Query 001506
Match_columns 1065
No_of_seqs 409 out of 584
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 02:32:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001506.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001506hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1999 RNA polymerase II tran 100.0 7E-216 2E-220 1883.3 75.3 943 77-1065 54-1024(1024)
2 COG5164 SPT5 Transcription elo 100.0 8E-78 1.7E-82 663.7 36.6 398 331-758 4-404 (607)
3 KOG1999 RNA polymerase II tran 100.0 3.1E-37 6.7E-42 367.3 41.9 301 327-637 316-723 (1024)
4 PRK08559 nusG transcription an 99.9 7.3E-22 1.6E-26 200.6 15.2 130 180-311 4-133 (153)
5 PF03439 Spt5-NGN: Early trans 99.9 3.3E-22 7.1E-27 183.6 9.0 82 183-264 1-84 (84)
6 COG5164 SPT5 Transcription elo 99.8 1.5E-19 3.3E-24 202.2 15.2 351 171-636 29-389 (607)
7 TIGR00405 L26e_arch ribosomal 99.7 1.8E-17 4E-22 166.8 14.2 125 185-311 1-125 (145)
8 COG0250 NusG Transcription ant 99.6 4.8E-15 1E-19 154.0 10.8 127 181-307 2-158 (178)
9 KOG0260 RNA polymerase II, lar 99.3 2.1E-11 4.5E-16 148.8 18.3 36 903-938 1556-1594(1605)
10 PF11942 Spt5_N: Spt5 transcri 99.3 5E-13 1.1E-17 126.3 2.9 88 90-177 1-97 (97)
11 PRK05609 nusG transcription an 99.3 1.8E-11 3.9E-16 127.5 13.7 128 180-307 4-161 (181)
12 TIGR00922 nusG transcription t 99.2 9.7E-11 2.1E-15 121.2 13.3 124 184-307 1-154 (172)
13 TIGR01956 NusG_myco NusG famil 99.2 6.9E-11 1.5E-15 128.1 12.5 125 183-307 1-240 (258)
14 KOG0260 RNA polymerase II, lar 99.2 1.9E-10 4.2E-15 140.6 17.0 8 580-587 1196-1203(1605)
15 PF12815 CTD: Spt5 C-terminal 99.0 3.7E-11 8.1E-16 117.8 0.0 37 797-833 12-56 (123)
16 PF12815 CTD: Spt5 C-terminal 98.9 4.5E-10 9.7E-15 110.3 0.0 52 781-832 1-67 (123)
17 smart00738 NGN In Spt5p, this 98.8 5.1E-09 1.1E-13 99.4 7.0 83 183-265 1-105 (106)
18 PRK09014 rfaH transcriptional 98.8 7.2E-09 1.6E-13 106.4 8.0 123 183-306 3-142 (162)
19 TIGR01955 RfaH transcriptional 98.8 1.6E-08 3.5E-13 103.3 7.8 122 184-306 1-141 (159)
20 KOG1832 HIV-1 Vpr-binding prot 97.9 3.9E-06 8.4E-11 101.6 2.1 26 2-27 1398-1423(1516)
21 KOG2837 Protein containing a U 97.8 7.6E-07 1.6E-11 96.1 -6.3 55 969-1031 254-309 (309)
22 PF00467 KOW: KOW motif; Inte 97.4 0.00022 4.8E-09 54.3 4.2 32 275-306 1-32 (32)
23 PF04931 DNA_pol_phi: DNA poly 97.1 0.00016 3.6E-09 91.6 1.2 12 145-156 739-750 (784)
24 PF10446 DUF2457: Protein of u 96.8 0.00062 1.4E-08 78.9 2.5 11 194-204 207-217 (458)
25 PF00467 KOW: KOW motif; Inte 96.8 0.0013 2.8E-08 50.1 3.1 31 708-738 1-31 (32)
26 KOG4315 G-patch nucleic acid b 96.7 0.0006 1.3E-08 78.2 1.1 103 959-1062 332-445 (455)
27 PF02357 NusG: Transcription t 96.7 0.0057 1.2E-07 56.9 7.4 65 183-249 2-78 (92)
28 PRK12281 rplX 50S ribosomal pr 96.0 0.009 2E-07 54.6 4.5 33 600-632 6-40 (76)
29 smart00739 KOW KOW (Kyprides, 95.7 0.016 3.5E-07 42.0 3.9 28 424-451 1-28 (28)
30 smart00739 KOW KOW (Kyprides, 95.6 0.014 3.1E-07 42.3 3.4 27 476-502 1-27 (28)
31 TIGR00405 L26e_arch ribosomal 94.8 0.042 9.2E-07 55.7 5.3 58 424-481 86-145 (145)
32 CHL00141 rpl24 ribosomal prote 94.8 0.038 8.3E-07 51.4 4.5 32 600-631 8-41 (83)
33 PRK00004 rplX 50S ribosomal pr 94.5 0.054 1.2E-06 52.5 5.0 33 600-632 4-38 (105)
34 KOG0262 RNA polymerase I, larg 93.9 0.097 2.1E-06 67.1 6.5 85 182-266 1440-1548(1640)
35 KOG1708 Mitochondrial/chloropl 93.6 0.12 2.7E-06 54.7 5.7 81 422-526 70-150 (236)
36 TIGR01079 rplX_bact ribosomal 93.4 0.12 2.5E-06 50.2 4.9 32 600-631 3-36 (104)
37 PF04147 Nop14: Nop14-like fam 93.4 0.053 1.2E-06 69.6 3.3 7 145-151 429-435 (840)
38 CHL00141 rpl24 ribosomal prote 93.3 0.15 3.3E-06 47.5 5.2 37 270-306 6-42 (83)
39 PRK08559 nusG transcription an 93.2 0.16 3.5E-06 52.3 5.9 50 706-755 95-148 (153)
40 PF04147 Nop14: Nop14-like fam 93.2 0.07 1.5E-06 68.6 3.9 12 145-156 444-455 (840)
41 PRK01191 rpl24p 50S ribosomal 93.1 0.18 3.9E-06 49.9 5.7 39 270-308 43-81 (120)
42 TIGR00922 nusG transcription t 92.8 0.17 3.6E-06 52.7 5.5 53 423-475 118-172 (172)
43 PRK01191 rpl24p 50S ribosomal 92.7 0.17 3.7E-06 50.1 5.0 33 600-632 45-79 (120)
44 COG0250 NusG Transcription ant 92.7 0.2 4.4E-06 52.9 5.9 56 421-476 120-177 (178)
45 PRK09014 rfaH transcriptional 92.6 0.18 3.8E-06 52.1 5.2 52 424-475 109-161 (162)
46 PRK12281 rplX 50S ribosomal pr 92.2 0.24 5.2E-06 45.4 4.9 36 271-306 5-40 (76)
47 PF02724 CDC45: CDC45-like pro 91.9 0.054 1.2E-06 67.4 0.5 18 225-242 356-373 (622)
48 PRK05609 nusG transcription an 91.8 0.28 6.1E-06 51.3 5.6 53 423-475 125-179 (181)
49 PF02724 CDC45: CDC45-like pro 91.1 0.083 1.8E-06 65.8 1.0 6 396-401 511-516 (622)
50 COG0198 RplX Ribosomal protein 91.0 0.47 1E-05 46.0 5.7 33 599-631 3-35 (104)
51 TIGR01080 rplX_A_E ribosomal p 90.9 0.35 7.5E-06 47.7 4.9 34 1014-1047 43-76 (114)
52 PTZ00194 60S ribosomal protein 90.7 0.32 7E-06 49.5 4.5 33 600-632 46-80 (143)
53 KOG2038 CAATT-binding transcri 90.4 0.17 3.7E-06 62.5 2.7 12 143-154 968-979 (988)
54 KOG0943 Predicted ubiquitin-pr 90.4 0.17 3.7E-06 64.3 2.7 14 182-195 1880-1893(3015)
55 TIGR01955 RfaH transcriptional 90.3 0.44 9.6E-06 48.8 5.4 51 423-473 107-158 (159)
56 PRK06763 F0F1 ATP synthase sub 90.2 2 4.3E-05 46.0 9.9 99 439-551 40-177 (213)
57 PRK00004 rplX 50S ribosomal pr 90.1 0.47 1E-05 46.1 5.0 35 272-306 4-38 (105)
58 TIGR01080 rplX_A_E ribosomal p 90.0 0.59 1.3E-05 46.1 5.6 48 258-307 29-76 (114)
59 KOG0943 Predicted ubiquitin-pr 89.8 0.15 3.2E-06 64.8 1.6 11 496-506 2286-2296(3015)
60 PTZ00194 60S ribosomal protein 89.7 0.62 1.3E-05 47.5 5.6 51 259-311 35-85 (143)
61 TIGR01956 NusG_myco NusG famil 89.5 0.54 1.2E-05 52.3 5.5 52 423-474 204-257 (258)
62 KOG0307 Vesicle coat complex C 89.0 10 0.00022 49.4 16.7 20 636-655 596-615 (1049)
63 PTZ00415 transmission-blocking 88.8 0.18 3.8E-06 66.4 1.3 14 89-102 208-221 (2849)
64 KOG4156 Claspin, protein media 88.3 0.048 1E-06 65.3 -3.9 14 88-101 1051-1064(1329)
65 COG0198 RplX Ribosomal protein 87.4 0.8 1.7E-05 44.4 4.4 33 423-455 3-35 (104)
66 TIGR01079 rplX_bact ribosomal 87.0 0.98 2.1E-05 43.9 4.8 35 272-306 3-37 (104)
67 KOG1991 Nuclear transport rece 86.0 0.39 8.4E-06 61.1 1.9 24 10-33 891-914 (1010)
68 PHA03378 EBNA-3B; Provisional 85.0 15 0.00033 45.6 14.2 10 719-728 542-551 (991)
69 PF04006 Mpp10: Mpp10 protein; 83.7 0.93 2E-05 56.5 3.8 17 78-94 175-192 (600)
70 PF00524 PPV_E1_N: E1 Protein, 82.3 0.56 1.2E-05 47.3 0.9 64 88-159 15-86 (130)
71 PF14632 SPT6_acidic: Acidic N 81.8 0.42 9.2E-06 45.4 -0.1 8 45-52 20-27 (92)
72 PTZ00415 transmission-blocking 81.5 0.6 1.3E-05 61.9 1.0 18 176-193 367-384 (2849)
73 KOG2141 Protein involved in hi 79.7 0.93 2E-05 56.1 1.7 15 143-157 334-348 (822)
74 cd04467 S1_aIF5A S1_aIF5A: Arc 78.9 4.1 9E-05 35.5 4.9 45 441-487 4-49 (57)
75 KOG1856 Transcription elongati 77.0 1.4 3E-05 57.1 2.2 34 422-455 586-632 (1299)
76 PRK12269 bifunctional cytidyla 76.3 65 0.0014 42.3 16.7 45 423-483 709-756 (863)
77 PTZ00223 40S ribosomal protein 74.5 6.8 0.00015 44.2 6.4 26 477-502 172-197 (273)
78 KOG0127 Nucleolar protein fibr 74.1 1.6 3.5E-05 52.5 1.6 23 222-244 332-354 (678)
79 KOG3118 Disrupter of silencing 73.0 1.5 3.2E-05 52.2 1.0 13 89-101 128-140 (517)
80 PF11623 DUF3252: Protein of u 72.8 7.3 0.00016 33.2 4.6 50 425-474 2-53 (53)
81 PRK04313 30S ribosomal protein 72.2 8.4 0.00018 42.7 6.4 42 477-518 172-218 (237)
82 COG2933 Predicted SAM-dependen 71.7 5.6 0.00012 44.6 4.9 58 186-247 5-62 (358)
83 KOG1708 Mitochondrial/chloropl 71.7 4 8.6E-05 43.8 3.6 30 475-504 71-100 (236)
84 PF11623 DUF3252: Protein of u 71.4 12 0.00027 31.9 5.6 44 709-752 5-52 (53)
85 COG1471 RPS4A Ribosomal protei 71.3 9 0.0002 42.1 6.2 34 468-501 163-198 (241)
86 PLN00036 40S ribosomal protein 71.1 9.7 0.00021 42.7 6.6 25 477-501 175-199 (261)
87 KOG2773 Apoptosis antagonizing 70.1 2.1 4.6E-05 50.7 1.3 15 176-193 214-228 (483)
88 PTZ00118 40S ribosomal protein 69.8 11 0.00024 42.3 6.7 25 477-501 175-199 (262)
89 TIGR00739 yajC preprotein tran 68.4 8.3 0.00018 36.1 4.6 42 708-754 40-81 (84)
90 smart00743 Agenet Tudor-like d 67.2 14 0.0003 31.8 5.5 54 424-477 2-57 (61)
91 CHL00010 infA translation init 67.1 34 0.00073 31.6 8.3 63 552-627 10-73 (78)
92 KOG2773 Apoptosis antagonizing 66.6 2.8 6E-05 49.8 1.3 12 88-99 126-137 (483)
93 PRK05886 yajC preprotein trans 66.2 9.9 0.00021 37.4 4.8 42 708-754 41-82 (109)
94 KOG0127 Nucleolar protein fibr 64.4 2.9 6.3E-05 50.5 1.0 21 224-244 496-516 (678)
95 PRK05886 yajC preprotein trans 64.3 16 0.00035 35.9 5.9 52 423-481 37-88 (109)
96 KOG2600 U3 small nucleolar rib 64.2 2.6 5.5E-05 50.9 0.5 14 78-91 170-184 (596)
97 PRK14635 hypothetical protein; 64.0 9 0.00019 40.1 4.4 50 705-754 95-155 (162)
98 PF11746 DUF3303: Protein of u 63.8 37 0.0008 32.2 8.1 75 185-259 2-85 (91)
99 smart00652 eIF1a eukaryotic tr 63.8 42 0.00091 31.4 8.3 65 549-627 5-70 (83)
100 PRK03879 ribonuclease P protei 62.6 18 0.00038 34.9 5.7 49 704-754 10-61 (96)
101 PRK05585 yajC preprotein trans 62.5 11 0.00025 36.8 4.5 43 708-755 55-97 (106)
102 KOG2076 RNA polymerase III tra 62.1 4.5 9.8E-05 51.5 2.1 10 174-185 201-210 (895)
103 KOG1984 Vesicle coat complex C 61.6 1E+02 0.0022 40.0 13.2 8 875-882 198-205 (1007)
104 KOG1991 Nuclear transport rece 61.3 2.7 6E-05 53.9 0.1 10 94-103 932-941 (1010)
105 KOG0699 Serine/threonine prote 61.0 3.7 8.1E-05 47.4 1.0 9 142-150 372-380 (542)
106 PRK14639 hypothetical protein; 60.9 15 0.00033 37.5 5.3 50 705-754 84-133 (140)
107 PRK04333 50S ribosomal protein 60.6 12 0.00027 35.1 4.2 29 708-736 6-35 (84)
108 PF05793 TFIIF_alpha: Transcri 60.6 2.8 6.1E-05 51.5 0.0 9 90-98 284-292 (527)
109 PHA03378 EBNA-3B; Provisional 60.0 88 0.0019 39.4 12.1 16 1003-1018 911-926 (991)
110 PRK05585 yajC preprotein trans 59.9 17 0.00037 35.6 5.2 49 422-477 50-98 (106)
111 KOG0262 RNA polymerase I, larg 59.1 7.7 0.00017 51.0 3.3 7 259-265 1560-1566(1640)
112 COG1588 POP4 RNase P/RNase MRP 59.0 18 0.0004 34.6 5.0 50 703-754 11-63 (95)
113 COG1862 YajC Preprotein transl 58.7 12 0.00025 36.2 3.8 41 709-754 47-87 (97)
114 KOG2418 Microtubule-associated 58.6 37 0.0008 39.6 8.2 12 1051-1062 424-435 (448)
115 PRK00276 infA translation init 58.6 56 0.0012 29.6 8.0 62 552-626 10-72 (72)
116 COG1862 YajC Preprotein transl 58.4 14 0.00031 35.6 4.3 53 423-482 42-94 (97)
117 PRK04333 50S ribosomal protein 58.3 17 0.00037 34.1 4.7 33 272-305 3-35 (84)
118 KOG0526 Nucleosome-binding fac 57.9 7.7 0.00017 47.0 2.9 13 144-156 581-593 (615)
119 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 57.7 44 0.00095 30.5 7.4 49 424-485 3-63 (86)
120 cd05793 S1_IF1A S1_IF1A: Trans 57.6 58 0.0013 30.1 8.0 63 551-627 2-65 (77)
121 KOG2393 Transcription initiati 56.8 8.6 0.00019 46.7 3.1 26 91-116 279-307 (555)
122 PRK04313 30S ribosomal protein 55.7 63 0.0014 36.1 9.2 73 975-1047 129-210 (237)
123 KOG2023 Nuclear transport rece 54.3 6.6 0.00014 48.8 1.6 10 89-98 377-386 (885)
124 PRK04012 translation initiatio 54.1 73 0.0016 31.0 8.3 74 540-627 11-86 (100)
125 PF02736 Myosin_N: Myosin N-te 53.4 25 0.00055 28.5 4.4 28 723-751 15-42 (42)
126 TIGR02760 TraI_TIGR conjugativ 52.8 52 0.0011 46.9 10.0 94 422-523 1327-1439(1960)
127 PRK11760 putative 23S rRNA C24 52.4 24 0.00052 41.4 5.6 58 185-246 4-61 (357)
128 smart00743 Agenet Tudor-like d 52.0 38 0.00083 29.1 5.6 50 476-527 2-57 (61)
129 COG2139 RPL21A Ribosomal prote 51.7 26 0.00056 33.7 4.7 53 423-475 31-93 (98)
130 PRK13709 conjugal transfer nic 51.6 67 0.0015 45.2 10.5 98 422-522 646-761 (1747)
131 COG2139 RPL21A Ribosomal prote 51.4 21 0.00044 34.4 4.0 56 470-525 26-93 (98)
132 cd04455 S1_NusA S1_NusA: N-uti 51.3 50 0.0011 29.0 6.3 42 441-486 7-50 (67)
133 PF04050 Upf2: Up-frameshift s 50.9 5.1 0.00011 42.1 0.0 11 146-156 68-78 (170)
134 PRK07594 type III secretion sy 50.8 2.4E+02 0.0052 34.3 13.8 62 420-509 8-69 (433)
135 PLN00208 translation initiatio 49.7 80 0.0017 32.7 8.2 76 538-627 20-97 (145)
136 smart00361 RRM_1 RNA recogniti 49.6 48 0.001 29.2 6.0 28 221-248 34-61 (70)
137 cd01734 YlxS_C YxlS is a Bacil 49.2 36 0.00079 31.5 5.3 51 426-476 23-77 (83)
138 cd04456 S1_IF1A_like S1_IF1A_l 49.1 1E+02 0.0023 28.5 8.2 64 550-627 1-66 (78)
139 cd05687 S1_RPS1_repeat_ec1_hs1 48.9 65 0.0014 28.1 6.7 43 441-486 4-54 (70)
140 PRK14638 hypothetical protein; 48.8 28 0.00061 36.0 5.0 48 705-754 96-143 (150)
141 KOG2023 Nuclear transport rece 48.3 8.3 0.00018 47.9 1.2 31 213-244 449-481 (885)
142 TIGR00739 yajC preprotein tran 48.3 28 0.00062 32.6 4.5 43 471-518 32-74 (84)
143 cd04454 S1_Rrp4_like S1_Rrp4_l 48.3 58 0.0013 29.5 6.5 47 426-485 5-59 (82)
144 KOG1980 Uncharacterized conser 48.3 4.7 0.0001 49.7 -0.9 8 235-242 536-543 (754)
145 KOG0526 Nucleosome-binding fac 47.8 9.9 0.00022 46.1 1.7 16 143-158 560-575 (615)
146 PRK00092 ribosome maturation p 47.5 30 0.00065 35.8 5.0 50 705-754 94-147 (154)
147 PF01868 UPF0086: Domain of un 47.4 51 0.0011 31.2 6.1 50 704-754 9-61 (89)
148 PF02576 DUF150: Uncharacteris 47.2 32 0.00068 35.0 5.0 50 705-754 83-138 (141)
149 TIGR00523 eIF-1A eukaryotic/ar 46.9 72 0.0016 31.0 7.1 64 548-627 18-85 (99)
150 PRK06531 yajC preprotein trans 46.6 23 0.00049 35.2 3.7 40 713-755 43-82 (113)
151 PRK14637 hypothetical protein; 46.6 37 0.00081 35.2 5.5 49 704-754 93-142 (151)
152 PRK14643 hypothetical protein; 46.5 30 0.00065 36.4 4.8 51 705-755 100-158 (164)
153 KOG0338 ATP-dependent RNA heli 46.5 6.7 0.00015 47.5 0.1 81 191-276 229-311 (691)
154 cd01734 YlxS_C YxlS is a Bacil 46.5 38 0.00083 31.3 5.1 50 705-754 21-76 (83)
155 PRK07400 30S ribosomal protein 46.1 1.8E+02 0.0038 33.8 11.4 51 423-486 27-85 (318)
156 PTZ00329 eukaryotic translatio 45.9 92 0.002 32.6 8.1 75 539-627 21-97 (155)
157 PRK04914 ATP-dependent helicas 45.9 59 0.0013 43.1 8.3 65 976-1045 18-82 (956)
158 KOG0699 Serine/threonine prote 45.6 13 0.00028 43.2 2.1 12 79-90 241-252 (542)
159 COG4547 CobT Cobalamin biosynt 45.6 16 0.00034 43.7 2.9 12 197-208 360-371 (620)
160 PF09953 DUF2187: Uncharacteri 45.3 45 0.00098 29.3 4.8 29 426-458 5-33 (57)
161 KOG2422 Uncharacterized conser 45.2 11 0.00025 46.2 1.7 52 214-267 242-297 (665)
162 PRK14644 hypothetical protein; 45.2 27 0.0006 35.6 4.2 49 705-753 81-135 (136)
163 PF11213 DUF3006: Protein of u 44.5 31 0.00068 31.1 4.0 42 442-485 1-42 (71)
164 cd05705 S1_Rrp5_repeat_hs14 S1 44.3 30 0.00064 31.3 3.9 22 471-502 45-66 (74)
165 PF11515 Cul7: Mouse developme 43.9 23 0.0005 32.8 3.0 31 271-301 16-49 (78)
166 PF01287 eIF-5a: Eukaryotic el 43.7 18 0.00039 32.7 2.3 43 441-483 5-52 (69)
167 PRK07400 30S ribosomal protein 43.3 2.2E+02 0.0048 33.0 11.7 64 423-502 74-140 (318)
168 COG4873 Uncharacterized protei 43.0 34 0.00074 30.7 3.8 32 423-458 22-53 (81)
169 KOG0299 U3 snoRNP-associated p 42.4 5 0.00011 47.6 -1.7 23 210-233 141-163 (479)
170 PRK14634 hypothetical protein; 42.1 38 0.00081 35.3 4.7 49 704-754 95-147 (155)
171 PRK12269 bifunctional cytidyla 42.1 67 0.0015 42.1 8.0 52 422-486 316-367 (863)
172 TIGR02760 TraI_TIGR conjugativ 42.0 1.2E+02 0.0026 43.5 10.9 93 422-518 679-792 (1960)
173 PTZ00223 40S ribosomal protein 41.9 85 0.0018 35.7 7.7 72 975-1047 130-209 (273)
174 KOG0772 Uncharacterized conser 41.7 13 0.00028 45.0 1.4 10 705-714 508-517 (641)
175 cd05790 S1_Rrp40 S1_Rrp40: Rrp 41.1 33 0.00072 32.4 3.7 49 426-484 5-57 (86)
176 COG5129 MAK16 Nuclear protein 41.0 12 0.00026 40.7 1.0 9 66-74 258-266 (303)
177 KOG2897 DNA-binding protein YL 40.4 11 0.00024 43.9 0.6 7 334-340 302-308 (390)
178 PF13051 DUF3912: Protein of u 40.2 44 0.00096 29.2 3.9 49 706-756 3-54 (68)
179 PF05641 Agenet: Agenet domain 39.7 78 0.0017 28.2 5.8 34 425-458 1-39 (68)
180 PHA02774 E1; Provisional 39.7 9.9 0.00021 47.2 0.1 20 140-159 65-84 (613)
181 PRK14645 hypothetical protein; 39.7 41 0.00089 35.0 4.6 46 705-753 98-143 (154)
182 PF01176 eIF-1a: Translation i 39.5 1.5E+02 0.0032 26.3 7.5 61 550-624 4-65 (65)
183 cd05791 S1_CSL4 S1_CSL4: CSL4, 39.5 52 0.0011 31.2 4.8 14 472-485 56-69 (92)
184 CHL00084 rpl19 ribosomal prote 39.4 1E+02 0.0022 30.9 6.9 38 421-458 19-67 (117)
185 smart00538 POP4 A domain found 39.1 77 0.0017 30.3 5.9 50 704-754 8-60 (92)
186 COG4547 CobT Cobalamin biosynt 39.1 24 0.00051 42.4 2.9 9 332-340 478-486 (620)
187 PRK04950 ProP expression regul 39.0 49 0.0011 36.3 5.1 45 707-753 168-212 (213)
188 PTZ00065 60S ribosomal protein 38.7 43 0.00093 34.0 4.3 34 272-306 7-40 (130)
189 PRK07899 rpsA 30S ribosomal pr 38.1 6.8E+02 0.015 30.9 15.2 45 252-307 60-104 (486)
190 PF09870 DUF2097: Uncharacteri 38.0 47 0.001 31.5 4.2 51 423-474 17-67 (86)
191 PRK14640 hypothetical protein; 37.8 57 0.0012 33.8 5.2 48 705-754 93-144 (152)
192 PF10842 DUF2642: Protein of u 37.7 79 0.0017 28.6 5.4 45 705-752 17-61 (66)
193 TIGR00717 rpsA ribosomal prote 37.6 3.5E+02 0.0076 33.1 12.9 46 252-308 211-256 (516)
194 CHL00125 psaE photosystem I su 37.4 53 0.0012 29.2 4.1 29 273-301 2-32 (64)
195 PRK14630 hypothetical protein; 37.4 66 0.0014 33.1 5.6 47 705-754 93-139 (143)
196 PTZ00065 60S ribosomal protein 37.2 30 0.00066 35.1 3.0 33 708-741 10-42 (130)
197 cd04451 S1_IF1 S1_IF1: Transla 37.1 1.7E+02 0.0036 25.6 7.4 58 553-623 5-63 (64)
198 COG5271 MDN1 AAA ATPase contai 37.0 25 0.00054 48.5 2.9 12 226-237 4204-4215(4600)
199 TIGR01651 CobT cobaltochelatas 37.0 23 0.0005 44.0 2.6 10 146-155 338-347 (600)
200 PRK14712 conjugal transfer nic 36.9 1.3E+02 0.0028 42.1 9.6 85 423-510 515-617 (1623)
201 PRK06763 F0F1 ATP synthase sub 36.8 2.9E+02 0.0063 30.2 10.2 26 494-519 43-68 (213)
202 PF14851 FAM176: FAM176 family 36.6 74 0.0016 33.3 5.8 11 145-155 119-129 (153)
203 PRK06531 yajC preprotein trans 35.9 53 0.0011 32.6 4.4 46 423-476 35-82 (113)
204 PRK00087 4-hydroxy-3-methylbut 35.6 3E+02 0.0065 35.1 12.1 156 424-641 474-639 (647)
205 COG1471 RPS4A Ribosomal protei 35.6 95 0.0021 34.5 6.6 71 976-1047 133-212 (241)
206 PF02427 PSI_PsaE: Photosystem 35.5 77 0.0017 28.1 4.7 29 273-301 1-31 (61)
207 PF03831 PhnA: PhnA protein; 35.2 20 0.00044 31.2 1.2 20 592-611 1-20 (56)
208 PRK09838 periplasmic copper-bi 34.3 81 0.0018 31.4 5.4 59 440-501 44-112 (115)
209 PRK02749 photosystem I reactio 34.2 52 0.0011 29.8 3.6 38 273-312 3-42 (71)
210 cd01854 YjeQ_engC YjeQ/EngC. 33.7 2.5E+02 0.0053 31.9 10.0 86 553-655 1-87 (287)
211 PLN00045 photosystem I reactio 33.0 42 0.00091 32.1 3.0 39 1008-1046 35-80 (101)
212 PF09507 CDC27: DNA polymerase 32.9 14 0.00031 43.5 0.0 6 89-94 366-371 (430)
213 PF03896 TRAP_alpha: Transloco 32.7 17 0.00038 41.4 0.6 13 303-315 251-263 (285)
214 PRK07899 rpsA 30S ribosomal pr 32.6 1.2E+02 0.0025 37.4 7.6 51 423-486 31-89 (486)
215 PF14001 YdfZ: YdfZ protein 32.4 48 0.001 29.6 3.1 31 593-626 2-32 (64)
216 TIGR01024 rplS_bact ribosomal 32.2 1.4E+02 0.003 29.8 6.6 38 421-458 15-63 (113)
217 PF09444 MRC1: MRC1-like domai 32.2 9.6 0.00021 39.3 -1.4 17 85-101 4-20 (145)
218 COG0779 Uncharacterized protei 32.1 94 0.002 32.5 5.7 48 705-754 95-146 (153)
219 PRK12366 replication factor A; 31.8 1.2E+03 0.026 29.8 18.0 16 424-439 344-359 (637)
220 PRK12288 GTPase RsgA; Reviewed 31.5 2.6E+02 0.0057 32.8 10.0 87 551-655 40-129 (347)
221 KOG0132 RNA polymerase II C-te 31.4 1.7E+02 0.0038 37.5 8.6 27 704-730 479-505 (894)
222 PF14563 DUF4444: Domain of un 31.2 91 0.002 25.8 4.2 33 1026-1059 7-39 (42)
223 PLN00036 40S ribosomal protein 31.2 69 0.0015 36.2 4.9 54 600-655 174-230 (261)
224 PF11604 CusF_Ec: Copper bindi 31.1 1.1E+02 0.0025 27.5 5.4 44 443-486 1-52 (70)
225 PF02699 YajC: Preprotein tran 31.0 16 0.00035 33.9 0.0 42 708-754 39-80 (82)
226 KOG4553 Uncharacterized conser 31.0 25 0.00054 45.9 1.6 9 91-99 1370-1378(1398)
227 TIGR00037 eIF_5A translation i 31.0 63 0.0014 32.7 4.2 63 421-487 56-119 (130)
228 COG0335 RplS Ribosomal protein 30.8 1.5E+02 0.0033 29.6 6.5 30 422-451 18-54 (115)
229 PF02699 YajC: Preprotein tran 30.8 17 0.00036 33.9 0.0 36 471-510 31-66 (82)
230 KOG1248 Uncharacterized conser 30.6 44 0.00096 44.3 3.7 70 31-100 970-1041(1176)
