 heat shock protein Gr 51.4 47 0.001 29.9 6.3 92 77-184 36-132 (191)
86 PF04420 CHD5: CHD5-like prote 51.3 54 0.0012 28.4 6.5 54 74-127 36-89 (161)
87 PF02132 RecR: RecR protein; 50.9 16 0.00034 24.5 2.4 13 138-150 14-26 (41)
88 PRK06424 transcription factor; 50.7 6.4 0.00014 33.8 0.6 8 144-151 3-10 (144)
89 PF09969 DUF2203: Uncharacteri 50.5 67 0.0015 26.7 6.6 27 74-100 46-72 (120)
90 PF14282 FlxA: FlxA-like prote 50.3 86 0.0019 25.3 7.1 53 43-97 18-70 (106)
91 PF02388 FemAB: FemAB family; 50.0 75 0.0016 31.4 8.1 48 38-95 243-290 (406)
92 COG4911 Uncharacterized conser 49.7 75 0.0016 26.3 6.5 55 37-99 11-65 (123)
93 PRK12495 hypothetical protein; 49.7 20 0.00044 33.0 3.7 12 141-152 42-53 (226)
94 PF06156 DUF972: Protein of un 49.3 1.2E+02 0.0025 24.8 7.7 46 75-125 5-50 (107)
95 PF10979 DUF2786: Protein of u 49.2 54 0.0012 22.4 4.9 35 83-119 3-37 (43)
96 KOG1666 V-SNARE [Intracellular 48.7 2.2E+02 0.0048 26.3 10.6 84 31-127 5-88 (220)
97 cd00729 rubredoxin_SM Rubredox 48.3 7.4 0.00016 25.2 0.5 11 140-150 17-27 (34)
98 PLN00204 CP12 gene family prot 48.1 55 0.0012 27.6 5.7 43 82-124 56-99 (126)
99 PRK11020 hypothetical protein; 47.7 1.4E+02 0.0031 24.9 7.9 20 78-97 31-50 (118)
100 TIGR02135 phoU_full phosphate 47.5 1.8E+02 0.0038 24.8 10.3 82 75-164 113-196 (212)
101 TIGR01554 major_cap_HK97 phage 47.4 46 0.001 32.3 6.0 42 82-123 3-46 (378)
102 COG1592 Rubrerythrin [Energy p 47.3 72 0.0016 28.2 6.6 8 141-148 134-141 (166)
103 PF07544 Med9: RNA polymerase 47.3 1.3E+02 0.0028 23.1 8.1 56 41-99 25-80 (83)
104 PRK10564 maltose regulon perip 46.7 25 0.00055 33.9 4.0 30 90-119 260-289 (303)
105 PRK10778 dksA RNA polymerase-b 46.7 98 0.0021 26.7 7.3 15 138-152 108-122 (151)
106 PLN02678 seryl-tRNA synthetase 46.5 62 0.0013 32.8 6.9 46 78-125 47-92 (448)
107 PF01025 GrpE: GrpE; InterPro 45.5 9.8 0.00021 32.4 0.9 36 149-184 66-106 (165)
108 PF03357 Snf7: Snf7; InterPro 45.5 1.1E+02 0.0024 25.6 7.4 52 75-126 12-63 (171)
109 KOG4552 Vitamin-D-receptor int 45.0 1.1E+02 0.0025 28.2 7.7 32 75-109 47-78 (272)
110 PRK00239 rpsT 30S ribosomal pr 44.6 57 0.0012 25.7 5.0 38 82-119 23-60 (88)
111 cd07973 Spt4 Transcription elo 44.5 7.5 0.00016 31.4 0.1 23 141-163 20-42 (98)
112 PF08317 Spc7: Spc7 kinetochor 44.3 2.4E+02 0.0053 27.0 10.4 20 34-54 140-159 (325)
113 PRK05431 seryl-tRNA synthetase 44.3 70 0.0015 32.0 6.9 46 78-125 42-87 (425)
114 TIGR02890 spore_yteA sporulati 44.2 1.2E+02 0.0026 26.4 7.5 31 140-174 85-115 (159)
115 KOG0835 Cyclin L [General func 43.5 16 0.00034 35.8 2.0 9 93-101 125-133 (367)
116 PF03119 DNA_ligase_ZBD: NAD-d 43.0 7.9 0.00017 24.1 -0.0 12 144-155 2-13 (28)
117 PF01396 zf-C4_Topoisom: Topoi 42.7 8.7 0.00019 25.6 0.2 13 142-154 2-14 (39)
118 PF13913 zf-C2HC_2: zinc-finge 42.5 17 0.00036 21.8 1.4 21 140-164 1-21 (25)
119 PF09237 GAGA: GAGA factor; I 42.2 6.5 0.00014 28.3 -0.6 21 139-159 22-42 (54)
120 COG3809 Uncharacterized protei 41.9 9 0.0002 29.9 0.1 15 141-155 1-15 (88)
121 PRK03918 chromosome segregatio 41.6 4.8E+02 0.01 28.0 15.1 16 142-157 433-448 (880)
122 PF07535 zf-DBF: DBF zinc fing 41.3 15 0.00032 26.0 1.1 41 138-184 2-42 (49)
123 PF12998 ING: Inhibitor of gro 41.1 1.7E+02 0.0036 22.6 8.0 73 43-116 21-94 (105)
124 PRK00420 hypothetical protein; 40.8 15 0.00033 30.3 1.3 20 138-157 37-56 (112)
125 COG0783 Dps DNA-binding ferrit 40.6 1.6E+02 0.0035 25.6 7.7 83 37-120 55-151 (156)
126 PF06632 XRCC4: DNA double-str 40.4 3.1E+02 0.0067 26.9 10.5 45 82-126 155-199 (342)
127 KOG3032 Uncharacterized conser 40.3 21 0.00046 33.2 2.3 35 140-184 34-68 (264)
128 PRK13169 DNA replication intia 39.9 2E+02 0.0043 23.7 7.7 49 74-127 4-52 (110)
129 TIGR00414 serS seryl-tRNA synt 39.8 95 0.0021 31.0 7.0 47 79-126 45-91 (418)
130 PF06721 DUF1204: Protein of u 39.3 1.1E+02 0.0024 27.8 6.6 70 78-150 50-120 (228)
131 TIGR00029 S20 ribosomal protei 39.0 89 0.0019 24.6 5.4 37 82-118 23-59 (87)
132 KOG0250 DNA repair protein RAD 39.0 2.5E+02 0.0054 31.7 10.4 78 5-88 168-252 (1074)
133 PRK12496 hypothetical protein; 38.6 12 0.00025 32.7 0.3 13 142-154 144-156 (164)
134 PF01649 Ribosomal_S20p: Ribos 38.5 95 0.0021 24.2 5.4 37 82-118 22-58 (84)
135 smart00746 TRASH metallochaper 38.3 6.8 0.00015 23.2 -0.9 24 144-169 1-24 (39)
136 smart00787 Spc7 Spc7 kinetocho 37.9 2.9E+02 0.0062 26.7 9.7 20 78-97 211-230 (312)
137 KOG0996 Structural maintenance 37.6 1.7E+02 0.0037 33.3 8.9 26 78-103 858-883 (1293)
138 PRK14145 heat shock protein Gr 37.5 1.6E+02 0.0034 26.7 7.4 90 79-184 46-137 (196)
139 PRK14156 heat shock protein Gr 37.2 1.3E+02 0.0028 26.8 6.7 85 82-182 31-117 (177)
140 PF07743 HSCB_C: HSCB C-termin 37.0 1.7E+02 0.0037 21.6 8.3 47 74-120 27-73 (78)
141 PF12230 PRP21_like_P: Pre-mRN 36.8 11 0.00025 34.1 0.0 37 138-184 165-201 (229)
142 PF05529 Bap31: B-cell recepto 36.8 2.4E+02 0.0052 24.6 8.5 36 80-127 156-191 (192)
143 TIGR00270 conserved hypothetic 36.7 13 0.00029 32.2 0.4 7 144-150 3-9 (154)
144 PF02388 FemAB: FemAB family; 36.2 90 0.0019 30.9 6.2 48 77-126 241-288 (406)
145 COG0172 SerS Seryl-tRNA synthe 36.1 95 0.0021 31.4 6.3 49 78-127 43-91 (429)
146 TIGR01206 lysW lysine biosynth 36.1 15 0.00033 26.5 0.5 15 141-155 2-16 (54)
147 PRK10325 heat shock protein Gr 36.0 1.3E+02 0.0027 27.2 6.5 44 139-182 84-133 (197)
148 cd00350 rubredoxin_like Rubred 36.0 15 0.00031 23.5 0.4 10 140-149 16-25 (33)
149 smart00531 TFIIE Transcription 35.7 16 0.00035 31.0 0.8 19 142-160 124-142 (147)
150 PRK14157 heat shock protein Gr 35.3 2E+02 0.0043 26.7 7.8 34 142-177 125-158 (227)
151 KOG2825 Putative arsenite-tran 34.9 78 0.0017 30.4 5.1 79 77-163 170-248 (323)
152 COG1340 Uncharacterized archae 34.7 1.3E+02 0.0028 28.9 6.7 28 30-61 128-155 (294)
153 PF05852 DUF848: Gammaherpesvi 34.5 1.9E+02 0.004 25.1 7.0 53 75-127 58-112 (146)
154 PF08792 A2L_zn_ribbon: A2L zi 34.4 15 0.00032 23.8 0.2 14 140-153 2-15 (33)
155 PF12329 TMF_DNA_bd: TATA elem 34.4 1.9E+02 0.004 21.9 6.3 45 77-126 4-48 (74)
156 KOG4765 Uncharacterized conser 34.4 32 0.0007 34.2 2.6 41 138-188 87-127 (419)
157 PF04880 NUDE_C: NUDE protein, 34.4 41 0.00088 29.7 3.0 25 103-127 23-47 (166)
158 PF05741 zf-nanos: Nanos RNA b 34.2 14 0.00031 26.8 0.1 10 141-150 33-42 (55)
159 smart00734 ZnF_Rad18 Rad18-lik 33.9 29 0.00063 21.1 1.5 20 142-165 2-21 (26)
160 PRK13130 H/ACA RNA-protein com 33.8 16 0.00034 26.6 0.3 11 140-150 4-14 (56)
161 PF07106 TBPIP: Tat binding pr 33.5 3.1E+02 0.0067 23.5 11.0 66 33-103 76-141 (169)
162 PF15070 GOLGA2L5: Putative go 33.3 4.8E+02 0.01 27.7 11.2 45 140-185 166-217 (617)
163 PF05700 BCAS2: Breast carcino 33.2 2E+02 0.0044 26.0 7.5 78 40-124 139-216 (221)
164 KOG4797 Transcriptional regula 33.1 1.2E+02 0.0027 25.1 5.4 51 48-106 45-95 (123)
165 COG4467 Regulator of replicati 32.8 2.7E+02 0.0058 23.1 7.3 49 74-127 4-52 (114)
166 KOG4602 Nanos and related prot 32.8 16 0.00035 34.5 0.3 9 142-150 269-277 (318)
167 PF08209 Sgf11: Sgf11 (transcr 32.6 18 0.0004 23.5 0.4 22 140-165 3-24 (33)
168 COG5188 PRP9 Splicing factor 3 32.6 20 0.00043 35.5 0.9 26 142-169 375-400 (470)
169 PF08898 DUF1843: Domain of un 32.4 1E+02 0.0023 22.2 4.3 33 86-124 18-51 (53)
170 COG4499 Predicted membrane pro 32.2 1.8E+02 0.0039 29.3 7.3 75 43-119 336-410 (434)
171 KOG2264 Exostosin EXT1L [Signa 32.2 1.9E+02 0.0041 30.7 7.7 40 74-113 103-147 (907)
172 PF05597 Phasin: Poly(hydroxya 32.1 2.7E+02 0.0059 23.5 7.6 23 77-99 108-130 (132)
173 smart00150 SPEC Spectrin repea 32.1 2E+02 0.0043 20.9 6.5 49 78-127 45-93 (101)
174 cd00890 Prefoldin Prefoldin is 32.0 1.8E+02 0.004 23.2 6.4 22 76-97 4-25 (129)
175 PF07967 zf-C3HC: C3HC zinc fi 32.0 15 0.00032 30.6 -0.1 17 138-154 40-56 (133)
176 KOG0250 DNA repair protein RAD 31.9 3.5E+02 0.0076 30.6 10.1 88 34-127 271-360 (1074)
177 KOG1510 RNA polymerase II holo 31.8 3.3E+02 0.0072 23.4 11.3 43 74-121 87-129 (139)
178 KOG2801 Probable Rab-GAPs [Int 31.8 15 0.00032 35.6 -0.1 22 145-169 402-423 (559)
179 PF11781 RRN7: RNA polymerase 31.3 19 0.00041 23.7 0.3 15 142-156 9-23 (36)
180 PRK08359 transcription factor; 31.0 17 0.00038 32.3 0.2 9 144-152 9-17 (176)
181 COG4477 EzrA Negative regulato 30.7 3.8E+02 0.0081 28.1 9.5 101 76-185 279-390 (570)
182 PRK11637 AmiB activator; Provi 30.6 4.4E+02 0.0095 26.1 10.0 19 78-96 75-93 (428)
183 TIGR01562 FdhE formate dehydro 30.4 1.3E+02 0.0029 29.0 6.0 12 141-152 184-195 (305)
184 PHA03161 hypothetical protein; 30.3 1.9E+02 0.0041 25.2 6.4 49 75-123 58-108 (150)
185 PF13945 NST1: Salt tolerance 30.1 37 0.00081 30.6 2.1 35 109-150 116-150 (190)
186 COG5188 PRP9 Splicing factor 3 30.0 18 0.00039 35.8 0.1 29 140-171 237-265 (470)
187 PLN02748 tRNA dimethylallyltra 30.0 28 0.00061 35.5 1.5 29 140-170 417-445 (468)
188 PRK03564 formate dehydrogenase 29.8 1.4E+02 0.003 28.9 6.1 13 140-152 186-198 (309)
189 PF01535 PPR: PPR repeat; Int 29.8 72 0.0016 18.3 2.8 23 93-115 6-28 (31)
190 TIGR00606 rad50 rad50. This fa 29.6 9.1E+02 0.02 27.8 14.1 32 139-170 675-706 (1311)
191 PF13922 PHD_3: PHD domain of 29.6 15 0.00032 27.7 -0.4 13 138-150 40-52 (69)
192 PF15003 HAUS2: HAUS augmin-li 29.4 5.1E+02 0.011 24.8 9.8 88 76-168 52-142 (277)
193 PRK13844 recombination protein 29.2 84 0.0018 28.6 4.3 9 162-170 101-109 (200)
194 PF10152 DUF2360: Predicted co 29.2 1.9E+02 0.0041 24.7 6.3 44 33-89 3-46 (148)
195 PRK14149 heat shock protein Gr 29.2 1.8E+02 0.004 26.2 6.4 43 142-184 84-131 (191)
196 PF14276 DUF4363: Domain of un 29.1 1.5E+02 0.0032 23.9 5.4 39 80-118 21-59 (121)
197 PF02318 FYVE_2: FYVE-type zin 28.7 2.4E+02 0.0052 22.9 6.6 15 140-154 53-67 (118)
198 PF06632 XRCC4: DNA double-str 28.7 2.7E+02 0.0058 27.3 7.9 43 80-127 139-181 (342)
199 smart00586 ZnF_DBF Zinc finger 28.6 36 0.00078 24.1 1.4 40 139-184 3-42 (49)
200 PF14828 Amnionless: Amnionles 28.5 17 0.00037 36.6 -0.3 15 142-156 227-241 (437)
201 PF13894 zf-C2H2_4: C2H2-type 28.4 21 0.00046 19.6 0.2 19 143-164 2-20 (24)
202 KOG3032 Uncharacterized conser 28.4 2.7E+02 0.0058 26.2 7.4 39 89-127 189-227 (264)
203 KOG2636 Splicing factor 3a, su 28.4 47 0.001 33.8 2.7 42 142-185 402-458 (497)
204 PF06751 EutB: Ethanolamine am 28.1 20 0.00044 36.0 0.1 30 139-169 310-346 (444)
205 PF06005 DUF904: Protein of un 27.8 2.7E+02 0.0059 21.1 7.3 18 80-97 6-23 (72)
206 TIGR00618 sbcc exonuclease Sbc 27.8 2.7E+02 0.0059 31.0 8.7 69 74-149 440-509 (1042)
207 smart00787 Spc7 Spc7 kinetocho 27.5 5.7E+02 0.012 24.7 10.0 20 34-54 135-154 (312)
208 PF04111 APG6: Autophagy prote 27.4 2E+02 0.0044 27.6 6.8 14 168-181 164-177 (314)
209 COG2023 RPR2 RNase P subunit R 27.3 2.6E+02 0.0056 23.0 6.3 64 82-157 9-72 (105)
210 COG5185 HEC1 Protein involved 27.1 2.8E+02 0.006 28.8 7.8 64 77-142 263-326 (622)
211 CHL00102 rps20 ribosomal prote 27.0 1.5E+02 0.0033 23.6 4.9 36 83-118 24-66 (93)
212 PF09862 DUF2089: Protein of u 26.6 23 0.0005 29.3 0.2 18 169-186 60-77 (113)
213 PF04111 APG6: Autophagy prote 26.5 2.6E+02 0.0056 26.9 7.3 8 17-24 14-21 (314)
214 PF04100 Vps53_N: Vps53-like, 26.4 6.4E+02 0.014 24.9 11.1 23 38-60 26-48 (383)
215 PF03980 Nnf1: Nnf1 ; InterPr 26.4 3.3E+02 0.0071 21.6 8.0 23 41-63 31-53 (109)
216 PF06694 Plant_NMP1: Plant nuc 25.9 5.2E+02 0.011 25.2 9.1 88 70-162 167-259 (325)
217 PRK00076 recR recombination pr 25.9 1.2E+02 0.0027 27.3 4.7 7 163-169 98-104 (196)
218 PF11062 DUF2863: Protein of u 25.9 30 0.00064 34.6 0.8 17 138-154 361-377 (398)
219 smart00030 CLb CLUSTERIN Beta 25.9 2.7E+02 0.0059 25.4 6.8 44 82-126 19-65 (206)
220 PLN03229 acetyl-coenzyme A car 25.8 4E+02 0.0088 29.0 9.1 39 16-56 440-478 (762)
221 TIGR02449 conserved hypothetic 25.4 2.7E+02 0.0059 20.8 5.7 43 80-127 2-44 (65)
222 PF06008 Laminin_I: Laminin Do 25.4 5.2E+02 0.011 23.7 9.0 86 33-119 49-138 (264)
223 cd00730 rubredoxin Rubredoxin; 25.4 28 0.0006 24.6 0.4 9 142-150 35-43 (50)
224 PF08271 TF_Zn_Ribbon: TFIIB z 25.3 27 0.00058 23.4 0.3 17 139-155 17-33 (43)
225 CHL00112 rpl28 ribosomal prote 25.2 26 0.00057 26.0 0.3 14 142-155 3-16 (63)
226 PF04065 Not3: Not1 N-terminal 25.0 5.4E+02 0.012 23.9 8.9 81 35-120 120-206 (233)
227 PF02591 DUF164: Putative zinc 25.0 29 0.00064 24.5 0.5 13 139-151 44-56 (56)
228 COG0353 RecR Recombinational D 24.9 1.2E+02 0.0026 27.6 4.4 7 164-170 100-106 (198)
229 PRK14159 heat shock protein Gr 24.9 2.4E+02 0.0053 25.0 6.3 82 85-182 30-116 (176)
230 TIGR03829 YokU_near_AblA uncha 24.9 29 0.00062 27.6 0.4 26 140-165 34-59 (89)
231 PRK04778 septation ring format 24.8 6.2E+02 0.013 26.2 10.3 34 87-120 177-210 (569)
232 PF07721 TPR_4: Tetratricopept 24.7 1.1E+02 0.0023 17.9 2.8 21 91-111 5-25 (26)
233 PLN02943 aminoacyl-tRNA ligase 24.5 1.8E+02 0.004 32.3 6.6 65 33-98 886-951 (958)
234 PRK00359 rpmB 50S ribosomal pr 24.4 37 0.0008 26.0 0.9 25 141-169 2-26 (76)
235 PLN02320 seryl-tRNA synthetase 24.4 2.1E+02 0.0045 29.6 6.6 48 77-127 106-153 (502)
236 PRK15067 ethanolamine ammonia 24.4 27 0.00059 35.3 0.3 28 141-169 322-356 (461)
237 COG5509 Uncharacterized small 24.3 99 0.0022 23.0 3.1 19 79-97 26-44 (65)
238 PF13248 zf-ribbon_3: zinc-rib 24.3 40 0.00087 20.2 0.9 10 142-151 3-12 (26)
239 TIGR02135 phoU_full phosphate 24.2 2.5E+02 0.0055 23.8 6.3 34 78-111 12-45 (212)
240 PF00301 Rubredoxin: Rubredoxi 24.1 30 0.00066 24.1 0.4 9 142-150 35-43 (47)
241 PF10146 zf-C4H2: Zinc finger- 23.9 5.8E+02 0.013 23.6 11.0 79 35-126 23-103 (230)
242 COG5136 U1 snRNP-specific prot 23.9 20 0.00044 31.6 -0.7 29 142-171 4-32 (188)
243 PF06170 DUF983: Protein of un 23.8 34 0.00074 26.8 0.7 18 141-158 8-25 (86)
244 PF04102 SlyX: SlyX; InterPro 23.6 1.5E+02 0.0033 21.9 4.1 21 78-98 32-52 (69)
245 PF04645 DUF603: Protein of un 23.6 3.5E+02 0.0075 24.2 6.9 54 74-127 108-161 (181)
246 PRK10698 phage shock protein P 23.5 5.6E+02 0.012 23.3 8.9 52 76-127 164-217 (222)
247 PF10191 COG7: Golgi complex c 23.5 5.5E+02 0.012 27.8 9.9 90 34-127 35-124 (766)
248 KOG4117 Heat shock factor bind 23.4 3E+02 0.0066 20.8 5.5 52 34-94 13-64 (73)
249 PF13041 PPR_2: PPR repeat fam 23.4 1.2E+02 0.0026 20.1 3.3 23 93-115 9-31 (50)
250 PRK00432 30S ribosomal protein 23.4 35 0.00075 24.1 0.6 16 140-155 19-35 (50)
251 PF15456 Uds1: Up-regulated Du 23.4 4.4E+02 0.0095 22.0 7.6 23 75-97 78-100 (124)
252 COG1340 Uncharacterized archae 23.3 6.8E+02 0.015 24.2 11.4 18 107-124 161-178 (294)
253 PF06160 EzrA: Septation ring 23.3 5.9E+02 0.013 26.4 9.7 86 36-122 100-208 (560)
254 TIGR01010 BexC_CtrB_KpsE polys 23.3 6.6E+02 0.014 24.0 10.1 62 37-98 170-234 (362)
255 PRK13729 conjugal transfer pil 23.2 3.1E+02 0.0067 28.2 7.4 44 78-126 76-119 (475)
256 PRK11788 tetratricopeptide rep 23.2 93 0.002 29.2 3.6 28 89-116 284-311 (389)
257 PF12718 Tropomyosin_1: Tropom 23.2 4.7E+02 0.01 22.2 9.2 22 106-127 68-89 (143)
258 PF06005 DUF904: Protein of un 23.1 3.4E+02 0.0073 20.5 7.8 44 78-126 18-61 (72)
259 PF02672 CP12: CP12 domain; I 23.1 28 0.0006 26.4 0.0 42 83-124 1-44 (71)
260 PRK13182 racA polar chromosome 22.9 4.2E+02 0.0092 23.4 7.5 52 76-127 90-141 (175)
261 KOG0113 U1 small nuclear ribon 22.8 91 0.002 30.3 3.4 13 173-185 151-163 (335)
262 PRK15178 Vi polysaccharide exp 22.7 6E+02 0.013 25.8 9.3 83 42-127 284-367 (434)
263 PF14257 DUF4349: Domain of un 22.7 4.4E+02 0.0095 24.1 7.9 55 73-127 127-185 (262)
264 KOG0963 Transcription factor/C 22.7 8.5E+02 0.018 26.0 10.5 23 75-97 282-304 (629)
265 TIGR03826 YvyF flagellar opero 22.7 59 0.0013 27.8 1.9 78 38-154 17-94 (137)
266 COG1645 Uncharacterized Zn-fin 22.5 34 0.00073 29.1 0.4 14 142-155 29-42 (131)
267 PF06160 EzrA: Septation ring 22.5 5.3E+02 0.011 26.8 9.2 89 30-124 61-149 (560)
268 PF01166 TSC22: TSC-22/dip/bun 22.4 66 0.0014 23.7 1.9 24 76-99 12-35 (59)
269 PF07765 KIP1: KIP1-like prote 22.4 3.7E+02 0.008 20.7 6.9 25 72-96 12-36 (74)
270 PF12907 zf-met2: Zinc-binding 22.3 31 0.00066 23.4 0.1 26 142-167 2-27 (40)
271 TIGR00756 PPR pentatricopeptid 22.2 1.5E+02 0.0033 17.0 3.3 21 94-114 7-27 (35)
272 cd00176 SPEC Spectrin repeats, 22.2 4.5E+02 0.0098 21.7 9.9 47 80-127 49-95 (213)
273 PF13174 TPR_6: Tetratricopept 22.0 1.5E+02 0.0033 17.2 3.3 24 90-113 3-26 (33)
274 PF02945 Endonuclease_7: Recom 21.9 23 0.00051 27.5 -0.6 30 140-169 21-51 (81)
275 PF12793 SgrR_N: Sugar transpo 21.9 1.3E+02 0.0029 24.6 3.9 27 85-111 68-94 (115)
276 PF02044 Bombesin: Bombesin-li 21.9 28 0.00062 18.4 -0.1 6 162-167 7-12 (14)
277 PRK14011 prefoldin subunit alp 21.9 2.1E+02 0.0047 24.5 5.2 15 138-152 49-63 (144)
278 COG4303 EutB Ethanolamine ammo 21.8 34 0.00073 33.6 0.3 10 160-169 346-355 (453)
279 TIGR02473 flagell_FliJ flagell 21.7 4.3E+02 0.0093 21.3 9.9 26 76-101 32-57 (141)
280 PF08946 Osmo_CC: Osmosensory 21.7 1.8E+02 0.004 20.3 3.8 22 76-97 17-38 (46)
281 PF12729 4HB_MCP_1: Four helix 21.6 4.2E+02 0.0092 21.1 9.6 35 76-110 110-144 (181)
282 PF06397 Desulfoferrod_N: Desu 21.6 20 0.00043 23.8 -0.9 16 138-153 3-18 (36)
283 PF05529 Bap31: B-cell recepto 21.6 3.3E+02 0.0071 23.8 6.6 47 80-126 127-176 (192)
284 KOG2906 RNA polymerase III sub 21.6 32 0.00068 28.0 0.1 15 141-155 1-15 (105)
285 PF00096 zf-C2H2: Zinc finger, 21.5 34 0.00075 19.2 0.2 19 143-164 2-20 (23)
286 PF11428 DUF3196: Protein of u 21.5 6.4E+02 0.014 24.3 8.8 86 1-91 8-94 (286)
287 PF08838 DUF1811: Protein of u 21.3 3.4E+02 0.0074 22.1 5.9 34 81-114 10-43 (102)
288 PF07106 TBPIP: Tat binding pr 21.3 4.8E+02 0.01 22.3 7.4 50 78-127 72-132 (169)
289 PF13374 TPR_10: Tetratricopep 21.3 2.1E+02 0.0044 17.4 4.9 31 89-119 4-34 (42)
290 PF11598 COMP: Cartilage oligo 21.3 2.2E+02 0.0049 19.7 4.2 9 140-148 37-45 (45)
291 PF05266 DUF724: Protein of un 21.3 5.1E+02 0.011 23.1 7.7 52 76-127 129-182 (190)
292 COG2178 Predicted RNA-binding 21.2 6.4E+02 0.014 23.1 8.9 48 76-123 18-65 (204)
293 PF10883 DUF2681: Protein of u 21.2 2.7E+02 0.0058 22.0 5.2 27 80-106 25-51 (87)
294 PRK06921 hypothetical protein; 21.1 94 0.002 28.9 3.1 37 108-150 5-41 (266)
295 PF02150 RNA_POL_M_15KD: RNA p 21.0 34 0.00074 22.2 0.1 14 141-154 1-14 (35)
296 KOG3576 Ovo and related transc 21.0 34 0.00075 31.5 0.2 40 139-184 210-251 (267)
297 PF12756 zf-C2H2_2: C2H2 type 21.0 51 0.0011 24.7 1.1 30 141-173 50-79 (100)
298 PF09543 DUF2379: Protein of u 20.6 3.2E+02 0.007 22.9 5.8 36 78-113 65-100 (121)
299 COG0268 RpsT Ribosomal protein 20.5 3.4E+02 0.0075 21.5 5.7 36 82-117 23-58 (88)
300 PRK14142 heat shock protein Gr 20.4 1.9E+02 0.0042 26.7 4.9 26 140-165 79-104 (223)
301 PF06825 HSBP1: Heat shock fac 20.4 3.4E+02 0.0073 19.6 5.3 20 37-56 3-22 (54)
302 PLN02372 violaxanthin de-epoxi 20.3 4.3E+02 0.0093 26.9 7.5 28 33-60 357-384 (455)
303 PF13465 zf-H2C2_2: Zinc-finge 20.3 39 0.00084 20.2 0.2 12 138-149 11-22 (26)
304 PF05605 zf-Di19: Drought indu 20.2 60 0.0013 22.6 1.3 20 142-165 3-22 (54)
305 KOG2698 GTP cyclohydrolase I [ 20.1 30 0.00065 31.8 -0.4 10 164-173 144-153 (247)
306 PF15011 CK2S: Casein Kinase 2 20.1 3E+02 0.0065 24.0 5.9 47 136-185 36-86 (168)
No 1
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=100.00 E-value=9.5e-56 Score=412.37 Aligned_cols=181 Identities=36% Similarity=0.608 Sum_probs=158.6
Q ss_pred CCCccccccCChhHHHHhhcCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHH
Q 022656 4 HLDCIPVKMCYYVCDCSFEKSPRHDAYVPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVL 83 (294)
Q Consensus 4 ~~~~~~~~~~~~~lK~~Ye~~~~~~~~~~~YE~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l 83 (294)
+|.|-| +||+++||++|+.+++..+| +||++|+.+|+.||.+|+++|+++++||+++.++ .......++++|..|
T Consensus 53 dlg~C~-kvHd~~lk~~Ye~~~k~~~~--~~E~d~~~~l~~~v~d~~rri~~~kerL~e~~ee--~~~e~~~k~~~v~~l 127 (319)
T KOG0796|consen 53 DLGPCP-KVHDEALKADYERASKERDY--GYEWDALEILERFVADVDRRIEKAKERLAETVEE--RSEEAARKAEKVHEL 127 (319)
T ss_pred ccCccc-chhhHHHHHHHhhchHhhhh--hhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh--hhhHHHHHHHHHHHH
Confidence 444444 89999999999999999999 9999999999999999999999999999987532 223344457889999
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH-HHHHHHHhhhhhhhhhhhhhhccccccccccccccCCchHHHHh
Q 022656 84 EEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNV-EKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAERTQS 162 (294)
Q Consensus 84 ~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~-er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~Rl~d 162 (294)
+++|+.|+++||+||++|+|++||++|.+||.|++ ++..++.+++.+.+.+.+++|||+||+||||||+++||++||||
T Consensus 128 ~e~I~~~l~~~E~LG~eG~Veeaq~~~~e~E~lk~~e~e~~~~~~~~~~~~~~~~~qkl~VCeVCGa~L~~~D~d~RlaD 207 (319)
T KOG0796|consen 128 EEKIGKLLEKAEELGEEGNVEEAQKAMKEVEELKAKEKEEAEESYNTTMPGASAQQQKLRVCEVCGAFLSVNDADRRLAD 207 (319)
T ss_pred HHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccCcchhhhhhhhhhHHHhhhHHHhccchHHHHHH
Confidence 99999999999999999999999999999999997 66666666633344456799999999999999999999999999
Q ss_pred hhcccccccHHHHHHHHHHHHHHHHHH
Q 022656 163 HISGKQHIGYGMVRDFITEYKEAKEKA 189 (294)
Q Consensus 163 H~~GK~HlGy~kIRe~l~eL~~~~~~~ 189 (294)
||+|||||||++||++|.+|++.....
T Consensus 208 Hf~GKlHlGy~~iR~~l~eLk~~~~~~ 234 (319)
T KOG0796|consen 208 HFGGKLHLGYVLIREKLAELKKEKAKR 234 (319)
T ss_pred hhcchHHHHHHHHHHHHHHHHHHHhHH
Confidence 999999999999999999999986554
No 2
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=100.00 E-value=5.9e-52 Score=382.69 Aligned_cols=180 Identities=37% Similarity=0.650 Sum_probs=158.0
Q ss_pred CCccccccCChhHHHHhhcCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHH
Q 022656 5 LDCIPVKMCYYVCDCSFEKSPRHDAYVPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLE 84 (294)
Q Consensus 5 ~~~~~~~~~~~~lK~~Ye~~~~~~~~~~~YE~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ 84 (294)
|---| +||+++||++|++++++..++ +||++|+.+|+.||.+||++|++|++||+.+++..+ .......+++|..|+
T Consensus 53 LG~C~-kiHd~~lk~~Ye~~~~~~~~~-~YE~e~~~~L~~~i~d~drrI~~~k~RL~~~~~~~~-~~~~~~~~~~i~~l~ 129 (254)
T PF03194_consen 53 LGPCP-KIHDEALKAEYEKASKKEKYG-GYEREFLRYLQRLIRDCDRRIERAKERLEQTQEEQA-KEADEEKAEKIDELD 129 (254)
T ss_pred cchhh-hhcCHHHHHHHHhCccccccc-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccccc-cchhhhHHHHHHHHH
Confidence 33335 899999999999999998885 699999999999999999999999999998764322 223333588999999
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH---hhhhh--hhhhhhhhhccccccccccccccCCchHH
Q 022656 85 EKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQ---QSQND--KVLMMAQEKKMALCEICGSFLVANDAAER 159 (294)
Q Consensus 85 ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~---~~~~~--~~~~~~~~qkm~VCeVCGA~Ls~~D~d~R 159 (294)
++|+.||++||+||++|+|++|+++|.+|+.|+++++.|++ ++ .+ .++.++++|+|+||+|||||||++||++|
T Consensus 130 ~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~le~~~~~~-~~~~~~~~~~~~qkl~VCeVCGA~Ls~~D~d~R 208 (254)
T PF03194_consen 130 EKIGELLKEAEELGEEGDVDEAQKLMEEVEKLKEEKEELEKELEEY-RNSIENSAQSQQQKLEVCEVCGAFLSVGDNDRR 208 (254)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhhhhhh-hhhhhhhhcccccCccchhhhhhHHhccchHHH
Confidence 99999999999999999999999999999999999999998 33 22 22334689999999999999999999999
Q ss_pred HHhhhcccccccHHHHHHHHHHHHHHHHH
Q 022656 160 TQSHISGKQHIGYGMVRDFITEYKEAKEK 188 (294)
Q Consensus 160 l~dH~~GK~HlGy~kIRe~l~eL~~~~~~ 188 (294)
|+|||+|||||||++||++|++|++...+
T Consensus 209 ladH~~GK~HlGy~~IR~~l~el~e~~~~ 237 (254)
T PF03194_consen 209 LADHFGGKQHLGYAKIREKLKELKEKREE 237 (254)
T ss_pred HHHHhccchhhhHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999998655
No 3
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=100.00 E-value=1.2e-35 Score=263.04 Aligned_cols=174 Identities=22% Similarity=0.316 Sum_probs=144.5
Q ss_pred CCccccccCChhHHHHhhcCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHH
Q 022656 5 LDCIPVKMCYYVCDCSFEKSPRHDAYVPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLE 84 (294)
Q Consensus 5 ~~~~~~~~~~~~lK~~Ye~~~~~~~~~~~YE~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ 84 (294)
|---| ++|.+-+|++||.+.....+ +|||+|+..|.++|.+|+..|..|-.++..+++ ....+.++.+.+..+.
T Consensus 54 lGkCp-~~H~~k~K~~YeR~~~~~~~--~yEweyl~~L~r~V~~cn~~I~~a~~~~~~t~e---e~~kI~e~~e~~~~~d 127 (258)
T COG5200 54 LGKCP-TSHEEKYKAEYERNGRERAE--EYEWEYLRLLVRIVLSCNDGIRAAGLEDRTTPE---EFGKIKEKEELFNRVD 127 (258)
T ss_pred cCCCc-chhHHHHHHHHhhhhhccch--hhhHHHHHHHHHHHHHhcchhhhhhhhccCCHH---HHHhHHHHHHHHHHHH
Confidence 44456 88889999999999888888 999999999999999999999999777743321 1223444555555555
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhh--hhhhhhhhhhccccccccccccccCCchHHHHh
Q 022656 85 EKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQN--DKVLMMAQEKKMALCEICGSFLVANDAAERTQS 162 (294)
Q Consensus 85 ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~--~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~Rl~d 162 (294)
+.|+.|..+++.|...-.|+.|+..+.+++.|+++++++..++ . ++|+++..+|||+||+|||||||.+|||+||||
T Consensus 128 ~sIg~lg~e~dalakrk~V~~a~~~f~el~rl~~~rkei~~~v-~sm~en~gq~thqklqvC~iCgayLsrlDtdrrlad 206 (258)
T COG5200 128 ESIGELGMEGDALAKRKLVERACSAFNELERLREERKEIKEAV-YSMVENNGQGTHQKLQVCGICGAYLSRLDTDRRLAD 206 (258)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHhhCcchhhhhhhhhhhhhhhHHHhcchhhHHHH
Confidence 5555555555555555559999999999999999999999887 4 567888899999999999999999999999999
Q ss_pred hhcccccccHHHHHHHHHHHHHH
Q 022656 163 HISGKQHIGYGMVRDFITEYKEA 185 (294)
Q Consensus 163 H~~GK~HlGy~kIRe~l~eL~~~ 185 (294)
||.||+|+||++||..|..|.+.
T Consensus 207 Hf~GklHlGy~~~R~dl~~llk~ 229 (258)
T COG5200 207 HFNGKLHLGYLLVRSDLADLLKK 229 (258)
T ss_pred HhccchhhhHHHHHHHHHHHHHH
Confidence 99999999999999999998775
No 4
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=95.68 E-value=0.16 Score=48.72 Aligned_cols=114 Identities=18% Similarity=0.159 Sum_probs=72.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 022656 34 FEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKV 113 (294)
Q Consensus 34 YE~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~v 113 (294)
++..++--. .|+..|.+-|.-+..+++..-+..... ..+..+......++|..|.++|+.|+.+-+--+.++.+.++
T Consensus 74 k~~~~~~E~-d~~~~l~~~v~d~~rri~~~kerL~e~--~ee~~~e~~~k~~~v~~l~e~I~~~l~~~E~LG~eG~Veea 150 (319)
T KOG0796|consen 74 KERDYGYEW-DALEILERFVADVDRRIEKAKERLAET--VEERSEEAARKAEKVHELEEKIGKLLEKAEELGEEGNVEEA 150 (319)
T ss_pred HhhhhhhhH-HHHHHHHHHHHHHHHHHHHHHHHHHhh--hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHH
Confidence 344444333 388888999999988876543212111 11233334444778999999999999998888889999999
Q ss_pred HHHHHHHHHHHH-hhhhh----hhhhhhhhhccccccccccc
Q 022656 114 EILNVEKTTLTQ-QSQND----KVLMMAQEKKMALCEICGSF 150 (294)
Q Consensus 114 e~Lk~er~~l~~-~~~~~----~~~~~~~~qkm~VCeVCGA~ 150 (294)
.++-.+.+.|.. +.... ..+++...-+-+.=.||...