231 COG5593 Nucleic-acid-binding p 30.2 13 0.00027 45.2 -1.1 9 90-98 766-774 (821)
232 COG0779 Uncharacterized protei 30.1 76 0.0016 33.2 4.6 48 425-476 96-147 (153)
233 PRK05338 rplS 50S ribosomal pr 30.1 1.9E+02 0.004 29.0 7.1 37 422-458 16-63 (116)
234 PLN00045 photosystem I reactio 30.0 88 0.0019 30.0 4.6 32 268-299 35-68 (101)
235 PF04050 Upf2: Up-frameshift s 30.0 17 0.00037 38.2 0.0 8 146-153 64-71 (170)
236 smart00333 TUDOR Tudor domain. 29.8 1.3E+02 0.0027 25.2 5.2 51 424-476 2-53 (57)
237 PF07076 DUF1344: Protein of u 29.8 1.3E+02 0.0028 26.9 5.2 44 440-486 4-47 (61)
238 PRK14633 hypothetical protein; 29.7 87 0.0019 32.5 5.0 49 705-754 90-142 (150)
239 KOG0970 DNA polymerase alpha, 29.5 31 0.00066 45.5 2.0 12 300-311 373-384 (1429)
240 PF04889 Cwf_Cwc_15: Cwf15/Cwc 29.4 26 0.00057 39.1 1.3 7 149-155 236-242 (244)
241 TIGR01622 SF-CC1 splicing fact 29.4 1.9E+02 0.004 34.6 8.5 67 195-264 383-454 (457)
242 PRK14632 hypothetical protein; 29.1 92 0.002 33.0 5.2 51 705-755 94-157 (172)
243 PF11942 Spt5_N: Spt5 transcri 29.0 22 0.00049 34.0 0.6 12 48-59 1-12 (97)
244 PTZ00118 40S ribosomal protein 28.7 83 0.0018 35.6 4.9 54 600-655 174-230 (262)
245 COG2163 RPL14A Ribosomal prote 28.5 73 0.0016 32.2 4.1 37 474-510 2-38 (125)
246 KOG0066 eIF2-interacting prote 28.5 49 0.0011 39.9 3.2 7 988-994 769-775 (807)
247 KOG3241 Uncharacterized conser 28.4 47 0.001 35.2 2.8 8 92-99 209-216 (227)
248 cd00164 S1_like S1_like: Ribos 28.3 92 0.002 25.6 4.2 42 442-486 2-51 (65)
249 PRK14636 hypothetical protein; 28.0 90 0.002 33.3 4.9 49 705-754 94-146 (176)
250 PF00924 MS_channel: Mechanose 27.8 66 0.0014 34.0 3.9 46 422-475 58-103 (206)
251 PRK06299 rpsA 30S ribosomal pr 27.6 6.3E+02 0.014 31.4 13.0 46 252-308 225-270 (565)
252 PRK05807 hypothetical protein; 27.6 2.3E+02 0.0051 28.8 7.6 15 472-486 44-58 (136)
253 PRK02001 hypothetical protein; 27.4 1.2E+02 0.0025 31.7 5.5 50 704-753 85-146 (152)
254 PRK00098 GTPase RsgA; Reviewed 27.1 3.8E+02 0.0083 30.6 10.1 87 553-655 3-89 (298)
255 KOG1856 Transcription elongati 27.1 33 0.00071 45.3 1.7 9 393-401 517-525 (1299)
256 KOG3130 Uncharacterized conser 26.8 31 0.00067 40.7 1.3 8 176-183 358-365 (514)
257 PRK06676 rpsA 30S ribosomal pr 26.7 6.3E+02 0.014 29.8 12.2 45 253-308 44-88 (390)
258 PF05470 eIF-3c_N: Eukaryotic 26.6 36 0.00077 42.8 1.8 7 306-312 335-341 (595)
259 PHA03247 large tegument protei 26.3 1.5E+03 0.032 34.1 16.3 31 507-537 2322-2359(3151)
260 PRK14638 hypothetical protein; 26.2 1.1E+02 0.0025 31.6 5.2 47 426-476 98-144 (150)
261 smart00316 S1 Ribosomal protei 26.2 2.5E+02 0.0055 23.4 6.6 42 442-486 7-56 (72)
262 TIGR03318 YdfZ_fam putative se 26.0 53 0.0011 29.3 2.2 31 593-626 3-33 (65)
263 cd04469 S1_Hex1 S1_Hex1: Hex1, 26.0 58 0.0013 30.1 2.6 38 444-481 6-48 (75)
264 COG3343 RpoE DNA-directed RNA 25.6 28 0.0006 36.8 0.6 9 96-104 158-166 (175)
265 PRK14646 hypothetical protein; 25.2 1.1E+02 0.0024 31.9 4.8 48 705-754 96-147 (155)
266 PRK12442 translation initiatio 25.2 3.4E+02 0.0074 25.9 7.5 61 553-626 11-72 (87)
267 KOG4264 Nucleo-cytoplasmic pro 25.1 49 0.0011 40.3 2.5 90 3-105 60-172 (694)
268 PF02576 DUF150: Uncharacteris 25.0 86 0.0019 31.8 4.0 51 426-476 85-139 (141)
269 COG3109 ProQ Activator of osmo 25.0 99 0.0021 32.9 4.4 44 708-753 164-207 (208)
270 PRK13709 conjugal transfer nic 24.7 3E+02 0.0066 39.1 10.1 89 423-521 1274-1382(1747)
271 PRK00409 recombination and DNA 24.5 95 0.0021 40.4 5.2 47 423-476 635-682 (782)
272 COG0361 InfA Translation initi 24.4 3.4E+02 0.0074 25.2 7.2 63 552-627 10-73 (75)
273 PRK08582 hypothetical protein; 24.4 2.3E+02 0.0049 29.0 6.9 15 472-486 45-59 (139)
274 PRK14647 hypothetical protein; 24.2 1.3E+02 0.0027 31.6 5.1 49 705-754 95-152 (159)
275 cd05703 S1_Rrp5_repeat_hs12_sc 24.1 46 0.001 29.9 1.6 46 441-486 4-56 (73)
276 KOG1824 TATA-binding protein-i 24.0 28 0.00061 45.1 0.3 24 222-245 477-500 (1233)
277 KOG0119 Splicing factor 1/bran 23.9 1E+03 0.023 29.4 12.9 14 389-402 57-70 (554)
278 PF01157 Ribosomal_L21e: Ribos 23.7 97 0.0021 30.2 3.8 58 469-526 25-98 (99)
279 COG5163 NOP7 Protein required 23.5 29 0.00062 40.9 0.2 12 145-156 568-579 (591)
280 COG0056 AtpA F0F1-type ATP syn 23.4 2E+02 0.0043 35.1 7.0 49 492-566 26-74 (504)
281 CHL00010 infA translation init 23.4 3E+02 0.0065 25.4 6.8 56 441-499 9-69 (78)
282 KOG0608 Warts/lats-like serine 23.2 9.4E+02 0.02 31.1 12.6 8 902-909 273-280 (1034)
283 PF14944 TCRP1: Tongue Cancer 23.2 2.5E+02 0.0054 29.4 6.7 9 903-911 72-80 (195)
284 PRK09521 exosome complex RNA-b 23.1 1.4E+02 0.003 31.8 5.3 53 423-485 60-127 (189)
285 PRK00092 ribosome maturation p 23.0 1.3E+02 0.0028 31.1 4.9 49 426-476 96-148 (154)
286 COG5129 MAK16 Nuclear protein 23.0 34 0.00073 37.4 0.6 13 71-83 260-272 (303)
287 PF08553 VID27: VID27 cytoplas 22.9 41 0.00088 43.5 1.4 15 486-500 649-663 (794)
288 smart00333 TUDOR Tudor domain. 22.7 1.2E+02 0.0026 25.4 3.8 39 974-1014 18-56 (57)
289 KOG2932 E3 ubiquitin ligase in 22.6 5.1E+02 0.011 30.2 9.5 12 620-631 135-146 (389)
290 KOG3416 Predicted nucleic acid 22.5 2.9E+02 0.0063 28.2 6.8 48 464-512 48-106 (134)
291 PRK04306 50S ribosomal protein 22.3 1.4E+02 0.003 29.1 4.5 53 423-475 33-95 (98)
292 PF12059 DUF3540: Protein of u 22.0 3.2E+02 0.0069 29.8 7.8 67 976-1047 3-72 (202)
293 PRK13806 rpsA 30S ribosomal pr 21.9 3.8E+02 0.0081 33.0 9.3 58 424-504 31-93 (491)
294 PF01157 Ribosomal_L21e: Ribos 21.8 1.9E+02 0.0041 28.2 5.3 53 423-475 31-97 (99)
295 PF04006 Mpp10: Mpp10 protein; 21.7 49 0.0011 41.6 1.8 8 200-207 397-404 (600)
296 KOG2418 Microtubule-associated 21.6 2.4E+02 0.0052 33.3 6.9 9 974-982 327-335 (448)
297 smart00357 CSP Cold shock prot 21.2 2.9E+02 0.0064 22.9 6.0 56 443-500 2-63 (64)
298 TIGR00686 phnA alkylphosphonat 21.2 65 0.0014 31.7 2.1 21 591-611 41-61 (109)
299 KOG3540 Beta amyloid precursor 21.0 53 0.0011 39.7 1.7 39 56-110 198-236 (615)
300 PRK07218 replication factor A; 20.9 9.8E+02 0.021 29.1 12.2 48 438-488 70-127 (423)
301 TIGR00008 infA translation ini 20.8 5.1E+02 0.011 23.7 7.4 59 552-623 8-67 (68)
302 KOG0415 Predicted peptidyl pro 20.7 1.4E+02 0.0031 35.0 4.9 102 139-249 200-306 (479)
303 PRK14640 hypothetical protein; 20.7 1.6E+02 0.0035 30.5 5.0 47 426-476 95-145 (152)
304 PF09122 DUF1930: Domain of un 20.6 1.1E+02 0.0023 27.5 3.0 25 285-312 44-68 (68)
305 TIGR00358 3_prime_RNase VacB a 20.5 4.7E+02 0.01 33.5 10.0 75 427-502 71-149 (654)
306 KOG0971 Microtubule-associated 20.3 1.7E+03 0.037 29.8 14.3 33 708-740 8-43 (1243)
307 PHA03169 hypothetical protein; 20.1 1.2E+02 0.0026 35.8 4.2 91 5-111 155-245 (413)
No 1
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=100.00 E-value=7.2e-216 Score=1883.31 Aligned_cols=943 Identities=49% Similarity=0.754 Sum_probs=805.0
Q ss_pred CCCcccccCCCCCCcccccccCCchhhhccc--ccccc-----ccCCCCCCCCCCCCCccCcCCCCCCCcchhhHHHHHH
Q 001506 77 ARKPKAKRRSGSEFFDLEAQVDSDEEEDEEE--GEDDF-----IVDGGAELPDEDGGRGIHRRPLLPREDEQEDVEALER 149 (1065)
Q Consensus 77 ~~~~krk~~~~~~FlD~EAeVdddeEeeeee--~~~~f-----i~~~~~~~~~~~~~~~~~r~~~~~~~~~~~d~ee~~~ 149 (1065)
+-++|+|+.+...||+.||+||||.||||++ +|+|+ |++.+.+++++..++|.||+.+.... +..|++++
T Consensus 54 ~~~~~~k~~s~~gf~~~e~dvDdeveddd~~~edEed~~~~~~ie~~e~~~~d~~~~~R~~~~~~~~~~---~~~e~~~~ 130 (1024)
T KOG1999|consen 54 EPDEKDKKESGGGFIDREADVDDEVEDDDDDEEDEEDIELHNDIEESEEDLPDERGDRRLRRYWDRQLN---ELEEELAK 130 (1024)
T ss_pred chhhhccccccccccccccccccccccccchhccCcchhhcccchhcccccccccccccchhhhhhhhh---HHHHHHHH
Confidence 4566778888999999999999988776663 34443 55555556665555555555332222 25566666
Q ss_pred HHHHHhcCCC-CC-CcccchhhhhhhhcCCCCCCCcEEEEEccCchHHHHHHHHHHHHHhhC---CCcceEEEEeeCCCc
Q 001506 150 RIQARYARSS-HT-EYDEETTDVEQQALLPSVRDPKLWMVKCAIGREREAAVCLMQKCIDKG---SELQIRSVIALDHLK 224 (1065)
Q Consensus 150 ~l~eRY~~~~-~~-~~~~~~~~v~q~~LlPsv~DP~lw~Vkck~G~Er~vv~~Lm~K~~~~~---~~l~I~Svf~~~~lk 224 (1065)
.+++||.... +. ..+++.++|+||+|||+++||+||+|||++|+||++|+|||+||+++. .+|+|+|||+++|||
T Consensus 131 r~aee~~~~~~~~~~~~~~~d~I~Q~~LLPsvkDP~LW~VKC~iG~Er~~a~~LMrK~i~~~~t~~plqI~Sv~a~D~lk 210 (1024)
T KOG1999|consen 131 RYAEEYIEKYGFEDGDDEDSDDIPQQALLPSVKDPNLWIVKCKIGREREVAFCLMRKFIELDKTDTPLQIKSVFAKDHLK 210 (1024)
T ss_pred HHHHhhcccccccccchhcccchhHHhhCCCCCCCCeeEEEeccccHHHHHHHHHHHHHhhcccCCCceEEEEEeccccc
Confidence 6666665332 33 333567899999999999999999999999999999999999999975 899999999999999
Q ss_pred cEEEEEecchHHHHHHHhcCcccceeeeeeeChhhhhhccccccccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEE
Q 001506 225 NYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVT 304 (1065)
Q Consensus 225 GYIYIEA~~~~~V~~ai~Gl~~v~~~~~~lVpi~Em~~vL~v~~~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~ 304 (1065)
|||||||++|+||++||+||++||.+++.||||+||++||+|.|+.+.|++|+|||||+|+||||||||+.|++++++|+
T Consensus 211 GyIYIEA~KqshV~~Ai~gv~niy~~~~~lVPikEM~dvLkV~K~~v~L~~gswVRiKrG~YKgDLAqVd~Vd~~~n~v~ 290 (1024)
T KOG1999|consen 211 GYIYIEADKQSHVKEAIEGVRNIYANRILLVPIKEMPDVLKVVKKVVQLSEGSWVRIKRGKYKGDLAQVDDVDENRNRVR 290 (1024)
T ss_pred eeEEEEechhHHHHHHHhhhhhheeccEEEEehhHhhhhhhhhhhhhccCccceEEEeccccccceeeeeeecccCCEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeeccchhhhhhhccccccccCCCCCCCCCCCCHHHHHhccccEeeeccCCCCceEEEecCceeccceEEEEEeccce
Q 001506 305 VKLIPRIDLQALANKLEGREVAKKKPFVPPPRFMNVDEARELHIRVERRRDPMTGDYFENIGGMLFKDGFLYKTVSMKSI 384 (1065)
Q Consensus 305 VkLvPRiD~~~~~~~~~~~~~~kkk~~RPp~rlFn~~e~~~~~~~v~~~r~~~~g~~~~~~~~~~~~dGfL~K~~~i~~l 384 (1065)
|||||||||+++..++. ....+|++||++||||..++++..++++.+++..+|+||++++|++|+||||||.|+|++|
T Consensus 291 lKlIPRIDyq~~~~~~~--~~~~~ka~~p~~R~~~~~~~~~~~ir~~~~~~~~~Gd~l~~~gn~~~~dGFLyK~v~i~sI 368 (1024)
T KOG1999|consen 291 LKLIPRIDYQKLLGKLE--ETTDKKAFRPAPRRPNQKEFDEEAIRSEGRRDHSRGDYLEFEGNELFKDGFLYKDVSISSI 368 (1024)
T ss_pred EEEeccccHHhhhcccc--ccchhhccCCcccCCCccccchhhhhhccccccccCceEEecCCceeccceeeeeeeccee
Confidence 99999999999998877 3345677899999999999999999999999999999999999999999999999999999
Q ss_pred eecCCCCChHHhhhccCCCCCCcchhhhhhHhhhcccc-cCcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCC
Q 001506 385 SAQNIQPTFDELEKFRTPGENGESDIASLSTLFANRKK-GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLP 463 (1065)
Q Consensus 385 ~~~~V~PTleEL~kF~~~~~~~~~dl~~ls~~~~~~~~-~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~ 463 (1065)
++++|+|||+||+||+...+ ++||.+++++++++.+ +.|++||+|+||.|||+|++|+|++|++.+|+|++++++|+
T Consensus 369 ~t~gV~PT~dELekF~~~~e--~~Dl~~~st~~~~r~~~~~F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~ 446 (1024)
T KOG1999|consen 369 ITDGVKPTLDELEKFNPSNE--EGDLEWVSTLKSNRKKKHLFSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLK 446 (1024)
T ss_pred eecCcccCHHHHHhhcCCCc--cccceeeeeeccccccccccCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCC
Confidence 99999999999999998766 6688888866665554 45999999999999999999999999999999999999999
Q ss_pred cceeeccccceeeccCCCcEEEeccccCCceeEEEEEeCcEEEEEeCCCCceEEEecccccccccccccccccCceeeee
Q 001506 464 KTLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRD 543 (1065)
Q Consensus 464 ~~l~v~~~~LrK~F~~GDhVkVi~G~~~getGlVVkVe~~~v~vlSD~t~~ei~V~~~dL~~~~e~~~g~~~~g~y~l~D 543 (1065)
.+|+|++++|||||++|||||||+|+|+|+|||||+|+++.|+||||++|+|++||++||++|++++++++++|+|+|||
T Consensus 447 ~pl~~~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe~~~vi~~Sd~t~eel~Vf~~dlq~c~ev~~gv~~~ge~e~hd 526 (1024)
T KOG1999|consen 447 GPLEVPASELRKYFEPGDHVKVIAGRYEGDTGLVVRVEQGDVILLSDLTMEELKVFARDLQLCSEVTLGVEKSGEYELHD 526 (1024)
T ss_pred CccccchHhhhhhccCCCeEEEEeccccCCcceEEEEeCCeEEEEecCccceeeEEehhcccchheeecccccccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEeCCCceEEEEEEccceEEEeccCCCCCcEEEEecchhhhccc-CCcccccCCCCeecCCCEEEEEcCCCCCceeeEE
Q 001506 544 LVLLDNNSFGVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLE-KKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVE 622 (1065)
Q Consensus 544 LVqLd~~tVGvIv~verd~~~VL~~~~~~g~v~~v~~~~I~~k~~-~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~ 622 (1065)
|||||.++||||++++++.|+||+++ |+|++|++++|.+|++ ++++|+|+++|+|+++|+|+++.||++||+|+|+
T Consensus 527 lVqLd~~~vgvI~rle~e~~~vl~~~---g~v~~i~~~~i~~kk~~r~~~~~D~~~n~I~~kD~Vkvi~Gp~~g~~G~v~ 603 (1024)
T KOG1999|consen 527 LVQLDNQNVGVIVRLERETFQVLGMN---GKVVTIRKSSITKKKDNRKAVAVDRNGNEIRVKDTVKVIGGPSKGREGEVL 603 (1024)
T ss_pred eeecCCCcEEEEEEecchheeeecCc---CceEEEeechhhhhhhhhhheeecccCCeecccceEEEecCCCCCccCccc
Confidence 99999999999999999999999985 7999999999999986 5699999999999999999999999999999999
Q ss_pred EEECCEEEEEecceeccceEEEEeCCceEEeeccCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 001506 623 HIYRGILFIHDRHHLEHAGFICAKSSSCVVVGGSRANGDRNGDAYSRFNSLRTPPRIPQSPGRYSRGGPPAGGRNRGGRG 702 (1065)
Q Consensus 623 HI~r~~lFl~~~~~~EN~Gifv~~a~~~~~~g~~~~~~~~~~~~~~~~~~~~~p~~~~~sp~~~~~~~~~~gg~~~~~~~ 702 (1065)
||||+++|||||+++||+||||||++||.++|++++.. .+....+.|++|+ |.++ ++|++++.+ +.++|+.+++||
T Consensus 604 ~i~r~~~F~h~r~~~En~Gv~vck~k~~~~~g~~~st~-~~~~~~~~l~~ms-P~r~-~sp~~~~~~-~ga~g~~gggrG 679 (1024)
T KOG1999|consen 604 HIYRPFVFLHSRKNLENGGVFVCKEKNLILAGGKKSTN-SLAFNKGALAPMS-PGRI-QSPMGPSGG-PGAFGGHGGGRG 679 (1024)
T ss_pred eeecceeeeeehhhcccCCeEEEecCCceeccccCccc-chhhcccccCCCC-cccc-cCCcCCCCC-CCCcCcCccCcc
Confidence 99999999999999999999999999999999976421 1111223344443 3322 444433211 112233333444
Q ss_pred C--CccccCcEEEEeeCCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCccccccccccccchhhhhhhhhhhhcccc
Q 001506 703 G--HDALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISDNVVVSTPYRYIELFFILFYHFLMLKL 780 (1065)
Q Consensus 703 ~--~d~liGktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 780 (1065)
| ++.+|||||+|+.||||||+|+|||+|+++||||||++|++|+|+|.++..+.+. ..-+ ....|
T Consensus 680 g~rd~~l~GktVrI~~Gp~KG~~GivkD~~~~~arVELhs~~~ti~vd~~~~~~v~~~-~~~g------------~~~sY 746 (1024)
T KOG1999|consen 680 GNRDDSLLGKTVRIRLGPKKGYLGIVKDVNGDTARVELHSKCVTIKVDRLKRKIVGST-RDGG------------ETSSY 746 (1024)
T ss_pred CcCcchhcCcEEEEecCCcccccceeEeccCCeeEEEEEeccEEEEechhhceEEeec-cCCC------------Ccccc
Confidence 4 4599999999999999999999999999999999999999999999999987642 1111 01135
Q ss_pred cceeeeccCCCCCC-CCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCC
Q 001506 781 TVHVIMFCSDTPRY-GMGSETPMHPSRTPLHP-YMTPMRDAGATPIHDGMRTPMRDRAWNPYTPMSPPR--DNWEDGNPG 856 (1065)
Q Consensus 781 ~~~~p~~~~~tp~y-~~G~~TP~~g~rTP~~~-~~TP~~~g~~TP~~~Gs~TP~~~~aw~p~~p~tp~~--~~~~~~~p~ 856 (1065)
+.+||+||++||+| ++||+|||||++||+|+ ++||++++++||+|+|+|||||++||+|+.++||++ ++|+++.++
T Consensus 747 g~~~~~~g~~~~~~~~~Gs~tp~~~s~tpl~~~s~tp~~~~~~Tp~~dG~rTP~r~~aW~~~~~~tPa~~~~~~~~g~~g 826 (1024)
T KOG1999|consen 747 GERTPGYGRVTPARYGMGSSTPMYGSNTPLWGGSRTPARDGGATPSHDGSRTPARGRAWNPYNGKTPARNFDNREPGFEG 826 (1024)
T ss_pred ccccccccccCccccCCCCcCccCCCCCCCCCcccCccccCCCCcCCCCCcCCCCCCCcCCCCCCCCccccCCcccCCCC
Confidence 67999999999988 78999999999999998 899999999999999999999999999999999988 678888888
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCc----CCCCCCCCCCCCC-CCCCCCCCCCCC
Q 001506 857 SWGTSPQYQPGSPPSRAYEAPTPGSGWASTPG-GNYSDAGTPRDSSSTYV----NAPSPYLPSTPGG-QPMTPNSASYLP 930 (1065)
Q Consensus 857 ~~~~tp~y~p~tp~~~~y~~~TPg~~~~~tP~-~~~~~~~tP~~~~~~y~----~~pspy~p~tp~~-~p~tP~~~~y~P 930 (1065)
.|+.+|+|. |.|+|||+.|+.+++ +.|+.+.||....|+|. ++|+| +++++ ++||||+.+|.|
T Consensus 827 ~~g~sp~~~--------~~a~Tpg~~~~~~~~~~~~~~~g~~~~~gsa~~~~~~~sps~---sp~~~~~~~tpss~s~~p 895 (1024)
T KOG1999|consen 827 SGGRSPQGY--------YSAPTPGSNWGSTGGGGAPAWPGTPNGNGSAWGPSGQNSPSP---SPWGYQNNPTPSSSSYGP 895 (1024)
T ss_pred CCCCCCCCC--------cCCCCCCCCCCcCCCCCCcCCCCCCCCCccccccccCCCCCC---CCccCccCCCCcccccCC
Confidence 888777653 678888888877754 45666677755556663 33333 34444 478999999999
Q ss_pred CCCCC-CCCCCCCCCCCCCCCcCCCCCCCCCccCcEEE-EcCCCcccEEEEEEeCCCCeEEEEeccCCCCceEEecCCCe
Q 001506 931 GTPGG-QPMTPGTGGLDAMSPVIGADNEGPWFMPDILV-RRSGEESVVGVIREVLPDGSCRVVLGSSGNGDTITALPNEI 1008 (1065)
Q Consensus 931 ~TPg~-~p~tp~~~g~~~~~~~~~~~~~~~W~~~~I~V-~~~g~~~~~GvI~~V~~~g~~~V~l~~~~~g~~v~v~~~~L 1008 (1065)
+|||+ +|||||++ ++.++... ++....| .++..+ ... -++.++||+|.+ |.|+|+|.++ +++++++++||
T Consensus 896 ~tpgg~~~~Tpgs~-~d~~~~~~-~~~~~~~-~~d~~~~~~~--~G~~~~ir~v~~-G~~sv~~~de--~~~~~~s~~~~ 967 (1024)
T KOG1999|consen 896 KTPGGGNPMTPGSG-LDSGSGNG-GDGNSSW-GPDTSLDTQL--VGQTGIIRSVAD-GGCSVWLGDE--GETISNSKPHL 967 (1024)
T ss_pred CCCCCCCCCCCCcc-ccccCCCC-CccceEe-ccccccccee--cccccceeeccC-CceeeecCCC--CcccccccccC
Confidence 99998 89999984 55555432 1222233 344333 111 156889999977 9999999985 78999999999
Q ss_pred eecCCCCCCcEEEEcCCCCCceEEEEEEeCCCcEEEecCCCceEEEeccchhcccCC
Q 001506 1009 EIVPPRKTDKIKIMGGPHRGATGKLIGVDGTDGIVKVDVSLDVKILDMAILAKLAQP 1065 (1065)
Q Consensus 1009 E~V~P~kgd~VkVi~G~~rG~tG~LisiD~~dgiVk~d~~~d~kil~~~~L~Kl~~~ 1065 (1065)
+++.|.+||.+||+.|.+||.+|+|+++|+.+||||+|.+.++|||++.+||||++|
T Consensus 968 a~~~p~~~d~~k~~~g~~~g~~~~~~~~dg~~g~~~~d~~~~~k~l~~~~~~k~~~~ 1024 (1024)
T KOG1999|consen 968 APAPPCKGDDVKSIWGDDRGSTGKLVGNDGWDGIVRIDETSDIKILNLGLLCKMVSP 1024 (1024)
T ss_pred ccCCCCCCCCccccccccccccccccCCCcccceecccccccchhhhhhhhhhccCC
Confidence 999999999999999999999999999999999999999999999999999999875
No 2
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=100.00 E-value=8e-78 Score=663.66 Aligned_cols=398 Identities=23% Similarity=0.252 Sum_probs=348.0
Q ss_pred CCCCCCCCCHHHHHhccccEeeeccCCCCceEEEecCceeccceEEEEEeccceeecCCCCChHHhhhccCCCCCCcchh
Q 001506 331 FVPPPRFMNVDEARELHIRVERRRDPMTGDYFENIGGMLFKDGFLYKTVSMKSISAQNIQPTFDELEKFRTPGENGESDI 410 (1065)
Q Consensus 331 ~RPp~rlFn~~e~~~~~~~v~~~r~~~~g~~~~~~~~~~~~dGfL~K~~~i~~l~~~~V~PTleEL~kF~~~~~~~~~dl 410 (1065)
.|||+||||+.|+.++.......|++. .| .|.|+.|.||||+|.|+++++++++++||+||+.+|....+ ++||
T Consensus 4 ~r~~~~lfn~t~a~~~~~~~~~kr~~r---~f-~~~ne~~~dgflvk~~Ris~~et~~~~pt~de~~~F~~~~~--dldl 77 (607)
T COG5164 4 HRAPPQLFNPTMALRLDQANLYKRDDR---HF-TYKNEDYIDGFLVKVKRISERETLMRIPTNDEKNVFSIICK--DLDL 77 (607)
T ss_pred ccCchhhcCchhhhhcChhhhhccCch---hc-cccCcccccceEEEEeeeceeeecccccccchhhhcCcccc--ccch
Confidence 499999999999999888666666553 34 58999999999999999999999999999999999987544 4788
Q ss_pred hhhhHhhhcccccCcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCcEEEecccc
Q 001506 411 ASLSTLFANRKKGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVVSGTQ 490 (1065)
Q Consensus 411 ~~ls~~~~~~~~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~F~~GDhVkVi~G~~ 490 (1065)
.+++.++++.. ..|||||+|||+.|++++..|+|.++.+++.+|... +.++|++|.+-|||.|..|||||||.|.|
T Consensus 78 ~s~~~s~kk~h-a~fqpgD~~Evl~Geqrg~~gVV~~~~~~I~tm~~~---~~~rl~~p~~~lRk~f~~gD~vkVI~g~~ 153 (607)
T COG5164 78 YSYVESFKKQH-AVFQPGDALEVLRGEQRGRVGVVPRQKEMIETMTYH---FEQRLCGPWGRLRKGFYKGDLVKVIEGGE 153 (607)
T ss_pred hHHHHHHhhcc-cccCCCCeeeeecceecccceeecccccceeeeeec---cCceeecchhhhhcccccCCeEEEecccc
Confidence 88888876654 459999999999999999999999999999998874 46789999999999999999999999999
Q ss_pred CCceeEEEEEeCcEEEEEeCCCCceEEEecccccccccccccccccCceeeeeeEEeCCCceEEEEEEccceEEEeccCC
Q 001506 491 AGATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDNNSFGVIIRVESEAFQVLKGVP 570 (1065)
Q Consensus 491 ~getGlVVkVe~~~v~vlSD~t~~ei~V~~~dL~~~~e~~~g~~~~g~y~l~DLVqLd~~tVGvIv~verd~~~VL~~~~ 570 (1065)
.+++|||++|+++.|+++|+++|.|++||+++|.++.+.+. ....|+|||||+|+..+|.||..|++|.++|+++
T Consensus 154 ~~d~g~V~rI~~~~vtF~s~~~~~e~tI~sr~l~ks~~tta---~ss~Y~lhd~V~l~~~~vaci~sid~Dv~kvide-- 228 (607)
T COG5164 154 MVDIGTVPRIDGEKVTFNSENFKSESTIKSRGLSKSIDTTA---TSSIYKLHDYVDLFLEKVACINSIDFDVEKVIDE-- 228 (607)
T ss_pred ccccceEEEecCceeEEccccccccceEEeccccccccccc---hhhhhhhhhhhhhhhcceeEEeecccchhhhhhh--
Confidence 99999999999999999999999999999999999988754 3458999999999999999999999999999997
Q ss_pred CCCcEEEEecchhhhccc-CC--cccccCCCCeecCCCEEEEEcCCCCCceeeEEEEECCEEEEEecceeccceEEEEeC
Q 001506 571 DRPEVALVKLREIKCKLE-KK--SNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRGILFIHDRHHLEHAGFICAKS 647 (1065)
Q Consensus 571 ~~g~v~~v~~~~I~~k~~-~r--~~a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~~lFl~~~~~~EN~Gifv~~a 647 (1065)
.|+|+++-+.+|..|++ +| .+++|+||++|++||.|+++-|. +++|+|+||||.|+|++++++.||+|+||++.
T Consensus 229 -~g~v~t~~~~sI~~kv~~~Rg~~i~~d~ng~eI~igd~VvE~~g~--~~egq~l~i~~~f~f~~t~~i~ennGVfv~~~ 305 (607)
T COG5164 229 -LGEVHTACPISIGDKVRVTRGELIGMDGNGREISIGDAVVESRGG--KFEGQSLGIVKHFDFGETVSIKENNGVFVKIE 305 (607)
T ss_pred -cCceeEecchhhhhhhecccceeEeeccccceEeeceeEEEecCC--ceeeEEEEEEEEEeeeeeeeeeccCceEEEec
Confidence 48999999999999986 45 59999999999999999999884 79999999999999999999999999999999
Q ss_pred CceEEeeccCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcEEEEeeCCCCCceeEEE
Q 001506 648 SSCVVVGGSRANGDRNGDAYSRFNSLRTPPRIPQSPGRYSRGGPPAGGRNRGGRGGHDALVGTTVKVRLGPYKGYRGRVV 727 (1065)
Q Consensus 648 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~p~~~~~sp~~~~~~~~~~gg~~~~~~~~~d~liGktV~I~~GpyKG~~G~Vk 727 (1065)
+|+.+++++...- . .-.+|++|| |+.+ ..+.. ++..- -....+|||.+|||||+|+.|+|||++|+||
T Consensus 306 ~nv~~VAtkd~~~-s---~k~dl~kmn-p~v~-~~~~~----p~~~~--l~r~i~gRd~aigktVrIr~g~yKG~lGVVK 373 (607)
T COG5164 306 GNVCIVATKDFTE-S---LKVDLDKMN-PPVT-VNLQN----PKTNE--LERKIVGRDPAIGKTVRIRCGEYKGHLGVVK 373 (607)
T ss_pred CceeEEEeccchh-h---hcccHhhcC-chhh-cCCCC----Ccchh--hhccccccccccCceEEEeecccccccceee
Confidence 9999999854211 1 124688998 4432 12111 11000 0112358999999999999999999999999
Q ss_pred eecCCeEEEEecCCCeEEEEecCCccccccc
Q 001506 728 DVKGQSVRVELESQMKVVTVDRSMISDNVVV 758 (1065)
Q Consensus 728 d~t~~~~rVELhs~~k~I~V~r~~l~~~~~~ 758 (1065)
|+++..|||||||++|.|||+|++|++.++.
T Consensus 374 dv~~~~arVeLhs~nK~VTI~K~~l~y~~re 404 (607)
T COG5164 374 DVDRNIARVELHSNNKFVTIEKSRLAYLGRE 404 (607)
T ss_pred eccCceEEEEEecCCceEEeehhheEEeccc
Confidence 9999999999999999999999999998763
No 3
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=100.00 E-value=3.1e-37 Score=367.26 Aligned_cols=301 Identities=17% Similarity=0.260 Sum_probs=204.4
Q ss_pred cCCCCCCCCCCCCHHHHHhccccEeeeccC---CCCceEEEecCceeccceEEEEEecccee-----ecCCCCChHH--h
Q 001506 327 KKKPFVPPPRFMNVDEARELHIRVERRRDP---MTGDYFENIGGMLFKDGFLYKTVSMKSIS-----AQNIQPTFDE--L 396 (1065)
Q Consensus 327 kkk~~RPp~rlFn~~e~~~~~~~v~~~r~~---~~g~~~~~~~~~~~~dGfL~K~~~i~~l~-----~~~V~PTleE--L 396 (1065)
+++..||+|++|.+..++..+.++-.+=+. -.+.+| .+|..| +=|.++.+...-++ ++--+|.-+| |
T Consensus 316 ~p~~R~~~~~~~~~~~ir~~~~~~~~~Gd~l~~~gn~~~--~dGFLy-K~v~i~sI~t~gV~PT~dELekF~~~~e~~Dl 392 (1024)
T KOG1999|consen 316 RPAPRRPNQKEFDEEAIRSEGRRDHSRGDYLEFEGNELF--KDGFLY-KDVSISSIITDGVKPTLDELEKFNPSNEEGDL 392 (1024)
T ss_pred CCcccCCCccccchhhhhhccccccccCceEEecCCcee--ccceee-eeeecceeeecCcccCHHHHHhhcCCCccccc
Confidence 344559999999999999887766433221 112233 344444 44778887776553 2223333331 1
Q ss_pred hh-------------ccCCCCC--Ccchhhhh---------------------hHhh---hcccccCcCCCCEEEEeccc
Q 001506 397 EK-------------FRTPGEN--GESDIASL---------------------STLF---ANRKKGHFMKGDAVIVIKGD 437 (1065)
Q Consensus 397 ~k-------------F~~~~~~--~~~dl~~l---------------------s~~~---~~~~~~~F~~GD~V~V~~Ge 437 (1065)
+. |+.+..- ...||..| ...| +..++++|++||||+|+.|.
T Consensus 393 ~~~st~~~~r~~~~~F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eLrKyF~~GDhVKVi~G~ 472 (1024)
T KOG1999|consen 393 EWVSTLKSNRKKKHLFSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASELRKYFEPGDHVKVIAGR 472 (1024)
T ss_pred eeeeeeccccccccccCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCCCccccchHhhhhhccCCCeEEEEecc
Confidence 11 5543210 01111111 1111 24468999999999999999
Q ss_pred ccCceeEEEEEcCCeEEEeecCCCCCcceeecccccee------------eccCCCcEEEeccccCCceeEEEEEeCcEE
Q 001506 438 LKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK------------YFEPGNHVKVVSGTQAGATGMVLKVEQHVL 505 (1065)
Q Consensus 438 l~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK------------~F~~GDhVkVi~G~~~getGlVVkVe~~~v 505 (1065)
++|-+|+|++|+...|+|+++. .+++|+|++++|++ .|+.+|.|..- +. .+|+|++++.+.+
T Consensus 473 ~eG~tGlVvrVe~~~vi~~Sd~--t~eel~Vf~~dlq~c~ev~~gv~~~ge~e~hdlVqLd---~~-~vgvI~rle~e~~ 546 (1024)
T KOG1999|consen 473 YEGDTGLVVRVEQGDVILLSDL--TMEELKVFARDLQLCSEVTLGVEKSGEYELHDLVQLD---NQ-NVGVIVRLERETF 546 (1024)
T ss_pred ccCCcceEEEEeCCeEEEEecC--ccceeeEEehhcccchheeecccccccccccceeecC---CC-cEEEEEEecchhe
Confidence 9999999999999999999974 37889999999995 37888888764 23 8999999999999
Q ss_pred EEEeCCCCceEEEeccccccccccccc--ccc-cCceeeeeeEEe----CCCceEEEEEEccceEEEec-cCCCCCcEEE
Q 001506 506 IILSDTTKEDIRVFADDVVESSEVTTG--ITK-IGDYELRDLVLL----DNNSFGVIIRVESEAFQVLK-GVPDRPEVAL 577 (1065)
Q Consensus 506 ~vlSD~t~~ei~V~~~dL~~~~e~~~g--~~~-~g~y~l~DLVqL----d~~tVGvIv~verd~~~VL~-~~~~~g~v~~ 577 (1065)
.|| +++...++|.+..+..+.+.... ++. .+.....|+|.. ..+..|=|.+|-|-.+++-+ .+-+++-|..
T Consensus 547 ~vl-~~~g~v~~i~~~~i~~kk~~r~~~~~D~~~n~I~~kD~Vkvi~Gp~~g~~G~v~~i~r~~~F~h~r~~~En~Gv~v 625 (1024)
T KOG1999|consen 547 QVL-GMNGKVVTIRKSSITKKKDNRKAVAVDRNGNEIRVKDTVKVIGGPSKGREGEVLHIYRPFVFLHSRKNLENGGVFV 625 (1024)
T ss_pred eee-cCcCceEEEeechhhhhhhhhhheeecccCCeecccceEEEecCCCCCccCccceeecceeeeeehhhcccCCeEE
Confidence 998 57789999999999877665332 332 578899999987 23566999999999877766 3456677777
Q ss_pred Eecchhhhc---ccC-------Ccccc------------cCC--------------CCeecCCCEEEEEcCCCCCceeeE
Q 001506 578 VKLREIKCK---LEK-------KSNVQ------------DRN--------------KNTVAVKDVVRIVEGPCKGKQGPV 621 (1065)
Q Consensus 578 v~~~~I~~k---~~~-------r~~a~------------D~~--------------gn~I~~~D~Vkvv~Gp~~gr~G~V 621 (1065)
|++..+.-. .++ -+.+. +.+ +..-..|.+|+|..||+||..|.|
T Consensus 626 ck~k~~~~~g~~~st~~~~~~~~~l~~msP~r~~sp~~~~~~~ga~g~~gggrGg~rd~~l~GktVrI~~Gp~KG~~Giv 705 (1024)
T KOG1999|consen 626 CKEKNLILAGGKKSTNSLAFNKGALAPMSPGRIQSPMGPSGGPGAFGGHGGGRGGNRDDSLLGKTVRIRLGPKKGYLGIV 705 (1024)
T ss_pred EecCCceeccccCcccchhhcccccCCCCcccccCCcCCCCCCCCcCcCccCccCcCcchhcCcEEEEecCCccccccee
Confidence 776654211 100 00010 000 112557889999999999999999
Q ss_pred EEEECCE--EEEEeccee
Q 001506 622 EHIYRGI--LFIHDRHHL 637 (1065)
Q Consensus 622 ~HI~r~~--lFl~~~~~~ 637 (1065)
+-+--++ +-||+..++
T Consensus 706 kD~~~~~arVELhs~~~t 723 (1024)
T KOG1999|consen 706 KDVNGDTARVELHSKCVT 723 (1024)
T ss_pred EeccCCeeEEEEEeccEE
Confidence 9999775 788876653
No 4
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=99.87 E-value=7.3e-22 Score=200.56 Aligned_cols=130 Identities=26% Similarity=0.426 Sum_probs=118.9
Q ss_pred CCCcEEEEEccCchHHHHHHHHHHHHHhhCCCcceEEEEeeCCCccEEEEEecchHHHHHHHhcCcccceeeeeeeChhh
Q 001506 180 RDPKLWMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIRE 259 (1065)
Q Consensus 180 ~DP~lw~Vkck~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~~~lkGYIYIEA~~~~~V~~ai~Gl~~v~~~~~~lVpi~E 259 (1065)
+||+||.|+|++|+|+.|+.+|++|+.. .++.|+++|++..++|||||||...+++|++|++++++++.-..++|.+|
T Consensus 4 ~~~~WYvv~t~sG~E~~V~~~L~~~~~~--~~~~i~~i~vp~~fpGYVfVe~~~~~~~~~~i~~v~~v~g~lg~~l~~~E 81 (153)
T PRK08559 4 EMSMIFAVKTTAGQERNVALMLAMRAKK--ENLPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVRGVVPGEISFEE 81 (153)
T ss_pred CCCcEEEEEeECChHHHHHHHHHHHHHh--CCCcEEEEEccCCCCcEEEEEEEChHHHHHHHhcCCCEeeeCCCCCCHHH
Confidence 7899999999999999999999999865 34559999999999999999999999999999999999975445899999
Q ss_pred hhhccccccccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEEEeecc
Q 001506 260 MTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLIPRI 311 (1065)
Q Consensus 260 m~~vL~v~~~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~VkLvPRi 311 (1065)
|..+|...+....+++|+||||+.|+|+|+.|+|.+++..+..|+|+|+-|-
T Consensus 82 i~~il~~~~~~~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~ 133 (153)
T PRK08559 82 VEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAA 133 (153)
T ss_pred HHHHHhccCcccCCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCc
Confidence 9999987655567999999999999999999999999999999999999875
No 5
>PF03439 Spt5-NGN: Early transcription elongation factor of RNA pol II, NGN section; InterPro: IPR005100 Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4 []. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit []. ; PDB: 3H7H_B 3QQC_D 3P8B_B 2EXU_A.
Probab=99.87 E-value=3.3e-22 Score=183.64 Aligned_cols=82 Identities=51% Similarity=0.835 Sum_probs=69.4
Q ss_pred cEEEEEccCchHHHHHHHHHHHHHhh--CCCcceEEEEeeCCCccEEEEEecchHHHHHHHhcCcccceeeeeeeChhhh
Q 001506 183 KLWMVKCAIGREREAAVCLMQKCIDK--GSELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIREM 260 (1065)
Q Consensus 183 ~lw~Vkck~G~Er~vv~~Lm~K~~~~--~~~l~I~Svf~~~~lkGYIYIEA~~~~~V~~ai~Gl~~v~~~~~~lVpi~Em 260 (1065)
+||+|||++|+|+++|.+||+|+++. ...++|+|||+++++||||||||+++.+|.+||+|++++++..+.+||++||
T Consensus 1 ~iw~Vkc~~G~E~~v~~~l~~k~~~~~~~~~l~I~Si~~~~~lkGyIyVEA~~~~~V~~ai~gi~~i~~~~~~~vp~~E~ 80 (84)
T PF03439_consen 1 KIWAVKCKPGQEREVAISLMNKAEDLAKKNNLNIYSIFAPDSLKGYIYVEAERESDVKEAIRGIRHIRGSRPGLVPIEEM 80 (84)
T ss_dssp EEEEEEE-TTTHHHHHHHHHHHHHHHHHHST----EEEE-TTSTSEEEEEESSHHHHHHHHTT-TTEEEECCEEB-GGGT
T ss_pred CEEEEEeCCChHHHHHHHHHHHHHHhhhcCCCceEEEEEeCCCceEEEEEeCCHHHHHHHHhcccceeeccceeECHHHH
Confidence 69999999999999999999998764 2449999999999999999999999999999999999999988999999999
Q ss_pred hhcc
Q 001506 261 TDVL 264 (1065)
Q Consensus 261 ~~vL 264 (1065)
+++|
T Consensus 81 ~~~L 84 (84)
T PF03439_consen 81 EDLL 84 (84)
T ss_dssp CGGH
T ss_pred HhhC
Confidence 9987
No 6
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=99.81 E-value=1.5e-19 Score=202.18 Aligned_cols=351 Identities=25% Similarity=0.326 Sum_probs=246.1
Q ss_pred hhhhcCCCCCCCcEEEEEccCchHHHHHHHHHHHHHhhCCCcceEEEEeeCCCccEEEEEecchHHHH----HHHhcCcc
Q 001506 171 EQQALLPSVRDPKLWMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHVK----EACKGLRN 246 (1065)
Q Consensus 171 ~q~~LlPsv~DP~lw~Vkck~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~~~lkGYIYIEA~~~~~V~----~ai~Gl~~ 246 (1065)
+|..|.|.-.-+..|.||.+.+.|+++... ... ..++..+++.+.+ |++|-|+|+.+..|+. ++|+-+++
T Consensus 29 ~r~f~~~ne~~~dgflvk~~Ris~~et~~~----~pt-~de~~~F~~~~~d-ldl~s~~~s~kk~ha~fqpgD~~Evl~G 102 (607)
T COG5164 29 DRHFTYKNEDYIDGFLVKVKRISERETLMR----IPT-NDEKNVFSIICKD-LDLYSYVESFKKQHAVFQPGDALEVLRG 102 (607)
T ss_pred chhccccCcccccceEEEEeeeceeeeccc----ccc-cchhhhcCccccc-cchhHHHHHHhhcccccCCCCeeeeecc
Confidence 577788887789999999999999977422 222 2566677776655 9999999999999999 88888888
Q ss_pred cceeeeeeeC-hhhhhhccccccccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEEEeeccchhhhhhhcccccc
Q 001506 247 IYSQKVMLVP-IREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLIPRIDLQALANKLEGREV 325 (1065)
Q Consensus 247 v~~~~~~lVp-i~Em~~vL~v~~~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~VkLvPRiD~~~~~~~~~~~~~ 325 (1065)
.-......|| .+||...|...- ..---+-|=||+.+.|+||+++|++ .+.++.+-+|||||-..
T Consensus 103 eqrg~~gVV~~~~~~I~tm~~~~--~~rl~~p~~~lRk~f~~gD~vkVI~---g~~~~d~g~V~rI~~~~---------- 167 (607)
T COG5164 103 EQRGRVGVVPRQKEMIETMTYHF--EQRLCGPWGRLRKGFYKGDLVKVIE---GGEMVDIGTVPRIDGEK---------- 167 (607)
T ss_pred eecccceeecccccceeeeeecc--CceeecchhhhhcccccCCeEEEec---cccccccceEEEecCce----------
Confidence 8766678888 788877776541 1112478999999999999999975 47889999999998321
Q ss_pred ccCCCCCCCCCCCCHHHHHhccccEeeeccC---CCCceEEEecCceeccceEEEEEeccceeecCCCCChHHhhhccCC
Q 001506 326 AKKKPFVPPPRFMNVDEARELHIRVERRRDP---MTGDYFENIGGMLFKDGFLYKTVSMKSISAQNIQPTFDELEKFRTP 402 (1065)
Q Consensus 326 ~kkk~~RPp~rlFn~~e~~~~~~~v~~~r~~---~~g~~~~~~~~~~~~dGfL~K~~~i~~l~~~~V~PTleEL~kF~~~ 402 (1065)
.+|+++.... ..-|..+-.. .+.-.-.+|.-+.|.++||.|..-+.++. .||-|++||+.+|...
T Consensus 168 ----------vtF~s~~~~~-e~tI~sr~l~ks~~tta~ss~Y~lhd~V~l~~~~vaci~sid-~Dv~kvide~g~v~t~ 235 (607)
T COG5164 168 ----------VTFNSENFKS-ESTIKSRGLSKSIDTTATSSIYKLHDYVDLFLEKVACINSID-FDVEKVIDELGEVHTA 235 (607)
T ss_pred ----------eEEccccccc-cceEEeccccccccccchhhhhhhhhhhhhhhcceeEEeecc-cchhhhhhhcCceeEe
Confidence 2455544321 1111111000 01111124667889999999988777776 5799999999999642
Q ss_pred CCCCcchhhhhhHhhhcccccCcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCc
Q 001506 403 GENGESDIASLSTLFANRKKGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNH 482 (1065)
Q Consensus 403 ~~~~~~dl~~ls~~~~~~~~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~F~~GDh 482 (1065)
...++||+|.+.+|+|.++.|.+-+|......+... ....+.....|.|+|-.|..
T Consensus 236 --------------------~~~sI~~kv~~~Rg~~i~~d~ng~eI~igd~VvE~~----g~~~egq~l~i~~~f~f~~t 291 (607)
T COG5164 236 --------------------CPISIGDKVRVTRGELIGMDGNGREISIGDAVVESR----GGKFEGQSLGIVKHFDFGET 291 (607)
T ss_pred --------------------cchhhhhhhecccceeEeeccccceEeeceeEEEec----CCceeeEEEEEEEEEeeeee
Confidence 346789999999999999888887776554333332 34577888899999999999
Q ss_pred EEEeccccCCceeEEEEEeCcEEEEEeCCCCceEEEecccccccccccccccccCceeeeeeEEeCCCceEEEEEEccce
Q 001506 483 VKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDNNSFGVIIRVESEA 562 (1065)
Q Consensus 483 VkVi~G~~~getGlVVkVe~~~v~vlSD~t~~ei~V~~~dL~~~~e~~~g~~~~g~y~l~DLVqLd~~tVGvIv~verd~ 562 (1065)
|++. ++.|++|+++++.++|.+--.+.+++|- |=.+++ -|++.
T Consensus 292 ~~i~-----ennGVfv~~~~nv~~VAtkd~~~s~k~d------------------------l~kmnp---~v~~~----- 334 (607)
T COG5164 292 VSIK-----ENNGVFVKIEGNVCIVATKDFTESLKVD------------------------LDKMNP---PVTVN----- 334 (607)
T ss_pred eeee-----ccCceEEEecCceeEEEeccchhhhccc------------------------HhhcCc---hhhcC-----
Confidence 8775 5899999999999998764333332221 111111 11110
Q ss_pred EEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCCceeeEEEEECCE--EEEEecce
Q 001506 563 FQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRGI--LFIHDRHH 636 (1065)
Q Consensus 563 ~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~~--lFl~~~~~ 636 (1065)
-|+ +. ...+++++ -|....+|-+|+|--|+|||.-|.||.+-++. +-||++..
T Consensus 335 ----~~~---p~-----~~~l~r~i---------~gRd~aigktVrIr~g~yKG~lGVVKdv~~~~arVeLhs~nK 389 (607)
T COG5164 335 ----LQN---PK-----TNELERKI---------VGRDPAIGKTVRIRCGEYKGHLGVVKDVDRNIARVELHSNNK 389 (607)
T ss_pred ----CCC---Cc-----chhhhccc---------cccccccCceEEEeecccccccceeeeccCceEEEEEecCCc
Confidence 011 21 12333443 34567789999999999999999999999995 78887664
No 7
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=99.74 E-value=1.8e-17 Score=166.80 Aligned_cols=125 Identities=26% Similarity=0.430 Sum_probs=110.5
Q ss_pred EEEEccCchHHHHHHHHHHHHHhhCCCcceEEEEeeCCCccEEEEEecchHHHHHHHhcCcccceeeeeeeChhhhhhcc
Q 001506 185 WMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIREMTDVL 264 (1065)
Q Consensus 185 w~Vkck~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~~~lkGYIYIEA~~~~~V~~ai~Gl~~v~~~~~~lVpi~Em~~vL 264 (1065)
|+|+|++|+|+.++..|.+|+-. ..+.|+++|.+..++||||||+....++|.+|++++|+.+.-...||.+||..++
T Consensus 1 Yvv~t~~g~E~~v~~~L~~~~~~--~~~~~~~~~vp~~fpGYvFV~~~~~~~~~~~i~~~~gv~~~v~~~i~~~ei~~l~ 78 (145)
T TIGR00405 1 FAVKTSVGQEKNVARLMARKARK--SGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVRGVVEGEIDFEEIERFL 78 (145)
T ss_pred CeEEeeCChHHHHHHHHHHHHhh--CCCcEEEEEccCCCCcEEEEEEECcHHHHHHHhCCCCEEeecCCCCCHHHHHHHh
Confidence 89999999999999888888644 4577999999999999999999999999999999999997544679999999999
Q ss_pred ccccccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEEEeecc
Q 001506 265 AVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLIPRI 311 (1065)
Q Consensus 265 ~v~~~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~VkLvPRi 311 (1065)
........+++|+||||++|||+|..|+|..++..+..|+|.|+-+-
T Consensus 79 ~~~~~~~~~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~~~ 125 (145)
T TIGR00405 79 TPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEAA 125 (145)
T ss_pred cccccccccCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEEcC
Confidence 75332345899999999999999999999999998999999998754
No 8
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=99.59 E-value=4.8e-15 Score=154.03 Aligned_cols=127 Identities=19% Similarity=0.288 Sum_probs=109.1
Q ss_pred CCcEEEEEccCchHHHHHHHHHHHHHhhCCC-----------------cceEEEEeeCCCccEEEEEecchHHHHHHHhc
Q 001506 181 DPKLWMVKCAIGREREAAVCLMQKCIDKGSE-----------------LQIRSVIALDHLKNYIYIEADKEAHVKEACKG 243 (1065)
Q Consensus 181 DP~lw~Vkck~G~Er~vv~~Lm~K~~~~~~~-----------------l~I~Svf~~~~lkGYIYIEA~~~~~V~~ai~G 243 (1065)
.++||+|+|.+|+|+.|+..|++|+...+.+ -+.+.+..++.++|||||||.....+|..|++
T Consensus 2 ~~~Wyvv~~~sg~E~~V~~~l~~~~~~~~~~~~~~~v~vp~E~v~e~~~~~~~~~e~~~fpGYVlVem~~~~~~w~~Vr~ 81 (178)
T COG0250 2 MKRWYVVQTYSGQEKKVKENLERKAELLGMEDLIFEVLVPTEEVVEVKGKRKVIVERKLFPGYVLVEMDMTDEAWHLVRN 81 (178)
T ss_pred CceEEEEEeeccHHHHHHHHHHHHHHhcCCccceeeEEeceEEEEEecCceEEEEecccCCcEEEEEEEcCCceEEEEec
Confidence 5899999999999999999999998775433 13555578899999999999999999999999
Q ss_pred Ccccce------eeeeeeChhhhhhcccc-------ccccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEEE
Q 001506 244 LRNIYS------QKVMLVPIREMTDVLAV-------ESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 307 (1065)
Q Consensus 244 l~~v~~------~~~~lVpi~Em~~vL~v-------~~~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~VkL 307 (1065)
++++.+ .++.+++.+|+.+.|.. .+....+++|+.|||..|+|+|..|+|.+||..+.+++|.|
T Consensus 82 tpgV~GfVg~~~~~P~pi~~~ei~~~l~~~~~~~~~~~~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v 158 (178)
T COG0250 82 TPGVTGFVGSGGAKPVPLSEEEIEHILGFLEEEVAPKKPKVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEV 158 (178)
T ss_pred CCCcEEEeccCCCCCcccCHHHHHHHHhhccccccCCcccccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEE
Confidence 999984 36788899999994433 22356899999999999999999999999999998888876
No 9
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=99.34 E-value=2.1e-11 Score=148.80 Aligned_cols=36 Identities=33% Similarity=0.707 Sum_probs=15.5
Q ss_pred CCcCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCC
Q 001506 903 TYVNAPSPYLPSTPGGQPMTPN---SASYLPGTPGGQPM 938 (1065)
Q Consensus 903 ~y~~~pspy~p~tp~~~p~tP~---~~~y~P~TPg~~p~ 938 (1065)
.|+|++++|+|.+|.|+|.+|+ .++|+|.+|-.+|.
T Consensus 1556 sysptsp~ysptspsysptspsys~~~~ysp~sp~yspt 1594 (1605)
T KOG0260|consen 1556 SYSPTSPSYSPTSPSYSPTSPSYSTSPSYSPTSPSYSPT 1594 (1605)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCC
Confidence 3444444444444444444442 23344444443333
No 10
>PF11942 Spt5_N: Spt5 transcription elongation factor, acidic N-terminal; InterPro: IPR022581 This is the very acidic N-terminal domain of the early transcription elongation factor Spt5 []. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4 [], nor is it essential for RNA polymerase II binding [].
Probab=99.33 E-value=5e-13 Score=126.27 Aligned_cols=88 Identities=45% Similarity=0.604 Sum_probs=60.4
Q ss_pred CcccccccCCchhhhcccc-ccccccCCCCCCCC--CCCCCccCcCCCCCC-CcchhhHHHHHHHHH--HHhcCCC---C
Q 001506 90 FFDLEAQVDSDEEEDEEEG-EDDFIVDGGAELPD--EDGGRGIHRRPLLPR-EDEQEDVEALERRIQ--ARYARSS---H 160 (1065)
Q Consensus 90 FlD~EAeVdddeEeeeee~-~~~fi~~~~~~~~~--~~~~~~~~r~~~~~~-~~~~~d~ee~~~~l~--eRY~~~~---~ 160 (1065)
|||+||+||||+||||+++ +.++|......+.+ .....++||++.+++ ....+++++||++|+ +||++++ .