T Consensus 151 q~~~~e~E~lk~~e~e~~~~~~~~~~~~~~~~~qkl~VCeVC 192 (319)
T KOG0796|consen 151 QKAMKEVEELKAKEKEEAEESYNTTMPGASAQQQKLRVCEVC 192 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCcchhhhhhhhhhHHHhh
Confidence 999988888875 22011 11222223345566777643
No 5
>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]
Probab=93.61 E-value=0.047 Score=53.72 Aligned_cols=10 Identities=20% Similarity=0.521 Sum_probs=4.9
Q ss_pred cccccHHHHH
Q 022656 167 KQHIGYGMVR 176 (294)
Q Consensus 167 K~HlGy~kIR 176 (294)
-||.-|+-|.
T Consensus 215 ~qhsr~ai~k 224 (479)
T KOG4676|consen 215 RQHSRRAIIK 224 (479)
T ss_pred hhhhhhhhcC
Confidence 4555554443
No 6
>KOG2888 consensus Putative RNA binding protein [General function prediction only]
Probab=93.56 E-value=0.044 Score=52.97 Aligned_cols=30 Identities=27% Similarity=0.325 Sum_probs=21.9
Q ss_pred HhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 98 GEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 98 GeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
|.-|=|.-|.-|+=++=.||--+.+|---+
T Consensus 120 gaggivSTAyCLLYklftlklTrKQ~~gll 149 (453)
T KOG2888|consen 120 GAGGIVSTAYCLLYKLFTLKLTRKQLIGLL 149 (453)
T ss_pred CcCcchhhHHHHHHHHHHHHhHHHHHHHHh
Confidence 455667888888888888887777765433
No 7
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=91.77 E-value=1.9 Score=39.52 Aligned_cols=126 Identities=14% Similarity=0.126 Sum_probs=77.0
Q ss_pred ChhhHHHHHH----HHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHH
Q 022656 30 YVPKFEAELA----QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDE 105 (294)
Q Consensus 30 ~~~~YE~e~l----~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~Vde 105 (294)
|...||+.-. .|--.++..+.+-+.....++.-.. .....+++...+|.++++.|+-+-..|+.||.+|+--.
T Consensus 65 ~K~~YeR~~~~~~~~yEweyl~~L~r~V~~cn~~I~~a~---~~~~~t~ee~~kI~e~~e~~~~~d~sIg~lg~e~dala 141 (258)
T COG5200 65 YKAEYERNGRERAEEYEWEYLRLLVRIVLSCNDGIRAAG---LEDRTTPEEFGKIKEKEELFNRVDESIGELGMEGDALA 141 (258)
T ss_pred HHHHHhhhhhccchhhhHHHHHHHHHHHHHhcchhhhhh---hhccCCHHHHHhHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence 4445665432 2566788888888888887774221 12345777888999999999999999999999997322
Q ss_pred H----HHHHHHHHHHHHHHHHHHHhhhhhhhhh--hhhhhccccccccccccccCCchHHHHh
Q 022656 106 A----EALMRKVEILNVEKTTLTQQSQNDKVLM--MAQEKKMALCEICGSFLVANDAAERTQS 162 (294)
Q Consensus 106 A----~~l~~~ve~Lk~er~~l~~~~~~~~~~~--~~~~qkm~VCeVCGA~Ls~~D~d~Rl~d 162 (294)
- ...|...-+|+.-+..+++-+ ..--++ ...+-.-+-=+|||.. +-.-.||+.
T Consensus 142 krk~V~~a~~~f~el~rl~~~rkei~-~~v~sm~en~gq~thqklqvC~iC---gayLsrlDt 200 (258)
T COG5200 142 KRKLVERACSAFNELERLREERKEIK-EAVYSMVENNGQGTHQKLQVCGIC---GAYLSRLDT 200 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHhhCcchhhhhhhhhhhhh---hhHHHhcch
Confidence 2 222233334444444343332 211112 3445566778999954 334566654
No 8
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=91.46 E-value=0.69 Score=43.01 Aligned_cols=19 Identities=26% Similarity=0.588 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHhh
Q 022656 42 CEKLVMDLDRRVRRGRERL 60 (294)
Q Consensus 42 L~~lI~d~dRkI~~~k~RL 60 (294)
++.=|.++..+|.++...|
T Consensus 64 ~e~ei~~~r~r~~~~e~kl 82 (239)
T COG1579 64 LESEIQEIRERIKRAEEKL 82 (239)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4555666777777776666
No 9
>PRK02224 chromosome segregation protein; Provisional
Probab=91.07 E-value=4.8 Score=43.28 Aligned_cols=14 Identities=21% Similarity=0.527 Sum_probs=10.6
Q ss_pred cccccccccccccc
Q 022656 140 KMALCEICGSFLVA 153 (294)
Q Consensus 140 km~VCeVCGA~Ls~ 153 (294)
...+|++||..+..
T Consensus 450 ~~~~Cp~C~r~~~~ 463 (880)
T PRK02224 450 EAGKCPECGQPVEG 463 (880)
T ss_pred hcccCCCCCCcCCC
Confidence 35899999986643
No 10
>PHA02562 46 endonuclease subunit; Provisional
Probab=90.56 E-value=5.3 Score=40.46 Aligned_cols=15 Identities=20% Similarity=0.503 Sum_probs=11.7
Q ss_pred ccccccccccccccC
Q 022656 140 KMALCEICGSFLVAN 154 (294)
Q Consensus 140 km~VCeVCGA~Ls~~ 154 (294)
.-.+|++||.-+...
T Consensus 283 ~~~~Cp~C~~~~~~~ 297 (562)
T PHA02562 283 KGGVCPTCTQQISEG 297 (562)
T ss_pred CCCCCCCCCCcCCCc
Confidence 346999999887654
No 11
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=90.15 E-value=0.13 Score=32.71 Aligned_cols=27 Identities=26% Similarity=0.636 Sum_probs=20.6
Q ss_pred ccccccccccccCCchHHHHhhhccccccc
Q 022656 142 ALCEICGSFLVANDAAERTQSHISGKQHIG 171 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlG 171 (294)
.-|++|+.++. ++ .=+..|+.||.|.-
T Consensus 4 ~~C~~C~~~~~--~~-~~~~~H~~gk~H~~ 30 (35)
T smart00451 4 FYCKLCNVTFT--DE-ISVEAHLKGKKHKK 30 (35)
T ss_pred eEccccCCccC--CH-HHHHHHHChHHHHH
Confidence 45999998766 33 34499999999954
No 12
>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=89.93 E-value=8.6 Score=41.89 Aligned_cols=24 Identities=17% Similarity=0.303 Sum_probs=17.9
Q ss_pred cccccccccccccCCchHHHHhhhc
Q 022656 141 MALCEICGSFLVANDAAERTQSHIS 165 (294)
Q Consensus 141 m~VCeVCGA~Ls~~D~d~Rl~dH~~ 165 (294)
...|+|||.-|.-. ....+.+|+.
T Consensus 457 ~~~CPvCg~~l~~~-~~~~~~~~~~ 480 (908)
T COG0419 457 GEKCPVCGQELPEE-HEKELLELYE 480 (908)
T ss_pred CCCCCCCCCCCCcH-HHHHHHHHHH
Confidence 47899999655433 3677888888
No 13
>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].
Probab=89.01 E-value=4.7 Score=36.16 Aligned_cols=82 Identities=22% Similarity=0.297 Sum_probs=66.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Q 022656 40 QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 119 (294)
Q Consensus 40 ~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 119 (294)
..|..+|.|++.-|..++.-|+... ........++..+...|..+..+|+.....|+=+-|...+.....+..+
T Consensus 26 ~~l~q~ird~e~~l~~a~~~~a~~~------a~~~~le~~~~~~~~~~~~~~~~A~~Al~~g~edLAr~al~~k~~~e~~ 99 (221)
T PF04012_consen 26 KMLEQAIRDMEEQLRKARQALARVM------ANQKRLERKLDEAEEEAEKWEKQAELALAAGREDLAREALQRKADLEEQ 99 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 7889999999999999999886432 2344567889999999999999999999999999997777777666666
Q ss_pred HHHHHHhh
Q 022656 120 KTTLTQQS 127 (294)
Q Consensus 120 r~~l~~~~ 127 (294)
...++..+
T Consensus 100 ~~~l~~~~ 107 (221)
T PF04012_consen 100 AERLEQQL 107 (221)
T ss_pred HHHHHHHH
Confidence 66655443
No 14
>PRK14143 heat shock protein GrpE; Provisional
Probab=87.62 E-value=2.5 Score=39.23 Aligned_cols=91 Identities=14% Similarity=0.262 Sum_probs=61.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccC
Q 022656 75 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVAN 154 (294)
Q Consensus 75 ~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~ 154 (294)
....++..|..+|..|-++++.|- +.-+.+.+..+.++.-...-.. ...+..+|.++-.||-+.
T Consensus 64 ~~~~~~~~l~~el~~l~~e~~elk-----d~~lR~~AdfeN~RKR~~kE~e-----------~~~~~a~~~~~~~lLpV~ 127 (238)
T PRK14143 64 DNAARLAQLEQELESLKQELEELN-----SQYMRIAADFDNFRKRTSREQE-----------DLRLQLKCNTLSEILPVV 127 (238)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHH
Confidence 345677888888888888888873 4456666666666543221111 124567788889999999
Q ss_pred CchHHHHhhhcc------cccccHHHHHHHHHH
Q 022656 155 DAAERTQSHISG------KQHIGYGMVRDFITE 181 (294)
Q Consensus 155 D~d~Rl~dH~~G------K~HlGy~kIRe~l~e 181 (294)
|+-.|.-.|+.. .++-||..|...|..
T Consensus 128 DnLerAl~~~~~~~~~~~~l~~Gve~i~k~l~~ 160 (238)
T PRK14143 128 DNFERARQQLKPEGEEAQALHRSYQGLYKQLVD 160 (238)
T ss_pred hHHHHHHhcccccchhHHHHHHHHHHHHHHHHH
Confidence 999997777742 367788887554443
No 15
>PRK01156 chromosome segregation protein; Provisional
Probab=86.94 E-value=5.8 Score=42.87 Aligned_cols=14 Identities=7% Similarity=-0.054 Sum_probs=10.1
Q ss_pred ccccccccccccCC
Q 022656 142 ALCEICGSFLVAND 155 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D 155 (294)
.+|+||+..+...+
T Consensus 450 ~~~~~Cp~c~~~~~ 463 (895)
T PRK01156 450 NGQSVCPVCGTTLG 463 (895)
T ss_pred ccCCCCCCCCCcCC
Confidence 37888887777666
No 16
>PRK06835 DNA replication protein DnaC; Validated
Probab=86.13 E-value=5.4 Score=38.56 Aligned_cols=67 Identities=15% Similarity=0.172 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCC---HHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhcccccccccc
Q 022656 79 QLSVLEEKIKNLLEQVETLGEAGK---VDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGS 149 (294)
Q Consensus 79 ~i~~l~ekI~~ll~eaE~LGeeG~---VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA 149 (294)
+|.+|+.+|..+-.++-.+...|+ -+....+-+++..|..++..|.... .-. ...-..-..|+.|+=
T Consensus 37 ~~~~id~~i~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~~~~lL~~~-g~~---~dyl~~~y~Cp~C~d 106 (329)
T PRK06835 37 EIAEIDDEIAKLGIKLSRAILKNPDKKEETLKELKEKITDLRVKKAELLVSN-GYP---PDYLEMKYTCPKCKD 106 (329)
T ss_pred cHHHHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHHHHHHHHc-CCC---hhhcCCCCCCCCCCC
Confidence 455666666666554444444555 5555677888889988888887654 111 111222357999975
No 17
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=86.12 E-value=1.7 Score=45.09 Aligned_cols=17 Identities=12% Similarity=0.329 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHHHH
Q 022656 107 EALMRKVEILNVEKTTL 123 (294)
Q Consensus 107 ~~l~~~ve~Lk~er~~l 123 (294)
.++|..++.|+.+..+.
T Consensus 257 ~~~~~~~~~~~~qh~~~ 273 (757)
T KOG4368|consen 257 LAFQQQIQTLKTQHEEF 273 (757)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 46778888887766553
No 18
>PRK14158 heat shock protein GrpE; Provisional
Probab=85.89 E-value=4.8 Score=36.31 Aligned_cols=95 Identities=15% Similarity=0.074 Sum_probs=61.1
Q ss_pred CchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhcccccccccccc
Q 022656 72 ISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFL 151 (294)
Q Consensus 72 ~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~L 151 (294)
........+..|+++|..+.++++.|- +.-+.+.++.+.++.-.+ .+. ...++..+..++-.||
T Consensus 34 ~~~~~~~~~~~le~~l~~le~e~~el~-----d~~lR~~AefeN~RkR~~---kE~--------e~~~~~a~~~~~~~lL 97 (194)
T PRK14158 34 QPVAAADRIKELEEALAAKEAEAAANW-----DKYLRERADLENYRKRVQ---KEK--------EELLKYGNESLILEIL 97 (194)
T ss_pred CCCCchhHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHH---HHH--------HHHHHHHHHHHHHHHH
Confidence 345566778899999999888888883 445556666665543221 111 1234556677788999
Q ss_pred ccCCchHHHHhhhcc----cccccHHHHHHHHHHH
Q 022656 152 VANDAAERTQSHISG----KQHIGYGMVRDFITEY 182 (294)
Q Consensus 152 s~~D~d~Rl~dH~~G----K~HlGy~kIRe~l~eL 182 (294)
.+.|+-.|.-.|... .++-|+.+|...+...
T Consensus 98 pV~DnLerAl~~~~~~~~~~i~~Gv~mi~k~l~~v 132 (194)
T PRK14158 98 PAVDNMERALDHADEESMSAIIEGIRMTLSMLLST 132 (194)
T ss_pred hHHhHHHHHHhccCcchHHHHHHHHHHHHHHHHHH
Confidence 999999997667542 3556666666555443
No 19
>PRK14144 heat shock protein GrpE; Provisional
Probab=85.22 E-value=4.2 Score=36.84 Aligned_cols=92 Identities=11% Similarity=0.138 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCc
Q 022656 77 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDA 156 (294)
Q Consensus 77 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~ 156 (294)
..++..+.++|..+-++++.| -+..+.+.++.+.++.-.+.-.+ ...+..+=.++-+||.+.|+
T Consensus 44 ~~~~~~l~~~i~~le~e~~el-----kdk~lR~~AefeN~RKR~~kE~e-----------~~~~~a~~~~~~~LLpV~Dn 107 (199)
T PRK14144 44 HPSYTALEEQLTLAEQKAHEN-----WEKSVRALAELENVRRRMEREVA-----------NAHKYGVEKLISALLPVVDS 107 (199)
T ss_pred chhHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhhHHhH
Confidence 355667888888888888877 35667777777777532211111 11233344566889999999
Q ss_pred hHHHHhhhc----ccccccHHHHHHHHHHHHH
Q 022656 157 AERTQSHIS----GKQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 157 d~Rl~dH~~----GK~HlGy~kIRe~l~eL~~ 184 (294)
-.|.-.|.. +.++-|+.+|...+...-+
T Consensus 108 LerAl~~~~~~~~~~i~~Gv~mi~k~l~~~L~ 139 (199)
T PRK14144 108 LEQALQLADKNSDPSMHEGLELTMKLFLDALQ 139 (199)
T ss_pred HHHHHHcccccchhHHHHHHHHHHHHHHHHHH
Confidence 999766653 4567788888776665544
No 20
>PRK15058 cytochrome b562; Provisional
Probab=84.75 E-value=9.8 Score=32.21 Aligned_cols=42 Identities=19% Similarity=0.251 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHH---HHHHHHhcCCHHHHHHHHHHHHHHHHH
Q 022656 78 EQLSVLEEKIKNLLE---QVETLGEAGKVDEAEALMRKVEILNVE 119 (294)
Q Consensus 78 e~i~~l~ekI~~ll~---eaE~LGeeG~VdeA~~l~~~ve~Lk~e 119 (294)
.++..+.+-++.|+. +++.|..+|++++|.....++..|+.+
T Consensus 78 ~e~K~Y~~G~d~Li~qID~a~~la~~GkL~eAK~~a~~l~~lR~e 122 (128)
T PRK15058 78 PEMKDFRHGFDILVGQIDGALKLANEGKVKEAQAAAEQLKTTRNA 122 (128)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 445555555555544 566799999999999999888888754
No 21
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=83.36 E-value=3.6 Score=31.16 Aligned_cols=60 Identities=20% Similarity=0.366 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCc
Q 022656 86 KIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDA 156 (294)
Q Consensus 86 kI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~ 156 (294)
.|+-|.+-|-.+...+..+-|..++..+..+-.+. ....++.-+..+|.-||.+|+.+-|
T Consensus 2 Ri~~L~~~a~~~~~~~~~~lsr~y~~~~~~i~~k~-----------~~~l~~~~kr~~Ck~C~~~liPG~~ 61 (85)
T PF04032_consen 2 RINFLYQAAHLLLADGSPSLSRHYMKLMRKISKKT-----------RIRLPPEIKRTICKKCGSLLIPGVN 61 (85)
T ss_dssp HHHHHHHHHH-HHCCC-HHHHHHHHHHHHHHHHHC-----------T---STTCCCTB-TTT--B--CTTT
T ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHh-----------CCCCChHHhcccccCCCCEEeCCCc
Confidence 56667777776778888888888887777765321 1123356688999999999998754
No 22
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=83.33 E-value=0.41 Score=29.04 Aligned_cols=25 Identities=20% Similarity=0.700 Sum_probs=20.0
Q ss_pred ccccccccccccCCchHHHHhhhccccc
Q 022656 142 ALCEICGSFLVANDAAERTQSHISGKQH 169 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~d~Rl~dH~~GK~H 169 (294)
.+|++|+..++ ++.=+..|+.||.|
T Consensus 2 ~~C~~C~k~f~---~~~~~~~H~~sk~H 26 (27)
T PF12171_consen 2 FYCDACDKYFS---SENQLKQHMKSKKH 26 (27)
T ss_dssp CBBTTTTBBBS---SHHHHHCCTTSHHH
T ss_pred CCcccCCCCcC---CHHHHHHHHccCCC
Confidence 47999996543 45778999999988
No 23
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=82.30 E-value=0.43 Score=28.04 Aligned_cols=24 Identities=25% Similarity=0.699 Sum_probs=18.9
Q ss_pred cccccccccccCCchHHHHhhhccccc
Q 022656 143 LCEICGSFLVANDAAERTQSHISGKQH 169 (294)
Q Consensus 143 VCeVCGA~Ls~~D~d~Rl~dH~~GK~H 169 (294)
.|+||..... +..=+..|+.||.|
T Consensus 2 ~C~~C~~~f~---s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 2 YCDICNKSFS---SENSLRQHLRSKKH 25 (25)
T ss_dssp EETTTTEEES---SHHHHHHHHTTHHH
T ss_pred CCCCCCCCcC---CHHHHHHHHCcCCC
Confidence 6999986543 45679999999987
No 24
>PRK14162 heat shock protein GrpE; Provisional
Probab=79.15 E-value=8.3 Score=34.80 Aligned_cols=94 Identities=19% Similarity=0.161 Sum_probs=60.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccC
Q 022656 75 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVAN 154 (294)
Q Consensus 75 ~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~ 154 (294)
+.+.++..|..+|..+-++++.| -+.-+.+.++.+.++.-.+.-.. ...+..+..++-.||.+.
T Consensus 36 ~~~~e~~~l~~~l~~l~~e~~el-----kd~~lR~~AEfeN~rkR~~kE~e-----------~~~~~a~~~~~~~LLpV~ 99 (194)
T PRK14162 36 EKQNPVEDLEKEIADLKAKNKDL-----EDKYLRSQAEIQNMQNRYAKERA-----------QLIKYESQSLAKDVLPAM 99 (194)
T ss_pred ccchhHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhhHH
Confidence 34567778888888888888877 24556666666666532211111 123445566778999999
Q ss_pred CchHHHHhhhcc-----cccccHHHHHHHHHHHHH
Q 022656 155 DAAERTQSHISG-----KQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 155 D~d~Rl~dH~~G-----K~HlGy~kIRe~l~eL~~ 184 (294)
|+-.|--.|... .++-|+.+|...|...-+
T Consensus 100 DnLerAl~~~~~~~~~~~l~~Gvemi~k~l~~vL~ 134 (194)
T PRK14162 100 DNLERALAVKADDEAAKQLKKGVQMTLDHLVKALK 134 (194)
T ss_pred hHHHHHHhccccchhHHHHHHHHHHHHHHHHHHHH
Confidence 999997667542 356677777766655444
No 25
>PRK09720 cybC cytochrome b562; Provisional
Probab=79.02 E-value=7.5 Score=31.56 Aligned_cols=42 Identities=24% Similarity=0.298 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHHH---HHHHHhcCCHHHHHHHHHHHHHHHH
Q 022656 77 SEQLSVLEEKIKNLLEQ---VETLGEAGKVDEAEALMRKVEILNV 118 (294)
Q Consensus 77 ~e~i~~l~ekI~~ll~e---aE~LGeeG~VdeA~~l~~~ve~Lk~ 118 (294)
..++..+..-+..|+.+ +..|..+|+++||.....++-.++.
T Consensus 49 s~e~K~y~~Gld~lI~qID~A~~La~~GkL~eAK~~a~~l~~~Rn 93 (100)
T PRK09720 49 SPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRN 93 (100)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 34555555555555554 5569999999999987776666654
No 26
>PRK14148 heat shock protein GrpE; Provisional
Probab=77.68 E-value=12 Score=33.84 Aligned_cols=91 Identities=18% Similarity=0.258 Sum_probs=57.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCch
Q 022656 78 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAA 157 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d 157 (294)
.++..|+.+|..|-+++++| -+.-+.+.++.+.++.-.. .+. ....+..++.++-.+|.+.|+-
T Consensus 40 ~e~~~l~~~l~~l~~e~~el-----kd~~lR~~Ae~eN~rKR~~---rE~--------e~~~~~a~~~~~~~LLpV~Dnl 103 (195)
T PRK14148 40 EQLERAKDTIKELEDSCDQF-----KDEALRAKAEMENIRKRAE---RDV--------SNARKFGIEKFAKELLPVIDSI 103 (195)
T ss_pred hHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHH---HHH--------HHHHHHHHHHHHHHHhhHHhHH
Confidence 45667777777777777776 2444555555555543211 111 1234556778888999999999
Q ss_pred HHHHhhhcc-----cccccHHHHHHHHHHHHH
Q 022656 158 ERTQSHISG-----KQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 158 ~Rl~dH~~G-----K~HlGy~kIRe~l~eL~~ 184 (294)
.|--.|... -++-|+.+|...|...-+
T Consensus 104 erAl~~~~~~~~~~~l~~Gv~mi~k~l~~vL~ 135 (195)
T PRK14148 104 EQALKHEVKLEEAIAMKEGIELTAKMLVDILK 135 (195)
T ss_pred HHHHhccccchhHHHHHHHHHHHHHHHHHHHH
Confidence 997777643 356677777666655443
No 27
>PF07361 Cytochrom_B562: Cytochrome b562; InterPro: IPR009155 Cytochrome b562 is a haem-containing protein that is expressed in the periplasm of Escherichia coli. In b-type cytochromes, the haem atom is not covalently attached to the polypeptide. Cytochrome b562 has a four-helical bundle structure that is structurally similar to that found in members of the cytochrome c family (IPR002321 from INTERPRO). Cytochrome b562 has a reduction potential of 167 mV, which sets the energy yield possible in metabolism and is also a key determinant of the rate at which redox reactions proceed [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding, 0042597 periplasmic space; PDB: 4ER9_A 3IQ6_G 2QLA_B 3FOO_A 3M79_C 256B_A 3NMI_F 3HNK_A 3NMK_D 2BC5_A ....
Probab=77.15 E-value=7.1 Score=31.47 Aligned_cols=41 Identities=37% Similarity=0.611 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHH---HHHHHHhcCCHHHHHHHHHHHHHHHHH
Q 022656 79 QLSVLEEKIKNLLE---QVETLGEAGKVDEAEALMRKVEILNVE 119 (294)
Q Consensus 79 ~i~~l~ekI~~ll~---eaE~LGeeG~VdeA~~l~~~ve~Lk~e 119 (294)
++..+.+-++.|+. .|+.|.+.|++++|...+.++..|+.+
T Consensus 54 ~~~~Y~~Gl~~li~~id~a~~~~~~G~l~~AK~~l~~l~~lR~e 97 (103)
T PF07361_consen 54 EVKDYQEGLDKLIDQIDKAEALAEAGKLDEAKAALKKLDDLRKE 97 (103)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34444544444443 567799999999999999999999865
No 28
>TIGR02977 phageshock_pspA phage shock protein A. Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.
Probab=77.04 E-value=30 Score=31.29 Aligned_cols=67 Identities=16% Similarity=0.240 Sum_probs=52.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 022656 40 QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRK 112 (294)
Q Consensus 40 ~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ 112 (294)
..|..+|.+++.-|..++.=|+... ........++..+...|..+..+|+.+-..|+=+-|...+.+
T Consensus 27 ~~l~q~irem~~~l~~ar~~lA~~~------a~~k~~e~~~~~~~~~~~~~~~~A~~Al~~G~EdLAr~Al~~ 93 (219)
T TIGR02977 27 KMIRLIIQEMEDTLVEVRTTSARTI------ADKKELERRVSRLEAQVADWQEKAELALSKGREDLARAALIE 93 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence 4678888888888888888886432 223345678999999999999999999999998888766433
No 29
>PF14282 FlxA: FlxA-like protein
Probab=77.01 E-value=9.7 Score=30.82 Aligned_cols=51 Identities=27% Similarity=0.452 Sum_probs=33.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 76 KSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 76 ~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
....|..|..+|..|.+++..|...+..+ +.....+++.|+.+...|..++
T Consensus 17 ~~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~-~e~k~~q~q~Lq~QI~~LqaQI 67 (106)
T PF14282_consen 17 SDSQIEQLQKQIKQLQEQLQELSQDSDLD-AEQKQQQIQLLQAQIQQLQAQI 67 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcccCCC-HHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999998843321 2222344555555555554443
No 30
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=76.60 E-value=8.6 Score=34.22 Aligned_cols=35 Identities=23% Similarity=0.302 Sum_probs=27.2
Q ss_pred hccccccccccccccCCchHHHHhhhcccccccHHHHHHHHHHHHHH
Q 022656 139 KKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKEA 185 (294)
Q Consensus 139 qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eL~~~ 185 (294)
...++|+.||+.|--.|+.. .+..+...+++|.+.
T Consensus 130 ~~~F~Cp~Cg~~L~~~d~s~------------~i~~l~~~i~~l~~~ 164 (176)
T COG1675 130 ELGFTCPKCGEDLEEYDSSE------------EIEELESELDELEEE 164 (176)
T ss_pred HhCCCCCCCCchhhhccchH------------HHHHHHHHHHHHHHH
Confidence 34599999999999999987 555666666666665
No 31
>PRK14151 heat shock protein GrpE; Provisional
Probab=76.58 E-value=8.8 Score=34.03 Aligned_cols=94 Identities=17% Similarity=0.200 Sum_probs=58.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccC
Q 022656 75 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVAN 154 (294)
Q Consensus 75 ~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~ 154 (294)
..+..+..+.++|..+-+++++|- +.-+.+.++.+.++.-. +.+. . ...+..+..++-.||.+.
T Consensus 17 ~~~~~~~~l~~~i~~le~e~~el~-----d~~lR~~Ae~eN~rkR~---~kE~-e-------~~~~~a~~~~~~~LLpv~ 80 (176)
T PRK14151 17 AEAAAGDDLTARVQELEEQLAAAK-----DQSLRAAADLQNVRRRA---EQDV-E-------KAHKFALEKFAGDLLPVV 80 (176)
T ss_pred ccccchhhHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHH---HHHH-H-------HHHHHHHHHHHHHHhhHH
Confidence 344556677777877777777773 44566666666664322 1111 0 123445566778999999
Q ss_pred CchHHHHhhhc------ccccccHHHHHHHHHHHHH
Q 022656 155 DAAERTQSHIS------GKQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 155 D~d~Rl~dH~~------GK~HlGy~kIRe~l~eL~~ 184 (294)
|+-.|.-.|.. ..++-|+.+|...+...-+
T Consensus 81 DnlerAl~~~~~~~~~~~~~~~Gv~mi~k~l~~~L~ 116 (176)
T PRK14151 81 DSLERGLELSSADDEAIKPMREGVELTLKMFQDTLK 116 (176)
T ss_pred hHHHHHHhcccccchhHHHHHHHHHHHHHHHHHHHH
Confidence 99999766654 2356677777766655433
No 32
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=76.00 E-value=13 Score=40.44 Aligned_cols=35 Identities=20% Similarity=0.588 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Q 022656 84 EEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNV 118 (294)
Q Consensus 84 ~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 118 (294)
...+..||.+||+|.++|..++|+.++.+++.+-+
T Consensus 537 ~~dL~~mmd~ie~la~~G~~~~A~q~L~qlq~mme 571 (820)
T PF13779_consen 537 QQDLQRMMDRIEELARSGRMDEARQLLEQLQQMME 571 (820)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 45577899999999999999999999998887754
No 33
>PRK14163 heat shock protein GrpE; Provisional
Probab=74.75 E-value=16 Score=33.51 Aligned_cols=89 Identities=11% Similarity=0.109 Sum_probs=56.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCch
Q 022656 78 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAA 157 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d 157 (294)
..+..|.++|..|-++++.| .+.-+.+.++.+.++.-...-.+ ...+..+=.++-.||.+.|+-
T Consensus 40 ~~~~~l~~~l~~l~~e~~el-----~d~~lR~~AEfeN~rkR~~kE~e-----------~~~~~a~~~~~~~LLpVlDnL 103 (214)
T PRK14163 40 AATAGLTAQLDQVRTALGER-----TADLQRLQAEYQNYRRRVERDRV-----------TVKEIAVANLLSELLPVLDDV 103 (214)
T ss_pred hhhHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhhhHhHH
Confidence 34567778888888888877 34556666666666532211111 112333344557889999999
Q ss_pred HHHHhhhcccccccHHHHHHHHHHHHH
Q 022656 158 ERTQSHISGKQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 158 ~Rl~dH~~GK~HlGy~kIRe~l~eL~~ 184 (294)
.|.-.|. .+.-|+.+|...|...-+
T Consensus 104 erAl~~~--~l~~Gv~mi~k~l~~~L~ 128 (214)
T PRK14163 104 GRAREHG--ELVGGFKSVAESLETTVA 128 (214)
T ss_pred HHHHhch--hHHHHHHHHHHHHHHHHH
Confidence 9987773 577888888777665444
No 34
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=74.49 E-value=13 Score=41.22 Aligned_cols=11 Identities=36% Similarity=0.772 Sum_probs=9.0
Q ss_pred ccccccccccc
Q 022656 140 KMALCEICGSF 150 (294)
Q Consensus 140 km~VCeVCGA~ 150 (294)
.=++|+|||+.
T Consensus 502 ~GePCPVCGS~ 512 (1047)
T PRK10246 502 AGQPCPLCGST 512 (1047)
T ss_pred CCCCcCCCCcc
Confidence 34899999984
No 35
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=74.24 E-value=64 Score=28.73 Aligned_cols=53 Identities=26% Similarity=0.399 Sum_probs=28.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 75 EKSEQLSVLEEKIKNLLEQVETLGEA-GKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 75 ~~~e~i~~l~ekI~~ll~eaE~LGee-G~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
....+|..+..+|..+..+++.+... ++.++-..++++++.|+.+.+.|..++
T Consensus 73 ~l~~~~~~~~~~i~~l~~~i~~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el 126 (188)
T PF03962_consen 73 KLQKEIEELEKKIEELEEKIEEAKKGREESEEREELLEELEELKKELKELKKEL 126 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555566666665555555322 223344556666666666666655544
No 36
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302. Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model.
Probab=74.06 E-value=11 Score=41.02 Aligned_cols=32 Identities=25% Similarity=0.577 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Q 022656 87 IKNLLEQVETLGEAGKVDEAEALMRKVEILNV 118 (294)
Q Consensus 87 I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 118 (294)
+..||..||+|.+.|..++|+.++.+++.+-+
T Consensus 570 Lq~Mmd~ieela~~G~~~~A~qlL~qlq~mme 601 (851)
T TIGR02302 570 LQNMMDQIENLARSGDRDQAKQLLSQLQQMMN 601 (851)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 77899999999999999999999999887754
No 37
>PRK03918 chromosome segregation protein; Provisional
Probab=73.65 E-value=40 Score=36.18 Aligned_cols=12 Identities=33% Similarity=0.847 Sum_probs=8.6
Q ss_pred cccccccccccc
Q 022656 142 ALCEICGSFLVA 153 (294)
Q Consensus 142 ~VCeVCGA~Ls~ 153 (294)
.||+|||.-|..
T Consensus 436 ~~Cp~c~~~L~~ 447 (880)
T PRK03918 436 GKCPVCGRELTE 447 (880)
T ss_pred CCCCCCCCcCCc
Confidence 578888877654
No 38
>PRK14154 heat shock protein GrpE; Provisional
Probab=72.62 E-value=13 Score=33.89 Aligned_cols=89 Identities=10% Similarity=0.069 Sum_probs=53.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCchH
Q 022656 79 QLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAE 158 (294)
Q Consensus 79 ~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~ 158 (294)
.+..|..+|..+-+++++| -+.-+.+.++.+.++.-.+.-.+ ...+..+..++-+||.+.|+-.
T Consensus 53 ~~~~l~~el~~le~e~~el-----kd~~lRl~ADfeNyRKR~~kE~e-----------~~~~~a~e~~~~~LLpVlDnLe 116 (208)
T PRK14154 53 SREKLEGQLTRMERKVDEY-----KTQYLRAQAEMDNLRKRIEREKA-----------DIIKFGSKQLITDLLPVADSLI 116 (208)
T ss_pred chhhHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhhHHhHHH
Confidence 3455666677777777766 24456666666666543222111 1234456667789999999999
Q ss_pred HHHhhhc------ccccccHHHHHHHHHHHH
Q 022656 159 RTQSHIS------GKQHIGYGMVRDFITEYK 183 (294)
Q Consensus 159 Rl~dH~~------GK~HlGy~kIRe~l~eL~ 183 (294)
|.-.|+. ..+.-|+.+|...|...-
T Consensus 117 RAL~~~~~~~~~~~~l~eGvemi~k~l~~vL 147 (208)
T PRK14154 117 HGLESPASEDPQVKSMRDGMSLTLDLLHNTL 147 (208)
T ss_pred HHHhcccccchhHHHHHHHHHHHHHHHHHHH
Confidence 9666653 235567766665555443
No 39
>PF13863 DUF4200: Domain of unknown function (DUF4200)
Probab=72.25 E-value=15 Score=29.75 Aligned_cols=51 Identities=18% Similarity=0.335 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 022656 41 FCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETL 97 (294)
Q Consensus 41 ~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~L 97 (294)
-+..||.+++.+..+|..+.++.. ........+|..|..+|..|-.++..|
T Consensus 50 ~f~~flken~~k~~rA~k~a~~e~------k~~~~k~~ei~~l~~~l~~l~~~~~k~ 100 (126)
T PF13863_consen 50 KFDKFLKENEAKRERAEKRAEEEK------KKKEEKEAEIKKLKAELEELKSEISKL 100 (126)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567788888888888887775432 122333444445554444444444433
No 40
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=71.95 E-value=11 Score=29.96 Aligned_cols=49 Identities=29% Similarity=0.397 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 77 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 77 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
..++..|..+-+.+.++|-.+...| +++..+++++..|+.+...++.++
T Consensus 42 ~~~~e~lr~~rN~~sk~I~~~~~~~--~~~~~l~~e~~~lk~~i~~le~~~ 90 (108)
T PF02403_consen 42 QQELEELRAERNELSKEIGKLKKAG--EDAEELKAEVKELKEEIKELEEQL 90 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCHTT--CCTHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhHHHHHHHHHhhCc--ccHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456677777777777777777777 667788888888888888887665
No 41
>PRK11115 transcriptional regulator PhoU; Provisional
Probab=69.34 E-value=55 Score=29.21 Aligned_cols=81 Identities=17% Similarity=0.065 Sum_probs=51.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhcccccccc--ccccccC
Q 022656 77 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEIC--GSFLVAN 154 (294)
Q Consensus 77 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVC--GA~Ls~~ 154 (294)
...|..+-+.+..++..+-..-..++++.|..+...-+.+......+.... -.. -.-..|.+. ..++.+.
T Consensus 125 ~~~l~~l~~~v~~~l~~a~~a~~~~d~~~a~~i~~~d~~Id~~~~~~~~~~-~~~-------l~~~~~~~~~~~~l~~i~ 196 (236)
T PRK11115 125 LVSLESLGRHTIQMLHDVLDAFARMDLDEAVRIYREDKKVDQEYEGIVRQL-MTY-------MMEDPRTIPSVLTVLWCA 196 (236)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH-HHH-------HHhCcccHHHHHHHHHHH
Confidence 355778888888888888888888999888877766555554433333222 000 011467765 3333366
Q ss_pred CchHHHHhhhc
Q 022656 155 DAAERTQSHIS 165 (294)
Q Consensus 155 D~d~Rl~dH~~ 165 (294)
..-+|++||..