T Consensus 1 Fid~EAeVDddeEEeee~ed~~~~~~~~~~~~~~~~~~~~d~~~r~~d~~r~~~~~~dae~lae~~k~~~RY~~~~~~~~ 80 (97)
T PF11942_consen 1 FIDDEAEVDDDEEEEEEDEDEADEIGEEDDEIEDAEAEEDDRRHRRLDRRREMEEEEDAEELAEYLKLSERYARSSESRY 80 (97)
T ss_pred CchhhcccCCcccccccccccchhhhcccccccccccchhHhhhhhhhhhHHHHhccCHHHHHHHHHHHHHhcccccccc
Confidence 9999999999988776432 23344222211211 123345777776554 466889999999999 9999864 2
Q ss_pred CCcccchhhhhhhhcCC
Q 001506 161 TEYDEETTDVEQQALLP 177 (1065)
Q Consensus 161 ~~~~~~~~~v~q~~LlP 177 (1065)
..+.+.++.|+||+|||
T Consensus 81 ~~~~~~~~~v~q~~LLP 97 (97)
T PF11942_consen 81 DGDDEDSDEVPQQLLLP 97 (97)
T ss_pred cccccccccchHhccCc
Confidence 34555788999999999
No 11
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=99.31 E-value=1.8e-11 Score=127.47 Aligned_cols=128 Identities=16% Similarity=0.201 Sum_probs=99.8
Q ss_pred CCCcEEEEEccCchHHHHHHHHHHHHHhhCCCcceEEEEee-----------------CCCccEEEEEecchHHHHHHHh
Q 001506 180 RDPKLWMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIAL-----------------DHLKNYIYIEADKEAHVKEACK 242 (1065)
Q Consensus 180 ~DP~lw~Vkck~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~-----------------~~lkGYIYIEA~~~~~V~~ai~ 242 (1065)
...+||+++|++|+|+.++..|.+++...+-.-.++.+|.| +.++|||||++......+..|+
T Consensus 4 ~~~~WYvl~~~~~~E~~v~~~L~~~~~~~~i~~~~~~~~~P~~~~~~~~~g~~~~~~~plfpgYvFv~~~~~~~~~~~i~ 83 (181)
T PRK05609 4 MKKRWYVVQTYSGYEKKVKENLENRIETLGMEDLIGEVLVPTEEVVEVKNGKKKKVERKFFPGYVLVKMVMTDESWHLVR 83 (181)
T ss_pred CCCeEEEEEeECCcHHHHHHHHHHHHHHCCCcceeeEEEeeeEEEEEccCCEEEEEEEecCCcEEEEEEEeCccHhHHhh
Confidence 34689999999999999999999886443221113444443 4599999999998778899999
Q ss_pred cCcccce------eeeeeeChhhhhhccccc-------cccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEEE
Q 001506 243 GLRNIYS------QKVMLVPIREMTDVLAVE-------SKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 307 (1065)
Q Consensus 243 Gl~~v~~------~~~~lVpi~Em~~vL~v~-------~~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~VkL 307 (1065)
.++++.+ ..+.+||.+||..++... .....+++|+.|||..|||+|-.|.|..++..+.+|+|.|
T Consensus 84 ~~~gv~~~v~~~g~~p~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l 161 (181)
T PRK05609 84 NTPGVTGFVGSTGSKPTPLSEKEVEKILKQLQEGVEKPKPKVDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLV 161 (181)
T ss_pred cCCCeEEEecCCCCCcccCCHHHHHHHHHHhhcccccCccccCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEE
Confidence 9998753 356789999999987621 1134688999999999999999999999997777777653
No 12
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=99.22 E-value=9.7e-11 Score=121.17 Aligned_cols=124 Identities=19% Similarity=0.197 Sum_probs=96.5
Q ss_pred EEEEEccCchHHHHHHHHHHHHHhhCCCcceEEEEe-----------------eCCCccEEEEEecchHHHHHHHhcCcc
Q 001506 184 LWMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIA-----------------LDHLKNYIYIEADKEAHVKEACKGLRN 246 (1065)
Q Consensus 184 lw~Vkck~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~-----------------~~~lkGYIYIEA~~~~~V~~ai~Gl~~ 246 (1065)
||+|+|++|+|+.++..|.+++...+-+-.++.+|. .+.++|||||++......+..|+.+++
T Consensus 1 WYvl~~~~~~E~~v~~~L~~~~~~~g~~~~~~~~~~P~~~~~~~~~g~~~~~~~plfPgYvFv~~~~~~~~~~~i~~~~g 80 (172)
T TIGR00922 1 WYVVQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPG 80 (172)
T ss_pred CEEEEeECChHHHHHHHHHHHHHHCCCccceeEEEcceEEEEEEcCCEEEEEEEecCCcEEEEEEEeCccHhHHhhcCCC
Confidence 899999999999999999888633321111233333 356899999999877788999999888
Q ss_pred cce-----eeeeeeCh-hhhhhcccccc-------ccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEEE
Q 001506 247 IYS-----QKVMLVPI-REMTDVLAVES-------KAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 307 (1065)
Q Consensus 247 v~~-----~~~~lVpi-~Em~~vL~v~~-------~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~VkL 307 (1065)
|.+ ..+..||. +||..++.... ....+++|+.|||..|||+|..|.|..++..+.+|+|.|
T Consensus 81 v~~~v~~~~~p~~I~~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~v 154 (172)
T TIGR00922 81 VTGFVGSGGKPKALSEDEEVKNILNALEEGKDKPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSV 154 (172)
T ss_pred ccEEcCcCCeeeccCCHHHHHHHHHHhhcccccCccccCCCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEE
Confidence 763 36888999 99999875321 123478999999999999999999999997777777653
No 13
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=99.22 E-value=6.9e-11 Score=128.13 Aligned_cols=125 Identities=18% Similarity=0.238 Sum_probs=98.9
Q ss_pred cEEEEEccCchHHHHHHHHHHHHHhhCCCcceEEE---------------------------------------------
Q 001506 183 KLWMVKCAIGREREAAVCLMQKCIDKGSELQIRSV--------------------------------------------- 217 (1065)
Q Consensus 183 ~lw~Vkck~G~Er~vv~~Lm~K~~~~~~~l~I~Sv--------------------------------------------- 217 (1065)
+||.|+|.+|+|..|...|.+|+.+.+..-.|.-|
T Consensus 1 kWYvv~t~sG~E~kV~~~l~~kv~~~~~ed~i~~v~Vp~e~~ve~~v~e~k~~~~p~~~k~~~~~~w~~~~~gk~~k~k~ 80 (258)
T TIGR01956 1 QWYIATTINGNEDEVIENIKAKVRALGLENYISDFKILKEREIEEKVFEPKNGQAPRSMKNTATTKWETLDETKYKKTKI 80 (258)
T ss_pred CeEEEEeeCCcHHHHHHHHHHHHHhCCCccEEEEEEEeeeEEEEEEEEEeecCcccccccccccccceeccCCccccEEE
Confidence 59999999999999999999998876533223222
Q ss_pred EeeCCCccEEEEEecchHHHHHHHhcCcccce---e-----eeeeeChhhh-hhcccccc--------------------
Q 001506 218 IALDHLKNYIYIEADKEAHVKEACKGLRNIYS---Q-----KVMLVPIREM-TDVLAVES-------------------- 268 (1065)
Q Consensus 218 f~~~~lkGYIYIEA~~~~~V~~ai~Gl~~v~~---~-----~~~lVpi~Em-~~vL~v~~-------------------- 268 (1065)
..+..++|||||+|.+.+++|.+|+++++|.| + +|.+++.+|. .++|....
T Consensus 81 ~er~~fPGYI~IkM~m~d~~W~~VRnt~gVTGFvGssg~g~kPiPls~~e~~~~ml~~~~~~~~~~~~~~~~~~~~~~~~ 160 (258)
T TIGR01956 81 SEKNKYNGYIYIKMIMTEDAWFLIRNTENVTGLVGSSGKGAKPIPISADADKLKMLKGISENTKKRVLVTNTAIVEMEEN 160 (258)
T ss_pred EEeeecCcEEEEEEEecccHhhheecCCCCCeecCCCCCCCCCcCCCHHHHHHHHhhhhhhccccccccccccccccccc
Confidence 23456899999999999999999999999974 2 5777777777 56654211
Q ss_pred -----------------------------------------ccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEEE
Q 001506 269 -----------------------------------------KAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 307 (1065)
Q Consensus 269 -----------------------------------------~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~VkL 307 (1065)
....+.+|+.|||..|+|+|..|.|.+++..+.+|+|.|
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV 240 (258)
T TIGR01956 161 KFDEKCQYILKHKQVKPEAIAQVSESGEIIDEIVEEFQLVDNLSKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEV 240 (258)
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccCCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEE
Confidence 123578999999999999999999999997777777653
No 14
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=99.21 E-value=1.9e-10 Score=140.59 Aligned_cols=8 Identities=25% Similarity=0.480 Sum_probs=3.2
Q ss_pred cchhhhcc
Q 001506 580 LREIKCKL 587 (1065)
Q Consensus 580 ~~~I~~k~ 587 (1065)
..+|.-|+
T Consensus 1196 m~~ia~~i 1203 (1605)
T KOG0260|consen 1196 MEQIAEKI 1203 (1605)
T ss_pred HHHHHHHH
Confidence 34444443
No 15
>PF12815 CTD: Spt5 C-terminal nonapeptide repeat binding Spt4; PDB: 2E70_A.
Probab=99.03 E-value=3.7e-11 Score=117.85 Aligned_cols=37 Identities=49% Similarity=0.644 Sum_probs=0.0
Q ss_pred CCCCCCC---CCCCCCC---CCCCCCCC-CCCCCC-CCCCCCCCC
Q 001506 797 GSETPMH---PSRTPLH---PYMTPMRD-AGATPI-HDGMRTPMR 833 (1065)
Q Consensus 797 G~~TP~~---g~rTP~~---~~~TP~~~-g~~TP~-~~Gs~TP~~ 833 (1065)
|+|||+| |+|||++ +++||++. |++||+ ++|+|||+.
T Consensus 12 g~rTPa~~~~gsrTP~~~~~g~rTPa~~~gsrTP~~~~gsrTPa~ 56 (123)
T PF12815_consen 12 GSRTPAWGNDGSRTPAPGADGSRTPAWGSGSRTPAFHDGSRTPAY 56 (123)
T ss_dssp ---------------------------------------------
T ss_pred CCCCcccccCCCCCcCCcCCCCcCcccccCCcCcccCCCCCCCcc
Confidence 4444444 4444443 34444443 456665 566666643
No 16
>PF12815 CTD: Spt5 C-terminal nonapeptide repeat binding Spt4; PDB: 2E70_A.
Probab=98.85 E-value=4.5e-10 Score=110.32 Aligned_cols=52 Identities=38% Similarity=0.503 Sum_probs=0.0
Q ss_pred cceeeec----cCCCCCC-CCCCCCCCC---CCCCCCC--CCCCCC-CCCCCCCCCCC----CCCCC
Q 001506 781 TVHVIMF----CSDTPRY-GMGSETPMH---PSRTPLH--PYMTPM-RDAGATPIHDG----MRTPM 832 (1065)
Q Consensus 781 ~~~~p~~----~~~tp~y-~~G~~TP~~---g~rTP~~--~~~TP~-~~g~~TP~~~G----s~TP~ 832 (1065)
++||||| |++||+| ..|+|||++ |+|||.+ +++||+ ++|++||+|.+ ++||+
T Consensus 1 g~rTPa~~~~~g~rTPa~~~~gsrTP~~~~~g~rTPa~~~gsrTP~~~~gsrTPa~~~~~~~~~TPa 67 (123)
T PF12815_consen 1 GSRTPAYGSASGSRTPAWGNDGSRTPAPGADGSRTPAWGSGSRTPAFHDGSRTPAYGGSSSPSRTPA 67 (123)
T ss_dssp -------------------------------------------------------------------
T ss_pred CCCCCcCcCCCCCCCcccccCCCCCcCCcCCCCcCcccccCCcCcccCCCCCCCccCCCCCCCCCcc
Confidence 3578886 4688888 568888887 6889887 778998 88899999875 47774
No 17
>smart00738 NGN In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. In Spt5p, this domain may confer affinity for Spt4p.Spt4p
Probab=98.84 E-value=5.1e-09 Score=99.44 Aligned_cols=83 Identities=29% Similarity=0.389 Sum_probs=70.0
Q ss_pred cEEEEEccCchHHHHHHHHHHHHHhhCCCcceEEEEee-----------------CCCccEEEEEecchHHHHHHHhcCc
Q 001506 183 KLWMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIAL-----------------DHLKNYIYIEADKEAHVKEACKGLR 245 (1065)
Q Consensus 183 ~lw~Vkck~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~-----------------~~lkGYIYIEA~~~~~V~~ai~Gl~ 245 (1065)
+||+|+|++|+|+.++..|.+++.+.+.+..+.++|+| ..++|||||++....+++.+|++++
T Consensus 1 ~Wyvv~~~~g~E~~v~~~L~~~~~~~~~~~~~~~~~~P~~~~~~~~~g~~~~~~~plfpGYvFv~~~~~~~~~~~i~~~~ 80 (106)
T smart00738 1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERPLFPGYIFVEADLEDEVWTAIRGTP 80 (106)
T ss_pred CEEEEEEeCCcHHHHHHHHHHHHHhcCCccccCEEEeeEEEEEEecCCEEEEEEEecCCCEEEEEEEeCCcHHHHHhcCC
Confidence 59999999999999999999998665444446677776 3356999999999999999999999
Q ss_pred ccce-----eeeeeeChhhhhhccc
Q 001506 246 NIYS-----QKVMLVPIREMTDVLA 265 (1065)
Q Consensus 246 ~v~~-----~~~~lVpi~Em~~vL~ 265 (1065)
++++ .++.+||.+||..+++
T Consensus 81 ~v~~~v~~~~~p~~v~~~e~~~l~~ 105 (106)
T smart00738 81 GVRGFVGGGGKPTPVPDDEIEKILK 105 (106)
T ss_pred CccEECCCCCeeeECCHHHHHHHhh
Confidence 9874 4688999999999885
No 18
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=98.83 E-value=7.2e-09 Score=106.43 Aligned_cols=123 Identities=15% Similarity=0.221 Sum_probs=90.1
Q ss_pred cEEEEEccCchHHHHHHHHHHHHHhhCCCc--------ceEEEEeeCCCccEEEEEecchHHHHHHHhcCcccc-----e
Q 001506 183 KLWMVKCAIGREREAAVCLMQKCIDKGSEL--------QIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIY-----S 249 (1065)
Q Consensus 183 ~lw~Vkck~G~Er~vv~~Lm~K~~~~~~~l--------~I~Svf~~~~lkGYIYIEA~~~~~V~~ai~Gl~~v~-----~ 249 (1065)
+||+++|++|+|+.++..|.++-+..=.|+ +-......+.++|||||.+..+...+..|+.++++. +
T Consensus 3 ~WYvl~t~~~~E~~v~~~L~~~gi~~~~P~~~~~~~~~gk~~~v~~plFPgYlFv~~~~~~~~~~~i~~~~gv~~~v~~g 82 (162)
T PRK09014 3 SWYLLYCKRGQLQRAQEHLERQGVECLYPMITLEKIVRGKRTEVSEPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVRFG 82 (162)
T ss_pred eEEEEEecCchHHHHHHHHHHCCCEEECCCEEEEEEECCeEEEEEEEcCCCeEEEEeccccCceEEEEecCCcceEeccC
Confidence 799999999999999988876532210111 111223357899999999987666666677777764 2
Q ss_pred eeeeeeChhhhhhcccccc----ccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEE
Q 001506 250 QKVMLVPIREMTDVLAVES----KAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 306 (1065)
Q Consensus 250 ~~~~lVpi~Em~~vL~v~~----~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~Vk 306 (1065)
..+.+||-+||..++.... ....+++|+.|||+.|||+|-.|.|..++ .+.++.|.
T Consensus 83 ~~p~~I~~~ei~~l~~~~~~~~~~~~~~~~G~~V~I~~Gp~~g~eg~v~~~~-~~~r~~v~ 142 (162)
T PRK09014 83 AQPAIVPSDVIYQLSVYKPEKIVDPETPKPGDKVIITEGAFEGLQAIYTEPD-GEARSILL 142 (162)
T ss_pred CCccccCHHHHHHHHhhcccccccccCCCCCCEEEEecCCCCCcEEEEEEeC-CCeEEEEe
Confidence 4688899889998875322 12347899999999999999999999998 56666554
No 19
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=98.76 E-value=1.6e-08 Score=103.28 Aligned_cols=122 Identities=18% Similarity=0.241 Sum_probs=88.1
Q ss_pred EEEEEccCchHHHHHHHHHHHHHhhCCCc--------ceEEEEeeCCCccEEEEEecchHHHHHHHhcCcccc-----ee
Q 001506 184 LWMVKCAIGREREAAVCLMQKCIDKGSEL--------QIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIY-----SQ 250 (1065)
Q Consensus 184 lw~Vkck~G~Er~vv~~Lm~K~~~~~~~l--------~I~Svf~~~~lkGYIYIEA~~~~~V~~ai~Gl~~v~-----~~ 250 (1065)
||+|+|++|+|+.++..|.++-+..=.|+ .-......+.++|||||......+.+..|..+.++. +.
T Consensus 1 WYvl~~~~~~E~~v~~~L~~~gi~~~~P~~~~~~~~~g~~~~~~~plfpgYvFv~~~~~~~~~~~i~~~~gv~~~v~~~~ 80 (159)
T TIGR01955 1 WYLLYCKPRQEQRAQEHLERQAVECYLPMITVEKIVRGKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTRGVSRFVRFGG 80 (159)
T ss_pred CEEEEEcCchHHHHHHHHHHCCCEEEccCEEEEEEECCcEEEEEEecCCCeEEEEEccCCCceEEEecCCCcCEEECCCC
Confidence 89999999999999988876532210111 112224457899999999987666666666666655 24
Q ss_pred eeeeeChhhhhhcccccc------ccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEE
Q 001506 251 KVMLVPIREMTDVLAVES------KAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 306 (1065)
Q Consensus 251 ~~~lVpi~Em~~vL~v~~------~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~Vk 306 (1065)
.+.+||-+||..++.... ....+++|+.|||+.|||+|-.|.|..++. +.+|.|.
T Consensus 81 ~p~~I~~~~i~~l~~~~~~~~~~~~~~~~~~G~~V~V~~GPf~g~~g~v~~~~~-~~r~~v~ 141 (159)
T TIGR01955 81 HPAPVPDDLIHQLRQYEPKDSVPPATTLPYKGDKVRITDGAFAGFEAIFLEPDG-EKRSMLL 141 (159)
T ss_pred CcccCCHHHHHHHHhccccccCCccccCCCCCCEEEEeccCCCCcEEEEEEECC-CceEEEE
Confidence 688899888887764321 123488999999999999999999999984 4566654
No 20
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=97.92 E-value=3.9e-06 Score=101.64 Aligned_cols=26 Identities=42% Similarity=0.677 Sum_probs=13.9
Q ss_pred CCCCCCCCcccccccchhhhhccCcc
Q 001506 2 PRRRDDDDDEMDAEEDEYDEQVMDDE 27 (1065)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~e 27 (1065)
.|+++-|||+|+|||+|+|+++||||
T Consensus 1398 GR~r~~~dd~DeeeD~e~Ed~dEddd 1423 (1516)
T KOG1832|consen 1398 GRRRPTDDDSDEEEDDETEDEDEDDD 1423 (1516)
T ss_pred cccCCCccccCccccchhhccccccc
Confidence 47777555555555555444433333
No 21
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=97.77 E-value=7.6e-07 Score=96.11 Aligned_cols=55 Identities=27% Similarity=0.452 Sum_probs=49.1
Q ss_pred cCCCc-ccEEEEEEeCCCCeEEEEeccCCCCceEEecCCCeeecCCCCCCcEEEEcCCCCCceE
Q 001506 969 RSGEE-SVVGVIREVLPDGSCRVVLGSSGNGDTITALPNEIEIVPPRKTDKIKIMGGPHRGATG 1031 (1065)
Q Consensus 969 ~~g~~-~~~GvI~~V~~~g~~~V~l~~~~~g~~v~v~~~~LE~V~P~kgd~VkVi~G~~rG~tG 1031 (1065)
.+|.+ +++|||+.|+++++..|+ +++ |.+|++||.|||+|||+ +||||+|||..+
T Consensus 254 ~l~~k~K~K~vv~~vid~y~~~~K-ld~--g~~lk~dq~~lEtvip~-----~~vng~yRg~~~ 309 (309)
T KOG2837|consen 254 SLGEKYKQKGVVKKVIDDYTGQIK-LDS--GTVLKVDQEHLETVIPQ-----MIVNGAYRGSEA 309 (309)
T ss_pred hhhHHhccccHHHHHHHhhhhhee-ccC--CceecccHHHHHHHhHH-----HHhhhhhccCCC
Confidence 46766 999999999999999999 455 79999999999999999 999999999753
No 22
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=97.39 E-value=0.00022 Score=54.28 Aligned_cols=32 Identities=34% Similarity=0.612 Sum_probs=30.0
Q ss_pred CCcEEEeecCCCCCCeeEEEEeeCCCCEEEEE
Q 001506 275 RDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 306 (1065)
Q Consensus 275 ~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~Vk 306 (1065)
+|++|+|++|+|+|..|+|.+++.++.+|+|+
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~ve 32 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTVE 32 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEES
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEEC
Confidence 69999999999999999999999999998873
No 23
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=97.10 E-value=0.00016 Score=91.58 Aligned_cols=12 Identities=25% Similarity=0.266 Sum_probs=9.9
Q ss_pred HHHHHHHHHHhc
Q 001506 145 EALERRIQARYA 156 (1065)
Q Consensus 145 ee~~~~l~eRY~ 156 (1065)
++||+.|++|-.
T Consensus 739 ~~La~~Fk~r~~ 750 (784)
T PF04931_consen 739 EQLAAIFKERKE 750 (784)
T ss_pred HHHHHHHHHHHh
Confidence 479999999965
No 24
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=96.80 E-value=0.00062 Score=78.88 Aligned_cols=11 Identities=27% Similarity=0.456 Sum_probs=5.4
Q ss_pred HHHHHHHHHHH
Q 001506 194 EREAAVCLMQK 204 (1065)
Q Consensus 194 Er~vv~~Lm~K 204 (1065)
|-.-+.||..|
T Consensus 207 E~AY~Scle~R 217 (458)
T PF10446_consen 207 EAAYISCLEAR 217 (458)
T ss_pred HHHHHHHHHHH
Confidence 44444555544
No 25
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=96.76 E-value=0.0013 Score=50.15 Aligned_cols=31 Identities=48% Similarity=0.830 Sum_probs=27.7
Q ss_pred cCcEEEEeeCCCCCceeEEEeecCCeEEEEe
Q 001506 708 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVEL 738 (1065)
Q Consensus 708 iGktV~I~~GpyKG~~G~Vkd~t~~~~rVEL 738 (1065)
.|.+|+|+.|||||..|.|.++.....+|.+
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~v 31 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTV 31 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEE
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEE
Confidence 3789999999999999999999988877765
No 26
>KOG4315 consensus G-patch nucleic acid binding protein [General function prediction only]
Probab=96.67 E-value=0.0006 Score=78.16 Aligned_cols=103 Identities=21% Similarity=0.368 Sum_probs=83.2
Q ss_pred CCccCcEEE--E----cCCCc-ccEEEEEEeCCCCeEEEEeccCCCCceE-EecCCCeeecCCC-CCCcEEEEcCCCCCc
Q 001506 959 PWFMPDILV--R----RSGEE-SVVGVIREVLPDGSCRVVLGSSGNGDTI-TALPNEIEIVPPR-KTDKIKIMGGPHRGA 1029 (1065)
Q Consensus 959 ~W~~~~I~V--~----~~g~~-~~~GvI~~V~~~g~~~V~l~~~~~g~~v-~v~~~~LE~V~P~-kgd~VkVi~G~~rG~ 1029 (1065)
.|+..+|.| + +.|.. .++.+|..|.+--+|.+.+.+.. +.+- .|+|+-|||++|. -|++|.|+.|.+.|.
T Consensus 332 ~wlR~dl~VR~is~d~Kgg~ly~~K~~i~dv~gp~scd~r~Dedq-~~~qg~irq~~lET~~pr~~Ge~vmvv~gkhkg~ 410 (455)
T KOG4315|consen 332 SWLRSDLKVRFISKDVKGGRLYEKKVRIVDVVGPTSCDIRMDEDQ-ELVQGNIRQELLETALPRRGGEKVMVVSGKHKGV 410 (455)
T ss_pred hhhhcceeEEeeccccccchhhhcccceecccCCCccceeccccc-cccccchHHHHHhhhcccccCceeEEEecccccc
Confidence 599999999 3 33433 88999999966568999987653 2233 3899999999996 677799999999999
Q ss_pred eEEEEEEeCC--CcEEEecCCCceEEEeccchhcc
Q 001506 1030 TGKLIGVDGT--DGIVKVDVSLDVKILDMAILAKL 1062 (1065)
Q Consensus 1030 tG~LisiD~~--dgiVk~d~~~d~kil~~~~L~Kl 1062 (1065)
.|.|++=|-. .++|++-.+.++..+-+..+|-.
T Consensus 411 ~g~llskd~~Ke~~~v~~~a~ndvv~~~~D~v~ey 445 (455)
T KOG4315|consen 411 YGSLLSKDLDKETGVVRLVATNDVVTVYLDQVCEY 445 (455)
T ss_pred hhhhhhhhhhhhhcceecccccchhhhhHHHHHHh
Confidence 9999988775 89999877778877788888754
No 27
>PF02357 NusG: Transcription termination factor nusG; InterPro: IPR006645 This sequence is identified by the NGN domain and is represented by the bacterial antitermination protein NusG. This protein influences transcription termination and anti-termination and acts as a component of the transcription complex. In addition to this, it interacts with the termination factor Rho and RNA polymerase [, ].; GO: 0032968 positive regulation of transcription elongation from RNA polymerase II promoter; PDB: 1NZ8_A 2OUG_C 1NPP_B 1M1G_D 1NPR_A 1M1H_A 2XHA_A 2XHC_A 2K06_A.
Probab=96.66 E-value=0.0057 Score=56.90 Aligned_cols=65 Identities=12% Similarity=0.302 Sum_probs=46.2
Q ss_pred cEEEEEccCchHHHHHHHHHHHHHh-h-------CC---Cc-ceEEEEeeCCCccEEEEEecchHHHHHHHhcCcccce
Q 001506 183 KLWMVKCAIGREREAAVCLMQKCID-K-------GS---EL-QIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYS 249 (1065)
Q Consensus 183 ~lw~Vkck~G~Er~vv~~Lm~K~~~-~-------~~---~l-~I~Svf~~~~lkGYIYIEA~~~~~V~~ai~Gl~~v~~ 249 (1065)
+||+|+|++|+|+.++..|.+.-+. . .. .= .+.. .....++|||||.+...+.++.+ +.+.++++
T Consensus 2 ~WYvl~~~~~~E~~v~~~L~~~~i~~~~P~~~~~~~~~~~g~~~~~-~~~plfpgYvFv~~~~~~~~~~i-~~~~gv~~ 78 (92)
T PF02357_consen 2 RWYVLRTKPGKEQKVAERLERQGIEAFLPMREVIRRRKPRGKKVKR-VERPLFPGYVFVRMDMEDELWKI-RSTPGVSG 78 (92)
T ss_dssp EEEEEEESTTTHHHHHHHHCHHHHHHE-SEEEEEECSSSSSCSEEE-EEEESSTTEEEEEE-TTHHHHHH-HHSTTEEE
T ss_pred EEEEEEEECChHHHHHHHHHHcCCceeccEEEEEEEEecCCceEEE-EEEEecCcEEEEEEEcchhhhhh-hcCCCeEE
Confidence 6999999999999999998555343 1 01 11 3444 56678999999999998555444 87777774
No 28
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=95.99 E-value=0.009 Score=54.57 Aligned_cols=33 Identities=27% Similarity=0.460 Sum_probs=28.9
Q ss_pred eecCCCEEEEEcCCCCCceeeEEEEECC--EEEEE
Q 001506 600 TVAVKDVVRIVEGPCKGKQGPVEHIYRG--ILFIH 632 (1065)
Q Consensus 600 ~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~--~lFl~ 632 (1065)
.|+.||.|.|+.|+++|++|+|+.|++. .+++.
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 40 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVE 40 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 5999999999999999999999999864 45553
No 29
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=95.66 E-value=0.016 Score=42.04 Aligned_cols=28 Identities=46% Similarity=0.564 Sum_probs=25.6
Q ss_pred CcCCCCEEEEecccccCceeEEEEEcCC
Q 001506 424 HFMKGDAVIVIKGDLKNLKGWVEKVDEE 451 (1065)
Q Consensus 424 ~F~~GD~V~V~~Gel~gl~G~V~~V~~d 451 (1065)
.|++||.|+|+.|.++|..|.|++|+.+
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~~ 28 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcCC
Confidence 4789999999999999999999999753
No 30
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=95.59 E-value=0.014 Score=42.29 Aligned_cols=27 Identities=41% Similarity=0.712 Sum_probs=25.0
Q ss_pred eccCCCcEEEeccccCCceeEEEEEeC
Q 001506 476 YFEPGNHVKVVSGTQAGATGMVLKVEQ 502 (1065)
Q Consensus 476 ~F~~GDhVkVi~G~~~getGlVVkVe~ 502 (1065)
.|++||.|+|++|.|+|.+|.|++++.
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 378999999999999999999999975
No 31
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=94.82 E-value=0.042 Score=55.74 Aligned_cols=58 Identities=24% Similarity=0.341 Sum_probs=44.6
Q ss_pred CcCCCCEEEEecccccCceeEEEEEcCCe--EEEeecCCCCCcceeeccccceeeccCCC
Q 001506 424 HFMKGDAVIVIKGDLKNLKGWVEKVDEEN--VHIRPEMKGLPKTLAVNSKELCKYFEPGN 481 (1065)
Q Consensus 424 ~F~~GD~V~V~~Gel~gl~G~V~~V~~d~--V~i~~~~~~l~~~l~v~~~~LrK~F~~GD 481 (1065)
.|++||.|+|++|=++|+.|+|+.+++.. |+|.-......-+++++.++|+|.=+.||
T Consensus 86 ~~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~~~~~~~v~v~~~~l~~~~~~~~ 145 (145)
T TIGR00405 86 SIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRIIQKEAD 145 (145)
T ss_pred ccCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEEcCccceEEEeeeEEEEecccCC
Confidence 49999999999999999999999998663 44433333333459999999988665554
No 32
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=94.82 E-value=0.038 Score=51.37 Aligned_cols=32 Identities=34% Similarity=0.560 Sum_probs=28.3
Q ss_pred eecCCCEEEEEcCCCCCceeeEEEEECC--EEEE
Q 001506 600 TVAVKDVVRIVEGPCKGKQGPVEHIYRG--ILFI 631 (1065)
Q Consensus 600 ~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~--~lFl 631 (1065)
.|+.||.|.|+.|+++|++|+|++|++. .+++
T Consensus 8 ~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~V 41 (83)
T CHL00141 8 HVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIV 41 (83)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEE
Confidence 5899999999999999999999999975 3444
No 33
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=94.51 E-value=0.054 Score=52.49 Aligned_cols=33 Identities=24% Similarity=0.422 Sum_probs=28.8
Q ss_pred eecCCCEEEEEcCCCCCceeeEEEEECC--EEEEE
Q 001506 600 TVAVKDVVRIVEGPCKGKQGPVEHIYRG--ILFIH 632 (1065)
Q Consensus 600 ~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~--~lFl~ 632 (1065)
.|+.||+|.|+.|+++|++|+|+.|++. .+++.
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 38 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVE 38 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 5899999999999999999999999954 45553
No 34
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=93.88 E-value=0.097 Score=67.14 Aligned_cols=85 Identities=14% Similarity=0.241 Sum_probs=47.0
Q ss_pred CcEEEEEc--cCchHHHHHHHHHHHHHhhC---CCcceEEEEeeC---CC--ccEEEEEecchHHHHHHH--hcCcccce
Q 001506 182 PKLWMVKC--AIGREREAAVCLMQKCIDKG---SELQIRSVIALD---HL--KNYIYIEADKEAHVKEAC--KGLRNIYS 249 (1065)
Q Consensus 182 P~lw~Vkc--k~G~Er~vv~~Lm~K~~~~~---~~l~I~Svf~~~---~l--kGYIYIEA~~~~~V~~ai--~Gl~~v~~ 249 (1065)
-+|..|+. -.++|+..+.+|.+++...- .--.|.-++..+ .. +-++--|.-.-.+.|+.. -.+.++|.
T Consensus 1440 ~~wcev~~~lp~~~~k~~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~~~k~~~~l~TeGVnl~a~~~~~d~LDv~~lyS 1519 (1640)
T KOG0262|consen 1440 GKWCEVELKLPLDKEKLDMSSIVESIAPKSVIHQVPGIERCVVSEPQDDVKEKSVLLTEGVNLPALFDHADILDVNRLYS 1519 (1640)
T ss_pred CcEEEEEEEecCCCcchHHHHHHHHHhcceeeeccCCceeeeccCCcccccccceehhcCccHHHHHHHHhhhhhhhhcc
Confidence 34555555 35789988888888865421 223455555532 11 125555555555666543 36667776
Q ss_pred eeeeee------------Chhhhhhcccc
Q 001506 250 QKVMLV------------PIREMTDVLAV 266 (1065)
Q Consensus 250 ~~~~lV------------pi~Em~~vL~v 266 (1065)
+.+..| =++||.+||.+
T Consensus 1520 NDI~ail~tyGVEAar~~Iv~Ev~~VF~v 1548 (1640)
T KOG0262|consen 1520 NDIHAILNTYGVEAARNAIVNEVNNVFKV 1548 (1640)
T ss_pred chHHHHHHHhhHHHHHHHHHHHHHHhhhh
Confidence 543222 25577777765
No 35
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=93.59 E-value=0.12 Score=54.67 Aligned_cols=81 Identities=25% Similarity=0.332 Sum_probs=55.0
Q ss_pred ccCcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCcEEEeccccCCceeEEEEEe
Q 001506 422 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLKVE 501 (1065)
Q Consensus 422 ~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~F~~GDhVkVi~G~~~getGlVVkVe 501 (1065)
.++|..||.|+|+.|.-+|-+|.|+.|.-+.-.|..+ +|+- |-+-+++.-+|+-|.||+.|
T Consensus 70 dw~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~--gln~-----------------k~r~~gsekeg~pgtivk~E 130 (236)
T KOG1708|consen 70 DWHFFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVK--GLNT-----------------KYRHMGSEKEGEPGTIVKSE 130 (236)
T ss_pred ceeEecCCEEEEEecccCCccceEEEEeecCceEEEc--ccch-----------------hhhhhcccccCCCceEEeec
Confidence 5899999999999999999999999996554333322 3321 11445667889999999998
Q ss_pred CcEEEEEeCCCCceEEEeccccccc
Q 001506 502 QHVLIILSDTTKEDIRVFADDVVES 526 (1065)
Q Consensus 502 ~~~v~vlSD~t~~ei~V~~~dL~~~ 526 (1065)
.-.- .+++-.-|-+.|.+-|
T Consensus 131 aPlh-----vsk~VmLvdp~d~q~t 150 (236)
T KOG1708|consen 131 APLH-----VSKQVMLVDPEDDQPT 150 (236)
T ss_pred CCce-----ecceeEEECccccCCc
Confidence 5321 1233444556665544
No 36
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=93.41 E-value=0.12 Score=50.19 Aligned_cols=32 Identities=25% Similarity=0.486 Sum_probs=28.2
Q ss_pred eecCCCEEEEEcCCCCCceeeEEEEECC--EEEE
Q 001506 600 TVAVKDVVRIVEGPCKGKQGPVEHIYRG--ILFI 631 (1065)
Q Consensus 600 ~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~--~lFl 631 (1065)
-|+.||.|.|+.|+.+|++|+|+.|++. .+++
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~V 36 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIV 36 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEE
Confidence 4899999999999999999999999965 4555
No 37
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=93.38 E-value=0.053 Score=69.64 Aligned_cols=7 Identities=29% Similarity=0.278 Sum_probs=2.8
Q ss_pred HHHHHHH
Q 001506 145 EALERRI 151 (1065)
Q Consensus 145 ee~~~~l 151 (1065)
+++.+.|
T Consensus 429 eel~~lL 435 (840)
T PF04147_consen 429 EELLELL 435 (840)
T ss_pred HHHHHHH
Confidence 3444333
No 38
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=93.27 E-value=0.15 Score=47.48 Aligned_cols=37 Identities=22% Similarity=0.357 Sum_probs=34.8
Q ss_pred cccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEE
Q 001506 270 AIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 306 (1065)
Q Consensus 270 ~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~Vk 306 (1065)
...|.+||-|.|.+|++||-.|+|..|+..+++|+|+
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 42 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVK 42 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 4579999999999999999999999999999999987
No 39
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=93.22 E-value=0.16 Score=52.31 Aligned_cols=50 Identities=34% Similarity=0.414 Sum_probs=42.0
Q ss_pred cccCcEEEEeeCCCCCceeEEEeec--CCeEEEEecCCCeE--EEEecCCcccc
Q 001506 706 ALVGTTVKVRLGPYKGYRGRVVDVK--GQSVRVELESQMKV--VTVDRSMISDN 755 (1065)
Q Consensus 706 ~liGktV~I~~GpyKG~~G~Vkd~t--~~~~rVELhs~~k~--I~V~r~~l~~~ 755 (1065)
-..|..|+|+.|||||+.|+|..+. ...|+|+|-.+.-. |+|+.+.|..+
T Consensus 95 ~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~~~~ 148 (153)
T PRK08559 95 IKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQVRVV 148 (153)
T ss_pred CCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEEEEe
Confidence 4579999999999999999999986 45788887777755 99999888754
No 40
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=93.19 E-value=0.07 Score=68.59 Aligned_cols=12 Identities=25% Similarity=0.454 Sum_probs=6.6
Q ss_pred HHHHHHHHHHhc
Q 001506 145 EALERRIQARYA 156 (1065)
Q Consensus 145 ee~~~~l~eRY~ 156 (1065)
.-|.+.|+.-|.
T Consensus 444 ~~iI~RIrk~~h 455 (840)
T PF04147_consen 444 PTIIQRIRKCYH 455 (840)
T ss_pred hHHHHHHHHhCC
Confidence 345556666664
No 41
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=93.07 E-value=0.18 Score=49.94 Aligned_cols=39 Identities=31% Similarity=0.523 Sum_probs=35.6
Q ss_pred cccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEEEe
Q 001506 270 AIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLI 308 (1065)
Q Consensus 270 ~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~VkLv 308 (1065)
...|+.||.|.|.+|+|||-.|+|..|+...++|+|+=|
T Consensus 43 ~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGv 81 (120)
T PRK01191 43 SLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGV 81 (120)
T ss_pred cceEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCc
Confidence 347899999999999999999999999999999999843
No 42
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=92.84 E-value=0.17 Score=52.67 Aligned_cols=53 Identities=25% Similarity=0.347 Sum_probs=41.4
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcC-C-eEEEeecCCCCCcceeecccccee
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDE-E-NVHIRPEMKGLPKTLAVNSKELCK 475 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~-d-~V~i~~~~~~l~~~l~v~~~~LrK 475 (1065)
..|++||.|+|++|-++|+.|.|++++. . .++|..+.=+....+++...+|+|
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~v~~~g~~~~v~v~~~~l~~ 172 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPVELEFSQVEK 172 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEEEECCCceEEEEcHHHeeC
Confidence 4699999999999999999999999983 3 677776543333457777777764
No 43
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=92.74 E-value=0.17 Score=50.11 Aligned_cols=33 Identities=24% Similarity=0.483 Sum_probs=29.5
Q ss_pred eecCCCEEEEEcCCCCCceeeEEEEECC--EEEEE
Q 001506 600 TVAVKDVVRIVEGPCKGKQGPVEHIYRG--ILFIH 632 (1065)
Q Consensus 600 ~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~--~lFl~ 632 (1065)
.|+.||.|+|+.|+++|++|+|+.|++. .+++.
T Consensus 45 ~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~Ve 79 (120)
T PRK01191 45 PVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVE 79 (120)
T ss_pred eEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEe
Confidence 6999999999999999999999999865 46664
No 44
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=92.72 E-value=0.2 Score=52.93 Aligned_cols=56 Identities=30% Similarity=0.478 Sum_probs=45.4
Q ss_pred cccCcCCCCEEEEecccccCceeEEEEEcCC--eEEEeecCCCCCcceeeccccceee
Q 001506 421 KKGHFMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCKY 476 (1065)
Q Consensus 421 ~~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d--~V~i~~~~~~l~~~l~v~~~~LrK~ 476 (1065)
....|.+||.|+|+.|=++|..|+|..|+.+ .+++....-+..-++++..++++|.
T Consensus 120 ~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~ifgr~tPVel~~~qVek~ 177 (178)
T COG0250 120 PKVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIFGRPTPVELEFDQVEKL 177 (178)
T ss_pred ccccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEEeCCceEEEEehhhEEEe
Confidence 3578999999999999999999999999998 4666655444455788888888763
No 45
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=92.57 E-value=0.18 Score=52.10 Aligned_cols=52 Identities=19% Similarity=0.256 Sum_probs=40.9
Q ss_pred CcCCCCEEEEecccccCceeEEEEEcCC-eEEEeecCCCCCcceeecccccee
Q 001506 424 HFMKGDAVIVIKGDLKNLKGWVEKVDEE-NVHIRPEMKGLPKTLAVNSKELCK 475 (1065)
Q Consensus 424 ~F~~GD~V~V~~Gel~gl~G~V~~V~~d-~V~i~~~~~~l~~~l~v~~~~LrK 475 (1065)
.|++||+|+|++|-++|+.|.|..+++. .+.|..+.=+..-+++++..+|.|
T Consensus 109 ~~~~G~~V~I~~Gp~~g~eg~v~~~~~~~r~~v~v~~~gr~~~v~v~~~~~~~ 161 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQFRK 161 (162)
T ss_pred CCCCCCEEEEecCCCCCcEEEEEEeCCCeEEEEeehhhCCcEEEEECHHHeec
Confidence 5999999999999999999999999866 455555432334468888888765
No 46
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=92.20 E-value=0.24 Score=45.43 Aligned_cols=36 Identities=28% Similarity=0.443 Sum_probs=34.1
Q ss_pred ccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEE
Q 001506 271 IDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 306 (1065)
Q Consensus 271 ~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~Vk 306 (1065)
..|+.||-|.|.+|++||-.|.|..|+..+++|+|+
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 40 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVE 40 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 368899999999999999999999999999999998
No 47
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=91.88 E-value=0.054 Score=67.38 Aligned_cols=18 Identities=17% Similarity=0.521 Sum_probs=8.0
Q ss_pred cEEEEEecchHHHHHHHh
Q 001506 225 NYIYIEADKEAHVKEACK 242 (1065)
Q Consensus 225 GYIYIEA~~~~~V~~ai~ 242 (1065)
-|.|+...-+..+...+.
T Consensus 356 ~y~~Md~~~K~~L~~~l~ 373 (622)
T PF02724_consen 356 KYSYMDMELKRELREKLE 373 (622)
T ss_pred CchhCCHHHHHHHHHHHH
Confidence 445544444444444443
No 48
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=91.76 E-value=0.28 Score=51.33 Aligned_cols=53 Identities=25% Similarity=0.376 Sum_probs=41.5
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcC-C-eEEEeecCCCCCcceeecccccee
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDE-E-NVHIRPEMKGLPKTLAVNSKELCK 475 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~-d-~V~i~~~~~~l~~~l~v~~~~LrK 475 (1065)
..|++||.|+|++|-++|+.|.|++++. . .++|....=+-.-.+++...+|+|
T Consensus 125 ~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l~~~G~~~~v~l~~~~l~~ 179 (181)
T PRK05609 125 VDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVSIFGRETPVELEFSQVEK 179 (181)
T ss_pred cCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEEEECCCceEEEEchHHEEE
Confidence 5699999999999999999999999973 3 677776543333457777777765
No 49
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=91.09 E-value=0.083 Score=65.77 Aligned_cols=6 Identities=50% Similarity=0.667 Sum_probs=2.4
Q ss_pred hhhccC
Q 001506 396 LEKFRT 401 (1065)
Q Consensus 396 L~kF~~ 401 (1065)
+..|..
T Consensus 511 ~~~F~~ 516 (622)
T PF02724_consen 511 LELFSH 516 (622)
T ss_pred HHHhCC
Confidence 344443
No 50
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=91.00 E-value=0.47 Score=45.98 Aligned_cols=33 Identities=27% Similarity=0.443 Sum_probs=28.7
Q ss_pred CeecCCCEEEEEcCCCCCceeeEEEEECCEEEE
Q 001506 599 NTVAVKDVVRIVEGPCKGKQGPVEHIYRGILFI 631 (1065)
Q Consensus 599 n~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~~lFl 631 (1065)
..|+.||+|+|+.|..||++|.|+-++.-.+++
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~V~V 35 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPKKVVV 35 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecCeEEE
Confidence 358999999999999999999999998766444
No 51
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=90.92 E-value=0.35 Score=47.67 Aligned_cols=34 Identities=38% Similarity=0.507 Sum_probs=31.0
Q ss_pred CCCCcEEEEcCCCCCceEEEEEEeCCCcEEEecC
Q 001506 1014 RKTDKIKIMGGPHRGATGKLIGVDGTDGIVKVDV 1047 (1065)
Q Consensus 1014 ~kgd~VkVi~G~~rG~tG~LisiD~~dgiVk~d~ 1047 (1065)
.+||+|+||.|.+.|.+|+++.|+..++.|-+++
T Consensus 43 kkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Veg 76 (114)
T TIGR01080 43 RKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEG 76 (114)
T ss_pred ecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcC
Confidence 6899999999999999999999999988776653
No 52
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=90.65 E-value=0.32 Score=49.53 Aligned_cols=33 Identities=36% Similarity=0.602 Sum_probs=29.2
Q ss_pred eecCCCEEEEEcCCCCCceeeEEEEECCE--EEEE
Q 001506 600 TVAVKDVVRIVEGPCKGKQGPVEHIYRGI--LFIH 632 (1065)
Q Consensus 600 ~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~~--lFl~ 632 (1065)
.|+.||+|+|+.|.++|++|.|+.|++.. +++.
T Consensus 46 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVE 80 (143)
T PTZ00194 46 PVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIE 80 (143)
T ss_pred eeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEe
Confidence 69999999999999999999999998763 5553
No 53
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=90.42 E-value=0.17 Score=62.53 Aligned_cols=12 Identities=8% Similarity=0.163 Sum_probs=6.3
Q ss_pred hHHHHHHHHHHH
Q 001506 143 DVEALERRIQAR 154 (1065)
Q Consensus 143 d~ee~~~~l~eR 154 (1065)
++|+.+..|.+.
T Consensus 968 saeey~hllD~d 979 (988)
T KOG2038|consen 968 SAEEYAHLLDQD 979 (988)
T ss_pred hHHHHHHHhhcc
Confidence 455555555443
No 54
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=90.38 E-value=0.17 Score=64.33 Aligned_cols=14 Identities=21% Similarity=0.233 Sum_probs=9.8
Q ss_pred CcEEEEEccCchHH
Q 001506 182 PKLWMVKCAIGRER 195 (1065)
Q Consensus 182 P~lw~Vkck~G~Er 195 (1065)
|.+|+++.....-|
T Consensus 1880 p~imAsiaaqsaaR 1893 (3015)
T KOG0943|consen 1880 PMIMASIAAQSAAR 1893 (3015)
T ss_pred hhHHHHHhhHHHHH
Confidence 88999888654333
No 55
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=90.34 E-value=0.44 Score=48.80 Aligned_cols=51 Identities=20% Similarity=0.234 Sum_probs=37.8
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcCC-eEEEeecCCCCCcceeeccccc
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEE-NVHIRPEMKGLPKTLAVNSKEL 473 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d-~V~i~~~~~~l~~~l~v~~~~L 473 (1065)
..|++||.|+|++|-++|+.|.|+.+++. .+.|..+.=+-.-.++++.++|
T Consensus 107 ~~~~~G~~V~V~~GPf~g~~g~v~~~~~~~r~~v~l~~~gr~~~v~~~~~~~ 158 (159)
T TIGR01955 107 TLPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKVSVPNTSV 158 (159)
T ss_pred cCCCCCCEEEEeccCCCCcEEEEEEECCCceEEEEEhhhCCceEEEecHHHc
Confidence 46999999999999999999999999855 4666655322223466665554
No 56
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=90.16 E-value=2 Score=46.01 Aligned_cols=99 Identities=19% Similarity=0.234 Sum_probs=64.9
Q ss_pred cCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCcEEEe----------------------cccc------
Q 001506 439 KNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVV----------------------SGTQ------ 490 (1065)
Q Consensus 439 ~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~F~~GDhVkVi----------------------~G~~------ 490 (1065)
.-..|+|+.|..+.+.|.++ ...+++.+- -+....+++||.||+. .|.|
T Consensus 40 ~tiEGrVvEV~~~~i~iesk--~yn~~v~i~-~d~~~nvKVGD~VKaTG~m~rnf~~ym~A~sVEk~~~~~G~h~~e~g~ 116 (213)
T PRK06763 40 STIEGRVVEVDNGVIVIKSK--QYEEPVSVY-IDSLSNVKVGDEVKATGSMMRNFTEYMVATAVENTTNKLGMHMKEDGS 116 (213)
T ss_pred ceeeeEEEEEeCCEEEEEec--cCCCceEEE-ecCCCCcccCcEEEEchHHHHhhHHhhhhhhheeeccCcceeecccCC
Confidence 45689999999999999887 446677776 4566778999999998 2444
Q ss_pred -CCceeEEEEEeC---------cEEEE-EeCCCCceEEEecccccccccccccccccCceeeeeeEEeCCCc
Q 001506 491 -AGATGMVLKVEQ---------HVLII-LSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDNNS 551 (1065)
Q Consensus 491 -~getGlVVkVe~---------~~v~v-lSD~t~~ei~V~~~dL~~~~e~~~g~~~~g~y~l~DLVqLd~~t 551 (1065)
.-..|-|.+|.. +.|+| ..+..++...|+ --+.+-..|.++|.|+++...
T Consensus 117 pdYvIG~Iskv~k~~~~~~~~~dyVvV~YP~~~G~~~~V~-----------V~LT~GQkFnVGDkVKV~~~~ 177 (213)
T PRK06763 117 PDYVIGEVSKVYTMEDDGDGATKYVVVEYPSLNGKKLIID-----------VFLTKGQVFHVGDKVKVDMKY 177 (213)
T ss_pred cceEEEEEEEecccccCCCCcccEEEEEcCCCCCCeeEEE-----------EEeccCCEEecCCEEEEEeee
Confidence 346788888854 23322 223333332222 112233579999999997544
No 57
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=90.13 E-value=0.47 Score=46.08 Aligned_cols=35 Identities=26% Similarity=0.333 Sum_probs=33.6
Q ss_pred cCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEE
Q 001506 272 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 306 (1065)
Q Consensus 272 ~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~Vk 306 (1065)
.|++||.|.|.+|++||-.|.|..|+..+++|.|+
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 38 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVE 38 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 58899999999999999999999999999999997
No 58
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=89.99 E-value=0.59 Score=46.10 Aligned_cols=48 Identities=29% Similarity=0.446 Sum_probs=38.7
Q ss_pred hhhhhccccccccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEEE
Q 001506 258 REMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 307 (1065)
Q Consensus 258 ~Em~~vL~v~~~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~VkL 307 (1065)
+|+...+.. ....|+.||-|+|.+|.|||-.|.|..|+..++.|+|+=
T Consensus 29 ~elr~~y~~--r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Veg 76 (114)
T TIGR01080 29 KELREKYGK--RALPVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEG 76 (114)
T ss_pred HHHHHHcCc--ccceeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcC
Confidence 344444432 234789999999999999999999999999999898873
No 59
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=89.82 E-value=0.15 Score=64.82 Aligned_cols=11 Identities=9% Similarity=0.247 Sum_probs=5.5
Q ss_pred EEEEEeCcEEE
Q 001506 496 MVLKVEQHVLI 506 (1065)
Q Consensus 496 lVVkVe~~~v~ 506 (1065)
+=|+++++.+.
T Consensus 2286 fE~rn~g~~La 2296 (3015)
T KOG0943|consen 2286 FEVRNDGNCLA 2296 (3015)
T ss_pred EEEecCCceee
Confidence 55555555443
No 60
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=89.66 E-value=0.62 Score=47.50 Aligned_cols=51 Identities=24% Similarity=0.276 Sum_probs=41.7
Q ss_pred hhhhccccccccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEEEeecc
Q 001506 259 EMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLIPRI 311 (1065)
Q Consensus 259 Em~~vL~v~~~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~VkLvPRi 311 (1065)
|+..-..+. ...|+.||-|.|.+|.|||-.|+|+.|+...++|+|+=|.+.
T Consensus 35 eLr~k~~~R--s~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~ 85 (143)
T PTZ00194 35 ELRAKYNVR--SMPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITRE 85 (143)
T ss_pred HHHHHhCCc--cceeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEE
Confidence 444444333 347899999999999999999999999999999999866555
No 61
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=89.52 E-value=0.54 Score=52.27 Aligned_cols=52 Identities=25% Similarity=0.448 Sum_probs=41.0
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcC--CeEEEeecCCCCCcceeeccccce
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDE--ENVHIRPEMKGLPKTLAVNSKELC 474 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~--d~V~i~~~~~~l~~~l~v~~~~Lr 474 (1065)
..|.+||.|+|+.|-+.|+.|.|+.++. ..+.|+...-+..-++++...+|+
T Consensus 204 ~~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV~IfGR~TpVeL~~~qVe 257 (258)
T TIGR01956 204 SKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVEILGKSVDVDLNFKHLK 257 (258)
T ss_pred cCCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEEEecCCcEEEEEchHHEE
Confidence 4699999999999999999999999984 467777664333446777777664
No 62
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=89.01 E-value=10 Score=49.36 Aligned_cols=20 Identities=30% Similarity=0.579 Sum_probs=8.7
Q ss_pred eeccceEEEEeCCceEEeec
Q 001506 636 HLEHAGFICAKSSSCVVVGG 655 (1065)
Q Consensus 636 ~~EN~Gifv~~a~~~~~~g~ 655 (1065)
.++|+|-+-..+.-|-+..|
T Consensus 596 rl~~~g~~~~~a~lcYi~ag 615 (1049)
T KOG0307|consen 596 RLENAGDLTSAAILCYICAG 615 (1049)
T ss_pred HHhhccchhhhhhHHhhhcc
Confidence 34555544334444444433
No 63
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=88.79 E-value=0.18 Score=66.38 Aligned_cols=14 Identities=29% Similarity=0.088 Sum_probs=8.8
Q ss_pred CCcccccccCCchh
Q 001506 89 EFFDLEAQVDSDEE 102 (1065)
Q Consensus 89 ~FlD~EAeVdddeE 102 (1065)
-|.-.||...|+-=
T Consensus 208 ~f~~~e~g~~d~~~ 221 (2849)
T PTZ00415 208 CFKFIEAGAGDDVF 221 (2849)
T ss_pred eeeeccCCCCCchh
Confidence 46666777766543
No 64
>KOG4156 consensus Claspin, protein mediating phosphorylation and activation of Chk1 protein kinase in the DNA replication checkpoint response [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=88.25 E-value=0.048 Score=65.29 Aligned_cols=14 Identities=21% Similarity=0.525 Sum_probs=10.8
Q ss_pred CCCcccccccCCch
Q 001506 88 SEFFDLEAQVDSDE 101 (1065)
Q Consensus 88 ~~FlD~EAeVddde 101 (1065)
..+|++||+|+-+|
T Consensus 1051 Rk~~eDEAevSGsD 1064 (1329)
T KOG4156|consen 1051 RKYLEDEAEVSGSD 1064 (1329)
T ss_pred HHhhcchhhcccCc
Confidence 36999999997444
No 65
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=87.38 E-value=0.8 Score=44.45 Aligned_cols=33 Identities=39% Similarity=0.378 Sum_probs=28.9
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcCCeEEE
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHI 455 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i 455 (1065)
..++.||.|.|+.|..+|-.|+|++|....|+|
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~V~V 35 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPKKVVV 35 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecCeEEE
Confidence 468899999999999999999999998776433
No 66
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=86.95 E-value=0.98 Score=43.88 Aligned_cols=35 Identities=26% Similarity=0.344 Sum_probs=33.2
Q ss_pred cCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEE
Q 001506 272 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 306 (1065)
Q Consensus 272 ~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~Vk 306 (1065)
.|+.||-|.|.+|++||-.|.|..|+..+++|.|+
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 37 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVE 37 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEC
Confidence 47899999999999999999999999999999987
No 67
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=86.00 E-value=0.39 Score=61.09 Aligned_cols=24 Identities=17% Similarity=0.428 Sum_probs=10.4
Q ss_pred cccccccchhhhhccCccchhhhh
Q 001506 10 DEMDAEEDEYDEQVMDDEIDEEEE 33 (1065)
Q Consensus 10 ~~~~~~~~~~~~~~~~~e~~~~d~ 33 (1065)
|+++++++++|+..++|+|.++++
T Consensus 891 e~~~~~~~~~e~~~~d~dD~d~~d 914 (1010)
T KOG1991|consen 891 EGEEEDDDEEEDFIDDEDDIDEDD 914 (1010)
T ss_pred cccCCCCcchhhccCccccccccc
Confidence 333334444444444444444444
No 68
>PHA03378 EBNA-3B; Provisional
Probab=85.04 E-value=15 Score=45.65 Aligned_cols=10 Identities=20% Similarity=0.056 Sum_probs=5.0
Q ss_pred CCCceeEEEe
Q 001506 719 YKGYRGRVVD 728 (1065)
Q Consensus 719 yKG~~G~Vkd 728 (1065)
|.+-++|-.|
T Consensus 542 y~~~l~ie~d 551 (991)
T PHA03378 542 YTEDLDIESD 551 (991)
T ss_pred eecccCcccC
Confidence 5555555444
No 69
>PF04006 Mpp10: Mpp10 protein; InterPro: IPR007151 This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites [].
Probab=83.74 E-value=0.93 Score=56.49 Aligned_cols=17 Identities=18% Similarity=0.458 Sum_probs=10.0
Q ss_pred CCcccccCCCC-CCcccc
Q 001506 78 RKPKAKRRSGS-EFFDLE 94 (1065)
Q Consensus 78 ~~~krk~~~~~-~FlD~E 94 (1065)
..+++++..++ .||+++
T Consensus 175 ~~~~~d~~glnD~FFsid 192 (600)
T PF04006_consen 175 EEKKEDKSGLNDGFFSID 192 (600)
T ss_pred ccccccCCCcCCCcCCHH
Confidence 33444555555 788884
No 70
>PF00524 PPV_E1_N: E1 Protein, N terminal domain; InterPro: IPR014000 Papillomaviruses are a large family of DNA tumour viruses which give rise to warts in their host species. The helicase E1 protein is an ATP-dependent DNA helicase required for initiation of viral DNA replication []. It forms a complex with the viral E2 protein, which is a site-specific DNA-binding transcriptional activator. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins []. The E1 protein is a 70 kDa polypeptide with a centrally-located DNA-binding domain and a C-terminal ATPase/helicase domain. It binds specific 18 bp DNA sequences at the origin of replication, melts the DNA duplex and functions as a 3' to 5' helicase []. In addition to E2 it also interacts with DNA polymerase alpha and replication protein A to effect DNA replication. The DNA-binding domain forms a five-stranded antiparallel beta sheet bordered by four loosely packed alpha helices on one side and two tightly packed helices on the other []. Two structural modules within this domain, an extended loop and a helix, contain conserved residues and are critical for DNA binding. In solution E1 is a monomer, but binds DNA as a dimer. Recruitment of more E1 subunits to the complex leads to melting of the origin and ultimately to the formation of an E1 hexamer with helicase activity []. This entry represents the N-terminal region of E1, which contains the nuclear localisation signal.; GO: 0016817 hydrolase activity, acting on acid anhydrides
Probab=82.34 E-value=0.56 Score=47.28 Aligned_cols=64 Identities=22% Similarity=0.407 Sum_probs=33.2
Q ss_pred CCCcccccccCCc----hhhhcc-c---cccccccCCCCCCCCCCCCCccCcCCCCCCCcchhhHHHHHHHHHHHhcCCC
Q 001506 88 SEFFDLEAQVDSD----EEEDEE-E---GEDDFIVDGGAELPDEDGGRGIHRRPLLPREDEQEDVEALERRIQARYARSS 159 (1065)
Q Consensus 88 ~~FlD~EAeVddd----eEeeee-e---~~~~fi~~~~~~~~~~~~~~~~~r~~~~~~~~~~~d~ee~~~~l~eRY~~~~ 159 (1065)
+.|+-+||+++++ +|.|+. | +..+||++.... ....++.|...+ +.+++ ++....||+||..+.
T Consensus 15 ~gw~~vEAec~dd~~s~de~E~~~d~~sd~~dfIDd~~~~------~qgnslaLf~~Q-~~~~d-~~~v~~LKRK~~~SP 86 (130)
T PF00524_consen 15 GGWFIVEAECSDDDISEDEDEDLFDSGSDISDFIDDSEVS------EQGNSLALFNQQ-EAEDD-ERAVQALKRKYLGSP 86 (130)
T ss_pred CcEEEEEEEEcCCCCCCCcccccccCCccccccccCCCcc------cccHHHHHHHHH-HHHHH-HHHHHHHHHHHcCCc
Confidence 4455569999982 221111 1 124788764321 223344433222 22333 455669999998654
No 71
>PF14632 SPT6_acidic: Acidic N-terminal SPT6
Probab=81.81 E-value=0.42 Score=45.36 Aligned_cols=8 Identities=50% Similarity=0.576 Sum_probs=5.1
Q ss_pred cccccccc
Q 001506 45 RSQFIDDV 52 (1065)
Q Consensus 45 ~~~~~~~~ 52 (1065)
..-||.|+
T Consensus 20 ~eGFIvDd 27 (92)
T PF14632_consen 20 REGFIVDD 27 (92)
T ss_pred hcCCccCC
Confidence 35677765
No 72
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=81.52 E-value=0.6 Score=61.86 Aligned_cols=18 Identities=22% Similarity=0.554 Sum_probs=8.7
Q ss_pred CCCCCCCcEEEEEccCch
Q 001506 176 LPSVRDPKLWMVKCAIGR 193 (1065)
Q Consensus 176 lPsv~DP~lw~Vkck~G~ 193 (1065)
-|-+..++-|-+=|-.|+
T Consensus 367 ppv~~~~~~~y~icdn~k 384 (2849)
T PTZ00415 367 PPVLHEAKKFYFICDNGK 384 (2849)
T ss_pred CCeeeccceEEEEeCCCc
Confidence 334445555555555444
No 73
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=79.72 E-value=0.93 Score=56.11 Aligned_cols=15 Identities=13% Similarity=0.217 Sum_probs=9.1
Q ss_pred hHHHHHHHHHHHhcC
Q 001506 143 DVEALERRIQARYAR 157 (1065)
Q Consensus 143 d~ee~~~~l~eRY~~ 157 (1065)
....|+.-|.+=|..
T Consensus 334 Ni~~I~~~i~~Ly~~ 348 (822)
T KOG2141|consen 334 NIIKIIAGIAELYMN 348 (822)
T ss_pred HHHHHHHHHHHHHHh
Confidence 344566666777763
No 74
>cd04467 S1_aIF5A S1_aIF5A: Archaeal translation Initiation Factor 5A (aIF5A), S1-like RNA-binding domain. aIF5A is a homolog of eukaryotic eIF5A. IF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is a post-translationally modified lysine and is essential for IF5A function. In yeast, eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the cold-shock domain which binds RNA. Moreover, IF5A prefers binding to the actively translating ribosome. This evidence suggests that IF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=78.88 E-value=4.1 Score=35.52 Aligned_cols=45 Identities=22% Similarity=0.338 Sum_probs=34.3
Q ss_pred ceeEEEEEcCCeEEEeecCCCCCcceeecc-ccceeeccCCCcEEEec
Q 001506 441 LKGWVEKVDEENVHIRPEMKGLPKTLAVNS-KELCKYFEPGNHVKVVS 487 (1065)
Q Consensus 441 l~G~V~~V~~d~V~i~~~~~~l~~~l~v~~-~~LrK~F~~GDhVkVi~ 487 (1065)
-.|.|++|.++.|.|| +.+.. ++++++. .+++-.+++|+.|.++.