T Consensus 197 ~~lERigDh~~ 207 (236)
T PRK11115 197 RSIERIGDRCQ 207 (236)
T ss_pred HHHHHHHHHHH
Confidence 67889999964
No 42
>PRK14147 heat shock protein GrpE; Provisional
Probab=69.17 E-value=15 Score=32.45 Aligned_cols=87 Identities=13% Similarity=0.134 Sum_probs=49.3
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCchHHHH
Q 022656 82 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAERTQ 161 (294)
Q Consensus 82 ~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~Rl~ 161 (294)
.+..+|..|.++++.|- +.-+.+.++.+.++.-. ..+. . ...+..+..++-.||.+.|+-.|.-
T Consensus 22 ~l~~~l~~l~~e~~elk-----d~~lR~~Ad~eN~rkR~---~kE~-e-------~~~~~a~~~~~~~lLpv~DnlerAl 85 (172)
T PRK14147 22 PLKAEVESLRSEIALVK-----ADALRERADLENQRKRI---ARDV-E-------QARKFANEKLLGELLPVFDSLDAGL 85 (172)
T ss_pred hHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHH---HHHH-H-------HHHHHHHHHHHHHHhhhhhHHHHHH
Confidence 34555555666666552 33345555555554321 1111 0 1234455677889999999999966
Q ss_pred hhhcc---cccccHHHHHHHHHHHHH
Q 022656 162 SHISG---KQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 162 dH~~G---K~HlGy~kIRe~l~eL~~ 184 (294)
.|... .++-|+.+|...|...-+
T Consensus 86 ~~~~~~~~~l~~Gv~mi~k~l~~~L~ 111 (172)
T PRK14147 86 TAAGTEPSPLRDGLELTYKQLLKVAA 111 (172)
T ss_pred hcccchHHHHHHHHHHHHHHHHHHHH
Confidence 66543 355677766666555433
No 43
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=68.35 E-value=10 Score=35.51 Aligned_cols=85 Identities=18% Similarity=0.168 Sum_probs=65.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHH--HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Q 022656 40 QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSV--LEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILN 117 (294)
Q Consensus 40 ~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~--l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk 117 (294)
.|-..|+..|.+-|...-.+++...+.....+... ..... ..++|..|.++|..|..+-+.-++++.+.++..|-
T Consensus 79 ~YE~e~~~~L~~~i~d~drrI~~~k~RL~~~~~~~---~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~ 155 (254)
T PF03194_consen 79 GYEREFLRYLQRLIRDCDRRIERAKERLEQTQEEQ---AKEADEEKAEKIDELDEKIGELLKEAEELGEEGDVDEAQKLM 155 (254)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcccc---ccchhhhHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
Confidence 48888999999999999999986543222111111 11112 28899999999999999988888899999999999
Q ss_pred HHHHHHHHhh
Q 022656 118 VEKTTLTQQS 127 (294)
Q Consensus 118 ~er~~l~~~~ 127 (294)
.+.+.|..+.
T Consensus 156 ~~~e~Lk~ek 165 (254)
T PF03194_consen 156 EEVEKLKEEK 165 (254)
T ss_pred HHHHHHHHHH
Confidence 9988888765
No 44
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=67.81 E-value=1.7 Score=32.40 Aligned_cols=26 Identities=23% Similarity=0.671 Sum_probs=19.0
Q ss_pred cccccccccc---------ccccCCchH-HHHhhhc
Q 022656 140 KMALCEICGS---------FLVANDAAE-RTQSHIS 165 (294)
Q Consensus 140 km~VCeVCGA---------~Ls~~D~d~-Rl~dH~~ 165 (294)
.-++|+|||. ||++.|++. =+|.-++
T Consensus 17 d~e~CP~Cgs~~~te~W~G~~iIidpe~SeIAkrlg 52 (64)
T COG2093 17 DTEICPVCGSTDLTEEWFGLLIIIDPEKSEIAKRLG 52 (64)
T ss_pred CCccCCCCCCcccchhhccEEEEEcCcHHHHHHHhC
Confidence 4478999998 578888887 3555444
No 45
>KOG1847 consensus mRNA splicing factor [RNA processing and modification]
Probab=67.75 E-value=5.4 Score=41.98 Aligned_cols=7 Identities=57% Similarity=0.994 Sum_probs=4.1
Q ss_pred ccccccc
Q 022656 165 SGKQHIG 171 (294)
Q Consensus 165 ~GK~HlG 171 (294)
+|+-||-
T Consensus 692 sg~R~l~ 698 (878)
T KOG1847|consen 692 SGKRHLH 698 (878)
T ss_pred CCCCcCc
Confidence 5666653
No 46
>PRK14141 heat shock protein GrpE; Provisional
Probab=66.93 E-value=20 Score=32.67 Aligned_cols=86 Identities=16% Similarity=0.183 Sum_probs=49.5
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCchHHHHh
Q 022656 83 LEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAERTQS 162 (294)
Q Consensus 83 l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~Rl~d 162 (294)
++.+|..|-+++++|- +.-+.+.++.+.++.-.+ .+. ....+..+..++-.||.+.|+-.|.-.
T Consensus 36 ~~~~i~~le~e~~elk-----d~~lR~~Ae~eN~RKR~~---kE~--------e~~~~~a~~~~~~dLLpViDnLerAl~ 99 (209)
T PRK14141 36 EPDPLEALKAENAELK-----DRMLRLAAEMENLRKRTQ---RDV--------ADARAYGIAGFARDMLSVSDNLRRALD 99 (209)
T ss_pred hHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHH---HHH--------HHHHHHHHHHHHHHHhhhHhHHHHHHh
Confidence 3444444444444441 334555556666653221 111 123455666778899999999999777
Q ss_pred hhcc-----------cccccHHHHHHHHHHHHH
Q 022656 163 HISG-----------KQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 163 H~~G-----------K~HlGy~kIRe~l~eL~~ 184 (294)
|+.. .++-|+.+|...|...-+
T Consensus 100 ~~~~~~~~~~~~~~~~l~eGv~mi~k~l~~vLe 132 (209)
T PRK14141 100 AIPAEARAAADAGLKALIEGVEMTERAMLNALE 132 (209)
T ss_pred ccccccccccchhHHHHHHHHHHHHHHHHHHHH
Confidence 7642 355677777666655443
No 47
>PRK10698 phage shock protein PspA; Provisional
Probab=66.21 E-value=74 Score=29.02 Aligned_cols=77 Identities=16% Similarity=0.149 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHH-------HHHH
Q 022656 40 QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEA-------LMRK 112 (294)
Q Consensus 40 ~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~-------l~~~ 112 (294)
..|..+|.+++.-+..++.=|+.. .+.......++..+...|...-.+|+.+...|+=+-|-. ...+
T Consensus 27 k~l~q~i~em~~~l~~~r~alA~~------~A~~k~~er~~~~~~~~~~~~e~kA~~Al~~G~EdLAr~AL~~K~~~~~~ 100 (222)
T PRK10698 27 KLVRLMIQEMEDTLVEVRSTSARA------LAEKKQLTRRIEQAEAQQVEWQEKAELALRKEKEDLARAALIEKQKLTDL 100 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 355666777776666665555432 122334567899999999999999999999999888877 5555
Q ss_pred HHHHHHHHHH
Q 022656 113 VEILNVEKTT 122 (294)
Q Consensus 113 ve~Lk~er~~ 122 (294)
+..|+.+.+.
T Consensus 101 ~~~l~~~~~~ 110 (222)
T PRK10698 101 IATLEHEVTL 110 (222)
T ss_pred HHHHHHHHHH
Confidence 5555555444
No 48
>PRK14160 heat shock protein GrpE; Provisional
Probab=66.14 E-value=34 Score=31.31 Aligned_cols=44 Identities=16% Similarity=0.058 Sum_probs=29.5
Q ss_pred hccccccccccccccCCchHHHHhhhc--ccccccHHHHHHHHHHH
Q 022656 139 KKMALCEICGSFLVANDAAERTQSHIS--GKQHIGYGMVRDFITEY 182 (294)
Q Consensus 139 qkm~VCeVCGA~Ls~~D~d~Rl~dH~~--GK~HlGy~kIRe~l~eL 182 (294)
.+..+..+.-.+|.+.|+-.|.-.|.. ..++-|+.+|...|...
T Consensus 106 ~~~a~e~~~~~LLpVlDnLerAl~~~~~~~~l~~Gv~mi~kql~~v 151 (211)
T PRK14160 106 YSDACEDVLKELLPVLDNLERAAAVEGSVEDLKKGIEMTVKQFKTS 151 (211)
T ss_pred HHHHHHHHHHHHhhHHhHHHHHHhcccchhHHHHHHHHHHHHHHHH
Confidence 455677788899999999999666532 23556766665554443
No 49
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=65.98 E-value=2 Score=38.88 Aligned_cols=28 Identities=25% Similarity=0.410 Sum_probs=0.0
Q ss_pred ccccccccccccccCCchHHHHhhhccccc
Q 022656 140 KMALCEICGSFLVANDAAERTQSHISGKQH 169 (294)
Q Consensus 140 km~VCeVCGA~Ls~~D~d~Rl~dH~~GK~H 169 (294)
+...|||||-+.-.+ -+=.+.||++--|
T Consensus 100 ~ey~CEICGN~~Y~G--rkaFekHF~E~rH 127 (196)
T PF11931_consen 100 VEYKCEICGNQSYKG--RKAFEKHFQEWRH 127 (196)
T ss_dssp ------------------------------
T ss_pred CeeeeEeCCCcceec--HHHHHHhcChhHH
Confidence 448999999987766 2338999999999
No 50
>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]
Probab=65.73 E-value=77 Score=29.19 Aligned_cols=82 Identities=18% Similarity=0.270 Sum_probs=62.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Q 022656 40 QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 119 (294)
Q Consensus 40 ~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 119 (294)
..|+..|.|++.-+..++.=+++.. ........++..+...+.++-.+++.+-..|+-+=|-.++.....|...
T Consensus 27 ~~l~Q~ird~~~~l~~ar~~~A~~~------a~~k~~e~~~~~~~~~~~k~e~~A~~Al~~g~E~LAr~al~~~~~le~~ 100 (225)
T COG1842 27 KMLEQAIRDMESELAKARQALAQAI------ARQKQLERKLEEAQARAEKLEEKAELALQAGNEDLAREALEEKQSLEDL 100 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 7788889988888888887776532 2344566789999999999999999999999988777777777776666
Q ss_pred HHHHHHhh
Q 022656 120 KTTLTQQS 127 (294)
Q Consensus 120 r~~l~~~~ 127 (294)
...+...+
T Consensus 101 ~~~~~~~~ 108 (225)
T COG1842 101 AKALEAEL 108 (225)
T ss_pred HHHHHHHH
Confidence 55554433
No 51
>PRK14155 heat shock protein GrpE; Provisional
Probab=65.28 E-value=19 Score=32.81 Aligned_cols=88 Identities=18% Similarity=0.146 Sum_probs=52.0
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCchHHH
Q 022656 81 SVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAERT 160 (294)
Q Consensus 81 ~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~Rl 160 (294)
..+..+|..+.+++++| -+..+.+.++.+.++.--+.-.+ ...+..+=.++-.||.+.|+-.|-
T Consensus 16 ~~l~~~l~~le~e~~el-----kd~~lR~~AefeN~RKR~~kE~e-----------~~~~~a~~~~~~~LLpV~DnLerA 79 (208)
T PRK14155 16 DDAAQEIEALKAEVAAL-----KDQALRYAAEAENTKRRAEREMN-----------DARAYAIQKFARDLLGAADNLGRA 79 (208)
T ss_pred cchHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhhHHhhHHHH
Confidence 45555666666666655 24456666666666532221111 112333344567889999999997
Q ss_pred Hhhhc--------ccccccHHHHHHHHHHHHH
Q 022656 161 QSHIS--------GKQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 161 ~dH~~--------GK~HlGy~kIRe~l~eL~~ 184 (294)
-.|+. ..++.|+.+|...|..+-+
T Consensus 80 l~~~~~~~~~~~~~~i~~Gvemi~k~~~~~L~ 111 (208)
T PRK14155 80 TAASPKDSADPAVKNFIIGVEMTEKELLGAFE 111 (208)
T ss_pred HhcccccccchHHHHHHHHHHHHHHHHHHHHH
Confidence 77764 2456788777766655444
No 52
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=64.93 E-value=11 Score=39.42 Aligned_cols=10 Identities=20% Similarity=0.345 Sum_probs=4.3
Q ss_pred HHHHHHHHHH
Q 022656 46 VMDLDRRVRR 55 (294)
Q Consensus 46 I~d~dRkI~~ 55 (294)
+.-|.||-++
T Consensus 171 ~~hcqrk~~~ 180 (757)
T KOG4368|consen 171 LHHCQRKQAR 180 (757)
T ss_pred HHHHHHHHHH
Confidence 3334444433
No 53
>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].
Probab=64.88 E-value=82 Score=26.26 Aligned_cols=70 Identities=27% Similarity=0.326 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 022656 36 AELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEI 115 (294)
Q Consensus 36 ~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~ 115 (294)
.-++..|..-|..++--|...+..|+. ...+-+.+.++|-.|+.+.+.+ .....++..
T Consensus 15 ~~~ve~L~s~lr~~E~E~~~l~~el~~-------------l~~~r~~l~~Eiv~l~~~~e~~---------~~~~~~~~~ 72 (120)
T PF12325_consen 15 VQLVERLQSQLRRLEGELASLQEELAR-------------LEAERDELREEIVKLMEENEEL---------RALKKEVEE 72 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHH
Confidence 346777888888888888888777752 2344456677777777777766 334444555
Q ss_pred HHHHHHHHHHhh
Q 022656 116 LNVEKTTLTQQS 127 (294)
Q Consensus 116 Lk~er~~l~~~~ 127 (294)
|+.+.+.|...+
T Consensus 73 L~~el~~l~~ry 84 (120)
T PF12325_consen 73 LEQELEELQQRY 84 (120)
T ss_pred HHHHHHHHHHHH
Confidence 555555555444
No 54
>COG3783 CybC Soluble cytochrome b562 [Energy production and conversion]
Probab=64.79 E-value=51 Score=26.71 Aligned_cols=26 Identities=23% Similarity=0.399 Sum_probs=21.8
Q ss_pred HHHHHHhcCCHHHHHHHHHHHHHHHH
Q 022656 93 QVETLGEAGKVDEAEALMRKVEILNV 118 (294)
Q Consensus 93 eaE~LGeeG~VdeA~~l~~~ve~Lk~ 118 (294)
++.+|..+|++++|.+...++..+..
T Consensus 68 ~a~klaqeGnl~eAKaaak~l~d~Rn 93 (100)
T COG3783 68 KADKLAQEGNLDEAKAAAKTLKDTRN 93 (100)
T ss_pred HHHHHHHcCChHHHHHHHHHHHHHHH
Confidence 67789999999999998888777653
No 55
>PRK14146 heat shock protein GrpE; Provisional
Probab=64.72 E-value=23 Score=32.40 Aligned_cols=46 Identities=22% Similarity=0.166 Sum_probs=32.0
Q ss_pred hccccccccccccccCCchHHHHhhhc-----ccccccHHHHHHHHHHHHH
Q 022656 139 KKMALCEICGSFLVANDAAERTQSHIS-----GKQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 139 qkm~VCeVCGA~Ls~~D~d~Rl~dH~~-----GK~HlGy~kIRe~l~eL~~ 184 (294)
.+..+..++-.||.+.|+-.|.-.|+. ..++-|+.+|...|...-+
T Consensus 99 ~~~a~e~~~~~lLpv~DnlerAl~~~~~~~~~~~l~~Gv~mi~k~l~~~L~ 149 (215)
T PRK14146 99 RKEAVKSLVSGFLNPIDNLERVGATQNQSEELKPFVEGVKMILKEFYSVLE 149 (215)
T ss_pred HHHHHHHHHHHHhhHHhHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHH
Confidence 455677788999999999999766753 2245677666665554433
No 56
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=64.65 E-value=16 Score=28.40 Aligned_cols=13 Identities=31% Similarity=0.685 Sum_probs=10.4
Q ss_pred ccccccccccccc
Q 022656 141 MALCEICGSFLVA 153 (294)
Q Consensus 141 m~VCeVCGA~Ls~ 153 (294)
..+|.|||-.|..
T Consensus 78 ~~~C~vC~k~l~~ 90 (109)
T PF10367_consen 78 STKCSVCGKPLGN 90 (109)
T ss_pred CCCccCcCCcCCC
Confidence 3679999998764
No 57
>PF02151 UVR: UvrB/uvrC motif; InterPro: IPR001943 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. UvrB and UvrC share a common domain of around 35 amino acids, the so called UVR domain. This domain in UvrB can interact with the homologous domain in UvrC throughout a putative coiled coil structure. This interaction is important for the incision of the damaged strand [].; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3PXG_D 3PXI_C 1E52_B 1QOJ_B 2D7D_B 2NMV_B.
Probab=64.15 E-value=24 Score=22.87 Aligned_cols=35 Identities=26% Similarity=0.332 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Q 022656 85 EKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 119 (294)
Q Consensus 85 ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 119 (294)
+.|..|..+.+.+.+..+.++|..+=.++..|+.+
T Consensus 2 ~~i~~l~~~m~~a~~~~dfE~Aa~~Rd~i~~l~~q 36 (36)
T PF02151_consen 2 KLIKELEEKMEEAVENEDFEKAARLRDQIKALKKQ 36 (36)
T ss_dssp HHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHcC
Confidence 56888889999999999999999998888888753
No 58
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=63.12 E-value=11 Score=33.18 Aligned_cols=39 Identities=23% Similarity=0.673 Sum_probs=29.0
Q ss_pred ccccccccccccCCchHHHHhhhcccccccHHHHHHHHHHHH
Q 022656 142 ALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYK 183 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eL~ 183 (294)
.-||-|-.|| .+|+..=--.|.+|+.|+-- ++..+.+..
T Consensus 4 YyCDYCdt~L-thDslsvRK~H~~GrkH~~n--vk~YY~k~~ 42 (165)
T KOG3454|consen 4 YYCDYCDTYL-THDSLSVRKTHCGGRKHKDN--VKDYYQKWM 42 (165)
T ss_pred chhhhhhhhh-hcccHHHHHhhhhhHHHHHH--HHHHHHHHH
Confidence 4699999998 57888888999999999753 233444443
No 59
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=61.30 E-value=13 Score=33.01 Aligned_cols=71 Identities=20% Similarity=0.288 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhcccccccccccc-ccCCch
Q 022656 79 QLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFL-VANDAA 157 (294)
Q Consensus 79 ~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~L-s~~D~d 157 (294)
.|..+..+|..|--+|+.|-.+++-...+.+..+++.|+-|..++..+. ....|+.|-+|=--| .++|.+
T Consensus 106 eL~s~~~ei~~L~~kI~~L~~~in~~~k~~~n~~i~slk~EL~d~iKe~---------e~~emeLyyecMkkL~~a~~~e 176 (181)
T PF04645_consen 106 ELKSIKKEIEILRLKISSLQKEINKNKKKDLNEEIESLKSELNDLIKER---------EIREMELYYECMKKLAKAHEVE 176 (181)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHhhhhhhh
Confidence 4556666777777777777777666666666666777777766665543 235677777776666 455555
Q ss_pred H
Q 022656 158 E 158 (294)
Q Consensus 158 ~ 158 (294)
.
T Consensus 177 s 177 (181)
T PF04645_consen 177 S 177 (181)
T ss_pred h
Confidence 4
No 60
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=61.12 E-value=4.8 Score=28.42 Aligned_cols=12 Identities=33% Similarity=0.789 Sum_probs=6.2
Q ss_pred cccccccccccC
Q 022656 143 LCEICGSFLVAN 154 (294)
Q Consensus 143 VCeVCGA~Ls~~ 154 (294)
+|+|||.-|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 999999876543
No 61
>PRK14139 heat shock protein GrpE; Provisional
Probab=60.74 E-value=39 Score=30.28 Aligned_cols=92 Identities=17% Similarity=0.143 Sum_probs=55.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCc
Q 022656 77 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDA 156 (294)
Q Consensus 77 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~ 156 (294)
..++..+..+|..+-+++++|- +.-+.+.++.+.++.-...-... ..+..+=.++-.||.+.|+
T Consensus 31 ~~e~~~l~~~l~~le~e~~elk-----d~~lR~~AefeN~rKR~~kE~e~-----------~~~~a~~~~~~~LLpv~Dn 94 (185)
T PRK14139 31 EDAAPALEAELAEAEAKAAELQ-----DSFLRAKAETENVRRRAQEDVAK-----------AHKFAIESFAESLLPVKDS 94 (185)
T ss_pred chhHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHhhHHhH
Confidence 3457778888888888888873 45566666666665322211111 1222333345678889999
Q ss_pred hHHHHhhhc---ccccccHHHHHHHHHHHHH
Q 022656 157 AERTQSHIS---GKQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 157 d~Rl~dH~~---GK~HlGy~kIRe~l~eL~~ 184 (294)
-.|.-.|.. ..+.-|+.+|...|..+-+
T Consensus 95 LerAl~~~~~~~~~l~~Gv~mi~k~l~~vL~ 125 (185)
T PRK14139 95 LEAALADESGDLEKLREGVELTLKQLTSAFE 125 (185)
T ss_pred HHHHHhcccchHHHHHHHHHHHHHHHHHHHH
Confidence 999656654 3456677777766655443
No 62
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=60.21 E-value=75 Score=27.37 Aligned_cols=112 Identities=19% Similarity=0.181 Sum_probs=60.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHH-HHHHHHHHHHHHHHHHHHHhcCCHH-----H--HHHH
Q 022656 38 LAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQ-LSVLEEKIKNLLEQVETLGEAGKVD-----E--AEAL 109 (294)
Q Consensus 38 ~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~-i~~l~ekI~~ll~eaE~LGeeG~Vd-----e--A~~l 109 (294)
+...++.=...++.-|..+++.+.... ..+.+.... ..-|..-|..+....+.+...-.++ + ...|
T Consensus 5 l~e~~~~~~~~L~~~le~a~e~~~~~~------elT~eEl~lv~~ylkRDl~~~a~~~~~~~~~~~~~~~lie~slw~~L 78 (146)
T PF07295_consen 5 LEEALEHSEEELQEALEKAKEYLVAAG------ELTREELALVSAYLKRDLEEFARYYEELREWLSPDLQLIEESLWDEL 78 (146)
T ss_pred HHHHHhcCHHHHHHHHHHHHHHHHHHh------hcCHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccHHHHHHHHHHHH
Confidence 344555666777888888888885432 122222222 2233444444444444422222221 1 2456
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhh---hhhhhhhccccccccccccccCCc
Q 022656 110 MRKVEILNVEKTTLTQQSQNDKV---LMMAQEKKMALCEICGSFLVANDA 156 (294)
Q Consensus 110 ~~~ve~Lk~er~~l~~~~~~~~~---~~~~~~qkm~VCeVCGA~Ls~~D~ 156 (294)
+.-+++.+.+..+|.+.+ .... +|.-.....-||.-||.-+....+
T Consensus 79 ~~ItDkTqvEw~el~~d~-~h~g~Y~sGE~~g~G~l~C~~Cg~~~~~~~~ 127 (146)
T PF07295_consen 79 SSITDKTQVEWAELAQDL-EHHGVYHSGEVVGPGTLVCENCGHEVELTHP 127 (146)
T ss_pred HhhhchhHHHHHHHHHHH-HhcCCeecCcEecCceEecccCCCEEEecCC
Confidence 666777777777777665 2211 112223467899999988777654
No 63
>PRK10884 SH3 domain-containing protein; Provisional
Probab=59.77 E-value=74 Score=28.89 Aligned_cols=54 Identities=20% Similarity=0.225 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 022656 42 CEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETL 97 (294)
Q Consensus 42 L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~L 97 (294)
+...|-.++..+...+..|++... .......+.++.+...+..|..|.++-.+|
T Consensus 91 ~~~rlp~le~el~~l~~~l~~~~~--~~~~~~~~l~~~~~~~~~~~~~L~~~n~~L 144 (206)
T PRK10884 91 LRTRVPDLENQVKTLTDKLNNIDN--TWNQRTAEMQQKVAQSDSVINGLKEENQKL 144 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556677777777777764321 112233444555556666666655555555
No 64
>PF01895 PhoU: PhoU domain; InterPro: IPR008170 This family contains phosphate regulatory proteins including PhoU. PhoU proteins are known to play a role in the regulation of phosphate uptake. The PhoU domain is composed of a three helix bundle []. The PhoU protein contains two copies of this domain. The domain binds to an iron cluster via its conserved E/DXXXD motif. Deletion of PhoU activates constitutive expression of the phosphate ABC transporter and allows phosphate transport, but causes a growth defect; suggesting that the protein has some secondary function []. ; PDB: 2I0M_A 1T72_B 1T8B_A 1SUM_B 1VCT_A 2BKN_A 2BKP_A 2BKO_A.
Probab=59.41 E-value=34 Score=24.85 Aligned_cols=82 Identities=13% Similarity=0.126 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCchHH
Q 022656 80 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAER 159 (294)
Q Consensus 80 i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~R 159 (294)
|..+.+.+..++..+-.+-..++.+.|..+...-+.+......+.... -.. ....+.+.-=.-+-.++.+..+-.|
T Consensus 1 i~~m~~~~~~~l~~~~~~~~~~d~~~a~~i~~~e~~id~~~~~~~~~~-~~~---~~~~~~~~~~~~~~~~~~i~~~lER 76 (88)
T PF01895_consen 1 ISEMGELVEEMLDDAIEAFEERDSELAQEIIQLEEEIDELYREIRRQI-LKI---LKNQNPLEELRELVGLLRIARDLER 76 (88)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHH-HHH---HHHHCGHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhHHHHHHHHHHHHHHH-HHH---HhhCCCHHHHHHHHHHHHHHHHHHH
Confidence 456777788888888888888888777666655555544444443332 110 0001111000113445666677888
Q ss_pred HHhhhc
Q 022656 160 TQSHIS 165 (294)
Q Consensus 160 l~dH~~ 165 (294)
++||..
T Consensus 77 igD~~~ 82 (88)
T PF01895_consen 77 IGDHAV 82 (88)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 888864
No 65
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=59.41 E-value=9 Score=37.40 Aligned_cols=18 Identities=11% Similarity=0.257 Sum_probs=12.5
Q ss_pred ccccHHHHHHHHHHHHHH
Q 022656 168 QHIGYGMVRDFITEYKEA 185 (294)
Q Consensus 168 ~HlGy~kIRe~l~eL~~~ 185 (294)
--.-|..|..+++.++.+
T Consensus 232 ~~p~~~li~~~vd~~k~~ 249 (367)
T KOG0835|consen 232 AKPDETLIEAFVDRLKRK 249 (367)
T ss_pred cccCHHHHHHHHHHhhHH
Confidence 335577788888887764
No 66
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=59.24 E-value=3.5 Score=36.65 Aligned_cols=32 Identities=31% Similarity=0.619 Sum_probs=24.8
Q ss_pred hhhhhccccccccccccccCCchHHHHhhhccccc
Q 022656 135 MAQEKKMALCEICGSFLVANDAAERTQSHISGKQH 169 (294)
Q Consensus 135 ~~~~qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~H 169 (294)
+..++--.-|+||-+ ++-|+-+ .-||++||.|
T Consensus 69 p~sq~~GyyCdVCdc--vvKDSin-flDHiNgKkH 100 (193)
T KOG4727|consen 69 PRSQKGGYYCDVCDC--VVKDSIN-FLDHINGKKH 100 (193)
T ss_pred cccccCceeeeecce--eehhhHH-HHHHhccHHH
Confidence 345666689999995 4777765 4489999999
No 67
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=58.68 E-value=44 Score=32.02 Aligned_cols=17 Identities=18% Similarity=0.210 Sum_probs=13.1
Q ss_pred hHHHHHHHHHHHHHHHH
Q 022656 33 KFEAELAQFCEKLVMDL 49 (294)
Q Consensus 33 ~YE~e~l~~L~~lI~d~ 49 (294)
++|-.+..+|..|+.++
T Consensus 97 ~r~p~w~~~L~alla~~ 113 (308)
T COG3058 97 PREPHWRKLLMALLAEL 113 (308)
T ss_pred CCCcHHHHHHHHHHHhc
Confidence 77778888888888654
No 68
>PRK01156 chromosome segregation protein; Provisional
Probab=58.56 E-value=37 Score=36.80 Aligned_cols=16 Identities=25% Similarity=0.717 Sum_probs=12.5
Q ss_pred ccccccccccccccCC
Q 022656 140 KMALCEICGSFLVAND 155 (294)
Q Consensus 140 km~VCeVCGA~Ls~~D 155 (294)
.--||+|||.-+--.=
T Consensus 451 ~~~~Cp~c~~~~~~e~ 466 (895)
T PRK01156 451 GQSVCPVCGTTLGEEK 466 (895)
T ss_pred cCCCCCCCCCcCChhh
Confidence 4589999999887444
No 69
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=58.32 E-value=65 Score=26.00 Aligned_cols=14 Identities=29% Similarity=0.636 Sum_probs=10.7
Q ss_pred hccccccccccccc
Q 022656 139 KKMALCEICGSFLV 152 (294)
Q Consensus 139 qkm~VCeVCGA~Ls 152 (294)
-...+|+.||..+.
T Consensus 78 g~yG~C~~Cge~I~ 91 (110)
T TIGR02420 78 GEYGYCEECGEEIG 91 (110)
T ss_pred CCCCchhccCCccc
Confidence 34579999998764
No 70
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=58.00 E-value=5.8 Score=35.11 Aligned_cols=34 Identities=26% Similarity=0.418 Sum_probs=26.4
Q ss_pred ccccccccccccccCCchHHHHhhhcccccccHHHHHHHHHHHHHH
Q 022656 140 KMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKEA 185 (294)
Q Consensus 140 km~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eL~~~ 185 (294)
--+.|++||..|.-.||..-+. .|.+.+++|++.
T Consensus 135 ~~F~Cp~Cg~~L~~~dn~~~~~------------~l~~~I~~l~~~ 168 (178)
T PRK06266 135 YGFRCPQCGEMLEEYDNSELIK------------ELKEQIKELEEE 168 (178)
T ss_pred cCCcCCCCCCCCeecccHHHHH------------HHHHHHHHHHHH
Confidence 4599999999999999887653 566777777654
No 71
>PF00435 Spectrin: Spectrin repeat; InterPro: IPR002017 Spectrin repeats [] are found in several proteins involved in cytoskeletal structure. These include spectrin alpha and beta subunits [, ], alpha-actinin [] and dystrophin. The spectrin repeat forms a three-helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.; GO: 0005515 protein binding; PDB: 1HCI_A 1QUU_A 3FB2_B 1S35_A 1U5P_A 1U4Q_A 1CUN_B 1YDI_B 3EDV_A 1AJ3_A ....
Probab=57.77 E-value=74 Score=23.40 Aligned_cols=83 Identities=19% Similarity=0.240 Sum_probs=49.0
Q ss_pred HHHHHHHHHHHHHHHHhhhhcCCCCCCCCCc-------hhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 022656 43 EKLVMDLDRRVRRGRERLSQEVEPAPPPPIS-------AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEI 115 (294)
Q Consensus 43 ~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~-------~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~ 115 (294)
..-+.++..=|......|.... .+...... ......|......|..+...+..| ....-..+..+...++.
T Consensus 7 ~~~~~~l~~Wl~~~e~~l~~~~-~~~~~~~~~~~~~~~~~~~~ei~~~~~~l~~l~~~~~~L-~~~~~~~~~~i~~~~~~ 84 (105)
T PF00435_consen 7 QQEADELLDWLQETEAKLSSSE-PGSDLEELEEQLKKHKELQEEIESRQERLESLNEQAQQL-IDSGPEDSDEIQEKLEE 84 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHCSCT-HSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHTTHTTHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhCCC-CCCCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHH-HHcCCCcHHHHHHHHHH
Confidence 4455566666777777773211 00000111 112344666677777777777778 44446677788888888
Q ss_pred HHHHHHHHHHhh
Q 022656 116 LNVEKTTLTQQS 127 (294)
Q Consensus 116 Lk~er~~l~~~~ 127 (294)
|......|...+
T Consensus 85 l~~~w~~l~~~~ 96 (105)
T PF00435_consen 85 LNQRWEALCELV 96 (105)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 888777776654
No 72
>PRK14161 heat shock protein GrpE; Provisional
Probab=57.13 E-value=46 Score=29.59 Aligned_cols=88 Identities=16% Similarity=0.209 Sum_probs=49.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCchH
Q 022656 79 QLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAE 158 (294)
Q Consensus 79 ~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~ 158 (294)
-+..+.++|..|-+++++|- +..+.+.++.+.++.--+.-. ....+..+=.++..+|.+.|+-.
T Consensus 20 ~~~~~~~ei~~l~~e~~elk-----d~~lR~~AefeN~rkR~~ke~-----------~~~~~~a~~~~~~~LLpv~Dnle 83 (178)
T PRK14161 20 IVETANPEITALKAEIEELK-----DKLIRTTAEIDNTRKRLEKAR-----------DEAKDYAIATFAKELLNVSDNLS 83 (178)
T ss_pred hhhhhHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhhHHhHHH
Confidence 34455556666666666652 444555555555543221111 11233444556788999999999
Q ss_pred HHHhhhcc-------cccccHHHHHHHHHHH
Q 022656 159 RTQSHISG-------KQHIGYGMVRDFITEY 182 (294)
Q Consensus 159 Rl~dH~~G-------K~HlGy~kIRe~l~eL 182 (294)
|--.|... .+.-|+.+|...+...
T Consensus 84 rAl~~~~~~~~~~~~~~~~Gv~mi~k~l~~v 114 (178)
T PRK14161 84 RALAHKPANSDVEVTNIIAGVQMTKDELDKV 114 (178)
T ss_pred HHHhcCccccchhHHHHHHHHHHHHHHHHHH
Confidence 96667542 3556776665555443
No 73
>KOG1847 consensus mRNA splicing factor [RNA processing and modification]
Probab=57.09 E-value=14 Score=39.03 Aligned_cols=14 Identities=29% Similarity=0.435 Sum_probs=6.9
Q ss_pred HHHHHhcCCHHHHH
Q 022656 94 VETLGEAGKVDEAE 107 (294)
Q Consensus 94 aE~LGeeG~VdeA~ 107 (294)
.|+|..+|+-..-|
T Consensus 637 ~eKLaqe~k~k~lq 650 (878)
T KOG1847|consen 637 EEKLAQEGKSKRLQ 650 (878)
T ss_pred HHHHHhhhhHHHHH
Confidence 35565555544333
No 74
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=56.76 E-value=53 Score=29.27 Aligned_cols=79 Identities=18% Similarity=0.294 Sum_probs=46.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Q 022656 39 AQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNV 118 (294)
Q Consensus 39 l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 118 (294)
+.-|+.=|..+..+|...+..|+....+......-....+++..|..++..|.++.+.+.. .+.+.-..+...+..++.
T Consensus 71 ~~~l~~~~~~~~~~i~~l~~~i~~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el~~~~~-~Dp~~i~~~~~~~~~~~~ 149 (188)
T PF03962_consen 71 LEKLQKEIEELEKKIEELEEKIEEAKKGREESEEREELLEELEELKKELKELKKELEKYSE-NDPEKIEKLKEEIKIAKE 149 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCHHHHHHHHHHHHHHHH
Confidence 4455555666666777777777644321222222334567788899999999999887655 344444444444444443
No 75
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=55.26 E-value=6.7 Score=26.12 Aligned_cols=32 Identities=22% Similarity=0.441 Sum_probs=17.0
Q ss_pred ccccccccccccCCchHHHHhhhcccccccHHH
Q 022656 142 ALCEICGSFLVANDAAERTQSHISGKQHIGYGM 174 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~k 174 (294)
.-||.|..||. +|+..=...|..|..|..-++
T Consensus 4 yyCdyC~~~~~-~d~~~~Rk~H~~G~kH~~nv~ 35 (38)
T PF06220_consen 4 YYCDYCKKYLT-HDSPSIRKQHERGWKHKENVK 35 (38)
T ss_dssp -B-TTT--B-S---SHHHHHHHT--THHHHHHH
T ss_pred eecccccceec-CCChHHHHHhhccHHHHHHHH
Confidence 57999999964 445544588999999986443
No 76
>PF12854 PPR_1: PPR repeat
Probab=54.24 E-value=16 Score=23.06 Aligned_cols=20 Identities=35% Similarity=0.513 Sum_probs=17.1
Q ss_pred HHHHHHhcCCHHHHHHHHHH
Q 022656 93 QVETLGEAGKVDEAEALMRK 112 (294)
Q Consensus 93 eaE~LGeeG~VdeA~~l~~~ 112 (294)
-|..+...|+|++|..++.+
T Consensus 13 lI~~~Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 13 LIDGYCKAGRVDEAFELFDE 32 (34)
T ss_pred HHHHHHHCCCHHHHHHHHHh
Confidence 46678999999999999865
No 77
>PRK03954 ribonuclease P protein component 4; Validated
Probab=54.17 E-value=31 Score=28.91 Aligned_cols=66 Identities=20% Similarity=0.259 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCc-hHHHH
Q 022656 84 EEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDA-AERTQ 161 (294)
Q Consensus 84 ~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~-d~Rl~ 161 (294)
.+.|+-|++.|+.+.. ++-+-|-..+..+..+-.. . ....+++-+-.+|.-|.+||+.+-| --||.
T Consensus 19 ~eRi~~L~~~A~~~~~-~~pelar~Yv~lar~Is~K-------~----rirlp~~~KR~~CK~C~t~LiPG~n~~vRi~ 85 (121)
T PRK03954 19 RERIDTLFTLAERVFP-YSPELANRYVELALAVQQK-------A----KVKLPRKWKRRYCKRCHSFLVPGVNARVRLR 85 (121)
T ss_pred HHHHHHHHHHHHHHhh-cCHHHHHHHHHHHHHHHHH-------h----ccCCCHHHHHHHhhcCCCeeecCCceEEEEe
Confidence 4778888888877763 3556666655555444211 1 1123456788999999999998754 33444
No 78
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=53.72 E-value=6.9 Score=33.90 Aligned_cols=21 Identities=29% Similarity=0.403 Sum_probs=17.8
Q ss_pred ccccccccccccccCCchHHH
Q 022656 140 KMALCEICGSFLVANDAAERT 160 (294)
Q Consensus 140 km~VCeVCGA~Ls~~D~d~Rl 160 (294)
--+.|++||+.|.-.||..-+
T Consensus 127 ~~F~Cp~Cg~~L~~~dn~~~i 147 (158)
T TIGR00373 127 LNFTCPRCGAMLDYLDNSEAI 147 (158)
T ss_pred cCCcCCCCCCEeeeccCHHHH
Confidence 459999999999999987654
No 79
>PRK14153 heat shock protein GrpE; Provisional
Probab=52.95 E-value=38 Score=30.57 Aligned_cols=89 Identities=17% Similarity=0.170 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCchHH
Q 022656 80 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAER 159 (294)
Q Consensus 80 i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~R 159 (294)
+..++.+|..+.++++.| -+.-+.+.++.+.++.-.+.-... ..+..+=.++-.||.+.|+-.|
T Consensus 35 ~~~~~~ei~~l~~e~~el-----kd~~lR~~AEfeN~rKR~~kE~e~-----------~~~~a~~~~~~~LLpv~DnLer 98 (194)
T PRK14153 35 DSTADSETEKCREEIESL-----KEQLFRLAAEFDNFRKRTAREMEE-----------NRKFVLEQVLLDLLEVTDNFER 98 (194)
T ss_pred cccchHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHhhHHhHHHH
Confidence 445666666666666666 234455555555554322211111 1222333455788999999999
Q ss_pred HHhhhc-----ccccccHHHHHHHHHHHHH
Q 022656 160 TQSHIS-----GKQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 160 l~dH~~-----GK~HlGy~kIRe~l~eL~~ 184 (294)
.-+|+. ..++.|+.+|...|..+-+
T Consensus 99 Al~~~~~~~~~~~l~~Gvemi~k~~~~vL~ 128 (194)
T PRK14153 99 ALESARTAEDMNSIVEGIEMVSKQFFSILE 128 (194)
T ss_pred HHhcccccchHHHHHHHHHHHHHHHHHHHH
Confidence 766653 2456777777666655443
No 80
>PRK14150 heat shock protein GrpE; Provisional
Probab=52.88 E-value=40 Score=30.28 Aligned_cols=46 Identities=17% Similarity=0.138 Sum_probs=32.0
Q ss_pred hccccccccccccccCCchHHHHhhhcc------cccccHHHHHHHHHHHHH
Q 022656 139 KKMALCEICGSFLVANDAAERTQSHISG------KQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 139 qkm~VCeVCGA~Ls~~D~d~Rl~dH~~G------K~HlGy~kIRe~l~eL~~ 184 (294)
++..+..++-.||.+.|+-.|.-.|... .++-|+.+|...|...-+
T Consensus 83 ~~~a~~~~~~~lL~v~DnlerAl~~~~~~~~~~~~~~~Gv~mi~~~l~~~L~ 134 (193)
T PRK14150 83 HKFALEKFANELLPVIDNLERALQAADKENEALKALIEGVELTLKSLLDTVA 134 (193)
T ss_pred HHHHHHHHHHHHHhHHhHHHHHHhcccccchhHHHHHHHHHHHHHHHHHHHH
Confidence 4556667788999999999996566532 356677777766655443
No 81
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=52.84 E-value=65 Score=34.52 Aligned_cols=20 Identities=30% Similarity=0.506 Sum_probs=16.5
Q ss_pred hhhccccccccccccccCCc
Q 022656 137 QEKKMALCEICGSFLVANDA 156 (294)
Q Consensus 137 ~~qkm~VCeVCGA~Ls~~D~ 156 (294)
..-.+.-||.||+-.+++|-
T Consensus 674 ~etRqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 674 YETRQRKCPKCNAAFGANDV 693 (698)
T ss_pred HHHhcCCCCCCCCCCCcccc
Confidence 45577999999999999883
No 82
>PF10475 DUF2450: Protein of unknown function N-terminal domain (DUF2450) ; InterPro: IPR019515 This entry represents Vacuolar protein sorting-associated protein 54, and is thought to be involved in retrograde transport from early and late endosomes to late Golgi found in eukaryotes, but its function is not known.