T Consensus 4 ~~aqVisi~g~~vQlM-D~eTY-eT~ev~~p~~~~~~i~~G~eV~y~~ 49 (57)
T cd04467 4 KTGQVLSIMGDVVQLM-DLETY-ETFEVPIPEEIKDKLEPGKEVEYWE 49 (57)
T ss_pred eEEEEEEEcCCEEEEe-ccccc-eeEEEecchhhcccCCCCCEEEEEe
Confidence 4699999999999999 55433 4666665 45656699999999875
No 75
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=76.97 E-value=1.4 Score=57.06 Aligned_cols=34 Identities=9% Similarity=0.164 Sum_probs=20.6
Q ss_pred ccCcCC--CC--------EEEEeccccc---CceeEEEEEcCCeEEE
Q 001506 422 KGHFMK--GD--------AVIVIKGDLK---NLKGWVEKVDEENVHI 455 (1065)
Q Consensus 422 ~~~F~~--GD--------~V~V~~Gel~---gl~G~V~~V~~d~V~i 455 (1065)
...|.| ++ +|..|.|.-. -+.++.++..|+.|-.
T Consensus 586 ~apy~p~~~~~~d~~~p~rvl~~~~~~~~~~a~f~v~vn~~Gd~vD~ 632 (1299)
T KOG1856|consen 586 QAPYRPDDDTFEDEKIPKRVLAVCGGTERSDAIFCVLVNFEGDLVDY 632 (1299)
T ss_pred cCCcCCCCCCcccccccceEEEeccCCCCCceEEEEEEcCCCceeee
Confidence 356777 55 6666666433 3566667767776533
No 76
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=76.34 E-value=65 Score=42.28 Aligned_cols=45 Identities=13% Similarity=0.220 Sum_probs=28.5
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcCC--eEEEeecCCCC-CcceeeccccceeeccCCCcE
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGL-PKTLAVNSKELCKYFEPGNHV 483 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d--~V~i~~~~~~l-~~~l~v~~~~LrK~F~~GDhV 483 (1065)
..|++||.|+| +|+.|+.+ .+.+..+ .+ .+ |...+-+.|++|+-|
T Consensus 709 ~~~kvGq~Vkv----------kVl~ID~e~rrI~LS~K--~l~~d----pw~~~~~~~~vG~iV 756 (863)
T PRK12269 709 HELEVGKEIEC----------MVIECDPQARRIRLGVK--QLSDN----PWQVFANAYGVGSTV 756 (863)
T ss_pred hccCCCCEEEE----------EEEEEeccCCEEEEEec--ccccC----hHHHHHhhCCCCCEE
Confidence 46999999997 58888765 3444332 22 12 333345567889866
No 77
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=74.46 E-value=6.8 Score=44.18 Aligned_cols=26 Identities=27% Similarity=0.489 Sum_probs=24.1
Q ss_pred ccCCCcEEEeccccCCceeEEEEEeC
Q 001506 477 FEPGNHVKVVSGTQAGATGMVLKVEQ 502 (1065)
Q Consensus 477 F~~GDhVkVi~G~~~getGlVVkVe~ 502 (1065)
|++|..|-|++|+|.|.+|.|+.++.
T Consensus 172 fe~G~l~~vtgG~n~GriG~I~~i~~ 197 (273)
T PTZ00223 172 NRNGKVVMVTGGANRGRIGEIVSIER 197 (273)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEEe
Confidence 78999999999999999999998863
No 78
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=74.10 E-value=1.6 Score=52.52 Aligned_cols=23 Identities=9% Similarity=0.219 Sum_probs=12.5
Q ss_pred CCccEEEEEecchHHHHHHHhcC
Q 001506 222 HLKNYIYIEADKEAHVKEACKGL 244 (1065)
Q Consensus 222 ~lkGYIYIEA~~~~~V~~ai~Gl 244 (1065)
+-+|--||--..+.+...+|.+.
T Consensus 332 ~skGtAFv~Fkt~~~~~~ci~~A 354 (678)
T KOG0127|consen 332 HSKGTAFVKFKTQIAAQNCIEAA 354 (678)
T ss_pred CcccceEEEeccHHHHHHHHHhc
Confidence 44555555555555555555544
No 79
>KOG3118 consensus Disrupter of silencing SAS10 [Chromatin structure and dynamics]
Probab=72.97 E-value=1.5 Score=52.15 Aligned_cols=13 Identities=15% Similarity=0.238 Sum_probs=5.6
Q ss_pred CCcccccccCCch
Q 001506 89 EFFDLEAQVDSDE 101 (1065)
Q Consensus 89 ~FlD~EAeVddde 101 (1065)
.|-|+++.-++++
T Consensus 128 d~dddd~s~e~ee 140 (517)
T KOG3118|consen 128 DVDDDDLSSEDEE 140 (517)
T ss_pred cccchhhccchHH
Confidence 3444444443333
No 80
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=72.81 E-value=7.3 Score=33.20 Aligned_cols=50 Identities=20% Similarity=0.271 Sum_probs=37.9
Q ss_pred cCCCCEEEEeccc--ccCceeEEEEEcCCeEEEeecCCCCCcceeeccccce
Q 001506 425 FMKGDAVIVIKGD--LKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELC 474 (1065)
Q Consensus 425 F~~GD~V~V~~Ge--l~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~Lr 474 (1065)
+.||-.|+|+..+ +-+..|.|.+|.++.+-|+-.-....+.++|+.++|.
T Consensus 2 ilPG~~V~V~n~~~~Y~~y~G~VQRvsdgkaaVLFEGGnWdKlvTf~l~eLe 53 (53)
T PF11623_consen 2 ILPGSTVRVKNPNDIYYGYEGFVQRVSDGKAAVLFEGGNWDKLVTFRLSELE 53 (53)
T ss_dssp --TT-EEEE--TTSTTTT-EEEEEEEETTEEEEEEEETTEEEEEEEEGGGEE
T ss_pred ccCCCEEEEeCCCCccchheEEEEEeeCCeEEEEecCCCceEEEEEEhhhCC
Confidence 5689999999876 6889999999999999888876666678999998873
No 81
>PRK04313 30S ribosomal protein S4e; Validated
Probab=72.21 E-value=8.4 Score=42.69 Aligned_cols=42 Identities=26% Similarity=0.500 Sum_probs=32.0
Q ss_pred ccCCCcEEEeccccCCceeEEEEEeCc-----EEEEEeCCCCceEEE
Q 001506 477 FEPGNHVKVVSGTQAGATGMVLKVEQH-----VLIILSDTTKEDIRV 518 (1065)
Q Consensus 477 F~~GDhVkVi~G~~~getGlVVkVe~~-----~v~vlSD~t~~ei~V 518 (1065)
|++|..|-|++|+|.|++|.|+.++.. ..+.+.|..++++.-
T Consensus 172 fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T 218 (237)
T PRK04313 172 FEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFET 218 (237)
T ss_pred cCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEE
Confidence 789999999999999999999999621 234445666665543
No 82
>COG2933 Predicted SAM-dependent methyltransferase [General function prediction only]
Probab=71.71 E-value=5.6 Score=44.59 Aligned_cols=58 Identities=19% Similarity=0.261 Sum_probs=48.5
Q ss_pred EEEccCchHHHHHHHHHHHHHhhCCCcceEEEEeeCCCccEEEEEecchHHHHHHHhcCccc
Q 001506 186 MVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNI 247 (1065)
Q Consensus 186 ~Vkck~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~~~lkGYIYIEA~~~~~V~~ai~Gl~~v 247 (1065)
+.-|++|.|++++.-|-.|+.. |.|+...-...-.|||..|.+..+++..+++.|+.-
T Consensus 5 ~lyCRpGFEkE~aAEi~d~Aa~----l~IfGfarvk~n~gyV~feCyq~d~adrL~r~lpf~ 62 (358)
T COG2933 5 ALYCRPGFEKECAAEITDKAAQ----LEIFGFARVKENSGYVIFECYQPDDADRLIRELPFR 62 (358)
T ss_pred eeeecCCCcHHHHHHHHHhhhh----hccccceeecccCceEEEEEcCcccHHHHHHhCcHH
Confidence 5679999999999999888754 677775444566899999999999999999998753
No 83
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=71.67 E-value=4 Score=43.75 Aligned_cols=30 Identities=33% Similarity=0.431 Sum_probs=26.7
Q ss_pred eeccCCCcEEEeccccCCceeEEEEEeCcE
Q 001506 475 KYFEPGNHVKVVSGTQAGATGMVLKVEQHV 504 (1065)
Q Consensus 475 K~F~~GDhVkVi~G~~~getGlVVkVe~~~ 504 (1065)
=+|..||.|+|+.|+.+|.-|.|++|-.+.
T Consensus 71 w~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~ 100 (236)
T KOG1708|consen 71 WHFFFGDTVEVLVGKDKGKQGEVTQVIRHR 100 (236)
T ss_pred eeEecCCEEEEEecccCCccceEEEEeecC
Confidence 378999999999999999999999996543
No 84
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=71.37 E-value=12 Score=31.88 Aligned_cols=44 Identities=36% Similarity=0.442 Sum_probs=34.5
Q ss_pred CcEEEEeeC--CCCCceeEEEeecCCeEEEEecCCC--eEEEEecCCc
Q 001506 709 GTTVKVRLG--PYKGYRGRVVDVKGQSVRVELESQM--KVVTVDRSMI 752 (1065)
Q Consensus 709 GktV~I~~G--pyKG~~G~Vkd~t~~~~rVELhs~~--k~I~V~r~~l 752 (1065)
|.+|+|+.- +|-||.|+|..+++..|-|...-.| |.||..-++|
T Consensus 5 G~~V~V~n~~~~Y~~y~G~VQRvsdgkaaVLFEGGnWdKlvTf~l~eL 52 (53)
T PF11623_consen 5 GSTVRVKNPNDIYYGYEGFVQRVSDGKAAVLFEGGNWDKLVTFRLSEL 52 (53)
T ss_dssp T-EEEE--TTSTTTT-EEEEEEEETTEEEEEEEETTEEEEEEEEGGGE
T ss_pred CCEEEEeCCCCccchheEEEEEeeCCeEEEEecCCCceEEEEEEhhhC
Confidence 668888754 6999999999999999999999888 8888876654
No 85
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=71.29 E-value=9 Score=42.13 Aligned_cols=34 Identities=26% Similarity=0.566 Sum_probs=27.6
Q ss_pred eccccceee--ccCCCcEEEeccccCCceeEEEEEe
Q 001506 468 VNSKELCKY--FEPGNHVKVVSGTQAGATGMVLKVE 501 (1065)
Q Consensus 468 v~~~~LrK~--F~~GDhVkVi~G~~~getGlVVkVe 501 (1065)
+|.+++..+ |++|-.|-|++|+|.|++|.|+.++
T Consensus 163 lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~ 198 (241)
T COG1471 163 LPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIE 198 (241)
T ss_pred CCChhheeEeccCCCcEEEEECCccccceEEEEEEE
Confidence 344444443 7899999999999999999999986
No 86
>PLN00036 40S ribosomal protein S4; Provisional
Probab=71.07 E-value=9.7 Score=42.72 Aligned_cols=25 Identities=36% Similarity=0.618 Sum_probs=23.8
Q ss_pred ccCCCcEEEeccccCCceeEEEEEe
Q 001506 477 FEPGNHVKVVSGTQAGATGMVLKVE 501 (1065)
Q Consensus 477 F~~GDhVkVi~G~~~getGlVVkVe 501 (1065)
|++|..|-|++|+|.|.+|.|+.++
T Consensus 175 fe~G~l~~vtgG~n~GrvG~I~~i~ 199 (261)
T PLN00036 175 FDVGNLVMVTGGRNRGRVGVIKNRE 199 (261)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEE
Confidence 7899999999999999999999887
No 87
>KOG2773 consensus Apoptosis antagonizing transcription factor/protein transport protein [Transcription; Intracellular trafficking, secretion, and vesicular transport]
Probab=70.12 E-value=2.1 Score=50.68 Aligned_cols=15 Identities=20% Similarity=0.308 Sum_probs=9.5
Q ss_pred CCCCCCCcEEEEEccCch
Q 001506 176 LPSVRDPKLWMVKCAIGR 193 (1065)
Q Consensus 176 lPsv~DP~lw~Vkck~G~ 193 (1065)
||+ |-+|..-|-.+.
T Consensus 214 LP~---~ev~~lf~sd~~ 228 (483)
T KOG2773|consen 214 LPQ---PEVLSLFKSDDE 228 (483)
T ss_pred CCC---hhhHHHhhcccc
Confidence 566 466777776555
No 88
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=69.84 E-value=11 Score=42.32 Aligned_cols=25 Identities=36% Similarity=0.651 Sum_probs=23.3
Q ss_pred ccCCCcEEEeccccCCceeEEEEEe
Q 001506 477 FEPGNHVKVVSGTQAGATGMVLKVE 501 (1065)
Q Consensus 477 F~~GDhVkVi~G~~~getGlVVkVe 501 (1065)
|++|..|-|++|+|.|.+|.|+.++
T Consensus 175 fe~G~l~~vtgG~n~GriG~I~~~~ 199 (262)
T PTZ00118 175 FEVGNLVMITGGHNVGRVGTIVSKE 199 (262)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEE
Confidence 7899999999999999999998765
No 89
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=68.44 E-value=8.3 Score=36.12 Aligned_cols=42 Identities=24% Similarity=0.460 Sum_probs=33.2
Q ss_pred cCcEEEEeeCCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 708 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 708 iGktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
.|..|. +.| |..|+|+++.++++.||+. .+-.|+++|+.|+-
T Consensus 40 ~Gd~Vv-T~g---Gi~G~V~~i~d~~v~vei~-~g~~i~~~r~aI~~ 81 (84)
T TIGR00739 40 KGDKVL-TIG---GIIGTVTKIAENTIVIELN-DNTEITFSKNAIVE 81 (84)
T ss_pred CCCEEE-ECC---CeEEEEEEEeCCEEEEEEC-CCeEEEEEhHHhhh
Confidence 455554 444 7999999999999999995 55669999998763
No 90
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=67.24 E-value=14 Score=31.79 Aligned_cols=54 Identities=24% Similarity=0.147 Sum_probs=39.0
Q ss_pred CcCCCCEEEEeccc-ccCceeEEEEEcC-CeEEEeecCCCCCcceeeccccceeec
Q 001506 424 HFMKGDAVIVIKGD-LKNLKGWVEKVDE-ENVHIRPEMKGLPKTLAVNSKELCKYF 477 (1065)
Q Consensus 424 ~F~~GD~V~V~~Ge-l~gl~G~V~~V~~-d~V~i~~~~~~l~~~l~v~~~~LrK~F 477 (1065)
.|++||.|+|..=+ -.=-.|+|+++.+ +...|.-.........+|+.++||-+.
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LRp~~ 57 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLGDGKYLVRYLTESEPLKETVDWSDLRPHP 57 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECCCCEEEEEECCCCcccEEEEeHHHcccCC
Confidence 69999999999533 2236799999998 556655544224567889999998654
No 91
>CHL00010 infA translation initiation factor 1
Probab=67.12 E-value=34 Score=31.59 Aligned_cols=63 Identities=19% Similarity=0.183 Sum_probs=42.3
Q ss_pred eEEEEEEc-cceEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCCceeeEEEEECC
Q 001506 552 FGVIIRVE-SEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRG 627 (1065)
Q Consensus 552 VGvIv~ve-rd~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~ 627 (1065)
.|+|+++- ...|.|... .|+++.++.. .|+. .+..-|.+||.|.+---++....|.|.|=|++
T Consensus 10 ~G~Vik~lg~~~y~V~~~---~g~~~~c~~r---Gklr-------~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~ 73 (78)
T CHL00010 10 EGLVTESLPNGMFRVRLD---NGCQVLGYIS---GKIR-------RNSIRILPGDRVKVELSPYDLTKGRIIYRLRN 73 (78)
T ss_pred EEEEEEEcCCCEEEEEeC---CCCEEEEEec---ccee-------cCCcccCCCCEEEEEEcccCCCeEEEEEEecC
Confidence 49999998 577888552 3566665522 2222 12345899999999754555567999998875
No 92
>KOG2773 consensus Apoptosis antagonizing transcription factor/protein transport protein [Transcription; Intracellular trafficking, secretion, and vesicular transport]
Probab=66.57 E-value=2.8 Score=49.76 Aligned_cols=12 Identities=25% Similarity=0.044 Sum_probs=8.6
Q ss_pred CCCcccccccCC
Q 001506 88 SEFFDLEAQVDS 99 (1065)
Q Consensus 88 ~~FlD~EAeVdd 99 (1065)
..+.|.||++.+
T Consensus 126 e~~~deEes~~s 137 (483)
T KOG2773|consen 126 EDKSDEEESDRS 137 (483)
T ss_pred ccccchhhcccc
Confidence 356678888777
No 93
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=66.23 E-value=9.9 Score=37.41 Aligned_cols=42 Identities=21% Similarity=0.313 Sum_probs=33.7
Q ss_pred cCcEEEEeeCCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 708 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 708 iGktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
.|..| |+.| |+.|+|+++++.++.||+. .+-.|++.|..|+-
T Consensus 41 ~GD~V-vT~g---Gi~G~V~~I~d~~v~leia-~gv~i~~~r~AI~~ 82 (109)
T PRK05886 41 PGDRV-HTTS---GLQATIVGITDDTVDLEIA-PGVVTTWMKLAVRD 82 (109)
T ss_pred CCCEE-EECC---CeEEEEEEEeCCEEEEEEC-CCeEEEEEhhheee
Confidence 35555 4555 8999999999999999995 45669999999884
No 94
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=64.43 E-value=2.9 Score=50.49 Aligned_cols=21 Identities=24% Similarity=0.403 Sum_probs=10.8
Q ss_pred ccEEEEEecchHHHHHHHhcC
Q 001506 224 KNYIYIEADKEAHVKEACKGL 244 (1065)
Q Consensus 224 kGYIYIEA~~~~~V~~ai~Gl 244 (1065)
.||-|+|-.--.|...|++-+
T Consensus 496 ~g~aF~~f~EhEhalkalk~~ 516 (678)
T KOG0127|consen 496 EGYAFVGFTEHEHALKALKVL 516 (678)
T ss_pred ccccccCccHHHHHHHhhhcc
Confidence 455666554444555554444
No 95
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=64.30 E-value=16 Score=35.95 Aligned_cols=52 Identities=12% Similarity=0.133 Sum_probs=37.0
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCC
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGN 481 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~F~~GD 481 (1065)
..+++||.|.-+ -|+.|+|++|+++.|+|.... +-.++|.-+.+.+...+.+
T Consensus 37 ~~Lk~GD~VvT~----gGi~G~V~~I~d~~v~leia~---gv~i~~~r~AI~~v~~p~~ 88 (109)
T PRK05886 37 ESLQPGDRVHTT----SGLQATIVGITDDTVDLEIAP---GVVTTWMKLAVRDRILPDD 88 (109)
T ss_pred HhcCCCCEEEEC----CCeEEEEEEEeCCEEEEEECC---CeEEEEEhhheeeecCCCc
Confidence 589999999998 457899999999988886531 2345665555555444444
No 96
>KOG2600 consensus U3 small nucleolar ribonucleoprotein (snoRNP) subunit - Mpp10p [RNA processing and modification]
Probab=64.21 E-value=2.6 Score=50.91 Aligned_cols=14 Identities=21% Similarity=0.387 Sum_probs=9.8
Q ss_pred CCcccccCCCC-CCc
Q 001506 78 RKPKAKRRSGS-EFF 91 (1065)
Q Consensus 78 ~~~krk~~~~~-~Fl 91 (1065)
++|++++...+ +||
T Consensus 170 q~K~~d~~gi~DkFF 184 (596)
T KOG2600|consen 170 QPKKFDKSGINDKFF 184 (596)
T ss_pred ccCcccccccccccc
Confidence 55666666766 798
No 97
>PRK14635 hypothetical protein; Provisional
Probab=64.01 E-value=9 Score=40.08 Aligned_cols=50 Identities=22% Similarity=0.250 Sum_probs=39.1
Q ss_pred ccccCcEEEEee-----CCCCCceeEEEeecCCeEEEEecCC------CeEEEEecCCccc
Q 001506 705 DALVGTTVKVRL-----GPYKGYRGRVVDVKGQSVRVELESQ------MKVVTVDRSMISD 754 (1065)
Q Consensus 705 d~liGktV~I~~-----GpyKG~~G~Vkd~t~~~~rVELhs~------~k~I~V~r~~l~~ 754 (1065)
..++|+.|+|+- ..|+|++|++++++++.+++++..+ .++++++.+.|.-
T Consensus 95 ~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~~v~l~~~~k~~~~~~~~~~~ip~~~I~k 155 (162)
T PRK14635 95 DRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGDQVELEKFQKGKKSKVKKQTTLNLKDILK 155 (162)
T ss_pred HHhCCCEEEEEEecCCCcEEEecceEEEEEcCCEEEEEEecccccccCCeEEEEEhHHeee
Confidence 578999988862 2577888899999999999988543 6678888777664
No 98
>PF11746 DUF3303: Protein of unknown function (DUF3303); InterPro: IPR021734 Several members are annotated as being LysM domain-like proteins, but these did not match any LysM domains reported in the literature.
Probab=63.81 E-value=37 Score=32.24 Aligned_cols=75 Identities=12% Similarity=0.243 Sum_probs=53.9
Q ss_pred EEEEc--cCchHHHHHHHHHHHHHhhC----CCcc---eEEEEeeCCCccEEEEEecchHHHHHHHhcCcccceeeeeee
Q 001506 185 WMVKC--AIGREREAAVCLMQKCIDKG----SELQ---IRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLV 255 (1065)
Q Consensus 185 w~Vkc--k~G~Er~vv~~Lm~K~~~~~----~~l~---I~Svf~~~~lkGYIYIEA~~~~~V~~ai~Gl~~v~~~~~~lV 255 (1065)
|+|.+ +++....-....+.++++.+ .+-+ |..++.+.+..||+.+||++...+.+.+.--+.++|..+..+
T Consensus 2 flv~w~f~~~~~~~~~~~~~~~~~~~G~~~~~peG~~~l~rw~~~~~g~g~~i~eadd~~~l~~~~~~W~~~fg~~~ei~ 81 (91)
T PF11746_consen 2 FLVIWQFPPGESQQEAYKAFERFMESGAPGDPPEGFKVLGRWHDPGGGRGFAIVEADDAKALFKHFAPWRDLFGMEFEIT 81 (91)
T ss_pred EEEEEEeCCcccchhHHHHHHHHHhcCCCCCCCCCEEEEEEEEecCCCcEEEEEEeCCHHHHHHHHhhhhhccCceEEEE
Confidence 45555 34555544556677777765 2222 445577889999999999999999999999999988777777
Q ss_pred Chhh
Q 001506 256 PIRE 259 (1065)
Q Consensus 256 pi~E 259 (1065)
|+=+
T Consensus 82 Pv~~ 85 (91)
T PF11746_consen 82 PVMT 85 (91)
T ss_pred eccc
Confidence 7543
No 99
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=63.77 E-value=42 Score=31.43 Aligned_cols=65 Identities=14% Similarity=0.186 Sum_probs=46.3
Q ss_pred CCceEEEEEEccc-eEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCCceeeEEEEECC
Q 001506 549 NNSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRG 627 (1065)
Q Consensus 549 ~~tVGvIv~verd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~ 627 (1065)
.+.+|.|+++-.+ .|.|.+. +|..+.+. |..|+.++ ==|+.||.|.|---|+.-..|.|.|+|+.
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~---dG~~~la~---ipgK~Rk~--------iwI~~GD~VlVe~~~~~~~kg~Iv~r~~~ 70 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCA---DGKERLAR---IPGKMRKK--------VWIRRGDIVLVDPWDFQDVKADIIYKYTK 70 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEEC---CCCEEEEE---Echhhccc--------EEEcCCCEEEEEecCCCCCEEEEEEEeCH
Confidence 4678999999875 5888874 36655443 44444321 24999999999877776678999999863
No 100
>PRK03879 ribonuclease P protein component 1; Validated
Probab=62.63 E-value=18 Score=34.88 Aligned_cols=49 Identities=27% Similarity=0.323 Sum_probs=41.9
Q ss_pred CccccCcEEEEeeCC---CCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 704 HDALVGTTVKVRLGP---YKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 704 ~d~liGktV~I~~Gp---yKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
+.+|+|-.|+|.+=+ |-|..|+|++-|..++.|+ +.++..+|+|+.-.+
T Consensus 10 ~~eliGl~v~Vv~S~npslvGi~GiVv~ETknt~~I~--~~~~~~~VPK~~~iF 61 (96)
T PRK03879 10 RHELIGLKVEVVDSTNPSLVGIKGRVVDETRNTLVIE--TDGKEWMVPKDGATF 61 (96)
T ss_pred HHHhcCCEEEEEEcCCCCcccceEEEEEeceeEEEEE--cCCcEEEEeCCCeEE
Confidence 468999999998765 5699999999999999999 778888999988443
No 101
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=62.54 E-value=11 Score=36.77 Aligned_cols=43 Identities=28% Similarity=0.391 Sum_probs=34.8
Q ss_pred cCcEEEEeeCCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCcccc
Q 001506 708 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISDN 755 (1065)
Q Consensus 708 iGktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~~ 755 (1065)
.|..|.- .| |..|+|+++.++++.||+ +.+-+|+++|..|+-+
T Consensus 55 ~Gd~VvT-~g---Gi~G~Vv~i~~~~v~lei-~~g~~i~~~r~aI~~v 97 (106)
T PRK05585 55 KGDEVVT-NG---GIIGKVTKVSEDFVIIEL-NDDTEIKIQKSAIAAV 97 (106)
T ss_pred CCCEEEE-CC---CeEEEEEEEeCCEEEEEE-CCCeEEEEEhHHhhhh
Confidence 5666654 44 799999999999999999 4567799999998854
No 102
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=62.12 E-value=4.5 Score=51.51 Aligned_cols=10 Identities=50% Similarity=0.963 Sum_probs=5.3
Q ss_pred hcCCCCCCCcEE
Q 001506 174 ALLPSVRDPKLW 185 (1065)
Q Consensus 174 ~LlPsv~DP~lw 185 (1065)
.|-|+ |+-+|
T Consensus 201 HL~p~--d~e~W 210 (895)
T KOG2076|consen 201 HLNPK--DYELW 210 (895)
T ss_pred hcCCC--ChHHH
Confidence 34454 55666
No 103
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=61.57 E-value=1e+02 Score=40.05 Aligned_cols=8 Identities=38% Similarity=0.974 Sum_probs=3.2
Q ss_pred CCCCCCCC
Q 001506 875 EAPTPGSG 882 (1065)
Q Consensus 875 ~~~TPg~~ 882 (1065)
.+++||.+
T Consensus 198 ~~p~p~~p 205 (1007)
T KOG1984|consen 198 QPPPPGAP 205 (1007)
T ss_pred CCCCCCCC
Confidence 33334443
No 104
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=61.26 E-value=2.7 Score=53.85 Aligned_cols=10 Identities=20% Similarity=0.156 Sum_probs=4.4
Q ss_pred ccccCCchhh
Q 001506 94 EAQVDSDEEE 103 (1065)
Q Consensus 94 EAeVdddeEe 103 (1065)
+..+||.||+
T Consensus 932 ~~~ddd~d~~ 941 (1010)
T KOG1991|consen 932 LDDDDDFDED 941 (1010)
T ss_pred ccccccccch
Confidence 4444444444
No 105
>KOG0699 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=61.04 E-value=3.7 Score=47.42 Aligned_cols=9 Identities=33% Similarity=0.239 Sum_probs=4.3
Q ss_pred hhHHHHHHH
Q 001506 142 EDVEALERR 150 (1065)
Q Consensus 142 ~d~ee~~~~ 150 (1065)
+|..|..+.
T Consensus 372 EDevE~~RI 380 (542)
T KOG0699|consen 372 EDEVETNRI 380 (542)
T ss_pred ccHHHHHHH
Confidence 444555543
No 106
>PRK14639 hypothetical protein; Provisional
Probab=60.91 E-value=15 Score=37.50 Aligned_cols=50 Identities=18% Similarity=0.325 Sum_probs=41.2
Q ss_pred ccccCcEEEEeeCCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 705 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 705 d~liGktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
..++|+.|+|+-..-|-+.|++++++++.+++++-.+.+++.++.+.|.-
T Consensus 84 ~r~~G~~v~v~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I~k 133 (140)
T PRK14639 84 AKSIGELVKITTNEKEKFEGKIVSVDDENITLENLENKEKTTINFNDIKK 133 (140)
T ss_pred HHhCCCEEEEEECCCcEEEEEEEEEeCCEEEEEEccCCcEEEEEhHHeee
Confidence 57899999998755688999999999999999874455678888877764
No 107
>PRK04333 50S ribosomal protein L14e; Validated
Probab=60.60 E-value=12 Score=35.08 Aligned_cols=29 Identities=28% Similarity=0.286 Sum_probs=25.0
Q ss_pred cCcEEEEeeCCCCCceeEEEeec-CCeEEE
Q 001506 708 VGTTVKVRLGPYKGYRGRVVDVK-GQSVRV 736 (1065)
Q Consensus 708 iGktV~I~~GpyKG~~G~Vkd~t-~~~~rV 736 (1065)
+|+-|.+..|+|+|-+++|.++- +..|-|
T Consensus 6 ~GrvV~~~~Grd~gk~~vIv~i~d~~~vlV 35 (84)
T PRK04333 6 VGRVCVKTAGREAGRKCVIVDIIDKNFVLV 35 (84)
T ss_pred ccEEEEEeccCCCCCEEEEEEEecCCEEEE
Confidence 78899999999999999999994 555555
No 108
>PF05793 TFIIF_alpha: Transcription initiation factor IIF, alpha subunit (TFIIF-alpha); InterPro: IPR008851 Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II [].; GO: 0003677 DNA binding, 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1F3U_F 1NHA_A 1I27_A 1J2X_A 2K7L_A 1ONV_A.
Probab=60.59 E-value=2.8 Score=51.51 Aligned_cols=9 Identities=0% Similarity=0.239 Sum_probs=0.0
Q ss_pred CcccccccC
Q 001506 90 FFDLEAQVD 98 (1065)
Q Consensus 90 FlD~EAeVd 98 (1065)
|++++...+
T Consensus 284 Y~SD~ss~e 292 (527)
T PF05793_consen 284 YMSDSSSSE 292 (527)
T ss_dssp ---------
T ss_pred ccccccccc
Confidence 444444333
No 109
>PHA03378 EBNA-3B; Provisional
Probab=60.02 E-value=88 Score=39.38 Aligned_cols=16 Identities=31% Similarity=0.397 Sum_probs=7.5
Q ss_pred ecCCCeeecCCCCCCc
Q 001506 1003 ALPNEIEIVPPRKTDK 1018 (1065)
Q Consensus 1003 v~~~~LE~V~P~kgd~ 1018 (1065)
+-.-|-+-+.|+|.-+
T Consensus 911 ~gpm~~~~i~p~kr~k 926 (991)
T PHA03378 911 VGPMHPTDIPPSKRAK 926 (991)
T ss_pred CCCCChhhCCCchhcc
Confidence 3334445555555433
No 110
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=59.92 E-value=17 Score=35.58 Aligned_cols=49 Identities=22% Similarity=0.308 Sum_probs=35.1
Q ss_pred ccCcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeec
Q 001506 422 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYF 477 (1065)
Q Consensus 422 ~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~F 477 (1065)
...+++||.|.-+ -|+.|+|++|++++|+|.... +-.++|.-+.+....