Probab=52.55 E-value=1.2e+02 Score=28.55 Aligned_cols=80 Identities=16% Similarity=0.099 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCC-Cch----------hhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHH
Q 022656 39 AQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPP-ISA----------EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAE 107 (294)
Q Consensus 39 l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~-~~~----------~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~ 107 (294)
+.-|+.-+..+-..|..+++.|....+...... ... .....|..+ ..|..+...++.|-++|+..+|+
T Consensus 69 v~el~~~l~~a~~~~~~~R~~L~~~~~~~~~~~L~Il~~~rkr~~l~~ll~~L~~i-~~v~~~~~~l~~ll~~~dy~~Al 147 (291)
T PF10475_consen 69 VQELQDELEEALVICKNLRRNLKSADENLTKSGLEILRLQRKRQNLKKLLEKLEQI-KTVQQTQSRLQELLEEGDYPGAL 147 (291)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhcCCHHHHH
Confidence 445555666666677777777764321110000 000 011112222 34556677888999999999999
Q ss_pred HHHHHHHHHHHH
Q 022656 108 ALMRKVEILNVE 119 (294)
Q Consensus 108 ~l~~~ve~Lk~e 119 (294)
.++.++..+-.+
T Consensus 148 ~li~~~~~~l~~ 159 (291)
T PF10475_consen 148 DLIEECQQLLEE 159 (291)
T ss_pred HHHHHHHHHHHh
Confidence 999999988654
No 83
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=52.53 E-value=5.2 Score=26.39 Aligned_cols=16 Identities=38% Similarity=0.719 Sum_probs=12.0
Q ss_pred hhhccccccccccccc
Q 022656 137 QEKKMALCEICGSFLV 152 (294)
Q Consensus 137 ~~qkm~VCeVCGA~Ls 152 (294)
+-+.-.||++||.-|+
T Consensus 17 pP~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 17 PPKVEGVCDNCGGELV 32 (36)
T ss_dssp --SSTTBCTTTTEBEB
T ss_pred CCCCCCccCCCCCeeE
Confidence 3466789999999776
No 84
>PF10458 Val_tRNA-synt_C: Valyl tRNA synthetase tRNA binding arm; InterPro: IPR019499 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the C-terminal domain of Valyl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IVS_B 1GAX_B.
Probab=52.46 E-value=58 Score=23.84 Aligned_cols=59 Identities=29% Similarity=0.416 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhcC-CCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHH
Q 022656 40 QFCEKLVMDLDRRVRRGRERLSQEV-EPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLG 98 (294)
Q Consensus 40 ~~L~~lI~d~dRkI~~~k~RL~~~~-e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LG 98 (294)
.-|++=+..+...|.....+|.... -...|+.......+++..+..+|..+...++.|+
T Consensus 7 ~rL~Kel~kl~~~i~~~~~kL~n~~F~~kAP~eVve~er~kl~~~~~~~~~l~~~l~~Lk 66 (66)
T PF10458_consen 7 ERLEKELEKLEKEIERLEKKLSNENFVEKAPEEVVEKEREKLEELEEELEKLEEALEQLK 66 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCSTTHHHHS-CCHHHHHHHHHHHHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4466777788888999999996321 0012233455566789999999999988888774
No 85
>PRK14140 heat shock protein GrpE; Provisional
Probab=51.43 E-value=47 Score=29.88 Aligned_cols=92 Identities=20% Similarity=0.167 Sum_probs=52.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCc
Q 022656 77 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDA 156 (294)
Q Consensus 77 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~ 156 (294)
.+.|..+..+|..+-+++..|- +.-+.+.+..+.++.-. ..+. ...++..+=.++..||.+.|+
T Consensus 36 ~~~~~~l~~~i~~l~~ei~elk-----d~~lR~~Ae~eN~rkR~---~rE~--------~~~~~~a~~~~~~~LLpvlDn 99 (191)
T PRK14140 36 AELLDEEQAKIAELEAKLDELE-----ERYLRLQADFENYKRRI---QKEN--------EAAEKYRAQSLASDLLPALDN 99 (191)
T ss_pred hhHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHH---HHHH--------HHHHHHHHHHHHHHHHHHHHH
Confidence 4567778888887777777662 33344444444443221 1111 112344455567889999999
Q ss_pred hHHHHhhhcc-----cccccHHHHHHHHHHHHH
Q 022656 157 AERTQSHISG-----KQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 157 d~Rl~dH~~G-----K~HlGy~kIRe~l~eL~~ 184 (294)
-.|--.|... .+.-|+.+|...+..+-+
T Consensus 100 LerAl~~~~~~~~~~~i~~Gv~mi~k~l~~~L~ 132 (191)
T PRK14140 100 FERALQIEADDEQTKSLLKGVEMVHRQLLEALK 132 (191)
T ss_pred HHHHHhccCccchHHHHHHHHHHHHHHHHHHHH
Confidence 9997666543 234566666655554433
No 86
>PF04420 CHD5: CHD5-like protein; InterPro: IPR007514 Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. The exact molecular function of these eukaryotic proteins is unknown.; PDB: 3SJA_H 3SJC_D 3SJB_D 3ZS8_D 3VLC_E.
Probab=51.29 E-value=54 Score=28.38 Aligned_cols=54 Identities=19% Similarity=0.267 Sum_probs=46.6
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 74 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 74 ~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
.....+...|..+|.++.+|....-.+.+....-++-.++++|.+|.+.+.+..
T Consensus 36 ~~~~~~~~~l~~Ei~~l~~E~~~iS~qDeFAkwaKl~Rk~~kl~~el~~~~~~~ 89 (161)
T PF04420_consen 36 SKSSKEQRQLRKEILQLKRELNAISAQDEFAKWAKLNRKLDKLEEELEKLNKSL 89 (161)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHTTS-TTTSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455677889999999999999999999999999999999999999998887765
No 87
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=50.89 E-value=16 Score=24.52 Aligned_cols=13 Identities=31% Similarity=1.127 Sum_probs=6.4
Q ss_pred hhccccccccccc
Q 022656 138 EKKMALCEICGSF 150 (294)
Q Consensus 138 ~qkm~VCeVCGA~ 150 (294)
..++..|.+||.|
T Consensus 14 ~~~i~~C~~C~nl 26 (41)
T PF02132_consen 14 KENIKFCSICGNL 26 (41)
T ss_dssp HHH-EE-SSS--E
T ss_pred HHcCCccCCCCCc
Confidence 3566888888876
No 88
>PRK06424 transcription factor; Provisional
Probab=50.73 E-value=6.4 Score=33.82 Aligned_cols=8 Identities=50% Similarity=1.427 Sum_probs=4.4
Q ss_pred cccccccc
Q 022656 144 CEICGSFL 151 (294)
Q Consensus 144 CeVCGA~L 151 (294)
||+||+.+
T Consensus 3 CE~CG~~~ 10 (144)
T PRK06424 3 CEMCGKKV 10 (144)
T ss_pred ccccCccc
Confidence 55665543
No 89
>PF09969 DUF2203: Uncharacterized conserved protein (DUF2203); InterPro: IPR018699 This family has no known function.
Probab=50.54 E-value=67 Score=26.66 Aligned_cols=27 Identities=26% Similarity=0.546 Sum_probs=20.1
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhc
Q 022656 74 AEKSEQLSVLEEKIKNLLEQVETLGEA 100 (294)
Q Consensus 74 ~~~~e~i~~l~ekI~~ll~eaE~LGee 100 (294)
.....++..+..+|..++.+++.||-+
T Consensus 46 ~~~~~~~~~~~~~~~~~i~~i~~~Gv~ 72 (120)
T PF09969_consen 46 NGLEAELEELEARLRELIDEIEELGVE 72 (120)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHcCcE
Confidence 345567788888888888888888753
No 90
>PF14282 FlxA: FlxA-like protein
Probab=50.25 E-value=86 Score=25.28 Aligned_cols=53 Identities=19% Similarity=0.376 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 022656 43 EKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETL 97 (294)
Q Consensus 43 ~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~L 97 (294)
...|..+...|....+.|..-... .......+..++..|..+|..|-.+|-.|
T Consensus 18 ~~~I~~L~~Qi~~Lq~ql~~l~~~--~~~~~e~k~~q~q~Lq~QI~~LqaQI~ql 70 (106)
T PF14282_consen 18 DSQIEQLQKQIKQLQEQLQELSQD--SDLDAEQKQQQIQLLQAQIQQLQAQIAQL 70 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcc--cCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567777778888877777543211 11123345667777777777776666443
No 91
>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []. These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.
Probab=50.01 E-value=75 Score=31.45 Aligned_cols=48 Identities=21% Similarity=0.391 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHH
Q 022656 38 LAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVE 95 (294)
Q Consensus 38 ~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE 95 (294)
++..|+.-+..+..+|.....+|++.+ ....++.+++.+|..+.++++
T Consensus 243 ~~~~l~~~~~~~~~~i~~l~~~l~~~~----------k~~~k~~~~~~q~~~~~k~~~ 290 (406)
T PF02388_consen 243 YLESLQEKLEKLEKEIEKLEEKLEKNP----------KKKNKLKELEEQLASLEKRIE 290 (406)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH-T----------HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCc----------chhhHHHHHHHHHHHHHHHHH
Confidence 445555555555566666655554321 333455555555554444443
No 92
>COG4911 Uncharacterized conserved protein [Function unknown]
Probab=49.67 E-value=75 Score=26.32 Aligned_cols=55 Identities=18% Similarity=0.171 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHh
Q 022656 37 ELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGE 99 (294)
Q Consensus 37 e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGe 99 (294)
+++..|.-++.++-.+.++-+...+.-. .++....|.+++.+++.++++|+++|-
T Consensus 11 e~~~el~P~l~d~~~~~r~~~n~~e~L~--------~qedk~~l~e~e~q~k~~l~~i~e~G~ 65 (123)
T COG4911 11 ETARELLPWLRDRLIQLRKIKNEIELLL--------VQEDKYALQEYESQTKKILDEIIEKGI 65 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhc--------ccccHHHHHHHHHHHHHHHHHHHHcCc
Confidence 5667777777777666666666665321 122246788999999999999999874
No 93
>PRK12495 hypothetical protein; Provisional
Probab=49.66 E-value=20 Score=33.02 Aligned_cols=12 Identities=33% Similarity=0.764 Sum_probs=10.7
Q ss_pred cccccccccccc
Q 022656 141 MALCEICGSFLV 152 (294)
Q Consensus 141 m~VCeVCGA~Ls 152 (294)
...|++||+.|.
T Consensus 42 a~hC~~CG~PIp 53 (226)
T PRK12495 42 NAHCDECGDPIF 53 (226)
T ss_pred hhhcccccCccc
Confidence 389999999988
No 94
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=49.28 E-value=1.2e+02 Score=24.83 Aligned_cols=46 Identities=28% Similarity=0.470 Sum_probs=29.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Q 022656 75 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQ 125 (294)
Q Consensus 75 ~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~ 125 (294)
++-..|..|+++|..|++++++|-. ....++++=..|+.|-+.|..
T Consensus 5 ~l~~~l~~le~~l~~l~~~~~~LK~-----~~~~l~EEN~~L~~EN~~Lr~ 50 (107)
T PF06156_consen 5 ELFDRLDQLEQQLGQLLEELEELKK-----QLQELLEENARLRIENEHLRE 50 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHH
Confidence 5667788888888888888888743 344455555555555444443
No 95
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=49.16 E-value=54 Score=22.39 Aligned_cols=35 Identities=34% Similarity=0.427 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Q 022656 83 LEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 119 (294)
Q Consensus 83 l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 119 (294)
+-.+|.+||..++. ..+.-.||+..+.++..|..+
T Consensus 3 il~kI~kLLalA~~--~~~~~~EA~~A~~kAq~Lm~k 37 (43)
T PF10979_consen 3 ILEKIRKLLALAES--TGSNEHEAEAALAKAQRLMAK 37 (43)
T ss_pred HHHHHHHHHHHhhC--CCCCHHHHHHHHHHHHHHHHH
Confidence 45678888877773 226777999999999988754
No 96
>KOG1666 consensus V-SNARE [Intracellular trafficking, secretion, and vesicular transport]
Probab=48.66 E-value=2.2e+02 Score=26.25 Aligned_cols=84 Identities=13% Similarity=0.225 Sum_probs=45.5
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHH
Q 022656 31 VPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALM 110 (294)
Q Consensus 31 ~~~YE~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~ 110 (294)
+.+||.+|-. +..++-.+|..+ + .. +..........|...-+++++|+.+++.-.-+--...---++
T Consensus 5 fe~yEqqy~~----l~a~it~k~~~~---~--~~----~~~ekk~~l~~i~~~leEa~ell~qMdlEvr~lp~~~Rs~~~ 71 (220)
T KOG1666|consen 5 FEGYEQQYRE----LSAEITKKIGRA---L--SL----PGSEKKQLLSEIDSKLEEANELLDQMDLEVRELPPNFRSSYL 71 (220)
T ss_pred HHHHHHHHHH----HHHHHHHhHHHH---h--cC----CchHHHHHHHHHHHhHHHHHHHHHHHHHHHHhCCchhhhHHH
Confidence 5688988854 445555666555 1 11 111222223344444445555555555443333333344677
Q ss_pred HHHHHHHHHHHHHHHhh
Q 022656 111 RKVEILNVEKTTLTQQS 127 (294)
Q Consensus 111 ~~ve~Lk~er~~l~~~~ 127 (294)
.++...|...+.|..++
T Consensus 72 ~KlR~yksdl~~l~~e~ 88 (220)
T KOG1666|consen 72 SKLREYKSDLKKLKREL 88 (220)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 78888887777777666
No 97
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=48.33 E-value=7.4 Score=25.20 Aligned_cols=11 Identities=36% Similarity=0.772 Sum_probs=9.0
Q ss_pred ccccccccccc
Q 022656 140 KMALCEICGSF 150 (294)
Q Consensus 140 km~VCeVCGA~ 150 (294)
...+|+||||-
T Consensus 17 ~p~~CP~Cg~~ 27 (34)
T cd00729 17 APEKCPICGAP 27 (34)
T ss_pred CCCcCcCCCCc
Confidence 45799999984
No 98
>PLN00204 CP12 gene family protein; Provisional
Probab=48.06 E-value=55 Score=27.62 Aligned_cols=43 Identities=19% Similarity=0.204 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHHHHHHHHHHHHH
Q 022656 82 VLEEKIKNLLEQVETLGEAG-KVDEAEALMRKVEILNVEKTTLT 124 (294)
Q Consensus 82 ~l~ekI~~ll~eaE~LGeeG-~VdeA~~l~~~ve~Lk~er~~l~ 124 (294)
.|+++|.+.+++|.++-.+| .-.++.....+||+|.++..-..
T Consensus 56 ~L~e~Ie~aI~eArevCa~g~~S~eCaaAWDeVEELqAeasHqr 99 (126)
T PLN00204 56 GISEKVEKSIKEAEETCADDPASGECVAAWDEVEELSAAASHAR 99 (126)
T ss_pred cHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHcc
Confidence 58889999999999988876 44678889999999998876543
No 99
>PRK11020 hypothetical protein; Provisional
Probab=47.71 E-value=1.4e+02 Score=24.87 Aligned_cols=20 Identities=20% Similarity=0.343 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 022656 78 EQLSVLEEKIKNLLEQVETL 97 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~L 97 (294)
+.|..+..+|..|.++|+.|
T Consensus 31 ~~i~qf~~E~~~l~k~I~~l 50 (118)
T PRK11020 31 EKYAQFEKEKATLEAEIARL 50 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44455555555555555555
No 100
>TIGR02135 phoU_full phosphate transport system regulatory protein PhoU. This model describes PhoU, a regulatory protein of unknown mechanism for high-affinity phosphate ABC transporter systems. The protein consists of two copies of the domain described by Pfam model pfam01895. Deletion of PhoU activates constitutive expression of the phosphate ABC transporter and allows phosphate transport, but causes a growth defect and so likely has some second function.
Probab=47.54 E-value=1.8e+02 Score=24.79 Aligned_cols=82 Identities=12% Similarity=0.039 Sum_probs=52.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhcccccc--ccccccc
Q 022656 75 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCE--ICGSFLV 152 (294)
Q Consensus 75 ~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCe--VCGA~Ls 152 (294)
.....|..+-..+..++..+-.+-..++.+.|..+...-+.+...-..+.... .. ..+. ..|+ .+-.|+.
T Consensus 113 ~~~~el~~m~~~v~~~l~~a~~al~~~d~~~~~~i~~~e~~id~l~~~i~~~~-~~----~~~~---~~~~~~~~~~~~~ 184 (212)
T TIGR02135 113 KHLEELEKMGKLALKMLKDALDAFLNKDAELARQVAEMDERVDELYRQIFREL-VT----YMKE---NPENIEAALDVLL 184 (212)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH-HH----HHHH---CcccHHHHHHHHH
Confidence 44567788888888888888888888888777666655555544333333322 11 0011 3465 4566677
Q ss_pred cCCchHHHHhhh
Q 022656 153 ANDAAERTQSHI 164 (294)
Q Consensus 153 ~~D~d~Rl~dH~ 164 (294)
+..+-.|+.||.
T Consensus 185 i~~~lERigD~~ 196 (212)
T TIGR02135 185 IARYLERIGDHA 196 (212)
T ss_pred HHHHHHHHHHHH
Confidence 778889999996
No 101
>TIGR01554 major_cap_HK97 phage major capsid protein, HK97 family. This family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease.
Probab=47.35 E-value=46 Score=32.28 Aligned_cols=42 Identities=19% Similarity=0.224 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHh--cCCHHHHHHHHHHHHHHHHHHHHH
Q 022656 82 VLEEKIKNLLEQVETLGE--AGKVDEAEALMRKVEILNVEKTTL 123 (294)
Q Consensus 82 ~l~ekI~~ll~eaE~LGe--eG~VdeA~~l~~~ve~Lk~er~~l 123 (294)
+|.++++.+.+++..|-+ +...+++.+...++.+|+.+.+.+
T Consensus 3 el~~~~~~~~~~~r~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 46 (378)
T TIGR01554 3 ELKEQREEIVAEIRSLLDKAEKLEKELTAAALEKEELETDVEKL 46 (378)
T ss_pred hHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 444555555555555544 444455555544444444444433
No 102
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=47.34 E-value=72 Score=28.17 Aligned_cols=8 Identities=38% Similarity=1.331 Sum_probs=6.3
Q ss_pred cccccccc
Q 022656 141 MALCEICG 148 (294)
Q Consensus 141 m~VCeVCG 148 (294)
.-||.|||
T Consensus 134 ~~vC~vCG 141 (166)
T COG1592 134 VWVCPVCG 141 (166)
T ss_pred EEEcCCCC
Confidence 67888887
No 103
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=47.28 E-value=1.3e+02 Score=23.15 Aligned_cols=56 Identities=18% Similarity=0.244 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHh
Q 022656 41 FCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGE 99 (294)
Q Consensus 41 ~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGe 99 (294)
.|..-+..+-.||.+|+.-|..-++ ......+...+|..|+++|..+-+-+..+++
T Consensus 25 d~~~~~~~lk~Klq~ar~~i~~lpg---i~~s~eeq~~~i~~Le~~i~~k~~~L~~~~~ 80 (83)
T PF07544_consen 25 DLDTATGSLKHKLQKARAAIRELPG---IDRSVEEQEEEIEELEEQIRKKREVLQKFKE 80 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCC---ccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455677778889999888865431 2233445566788888888877777666654
No 104
>PRK10564 maltose regulon periplasmic protein; Provisional
Probab=46.74 E-value=25 Score=33.88 Aligned_cols=30 Identities=23% Similarity=0.324 Sum_probs=25.5
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Q 022656 90 LLEQVETLGEAGKVDEAEALMRKVEILNVE 119 (294)
Q Consensus 90 ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 119 (294)
....|++....|+|+.|+.|+.|+|.|--.
T Consensus 260 y~~aI~~AVk~gDi~KAL~LldEAe~LG~~ 289 (303)
T PRK10564 260 FNQAIKQAVKKGDVDKALKLLDEAERLGST 289 (303)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHhCCc
Confidence 346788889999999999999999999543
No 105
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=46.70 E-value=98 Score=26.74 Aligned_cols=15 Identities=27% Similarity=0.722 Sum_probs=11.7
Q ss_pred hhccccccccccccc
Q 022656 138 EKKMALCEICGSFLV 152 (294)
Q Consensus 138 ~qkm~VCeVCGA~Ls 152 (294)
.-..-+|+.||-.+.
T Consensus 108 ~gtYG~Ce~CGe~I~ 122 (151)
T PRK10778 108 DEDFGYCESCGVEIG 122 (151)
T ss_pred CCCCceeccCCCccc
Confidence 346689999998764
No 106
>PLN02678 seryl-tRNA synthetase
Probab=46.54 E-value=62 Score=32.84 Aligned_cols=46 Identities=24% Similarity=0.273 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Q 022656 78 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQ 125 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~ 125 (294)
.+|..|..+++.+.++|-.+...+ +++..+++++..|+++...|+.
T Consensus 47 ~~~e~lr~erN~~sk~I~~~k~~~--~~~~~l~~~~~~Lk~ei~~le~ 92 (448)
T PLN02678 47 FELDSLRKEFNKLNKEVAKLKIAK--EDATELIAETKELKKEITEKEA 92 (448)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhCC--CcHHHHHHHHHHHHHHHHHHHH
Confidence 344455555555555554433333 2344455555555555554443
No 107
>PF01025 GrpE: GrpE; InterPro: IPR000740 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolysing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. In prokaryotes the grpE protein. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold []. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. The X-ray crystal structure of GrpE in complex with the ATPase domain of DnaK revealed that GrpE is an asymmetric homodimer, bent in a manner that favours extensive contacts with only one DnaKATPase monomer []. GrpE does not actively compete for the atomic positions occupied by the nucleotide. GrpE and ADP mutually reduce one another's affinity for DnaK 200-fold, and ATP instantly dissociates GrpE from DnaK.; GO: 0000774 adenyl-nucleotide exchange factor activity, 0042803 protein homodimerization activity, 0051087 chaperone binding, 0006457 protein folding; PDB: 3A6M_A 4ANI_A 1DKG_B.
Probab=45.51 E-value=9.8 Score=32.44 Aligned_cols=36 Identities=19% Similarity=0.180 Sum_probs=22.5
Q ss_pred cccccCCchHHHHhhhc-----ccccccHHHHHHHHHHHHH
Q 022656 149 SFLVANDAAERTQSHIS-----GKQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 149 A~Ls~~D~d~Rl~dH~~-----GK~HlGy~kIRe~l~eL~~ 184 (294)
.+|.+.|+-.+...|+. +.++-||..|...|..+-+
T Consensus 66 ~ll~v~D~l~~a~~~~~~~~~~~~~~~g~~~~~~~l~~~L~ 106 (165)
T PF01025_consen 66 DLLPVLDNLERALEAAKSNEEEESLLEGLEMILKQLEDILE 106 (165)
T ss_dssp HHHHHHHHHHHHHCC-SHHCTCHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHHHHHH
Confidence 35566666677777663 4566777777776666544
No 108
>PF03357 Snf7: Snf7; InterPro: IPR005024 This is a family of eukaryotic proteins which are variously described as either hypothetical protein, developmental protein or related to yeast SNF7. The family contains human CHMP1. CHMP1 (CHromatin Modifying Protein; CHarged Multivesicular body Protein), is encoded by an alternative open reading frame in the PRSM1 gene [] and is conserved in both complex and simple eukaryotes. CHMP1 contains a predicted bipartite nuclear localisation signal and distributes as distinct forms to the cytoplasm and the nuclear matrix in all cell lines tested. Human CHMP1 is strongly implicated in multivesicular body formation. A multivesicular body is a vesicle-filled endosome that targets proteins to the interior of lysosomes. Immunocytochemistry and biochemical fractionation localise CHMP1 to early endosomes and CHMP1 physically interacts with SKD1/VPS4, a highly conserved protein directly linked to multivesicular body sorting in yeast. Similar to the action of a mutant SKD1 protein, over expression of a fusion derivative of human CHMP1 dilates endosomal compartments and disrupts the normal distribution of several endosomal markers. Genetic studies in Saccharomyces cerevisiae (Baker's yeast) further support a conserved role of CHMP1 in vesicle trafficking. Deletion of CHM1, the budding yeast homologue of CHMP1, results in defective sorting of carboxypeptidases S and Y and produces abnormal, multi-lamellar prevacuolar compartments. This phenotype classifies CHM1 as a member of the class E vacuolar protein sorting genes []. ; GO: 0015031 protein transport; PDB: 2V6X_B 2W2U_D 2GD5_D 3FRT_B 3FRV_A 4ABM_D 3EAB_H 3HTU_D.
Probab=45.48 E-value=1.1e+02 Score=25.59 Aligned_cols=52 Identities=23% Similarity=0.319 Sum_probs=42.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHh
Q 022656 75 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQ 126 (294)
Q Consensus 75 ~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~ 126 (294)
.+...+..|+.+|..+..+|-.+...|+.+.|..++...-.+......+...
T Consensus 12 ~L~~~~~~le~~i~~~~~~~k~~~~~~~~~~A~~~lk~~k~~~k~~~~~~~~ 63 (171)
T PF03357_consen 12 RLEKQIKRLEKKIKKLEKKAKKAIKKGNKERAKIYLKRKKRLEKQLEKLLNQ 63 (171)
T ss_dssp HHHHHHHHHHHHHHHCHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456788899999999999999999999999999988888887777665543
No 109
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=45.03 E-value=1.1e+02 Score=28.18 Aligned_cols=32 Identities=16% Similarity=0.163 Sum_probs=22.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHH
Q 022656 75 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEAL 109 (294)
Q Consensus 75 ~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l 109 (294)
.+.+-+..-+..|+.||+-|.+ +|+|++++..
T Consensus 47 ~il~Ll~~kd~ef~~llkla~e---q~k~e~~m~~ 78 (272)
T KOG4552|consen 47 NILKLLDSKDDEFKTLLKLAPE---QQKREQLMRT 78 (272)
T ss_pred HHHHHHHhccHHHHHHHHHhHh---HHHHHHHHHH
Confidence 4556666778889999888765 4566665543
No 110
>PRK00239 rpsT 30S ribosomal protein S20; Reviewed
Probab=44.59 E-value=57 Score=25.71 Aligned_cols=38 Identities=16% Similarity=0.240 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Q 022656 82 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 119 (294)
Q Consensus 82 ~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 119 (294)
.+-..|...+.+++.+.++|+.++|..++.++..+-..
T Consensus 23 ~~kS~~kT~iKk~~~ai~~~~~~~a~~~~~~a~s~iDk 60 (88)
T PRK00239 23 SRKSRVRTAIKKVEAAIAAGDKEAAEEALKAAQSKIDK 60 (88)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 44556777778888888899999999999988877543
No 111
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=44.52 E-value=7.5 Score=31.37 Aligned_cols=23 Identities=22% Similarity=0.349 Sum_probs=17.6
Q ss_pred cccccccccccccCCchHHHHhh
Q 022656 141 MALCEICGSFLVANDAAERTQSH 163 (294)
Q Consensus 141 m~VCeVCGA~Ls~~D~d~Rl~dH 163 (294)
-..|++||.||...++..++.|-
T Consensus 20 ~~gCpnC~~~l~~~g~~~~v~~~ 42 (98)
T cd07973 20 RDGCPNCEGYLDMKGNHERVYDC 42 (98)
T ss_pred CCCCCCCcchhccCCCccccccc
Confidence 47999999999877776655554
No 112
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=44.29 E-value=2.4e+02 Score=26.97 Aligned_cols=20 Identities=25% Similarity=0.343 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 022656 34 FEAELAQFCEKLVMDLDRRVR 54 (294)
Q Consensus 34 YE~e~l~~L~~lI~d~dRkI~ 54 (294)
|||. +..++.|+..++..+.
T Consensus 140 YeWR-~~ll~gl~~~L~~~~~ 159 (325)
T PF08317_consen 140 YEWR-MQLLEGLKEGLEENLE 159 (325)
T ss_pred HHHH-HHHHHHHHHHHHHHHH
Confidence 5664 4444555555544433
No 113
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=44.27 E-value=70 Score=32.02 Aligned_cols=46 Identities=26% Similarity=0.367 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Q 022656 78 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQ 125 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~ 125 (294)
.+|..|..+++++.++|-.+...++ ++..+++++..|+++...|++
T Consensus 42 ~~~~~lr~~rn~~sk~i~~~~~~~~--~~~~l~~~~~~l~~~~~~~~~ 87 (425)
T PRK05431 42 TELEELQAERNALSKEIGQAKRKGE--DAEALIAEVKELKEEIKALEA 87 (425)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcCC--cHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555555544333331 233344455555554444443
No 114
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=44.23 E-value=1.2e+02 Score=26.40 Aligned_cols=31 Identities=19% Similarity=0.421 Sum_probs=18.3
Q ss_pred ccccccccccccccCCchHHHHhhhcccccccHHH
Q 022656 140 KMALCEICGSFLVANDAAERTQSHISGKQHIGYGM 174 (294)
Q Consensus 140 km~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~k 174 (294)
..-+|++||..+. ..||.--=.=..-+..+.
T Consensus 85 ~YG~Ce~CGe~I~----~~RL~a~P~a~~Ci~Cq~ 115 (159)
T TIGR02890 85 TYGICEVCGKPIP----YERLEAIPTATTCVECQN 115 (159)
T ss_pred CCCeecccCCccc----HHHHhhCCCcchhHHHHH
Confidence 4579999998864 346554443333344333
No 115
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=43.50 E-value=16 Score=35.77 Aligned_cols=9 Identities=33% Similarity=0.427 Sum_probs=3.6
Q ss_pred HHHHHHhcC
Q 022656 93 QVETLGEAG 101 (294)
Q Consensus 93 eaE~LGeeG 101 (294)
+-+.|-+-|
T Consensus 125 e~~ILr~LG 133 (367)
T KOG0835|consen 125 ERRILRELG 133 (367)
T ss_pred HHHHHHHhC
Confidence 334444444
No 116
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=43.02 E-value=7.9 Score=24.05 Aligned_cols=12 Identities=50% Similarity=1.151 Sum_probs=6.6
Q ss_pred ccccccccccCC
Q 022656 144 CEICGSFLVAND 155 (294)
Q Consensus 144 CeVCGA~Ls~~D 155 (294)
|+|||+-|+..+
T Consensus 2 CP~C~s~l~~~~ 13 (28)
T PF03119_consen 2 CPVCGSKLVREE 13 (28)
T ss_dssp -TTT--BEEE-C
T ss_pred cCCCCCEeEcCC
Confidence 999999998444
No 117
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=42.73 E-value=8.7 Score=25.58 Aligned_cols=13 Identities=38% Similarity=0.718 Sum_probs=10.6
Q ss_pred ccccccccccccC
Q 022656 142 ALCEICGSFLVAN 154 (294)
Q Consensus 142 ~VCeVCGA~Ls~~ 154 (294)
..|+.||+.|+.-
T Consensus 2 ~~CP~Cg~~lv~r 14 (39)
T PF01396_consen 2 EKCPKCGGPLVLR 14 (39)
T ss_pred cCCCCCCceeEEE
Confidence 5799999998753
No 118
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=42.50 E-value=17 Score=21.84 Aligned_cols=21 Identities=29% Similarity=0.708 Sum_probs=15.8
Q ss_pred ccccccccccccccCCchHHHHhhh
Q 022656 140 KMALCEICGSFLVANDAAERTQSHI 164 (294)
Q Consensus 140 km~VCeVCGA~Ls~~D~d~Rl~dH~ 164 (294)
.|..|++||--. +..+|+.|+
T Consensus 1 ~l~~C~~CgR~F----~~~~l~~H~ 21 (25)
T PF13913_consen 1 ELVPCPICGRKF----NPDRLEKHE 21 (25)
T ss_pred CCCcCCCCCCEE----CHHHHHHHH
Confidence 378999999643 567888885
No 119
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=42.24 E-value=6.5 Score=28.31 Aligned_cols=21 Identities=29% Similarity=0.643 Sum_probs=12.1
Q ss_pred hccccccccccccccCCchHH
Q 022656 139 KKMALCEICGSFLVANDAAER 159 (294)
Q Consensus 139 qkm~VCeVCGA~Ls~~D~d~R 159 (294)
-+...|+||||.+...-|-+|
T Consensus 22 ~~PatCP~C~a~~~~srnLrR 42 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRR 42 (54)
T ss_dssp S--EE-TTT--EESSHHHHHH
T ss_pred CCCCCCCcchhhccchhhHHH
Confidence 355789999999987755555
No 120
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.93 E-value=9 Score=29.92 Aligned_cols=15 Identities=53% Similarity=0.888 Sum_probs=11.8
Q ss_pred cccccccccccccCC
Q 022656 141 MALCEICGSFLVAND 155 (294)
Q Consensus 141 m~VCeVCGA~Ls~~D 155 (294)
|-+|+|||+-|...+
T Consensus 1 ~llCP~C~v~l~~~~ 15 (88)
T COG3809 1 MLLCPICGVELVMSV 15 (88)
T ss_pred CcccCcCCceeeeee
Confidence 568999999887553
No 121
>PRK03918 chromosome segregation protein; Provisional
Probab=41.62 E-value=4.8e+02 Score=28.05 Aligned_cols=16 Identities=6% Similarity=-0.176 Sum_probs=12.3
Q ss_pred ccccccccccccCCch
Q 022656 142 ALCEICGSFLVANDAA 157 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~d 157 (294)
.+|+||+..-...+.+
T Consensus 433 ~~~~~Cp~c~~~L~~~ 448 (880)
T PRK03918 433 KAKGKCPVCGRELTEE 448 (880)
T ss_pred hcCCCCCCCCCcCCch
Confidence 5999999866666654
No 122
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=41.28 E-value=15 Score=26.02 Aligned_cols=41 Identities=24% Similarity=0.400 Sum_probs=29.0
Q ss_pred hhccccccccccccccCCchHHHHhhhcccccccHHHHHHHHHHHHH
Q 022656 138 EKKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 138 ~qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eL~~ 184 (294)
+++--.||+|-.- .+ =|+.|+.+++|..|+.=-.-+..|..
T Consensus 2 ~~k~GYCE~C~~k---y~---~l~~Hi~s~~Hr~FA~~~~Nf~~lD~ 42 (49)
T PF07535_consen 2 DKKPGYCENCRVK---YD---DLEEHIQSEKHRKFAENDSNFKELDS 42 (49)
T ss_pred CCCCccCccccch---hh---hHHHHhCCHHHHHHHcCcccHHHHHH
Confidence 3566789999854 22 38999999999888755555555444
No 123
>PF12998 ING: Inhibitor of growth proteins N-terminal histone-binding; InterPro: IPR024610 Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterised C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail. This entry represents the N-terminal histone binding domain found in inhibitor proteins.; PDB: 4AFL_A.
Probab=41.10 E-value=1.7e+02 Score=22.61 Aligned_cols=73 Identities=21% Similarity=0.194 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHHhhhhcCCC-CCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 022656 43 EKLVMDLDRRVRRGRERLSQEVEP-APPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEIL 116 (294)
Q Consensus 43 ~~lI~d~dRkI~~~k~RL~~~~e~-~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~L 116 (294)
-..|.++|.++......+.+.... ......+.....+...+-.+|...+.++..|+.+ +|.-|..+...|+.-
T Consensus 21 l~~irelD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~l~de-Kv~lA~~~~d~v~~h 94 (105)
T PF12998_consen 21 LTLIRELDAKSQDLLEELDQQIQKFIKNHGSPSLSPEKRRELLKEIQEEYERALELSDE-KVALAQQAYDLVDRH 94 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTCTTS--S-HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHHHHhhcccccCChHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Confidence 345666666665555555421100 0000010111125556777888888888888765 455555555555444
No 124
>PRK00420 hypothetical protein; Validated
Probab=40.79 E-value=15 Score=30.34 Aligned_cols=20 Identities=10% Similarity=0.406 Sum_probs=15.8
Q ss_pred hhccccccccccccccCCch
Q 022656 138 EKKMALCEICGSFLVANDAA 157 (294)
Q Consensus 138 ~qkm~VCeVCGA~Ls~~D~d 157 (294)
.+...+|++||.++.+.+.+
T Consensus 37 k~g~~~Cp~Cg~~~~v~~~e 56 (112)
T PRK00420 37 KDGEVVCPVHGKVYIVKSDE 56 (112)
T ss_pred CCCceECCCCCCeeeeccHH
Confidence 35668999999999887755
No 125
>COG0783 Dps DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]
Probab=40.60 E-value=1.6e+02 Score=25.59 Aligned_cols=83 Identities=19% Similarity=0.155 Sum_probs=47.1
Q ss_pred HHHHHHHHHHHHHHHHHHH--------HHHhhhhc--CCCCCCCCC----chhhHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 022656 37 ELAQFCEKLVMDLDRRVRR--------GRERLSQE--VEPAPPPPI----SAEKSEQLSVLEEKIKNLLEQVETLGEAGK 102 (294)
Q Consensus 37 e~l~~L~~lI~d~dRkI~~--------~k~RL~~~--~e~~~~~~~----~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~ 102 (294)
+++..|..+|++|--||.. -.+=++.. .+.+. ... ...+.+....|...|.+.++-++++|..|=
T Consensus 55 e~y~el~~~~DeiAERi~~LGg~p~~t~~~~~~~s~ike~~~-~~~~~~~l~~l~~~~~~l~~~~r~~~~~a~e~gD~~T 133 (156)
T COG0783 55 ELYEELAEHVDEIAERIRALGGVPLGTLSEYLKLSSIKEEPG-DYTAREMLKELVEDYEYLIKELRKGIELADEAGDEVT 133 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCcccHHHHHHhCCCcccCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCChhH
Confidence 4677777788887777754 11111111 11011 111 112233445566666677777777777777
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 022656 103 VDEAEALMRKVEILNVEK 120 (294)
Q Consensus 103 VdeA~~l~~~ve~Lk~er 120 (294)
.+-....+..+|+.....