T Consensus 50 ~~~Lk~Gd~VvT~----gGi~G~Vv~i~~~~v~lei~~---g~~i~~~r~aI~~v~ 98 (106)
T PRK05585 50 LSSLAKGDEVVTN----GGIIGKVTKVSEDFVIIELND---DTEIKIQKSAIAAVL 98 (106)
T ss_pred HHhcCCCCEEEEC----CCeEEEEEEEeCCEEEEEECC---CeEEEEEhHHhhhhc
Confidence 4589999999998 457899999999988887532 134555555444433
No 111
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=59.13 E-value=7.7 Score=50.97 Aligned_cols=7 Identities=14% Similarity=0.349 Sum_probs=3.1
Q ss_pred hhhhccc
Q 001506 259 EMTDVLA 265 (1065)
Q Consensus 259 Em~~vL~ 265 (1065)
=++|+++
T Consensus 1560 LiADYMT 1566 (1640)
T KOG0262|consen 1560 LIADYMT 1566 (1640)
T ss_pred HHHHHHh
Confidence 3444444
No 112
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=58.99 E-value=18 Score=34.59 Aligned_cols=50 Identities=26% Similarity=0.335 Sum_probs=41.1
Q ss_pred CCccccCcEEEEeeCC---CCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 703 GHDALVGTTVKVRLGP---YKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 703 ~~d~liGktV~I~~Gp---yKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
=+..|||..|+|..-+ |-|.-|.|+|-|-++..++-.+ +.+.|.|....+
T Consensus 11 ~~hEliGl~vrVv~s~~~s~vGI~G~VVdETkNtLvi~t~~--~~~~VpK~~~vf 63 (95)
T COG1588 11 IRHELIGLEVRVVRSTNPSYVGIEGRVVDETKNTLVIDTGS--REKVVPKDGAVF 63 (95)
T ss_pred ChHHhcCcEEEEEecCCCCccceeEEEEeeeccEEEEECCC--ceEEEecCcEEE
Confidence 3589999999999876 5677888999999999887766 777888877554
No 113
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=58.70 E-value=12 Score=36.19 Aligned_cols=41 Identities=27% Similarity=0.482 Sum_probs=34.5
Q ss_pred CcEEEEeeCCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 709 GTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 709 GktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
|..|. +.| |+.|+|..+.++++.|+|. .+-.|++.|+.++.
T Consensus 47 GD~Vv-T~g---Gi~G~V~~v~d~~v~I~l~-~~~~i~~~k~aI~~ 87 (97)
T COG1862 47 GDEVV-TIG---GIVGTVTKVGDDTVEIELG-DGTKIKFEKEAIAT 87 (97)
T ss_pred CCEEE-EcC---CeEEEEEEEecCcEEEEEC-CCeEEEEEHHHHHh
Confidence 55554 444 8999999999999999999 78889999999885
No 114
>KOG2418 consensus Microtubule-associated protein TAU [Cytoskeleton]
Probab=58.63 E-value=37 Score=39.63 Aligned_cols=12 Identities=42% Similarity=0.628 Sum_probs=5.8
Q ss_pred eEEEeccchhcc
Q 001506 1051 VKILDMAILAKL 1062 (1065)
Q Consensus 1051 ~kil~~~~L~Kl 1062 (1065)
|-+|+-..||-|
T Consensus 424 idll~spqlatl 435 (448)
T KOG2418|consen 424 IDLLDSPQLATL 435 (448)
T ss_pred cccccCcccchh
Confidence 445555545443
No 115
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=58.62 E-value=56 Score=29.56 Aligned_cols=62 Identities=18% Similarity=0.205 Sum_probs=40.8
Q ss_pred eEEEEEEccc-eEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCCceeeEEEEEC
Q 001506 552 FGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYR 626 (1065)
Q Consensus 552 VGvIv~verd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~HI~r 626 (1065)
.|.|+++-.+ .|.|.+. .|.++.++.. .|+.+ +...+.+||.|.+---++....|.|.|=||
T Consensus 10 ~G~Vi~~~~~~~y~V~~~---~g~~~~c~~~---Gklr~-------~~i~i~vGD~V~ve~~~~~~~~g~Iv~r~~ 72 (72)
T PRK00276 10 EGTVVEALPNAMFRVELE---NGHEVLAHIS---GKMRK-------NYIRILPGDKVTVELSPYDLTKGRITYRHK 72 (72)
T ss_pred EEEEEEEcCCCEEEEEeC---CCCEEEEEEc---cceee-------CCcccCCCCEEEEEEcccCCCeEEEEEEeC
Confidence 3899999877 7777552 3566665532 22221 133489999999985555556788888665
No 116
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=58.37 E-value=14 Score=35.56 Aligned_cols=53 Identities=25% Similarity=0.409 Sum_probs=38.0
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCc
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNH 482 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~F~~GDh 482 (1065)
..+++||.|.-+ -|+.|+|++|.++.++|.... +-.++|.-+.+....+.|+.
T Consensus 42 ~sL~kGD~VvT~----gGi~G~V~~v~d~~v~I~l~~---~~~i~~~k~aI~~v~~~~~~ 94 (97)
T COG1862 42 NSLKKGDEVVTI----GGIVGTVTKVGDDTVEIELGD---GTKIKFEKEAIATVLEKGDL 94 (97)
T ss_pred HhccCCCEEEEc----CCeEEEEEEEecCcEEEEECC---CeEEEEEHHHHHhhccCccc
Confidence 579999999988 458899999999988887752 23466665555544444443
No 117
>PRK04333 50S ribosomal protein L14e; Validated
Probab=58.28 E-value=17 Score=34.12 Aligned_cols=33 Identities=18% Similarity=0.195 Sum_probs=28.1
Q ss_pred cCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEE
Q 001506 272 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTV 305 (1065)
Q Consensus 272 ~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~V 305 (1065)
.+++|..|.+..|.|+|-+|.|+++.. .++|.|
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d-~~~vlV 35 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIID-KNFVLV 35 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEec-CCEEEE
Confidence 578999999999999999999999854 356655
No 118
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=57.94 E-value=7.7 Score=46.98 Aligned_cols=13 Identities=23% Similarity=0.156 Sum_probs=6.0
Q ss_pred HHHHHHHHHHHhc
Q 001506 144 VEALERRIQARYA 156 (1065)
Q Consensus 144 ~ee~~~~l~eRY~ 156 (1065)
+|+-|+.=++||.
T Consensus 581 we~ka~~dk~ry~ 593 (615)
T KOG0526|consen 581 WEDKAAVDKQRYE 593 (615)
T ss_pred hhHHHHHHHHHHH
Confidence 3344444455554
No 119
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=57.69 E-value=44 Score=30.50 Aligned_cols=49 Identities=18% Similarity=0.222 Sum_probs=30.2
Q ss_pred CcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeecc------------ccceeeccCCCcEEE
Q 001506 424 HFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNS------------KELCKYFEPGNHVKV 485 (1065)
Q Consensus 424 ~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~------------~~LrK~F~~GDhVkV 485 (1065)
.+++||.|+ |+|++|.++.+.+....+ -+--++. .++.+.|++||.|++
T Consensus 3 ~p~~GdiV~----------g~V~~i~~~g~~v~i~~~---~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~ 63 (86)
T cd05789 3 IPEVGDVVI----------GRVTEVGFKRWKVDINSP---YDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVA 63 (86)
T ss_pred cCCCCCEEE----------EEEEEECCCEEEEECCCC---eEEEEEHHHccCCCCccchHHHHhhCCCCCEEEE
Confidence 346777774 778888888666543311 1122333 344557999999976
No 120
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=57.63 E-value=58 Score=30.07 Aligned_cols=63 Identities=14% Similarity=0.169 Sum_probs=45.1
Q ss_pred ceEEEEEEccc-eEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCCceeeEEEEECC
Q 001506 551 SFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRG 627 (1065)
Q Consensus 551 tVGvIv~verd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~ 627 (1065)
..|.|+++-.+ .|.|...+ |..+.+ .|..|+.++ =-|..||.|.|---|+.-..|.|.|.|..
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~---g~~~la---~i~gK~rk~--------iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~~ 65 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFD---GKKRLC---RIRGKMRKR--------VWINEGDIVLVAPWDFQDDKADIIYKYTP 65 (77)
T ss_pred EEEEEEEEcCCCEEEEEECC---CCEEEE---EEchhhccc--------EEEcCCCEEEEEeccccCCEEEEEEEcCH
Confidence 46888888765 58888753 555443 344444321 24999999999877888889999999864
No 121
>KOG2393 consensus Transcription initiation factor IIF, large subunit (RAP74) [Transcription]
Probab=56.84 E-value=8.6 Score=46.66 Aligned_cols=26 Identities=27% Similarity=0.331 Sum_probs=13.7
Q ss_pred cccccccCCchhhhcc---ccccccccCC
Q 001506 91 FDLEAQVDSDEEEDEE---EGEDDFIVDG 116 (1065)
Q Consensus 91 lD~EAeVdddeEeeee---e~~~~fi~~~ 116 (1065)
.|++|-+..|+-|.++ |++++|-++.
T Consensus 279 ~Dd~a~eesdd~d~e~~E~DYdee~addE 307 (555)
T KOG2393|consen 279 VDDEAFEESDDGDNEGRELDYDEESADDE 307 (555)
T ss_pred CcccccccCCCccccccccccccccCCcc
Confidence 4888866554433322 4445555443
No 122
>PRK04313 30S ribosomal protein S4e; Validated
Probab=55.74 E-value=63 Score=36.05 Aligned_cols=73 Identities=26% Similarity=0.396 Sum_probs=50.2
Q ss_pred cEEEEEEeCCCCeEEEEe--ccCCCCceEEec-CCC--eeecCCCCCCcEEEEcCCCCCceEEEEEEeC----CCcEEEe
Q 001506 975 VVGVIREVLPDGSCRVVL--GSSGNGDTITAL-PNE--IEIVPPRKTDKIKIMGGPHRGATGKLIGVDG----TDGIVKV 1045 (1065)
Q Consensus 975 ~~GvI~~V~~~g~~~V~l--~~~~~g~~v~v~-~~~--LE~V~P~kgd~VkVi~G~~rG~tG~LisiD~----~dgiVk~ 1045 (1065)
+.|++.=++-||.+-++- ..-..+++|.++ .++ ++.+.-..|..+.|+.|.+.|.+|++.+|.. ..-+|.+
T Consensus 129 ~gG~~ql~~hDGrni~~~~~~~~k~~Dtv~i~l~~~kI~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i 208 (237)
T PRK04313 129 KGGKIQLNLHDGRNILVDVEDDYKTGDSLLISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTL 208 (237)
T ss_pred cCCEEEEEecCCceEEccCccccccCCEEEEECCCCceeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEE
Confidence 345565566677764432 121125666666 233 6666679999999999999999999999973 4567877
Q ss_pred cC
Q 001506 1046 DV 1047 (1065)
Q Consensus 1046 d~ 1047 (1065)
.+
T Consensus 209 ~d 210 (237)
T PRK04313 209 ED 210 (237)
T ss_pred Ec
Confidence 63
No 123
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=54.31 E-value=6.6 Score=48.75 Aligned_cols=10 Identities=30% Similarity=0.182 Sum_probs=6.7
Q ss_pred CCcccccccC
Q 001506 89 EFFDLEAQVD 98 (1065)
Q Consensus 89 ~FlD~EAeVd 98 (1065)
++||+-|-|=
T Consensus 377 AaLDVLanvf 386 (885)
T KOG2023|consen 377 AALDVLANVF 386 (885)
T ss_pred HHHHHHHHhh
Confidence 5777777653
No 124
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=54.12 E-value=73 Score=31.00 Aligned_cols=74 Identities=16% Similarity=0.155 Sum_probs=50.7
Q ss_pred eeeeeEEeCC-CceEEEEEEccc-eEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCCc
Q 001506 540 ELRDLVLLDN-NSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGK 617 (1065)
Q Consensus 540 ~l~DLVqLd~-~tVGvIv~verd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr 617 (1065)
..++|+..+. +..|.|+++-.+ .|.|... +|..+.+. |..|+.++ =-|..||.|.|---||.--
T Consensus 11 ~~~~~~~p~e~e~~g~V~~~lG~~~~~V~~~---dG~~~la~---i~GK~Rk~--------IwI~~GD~VlVe~~~~~~~ 76 (100)
T PRK04012 11 TRVRLPMPEEGEVFGVVEQMLGANRVRVRCM---DGVERMGR---IPGKMKKR--------MWIREGDVVIVAPWDFQDE 76 (100)
T ss_pred eeEEccCCCCCEEEEEEEEEcCCCEEEEEeC---CCCEEEEE---Echhhccc--------EEecCCCEEEEEecccCCC
Confidence 4566777754 567999998765 5888874 35555443 33444321 1488999999987677666
Q ss_pred eeeEEEEECC
Q 001506 618 QGPVEHIYRG 627 (1065)
Q Consensus 618 ~G~V~HI~r~ 627 (1065)
.|.|.|.|..
T Consensus 77 kg~Iv~r~~~ 86 (100)
T PRK04012 77 KADIIWRYTK 86 (100)
T ss_pred EEEEEEEcCH
Confidence 8999999863
No 125
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=53.43 E-value=25 Score=28.54 Aligned_cols=28 Identities=32% Similarity=0.523 Sum_probs=25.2
Q ss_pred eeEEEeecCCeEEEEecCCCeEEEEecCC
Q 001506 723 RGRVVDVKGQSVRVELESQMKVVTVDRSM 751 (1065)
Q Consensus 723 ~G~Vkd~t~~~~rVELhs~~k~I~V~r~~ 751 (1065)
+|.|++..+..++|++.. .++++|.+++
T Consensus 15 ~g~I~~~~g~~vtV~~~~-G~~~tv~~dd 42 (42)
T PF02736_consen 15 KGEIIEEEGDKVTVKTED-GKEVTVKKDD 42 (42)
T ss_dssp EEEEEEEESSEEEEEETT-TEEEEEEGGG
T ss_pred EEEEEEEcCCEEEEEECC-CCEEEeCCCC
Confidence 589999999999999999 8899998753
No 126
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=52.80 E-value=52 Score=46.90 Aligned_cols=94 Identities=15% Similarity=0.178 Sum_probs=66.1
Q ss_pred ccCcCCCCEEEEecccccCceeEEEEEcCC--eEEEee-cCCCCCcceeecccccee-----------eccCCCcEEEec
Q 001506 422 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRP-EMKGLPKTLAVNSKELCK-----------YFEPGNHVKVVS 487 (1065)
Q Consensus 422 ~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d--~V~i~~-~~~~l~~~l~v~~~~LrK-----------~F~~GDhVkVi~ 487 (1065)
...|++|+.|+.-.| ....|+.|+.+ .|++.. .. +....|.++.+.+ -|..||.|+...
T Consensus 1327 ~~~Y~~G~vv~~~~~----~y~~V~~vd~~~~~v~l~~~~~---G~~~~~~p~~~~~~~~~~y~~~~~~l~~GDri~~t~ 1399 (1960)
T TIGR02760 1327 MMPFEKGAVLRLKKD----AYLTIADIDREHGKLTVADIKT---GSERDILPRQLDHTFTSLYSDSELPLAKGDKIRLRA 1399 (1960)
T ss_pred ccccCCCcEEEecCC----cEEEEEEecCCCCEEEEEecCC---CCeEeeChhhcCcccceeeccccccccCCCEEEEee
Confidence 357999999996655 45678888754 555543 21 3345566665542 578999999874
Q ss_pred c-----ccCCceeEEEEEeCcEEEEEeCCCCceEEEecccc
Q 001506 488 G-----TQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDV 523 (1065)
Q Consensus 488 G-----~~~getGlVVkVe~~~v~vlSD~t~~ei~V~~~dL 523 (1065)
. .-.|+.+.|+.|+.+.+++.+|. ++++++.+.+.
T Consensus 1400 ~d~~~g~~n~~~~~V~~v~~~~~~~~~~~-~~~~~l~~~~~ 1439 (1960)
T TIGR02760 1400 TDKNRGIKANEVYTVTQVVNGLSVQLSKV-KNSLSLKPIQA 1439 (1960)
T ss_pred cCcccccccCCeEEEEEEcCCcEEEEcCC-CceEEecCchh
Confidence 3 34589999999988888888775 57788866544
No 127
>PRK11760 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional
Probab=52.36 E-value=24 Score=41.35 Aligned_cols=58 Identities=17% Similarity=0.283 Sum_probs=46.5
Q ss_pred EEEEccCchHHHHHHHHHHHHHhhCCCcceEEEEeeCCCccEEEEEecchHHHHHHHhcCcc
Q 001506 185 WMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRN 246 (1065)
Q Consensus 185 w~Vkck~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~~~lkGYIYIEA~~~~~V~~ai~Gl~~ 246 (1065)
|..-|++|.|++.+.-|..|+-. +.|+...-...-.|||..|.+...+...+++.++-
T Consensus 4 l~lyCR~GFE~e~aaEi~~~a~~----~~~~G~~~~~~~sgyv~f~~~~~~~~~~l~~~l~~ 61 (357)
T PRK11760 4 LLLYCRPGFEKECAAEITDKAAE----LGVFGYARVKENSGYVIFECYQPDDADRLARELPF 61 (357)
T ss_pred EEEEeCCCchHHHHHHHHHHHHh----cCCcccccccCCCeEEEEEecCcchHHHHHhhCCc
Confidence 88999999999999999999765 34555433445579999999998999988887654
No 128
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=52.01 E-value=38 Score=29.06 Aligned_cols=50 Identities=22% Similarity=0.122 Sum_probs=37.6
Q ss_pred eccCCCcEEEec---cccCCceeEEEEEeC-cEEEEEeCC--CCceEEEecccccccc
Q 001506 476 YFEPGNHVKVVS---GTQAGATGMVLKVEQ-HVLIILSDT--TKEDIRVFADDVVESS 527 (1065)
Q Consensus 476 ~F~~GDhVkVi~---G~~~getGlVVkVe~-~~v~vlSD~--t~~ei~V~~~dL~~~~ 527 (1065)
.|++||.|-+-. |.+ -.|+|+++.+ +.+.|.-+. +..+.+|-..+|+-+.
T Consensus 2 ~~~~G~~Ve~~~~~~~~W--~~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LRp~~ 57 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSW--WEAVVTKVLGDGKYLVRYLTESEPLKETVDWSDLRPHP 57 (61)
T ss_pred CcCCCCEEEEEECCCCEE--EEEEEEEECCCCEEEEEECCCCcccEEEEeHHHcccCC
Confidence 589999998873 222 3799999988 667666666 7778888888887654
No 129
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=51.70 E-value=26 Score=33.73 Aligned_cols=53 Identities=25% Similarity=0.238 Sum_probs=40.8
Q ss_pred cCcCCCCEEEEe------cc----cccCceeEEEEEcCCeEEEeecCCCCCcceeecccccee
Q 001506 423 GHFMKGDAVIVI------KG----DLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK 475 (1065)
Q Consensus 423 ~~F~~GD~V~V~------~G----el~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK 475 (1065)
..|.+||.|-|. .| .+.|.+|+|+.+.++-..|.....+..+.|-+.+..|+.
T Consensus 31 ~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~~G~k~K~liv~peHLk~ 93 (98)
T COG2139 31 QEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVYDGNKEKTLIVRPEHLKP 93 (98)
T ss_pred hhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEecCCceEEEEeCHHHccc
Confidence 579999999774 23 468899999999999776666666666778777777765
No 130
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=51.60 E-value=67 Score=45.16 Aligned_cols=98 Identities=15% Similarity=0.194 Sum_probs=70.2
Q ss_pred ccCcCCCCEEEEeccc-ccCceeEEEEEcCC--eEEEeecCCCCCcceeecccccee----------eccCCCcEEEecc
Q 001506 422 KGHFMKGDAVIVIKGD-LKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCK----------YFEPGNHVKVVSG 488 (1065)
Q Consensus 422 ~~~F~~GD~V~V~~Ge-l~gl~G~V~~V~~d--~V~i~~~~~~l~~~l~v~~~~LrK----------~F~~GDhVkVi~G 488 (1065)
..+|++|+.|+-.... +++...+|+.|+.+ .++|.... +..+.|.++.+.+ .|..||.+++...
T Consensus 646 a~~Y~~G~vi~~~~~~~~~~~~y~V~~v~~~~n~LtL~~~~---G~~~~~~p~~~~~~~~vy~~~~ieiA~GDrLr~T~n 722 (1747)
T PRK13709 646 RDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQ---GETQVVKISSLDSSWSLFRPEKMPVADGERLRVLGK 722 (1747)
T ss_pred hhcCCCCcEEEeeccccccCccEEEEEEcCCCCEEEEEcCC---CCEEEeChHHhcccceeccccccccCCCCEEEEccC
Confidence 4689999999986643 34656799999876 45554433 3456777766632 3688999999854
Q ss_pred -----ccCCceeEEEEEeCcEEEEEeCCCCceEEEeccc
Q 001506 489 -----TQAGATGMVLKVEQHVLIILSDTTKEDIRVFADD 522 (1065)
Q Consensus 489 -----~~~getGlVVkVe~~~v~vlSD~t~~ei~V~~~d 522 (1065)
...|+.+.|+.|+++.++|-.+-..+++++-.+.
T Consensus 723 d~~~~l~Ngd~~tV~~i~~~~i~l~~~~~gk~~~L~~~~ 761 (1747)
T PRK13709 723 IPGLRLKGGDRLQVTSVSEDGLTVVVPGRAEPATLPVDD 761 (1747)
T ss_pred CcccCccCCCEEEEEEecCCeEEEEECCCceEEEeCCcc
Confidence 2468999999999999999876555667664443
No 131
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=51.39 E-value=21 Score=34.38 Aligned_cols=56 Identities=16% Similarity=0.287 Sum_probs=40.5
Q ss_pred cccceeeccCCCcEEEe------cc----ccCCceeEEEEEeCcEEEE--EeCCCCceEEEecccccc
Q 001506 470 SKELCKYFEPGNHVKVV------SG----TQAGATGMVLKVEQHVLII--LSDTTKEDIRVFADDVVE 525 (1065)
Q Consensus 470 ~~~LrK~F~~GDhVkVi------~G----~~~getGlVVkVe~~~v~v--lSD~t~~ei~V~~~dL~~ 525 (1065)
.+-+-+-|++||.|-++ .| +|.|-||.|+-+-++.+.| ......+.|-|.|.+|+-
T Consensus 26 lsr~l~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~~G~k~K~liv~peHLk~ 93 (98)
T COG2139 26 LSRYLQEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVYDGNKEKTLIVRPEHLKP 93 (98)
T ss_pred hhhHHhhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEecCCceEEEEeCHHHccc
Confidence 34444569999999665 34 4789999999999886544 333456778888888864
No 132
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=51.27 E-value=50 Score=29.02 Aligned_cols=42 Identities=26% Similarity=0.427 Sum_probs=29.0
Q ss_pred ceeEEEEEcCCeEEEeecCCCCCcceeeccccce--eeccCCCcEEEe
Q 001506 441 LKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELC--KYFEPGNHVKVV 486 (1065)
Q Consensus 441 l~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~Lr--K~F~~GDhVkVi 486 (1065)
++|+|++++.+.+.|... . -+--+|.+++. ..|++||+|+|.
T Consensus 7 V~G~V~~~~~~~~~vdig--~--~eg~lp~~e~~~~~~~~~Gd~v~v~ 50 (67)
T cd04455 7 VTGIVKRVDRGNVIVDLG--K--VEAILPKKEQIPGESYRPGDRIKAY 50 (67)
T ss_pred EEEEEEEEcCCCEEEEcC--C--eEEEeeHHHCCCCCcCCCCCEEEEE
Confidence 468999998887666432 2 23455666664 579999999874
No 133
>PF04050 Upf2: Up-frameshift suppressor 2 ; InterPro: IPR007193 This entry represents Up-frameshift suppressor 2 (also known as Nonsense-mediated mRNA decay protein 2). Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay [].; PDB: 2WJV_D.
Probab=50.95 E-value=5.1 Score=42.11 Aligned_cols=11 Identities=0% Similarity=0.208 Sum_probs=6.5
Q ss_pred HHHHHHHHHhc
Q 001506 146 ALERRIQARYA 156 (1065)
Q Consensus 146 e~~~~l~eRY~ 156 (1065)
++++++.+=|.
T Consensus 68 ef~kmm~eS~~ 78 (170)
T PF04050_consen 68 EFQKMMAESLE 78 (170)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHH
Confidence 56666666554
No 134
>PRK07594 type III secretion system ATPase SsaN; Validated
Probab=50.76 E-value=2.4e+02 Score=34.33 Aligned_cols=62 Identities=10% Similarity=0.052 Sum_probs=44.6
Q ss_pred ccccCcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCcEEEeccccCCceeEEEE
Q 001506 420 RKKGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLK 499 (1065)
Q Consensus 420 ~~~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~F~~GDhVkVi~G~~~getGlVVk 499 (1065)
+.+-.|-||+.+..+ |+|++|.+..|.+... ....|+.|.|-. .+..|.|+.
T Consensus 8 ~~~~~~~~~~~~~~~--------G~v~~v~g~~~~~~~~-----------------~~~~ge~~~i~~---~~~~~eVv~ 59 (433)
T PRK07594 8 RLRLKYPPPDGYCRW--------GRIQDVSATLLNAWLP-----------------GVFMGELCCIKP---GEELAEVVG 59 (433)
T ss_pred hCccCCCCCCcccee--------eEEEEEECCEEEEEEC-----------------CcCCCCEEEEec---CCeEEEEEE
Confidence 345567787777655 9999999998887632 135778887722 346899999
Q ss_pred EeCcEEEEEe
Q 001506 500 VEQHVLIILS 509 (1065)
Q Consensus 500 Ve~~~v~vlS 509 (1065)
++++.+.+..
T Consensus 60 ~~~~~~~l~~ 69 (433)
T PRK07594 60 INGSKALLSP 69 (433)
T ss_pred EcCCeEEEEE
Confidence 9999877643
No 135
>PLN00208 translation initiation factor (eIF); Provisional
Probab=49.70 E-value=80 Score=32.73 Aligned_cols=76 Identities=20% Similarity=0.247 Sum_probs=55.2
Q ss_pred ceeeeeeEEeC-CCceEEEEEEccc-eEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCC
Q 001506 538 DYELRDLVLLD-NNSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCK 615 (1065)
Q Consensus 538 ~y~l~DLVqLd-~~tVGvIv~verd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~ 615 (1065)
.-+..+|+..+ .+.+|.|+++-.+ .|.|.+.+ |..+.+. |..|+.++ -=|+.||.|.|---+|.
T Consensus 20 ~~~~~el~~p~egq~~g~V~~~lGn~~~~V~c~d---G~~rLa~---IpGKmRKr--------IWI~~GD~VlVel~~~d 85 (145)
T PLN00208 20 DDEKRELIFKEDGQEYAQVLRMLGNGRCEALCID---GTKRLCH---IRGKMRKK--------VWIAAGDIILVGLRDYQ 85 (145)
T ss_pred ccceeecccCCCCcEEEEEEEEcCCCEEEEEECC---CCEEEEE---Eeccceee--------EEecCCCEEEEEccCCC
Confidence 45677888775 4678999999875 58888753 5555433 44444332 24999999999888888
Q ss_pred CceeeEEEEECC
Q 001506 616 GKQGPVEHIYRG 627 (1065)
Q Consensus 616 gr~G~V~HI~r~ 627 (1065)
--.|.|.|.|..
T Consensus 86 ~~KgdIv~ry~~ 97 (145)
T PLN00208 86 DDKADVILKYMP 97 (145)
T ss_pred CCEEEEEEEcCH
Confidence 789999999865
No 136
>smart00361 RRM_1 RNA recognition motif.
Probab=49.64 E-value=48 Score=29.24 Aligned_cols=28 Identities=21% Similarity=0.432 Sum_probs=25.2
Q ss_pred CCCccEEEEEecchHHHHHHHhcCcccc
Q 001506 221 DHLKNYIYIEADKEAHVKEACKGLRNIY 248 (1065)
Q Consensus 221 ~~lkGYIYIEA~~~~~V~~ai~Gl~~v~ 248 (1065)
.+.+||.||+-....+...||+.|.+-.
T Consensus 34 ~~~rG~~fV~f~~~~dA~~A~~~l~g~~ 61 (70)
T smart00361 34 NHKRGNVYITFERSEDAARAIVDLNGRY 61 (70)
T ss_pred CCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence 4579999999999999999999988855
No 137
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=49.16 E-value=36 Score=31.48 Aligned_cols=51 Identities=24% Similarity=0.298 Sum_probs=37.6
Q ss_pred CCCCEEEEec----ccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceee
Q 001506 426 MKGDAVIVIK----GDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 476 (1065)
Q Consensus 426 ~~GD~V~V~~----Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~ 476 (1065)
..|-.|+|.- +..+...|.+.+++++.|+|..+.+.-.+++.++..+++|+
T Consensus 23 ~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~~~~~~~~~i~~~~I~ka 77 (83)
T cd01734 23 AVGKYVHVKLYQPIDGQKEFEGTLLGVDDDTVTLEVDIKTRGKTVEIPLDKIAKA 77 (83)
T ss_pred hCCCEEEEEEEcccCCeEEEEEEEEeEeCCEEEEEEecCCCCeEEEEEhHHeeEE
Confidence 3577777743 44567899999999999999875332346788898888874
No 138
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=49.05 E-value=1e+02 Score=28.52 Aligned_cols=64 Identities=16% Similarity=0.118 Sum_probs=44.9
Q ss_pred CceEEEEEEccc-eEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCC-CCceeeEEEEECC
Q 001506 550 NSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPC-KGKQGPVEHIYRG 627 (1065)
Q Consensus 550 ~tVGvIv~verd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~-~gr~G~V~HI~r~ 627 (1065)
+.+|.|+++-.+ .|.|.+. +|..+.+. |..|+.++ ==|..||.|.|---|+ .--.|.|.|.|+.
T Consensus 1 q~i~~V~~~lG~~~~~V~~~---dg~~~l~~---i~gK~Rk~--------iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~~ 66 (78)
T cd04456 1 QQIVRVLRMLGNNRHEVECA---DGQRRLVS---IPGKLRKN--------IWIKRGDFLIVDPIEEGEDVKADIIFVYCK 66 (78)
T ss_pred CeEEEEEEECCCCEEEEEEC---CCCEEEEE---EchhhccC--------EEEcCCCEEEEEecccCCCceEEEEEEeCH
Confidence 357889988865 5788874 36555543 44444331 2499999999987777 4578999999874
No 139
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=48.86 E-value=65 Score=28.08 Aligned_cols=43 Identities=23% Similarity=0.301 Sum_probs=27.8
Q ss_pred ceeEEEEEcCCeEEEeecCCCCCcceeeccccce--------eeccCCCcEEEe
Q 001506 441 LKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELC--------KYFEPGNHVKVV 486 (1065)
Q Consensus 441 l~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~Lr--------K~F~~GDhVkVi 486 (1065)
.+|+|++|....+.|.-.. ..+-.++.+++. +.|++||.+++.