T Consensus 134 adl~~~~~~~~EK~~Wml 151 (156)
T COG0783 134 ADLLTDIIRELEKTLWML 151 (156)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 777788888887776544
No 126
>PF06632 XRCC4: DNA double-strand break repair and V(D)J recombination protein XRCC4; InterPro: IPR010585 This entry represents the DNA double-strand break repair and V(D)J recombination protein XRCC4, which is found in certain Metazoans, fungi and plants. XRCC4 binds to DNA, and to DNA ligase IV (LIG4) to form the LIG4-XRCC4 complex []. The LIG4-XRCC4 complex is responsible for the ligation step in the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair. XRCC4 enhances the joining activity of LIG4. It is thought that XRCC4 and LIG4 are essential for alignment-based gap filling, as well as for final ligation of the breaks []. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. ; GO: 0003677 DNA binding, 0006302 double-strand break repair, 0006310 DNA recombination, 0005634 nucleus; PDB: 3RWR_R 1IK9_B 3SR2_E 3Q4F_H 3II6_B 1FU1_A 3MUD_B.
Probab=40.37 E-value=3.1e+02 Score=26.90 Aligned_cols=45 Identities=27% Similarity=0.350 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHh
Q 022656 82 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQ 126 (294)
Q Consensus 82 ~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~ 126 (294)
.|...++.+++++|++..+-.--|..-+..=|--|+++|+.|.+.
T Consensus 155 rL~~e~~~~~~qlE~~v~~K~~~E~~L~~KF~~vLNeKK~KIR~l 199 (342)
T PF06632_consen 155 RLESEANKLLKQLEKFVNAKEEHEEDLYAKFVLVLNEKKAKIREL 199 (342)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 455666666677777666665557766666677777777776543
No 127
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.33 E-value=21 Score=33.22 Aligned_cols=35 Identities=23% Similarity=0.479 Sum_probs=28.2
Q ss_pred ccccccccccccccCCchHHHHhhhcccccccHHHHHHHHHHHHH
Q 022656 140 KMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 140 km~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eL~~ 184 (294)
..-||=||-+.|= ..=-+-|+.||+| |+.++.|+.
T Consensus 34 gql~C~vCn~piK----p~lW~vHvnsKkH------re~id~lKs 68 (264)
T KOG3032|consen 34 GQLVCRVCNVPIK----PSLWDVHVNSKKH------REAIDSLKS 68 (264)
T ss_pred CCeeEEEecCccc----HHHHHHHhccHHH------HHHHHHHHh
Confidence 4479999998764 5567889999999 788888884
No 128
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=39.91 E-value=2e+02 Score=23.69 Aligned_cols=49 Identities=22% Similarity=0.341 Sum_probs=33.3
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 74 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 74 ~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
.++-..|..|+.+|+.|+++++.|-. ....++++-..|+.|-+.|...+
T Consensus 4 ~elfd~l~~le~~l~~l~~el~~LK~-----~~~el~EEN~~L~iEN~~Lr~~l 52 (110)
T PRK13169 4 KEIFDALDDLEQNLGVLLKELGALKK-----QLAELLEENTALRLENDKLRERL 52 (110)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35667888889999999988888843 35556666666666655554433
No 129
>TIGR00414 serS seryl-tRNA synthetase. This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model.
Probab=39.82 E-value=95 Score=31.01 Aligned_cols=47 Identities=23% Similarity=0.315 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHh
Q 022656 79 QLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQ 126 (294)
Q Consensus 79 ~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~ 126 (294)
++..|..+.+.+.++|-.+...|+ +++..+.+++..|+++...|+++
T Consensus 45 ~~~~l~~erN~~sk~i~~~~~~~~-~~~~~l~~~~~~l~~~~~~~~~~ 91 (418)
T TIGR00414 45 EIEELQAKRNELSKQIGKAKGQKK-DKIEEIKKELKELKEELTELSAA 91 (418)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCc-chHHHHHHHHHHHHHHHHHHHHH
Confidence 344444555555555544433342 11455556666666655555443
No 130
>PF06721 DUF1204: Protein of unknown function (DUF1204); InterPro: IPR009596 This family represents the C terminus of a number of Arabidopsis thaliana hypothetical proteins of unknown function. Family members contain a conserved DFD motif.
Probab=39.27 E-value=1.1e+02 Score=27.76 Aligned_cols=70 Identities=13% Similarity=0.233 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHHHHHH-HHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccc
Q 022656 78 EQLSVLEEKIKNLLEQVET-LGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSF 150 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~-LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~ 150 (294)
.+..+|+..|..-++..+. -.+-.+..-..+|..-++.+++....+...+ .+. .....+-|+.|+|||..
T Consensus 50 ~K~deLedr~~se~KRLRsrR~~~AEn~rrs~L~kv~~l~QARidRvK~Hi-Ddk--ia~ePkFle~nQV~Gni 120 (228)
T PF06721_consen 50 VKFDELEDRISSEQKRLRSRRINYAENNRRSALEKVASLYQARIDRVKAHI-DDK--IADEPKFLEFNQVKGNI 120 (228)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hhh--hhcchHHHHHHHhhchH
Confidence 3444555555544444433 1111122224556666667777777777766 332 12234678889999964
No 131
>TIGR00029 S20 ribosomal protein S20. This family consists of bacterial (and chloroplast) examples of the bacteria ribosomal small subunit protein S20.
Probab=39.01 E-value=89 Score=24.59 Aligned_cols=37 Identities=19% Similarity=0.220 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Q 022656 82 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNV 118 (294)
Q Consensus 82 ~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 118 (294)
.+-..|...+.+++.+.++|+.++|+.++.++..+-.
T Consensus 23 ~~kS~~kT~iKk~~~ai~~~d~~~a~~~l~~a~s~iD 59 (87)
T TIGR00029 23 SQKSKMKTIIKKVYAAIAAGDKDKAQEAFKEAAKKLD 59 (87)
T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4456677788889999999999999999988877643
No 132
>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]
Probab=39.01 E-value=2.5e+02 Score=31.70 Aligned_cols=78 Identities=15% Similarity=0.150 Sum_probs=52.4
Q ss_pred CCccccccCChhH------HHHhh-cCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhH
Q 022656 5 LDCIPVKMCYYVC------DCSFE-KSPRHDAYVPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKS 77 (294)
Q Consensus 5 ~~~~~~~~~~~~l------K~~Ye-~~~~~~~~~~~YE~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~ 77 (294)
||+..|-|-++.+ -.+|- +..+..+|..+|+.-.|+.|......|---+..+++.|.+..+ ....+.
T Consensus 168 v~~f~I~veNP~~~lsQD~aR~FL~~~~p~dkYklfmkaT~L~qi~~~~~~~~~~~~~~~~~i~~~~e------~i~~l~ 241 (1074)
T KOG0250|consen 168 VDHFNIQVENPMFVLSQDAARSFLANSNPKDKYKLFMKATQLEQITESYSEIMESLDHAKELIDLKEE------EIKNLK 241 (1074)
T ss_pred HHHhCcCCCCcchhhcHHHHHHHHhcCChHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHh------hhHHHH
Confidence 4556666666654 33443 3456778888999999999999999999999999999965321 222344
Q ss_pred HHHHHHHHHHH
Q 022656 78 EQLSVLEEKIK 88 (294)
Q Consensus 78 e~i~~l~ekI~ 88 (294)
.+|.++.+++.
T Consensus 242 k~i~e~~e~~~ 252 (1074)
T KOG0250|consen 242 KKIKEEEEKLD 252 (1074)
T ss_pred HHHHHHHHHHH
Confidence 45555555444
No 133
>PRK12496 hypothetical protein; Provisional
Probab=38.61 E-value=12 Score=32.72 Aligned_cols=13 Identities=46% Similarity=0.958 Sum_probs=10.4
Q ss_pred ccccccccccccC
Q 022656 142 ALCEICGSFLVAN 154 (294)
Q Consensus 142 ~VCeVCGA~Ls~~ 154 (294)
.+|+|||+-|..-
T Consensus 144 ~~C~~CG~~~~r~ 156 (164)
T PRK12496 144 DVCEICGSPVKRK 156 (164)
T ss_pred CcCCCCCChhhhc
Confidence 6799999987644
No 134
>PF01649 Ribosomal_S20p: Ribosomal protein S20; InterPro: IPR002583 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 [, ]. This family consists of bacterial (and chloroplast) examples of the ribosomal small subunit protein S20. Bacterial ribosomal protein S20 forms part of the 30S ribosomal subunit, and interacts with 16S rRNA.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1I94_T 1FJG_T 4DH9_T 3KNJ_T 3TVG_W 3UYF_W 3V28_T 3KIS_t 3HUY_T 1HNX_T ....
Probab=38.49 E-value=95 Score=24.17 Aligned_cols=37 Identities=22% Similarity=0.280 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Q 022656 82 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNV 118 (294)
Q Consensus 82 ~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 118 (294)
..-..|..++.+++.+.+.|+.++|+.++..+..+-.
T Consensus 22 ~~kS~~rT~iKk~~~ai~~~~~~~a~~~l~~a~s~iD 58 (84)
T PF01649_consen 22 SRKSRVRTAIKKFREAIEAGDKEEAKELLRKAYSAID 58 (84)
T ss_dssp HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHH
Confidence 4556788889999999999999999999988877643
No 135
>smart00746 TRASH metallochaperone-like domain.
Probab=38.30 E-value=6.8 Score=23.21 Aligned_cols=24 Identities=21% Similarity=0.398 Sum_probs=13.9
Q ss_pred ccccccccccCCchHHHHhhhccccc
Q 022656 144 CEICGSFLVANDAAERTQSHISGKQH 169 (294)
Q Consensus 144 CeVCGA~Ls~~D~d~Rl~dH~~GK~H 169 (294)
|++||..+........+ . +.|+++
T Consensus 1 c~~C~~~~~~~~~~~~~-~-~~g~~~ 24 (39)
T smart00746 1 CSFCGKDIYNPGTGIMV-V-NDGKVF 24 (39)
T ss_pred CCCCCCCccCCCCceEE-E-ECCEEE
Confidence 89999988643332222 2 555554
No 136
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=37.89 E-value=2.9e+02 Score=26.66 Aligned_cols=20 Identities=30% Similarity=0.386 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 022656 78 EQLSVLEEKIKNLLEQVETL 97 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~L 97 (294)
++|..+..+|..+..+++++
T Consensus 211 ~~l~~~~~ei~~~~~~l~e~ 230 (312)
T smart00787 211 EKLKKLLQEIMIKVKKLEEL 230 (312)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444444433
No 137
>KOG0996 consensus Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]
Probab=37.61 E-value=1.7e+02 Score=33.33 Aligned_cols=26 Identities=38% Similarity=0.514 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCH
Q 022656 78 EQLSVLEEKIKNLLEQVETLGEAGKV 103 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~LGeeG~V 103 (294)
+.+.++.++|..+-.++|.|+++|-.
T Consensus 858 ~~l~~~~~~ie~l~kE~e~~qe~~~K 883 (1293)
T KOG0996|consen 858 KRLKELEEQIEELKKEVEELQEKAAK 883 (1293)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhH
Confidence 55677777788888888888765544
No 138
>PRK14145 heat shock protein GrpE; Provisional
Probab=37.48 E-value=1.6e+02 Score=26.72 Aligned_cols=90 Identities=12% Similarity=0.099 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCchH
Q 022656 79 QLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAE 158 (294)
Q Consensus 79 ~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~ 158 (294)
++..|.++|..+-+++..|- +..+.+.++.+.++.--+.-.. ...+..+=.++-+||-+.|+-.
T Consensus 46 e~~~l~~~l~~le~e~~el~-----d~~lR~~AEfeN~rkR~~kE~e-----------~~~~~a~e~~~~~LLpV~DnLe 109 (196)
T PRK14145 46 EIEELKQKLQQKEVEAQEYL-----DIAQRLKAEFENYRKRTEKEKS-----------EMVEYGKEQVILELLPVMDNFE 109 (196)
T ss_pred HHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhHHhHHH
Confidence 45555666655555555542 3344555555555432111111 1223334445678899999999
Q ss_pred HHHhhhcc--cccccHHHHHHHHHHHHH
Q 022656 159 RTQSHISG--KQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 159 Rl~dH~~G--K~HlGy~kIRe~l~eL~~ 184 (294)
|.-.|... .++-|+.+|...|...-+
T Consensus 110 rAl~~~~~~~~l~~Gv~mi~k~l~~vL~ 137 (196)
T PRK14145 110 RALASSGDYNSLKEGIELIYRQFKKILD 137 (196)
T ss_pred HHHhccccHHHHHHHHHHHHHHHHHHHH
Confidence 96666322 234566666665554433
No 139
>PRK14156 heat shock protein GrpE; Provisional
Probab=37.17 E-value=1.3e+02 Score=26.80 Aligned_cols=85 Identities=11% Similarity=0.131 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCchHHHH
Q 022656 82 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAERTQ 161 (294)
Q Consensus 82 ~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~Rl~ 161 (294)
.+..+|..+.++++.|- +.-+.+.++.+.++.-.. .+. ....+..+=.++-.||.+.|+-.|--
T Consensus 31 ~~~~~l~~l~~e~~elk-----d~~lR~~AEfeN~rKR~~---rE~--------e~~~~~a~~~~~~~LLpVlDnLerAl 94 (177)
T PRK14156 31 PEKSELELANERADEFE-----NKYLRAHAEMQNIQRRAN---EER--------QQLQRYRSQDLAKAILPSLDNLERAL 94 (177)
T ss_pred ccHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHH---HHH--------HHHHHHHHHHHHHHHhhHHhHHHHHH
Confidence 34555555666666552 334444555555442211 111 01123333445678899999999965
Q ss_pred hhhc--ccccccHHHHHHHHHHH
Q 022656 162 SHIS--GKQHIGYGMVRDFITEY 182 (294)
Q Consensus 162 dH~~--GK~HlGy~kIRe~l~eL 182 (294)
.|.. +.++-|+.+|...|...
T Consensus 95 ~~~~~~~~l~~Gv~mi~k~l~~~ 117 (177)
T PRK14156 95 AVEGLTDDVKKGLEMVQESLIQA 117 (177)
T ss_pred hCcccchhHHHHHHHHHHHHHHH
Confidence 5543 34567887777666443
No 140
>PF07743 HSCB_C: HSCB C-terminal oligomerisation domain; InterPro: IPR009073 This entry represents the C-terminal oligomerisation domain found in HscB (heat shock cognate protein B), which is also known as HSC20 (20K heat shock cognate protein). HscB acts as a co-chaperone to regulate the ATPase activity and peptide-binding specificity of the molecular chaperone HscA, also known as HSC66 (HSP70 class). HscB proteins contain two domains, an N-terminal J-domain, which is involved in interactions with HscA, connected by a short loop to the C-terminal oligomerisation domain; the two domains make contact through a hydrophobic interface. The core of the oligomerisation domain is thought to bind and target proteins to HscA and consists of an open, three-helical bundle []. HscB, along with HscA, has been shown to play a role in the biogenesis of iron-sulphur proteins.; GO: 0006457 protein folding; PDB: 1FPO_C 3BVO_B 3HHO_A 3UO2_B 3UO3_B.
Probab=36.98 E-value=1.7e+02 Score=21.61 Aligned_cols=47 Identities=30% Similarity=0.354 Sum_probs=36.6
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHH
Q 022656 74 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEK 120 (294)
Q Consensus 74 ~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er 120 (294)
..+..-...++..|..++.++..+-..++.+.|...+.++-=+..-.
T Consensus 27 ~~L~~l~~~~~~~~~~~~~~l~~~f~~~d~~~A~~~~~kLky~~kl~ 73 (78)
T PF07743_consen 27 AELEELKKEIEERIKELIKELAEAFDAKDWEEAKEALRKLKYLQKLL 73 (78)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHHHHHH
Confidence 45556677888999999999999999999999998887775554433
No 141
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=36.81 E-value=11 Score=34.12 Aligned_cols=37 Identities=22% Similarity=0.490 Sum_probs=0.0
Q ss_pred hhccccccccccccccCCchHHHHhhhcccccccHHHHHHHHHHHHH
Q 022656 138 EKKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 138 ~qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eL~~ 184 (294)
..+|.+|+|||-.+-+..-+ . ||=+..|-=.+++-++
T Consensus 165 ~~~~~~cPitGe~IP~~e~~----e------HmRi~LlDP~wkEqr~ 201 (229)
T PF12230_consen 165 KEKMIICPITGEMIPADEMD----E------HMRIELLDPRWKEQRD 201 (229)
T ss_dssp -----------------------------------------------
T ss_pred cccccccccccccccccccc----c------cccccccccccccccc
Confidence 45789999999998877644 3 4445555544444433
No 142
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=36.79 E-value=2.4e+02 Score=24.62 Aligned_cols=36 Identities=22% Similarity=0.329 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 80 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 80 i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
...++++|..+-+++++ .-.+++.||.+.+.+..+|
T Consensus 156 ~~~~~~ei~~lk~el~~------------~~~~~~~LkkQ~~~l~~ey 191 (192)
T PF05529_consen 156 NKKLSEEIEKLKKELEK------------KEKEIEALKKQSEGLQKEY 191 (192)
T ss_pred hhhhHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHhhc
Confidence 33444555555554444 3334455555555554443
No 143
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=36.73 E-value=13 Score=32.17 Aligned_cols=7 Identities=71% Similarity=1.602 Sum_probs=4.4
Q ss_pred ccccccc
Q 022656 144 CEICGSF 150 (294)
Q Consensus 144 CeVCGA~ 150 (294)
||+||+-
T Consensus 3 CEiCG~~ 9 (154)
T TIGR00270 3 CEICGRK 9 (154)
T ss_pred cccCCCc
Confidence 6677654
No 144
>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []. These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.
Probab=36.21 E-value=90 Score=30.89 Aligned_cols=48 Identities=25% Similarity=0.392 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHh
Q 022656 77 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQ 126 (294)
Q Consensus 77 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~ 126 (294)
.+-+..|+++|..+.+++++|.+. +++..+.-.++..|..+.+.++..
T Consensus 241 ~~~~~~l~~~~~~~~~~i~~l~~~--l~~~~k~~~k~~~~~~q~~~~~k~ 288 (406)
T PF02388_consen 241 KEYLESLQEKLEKLEKEIEKLEEK--LEKNPKKKNKLKELEEQLASLEKR 288 (406)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH--HHH-THHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH--HHhCcchhhHHHHHHHHHHHHHHH
Confidence 455777777777777777777553 000013444444454444444443
No 145
>COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=36.14 E-value=95 Score=31.43 Aligned_cols=49 Identities=20% Similarity=0.264 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 78 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
.++..|..+.+.+.++|-..+..|.- .++.+++++..|+.+.+.++.+.
T Consensus 43 ~~~e~l~~~rn~~sk~ig~~~~~~~~-~~~~l~~e~~~l~~~l~~~e~~~ 91 (429)
T COG0172 43 RELEELQAERNELSKEIGRALKRGED-DAEELIAEVKELKEKLKELEAAL 91 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhccch-hHHHHHHHHHHHHHHHHhccHHH
Confidence 34556666666666666655554443 67788888888888877766544
No 146
>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=36.14 E-value=15 Score=26.45 Aligned_cols=15 Identities=20% Similarity=0.428 Sum_probs=9.7
Q ss_pred cccccccccccccCC
Q 022656 141 MALCEICGSFLVAND 155 (294)
Q Consensus 141 m~VCeVCGA~Ls~~D 155 (294)
+..|++||+-+-+.|
T Consensus 2 ~~~CP~CG~~iev~~ 16 (54)
T TIGR01206 2 QFECPDCGAEIELEN 16 (54)
T ss_pred ccCCCCCCCEEecCC
Confidence 356777777666554
No 147
>PRK10325 heat shock protein GrpE; Provisional
Probab=36.04 E-value=1.3e+02 Score=27.18 Aligned_cols=44 Identities=16% Similarity=0.153 Sum_probs=29.3
Q ss_pred hccccccccccccccCCchHHHHhhhcc------cccccHHHHHHHHHHH
Q 022656 139 KKMALCEICGSFLVANDAAERTQSHISG------KQHIGYGMVRDFITEY 182 (294)
Q Consensus 139 qkm~VCeVCGA~Ls~~D~d~Rl~dH~~G------K~HlGy~kIRe~l~eL 182 (294)
.+..+..++-.||.+.|+-.|--.|... -++-|+.+|...|...
T Consensus 84 ~~~a~~~~~~~lLpv~DnlerAl~~~~~~~~~~~~l~~Gv~m~~~~l~~~ 133 (197)
T PRK10325 84 HKFALEKFINELLPVIDSLDRALEVADKANPDMSAMVEGIELTLKSMLDV 133 (197)
T ss_pred HHHHHHHHHHHHhhHHhHHHHHHhcccccchhHHHHHHHHHHHHHHHHHH
Confidence 3445666778899999999997677531 2456666665555443
No 148
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=35.97 E-value=15 Score=23.48 Aligned_cols=10 Identities=30% Similarity=0.956 Sum_probs=8.5
Q ss_pred cccccccccc
Q 022656 140 KMALCEICGS 149 (294)
Q Consensus 140 km~VCeVCGA 149 (294)
...+|+||||
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 5679999998
No 149
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=35.68 E-value=16 Score=31.00 Aligned_cols=19 Identities=32% Similarity=0.550 Sum_probs=16.2
Q ss_pred ccccccccccccCCchHHH
Q 022656 142 ALCEICGSFLVANDAAERT 160 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~d~Rl 160 (294)
.+|+.||+-|...||..-+
T Consensus 124 f~Cp~Cg~~l~~~dn~~~~ 142 (147)
T smart00531 124 FTCPRCGEELEEDDNSEPI 142 (147)
T ss_pred EECCCCCCEEEEcCchhhH
Confidence 8999999999999886543
No 150
>PRK14157 heat shock protein GrpE; Provisional
Probab=35.28 E-value=2e+02 Score=26.72 Aligned_cols=34 Identities=18% Similarity=0.280 Sum_probs=23.8
Q ss_pred ccccccccccccCCchHHHHhhhcccccccHHHHHH
Q 022656 142 ALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRD 177 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe 177 (294)
.+=.++-.||-+.|+-.|.-.|.. +--||..|..
T Consensus 125 a~~~~~~dLLpvlDnLeRAl~~~~--~~~~~~~i~k 158 (227)
T PRK14157 125 GIIDVLTALLPALDDIDRIREHSE--MDDSFKAVAA 158 (227)
T ss_pred HHHHHHHHHhhhhhhHHHHHhccc--cchHHHHHHH
Confidence 344577899999999999877764 3345665533
No 151
>KOG2825 consensus Putative arsenite-translocating ATPase [Inorganic ion transport and metabolism]
Probab=34.89 E-value=78 Score=30.36 Aligned_cols=79 Identities=22% Similarity=0.219 Sum_probs=53.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCc
Q 022656 77 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDA 156 (294)
Q Consensus 77 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~ 156 (294)
..+|-.|..+|.-++.++-.+-..|+. .+..+..+++.|++-...+.+++ ++ +.+...||=-=.-||++..+
T Consensus 170 lgKl~~l~~k~~pm~sq~~sm~g~~~~-~~~~l~~kle~~~~~i~~vn~qF-kd------pd~TtFVcVcI~eflslyEt 241 (323)
T KOG2825|consen 170 LGKLLSLKNKIGPMLSQMGSMFGMEDA-GADDLAGKLEELLEVIEKVNEQF-KD------PDCTTFVCVCIAEFLSLYET 241 (323)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhccccC-CHHHHHHHHHHHHHHHHHHHHHc-CC------CCCceEEEEEHHHHHhHHHH
Confidence 456778888888888765443222222 23456677788888777888887 44 46788999444559999988
Q ss_pred hHHHHhh
Q 022656 157 AERTQSH 163 (294)
Q Consensus 157 d~Rl~dH 163 (294)
++=+++-
T Consensus 242 eRliqeL 248 (323)
T KOG2825|consen 242 ERLIQEL 248 (323)
T ss_pred HHHHHHH
Confidence 7777754
No 152
>COG1340 Uncharacterized archaeal coiled-coil protein [Function unknown]
Probab=34.73 E-value=1.3e+02 Score=28.95 Aligned_cols=28 Identities=25% Similarity=0.394 Sum_probs=14.6
Q ss_pred ChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022656 30 YVPKFEAELAQFCEKLVMDLDRRVRRGRERLS 61 (294)
Q Consensus 30 ~~~~YE~e~l~~L~~lI~d~dRkI~~~k~RL~ 61 (294)
..|..|..+...|.. +...+..++.-+.
T Consensus 128 L~~e~E~~lvq~I~~----L~k~le~~~k~~e 155 (294)
T COG1340 128 LTPEEERELVQKIKE----LRKELEDAKKALE 155 (294)
T ss_pred CChHHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence 334556666554444 4555555555553
No 153
>PF05852 DUF848: Gammaherpesvirus protein of unknown function (DUF848); InterPro: IPR008566 This family consists of several uncharacterised proteins from the Gammaherpesvirinae.
Probab=34.53 E-value=1.9e+02 Score=25.11 Aligned_cols=53 Identities=26% Similarity=0.305 Sum_probs=41.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHH--hcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 75 EKSEQLSVLEEKIKNLLEQVETLG--EAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 75 ~~~e~i~~l~ekI~~ll~eaE~LG--eeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
.....|..++..|.....++..|- .-.+|+.+.+|...|..|+++.+.-...+
T Consensus 58 ~~~~~v~~~~~~i~~k~~El~~L~~~d~~kv~~~E~L~d~v~eLkeel~~el~~l 112 (146)
T PF05852_consen 58 EIKNKVSSLETEISEKKKELSHLKKFDRKKVEDLEKLTDRVEELKEELEFELERL 112 (146)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455677888888888888888874 45789999999999999998776544433
No 154
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=34.45 E-value=15 Score=23.81 Aligned_cols=14 Identities=21% Similarity=0.593 Sum_probs=11.0
Q ss_pred cccccccccccccc
Q 022656 140 KMALCEICGSFLVA 153 (294)
Q Consensus 140 km~VCeVCGA~Ls~ 153 (294)
++.+|.+||+.+++
T Consensus 2 ~~~~C~~C~~~~i~ 15 (33)
T PF08792_consen 2 NLKKCSKCGGNGIV 15 (33)
T ss_pred CceEcCCCCCCeEE
Confidence 35688889888877
No 155
>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.
Probab=34.44 E-value=1.9e+02 Score=21.89 Aligned_cols=45 Identities=24% Similarity=0.347 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHh
Q 022656 77 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQ 126 (294)
Q Consensus 77 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~ 126 (294)
...|.+-+++|..||++.|.|--. =+.+...+-.|+.+...++..
T Consensus 4 ~~~l~EKDe~Ia~L~eEGekLSk~-----el~~~~~IKKLr~~~~e~e~~ 48 (74)
T PF12329_consen 4 EKKLAEKDEQIAQLMEEGEKLSKK-----ELKLNNTIKKLRAKIKELEKQ 48 (74)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHH-----HHhhHHHHHHHHHHHHHHHHH
Confidence 455666777777777777776321 134445555555555444443
No 156
>KOG4765 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.40 E-value=32 Score=34.21 Aligned_cols=41 Identities=24% Similarity=0.475 Sum_probs=28.9
Q ss_pred hhccccccccccccccCCchHHHHhhhcccccccHHHHHHHHHHHHHHHHH
Q 022656 138 EKKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKEAKEK 188 (294)
Q Consensus 138 ~qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eL~~~~~~ 188 (294)
..-|-+|++|||||...-.++ -+-|...-...++++++.+.
T Consensus 87 d~D~lkCe~C~a~L~~s~pq~----------s~s~d~~n~~~ek~~kkLet 127 (419)
T KOG4765|consen 87 DCDMLKCESCGAFLCASLPQQ----------SFSFDRYNQRCEKFKKKLET 127 (419)
T ss_pred cCCeeehhhhhhHHhccCCcc----------ccChHHHHhHHHHHHHHHHH
Confidence 357889999999998664432 34566777777777776544
No 157
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins. Emericella nidulans (Aspergillus nidulans) NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei []. It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.; PDB: 2V66_B 2V71_B.
Probab=34.39 E-value=41 Score=29.71 Aligned_cols=25 Identities=36% Similarity=0.391 Sum_probs=6.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 103 VDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 103 VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
|+|-..|..+|+.|+.|..+|.+++
T Consensus 23 LdEKE~L~~~~QRLkDE~RDLKqEl 47 (166)
T PF04880_consen 23 LDEKENLREEVQRLKDELRDLKQEL 47 (166)
T ss_dssp HHHHHHHHHCH--------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3556666666666666666655543
No 158
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=34.18 E-value=14 Score=26.78 Aligned_cols=10 Identities=40% Similarity=1.006 Sum_probs=3.4
Q ss_pred cccccccccc
Q 022656 141 MALCEICGSF 150 (294)
Q Consensus 141 m~VCeVCGA~ 150 (294)
-.||++|||-
T Consensus 33 ~y~Cp~CgAt 42 (55)
T PF05741_consen 33 KYVCPICGAT 42 (55)
T ss_dssp G---TTT---
T ss_pred cCcCCCCcCc
Confidence 3799999984
No 159
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=33.87 E-value=29 Score=21.10 Aligned_cols=20 Identities=20% Similarity=0.454 Sum_probs=14.4
Q ss_pred ccccccccccccCCchHHHHhhhc
Q 022656 142 ALCEICGSFLVANDAAERTQSHIS 165 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~d~Rl~dH~~ 165 (294)
-.|+||+..+ ...-+.+|+-
T Consensus 2 v~CPiC~~~v----~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV----PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc----cHHHHHHHHH
Confidence 4699999886 3456777765
No 160
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=33.76 E-value=16 Score=26.62 Aligned_cols=11 Identities=36% Similarity=1.032 Sum_probs=6.5
Q ss_pred ccccccccccc
Q 022656 140 KMALCEICGSF 150 (294)
Q Consensus 140 km~VCeVCGA~ 150 (294)
+|.+|+.||.|
T Consensus 4 ~mr~C~~CgvY 14 (56)
T PRK13130 4 KIRKCPKCGVY 14 (56)
T ss_pred cceECCCCCCE
Confidence 45666666655
No 161
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=33.45 E-value=3.1e+02 Score=23.47 Aligned_cols=66 Identities=26% Similarity=0.367 Sum_probs=47.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCH
Q 022656 33 KFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKV 103 (294)
Q Consensus 33 ~YE~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~V 103 (294)
.++.+ +.-|..=+..+...+......|..-. ..+...+....|..|..+|..|..+++.|-..+..
T Consensus 76 ~ld~e-i~~L~~el~~l~~~~k~l~~eL~~L~----~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~~~ 141 (169)
T PF07106_consen 76 ELDAE-IKELREELAELKKEVKSLEAELASLS----SEPTNEELREEIEELEEEIEELEEKLEKLRSGSKP 141 (169)
T ss_pred HHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHh----cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 44555 56666667777777777777775432 22456678889999999999999999999874443
No 162
>PF15070 GOLGA2L5: Putative golgin subfamily A member 2-like protein 5
Probab=33.34 E-value=4.8e+02 Score=27.69 Aligned_cols=45 Identities=22% Similarity=0.361 Sum_probs=26.4
Q ss_pred ccccccccccccccCCchHH-HHhhhccccccc------HHHHHHHHHHHHHH
Q 022656 140 KMALCEICGSFLVANDAAER-TQSHISGKQHIG------YGMVRDFITEYKEA 185 (294)
Q Consensus 140 km~VCeVCGA~Ls~~D~d~R-l~dH~~GK~HlG------y~kIRe~l~eL~~~ 185 (294)
|-++++.=-+|..++ |+.- |.+-+..-+|++ |..+.+.+..|++.
T Consensus 166 K~QL~Elq~~Fv~lt-ne~~elt~~lq~Eq~~~keL~~kl~~l~~~l~~~~e~ 217 (617)
T PF15070_consen 166 KEQLAELQDAFVKLT-NENMELTSALQSEQHVKKELQKKLGELQEKLHNLKEK 217 (617)
T ss_pred HHHHHHHHHHHHHHH-HhhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 446777766776655 3332 555555666665 45566666666554
No 163
>PF05700 BCAS2: Breast carcinoma amplified sequence 2 (BCAS2); InterPro: IPR008409 This family consists of several eukaryotic sequences of unknown function. The mammalian members of this family are annotated as breast carcinoma amplified sequence 2 (BCAS2) proteins []. BCAS2 is a putative spliceosome associated protein [].
Probab=33.17 E-value=2e+02 Score=26.01 Aligned_cols=78 Identities=18% Similarity=0.268 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Q 022656 40 QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 119 (294)
Q Consensus 40 ~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 119 (294)
..|+.++..++..+...++.++.-. ..-.........+|..|+.+-..++.+.=++.. .+..|-.+|..|+.+
T Consensus 139 ~~Le~~~~~le~~l~~~k~~ie~vN--~~RK~~Q~~~~~~L~~Le~~W~~~v~kn~eie~-----a~~~Le~ei~~l~~~ 211 (221)
T PF05700_consen 139 EQLEAMLKRLEKELAKLKKEIEEVN--RERKRRQEEAGEELRYLEQRWKELVSKNLEIEV-----ACEELEQEIEQLKRK 211 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHH
Confidence 4445555555555555555443210 000000112334566666666666655554432 245555666666655
Q ss_pred HHHHH
Q 022656 120 KTTLT 124 (294)
Q Consensus 120 r~~l~ 124 (294)
..+++
T Consensus 212 ~~~~~ 216 (221)
T PF05700_consen 212 AAELK 216 (221)
T ss_pred HHHHh
Confidence 54444
No 164
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=33.13 E-value=1.2e+02 Score=25.08 Aligned_cols=51 Identities=18% Similarity=0.336 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHH
Q 022656 48 DLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEA 106 (294)
Q Consensus 48 d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA 106 (294)
-+|.||+.|-.=+..+ ..-.+.+++..|.++|.+|.+....|-.|..+-..
T Consensus 45 aIDNKIeQAMDLVKtH--------LmfAVREEVe~Lk~qI~eL~er~~~Le~EN~lLk~ 95 (123)
T KOG4797|consen 45 AIDNKIEQAMDLVKTH--------LMFAVREEVEVLKEQIRELEERNSALERENSLLKT 95 (123)
T ss_pred eechHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3567777764433211 12345677778888888887777777555544333
No 165
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=32.82 E-value=2.7e+02 Score=23.09 Aligned_cols=49 Identities=24% Similarity=0.336 Sum_probs=35.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 74 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 74 ~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
.++-.+|..|+++|+.+++++..|-. .+..+|++--.|+-|-+.|...+
T Consensus 4 keiFd~v~~le~~l~~l~~el~~lK~-----~l~~lvEEN~~L~lENe~LR~RL 52 (114)
T COG4467 4 KEIFDQVDNLEEQLGVLLAELGGLKQ-----HLGSLVEENTALRLENEKLRERL 52 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHhhHHHHhhHHHHHHHh
Confidence 45678899999999999999988743 34556666666666666665544
No 166
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=32.77 E-value=16 Score=34.52 Aligned_cols=9 Identities=44% Similarity=1.169 Sum_probs=7.8
Q ss_pred ccccccccc
Q 022656 142 ALCEICGSF 150 (294)
Q Consensus 142 ~VCeVCGA~ 150 (294)
.||.||||-
T Consensus 269 YVCPiCGAT 277 (318)
T KOG4602|consen 269 YVCPICGAT 277 (318)
T ss_pred hcCcccccc
Confidence 799999983
No 167
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=32.60 E-value=18 Score=23.47 Aligned_cols=22 Identities=27% Similarity=0.531 Sum_probs=16.1
Q ss_pred ccccccccccccccCCchHHHHhhhc
Q 022656 140 KMALCEICGSFLVANDAAERTQSHIS 165 (294)
Q Consensus 140 km~VCeVCGA~Ls~~D~d~Rl~dH~~ 165 (294)
...+|+.||-.++. .|+|-||.
T Consensus 3 ~~~~C~nC~R~v~a----~RfA~HLe 24 (33)
T PF08209_consen 3 PYVECPNCGRPVAA----SRFAPHLE 24 (33)
T ss_dssp -EEE-TTTSSEEEG----GGHHHHHH
T ss_pred CeEECCCCcCCcch----hhhHHHHH
Confidence 45789999987765 59999985
No 168
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=32.59 E-value=20 Score=35.45 Aligned_cols=26 Identities=31% Similarity=0.727 Sum_probs=21.5
Q ss_pred ccccccccccccCCchHHHHhhhccccc
Q 022656 142 ALCEICGSFLVANDAAERTQSHISGKQH 169 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~d~Rl~dH~~GK~H 169 (294)
..|+|||.|.--+ -.+.+-||+.--|
T Consensus 375 f~CEICgNyvy~G--R~~FdrHF~E~rH 400 (470)
T COG5188 375 FECEICGNYVYYG--RDRFDRHFEEDRH 400 (470)
T ss_pred eeeeecccccccc--hHHHHhhhhhhhh
Confidence 7899999985544 5779999998888
No 169
>PF08898 DUF1843: Domain of unknown function (DUF1843); InterPro: IPR014994 This domain is found in functionally uncharacterised proteins. It can be found independently or at the C terminus of the protein.
Probab=32.41 E-value=1e+02 Score=22.22 Aligned_cols=33 Identities=39% Similarity=0.538 Sum_probs=20.6
Q ss_pred HHHHHHHHHHH-HHhcCCHHHHHHHHHHHHHHHHHHHHHH
Q 022656 86 KIKNLLEQVET-LGEAGKVDEAEALMRKVEILNVEKTTLT 124 (294)
Q Consensus 86 kI~~ll~eaE~-LGeeG~VdeA~~l~~~ve~Lk~er~~l~ 124 (294)
+++.|+.++|+ |.+.|+|-.| ++.|+.|...|+
T Consensus 18 ~MK~l~~~aeq~L~~~~~i~~a------l~~Lk~EIaklE 51 (53)
T PF08898_consen 18 QMKALAAQAEQQLAEAGDIAAA------LEKLKAEIAKLE 51 (53)
T ss_pred HHHHHHHHHHHHHccchHHHHH------HHHHHHHHHHHh
Confidence 44556666665 6666666544 566777776665
No 170
>COG4499 Predicted membrane protein [Function unknown]
Probab=32.24 E-value=1.8e+02 Score=29.28 Aligned_cols=75 Identities=13% Similarity=0.116 Sum_probs=46.0
Q ss_pred HHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Q 022656 43 EKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 119 (294)
Q Consensus 43 ~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 119 (294)
.+.+.|.+=-.=..-.++++.. +.+...-.+.++.|.+++.+|+.++++.+++..+-+-+++...-.+-|+++.+
T Consensus 336 Ar~L~D~d~~~~Al~k~~eevk--sn~~lsg~~r~e~lk~~n~~lqd~~k~~~e~k~e~das~~aeaka~eek~~~e 410 (434)
T COG4499 336 ARNLDDNDLTLLALTKLYEEVK--SNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQE 410 (434)
T ss_pred HHhCCcchhHHHHHHHHHHHHh--cccCCCchHHHHHHHHHHHHHHHHHHHHHHhhcccccchhhHhhhhhhhhhhh
Confidence 3444444443333334443332 22334456788899999999999999999999876665554444444455443
No 171
>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]
Probab=32.19 E-value=1.9e+02 Score=30.73 Aligned_cols=40 Identities=15% Similarity=0.324 Sum_probs=23.3
Q ss_pred hhhHHHHHHHHHHHHHHHHHHH-----HHHhcCCHHHHHHHHHHH
Q 022656 74 AEKSEQLSVLEEKIKNLLEQVE-----TLGEAGKVDEAEALMRKV 113 (294)
Q Consensus 74 ~~~~e~i~~l~ekI~~ll~eaE-----~LGeeG~VdeA~~l~~~v 113 (294)
++.+.+|.+++.+|.++-+.|+ -+.-+|.|++||...+++
T Consensus 103 qel~seI~~~n~kiEelk~~i~~~q~eL~~Lk~~ieqaq~~~~El 147 (907)
T KOG2264|consen 103 QELNSEIEEINTKIEELKRLIPQKQLELSALKGEIEQAQRQLEEL 147 (907)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHHHHHHHH
Confidence 4455566677777766654443 344467777776655443
No 172
>PF05597 Phasin: Poly(hydroxyalcanoate) granule associated protein (phasin); InterPro: IPR008769 Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.
Probab=32.14 E-value=2.7e+02 Score=23.54 Aligned_cols=23 Identities=30% Similarity=0.489 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Q 022656 77 SEQLSVLEEKIKNLLEQVETLGE 99 (294)
Q Consensus 77 ~e~i~~l~ekI~~ll~eaE~LGe 99 (294)
...|..|..+|..|..+++.|-.
T Consensus 108 ~~dv~~L~~rId~L~~~v~~l~~ 130 (132)
T PF05597_consen 108 RKDVEALSARIDQLTAQVERLAN 130 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 46788888888888888887743
No 173
>smart00150 SPEC Spectrin repeats.
Probab=32.13 E-value=2e+02 Score=20.91 Aligned_cols=49 Identities=31% Similarity=0.362 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 78 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
..|......|..+...++.|...|.. .+..+...++.|+.....|...+
T Consensus 45 ~e~~~~~~~v~~~~~~~~~L~~~~~~-~~~~i~~~~~~l~~~w~~l~~~~ 93 (101)
T smart00150 45 AELEAHEERVEALNELGEQLIEEGHP-DAEEIEERLEELNERWEELKELA 93 (101)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556666667777777777777643 45667777788877777766544
No 174
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=32.05 E-value=1.8e+02 Score=23.18 Aligned_cols=22 Identities=27% Similarity=0.477 Sum_probs=12.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHH
Q 022656 76 KSEQLSVLEEKIKNLLEQVETL 97 (294)
Q Consensus 76 ~~e~i~~l~ekI~~ll~eaE~L 97 (294)
...++..|..+|+.+......|
T Consensus 4 l~~~~~~l~~~i~~l~~~~~~l 25 (129)
T cd00890 4 LAAQLQQLQQQLEALQQQLQKL 25 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3345555666666665555544
No 175
>PF07967 zf-C3HC: C3HC zinc finger-like ; InterPro: IPR012935 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) and other proteins. NIPA is thought to perform an antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signalling events []. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe protein containing this domain (O94506 from SWISSPROT) is involved in mRNA export from the nucleus []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=31.96 E-value=15 Score=30.63 Aligned_cols=17 Identities=41% Similarity=0.767 Sum_probs=15.2
Q ss_pred hhccccccccccccccC
Q 022656 138 EKKMALCEICGSFLVAN 154 (294)
Q Consensus 138 ~qkm~VCeVCGA~Ls~~ 154 (294)
.+.+-.|+.||++|++.
T Consensus 40 ~~d~l~C~~C~~~l~~~ 56 (133)
T PF07967_consen 40 SKDMLKCESCGARLCVK 56 (133)
T ss_pred CCCEEEeCCCCCEEEEe
Confidence 47788999999999988
No 176
>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]
Probab=31.87 E-value=3.5e+02 Score=30.61 Aligned_cols=88 Identities=14% Similarity=0.220 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHH--HHHHHHH
Q 022656 34 FEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVD--EAEALMR 111 (294)
Q Consensus 34 YE~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~Vd--eA~~l~~ 111 (294)
|=|-++--.++=+..|...|...++++..-++ ........+..+..++...-+++.++-.++++- +.+.+-+
T Consensus 271 ~~W~~V~~~~~ql~~~~~~i~~~qek~~~l~~------ki~~~~~k~~~~r~k~teiea~i~~~~~e~~~~d~Ei~~~r~ 344 (1074)
T KOG0250|consen 271 MAWAWVNEVERQLNNQEEEIKKKQEKVDTLQE------KIEEKQGKIEEARQKLTEIEAKIGELKDEVDAQDEEIEEARK 344 (1074)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHhhhhhHHHHHHHHHHHhhhhhhHHHHHHHH
Confidence 33444444444555566666666666653221 122333445555555555555555555555543 2344555
Q ss_pred HHHHHHHHHHHHHHhh
Q 022656 112 KVEILNVEKTTLTQQS 127 (294)
Q Consensus 112 ~ve~Lk~er~~l~~~~ 127 (294)
-++.++.+..+++.++
T Consensus 345 ~~~~~~re~~~~~~~~ 360 (1074)
T KOG0250|consen 345 DLDDLRREVNDLKEEI 360 (1074)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5555555555555554
No 177
>KOG1510 consensus RNA polymerase II holoenzyme and mediator subcomplex, subunit SURB7/SRB7 [Transcription]
Probab=31.83 E-value=3.3e+02 Score=23.38 Aligned_cols=43 Identities=23% Similarity=0.353 Sum_probs=28.4
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Q 022656 74 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKT 121 (294)
Q Consensus 74 ~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~ 121 (294)
....++|..|++++.+...+.+.+ |.++..|+.+|+.+-+...
T Consensus 87 e~Ql~~i~kLq~en~e~~~el~~~-----v~~~e~Ll~~vq~~le~~a 129 (139)
T KOG1510|consen 87 EAQLEKIKKLQEENEEVALELEEL-----VSKGEKLLEQVQSLLEDIA 129 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHH
Confidence 344566888888887777766665 4556667777776655543
No 178
>KOG2801 consensus Probable Rab-GAPs [Intracellular trafficking, secretion, and vesicular transport]
Probab=31.82 E-value=15 Score=35.63 Aligned_cols=22 Identities=27% Similarity=0.666 Sum_probs=16.4
Q ss_pred cccccccccCCchHHHHhhhccccc
Q 022656 145 EICGSFLVANDAAERTQSHISGKQH 169 (294)
Q Consensus 145 eVCGA~Ls~~D~d~Rl~dH~~GK~H 169 (294)
+||||||+..=++ .+.|+||+-
T Consensus 402 evcgaylstdwse---rnkfggklg 423 (559)
T KOG2801|consen 402 EVCGAYLSTDWSE---RNKFGGKLG 423 (559)
T ss_pred HHhhHhcccchhh---hcccCceec
Confidence 7999999865333 368999963
No 179
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=31.34 E-value=19 Score=23.71 Aligned_cols=15 Identities=33% Similarity=0.698 Sum_probs=11.2
Q ss_pred ccccccccccccCCc
Q 022656 142 ALCEICGSFLVANDA 156 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~ 156 (294)
..|+|||+.+...+.
T Consensus 9 ~~C~~C~~~~~~~~d 23 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDD 23 (36)
T ss_pred CcCCCCCCeEeEccC
Confidence 459999998666553
No 180
>PRK08359 transcription factor; Validated
Probab=31.00 E-value=17 Score=32.26 Aligned_cols=9 Identities=56% Similarity=1.302 Sum_probs=7.1
Q ss_pred ccccccccc
Q 022656 144 CEICGSFLV 152 (294)
Q Consensus 144 CeVCGA~Ls 152 (294)
||+||+-+.
T Consensus 9 CEiCG~~i~ 17 (176)
T PRK08359 9 CEICGAEIR 17 (176)
T ss_pred eecCCCccC
Confidence 999998653
No 181
>COG4477 EzrA Negative regulator of septation ring formation [Cell division and chromosome partitioning]
Probab=30.73 E-value=3.8e+02 Score=28.14 Aligned_cols=101 Identities=23% Similarity=0.231 Sum_probs=50.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcCCHHHH---------HHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhcc--ccc
Q 022656 76 KSEQLSVLEEKIKNLLEQVETLGEAGKVDEA---------EALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKM--ALC 144 (294)
Q Consensus 76 ~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA---------~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm--~VC 144 (294)
..+.|..++++|..|..-.|-=.+.+++-+. ..+-..-+.|+++.+.+.+.| .-........++. ..-
T Consensus 279 aeeel~~I~e~ie~lYd~lE~EveA~~~V~~~~~~l~~~l~k~ke~n~~L~~Eie~V~~sY-~l~e~e~~~vr~~e~eL~ 357 (570)
T COG4477 279 AEEELGLIQEKIESLYDLLEREVEAKNVVEENLPILPDYLEKAKENNEHLKEEIERVKESY-RLAETELGSVRKFEKELK 357 (570)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHHHh-ccChhHHHHHHHHHHHHH
Confidence 3456777777777777777766666655332 122222334444444444443 1100001011111 111
Q ss_pred cccccccccCCchHHHHhhhcccccccHHHHHHHHHHHHHH
Q 022656 145 EICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKEA 185 (294)
Q Consensus 145 eVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eL~~~ 185 (294)
++=..|..+ .-.++.+|+.|.-+.++++++...
T Consensus 358 el~~~~~~i--------~~~~~~~~~~yS~lq~~l~~~~~~ 390 (570)
T COG4477 358 ELESVLDEI--------LENIEAQEVAYSELQDNLEEIEKA 390 (570)
T ss_pred HHHHHHHHH--------HHHhhcccccHHHHHHHHHHHHHH
Confidence 111111111 124688999999999999998775
No 182
>PRK11637 AmiB activator; Provisional
Probab=30.56 E-value=4.4e+02 Score=26.07 Aligned_cols=19 Identities=26% Similarity=0.279 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 022656 78 EQLSVLEEKIKNLLEQVET 96 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~ 96 (294)
.+|..++.+|..+..++..
T Consensus 75 ~~l~~l~~qi~~~~~~i~~ 93 (428)
T PRK11637 75 AQLKKQEEAISQASRKLRE 93 (428)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444443
No 183
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=30.42 E-value=1.3e+02 Score=29.00 Aligned_cols=12 Identities=50% Similarity=0.852 Sum_probs=9.6
Q ss_pred cccccccccccc
Q 022656 141 MALCEICGSFLV 152 (294)
Q Consensus 141 m~VCeVCGA~Ls 152 (294)
-.+|+|||+.-+
T Consensus 184 ~~~CPvCGs~P~ 195 (305)
T TIGR01562 184 RTLCPACGSPPV 195 (305)
T ss_pred CCcCCCCCChhh
Confidence 459999999864
No 184
>PHA03161 hypothetical protein; Provisional
Probab=30.28 E-value=1.9e+02 Score=25.21 Aligned_cols=49 Identities=18% Similarity=0.153 Sum_probs=40.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHh--cCCHHHHHHHHHHHHHHHHHHHHH
Q 022656 75 EKSEQLSVLEEKIKNLLEQVETLGE--AGKVDEAEALMRKVEILNVEKTTL 123 (294)
Q Consensus 75 ~~~e~i~~l~ekI~~ll~eaE~LGe--eG~VdeA~~l~~~ve~Lk~er~~l 123 (294)
.+...|..++..|..+-++++.|-. -.+|+.+.+|...|+.|+.+..--
T Consensus 58 ~i~~~v~~l~~~I~~k~kE~~~L~~fd~kkl~~~E~L~drv~eLkeel~~E 108 (150)
T PHA03161 58 SIEGMLQAVDLSIQEKKKELSLLKAFDRHKLSAAEDLQDKILELKEDIHFE 108 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566788899999999999998864 578999999999999998876543
No 185
>PF13945 NST1: Salt tolerance down-regulator
Probab=30.06 E-value=37 Score=30.59 Aligned_cols=35 Identities=20% Similarity=0.501 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccc
Q 022656 109 LMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSF 150 (294)
Q Consensus 109 l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~ 150 (294)
.-+.-..|+.++++|...+ .. +++--=.|.|||--
T Consensus 116 eeERr~LVkIEKe~VLkkm-Ke------qq~h~C~C~vCgr~ 150 (190)
T PF13945_consen 116 EEERRSLVKIEKEAVLKKM-KE------QQKHSCSCSVCGRK 150 (190)
T ss_pred HHHHHHHHHhhHHHHHHHH-HH------HhccCcccHHHhch
Confidence 3345566777777777665 32 34555789999954
No 186
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=30.00 E-value=18 Score=35.75 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=23.1
Q ss_pred ccccccccccccccCCchHHHHhhhccccccc
Q 022656 140 KMALCEICGSFLVANDAAERTQSHISGKQHIG 171 (294)
Q Consensus 140 km~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlG 171 (294)
+-.-|++||-+.+.. .=...|+.||.|.-
T Consensus 237 ~~~YC~~C~r~f~~~---~VFe~Hl~gK~H~k 265 (470)
T COG5188 237 PKVYCVKCGREFSRS---KVFEYHLEGKRHCK 265 (470)
T ss_pred cceeeHhhhhHhhhh---HHHHHHHhhhhhhh
Confidence 447899999998754 34789999999954
No 187
>PLN02748 tRNA dimethylallyltransferase
Probab=29.97 E-value=28 Score=35.49 Aligned_cols=29 Identities=24% Similarity=0.541 Sum_probs=21.5
Q ss_pred ccccccccccccccCCchHHHHhhhcccccc
Q 022656 140 KMALCEICGSFLVANDAAERTQSHISGKQHI 170 (294)
Q Consensus 140 km~VCeVCGA~Ls~~D~d~Rl~dH~~GK~Hl 170 (294)
+..+||||+.-.++++ .=-+-|+.|+.|-
T Consensus 417 ~~~~Ce~C~~~~~~G~--~eW~~Hlksr~Hk 445 (468)
T PLN02748 417 TQYVCEACGNKVLRGA--HEWEQHKQGRGHR 445 (468)
T ss_pred ccccccCCCCcccCCH--HHHHHHhcchHHH
Confidence 5568999996444554 4477899999994
No 188
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=29.84 E-value=1.4e+02 Score=28.89 Aligned_cols=13 Identities=38% Similarity=0.991 Sum_probs=10.4
Q ss_pred ccccccccccccc
Q 022656 140 KMALCEICGSFLV 152 (294)
Q Consensus 140 km~VCeVCGA~Ls 152 (294)
.-.+|+|||+.-+
T Consensus 186 ~~~~CPvCGs~P~ 198 (309)
T PRK03564 186 QRQFCPVCGSMPV 198 (309)
T ss_pred CCCCCCCCCCcch
Confidence 3589999999854
No 189
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=29.84 E-value=72 Score=18.33 Aligned_cols=23 Identities=13% Similarity=0.245 Sum_probs=18.4
Q ss_pred HHHHHHhcCCHHHHHHHHHHHHH
Q 022656 93 QVETLGEAGKVDEAEALMRKVEI 115 (294)
Q Consensus 93 eaE~LGeeG~VdeA~~l~~~ve~ 115 (294)
=+..++..|++++|..++.+..+
T Consensus 6 li~~~~~~~~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 6 LISGYCKMGQFEEALEVFDEMRE 28 (31)
T ss_pred HHHHHHccchHHHHHHHHHHHhH
Confidence 35678999999999998876543
No 190
>TIGR00606 rad50 rad50. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.64 E-value=9.1e+02 Score=27.77 Aligned_cols=32 Identities=13% Similarity=0.362 Sum_probs=19.6
Q ss_pred hccccccccccccccCCchHHHHhhhcccccc
Q 022656 139 KKMALCEICGSFLVANDAAERTQSHISGKQHI 170 (294)
Q Consensus 139 qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~Hl 170 (294)
..-.+|++|.--+...+.-..+-.++..++--
T Consensus 675 ~~~~~C~LC~R~f~~eee~~~f~~~L~~~~~~ 706 (1311)
T TIGR00606 675 ENQSCCPVCQRVFQTEAELQEFISDLQSKLRL 706 (1311)
T ss_pred ccCCcCCCCCCCCCChhHHHHHHHHHHHHHhc
Confidence 34469999998765554434555555555443
No 191
>PF13922 PHD_3: PHD domain of transcriptional enhancer, Asx
Probab=29.57 E-value=15 Score=27.72 Aligned_cols=13 Identities=46% Similarity=1.055 Sum_probs=11.7
Q ss_pred hhccccccccccc
Q 022656 138 EKKMALCEICGSF 150 (294)
Q Consensus 138 ~qkm~VCeVCGA~ 150 (294)
-+-|-+|.-||||
T Consensus 40 LkAMi~Cq~CGAF 52 (69)
T PF13922_consen 40 LKAMIMCQGCGAF 52 (69)
T ss_pred hHHHHHHhhccch
Confidence 4689999999999
No 192
>PF15003 HAUS2: HAUS augmin-like complex subunit 2
Probab=29.45 E-value=5.1e+02 Score=24.79 Aligned_cols=88 Identities=17% Similarity=0.187 Sum_probs=54.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcCCHHHH---HHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccc
Q 022656 76 KSEQLSVLEEKIKNLLEQVETLGEAGKVDEA---EALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLV 152 (294)
Q Consensus 76 ~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA---~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls 152 (294)
...+|..+..+|.++--++|.|-.+-++-.. ..+..+++.|+.--.-|+.-+ .++....+--|+ +.||-+|-
T Consensus 52 ~L~QIt~iQaeI~q~nlEielLkleKeTADltH~~~L~~K~~~Lq~m~shLe~VL-k~K~~Lr~RLqk----P~~qe~LP 126 (277)
T PF15003_consen 52 RLRQITNIQAEIDQLNLEIELLKLEKETADLTHPDYLAEKCEALQSMNSHLEAVL-KEKDRLRQRLQK----PYCQENLP 126 (277)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHhhcchHhhhCHHHHHHHHHHHHHHHHHHHHHH-HhHHHHHHHHHh----hhhhcCcc
Confidence 3567888999999999999999888777654 456666666665544444433 221111111111 23788888
Q ss_pred cCCchHHHHhhhcccc
Q 022656 153 ANDAAERTQSHISGKQ 168 (294)
Q Consensus 153 ~~D~d~Rl~dH~~GK~ 168 (294)
+.-.-.|-.-||...+
T Consensus 127 VEA~yHr~vVeLL~la 142 (277)
T PF15003_consen 127 VEAQYHRYVVELLELA 142 (277)
T ss_pred chhhhhHHHHHHHHHH
Confidence 8777777666665543
No 193
>PRK13844 recombination protein RecR; Provisional
Probab=29.25 E-value=84 Score=28.56 Aligned_cols=9 Identities=22% Similarity=0.312 Sum_probs=6.0
Q ss_pred hhhcccccc
Q 022656 162 SHISGKQHI 170 (294)
Q Consensus 162 dH~~GK~Hl 170 (294)
..|.|+=||
T Consensus 101 ~~y~G~YhV 109 (200)
T PRK13844 101 GIYRGKYFV 109 (200)
T ss_pred CccceEEEE
Confidence 467777773
No 194
>PF10152 DUF2360: Predicted coiled-coil domain-containing protein (DUF2360); InterPro: IPR019309 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53.
Probab=29.23 E-value=1.9e+02 Score=24.73 Aligned_cols=44 Identities=20% Similarity=0.373 Sum_probs=32.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHH
Q 022656 33 KFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKN 89 (294)
Q Consensus 33 ~YE~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ 89 (294)
.|=.-..+||.+|...|+-|+.....||.+ +...|..|+.++..
T Consensus 3 ~Fi~~tv~fLN~F~~~cE~kL~~~e~~Lq~-------------~E~~l~iLEaKL~S 46 (148)
T PF10152_consen 3 HFIVHTVQFLNRFASVCEEKLSDMEQRLQR-------------LEATLNILEAKLSS 46 (148)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHhc
Confidence 456667899999999999999999888842 23455666666543
No 195
>PRK14149 heat shock protein GrpE; Provisional
Probab=29.23 E-value=1.8e+02 Score=26.15 Aligned_cols=43 Identities=16% Similarity=0.074 Sum_probs=28.6
Q ss_pred ccccccccccccCCchHHHHhhhc-----ccccccHHHHHHHHHHHHH
Q 022656 142 ALCEICGSFLVANDAAERTQSHIS-----GKQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~d~Rl~dH~~-----GK~HlGy~kIRe~l~eL~~ 184 (294)
.+=.++..||.+.|+-.|.-.|.. +.+.-|+.+|...|..+-+
T Consensus 84 a~~~~~~~LLpVlDnLerAl~~~~~~~~~~~l~~Gv~mi~k~l~~vL~ 131 (191)
T PRK14149 84 AYEKIALDLLPVIDALLGALKSAAEVDKESALTKGLELTMEKLHEVLA 131 (191)
T ss_pred HHHHHHHHHhhHHhHHHHHHhccccccchHHHHHHHHHHHHHHHHHHH
Confidence 333455788999999999766654 3456677777666655443
No 196
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=29.13 E-value=1.5e+02 Score=23.90 Aligned_cols=39 Identities=23% Similarity=0.129 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Q 022656 80 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNV 118 (294)
Q Consensus 80 i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 118 (294)
+......|...+..+++....++.++|...+.++...=.
T Consensus 21 l~~~~~~i~~~l~~i~~~i~~~dW~~A~~~~~~l~~~W~ 59 (121)
T PF14276_consen 21 LNNSTDSIEEQLEQIEEAIENEDWEKAYKETEELEKEWD 59 (121)
T ss_pred hhhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHH
Confidence 445677888888999999999999999988877776633
No 197
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=28.71 E-value=2.4e+02 Score=22.89 Aligned_cols=15 Identities=20% Similarity=0.253 Sum_probs=8.0
Q ss_pred ccccccccccccccC
Q 022656 140 KMALCEICGSFLVAN 154 (294)
Q Consensus 140 km~VCeVCGA~Ls~~ 154 (294)
.-..|-.||..+...
T Consensus 53 ~~~~C~~C~~~fg~l 67 (118)
T PF02318_consen 53 GERHCARCGKPFGFL 67 (118)
T ss_dssp CCSB-TTTS-BCSCT
T ss_pred CCcchhhhCCccccc
Confidence 456788888754433
No 198
>PF06632 XRCC4: DNA double-strand break repair and V(D)J recombination protein XRCC4; InterPro: IPR010585 This entry represents the DNA double-strand break repair and V(D)J recombination protein XRCC4, which is found in certain Metazoans, fungi and plants. XRCC4 binds to DNA, and to DNA ligase IV (LIG4) to form the LIG4-XRCC4 complex []. The LIG4-XRCC4 complex is responsible for the ligation step in the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair. XRCC4 enhances the joining activity of LIG4. It is thought that XRCC4 and LIG4 are essential for alignment-based gap filling, as well as for final ligation of the breaks []. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. ; GO: 0003677 DNA binding, 0006302 double-strand break repair, 0006310 DNA recombination, 0005634 nucleus; PDB: 3RWR_R 1IK9_B 3SR2_E 3Q4F_H 3II6_B 1FU1_A 3MUD_B.
Probab=28.67 E-value=2.7e+02 Score=27.34 Aligned_cols=43 Identities=23% Similarity=0.264 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 80 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 80 i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
+..|.+++..|..+.+.|- .++..+..++|++...|++++..+
T Consensus 139 ~~~l~~~~~~L~~enerL~-----~e~~~~~~qlE~~v~~K~~~E~~L 181 (342)
T PF06632_consen 139 NSRLQAENEHLQKENERLE-----SEANKLLKQLEKFVNAKEEHEEDL 181 (342)
T ss_dssp HHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455666666666666663 355677777777777777777665
No 199
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=28.58 E-value=36 Score=24.10 Aligned_cols=40 Identities=23% Similarity=0.409 Sum_probs=28.5
Q ss_pred hccccccccccccccCCchHHHHhhhcccccccHHHHHHHHHHHHH
Q 022656 139 KKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKE 184 (294)
Q Consensus 139 qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eL~~ 184 (294)
+|-..||+|-.- .| =++.|+.++.|.-|++=-..+..|..
T Consensus 3 ~k~GYCE~Cr~k---fd---~l~~Hi~s~~Hr~FA~~~~Nf~~lD~ 42 (49)
T smart00586 3 KKPGYCENCREK---YD---DLETHLLSEKHRRFAENNDNFQALDD 42 (49)
T ss_pred CCCcccccHhHH---Hh---hHHHHhccHHHHHHHcCchhHHHHHH
Confidence 566899999754 22 37889999999877665555555544
No 200
>PF14828 Amnionless: Amnionless
Probab=28.46 E-value=17 Score=36.62 Aligned_cols=15 Identities=27% Similarity=0.727 Sum_probs=12.1
Q ss_pred ccccccccccccCCc
Q 022656 142 ALCEICGSFLVANDA 156 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~ 156 (294)
.=|+||||+|...-+
T Consensus 227 hCC~iCGa~v~~~~~ 241 (437)
T PF14828_consen 227 HCCPICGAIVTLEYS 241 (437)
T ss_pred CchhhcceEEEEeec
Confidence 679999999886544
No 201
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=28.44 E-value=21 Score=19.62 Aligned_cols=19 Identities=26% Similarity=0.684 Sum_probs=10.5
Q ss_pred cccccccccccCCchHHHHhhh
Q 022656 143 LCEICGSFLVANDAAERTQSHI 164 (294)
Q Consensus 143 VCeVCGA~Ls~~D~d~Rl~dH~ 164 (294)
+|++||.-.. +..-+..|+
T Consensus 2 ~C~~C~~~~~---~~~~l~~H~ 20 (24)
T PF13894_consen 2 QCPICGKSFR---SKSELRQHM 20 (24)
T ss_dssp E-SSTS-EES---SHHHHHHHH
T ss_pred CCcCCCCcCC---cHHHHHHHH
Confidence 6999997543 334555554
No 202
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.41 E-value=2.7e+02 Score=26.18 Aligned_cols=39 Identities=26% Similarity=0.262 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 89 NLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 89 ~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
+.-+.+..--+.|+|++-+....+|+.|+.++..|..+.
T Consensus 189 Eeeed~~l~reieeidEQi~~~kkvekl~~qK~ellnkk 227 (264)
T KOG3032|consen 189 EEEEDAALTREIEEIDEQISYKKKVEKLKRQKMELLNKK 227 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333334455778888899999999999999988765
No 203
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=28.40 E-value=47 Score=33.81 Aligned_cols=42 Identities=21% Similarity=0.525 Sum_probs=30.5
Q ss_pred ccccccccccccCCchHHHHhhhccccc------c---------cHHHHHHHHHHHHHH
Q 022656 142 ALCEICGSFLVANDAAERTQSHISGKQH------I---------GYGMVRDFITEYKEA 185 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~d~Rl~dH~~GK~H------l---------Gy~kIRe~l~eL~~~ 185 (294)
.-|+|||-|.--+ ....+-||.---| | |-.+|-++++-.+..
T Consensus 402 y~CEICGNy~Y~G--rkaF~RHF~EwRH~hGmrCLGIpnt~~F~~IT~I~eA~~LW~k~ 458 (497)
T KOG2636|consen 402 YNCEICGNYVYKG--RKAFDRHFNEWRHAHGMRCLGIPNTSVFKGITKIEEALELWKKM 458 (497)
T ss_pred cceeeccCccccC--cHHHHHHhHHHHHhhcceecCCCCcHHhcccccHHHHHHHHHHH
Confidence 7899999985555 5779999997777 3 346777777655543
No 204
>PF06751 EutB: Ethanolamine ammonia lyase large subunit (EutB); InterPro: IPR010628 This family consists of several bacterial ethanolamine ammonia lyase large subunit (EutB) proteins. Ethanolamine ammonia-lyase is a bacterial enzyme that catalyses the adenosylcobalamin-dependent conversion of certain vicinal amino alcohols to oxo compounds and ammonia. The enzyme is a heterodimer composed of subunits of Mr approximately 55,000 (EutB) and 35,000 (EutC) [].; GO: 0008851 ethanolamine ammonia-lyase activity, 0006520 cellular amino acid metabolic process; PDB: 3ABQ_C 3ABS_C 3AO0_A 3ABR_A 3ABO_C 3ANY_A 2QEZ_B.
Probab=28.06 E-value=20 Score=35.99 Aligned_cols=30 Identities=23% Similarity=0.421 Sum_probs=20.0
Q ss_pred hccccccccccccc---cCCchH--H--HHhhhccccc
Q 022656 139 KKMALCEICGSFLV---ANDAAE--R--TQSHISGKQH 169 (294)
Q Consensus 139 qkm~VCeVCGA~Ls---~~D~d~--R--l~dH~~GK~H 169 (294)
+.+-|=.|-| |+. ..|..| | |+|||+||+|
T Consensus 310 ~P~lVNtVvG-FIGPEylyd~kQiiRAgLEDhF~GKL~ 346 (444)
T PF06751_consen 310 DPFLVNTVVG-FIGPEYLYDGKQIIRAGLEDHFMGKLL 346 (444)
T ss_dssp -ESEEEEECC-CSSTTTSSBCHHHHHHHHHHHHHHHHC
T ss_pred CceeEeecce-ecccceeeccchheecchHhhhhhhhc
Confidence 3445666766 333 456665 3 8899999999
No 205
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=27.77 E-value=2.7e+02 Score=21.05 Aligned_cols=18 Identities=44% Similarity=0.617 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 022656 80 LSVLEEKIKNLLEQVETL 97 (294)
Q Consensus 80 i~~l~ekI~~ll~eaE~L 97 (294)
+..|+.+|+.++..|..|
T Consensus 6 l~~LE~ki~~aveti~~L 23 (72)
T PF06005_consen 6 LEQLEEKIQQAVETIALL 23 (72)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 444444444444444444
No 206
>TIGR00618 sbcc exonuclease SbcC. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.76 E-value=2.7e+02 Score=31.01 Aligned_cols=69 Identities=19% Similarity=0.202 Sum_probs=0.0
Q ss_pred hhhHHHHHHHHH-HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhcccccccccc
Q 022656 74 AEKSEQLSVLEE-KIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGS 149 (294)
Q Consensus 74 ~~~~e~i~~l~e-kI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA 149 (294)
.....++..++. .+..+..+.+.+-.. +..+...+..++.+-.....+.... .....-..-.+|++||+
T Consensus 440 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~l~~~~~~~~~~~~~~~~~-----~~r~~l~~~~~cplcgs 509 (1042)
T TIGR00618 440 AELCAAAITCTAQCEKLEKIHLQESAQS--LKEREQQLQTKEQIHLQETRKKAVV-----LARLLELQEEPCPLCGS 509 (1042)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHhcCCCCCCCCCCC
No 207
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=27.48 E-value=5.7e+02 Score=24.65 Aligned_cols=20 Identities=25% Similarity=0.356 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 022656 34 FEAELAQFCEKLVMDLDRRVR 54 (294)
Q Consensus 34 YE~e~l~~L~~lI~d~dRkI~ 54 (294)
|||. +..|+.|+..++..+.
T Consensus 135 YeWR-~kllegLk~~L~~~~~ 154 (312)
T smart00787 135 YEWR-MKLLEGLKEGLDENLE 154 (312)
T ss_pred HHHH-HHHHHHHHHHHHHHHH
Confidence 5663 3445555555555443
No 208
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=27.35 E-value=2e+02 Score=27.58 Aligned_cols=14 Identities=0% Similarity=0.045 Sum_probs=6.8
Q ss_pred ccccHHHHHHHHHH
Q 022656 168 QHIGYGMVRDFITE 181 (294)
Q Consensus 168 ~HlGy~kIRe~l~e 181 (294)
..|.|..|-.++-.
T Consensus 164 ~~V~W~EINAA~Gq 177 (314)
T PF04111_consen 164 VPVEWNEINAAWGQ 177 (314)
T ss_dssp B---HHHHHHHHHH
T ss_pred CCCChHHHHHHHHH
Confidence 34667777666643
No 209
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=27.31 E-value=2.6e+02 Score=22.97 Aligned_cols=64 Identities=22% Similarity=0.341 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCch
Q 022656 82 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAA 157 (294)
Q Consensus 82 ~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d 157 (294)
...+.|.-|.+-|+.....| -+-|-..++.++.+-.. .. ...+..=|=..|.-|.+||+.+=|.
T Consensus 9 ia~eRi~~L~~lA~~~~~~~-~~laRrYv~la~~Is~K----------~r-v~lp~~iKR~~CkkC~t~Lvpg~n~ 72 (105)
T COG2023 9 IAAERIDYLYSLAEETFRTG-PDLARRYVKLARRISMK----------YR-VRLPREIKRTICKKCYTPLVPGKNA 72 (105)
T ss_pred HHHHHHHHHHHHHHHHHhcC-cHHHHHHHHHHHHHHHh----------hc-cccCHHHHHHhccccCcccccCcce
Confidence 44678999999999999999 57777777666655321 11 1133455668899999999987554
No 210
>COG5185 HEC1 Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]
Probab=27.08 E-value=2.8e+02 Score=28.79 Aligned_cols=64 Identities=23% Similarity=0.290 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccc
Q 022656 77 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMA 142 (294)
Q Consensus 77 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~ 142 (294)
.+....|..+|..|-.+-+.|.+ ++.+|+++...++.|.+.+.+|..-.+.-.+.+.+..+||+
T Consensus 263 ~~~~~~i~~~i~~lk~~n~~l~e--~i~ea~k~s~~i~~l~ek~r~l~~D~nk~~~~~~~mk~K~~ 326 (622)
T COG5185 263 EKFVHIINTDIANLKTQNDNLYE--KIQEAMKISQKIKTLREKWRALKSDSNKYENYVNAMKQKSQ 326 (622)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHH
Confidence 45677888888888888888765 58899999999999998888886433122333333344443
No 211
>CHL00102 rps20 ribosomal protein S20
Probab=27.02 E-value=1.5e+02 Score=23.65 Aligned_cols=36 Identities=11% Similarity=0.052 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHHHhc-------CCHHHHHHHHHHHHHHHH
Q 022656 83 LEEKIKNLLEQVETLGEA-------GKVDEAEALMRKVEILNV 118 (294)
Q Consensus 83 l~ekI~~ll~eaE~LGee-------G~VdeA~~l~~~ve~Lk~ 118 (294)
.-..|..++.+++.+.+. |++++|+.++..+..+-.
T Consensus 24 ~kS~~rT~iKk~~~ai~~~~~~~~~~d~~~a~~~l~~a~s~iD 66 (93)
T CHL00102 24 YKSSVKTLIKKYLKNLEDYKTSPNSNNKKKVQETLSSVYSKID 66 (93)
T ss_pred HHHHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHH
Confidence 344555666677777766 999999999988887654
No 212
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=26.63 E-value=23 Score=29.32 Aligned_cols=18 Identities=28% Similarity=0.335 Sum_probs=14.4
Q ss_pred cccHHHHHHHHHHHHHHH
Q 022656 169 HIGYGMVRDFITEYKEAK 186 (294)
Q Consensus 169 HlGy~kIRe~l~eL~~~~ 186 (294)
-+.|-.||..|++|-++.
T Consensus 60 giSYPTvR~rLd~ii~~l 77 (113)
T PF09862_consen 60 GISYPTVRNRLDKIIEKL 77 (113)
T ss_pred CCCcHHHHHHHHHHHHHh
Confidence 377999999998887763
No 213
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=26.49 E-value=2.6e+02 Score=26.89 Aligned_cols=8 Identities=25% Similarity=0.368 Sum_probs=0.0
Q ss_pred HHHHhhcC
Q 022656 17 CDCSFEKS 24 (294)
Q Consensus 17 lK~~Ye~~ 24 (294)
|+.+|+.+
T Consensus 14 l~~~~~~~ 21 (314)
T PF04111_consen 14 LDKQLEQA 21 (314)
T ss_dssp --------
T ss_pred HHHHHHHH
Confidence 45555554
No 214
>PF04100 Vps53_N: Vps53-like, N-terminal ; InterPro: IPR007234 Vps53 complexes with Vps52 and Vps54 to form a multi-subunit complex involved in regulating membrane trafficking events [].
Probab=26.44 E-value=6.4e+02 Score=24.90 Aligned_cols=23 Identities=17% Similarity=0.170 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Q 022656 38 LAQFCEKLVMDLDRRVRRGRERL 60 (294)
Q Consensus 38 ~l~~L~~lI~d~dRkI~~~k~RL 60 (294)
++..|...|..+|.-|..+..-.
T Consensus 26 ~i~~l~~~i~~ld~eI~~~v~~q 48 (383)
T PF04100_consen 26 LIAKLRKEIRELDEEIKELVREQ 48 (383)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555566666666666554444
No 215
>PF03980 Nnf1: Nnf1 ; InterPro: IPR007128 NNF1 is an essential yeast gene required for proper spindle orientation, nucleolar and nuclear envelope structure and mRNA export [].
Probab=26.37 E-value=3.3e+02 Score=21.55 Aligned_cols=23 Identities=17% Similarity=0.260 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhc
Q 022656 41 FCEKLVMDLDRRVRRGRERLSQE 63 (294)
Q Consensus 41 ~L~~lI~d~dRkI~~~k~RL~~~ 63 (294)
-|...++++|.-|..|+.|....
T Consensus 31 ~v~~kLneLd~Li~eA~~r~~~~ 53 (109)
T PF03980_consen 31 DVVEKLNELDKLIEEAKERKNSG 53 (109)
T ss_pred hHHHHHHHHHHHHHHHHHhHhcc
Confidence 34567888999999999998643
No 216
>PF06694 Plant_NMP1: Plant nuclear matrix protein 1 (NMP1); InterPro: IPR010604 This family consists of several plant specific nuclear matrix protein 1 (NMP1) sequences. Nuclear Matrix Protein 1 is a ubiquitously expressed 36 kDa protein, which has no homologues in animals and fungi, but is highly conserved among flowering and non-flowering plants. NMP1 is located both in the cytoplasm and nucleus and that the nuclear fraction is associated with the nuclear matrix. NMP1 is a candidate for a plant-specific structural protein with a function both in the nucleus and cytoplasm [].
Probab=25.93 E-value=5.2e+02 Score=25.20 Aligned_cols=88 Identities=22% Similarity=0.200 Sum_probs=59.5
Q ss_pred CCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhh-----hhhhhccccc
Q 022656 70 PPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLM-----MAQEKKMALC 144 (294)
Q Consensus 70 ~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~-----~~~~qkm~VC 144 (294)
.+-..+...++..+..++..+.+.++.|...+.+.-=+.....+..|+.+.+.+.+.+ ..=+.. -+=-..|.|=
T Consensus 167 lPD~seLe~~~s~~sk~Lq~lqq~v~~Lask~~y~pd~~~~e~~~~Lr~~L~tflq~~-~~F~~~Y~~EIrpWch~~~~P 245 (325)
T PF06694_consen 167 LPDVSELEKKASELSKQLQSLQQQVAELASKHPYNPDEEYVEKESQLRLELETFLQTA-AGFNHCYEKEIRPWCHMMEVP 245 (325)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcchhhHHHHHHHHHHHHHHHHHH-HHHHHHHHhcchhhhccCccc
Confidence 3445667888999999999999999999999888766666677777888777777654 221100 1112355776
Q ss_pred cccccccccCCchHHHHh
Q 022656 145 EICGSFLVANDAAERTQS 162 (294)
Q Consensus 145 eVCGA~Ls~~D~d~Rl~d 162 (294)
+.|| .+-+-.|+-+
T Consensus 246 ~L~g----LGPAa~Rlle 259 (325)
T PF06694_consen 246 QLHG----LGPAANRLLE 259 (325)
T ss_pred hhhc----ccHHHHHHHH
Confidence 6777 3444556544
No 217
>PRK00076 recR recombination protein RecR; Reviewed
Probab=25.91 E-value=1.2e+02 Score=27.34 Aligned_cols=7 Identities=29% Similarity=0.396 Sum_probs=5.0
Q ss_pred hhccccc
Q 022656 163 HISGKQH 169 (294)
Q Consensus 163 H~~GK~H 169 (294)
.|.|+=|
T Consensus 98 ~y~G~Yh 104 (196)
T PRK00076 98 EYRGLYH 104 (196)
T ss_pred cCceEEE
Confidence 4777777
No 218
>PF11062 DUF2863: Protein of unknown function (DUF2863); InterPro: IPR021292 This bacterial family of proteins have no known function.
Probab=25.91 E-value=30 Score=34.56 Aligned_cols=17 Identities=24% Similarity=0.536 Sum_probs=13.8
Q ss_pred hhccccccccccccccC
Q 022656 138 EKKMALCEICGSFLVAN 154 (294)
Q Consensus 138 ~qkm~VCeVCGA~Ls~~ 154 (294)
.=.|+.||-|||.|..+
T Consensus 361 ~f~~E~CdDCGaPlypd 377 (398)
T PF11062_consen 361 RFPPEFCDDCGAPLYPD 377 (398)
T ss_pred cCCchhcccCCCCCCCC
Confidence 34789999999998765
No 219
>smart00030 CLb CLUSTERIN Beta chain.
Probab=25.89 E-value=2.7e+02 Score=25.44 Aligned_cols=44 Identities=23% Similarity=0.333 Sum_probs=25.3
Q ss_pred HHHHHHHHH---HHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHh
Q 022656 82 VLEEKIKNL---LEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQ 126 (294)
Q Consensus 82 ~l~ekI~~l---l~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~ 126 (294)
-++++|++. ++++-.|.+.-+.+ =+.+|.-+++.+++|+.....
T Consensus 19 yvd~EI~nAl~GvKqMK~~mer~~ee-h~~ll~tLe~~kk~KeeAlk~ 65 (206)
T smart00030 19 YINKEIKNALKGVKQIKTLIEKTNKE-RKSLLSTLEEAKKKKEEALKD 65 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHH-HHHHHHHHHHHHHHHHHHHHH
Confidence 345555533 34444555555543 457787888877777665443
No 220
>PLN03229 acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha; Provisional
Probab=25.76 E-value=4e+02 Score=29.01 Aligned_cols=39 Identities=18% Similarity=0.145 Sum_probs=28.0
Q ss_pred hHHHHhhcCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHH
Q 022656 16 VCDCSFEKSPRHDAYVPKFEAELAQFCEKLVMDLDRRVRRG 56 (294)
Q Consensus 16 ~lK~~Ye~~~~~~~~~~~YE~e~l~~L~~lI~d~dRkI~~~ 56 (294)
.||+++-+++..... --+.-+...|++|-.++|..+..|
T Consensus 440 kLk~eilKAk~s~~~--~~~~~L~e~IeKLk~E~d~e~S~A 478 (762)
T PLN03229 440 KLKEQILKAKESSSK--PSELALNEMIEKLKKEIDLEYTEA 478 (762)
T ss_pred HHHHHHHhcccccCC--CCChHHHHHHHHHHHHHHHHHHHh
Confidence 367777776533332 346778888999999999998776
No 221
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=25.45 E-value=2.7e+02 Score=20.80 Aligned_cols=43 Identities=23% Similarity=0.361 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 80 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 80 i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
+..|+.+|..|+...+.|-.+. ..|-.++..+..++..|.+..
T Consensus 2 L~~Le~kle~Li~~~~~L~~EN-----~~Lr~q~~~~~~ER~~L~ekn 44 (65)
T TIGR02449 2 LQALAAQVEHLLEYLERLKSEN-----RLLRAQEKTWREERAQLLEKN 44 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHH
Confidence 5688999999999999997655 356667777888887776543
No 222
>PF06008 Laminin_I: Laminin Domain I; InterPro: IPR009254 Laminins are glycoproteins that are major constituents of the basement membrane of cells. Laminins are trimeric molecules; laminin-1 is an alpha1 beta1 gamma1 trimer. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure []. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components.; GO: 0005102 receptor binding, 0030155 regulation of cell adhesion, 0030334 regulation of cell migration, 0045995 regulation of embryonic development, 0005606 laminin-1 complex
Probab=25.43 E-value=5.2e+02 Score=23.71 Aligned_cols=86 Identities=19% Similarity=0.232 Sum_probs=47.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC-CCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHh---cCCHHHHHH
Q 022656 33 KFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEP-APPPPISAEKSEQLSVLEEKIKNLLEQVETLGE---AGKVDEAEA 108 (294)
Q Consensus 33 ~YE~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~-~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGe---eG~VdeA~~ 108 (294)
.+|.+ +.-|..-+..+..++..+.....+-... ..+..........|..+...|..++.++..||. .+-...-..
T Consensus 49 ~~e~~-l~~L~~d~~~L~~k~~~~~~~~~~l~~~t~~t~~~a~~L~~~i~~l~~~i~~l~~~~~~l~~~~~~~~~~~l~~ 127 (264)
T PF06008_consen 49 PLEKE-LESLEQDVENLQEKATKVSRKAQQLNNNTERTLQRAQDLEQFIQNLQDNIQELIEQVESLNENGDQLPSEDLQR 127 (264)
T ss_pred HHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcccCCCCHHHHHH
Confidence 44544 4444555555555555554443211100 001112344566788999999999999999999 444444455
Q ss_pred HHHHHHHHHHH
Q 022656 109 LMRKVEILNVE 119 (294)
Q Consensus 109 l~~~ve~Lk~e 119 (294)
.+++|+.+-.+
T Consensus 128 ~l~ea~~mL~e 138 (264)
T PF06008_consen 128 ALAEAQRMLEE 138 (264)
T ss_pred HHHHHHHHHHH
Confidence 55555555443
No 223
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=25.39 E-value=28 Score=24.65 Aligned_cols=9 Identities=33% Similarity=0.973 Sum_probs=7.8
Q ss_pred ccccccccc
Q 022656 142 ALCEICGSF 150 (294)
Q Consensus 142 ~VCeVCGA~ 150 (294)
-+|+||||-
T Consensus 35 w~CP~C~a~ 43 (50)
T cd00730 35 WVCPVCGAG 43 (50)
T ss_pred CCCCCCCCc
Confidence 599999984
No 224
>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=25.33 E-value=27 Score=23.40 Aligned_cols=17 Identities=29% Similarity=0.522 Sum_probs=10.6
Q ss_pred hccccccccccccccCC
Q 022656 139 KKMALCEICGSFLVAND 155 (294)
Q Consensus 139 qkm~VCeVCGA~Ls~~D 155 (294)
..-.||..||+.|--+.
T Consensus 17 ~g~~vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 17 RGELVCPNCGLVLEENI 33 (43)
T ss_dssp TTEEEETTT-BBEE-TT
T ss_pred CCeEECCCCCCEeeccc
Confidence 34469999998876443
No 225
>CHL00112 rpl28 ribosomal protein L28; Provisional
Probab=25.20 E-value=26 Score=25.98 Aligned_cols=14 Identities=14% Similarity=0.247 Sum_probs=10.8
Q ss_pred ccccccccccccCC
Q 022656 142 ALCEICGSFLVAND 155 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D 155 (294)
.+|+|||--...+-
T Consensus 3 r~C~i~GK~~~~Gn 16 (63)
T CHL00112 3 KKCQLTGKKANNGY 16 (63)
T ss_pred CeeccCCCcCccCc
Confidence 58999998766653
No 226
>PF04065 Not3: Not1 N-terminal domain, CCR4-Not complex component ; InterPro: IPR007207 The Ccr4-Not complex (Not1, Not2, Not3, Not4 and Not5) is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID []. This domain is the N-terminal region of the Not proteins.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=25.00 E-value=5.4e+02 Score=23.89 Aligned_cols=81 Identities=17% Similarity=0.264 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHH------HHHHHHHHHHhcCCHHHHHH
Q 022656 35 EAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIK------NLLEQVETLGEAGKVDEAEA 108 (294)
Q Consensus 35 E~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~------~ll~eaE~LGeeG~VdeA~~ 108 (294)
-.+...||..+|..+...|+....-++.-.....-.......+..|..|...|. ..|+.+=.|-..|.|+-
T Consensus 120 k~e~~~wl~~~Id~L~~QiE~~E~E~E~L~~~~kKkk~~~~~~~r~~~l~~~ierhk~Hi~kLE~lLR~L~N~~l~~--- 196 (233)
T PF04065_consen 120 KEEARDWLKDSIDELNRQIEQLEAEIESLSSQKKKKKKDSTKQERIEELESRIERHKFHIEKLELLLRLLDNDELDP--- 196 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCccCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCH---
Confidence 356788999999999999998877765221000000111234445555555554 33455555677788754
Q ss_pred HHHHHHHHHHHH
Q 022656 109 LMRKVEILNVEK 120 (294)
Q Consensus 109 l~~~ve~Lk~er 120 (294)
..|+.|+.-.
T Consensus 197 --e~V~~ikedi 206 (233)
T PF04065_consen 197 --EQVEDIKEDI 206 (233)
T ss_pred --HHHHHHHHHH
Confidence 3445555443
No 227
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=24.99 E-value=29 Score=24.49 Aligned_cols=13 Identities=31% Similarity=0.958 Sum_probs=11.3
Q ss_pred hcccccccccccc
Q 022656 139 KKMALCEICGSFL 151 (294)
Q Consensus 139 qkm~VCeVCGA~L 151 (294)
..+..|+-||.+|
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 5788999999987
No 228
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=24.91 E-value=1.2e+02 Score=27.62 Aligned_cols=7 Identities=29% Similarity=0.605 Sum_probs=4.1
Q ss_pred hcccccc
Q 022656 164 ISGKQHI 170 (294)
Q Consensus 164 ~~GK~Hl 170 (294)
|.|.-||
T Consensus 100 f~G~YhV 106 (198)
T COG0353 100 FRGLYHV 106 (198)
T ss_pred cCeeEEE
Confidence 5666663
No 229
>PRK14159 heat shock protein GrpE; Provisional
Probab=24.91 E-value=2.4e+02 Score=24.98 Aligned_cols=82 Identities=15% Similarity=0.030 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccccccCCchHHHHhhh
Q 022656 85 EKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAERTQSHI 164 (294)
Q Consensus 85 ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~Rl~dH~ 164 (294)
.+|..+-++++.| -+.-+.+.++++.++.-.+.-... ..+..+=.++..||.+.|+-.|.-.|.
T Consensus 30 ~~i~~l~~e~~el-----kd~~lR~~AdfeN~rkR~~rE~e~-----------~~~~a~~~~~~~LLpV~DnlerAl~~~ 93 (176)
T PRK14159 30 VEQNKLQKDYDEL-----KDKYMRANAEFENIKKRMEKEKLS-----------AMAYANESFAKDLLDVLDALEAAVNVE 93 (176)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHhhHHhHHHHHHhcc
Confidence 4444555555554 234456666666664322211111 122333445678999999999976665
Q ss_pred cc-----cccccHHHHHHHHHHH
Q 022656 165 SG-----KQHIGYGMVRDFITEY 182 (294)
Q Consensus 165 ~G-----K~HlGy~kIRe~l~eL 182 (294)
.. .++-|+.+|...+...
T Consensus 94 ~~~~~~~~l~~Gv~mi~k~l~~v 116 (176)
T PRK14159 94 CHDEISLKIKEGVQNTLDLFLKK 116 (176)
T ss_pred cccchHHHHHHHHHHHHHHHHHH
Confidence 42 3455666665555443
No 230
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=24.86 E-value=29 Score=27.62 Aligned_cols=26 Identities=12% Similarity=0.304 Sum_probs=22.8
Q ss_pred ccccccccccccccCCchHHHHhhhc
Q 022656 140 KMALCEICGSFLVANDAAERTQSHIS 165 (294)
Q Consensus 140 km~VCeVCGA~Ls~~D~d~Rl~dH~~ 165 (294)
.-.||+.||..-...+.-+.|.+.|.
T Consensus 34 Pa~~C~~CGe~y~~dev~~eIE~~l~ 59 (89)
T TIGR03829 34 PSISCSHCGMEYQDDTTVKEIEDQLL 59 (89)
T ss_pred CcccccCCCcEeecHHHHHHHHhhhE
Confidence 45899999999888889999999885
No 231
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=24.82 E-value=6.2e+02 Score=26.22 Aligned_cols=34 Identities=21% Similarity=0.236 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHH
Q 022656 87 IKNLLEQVETLGEAGKVDEAEALMRKVEILNVEK 120 (294)
Q Consensus 87 I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er 120 (294)
|.....+.+.|.+.|+..+|..++.+++.--...
T Consensus 177 ~e~~f~~f~~l~~~Gd~~~A~e~l~~l~~~~~~l 210 (569)
T PRK04778 177 LEEEFSQFVELTESGDYVEAREILDQLEEELAAL 210 (569)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHH
Confidence 3455668889999999999988876665544433
No 232
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=24.69 E-value=1.1e+02 Score=17.95 Aligned_cols=21 Identities=43% Similarity=0.531 Sum_probs=17.4
Q ss_pred HHHHHHHHhcCCHHHHHHHHH
Q 022656 91 LEQVETLGEAGKVDEAEALMR 111 (294)
Q Consensus 91 l~eaE~LGeeG~VdeA~~l~~ 111 (294)
+.-+..+...|+.++|..++.
T Consensus 5 ~~la~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 5 LALARALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHHHHHcCCHHHHHHHHh
Confidence 456788999999999998875
No 233
>PLN02943 aminoacyl-tRNA ligase
Probab=24.48 E-value=1.8e+02 Score=32.27 Aligned_cols=65 Identities=22% Similarity=0.197 Sum_probs=41.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC-CCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHH
Q 022656 33 KFEAELAQFCEKLVMDLDRRVRRGRERLSQEV-EPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLG 98 (294)
Q Consensus 33 ~YE~e~l~~L~~lI~d~dRkI~~~k~RL~~~~-e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LG 98 (294)
+++.+..+ |++-+..++..|.+.+.+|.... ....++.......+++.++.++|..+.+.+..|+
T Consensus 886 D~~~E~~r-L~K~l~klekei~~~~~kLsN~~F~~KAP~evv~~e~~kl~~~~~~l~~~~~~l~~l~ 951 (958)
T PLN02943 886 DISAEVER-LSKRLSKMQTEYDALAARLSSPKFVEKAPEDVVRGVREKAAEAEEKIKLTKNRLAFLK 951 (958)
T ss_pred cHHHHHHH-HHHHHHHHHHHHHHHHHHhCCchhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35666555 78888888899999999995321 0111222333345567777777777777777765
No 234
>PRK00359 rpmB 50S ribosomal protein L28; Reviewed
Probab=24.45 E-value=37 Score=26.05 Aligned_cols=25 Identities=24% Similarity=0.417 Sum_probs=17.2
Q ss_pred cccccccccccccCCchHHHHhhhccccc
Q 022656 141 MALCEICGSFLVANDAAERTQSHISGKQH 169 (294)
Q Consensus 141 m~VCeVCGA~Ls~~D~d~Rl~dH~~GK~H 169 (294)
+.+|+|||.-...+-+-. |..+|-+
T Consensus 2 sr~C~i~GK~~~~Gn~vS----hs~~kTk 26 (76)
T PRK00359 2 SRVCEITGKGPMVGNNVS----HSNNKTK 26 (76)
T ss_pred CCccccCCCCCccCCeee----ecCCccC
Confidence 478999999887775443 5555543
No 235
>PLN02320 seryl-tRNA synthetase
Probab=24.43 E-value=2.1e+02 Score=29.61 Aligned_cols=48 Identities=15% Similarity=0.153 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 77 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 77 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
..++..|..+.+.+.+++-.. ..+ ++++++.+++..|+.+...|++++
T Consensus 106 ~~~~~~lr~ern~~sk~i~~~-~~~--~~~~~l~~~~k~lk~~i~~le~~~ 153 (502)
T PLN02320 106 QKEVERLRAERNAVANKMKGK-LEP--SERQALVEEGKNLKEGLVTLEEDL 153 (502)
T ss_pred HHHHHHHHHHHHHHHHHHHhh-hCC--CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 445666666666666666441 122 345677777777777777766543
No 236
>PRK15067 ethanolamine ammonia lyase large subunit; Provisional
Probab=24.38 E-value=27 Score=35.27 Aligned_cols=28 Identities=25% Similarity=0.467 Sum_probs=17.6
Q ss_pred cccccccccccc---cCCchH--H--HHhhhccccc
Q 022656 141 MALCEICGSFLV---ANDAAE--R--TQSHISGKQH 169 (294)
Q Consensus 141 m~VCeVCGA~Ls---~~D~d~--R--l~dH~~GK~H 169 (294)
+-|=.|-| |+. ..|..| | |+|||.||+|
T Consensus 322 ~LVNtVvG-FIGPEyLyd~kQiiRAgLEDhf~GKLl 356 (461)
T PRK15067 322 LLVNTVVG-FIGPEYLYDGKQIIRAGLEDHFMGKLL 356 (461)
T ss_pred eeeeecce-eccchhcccchhhhhcchHhhhhhhhh
Confidence 34555555 222 345444 3 8999999999
No 237
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=24.31 E-value=99 Score=22.97 Aligned_cols=19 Identities=37% Similarity=0.532 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 022656 79 QLSVLEEKIKNLLEQVETL 97 (294)
Q Consensus 79 ~i~~l~ekI~~ll~eaE~L 97 (294)
-+.+|++.|..|..+|+-|
T Consensus 26 sV~El~eRIalLq~EIeRl 44 (65)
T COG5509 26 SVAELEERIALLQAEIERL 44 (65)
T ss_pred hHHHHHHHHHHHHHHHHHH
Confidence 3678899999888888877
No 238
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=24.26 E-value=40 Score=20.25 Aligned_cols=10 Identities=30% Similarity=0.919 Sum_probs=5.6
Q ss_pred cccccccccc
Q 022656 142 ALCEICGSFL 151 (294)
Q Consensus 142 ~VCeVCGA~L 151 (294)
.+|.-||+.+
T Consensus 3 ~~Cp~Cg~~~ 12 (26)
T PF13248_consen 3 MFCPNCGAEI 12 (26)
T ss_pred CCCcccCCcC
Confidence 3566666643
No 239
>TIGR02135 phoU_full phosphate transport system regulatory protein PhoU. This model describes PhoU, a regulatory protein of unknown mechanism for high-affinity phosphate ABC transporter systems. The protein consists of two copies of the domain described by Pfam model pfam01895. Deletion of PhoU activates constitutive expression of the phosphate ABC transporter and allows phosphate transport, but causes a growth defect and so likely has some second function.
Probab=24.24 E-value=2.5e+02 Score=23.80 Aligned_cols=34 Identities=15% Similarity=0.132 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHH
Q 022656 78 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMR 111 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~ 111 (294)
..|..+...+..++..+..+-..++.+.|+.+..
T Consensus 12 ~el~~m~~~~~~ml~~~~~~~~~~d~~~~~~i~~ 45 (212)
T TIGR02135 12 EELLEMGGLVEEQLEDAVRALTEKDRELARKVIE 45 (212)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHH
Confidence 4445555555555555555555555544444433
No 240
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=24.14 E-value=30 Score=24.13 Aligned_cols=9 Identities=33% Similarity=1.025 Sum_probs=6.2
Q ss_pred ccccccccc
Q 022656 142 ALCEICGSF 150 (294)
Q Consensus 142 ~VCeVCGA~ 150 (294)
-+|+||||-
T Consensus 35 w~CP~C~a~ 43 (47)
T PF00301_consen 35 WVCPVCGAP 43 (47)
T ss_dssp -B-TTTSSB
T ss_pred CcCcCCCCc
Confidence 699999984
No 241
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 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 family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=23.94 E-value=5.8e+02 Score=23.55 Aligned_cols=79 Identities=19% Similarity=0.251 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhc--CCHHHHHHHHHH
Q 022656 35 EAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEA--GKVDEAEALMRK 112 (294)
Q Consensus 35 E~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGee--G~VdeA~~l~~~ 112 (294)
|.+++.-...+|.||..-+.. |.++ .....++|..|+..|+.|-..|..+-.+ --.+.+..++.+
T Consensus 23 e~~~~e~ee~~L~e~~kE~~~----L~~E---------r~~h~eeLrqI~~DIn~lE~iIkqa~~er~~~~~~i~r~~ee 89 (230)
T PF10146_consen 23 EVESLENEEKCLEEYRKEMEE----LLQE---------RMAHVEELRQINQDINTLENIIKQAESERNKRQEKIQRLYEE 89 (230)
T ss_pred HHHHHHHHHHHHHHHHHHHHH----HHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555566666666655543 2111 1123344444455555444444333222 135567778888
Q ss_pred HHHHHHHHHHHHHh
Q 022656 113 VEILNVEKTTLTQQ 126 (294)
Q Consensus 113 ve~Lk~er~~l~~~ 126 (294)
+..|+.+...+..+
T Consensus 90 y~~Lk~~in~~R~e 103 (230)
T PF10146_consen 90 YKPLKDEINELRKE 103 (230)
T ss_pred HHHHHHHHHHHHHH
Confidence 88888887777665
No 242
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=23.85 E-value=20 Score=31.59 Aligned_cols=29 Identities=28% Similarity=0.515 Sum_probs=24.4
Q ss_pred ccccccccccccCCchHHHHhhhccccccc
Q 022656 142 ALCEICGSFLVANDAAERTQSHISGKQHIG 171 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlG 171 (294)
..||-|-.+| .+|+..=-..|..|+.|+-
T Consensus 4 Y~CeyC~~~L-thD~lsvRk~H~~G~~H~~ 32 (188)
T COG5136 4 YFCEYCNKML-THDRLSVRKMHCGGAKHGL 32 (188)
T ss_pred hHHHHHHHHH-hccHHHHHHHhhhhHHHHH
Confidence 4699999998 5778877889999999964
No 243
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=23.81 E-value=34 Score=26.82 Aligned_cols=18 Identities=22% Similarity=0.373 Sum_probs=14.4
Q ss_pred cccccccccccccCCchH
Q 022656 141 MALCEICGSFLVANDAAE 158 (294)
Q Consensus 141 m~VCeVCGA~Ls~~D~d~ 158 (294)
-.-|++||.=+...|++-
T Consensus 8 ~~~C~~CG~d~~~~~adD 25 (86)
T PF06170_consen 8 APRCPHCGLDYSHARADD 25 (86)
T ss_pred CCcccccCCccccCCcCc
Confidence 367999999988887653
No 244
>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function. It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.
Probab=23.63 E-value=1.5e+02 Score=21.94 Aligned_cols=21 Identities=24% Similarity=0.425 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 022656 78 EQLSVLEEKIKNLLEQVETLG 98 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~LG 98 (294)
.+|..|..+|..|..++..+.
T Consensus 32 ~~I~~L~~~l~~L~~rl~~~~ 52 (69)
T PF04102_consen 32 RQIDRLQRQLRLLRERLRELE 52 (69)
T ss_dssp HHHHHHHHHHHHHHHT-----
T ss_pred HHHHHHHHHHHHHHHHHHHhc
Confidence 344455555555544444443
No 245
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=23.62 E-value=3.5e+02 Score=24.24 Aligned_cols=54 Identities=17% Similarity=0.203 Sum_probs=42.5
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 74 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 74 ~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
.....+|..|+-+|..|-.+++.=-..+--.+-+.+-.+++.|+.+++.++-++
T Consensus 108 ~s~~~ei~~L~~kI~~L~~~in~~~k~~~n~~i~slk~EL~d~iKe~e~~emeL 161 (181)
T PF04645_consen 108 KSIKKEIEILRLKISSLQKEINKNKKKDLNEEIESLKSELNDLIKEREIREMEL 161 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 456788999999999999999986665544455678888999999888877654
No 246
>PRK10698 phage shock protein PspA; Provisional
Probab=23.53 E-value=5.6e+02 Score=23.26 Aligned_cols=52 Identities=13% Similarity=0.223 Sum_probs=32.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 76 KSEQLSVLEEKIKNLLEQVETLGEAG--KVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 76 ~~e~i~~l~ekI~~ll~eaE~LGeeG--~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
....+..++++|..+..+++.++.-+ .++.-+..+..-+.+-.+.+.|...+
T Consensus 164 a~~~f~rmE~ki~~~Ea~aea~~~~~~~~l~~e~~~le~~~~ve~ELa~LK~~~ 217 (222)
T PRK10698 164 AMARFESFERRIDQMEAEAESHGFGKQKSLDQQFAELKADDEISEQLAALKAKM 217 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHhHhhccCCCCHHHHHHHhhccchHHHHHHHHHHHh
Confidence 34567789999999999999886521 25555444443334455555555443
No 247
>PF10191 COG7: Golgi complex component 7 (COG7); InterPro: IPR019335 The conserved oligomeric Golgi (COG) complex is an eight-subunit (Cog1-8) peripheral Golgi protein involved in membrane trafficking and glycoconjugate synthesis []. COG7 is required for normal Golgi morphology and trafficking. Mutation in COG7 causes a congenital disorder of glycosylation [].
Probab=23.50 E-value=5.5e+02 Score=27.83 Aligned_cols=90 Identities=8% Similarity=0.103 Sum_probs=59.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 022656 34 FEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKV 113 (294)
Q Consensus 34 YE~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~v 113 (294)
|=..+...|+-++.+|..-|+..-..+-..- +-+......+...+..|..++..+.+++.. .+++...++..+.++
T Consensus 35 ~ls~l~~kLql~~qe~~~~le~~~~q~l~~~--Pr~~~ev~~l~~ea~~L~~~~~~v~~~~~~--~e~~t~~s~~~L~~l 110 (766)
T PF10191_consen 35 HLSSLVMKLQLYSQEVNASLEETSQQALQRV--PRVLREVDRLRQEAASLQEQMASVQEEIKA--VEQDTAQSMAQLAEL 110 (766)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--cHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--hhccHHHHHHHHHHH
Confidence 4556666667777777666666544443221 111111233556777888999999988876 477888899999999
Q ss_pred HHHHHHHHHHHHhh
Q 022656 114 EILNVEKTTLTQQS 127 (294)
Q Consensus 114 e~Lk~er~~l~~~~ 127 (294)
+..|...+.....+
T Consensus 111 d~vK~rm~~a~~~L 124 (766)
T PF10191_consen 111 DSVKSRMEAARETL 124 (766)
T ss_pred HHHHHHHHHHHHHH
Confidence 99988776655444
No 248
>KOG4117 consensus Heat shock factor binding protein [Transcription; Posttranslational modification, protein turnover, chaperones]
Probab=23.45 E-value=3e+02 Score=20.75 Aligned_cols=52 Identities=15% Similarity=0.240 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHH
Q 022656 34 FEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQV 94 (294)
Q Consensus 34 YE~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~ea 94 (294)
-+.++-.+++.++..+.-|..---..+ ...+......|+.|++.|+.||.++
T Consensus 13 Nmq~LTs~vQ~lLQq~QDkFQtMSDQI---------I~RiDDM~~riDDLEKnIaDLm~qa 64 (73)
T KOG4117|consen 13 NMQDLTSVVQGLLQQTQDKFQTMSDQI---------IGRIDDMSSRIDDLEKNIADLMTQA 64 (73)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHhhhhhhhHHHHHHHHHHHHHc
Confidence 466777777777766555543322222 1122233456667777777776654
No 249
>PF13041 PPR_2: PPR repeat family
Probab=23.44 E-value=1.2e+02 Score=20.12 Aligned_cols=23 Identities=26% Similarity=0.404 Sum_probs=18.6
Q ss_pred HHHHHHhcCCHHHHHHHHHHHHH
Q 022656 93 QVETLGEAGKVDEAEALMRKVEI 115 (294)
Q Consensus 93 eaE~LGeeG~VdeA~~l~~~ve~ 115 (294)
-+..+...|++++|..++.+...
T Consensus 9 li~~~~~~~~~~~a~~l~~~M~~ 31 (50)
T PF13041_consen 9 LISGYCKAGKFEEALKLFKEMKK 31 (50)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHH
Confidence 35678899999999999976653
No 250
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=23.40 E-value=35 Score=24.05 Aligned_cols=16 Identities=38% Similarity=0.804 Sum_probs=12.6
Q ss_pred cccccccccc-ccccCC
Q 022656 140 KMALCEICGS-FLVAND 155 (294)
Q Consensus 140 km~VCeVCGA-~Ls~~D 155 (294)
....|+.||+ ||....
T Consensus 19 ~~~fCP~Cg~~~m~~~~ 35 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL 35 (50)
T ss_pred ccCcCcCCCcchheccC
Confidence 4579999999 877654
No 251
>PF15456 Uds1: Up-regulated During Septation
Probab=23.39 E-value=4.4e+02 Score=21.99 Aligned_cols=23 Identities=22% Similarity=0.328 Sum_probs=13.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHH
Q 022656 75 EKSEQLSVLEEKIKNLLEQVETL 97 (294)
Q Consensus 75 ~~~e~i~~l~ekI~~ll~eaE~L 97 (294)
...+++..++.+|.++..+++.|
T Consensus 78 ~~eeel~~~~rk~ee~~~eL~~l 100 (124)
T PF15456_consen 78 KAEEELAESDRKCEELAQELWKL 100 (124)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHH
Confidence 34455666666666666555554
No 252
>COG1340 Uncharacterized archaeal coiled-coil protein [Function unknown]
Probab=23.32 E-value=6.8e+02 Score=24.16 Aligned_cols=18 Identities=11% Similarity=0.254 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 022656 107 EALMRKVEILNVEKTTLT 124 (294)
Q Consensus 107 ~~l~~~ve~Lk~er~~l~ 124 (294)
+.+.++++.|+.+...+.
T Consensus 161 ~el~aei~~lk~~~~e~~ 178 (294)
T COG1340 161 KELKAEIDELKKKAREIH 178 (294)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 344444444444444443
No 253
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=23.28 E-value=5.9e+02 Score=26.41 Aligned_cols=86 Identities=17% Similarity=0.190 Sum_probs=49.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCC--CCc---------------------hhhHHHHHHHHHHHHHHHH
Q 022656 36 AELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPP--PIS---------------------AEKSEQLSVLEEKIKNLLE 92 (294)
Q Consensus 36 ~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~--~~~---------------------~~~~e~i~~l~ekI~~ll~ 92 (294)
...+..++.+|..++..|..-...|.+-.+ .... ... ..-...|...=..|.....
T Consensus 100 ~~~i~~~~~~l~~~e~~i~~i~~~l~~L~~-~e~~nr~~i~~l~~~y~~lrk~ll~~~~~~G~a~~~Le~~L~~ie~~F~ 178 (560)
T PF06160_consen 100 KQAIKEIEEQLDEIEEDIKEILDELDELLE-SEEKNREEIEELKEKYRELRKELLAHSFSYGPAIEELEKQLENIEEEFS 178 (560)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhchhHHHHHHHHHHHHHHHH
Confidence 345677788888888888777666642110 0000 000 0001112222234445667
Q ss_pred HHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Q 022656 93 QVETLGEAGKVDEAEALMRKVEILNVEKTT 122 (294)
Q Consensus 93 eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~ 122 (294)
+.++|.+.|+..+|..++.+++.--.....
T Consensus 179 ~f~~lt~~GD~~~A~eil~~l~~~~~~l~~ 208 (560)
T PF06160_consen 179 EFEELTENGDYLEAREILEKLKEETDELEE 208 (560)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 888999999999999888776655444433
No 254
>TIGR01010 BexC_CtrB_KpsE polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family. This family contains gamma proteobacterial proteins involved in capsule polysaccharide export.
Probab=23.26 E-value=6.6e+02 Score=24.01 Aligned_cols=62 Identities=19% Similarity=0.252 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCC-CC--CchhhHHHHHHHHHHHHHHHHHHHHHH
Q 022656 37 ELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPP-PP--ISAEKSEQLSVLEEKIKNLLEQVETLG 98 (294)
Q Consensus 37 e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~-~~--~~~~~~e~i~~l~ekI~~ll~eaE~LG 98 (294)
+...||+.-|..+..++..++..|..-...... .+ ........|..|..++..+-.+..+|.
T Consensus 170 ~a~~fl~~ql~~~~~~l~~ae~~l~~fr~~~~~~d~~~~~~~~~~~i~~L~~~l~~~~~~l~~l~ 234 (362)
T TIGR01010 170 DTIAFAENEVKEAEQRLNATKAELLKYQIKNKVFDPKAQSSAQLSLISTLEGELIRVQAQLAQLR 234 (362)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666666666777777776666532110100 00 111233445566666555555554443
No 255
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=23.21 E-value=3.1e+02 Score=28.24 Aligned_cols=44 Identities=14% Similarity=0.296 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHh
Q 022656 78 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQ 126 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~ 126 (294)
.++.+|+++|..|-.+.+.|..... .+-.+++.|..+.+.|+.+
T Consensus 76 ~kasELEKqLaaLrqElq~~saq~~-----dle~KIkeLEaE~~~Lk~Q 119 (475)
T PRK13729 76 VTAAQMQKQYEEIRRELDVLNKQRG-----DDQRRIEKLGQDNAALAEQ 119 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhh-----hHHHHHHHHHHHHHHHHHH
Confidence 4455666666666555554433322 2233444444555444444
No 256
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=23.18 E-value=93 Score=29.18 Aligned_cols=28 Identities=29% Similarity=0.238 Sum_probs=20.7
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 022656 89 NLLEQVETLGEAGKVDEAEALMRKVEIL 116 (294)
Q Consensus 89 ~ll~eaE~LGeeG~VdeA~~l~~~ve~L 116 (294)
..+..+..+...|++++|..++.++-.+
T Consensus 284 ~~~~la~~~~~~g~~~~A~~~l~~~l~~ 311 (389)
T PRK11788 284 LLLALAQLLEEQEGPEAAQALLREQLRR 311 (389)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence 3456677788889999998888766443
No 257
>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].
Probab=23.16 E-value=4.7e+02 Score=22.18 Aligned_cols=22 Identities=23% Similarity=0.170 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q 022656 106 AEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 106 A~~l~~~ve~Lk~er~~l~~~~ 127 (294)
+......++.|......|+.++
T Consensus 68 ~~~~~~~~E~l~rriq~LEeel 89 (143)
T PF12718_consen 68 SEKRKSNAEQLNRRIQLLEEEL 89 (143)
T ss_pred HHHHHHhHHHHHhhHHHHHHHH
Confidence 3333334444554444454444
No 258
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=23.13 E-value=3.4e+02 Score=20.54 Aligned_cols=44 Identities=25% Similarity=0.369 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHh
Q 022656 78 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQ 126 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~ 126 (294)
+.|..|..+|..|-++...|. ++...|..+.+.|+.+.......
T Consensus 18 eti~~Lq~e~eeLke~n~~L~-----~e~~~L~~en~~L~~e~~~~~~r 61 (72)
T PF06005_consen 18 ETIALLQMENEELKEKNNELK-----EENEELKEENEQLKQERNAWQER 61 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhHH-----HHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555555555555555 55566666677777666554443
No 259
>PF02672 CP12: CP12 domain; InterPro: IPR003823 This entry represents an uncharacterised domain in proteins of unknown function. This domain is found associated with CBS domains in some proteins IPR000644 from INTERPRO.; PDB: 3B1K_I 3B1J_D 3RVD_N 3QV1_I 2LJ9_A.
Probab=23.10 E-value=28 Score=26.41 Aligned_cols=42 Identities=29% Similarity=0.356 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHHHHHHH
Q 022656 83 LEEKIKNLLEQVETLGEAG--KVDEAEALMRKVEILNVEKTTLT 124 (294)
Q Consensus 83 l~ekI~~ll~eaE~LGeeG--~VdeA~~l~~~ve~Lk~er~~l~ 124 (294)
|+++|...++++.++-.++ .-.++-.....|+.|..++.-..
T Consensus 1 l~e~Ie~~i~eA~~~c~~~g~~s~ec~~AWdeVEELqa~~~h~~ 44 (71)
T PF02672_consen 1 LEEKIEKAIEEAREACAEGGANSAECRHAWDEVEELQAEASHQR 44 (71)
T ss_dssp --------------------------------------------
T ss_pred ChHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHcc
Confidence 5678888888888888888 77788888889999988765443
No 260
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=22.89 E-value=4.2e+02 Score=23.36 Aligned_cols=52 Identities=13% Similarity=0.113 Sum_probs=33.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 76 KSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 76 ~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
..+++..+.++|..|-...+.+....-.=+-...-.++|++......|++.+
T Consensus 90 Le~~~~~l~~ri~eLe~~l~~kad~vvsYqll~hr~e~ee~~~~l~~le~~~ 141 (175)
T PRK13182 90 LEAQLNTITRRLDELERQLQQKADDVVSYQLLQHRREMEEMLERLQKLEARL 141 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 4566777788888887777777766654444455556666666655555543
No 261
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]
Probab=22.81 E-value=91 Score=30.25 Aligned_cols=13 Identities=38% Similarity=0.554 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHHH
Q 022656 173 GMVRDFITEYKEA 185 (294)
Q Consensus 173 ~kIRe~l~eL~~~ 185 (294)
..=++++..++++
T Consensus 151 e~erdm~~AYK~a 163 (335)
T KOG0113|consen 151 EHERDMKAAYKDA 163 (335)
T ss_pred ccHHHHHHHHHhc
Confidence 3447777777664
No 262
>PRK15178 Vi polysaccharide export inner membrane protein VexD; Provisional
Probab=22.75 E-value=6e+02 Score=25.83 Aligned_cols=83 Identities=13% Similarity=0.177 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHhhhhcCC-CCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHH
Q 022656 42 CEKLVMDLDRRVRRGRERLSQEVE-PAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEK 120 (294)
Q Consensus 42 L~~lI~d~dRkI~~~k~RL~~~~e-~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er 120 (294)
+..+|..++..+...+..|+.-.. -.+..+.......+|..|+.+|.....+ |+..|....--..+.+.+.|..+.
T Consensus 284 ~~~lI~~Le~qLa~~~aeL~~L~~~~~p~sPqV~~l~~rI~aLe~QIa~er~k---l~~~~g~~~la~~laeYe~L~le~ 360 (434)
T PRK15178 284 IYQLIAGFETQLAEAKAEYAQLMVNGLDQNPLIPRLSAKIKVLEKQIGEQRNR---LSNKLGSQGSSESLSLFEDLRLQS 360 (434)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCchhHHHHHHHHHHHHHHHHHHH---hhcCCCCCchhHHHHHHHHHHHHH
Q ss_pred HHHHHhh
Q 022656 121 TTLTQQS 127 (294)
Q Consensus 121 ~~l~~~~ 127 (294)
+-.++.+
T Consensus 361 efAe~~y 367 (434)
T PRK15178 361 EIAKARW 367 (434)
T ss_pred HHHHHHH
No 263
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=22.72 E-value=4.4e+02 Score=24.11 Aligned_cols=55 Identities=29% Similarity=0.332 Sum_probs=38.6
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHH----HHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 73 SAEKSEQLSVLEEKIKNLLEQVET----LGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 73 ~~~~~e~i~~l~ekI~~ll~eaE~----LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
...+..++..++.+|+.+-++.+. |...+.|++-+++-.++...+.+.+.++.+.
T Consensus 127 ~~DvT~~y~D~~arl~~l~~~~~rl~~ll~ka~~~~d~l~ie~~L~~v~~eIe~~~~~~ 185 (262)
T PF14257_consen 127 SEDVTEQYVDLEARLKNLEAEEERLLELLEKAKTVEDLLEIERELSRVRSEIEQLEGQL 185 (262)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334555666666666655555444 3345799999999999999999998888765
No 264
>KOG0963 consensus Transcription factor/CCAAT displacement protein CDP1 [Transcription]
Probab=22.67 E-value=8.5e+02 Score=25.99 Aligned_cols=23 Identities=22% Similarity=0.305 Sum_probs=15.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHH
Q 022656 75 EKSEQLSVLEEKIKNLLEQVETL 97 (294)
Q Consensus 75 ~~~e~i~~l~ekI~~ll~eaE~L 97 (294)
.....+..++..|..|+..++.+
T Consensus 282 ~~~~~L~~kd~~i~~L~~di~~~ 304 (629)
T KOG0963|consen 282 ALGSVLNQKDSEIAQLSNDIERL 304 (629)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHH
Confidence 34445666777888888877765
No 265
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=22.65 E-value=59 Score=27.76 Aligned_cols=78 Identities=12% Similarity=0.109 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Q 022656 38 LAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILN 117 (294)
Q Consensus 38 ~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk 117 (294)
.-.+|..-..+.+..-.+.++=|...+.. .+... ++.+..+.-.+.|..+..+|.+.-+.
T Consensus 17 ~~~iCp~C~~~~e~~f~kV~~yLr~~p~~---~ati~-------eV~e~tgVs~~~I~~~IreGRL~~~~---------- 76 (137)
T TIGR03826 17 GRDVCPSCYEEEEREFEKVYKFLRKHENR---QATVS-------EIVEETGVSEKLILKFIREGRLQLKH---------- 76 (137)
T ss_pred CCccCHHHhHHHHHHHHHHHHHHHHCCCC---CCCHH-------HHHHHHCcCHHHHHHHHHcCCeeccC----------
Confidence 34466777777777777888888644311 11222 33333344445666677777664331
Q ss_pred HHHHHHHHhhhhhhhhhhhhhhccccccccccccccC
Q 022656 118 VEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVAN 154 (294)
Q Consensus 118 ~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~ 154 (294)
..+ -.-+||.||+.+-.+
T Consensus 77 ------------~~n-------l~~~CE~CG~~I~~G 94 (137)
T TIGR03826 77 ------------FPN-------LGYPCERCGTSIREG 94 (137)
T ss_pred ------------CCC-------CcCcccccCCcCCCC
Confidence 112 237899999987655
No 266
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=22.55 E-value=34 Score=29.13 Aligned_cols=14 Identities=36% Similarity=0.748 Sum_probs=11.7
Q ss_pred ccccccccccccCC
Q 022656 142 ALCEICGSFLVAND 155 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D 155 (294)
.-|++||+.|+.-|
T Consensus 29 ~hCp~Cg~PLF~Kd 42 (131)
T COG1645 29 KHCPKCGTPLFRKD 42 (131)
T ss_pred hhCcccCCcceeeC
Confidence 67999999998753
No 267
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=22.50 E-value=5.3e+02 Score=26.76 Aligned_cols=89 Identities=19% Similarity=0.244 Sum_probs=52.9
Q ss_pred ChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHH
Q 022656 30 YVPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEAL 109 (294)
Q Consensus 30 ~~~~YE~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l 109 (294)
.+..|..+|-.....-+.+|+..+-.+..-+..-. -..+........+.|..++++|..++.+++.|-+. -...
T Consensus 61 ~fe~w~~~w~~i~~~~~~~ie~~L~~ae~~~~~~r-f~ka~~~i~~~~~~l~~~e~~i~~i~~~l~~L~~~-----e~~n 134 (560)
T PF06160_consen 61 KFEEWRQKWDEIVTKQLPEIEEQLFEAEEYADKYR-FKKAKQAIKEIEEQLDEIEEDIKEILDELDELLES-----EEKN 134 (560)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhccc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHH
Confidence 34556677777777777888888877665553210 00011223445677888888999888888888543 3334
Q ss_pred HHHHHHHHHHHHHHH
Q 022656 110 MRKVEILNVEKTTLT 124 (294)
Q Consensus 110 ~~~ve~Lk~er~~l~ 124 (294)
-.+++.|+..-..+.
T Consensus 135 r~~i~~l~~~y~~lr 149 (560)
T PF06160_consen 135 REEIEELKEKYRELR 149 (560)
T ss_pred HHHHHHHHHHHHHHH
Confidence 444555554444443
No 268
>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.
Probab=22.44 E-value=66 Score=23.68 Aligned_cols=24 Identities=38% Similarity=0.483 Sum_probs=17.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHh
Q 022656 76 KSEQLSVLEEKIKNLLEQVETLGE 99 (294)
Q Consensus 76 ~~e~i~~l~ekI~~ll~eaE~LGe 99 (294)
+-+++..|-++|.+|..+..+|-.
T Consensus 12 VrEEVevLK~~I~eL~~~n~~Le~ 35 (59)
T PF01166_consen 12 VREEVEVLKEQIAELEERNSQLEE 35 (59)
T ss_dssp -TTSHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 446788888888888887777633
No 269
>PF07765 KIP1: KIP1-like protein; InterPro: IPR011684 This is a group of sequences found exclusively in plants. They are similar to kinase interacting protein 1 (KIP1), which has been found to interact with the kinase domain of PRK1, a receptor-like kinase []. This particular region contains two coiled-coils, which are described as motifs involved in protein-protein interactions []. It has also been suggested that the coiled-coils of the protein allow it to dimerise in vivo [].
Probab=22.42 E-value=3.7e+02 Score=20.71 Aligned_cols=25 Identities=36% Similarity=0.436 Sum_probs=20.1
Q ss_pred CchhhHHHHHHHHHHHHHHHHHHHH
Q 022656 72 ISAEKSEQLSVLEEKIKNLLEQVET 96 (294)
Q Consensus 72 ~~~~~~e~i~~l~ekI~~ll~eaE~ 96 (294)
.++-++..|.+++++++.||+-|++
T Consensus 12 ~skWL~~~l~dmd~kvk~mlkliee 36 (74)
T PF07765_consen 12 QSKWLQENLSDMDEKVKAMLKLIEE 36 (74)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3445778899999999999888766
No 270
>PF12907 zf-met2: Zinc-binding
Probab=22.33 E-value=31 Score=23.44 Aligned_cols=26 Identities=19% Similarity=0.529 Sum_probs=18.5
Q ss_pred ccccccccccccCCchHHHHhhhccc
Q 022656 142 ALCEICGSFLVANDAAERTQSHISGK 167 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~d~Rl~dH~~GK 167 (294)
-+|.||=+-....-+..=|.+|+..|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enK 27 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENK 27 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHcc
Confidence 47999985444444566699999876
No 271
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=22.24 E-value=1.5e+02 Score=17.03 Aligned_cols=21 Identities=33% Similarity=0.591 Sum_probs=17.1
Q ss_pred HHHHHhcCCHHHHHHHHHHHH
Q 022656 94 VETLGEAGKVDEAEALMRKVE 114 (294)
Q Consensus 94 aE~LGeeG~VdeA~~l~~~ve 114 (294)
+..+...|++++|..++.+..
T Consensus 7 i~~~~~~~~~~~a~~~~~~M~ 27 (35)
T TIGR00756 7 IDGLCKAGRVEEALELFKEML 27 (35)
T ss_pred HHHHHHCCCHHHHHHHHHHHH
Confidence 566889999999999887654
No 272
>cd00176 SPEC Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here
Probab=22.23 E-value=4.5e+02 Score=21.69 Aligned_cols=47 Identities=32% Similarity=0.387 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 80 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 80 i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
|......|..+...++.|...+. ..+..+...++.|+.....|....
T Consensus 49 ~~~~~~~~~~l~~~~~~L~~~~~-~~~~~i~~~~~~l~~~w~~l~~~~ 95 (213)
T cd00176 49 LAAHEERVEALNELGEQLIEEGH-PDAEEIQERLEELNQRWEELRELA 95 (213)
T ss_pred HHHCHHHHHHHHHHHHHHHhcCC-CChHHHHHHHHHHHHHHHHHHHHH
Confidence 44456666777788888888876 567778888888887777765543
No 273
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=21.96 E-value=1.5e+02 Score=17.16 Aligned_cols=24 Identities=21% Similarity=0.285 Sum_probs=17.3
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHH
Q 022656 90 LLEQVETLGEAGKVDEAEALMRKV 113 (294)
Q Consensus 90 ll~eaE~LGeeG~VdeA~~l~~~v 113 (294)
++..+..+...|+.++|...+.++
T Consensus 3 ~~~~a~~~~~~g~~~~A~~~~~~~ 26 (33)
T PF13174_consen 3 LYRLARCYYKLGDYDEAIEYFQRL 26 (33)
T ss_dssp HHHHHHHHHHHCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHccCHHHHHHHHHHH
Confidence 455566667778888888877655
No 274
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=21.94 E-value=23 Score=27.46 Aligned_cols=30 Identities=23% Similarity=0.442 Sum_probs=14.0
Q ss_pred ccccccccccccccCCchHHHH-hhhccccc
Q 022656 140 KMALCEICGSFLVANDAAERTQ-SHISGKQH 169 (294)
Q Consensus 140 km~VCeVCGA~Ls~~D~d~Rl~-dH~~GK~H 169 (294)
+--+|.|||.-+......-=++ ||.+|..-
T Consensus 21 q~~~C~iC~~~~~~~~~~~~vDHdH~tG~vR 51 (81)
T PF02945_consen 21 QGGRCAICGKPLPGESRKLVVDHDHKTGRVR 51 (81)
T ss_dssp TTTE-TTT-SEEETTCGGCEEEE-TTTTBEE
T ss_pred hCCcCcCCCCCcccCCCcceecCCCCCCCch
Confidence 3359999998433332111122 67777753
No 275
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=21.93 E-value=1.3e+02 Score=24.57 Aligned_cols=27 Identities=33% Similarity=0.326 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHH
Q 022656 85 EKIKNLLEQVETLGEAGKVDEAEALMR 111 (294)
Q Consensus 85 ekI~~ll~eaE~LGeeG~VdeA~~l~~ 111 (294)
.-...++..++.+.++|+|+.|..++.
T Consensus 68 ~~~~~~~~~~~~~l~~g~~~~a~~ll~ 94 (115)
T PF12793_consen 68 SPEELLEQQAEELLEQGKYEQALQLLD 94 (115)
T ss_pred CHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 334556789999999999999999987
No 276
>PF02044 Bombesin: Bombesin-like peptide; InterPro: IPR000874 Bombesin-like peptides comprise a large family of peptides which were initially isolated from amphibian skin, where they stimulate smooth muscle contraction. They were later found to be widely distributed in mammalian neural and endocrine cells. The amphibian peptides which belong to this family are currently classified into three subfamilies [, ]; the Bombesin group, which includes bombesin and alytesin; the Ranatensin group, which includes ranatensins, litorin, and Rohdei litorin; and the Phyllolitorin group, which includes Leu(8)- and Phe(8)-phyllolitorins. In mammals and birds two categories of bombesin-like peptides are known [, ], gastrin-releasing peptide (GRP), which stimulates the release of gastrin as well as other gastrointestinal hormones, and neuromedin B (NMB), a neuropeptide whose function is not yet clear. Bombesin-like peptides, like many other active peptides, are synthesized as larger protein precursors that are enzymatically converted to their mature forms. The final peptides are eight to fourteen residues long.; GO: 0007218 neuropeptide signaling pathway; PDB: 1C9A_A 1C98_A.
Probab=21.92 E-value=28 Score=18.39 Aligned_cols=6 Identities=50% Similarity=0.878 Sum_probs=2.2
Q ss_pred hhhccc
Q 022656 162 SHISGK 167 (294)
Q Consensus 162 dH~~GK 167 (294)
-||+||
T Consensus 7 Gh~Mgk 12 (14)
T PF02044_consen 7 GHFMGK 12 (14)
T ss_dssp HCT---
T ss_pred eeeecc
Confidence 588887
No 277
>PRK14011 prefoldin subunit alpha; Provisional
Probab=21.91 E-value=2.1e+02 Score=24.47 Aligned_cols=15 Identities=20% Similarity=0.228 Sum_probs=12.0
Q ss_pred hhccccccccccccc
Q 022656 138 EKKMALCEICGSFLV 152 (294)
Q Consensus 138 ~qkm~VCeVCGA~Ls 152 (294)
.+.+-||=.||+|+-
T Consensus 49 ~~eiLVPLg~s~yV~ 63 (144)
T PRK14011 49 SEEILIPLGPGAFLK 63 (144)
T ss_pred CCeEEEEcCCCcEEe
Confidence 577888888888876
No 278
>COG4303 EutB Ethanolamine ammonia-lyase, large subunit [Amino acid transport and metabolism]
Probab=21.77 E-value=34 Score=33.64 Aligned_cols=10 Identities=30% Similarity=0.484 Sum_probs=9.4
Q ss_pred HHhhhccccc
Q 022656 160 TQSHISGKQH 169 (294)
Q Consensus 160 l~dH~~GK~H 169 (294)
|.|||+||+|
T Consensus 346 LEDHFmGKL~ 355 (453)
T COG4303 346 LEDHFMGKLS 355 (453)
T ss_pred hHhhhhhhhc
Confidence 7899999998
No 279
>TIGR02473 flagell_FliJ flagellar export protein FliJ. Members of this family are the FliJ protein found, in nearly every case, in the midst of other flagellar biosynthesis genes in bacgterial genomes. Typically the fliJ gene is found adjacent to the gene for the flagellum-specific ATPase FliI. Sequence scoring in the gray zone between trusted and noise cutoffs include both probable FliJ proteins and components of bacterial type III secretion systems.
Probab=21.70 E-value=4.3e+02 Score=21.26 Aligned_cols=26 Identities=23% Similarity=0.068 Sum_probs=14.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcC
Q 022656 76 KSEQLSVLEEKIKNLLEQVETLGEAG 101 (294)
Q Consensus 76 ~~e~i~~l~ekI~~ll~eaE~LGeeG 101 (294)
...+|..|...+......+...+..|
T Consensus 32 ~~~~l~~l~~~~~~~~~~~~~~~~~g 57 (141)
T TIGR02473 32 LETQLQQLIKYREEYEQQALEKVGAG 57 (141)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 33455555555555555555555555
No 280
>PF08946 Osmo_CC: Osmosensory transporter coiled coil; InterPro: IPR015041 The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function []. ; PDB: 1R48_B.
Probab=21.68 E-value=1.8e+02 Score=20.34 Aligned_cols=22 Identities=18% Similarity=0.345 Sum_probs=12.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHH
Q 022656 76 KSEQLSVLEEKIKNLLEQVETL 97 (294)
Q Consensus 76 ~~e~i~~l~ekI~~ll~eaE~L 97 (294)
+..+|..|+++|..|-++-+.|
T Consensus 17 IEqkiedid~qIaeLe~KR~~L 38 (46)
T PF08946_consen 17 IEQKIEDIDEQIAELEAKRQRL 38 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHhHHHHHHHHHHHHHHHHHH
Confidence 4455666666665555554444
No 281
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=21.61 E-value=4.2e+02 Score=21.13 Aligned_cols=35 Identities=29% Similarity=0.363 Sum_probs=21.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHH
Q 022656 76 KSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALM 110 (294)
Q Consensus 76 ~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~ 110 (294)
...++...-........++-.|...|+.++|..++
T Consensus 110 ~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~a~~~~ 144 (181)
T PF12729_consen 110 LLEEFKEAWKAYRKLRDQVIELAKSGDNDEARAIL 144 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
Confidence 33445555555556666666777778777775544
No 282
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=21.59 E-value=20 Score=23.82 Aligned_cols=16 Identities=25% Similarity=0.657 Sum_probs=9.3
Q ss_pred hhcccccccccccccc
Q 022656 138 EKKMALCEICGSFLVA 153 (294)
Q Consensus 138 ~qkm~VCeVCGA~Ls~ 153 (294)
..+...|++||...-+
T Consensus 3 ~~~~YkC~~CGniVev 18 (36)
T PF06397_consen 3 KGEFYKCEHCGNIVEV 18 (36)
T ss_dssp TTEEEE-TTT--EEEE
T ss_pred cccEEEccCCCCEEEE
Confidence 3466899999987654
No 283
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=21.56 E-value=3.3e+02 Score=23.78 Aligned_cols=47 Identities=32% Similarity=0.398 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCC---HHHHHHHHHHHHHHHHHHHHHHHh
Q 022656 80 LSVLEEKIKNLLEQVETLGEAGK---VDEAEALMRKVEILNVEKTTLTQQ 126 (294)
Q Consensus 80 i~~l~ekI~~ll~eaE~LGeeG~---VdeA~~l~~~ve~Lk~er~~l~~~ 126 (294)
+..+++++..+.++++...+..+ .++....-++++.|+.+.+..+..
T Consensus 127 l~~~~~~~~~~~kq~~~~~~~~~~~~~~~~~~~~~ei~~lk~el~~~~~~ 176 (192)
T PF05529_consen 127 LIKLEEKLEALKKQAESASEAAEKLLKEENKKLSEEIEKLKKELEKKEKE 176 (192)
T ss_pred HHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHH
Confidence 44555555556665555443332 234445556666666665554433
No 284
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=21.55 E-value=32 Score=28.01 Aligned_cols=15 Identities=33% Similarity=0.992 Sum_probs=12.5
Q ss_pred cccccccccccccCC
Q 022656 141 MALCEICGSFLVAND 155 (294)
Q Consensus 141 m~VCeVCGA~Ls~~D 155 (294)
|.-|+.||.+|++.-
T Consensus 1 m~FCP~Cgn~Live~ 15 (105)
T KOG2906|consen 1 MLFCPTCGNMLIVES 15 (105)
T ss_pred CcccCCCCCEEEEec
Confidence 678999999999753
No 285
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=21.51 E-value=34 Score=19.16 Aligned_cols=19 Identities=26% Similarity=0.705 Sum_probs=11.7
Q ss_pred cccccccccccCCchHHHHhhh
Q 022656 143 LCEICGSFLVANDAAERTQSHI 164 (294)
Q Consensus 143 VCeVCGA~Ls~~D~d~Rl~dH~ 164 (294)
+|++||...... .-|..|+
T Consensus 2 ~C~~C~~~f~~~---~~l~~H~ 20 (23)
T PF00096_consen 2 KCPICGKSFSSK---SNLKRHM 20 (23)
T ss_dssp EETTTTEEESSH---HHHHHHH
T ss_pred CCCCCCCccCCH---HHHHHHH
Confidence 799999764432 3444454
No 286
>PF11428 DUF3196: Protein of unknown function (DUF3196); InterPro: IPR024503 The entry comprises bacterial proteins of unknown function. One of the proteins in this entry, MPN330, is thought to involved in a cellular function that has yet to be characterised. The protein has 11 helices and a novel fold. No function is currently known for this protein.; PDB: 1TD6_A.
Probab=21.51 E-value=6.4e+02 Score=24.26 Aligned_cols=86 Identities=20% Similarity=0.307 Sum_probs=49.1
Q ss_pred CCCCCCccccccCChh-HHHHhhcCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHH
Q 022656 1 MINHLDCIPVKMCYYV-CDCSFEKSPRHDAYVPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQ 79 (294)
Q Consensus 1 ~~~~~~~~~~~~~~~~-lK~~Ye~~~~~~~~~~~YE~e~l~~L~~lI~d~dRkI~~~k~RL~~~~e~~~~~~~~~~~~e~ 79 (294)
+||||++.--..|++. +++.+-+.-........|=.+.+.-++.+|. ++....|...+.++- ..|-.+......
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~yYd~il~~i~~ll~--~~~y~~A~~lI~~EL---~mPYIP~~~~~~ 82 (286)
T PF11428_consen 8 FINHLMTLKKHFHTYNEIKKDFKKYEKNNDQITNYYDEILKKIKQLLD--KKDYKEALELINEEL---SMPYIPLPLESK 82 (286)
T ss_dssp SSTT-SB-----SSHHHHHHHHHHHHTTTSSHHHHHHHHHHHHHHHHH--TT-HHHHHHHHHHHT---T-TTS-HHHHHH
T ss_pred HHHHHHHHHHhHhhHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHHHH--HhhHHHHHHHHHHHh---cCCCCChHHHHH
Confidence 4899999999999986 6776655411224445665667777777776 456788888887653 334455555566
Q ss_pred HHHHHHHHHHHH
Q 022656 80 LSVLEEKIKNLL 91 (294)
Q Consensus 80 i~~l~ekI~~ll 91 (294)
+..+--.|+..+
T Consensus 83 fe~~l~~ik~~~ 94 (286)
T PF11428_consen 83 FESLLQEIKKDL 94 (286)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 666666666544
No 287
>PF08838 DUF1811: Protein of unknown function (DUF1811); InterPro: IPR014938 This entry consists uncharacterised bacterial proteins. Some of the proteins are annotated as being transcriptional regulators (see Q4MQL7 from SWISSPROT, Q65MA2 from SWISSPROT). The structure of one of the proteins has revealed a beta-barrel like structure with helix-turn-helix like motif. ; PDB: 2YXY_A 1SF9_A.
Probab=21.34 E-value=3.4e+02 Score=22.15 Aligned_cols=34 Identities=26% Similarity=0.330 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 022656 81 SVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVE 114 (294)
Q Consensus 81 ~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve 114 (294)
.+|..+|..|.+++.++=..|.|.+-.-++.++.
T Consensus 10 ~EL~~Ei~~L~ekarKAEq~G~~nE~aV~erK~~ 43 (102)
T PF08838_consen 10 EELRQEIARLKEKARKAEQLGIVNEYAVYERKII 43 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHcCCccHHHHHHHHHH
Confidence 3677778888888888777788877655554443
No 288
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=21.34 E-value=4.8e+02 Score=22.25 Aligned_cols=50 Identities=34% Similarity=0.395 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCHHHH-----------HHHHHHHHHHHHHHHHHHHhh
Q 022656 78 EQLSVLEEKIKNLLEQVETLGEAGKVDEA-----------EALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA-----------~~l~~~ve~Lk~er~~l~~~~ 127 (294)
+++..|+.+|..|.+++..|..+-..-.+ ..+...++.|+.+...|+..+
T Consensus 72 eel~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL 132 (169)
T PF07106_consen 72 EELAELDAEIKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKL 132 (169)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 44556666666666665555443322222 234455555555555555544
No 289
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=21.33 E-value=2.1e+02 Score=17.39 Aligned_cols=31 Identities=16% Similarity=0.207 Sum_probs=22.1
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Q 022656 89 NLLEQVETLGEAGKVDEAEALMRKVEILNVE 119 (294)
Q Consensus 89 ~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 119 (294)
.+..-+..+...|+.++|..+..++=.+.+.
T Consensus 4 ~~~~la~~~~~~g~~~~A~~~~~~al~~~~~ 34 (42)
T PF13374_consen 4 ALNNLANAYRAQGRYEEALELLEEALEIRER 34 (42)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHhhhhcchhhHHHHHHHHHHHH
Confidence 3455677788999999999999888666543
No 290
>PF11598 COMP: Cartilage oligomeric matrix protein; InterPro: IPR024665 Thrombospondins are adhesive glycoproteins that mediate cell-to-cell and cell-to-matrix interactions. Cartilage oligomeric matrix protein may play a role in the structural integrity of cartilage via its interaction with other extracellular matrix proteins such as collagen and fibronectin [, ]. Thrombospondin 3 and 4 and cartilage oligomeric matrix proteins contain a five-stranded coiled-coil domain represented by this entry. This domain has a binding site between two internal rings formed by Leu37 and Thr40 [].; PDB: 1MZ9_D 1FBM_A 1VDF_E.
Probab=21.32 E-value=2.2e+02 Score=19.74 Aligned_cols=9 Identities=33% Similarity=1.095 Sum_probs=5.3
Q ss_pred ccccccccc
Q 022656 140 KMALCEICG 148 (294)
Q Consensus 140 km~VCeVCG 148 (294)
.+.-|+.||
T Consensus 37 tI~eC~aCg 45 (45)
T PF11598_consen 37 TIMECQACG 45 (45)
T ss_dssp HHHT-TTG-
T ss_pred HHHHhcccC
Confidence 456799998
No 291
>PF05266 DUF724: Protein of unknown function (DUF724); InterPro: IPR007930 This family contains several uncharacterised proteins found exclusively in Arabidopsis thaliana.
Probab=21.25 E-value=5.1e+02 Score=23.12 Aligned_cols=52 Identities=27% Similarity=0.219 Sum_probs=25.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 76 KSEQLSVLEEKIKNLLEQVETLGEAG--KVDEAEALMRKVEILNVEKTTLTQQS 127 (294)
Q Consensus 76 ~~e~i~~l~ekI~~ll~eaE~LGeeG--~VdeA~~l~~~ve~Lk~er~~l~~~~ 127 (294)
....|.+|+.+|..|-.++..|..+- .-.+...+-..++.++++...++.++
T Consensus 129 ~e~~i~~Le~ki~el~~~~~~~~~~ke~~~~ei~~lks~~~~l~~~~~~~e~~F 182 (190)
T PF05266_consen 129 LESEIKELEMKILELQRQAAKLKEKKEAKDKEISRLKSEAEALKEEIENAELEF 182 (190)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556666666666666555554221 11223344445555555555554444
No 292
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=21.17 E-value=6.4e+02 Score=23.06 Aligned_cols=48 Identities=23% Similarity=0.186 Sum_probs=33.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHH
Q 022656 76 KSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTL 123 (294)
Q Consensus 76 ~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~er~~l 123 (294)
.-+++-.|.-+|--+-..+=.+.-.|++++|...++++..+-++...+
T Consensus 18 ~REE~l~lsRei~r~s~~aI~~~H~~~~eeA~~~l~~a~~~v~~Lk~~ 65 (204)
T COG2178 18 AREEALKLSREIVRLSGEAIFLLHRGDFEEAEKKLKKASEAVEKLKRL 65 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHH
Confidence 445666777777777777777778888888877777766665555543
No 293
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=21.15 E-value=2.7e+02 Score=22.03 Aligned_cols=27 Identities=19% Similarity=0.197 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHH
Q 022656 80 LSVLEEKIKNLLEQVETLGEAGKVDEA 106 (294)
Q Consensus 80 i~~l~ekI~~ll~eaE~LGeeG~VdeA 106 (294)
+..+..+|..|.++.++|-.+-.|-++
T Consensus 25 ~~ka~~~~~kL~~en~qlk~Ek~~~~~ 51 (87)
T PF10883_consen 25 VKKAKKQNAKLQKENEQLKTEKAVAET 51 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555566666666666544444333
No 294
>PRK06921 hypothetical protein; Provisional
Probab=21.06 E-value=94 Score=28.91 Aligned_cols=37 Identities=14% Similarity=0.175 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccccc
Q 022656 108 ALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSF 150 (294)
Q Consensus 108 ~l~~~ve~Lk~er~~l~~~~~~~~~~~~~~~qkm~VCeVCGA~ 150 (294)
.++.++..|..++..|.... .- + .......|++|+=-
T Consensus 5 ~~~~~~~~l~~~~~~~l~~~-g~----~-~~~~~~~Cp~C~dt 41 (266)
T PRK06921 5 TIEEKAAELLMRERPSTTTK-PE----E-SDAERYDCPKCKDR 41 (266)
T ss_pred HHHHHHHHHHHHHHHHHHhC-CC----C-CcCCCCCCCCCCCC
Confidence 46677777877777766543 11 1 12334679999853
No 295
>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=21.00 E-value=34 Score=22.23 Aligned_cols=14 Identities=36% Similarity=0.928 Sum_probs=9.9
Q ss_pred cccccccccccccC
Q 022656 141 MALCEICGSFLVAN 154 (294)
Q Consensus 141 m~VCeVCGA~Ls~~ 154 (294)
|.-|+-||.+|.+-
T Consensus 1 m~FCp~C~nlL~p~ 14 (35)
T PF02150_consen 1 MRFCPECGNLLYPK 14 (35)
T ss_dssp --BETTTTSBEEEE
T ss_pred CeeCCCCCccceEc
Confidence 56799999998754
No 296
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=20.97 E-value=34 Score=31.52 Aligned_cols=40 Identities=25% Similarity=0.251 Sum_probs=22.3
Q ss_pred hccccccccccccccCCchHHHHhhhc-cccc-ccHHHHHHHHHHHHH
Q 022656 139 KKMALCEICGSFLVANDAAERTQSHIS-GKQH-IGYGMVRDFITEYKE 184 (294)
Q Consensus 139 qkm~VCeVCGA~Ls~~D~d~Rl~dH~~-GK~H-lGy~kIRe~l~eL~~ 184 (294)
.||.|||-||.-- .+-+.|+. =|.| -+-..+..+.+.+-+
T Consensus 210 ~kl~vcedcg~t~------~~~e~~~~h~~~~hp~SpallKfsKk~a~ 251 (267)
T KOG3576|consen 210 AKLYVCEDCGYTS------ERPEVYYLHLKLHHPFSPALLKFSKKQAQ 251 (267)
T ss_pred hheeeecccCCCC------CChhHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence 5899999999642 33333332 1333 344556666655443
No 297
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=20.96 E-value=51 Score=24.67 Aligned_cols=30 Identities=23% Similarity=0.339 Sum_probs=23.6
Q ss_pred cccccccccccccCCchHHHHhhhcccccccHH
Q 022656 141 MALCEICGSFLVANDAAERTQSHISGKQHIGYG 173 (294)
Q Consensus 141 m~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~ 173 (294)
.-.|.+|+.- .++..-|..|+..+-|.-+.
T Consensus 50 ~~~C~~C~~~---f~s~~~l~~Hm~~~~H~~~~ 79 (100)
T PF12756_consen 50 SFRCPYCNKT---FRSREALQEHMRSKHHKKRN 79 (100)
T ss_dssp SEEBSSSS-E---ESSHHHHHHHHHHTTTTC-S
T ss_pred CCCCCccCCC---CcCHHHHHHHHcCccCCCcc
Confidence 4789999987 45778899999999998763
No 298
>PF09543 DUF2379: Protein of unknown function (DUF2379); InterPro: IPR011753 This family consists of at least 7 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. The function is unknown.
Probab=20.62 E-value=3.2e+02 Score=22.94 Aligned_cols=36 Identities=25% Similarity=0.378 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 022656 78 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKV 113 (294)
Q Consensus 78 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~v 113 (294)
..|.+=+..+...+-.+-.+-..|++|.|...|..|
T Consensus 65 rRIr~GS~RL~~al~r~~~~~daGD~dgARq~m~dv 100 (121)
T PF09543_consen 65 RRIRDGSRRLSRALHRMYRLRDAGDLDGARQEMRDV 100 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhccCHHHHHHHHHHH
Confidence 344455555555667788899999999999988665
No 299
>COG0268 RpsT Ribosomal protein S20 [Translation, ribosomal structure and biogenesis]
Probab=20.48 E-value=3.4e+02 Score=21.51 Aligned_cols=36 Identities=19% Similarity=0.283 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Q 022656 82 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILN 117 (294)
Q Consensus 82 ~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk 117 (294)
..-..|...+.+++...+.|+++.|+.++..+...-
T Consensus 23 ~~kS~~rT~iKk~~~ai~~gd~~~A~~~l~~a~~~i 58 (88)
T COG0268 23 SRKSALRTAIKKVEAAIEAGDKEAAKAALKEAQKKI 58 (88)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence 445667788889999999999999999998887654
No 300
>PRK14142 heat shock protein GrpE; Provisional
Probab=20.44 E-value=1.9e+02 Score=26.72 Aligned_cols=26 Identities=23% Similarity=0.245 Sum_probs=20.0
Q ss_pred ccccccccccccccCCchHHHHhhhc
Q 022656 140 KMALCEICGSFLVANDAAERTQSHIS 165 (294)
Q Consensus 140 km~VCeVCGA~Ls~~D~d~Rl~dH~~ 165 (294)
+-.+..++-.||-+.|+-.|--.|..
T Consensus 79 ~~A~e~~~kdLLpVlDnLERAL~~~~ 104 (223)
T PRK14142 79 DRAKASVVSQLLGVLDDLERARKHGD 104 (223)
T ss_pred HHHHHHHHHHHhchHhHHHHHHhccc
Confidence 34556677899999999999767754
No 301
>PF06825 HSBP1: Heat shock factor binding protein 1; InterPro: IPR009643 Heat shock factor binding protein 1 (HSBP1) appears to be a negative regulator of the heat shock response [].; PDB: 3CI9_A.
Probab=20.43 E-value=3.4e+02 Score=19.56 Aligned_cols=20 Identities=20% Similarity=0.454 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 022656 37 ELAQFCEKLVMDLDRRVRRG 56 (294)
Q Consensus 37 e~l~~L~~lI~d~dRkI~~~ 56 (294)
++-.|++.|+..+.-|....
T Consensus 3 elt~~v~~lL~qmq~kFq~m 22 (54)
T PF06825_consen 3 ELTAFVQNLLQQMQDKFQTM 22 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 45666777777766666543
No 302
>PLN02372 violaxanthin de-epoxidase
Probab=20.32 E-value=4.3e+02 Score=26.90 Aligned_cols=28 Identities=18% Similarity=0.158 Sum_probs=17.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022656 33 KFEAELAQFCEKLVMDLDRRVRRGRERL 60 (294)
Q Consensus 33 ~YE~e~l~~L~~lI~d~dRkI~~~k~RL 60 (294)
|=|-.++..|++-|.+.++.|-+--..+
T Consensus 357 gpep~l~~~l~~~~e~~e~~i~~e~~~~ 384 (455)
T PLN02372 357 GPEPPLLERLEKDVEEGEKTIVKEARQI 384 (455)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455567777777777777776653333
No 303
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=20.30 E-value=39 Score=20.17 Aligned_cols=12 Identities=33% Similarity=0.706 Sum_probs=9.8
Q ss_pred hhcccccccccc
Q 022656 138 EKKMALCEICGS 149 (294)
Q Consensus 138 ~qkm~VCeVCGA 149 (294)
.++...|++||.
T Consensus 11 ~~k~~~C~~C~k 22 (26)
T PF13465_consen 11 GEKPYKCPYCGK 22 (26)
T ss_dssp SSSSEEESSSSE
T ss_pred CCCCCCCCCCcC
Confidence 457799999985
No 304
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=20.20 E-value=60 Score=22.64 Aligned_cols=20 Identities=20% Similarity=0.388 Sum_probs=11.1
Q ss_pred ccccccccccccCCchHHHHhhhc
Q 022656 142 ALCEICGSFLVANDAAERTQSHIS 165 (294)
Q Consensus 142 ~VCeVCGA~Ls~~D~d~Rl~dH~~ 165 (294)
..|+.||..++ ...|..|+.
T Consensus 3 f~CP~C~~~~~----~~~L~~H~~ 22 (54)
T PF05605_consen 3 FTCPYCGKGFS----ESSLVEHCE 22 (54)
T ss_pred cCCCCCCCccC----HHHHHHHHH
Confidence 56777776322 234666654
No 305
>KOG2698 consensus GTP cyclohydrolase I [Coenzyme transport and metabolism]
Probab=20.13 E-value=30 Score=31.81 Aligned_cols=10 Identities=60% Similarity=0.909 Sum_probs=9.0
Q ss_pred hcccccccHH
Q 022656 164 ISGKQHIGYG 173 (294)
Q Consensus 164 ~~GK~HlGy~ 173 (294)
|.||.|+||.
T Consensus 144 F~GkVhIGY~ 153 (247)
T KOG2698|consen 144 FYGKVHIGYI 153 (247)
T ss_pred ceeeEEEeec
Confidence 7899999995
No 306
>PF15011 CK2S: Casein Kinase 2 substrate
Probab=20.12 E-value=3e+02 Score=24.03 Aligned_cols=47 Identities=17% Similarity=0.162 Sum_probs=34.2
Q ss_pred hhhhccccccccccccccCCchHHHHhhhccccccc----HHHHHHHHHHHHHH
Q 022656 136 AQEKKMALCEICGSFLVANDAAERTQSHISGKQHIG----YGMVRDFITEYKEA 185 (294)
Q Consensus 136 ~~~qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlG----y~kIRe~l~eL~~~ 185 (294)
.+.+-++-+..||+.|...+ =|.+.+..||-.+ +++|++++++|.+.
T Consensus 36 eqL~al~~~~~~~~pL~~fp---dl~~rL~~Kq~~ale~vl~~L~e~l~~l~~v 86 (168)
T PF15011_consen 36 EQLQALQNVKNYGTPLRSFP---DLQERLRRKQLEALETVLAKLRETLEELQKV 86 (168)
T ss_pred HHHHHHHhccccCCcccccc---cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35566777888998766553 2566677777766 68899999998875
Done!