T Consensus 4 v~g~V~~i~~~~~~v~l~~---~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~ 54 (70)
T cd05687 4 VKGTVVSVDDDEVLVDIGY---KSEGIIPISEFSDDPIENGEDEVKVGDEVEVY 54 (70)
T ss_pred EEEEEEEEeCCEEEEEeCC---CceEEEEHHHhCccccCCHhHcCCCCCEEEEE
Confidence 4689999988866665421 122334445553 569999999874
No 140
>PRK14638 hypothetical protein; Provisional
Probab=48.82 E-value=28 Score=36.03 Aligned_cols=48 Identities=10% Similarity=0.155 Sum_probs=39.1
Q ss_pred ccccCcEEEEeeCCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 705 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 705 d~liGktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
..++|+.|+|+-..-|-+.|+++++++..++++. +.+++.++.+.|.-
T Consensus 96 ~r~~G~~v~V~~~~~k~~~G~L~~~~~~~i~l~~--~~~~~~i~~~~I~~ 143 (150)
T PRK14638 96 VRFTGKLAKIVTKDGKTFIGRIESFVDGTITISD--EKEKYEINIDDVKR 143 (150)
T ss_pred HHhCCCEEEEEECCCcEEEEEEEEEeCCEEEEEE--CCcEEEEEhHHcce
Confidence 5789999999753348899999999999999874 56778888877764
No 141
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=48.32 E-value=8.3 Score=47.92 Aligned_cols=31 Identities=19% Similarity=0.450 Sum_probs=15.2
Q ss_pred ceEEEEe--eCCCccEEEEEecchHHHHHHHhcC
Q 001506 213 QIRSVIA--LDHLKNYIYIEADKEAHVKEACKGL 244 (1065)
Q Consensus 213 ~I~Svf~--~~~lkGYIYIEA~~~~~V~~ai~Gl 244 (1065)
-|.|+-+ ...+.-||.=+. .+...+..+.|+
T Consensus 449 lVRsITCWTLsRys~wv~~~~-~~~~f~pvL~~l 481 (885)
T KOG2023|consen 449 LVRSITCWTLSRYSKWVVQDS-RDEYFKPVLEGL 481 (885)
T ss_pred ceeeeeeeeHhhhhhhHhcCC-hHhhhHHHHHHH
Confidence 3555533 344555555544 334455555554
No 142
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=48.31 E-value=28 Score=32.59 Aligned_cols=43 Identities=23% Similarity=0.461 Sum_probs=31.7
Q ss_pred ccceeeccCCCcEEEeccccCCceeEEEEEeCcEEEEEeCCCCceEEE
Q 001506 471 KELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRV 518 (1065)
Q Consensus 471 ~~LrK~F~~GDhVkVi~G~~~getGlVVkVe~~~v~vlSD~t~~ei~V 518 (1065)
++++...++||.|.-++|-| |.|+.++++.++|-.. .+.++++
T Consensus 32 ~~m~~~L~~Gd~VvT~gGi~----G~V~~i~d~~v~vei~-~g~~i~~ 74 (84)
T TIGR00739 32 KKLIESLKKGDKVLTIGGII----GTVTKIAENTIVIELN-DNTEITF 74 (84)
T ss_pred HHHHHhCCCCCEEEECCCeE----EEEEEEeCCEEEEEEC-CCeEEEE
Confidence 35667789999998888755 9999999998876432 2344444
No 143
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=48.31 E-value=58 Score=29.53 Aligned_cols=47 Identities=28% Similarity=0.375 Sum_probs=30.9
Q ss_pred CCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeec--------cccceeeccCCCcEEE
Q 001506 426 MKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVN--------SKELCKYFEPGNHVKV 485 (1065)
Q Consensus 426 ~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~--------~~~LrK~F~~GDhVkV 485 (1065)
++||.|. |+|++|.++.+.|..... -+-.++ .+++...|++||.+++
T Consensus 5 ~~GdiV~----------G~V~~v~~~~~~V~i~~~---~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~ 59 (82)
T cd04454 5 DVGDIVI----------GIVTEVNSRFWKVDILSR---GTARLEDSSATEKDKKEIRKSLQPGDLILA 59 (82)
T ss_pred CCCCEEE----------EEEEEEcCCEEEEEeCCC---ceEEeechhccCcchHHHHhcCCCCCEEEE
Confidence 5677663 889999999777655321 112222 3455677999999976
No 144
>KOG1980 consensus Uncharacterized conserved protein [Function unknown]
Probab=48.25 E-value=4.7 Score=49.68 Aligned_cols=8 Identities=38% Similarity=0.376 Sum_probs=4.3
Q ss_pred HHHHHHHh
Q 001506 235 AHVKEACK 242 (1065)
Q Consensus 235 ~~V~~ai~ 242 (1065)
-.|+++++
T Consensus 536 ~~i~E~~~ 543 (754)
T KOG1980|consen 536 VSILEAIK 543 (754)
T ss_pred HHHHHHHh
Confidence 44555555
No 145
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=47.83 E-value=9.9 Score=46.09 Aligned_cols=16 Identities=6% Similarity=0.308 Sum_probs=9.6
Q ss_pred hHHHHHHHHHHHhcCC
Q 001506 143 DVEALERRIQARYARS 158 (1065)
Q Consensus 143 d~ee~~~~l~eRY~~~ 158 (1065)
..-++++..=+++...
T Consensus 560 ~~~dv~kk~g~~wk~m 575 (615)
T KOG0526|consen 560 SVGDVAKKAGEKWKQM 575 (615)
T ss_pred hHHHHHHHHhHHHhhh
Confidence 4456666666666543
No 146
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=47.51 E-value=30 Score=35.80 Aligned_cols=50 Identities=28% Similarity=0.502 Sum_probs=39.0
Q ss_pred ccccCcEEEEe----eCCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 705 DALVGTTVKVR----LGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 705 d~liGktV~I~----~GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
..++|+.|+|+ .+.-|=+.|++.+++++.+.++...+.|+++++.+.|.-
T Consensus 94 ~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I~~ 147 (154)
T PRK00092 94 RRFIGREVKVKLYEPIDGRKKFQGILLAVDGETVTLEVEGKEKEVEIPLDNIAK 147 (154)
T ss_pred HHhCCCeEEEEEEcccCCceEEEEEEEEeeCCEEEEEECCCeEEEEEEHHHcce
Confidence 57899999997 244466789999999999988876443488888888764
No 147
>PF01868 UPF0086: Domain of unknown function UPF0086; InterPro: IPR002730 The p29 subunit (also known as Rpp29 or Pop4) of the related ribonucleoproteins ribonuclease (RNase) P and RNase MRP can be found in both eukaryotes and arachea []. The structure of the RNase P subunit, Rpp29, from Methanobacterium thermoautotrophicum has been determined. Mth Rpp29 is a member of the oligonucleotide/oligosaccharide binding fold family. It contains a structured beta-barrel core and unstructured N- and C-terminal extensions bearing several highly conserved amino acid residues that could be involved in RNA contacts in the protein-RNA complex []. Rpp29 (3.1.26.5 from EC) catalyses the endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. It interacts with the Rpp25 and Pop5 subunits. RNase P is a ubiquitous ribonucleoprotein enzyme primarily responsible for cleaving the 5' leader sequence during maturation of tRNAs in all three domains of life. In eubacteria, this enzyme is made up of two subunits: a large RNA (approximately 120 kDa) responsible for mediating catalysis, and a small protein cofactor (approximately 15 kDa) that modulates substrate recognition and is required for efficient in vivo catalysis. In contrast, multiple proteins are associated with eukaryotic and archaeal RNase P, and these proteins exhibit no recognizable homology to the conserved bacterial protein subunit. In reconstitution experiments with recombinantly expressed and purified protein subunits Mth Rpp29, a homologue of the Rpp29 protein subunit from eukaryotic RNase P, is an essential protein component of the archaeal holoenzyme []. In Saccharomyces cerevisiae (Baker's yeast), RNase P consists of 9 protein subunits (Pop1, Pop3-8, Rpr2 and Rpp1), while in humans there are 10 subunits (Rpp14, 20, 21, 25, 29, 30, 38, 40, hPop1, 5). RNase MRP (mitochondrial RNA processing) is an rRNA processing enzyme that cleaves a specific site within precursor rRNA to generate the mature 5'-end of 5.8S rRNA []. RNase MRP also cleaves primers for mitochondrial DNA replication and CLB2 mRNA. In yeast, RNase MRP possesses one putatively catalytic RNA and at least 9 protein subunits and is highly related to RNase P (Pop1, Pop3-Pop8, Rpp1, Snm1 and Rmp1).; GO: 0003723 RNA binding, 0004540 ribonuclease activity, 0006364 rRNA processing, 0006379 mRNA cleavage, 0008033 tRNA processing, 0000172 ribonuclease MRP complex, 0030677 ribonuclease P complex; PDB: 1V76_B 2ZAE_C 1OQK_A 2KI7_A 1TSF_A 1TS9_A 1PC0_A.
Probab=47.41 E-value=51 Score=31.17 Aligned_cols=50 Identities=22% Similarity=0.248 Sum_probs=38.9
Q ss_pred CccccCcEEEEeeCC---CCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 704 HDALVGTTVKVRLGP---YKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 704 ~d~liGktV~I~~Gp---yKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
+.+|+|-.|+|.+=+ |-|..|+|++-|..+++|. ...+|+++|.|.+-.+
T Consensus 9 ~~dl~G~~i~V~~s~~pslvG~~GiVV~ETknt~~I~-t~~~~~~~IpK~~~vF 61 (89)
T PF01868_consen 9 KADLIGAKIEVVRSKNPSLVGIEGIVVDETKNTFVIV-TEDGKVKTIPKAGSVF 61 (89)
T ss_dssp TS--TT-EEEEEEESSCCCTTEEEEEEEEETTEEEEE-ETTEEEEEEESTTEEE
T ss_pred hhhhcCCEEEEEEcCCCCccCCEEEEEEcccceEEEE-ecCCcEEEEecCCEEE
Confidence 367899999998765 7799999999999999986 4455789999988664
No 148
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=47.15 E-value=32 Score=34.96 Aligned_cols=50 Identities=30% Similarity=0.556 Sum_probs=35.8
Q ss_pred ccccCcEEEEee-CCC---CCceeEEEeecCCeEEEEecCCC--eEEEEecCCccc
Q 001506 705 DALVGTTVKVRL-GPY---KGYRGRVVDVKGQSVRVELESQM--KVVTVDRSMISD 754 (1065)
Q Consensus 705 d~liGktV~I~~-Gpy---KG~~G~Vkd~t~~~~rVELhs~~--k~I~V~r~~l~~ 754 (1065)
..++|+.|+|+- -+. |=+.|++.++++..+++++..+. ++++|+.++|.-
T Consensus 83 ~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~~I~~~~I~k 138 (141)
T PF02576_consen 83 ERFIGRKVKVKLKQPVNGRKEFEGKLLEVDEDEITLEVEGKGKKKEVEIPFSDIKK 138 (141)
T ss_dssp HHH-SEEEEEE-SS-SSS-SEEEEEEEEEETTEEEEEEE-SS-EEEEEE-SS--SS
T ss_pred HHhcCCeEEEEEeccCCCcEEEEEEEEEEeCCEEEEEECCccceEEEEEEHHHCce
Confidence 578999999995 333 44799999999999999998874 688998887753
No 149
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=46.93 E-value=72 Score=30.97 Aligned_cols=64 Identities=22% Similarity=0.202 Sum_probs=42.7
Q ss_pred CCCceEEEEEEccc-eEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCCc---eeeEEE
Q 001506 548 DNNSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGK---QGPVEH 623 (1065)
Q Consensus 548 d~~tVGvIv~verd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr---~G~V~H 623 (1065)
+.+..|.|+++-.+ .|.|.+. +|..+.+ .|..|+.++ ==|..||.|.| .||.-- .|.|.|
T Consensus 18 e~e~~g~V~~~lG~~~~~V~~~---dG~~~la---~i~GK~Rk~--------iwI~~GD~VlV--sp~d~~~~~kg~Iv~ 81 (99)
T TIGR00523 18 EGEILGVIEQMLGAGRVKVRCL---DGKTRLG---RIPGKLKKR--------IWIREGDVVIV--KPWEFQGDDKCDIVW 81 (99)
T ss_pred CCEEEEEEEEEcCCCEEEEEeC---CCCEEEE---EEchhhccc--------EEecCCCEEEE--EEccCCCCccEEEEE
Confidence 34678999999865 5888874 3555543 344444321 24899999999 355433 699999
Q ss_pred EECC
Q 001506 624 IYRG 627 (1065)
Q Consensus 624 I~r~ 627 (1065)
.|..
T Consensus 82 r~~~ 85 (99)
T TIGR00523 82 RYTK 85 (99)
T ss_pred EcCH
Confidence 9864
No 150
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=46.59 E-value=23 Score=35.16 Aligned_cols=40 Identities=23% Similarity=0.313 Sum_probs=29.0
Q ss_pred EEeeCCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCcccc
Q 001506 713 KVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISDN 755 (1065)
Q Consensus 713 ~I~~GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~~ 755 (1065)
.|+.| |+.|+|.++.++..+|+|...+-.|+|.|+.|+-+
T Consensus 43 VvT~G---Gi~G~V~~I~~~~~~v~le~~gv~i~v~r~AI~~V 82 (113)
T PRK06531 43 VVTIG---GLYGTVDEVDTEAKTIVLDVDGVYLTFELAAIKRV 82 (113)
T ss_pred EEECC---CcEEEEEEEecCCCEEEEEECCEEEEEEhhHhhhh
Confidence 35666 99999999987544444433567799999988853
No 151
>PRK14637 hypothetical protein; Provisional
Probab=46.56 E-value=37 Score=35.23 Aligned_cols=49 Identities=20% Similarity=0.237 Sum_probs=38.1
Q ss_pred CccccCcEEEEeeCCCCCc-eeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 704 HDALVGTTVKVRLGPYKGY-RGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 704 ~d~liGktV~I~~GpyKG~-~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
...++|+.|+|+-..-|.+ .|++++++++.+.++. ..+++.++.+.|.-
T Consensus 93 f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~~v~l~~--~~~~~~i~~~~I~k 142 (151)
T PRK14637 93 FSIFVGETVKVWFECTGQWQVGTIAEADETCLVLTS--DGVPVTIPYVQITK 142 (151)
T ss_pred HHHhCCCEEEEEECCCCcEEEEEEEEEeCCEEEEEE--CCEEEEEEHHHeee
Confidence 3678999999986223567 5999999999998885 56778888777664
No 152
>PRK14643 hypothetical protein; Provisional
Probab=46.54 E-value=30 Score=36.40 Aligned_cols=51 Identities=20% Similarity=0.145 Sum_probs=39.9
Q ss_pred ccccCcEEEEee-CCC---CCceeEEEeecCCeEEEEec----CCCeEEEEecCCcccc
Q 001506 705 DALVGTTVKVRL-GPY---KGYRGRVVDVKGQSVRVELE----SQMKVVTVDRSMISDN 755 (1065)
Q Consensus 705 d~liGktV~I~~-Gpy---KG~~G~Vkd~t~~~~rVELh----s~~k~I~V~r~~l~~~ 755 (1065)
..++|+.|+|+- .|+ |-+.|+++++.++.++++|+ ...+++.++++.|.-+
T Consensus 100 ~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l~~~~~~~~~~~~ip~~~I~ka 158 (164)
T PRK14643 100 VKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRFTFFIKGQKKKLDVKYEQIKFI 158 (164)
T ss_pred HHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEEEeeccCcCcEEEEeHHHhhhe
Confidence 578999999963 444 44889999999998888864 4467899998887753
No 153
>KOG0338 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=46.49 E-value=6.7 Score=47.48 Aligned_cols=81 Identities=12% Similarity=0.174 Sum_probs=35.5
Q ss_pred CchHHHHHHHHHHHHHhhCCCcceEEEEee-CCCccEEEEEecchHHHHHHHhcCcccc-eeeeeeeChhhhhhcccccc
Q 001506 191 IGREREAAVCLMQKCIDKGSELQIRSVIAL-DHLKNYIYIEADKEAHVKEACKGLRNIY-SQKVMLVPIREMTDVLAVES 268 (1065)
Q Consensus 191 ~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~-~~lkGYIYIEA~~~~~V~~ai~Gl~~v~-~~~~~lVpi~Em~~vL~v~~ 268 (1065)
.|+--..++-++.|++.+.....+.-|++. +. .- + |-.-..|-.-|..+..|. +--+.-+.++.=..+|+..+
T Consensus 229 sGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PT-RE-L---aiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs~P 303 (691)
T KOG0338|consen 229 SGKTAAFALPILERLLYRPKKVAATRVLVLVPT-RE-L---AIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSRP 303 (691)
T ss_pred CCchhhhHHHHHHHHhcCcccCcceeEEEEecc-HH-H---HHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhhCC
Confidence 466666666666777665444444444321 00 00 0 000112222233333333 33445556666666666555
Q ss_pred ccccCCCC
Q 001506 269 KAIDLSRD 276 (1065)
Q Consensus 269 ~~~~l~~G 276 (1065)
..+-..||
T Consensus 304 DIVIATPG 311 (691)
T KOG0338|consen 304 DIVIATPG 311 (691)
T ss_pred CEEEecch
Confidence 44434444
No 154
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=46.48 E-value=38 Score=31.32 Aligned_cols=50 Identities=24% Similarity=0.408 Sum_probs=38.3
Q ss_pred ccccCcEEEEe-e---CCCCCceeEEEeecCCeEEEEecCC--CeEEEEecCCccc
Q 001506 705 DALVGTTVKVR-L---GPYKGYRGRVVDVKGQSVRVELESQ--MKVVTVDRSMISD 754 (1065)
Q Consensus 705 d~liGktV~I~-~---GpyKG~~G~Vkd~t~~~~rVELhs~--~k~I~V~r~~l~~ 754 (1065)
..++|+.|+|+ . +.-|-+.|++.+++++.+++++..+ .++++++.++|.-
T Consensus 21 ~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~~~~~~~~~i~~~~I~k 76 (83)
T cd01734 21 ERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDDTVTLEVDIKTRGKTVEIPLDKIAK 76 (83)
T ss_pred HHhCCCEEEEEEEcccCCeEEEEEEEEeEeCCEEEEEEecCCCCeEEEEEhHHeeE
Confidence 57899999995 3 3335578999999999998887643 5678888777764
No 155
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=46.15 E-value=1.8e+02 Score=33.83 Aligned_cols=51 Identities=18% Similarity=0.173 Sum_probs=31.9
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccc--------cceeeccCCCcEEEe
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSK--------ELCKYFEPGNHVKVV 486 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~--------~LrK~F~~GDhVkVi 486 (1065)
..|++||.|+ |+|++|..+.+.|.... +..=-+|.+ .+.++|++||.|++.
T Consensus 27 ~~~~~G~iv~----------G~V~~i~~~g~~Vdig~---k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~ 85 (318)
T PRK07400 27 YHFKPGDIVN----------GTVFSLEPRGALIDIGA---KTAAFMPIQEMSINRVEGPEEVLQPNETREFF 85 (318)
T ss_pred hhcCCCCEEE----------EEEEEEECCEEEEEECC---CeEEEEEHHHhccccccCHHHccCCCCEEEEE
Confidence 3588998874 77888887766555421 111122333 345679999998764
No 156
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=45.93 E-value=92 Score=32.64 Aligned_cols=75 Identities=16% Similarity=0.220 Sum_probs=53.5
Q ss_pred eeeeeeEEeC-CCceEEEEEEccc-eEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCC
Q 001506 539 YELRDLVLLD-NNSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKG 616 (1065)
Q Consensus 539 y~l~DLVqLd-~~tVGvIv~verd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~g 616 (1065)
-+..+|+.=. .+.+|+|+++-.+ .|.|.+.+ |..+.+ .|..|+.++ --|..||.|.|---||.-
T Consensus 21 ~~~rel~~~eegq~~g~V~~~LGn~~f~V~c~d---G~~rLa---~I~GKmRK~--------IWI~~GD~VlVel~~yd~ 86 (155)
T PTZ00329 21 GEKRELVFKEEGQEYAQVLRMLGNGRLEAYCFD---GVKRLC---HIRGKMRKR--------VWINIGDIILVSLRDFQD 86 (155)
T ss_pred cceeeeccCCCCcEEEEEEEEcCCCEEEEEECC---CCEEEE---Eeeccceee--------EEecCCCEEEEeccCCCC
Confidence 3455565543 4678999999875 58888753 555443 344555432 249999999998888888
Q ss_pred ceeeEEEEECC
Q 001506 617 KQGPVEHIYRG 627 (1065)
Q Consensus 617 r~G~V~HI~r~ 627 (1065)
-.|.|.|.|..
T Consensus 87 ~KgdIi~Ry~~ 97 (155)
T PTZ00329 87 SKADVILKYTP 97 (155)
T ss_pred CEEEEEEEcCH
Confidence 88999999876
No 157
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=45.91 E-value=59 Score=43.14 Aligned_cols=65 Identities=14% Similarity=0.161 Sum_probs=55.4
Q ss_pred EEEEEEeCCCCeEEEEeccCCCCceEEecCCCeeecCCCCCCcEEEEcCCCCCceEEEEEEeCCCcEEEe
Q 001506 976 VGVIREVLPDGSCRVVLGSSGNGDTITALPNEIEIVPPRKTDKIKIMGGPHRGATGKLIGVDGTDGIVKV 1045 (1065)
Q Consensus 976 ~GvI~~V~~~g~~~V~l~~~~~g~~v~v~~~~LE~V~P~kgd~VkVi~G~~rG~tG~LisiD~~dgiVk~ 1045 (1065)
.|+|.+|.+ ++++|..+.+++.+...+...-|.-|++.+|++|.+..| ...++..|...+|++..
T Consensus 18 lG~v~~~d~-r~vtv~fpas~e~R~ya~~~apl~Rv~~~~g~~v~~~~~----~~~~v~~v~~~~gl~~y 82 (956)
T PRK04914 18 LGTVVAVDG-RTVTLLFPATGENRLYARNDAPLTRVMFNPGDTITSHEG----WQLTVEEVEEENGLLTY 82 (956)
T ss_pred cEEEEEEeC-CEEEEEecCCCCceeeecCCCCceeeecCCCCEEEecCC----CEEEEEEEeccCCcEEE
Confidence 789999966 889999999987788889999999999999999997665 56777778778888775
No 158
>KOG0699 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=45.56 E-value=13 Score=43.21 Aligned_cols=12 Identities=42% Similarity=0.487 Sum_probs=6.1
Q ss_pred CcccccCCCCCC
Q 001506 79 KPKAKRRSGSEF 90 (1065)
Q Consensus 79 ~~krk~~~~~~F 90 (1065)
.+|-.+.+.+.|
T Consensus 241 s~Kl~q~sKsef 252 (542)
T KOG0699|consen 241 SKKLNQSSKSEF 252 (542)
T ss_pred hhhccccccccc
Confidence 444445555555
No 159
>COG4547 CobT Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]
Probab=45.56 E-value=16 Score=43.74 Aligned_cols=12 Identities=17% Similarity=0.174 Sum_probs=6.7
Q ss_pred HHHHHHHHHHhh
Q 001506 197 AAVCLMQKCIDK 208 (1065)
Q Consensus 197 vv~~Lm~K~~~~ 208 (1065)
++..|.+|++++
T Consensus 360 lanrlqrRlmAq 371 (620)
T COG4547 360 LANRLQRRLMAQ 371 (620)
T ss_pred HHHHHHHHHHHh
Confidence 345556666654
No 160
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=45.32 E-value=45 Score=29.25 Aligned_cols=29 Identities=31% Similarity=0.359 Sum_probs=23.3
Q ss_pred CCCCEEEEecccccCceeEEEEEcCCeEEEeec
Q 001506 426 MKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPE 458 (1065)
Q Consensus 426 ~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~ 458 (1065)
.+||.|+.- .+++|+|++|..+.|.+.-.
T Consensus 5 ~vGdiIefk----~g~~G~V~kv~eNSVIVdIT 33 (57)
T PF09953_consen 5 KVGDIIEFK----DGFTGIVEKVYENSVIVDIT 33 (57)
T ss_pred ccCcEEEEc----CCcEEEEEEEecCcEEEEEE
Confidence 589999973 57999999999997766543
No 161
>KOG2422 consensus Uncharacterized conserved protein [Function unknown]
Probab=45.22 E-value=11 Score=46.17 Aligned_cols=52 Identities=13% Similarity=0.222 Sum_probs=23.0
Q ss_pred eEEEEeeCCCccEEEEEecchHHHHHHHhcCcccc---eeeeeeeC-hhhhhhccccc
Q 001506 214 IRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIY---SQKVMLVP-IREMTDVLAVE 267 (1065)
Q Consensus 214 I~Svf~~~~lkGYIYIEA~~~~~V~~ai~Gl~~v~---~~~~~lVp-i~Em~~vL~v~ 267 (1065)
-.|.|.-.+..-|- +|.+.--+..++-...+|. ...|--|+ +-.|.++++..
T Consensus 242 ~isfF~~~hs~sYe--qaq~~F~~av~~~d~n~v~~lL~ssPYHvdsLLqva~~~r~q 297 (665)
T KOG2422|consen 242 GISFFKFEHSNSYE--QAQRDFYLAVIVHDPNNVLILLISSPYHVDSLLQVADIFRFQ 297 (665)
T ss_pred ceeEEEeecchHHH--HHHHHHHHHHhhcCCcceeeeeccCCcchhHHHHHHHHHHHh
Confidence 44556666655544 3333222223333333433 23333333 44666666544
No 162
>PRK14644 hypothetical protein; Provisional
Probab=45.19 E-value=27 Score=35.58 Aligned_cols=49 Identities=14% Similarity=0.343 Sum_probs=36.6
Q ss_pred ccccCcEEEEee-CC---CCCceeEEEeecCCeEEEEe--cCCCeEEEEecCCcc
Q 001506 705 DALVGTTVKVRL-GP---YKGYRGRVVDVKGQSVRVEL--ESQMKVVTVDRSMIS 753 (1065)
Q Consensus 705 d~liGktV~I~~-Gp---yKG~~G~Vkd~t~~~~rVEL--hs~~k~I~V~r~~l~ 753 (1065)
..++|+.|+|+- .+ -|=+.|+++++.+..++++. ..+-++|++++++|+
T Consensus 81 ~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~~i~l~~~~k~~~~~i~~~~~~i~ 135 (136)
T PRK14644 81 ENHIGEIIDVSLNKEVNKTDFITGELLENNPETITLKWNCKGQFRKVEINKENIK 135 (136)
T ss_pred HHhCCCeEEEEEccCcCCeEEEEEEEEEEeCCEEEEEEecCCcEEEEEECHHHhc
Confidence 578999999963 22 36688999999999999864 444467777777664
No 163
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=44.49 E-value=31 Score=31.12 Aligned_cols=42 Identities=17% Similarity=0.260 Sum_probs=35.3
Q ss_pred eeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCcEEE
Q 001506 442 KGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKV 485 (1065)
Q Consensus 442 ~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~F~~GDhVkV 485 (1065)
++.|-+++++.+.+...... +.+.||.+.|=.-.++||.+.+
T Consensus 1 k~ivDRiE~~~AVl~~~~~~--~~~~vp~~~LP~~~keGDvl~i 42 (71)
T PF11213_consen 1 KAIVDRIEGDYAVLELEDGE--KEIDVPRSRLPEGAKEGDVLEI 42 (71)
T ss_pred CeEEEEEeCCEEEEEECCCe--EEEEEEHHHCCCCCCcccEEEE
Confidence 46889999998888876543 5799999999999999998877
No 164
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=44.33 E-value=30 Score=31.27 Aligned_cols=22 Identities=27% Similarity=0.389 Sum_probs=16.5
Q ss_pred ccceeeccCCCcEEEeccccCCceeEEEEEeC
Q 001506 471 KELCKYFEPGNHVKVVSGTQAGATGMVLKVEQ 502 (1065)
Q Consensus 471 ~~LrK~F~~GDhVkVi~G~~~getGlVVkVe~ 502 (1065)
+++.++|++||.|++ .|+.|+.
T Consensus 45 ~~~~~~~~~G~~v~~----------kVl~id~ 66 (74)
T cd05705 45 SLYNKYLPEGKLLTA----------KVLSVNS 66 (74)
T ss_pred hhHhcccCCCCEEEE----------EEEEEEC
Confidence 446789999999976 4677754
No 165
>PF11515 Cul7: Mouse development and cellular proliferation protein Cullin-7; InterPro: IPR021097 The CPH domain is found in the Cullin-7, PARC and HERC2 proteins, which are all components of known or predicted E3-ubiquitin ligases. The CPH domain is a protein-protein interaction module that binds the teramerisation domain of the tumour suppressor protein p53 []. Structurally it forms a beta-barrel fold similar to the SH3, Tudor and KOW and domains. Unlike the SH3 and Tudor domains, which bind to small peptides, the CPH domain appears to bind to an extended surface on p53.; PDB: 2JUF_A 2JNG_A.
Probab=43.89 E-value=23 Score=32.80 Aligned_cols=31 Identities=19% Similarity=0.082 Sum_probs=19.9
Q ss_pred ccCCCCcEEEeec---CCCCCCeeEEEEeeCCCC
Q 001506 271 IDLSRDTWVRMKI---GNYKGDLAKVVDVDNVRQ 301 (1065)
Q Consensus 271 ~~l~~G~wVRIk~---G~YkGDlAqV~~Vd~~~~ 301 (1065)
..|++|+.||+.+ ...+||.|+|..++.++.
T Consensus 16 ~~i~~GM~VRc~~~yeeV~~GD~G~V~k~~~dg~ 49 (78)
T PF11515_consen 16 DNIQPGMRVRCCRDYEEVRAGDEGEVFKQDRDGL 49 (78)
T ss_dssp HH--TT-EEEESS-BTTB-TT-EEE-EEEE-TTS
T ss_pred HhCCCCcEEEEecccccccccccceeEeeccCCC
Confidence 3689999999996 589999999998886543
No 166
>PF01287 eIF-5a: Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold; InterPro: IPR020189 A five-stranded beta-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease and aspartyl-tRNA synthetase) or oligosaccharides (B subunits of enterotoxin and verotoxin-1), and has been termed the oligonucleotide/oligosaccharide binding motif, or OB fold, a five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha helix located between the third and fourth strands []. Two ribosomal proteins, S17 and S1, are members of this class, and have different variations of the OB fold theme. Comparisons with other OB fold nucleic acid binding proteins suggest somewhat different mechanisms of nucleic acid recognition in each case []. There are many nucleic acid-binding proteins that contain domains with this OB-fold structure, including anticodon-binding tRNA synthetases, ssDNA-binding proteins (CDC13, telomere-end binding proteins), phage ssDNA-binding proteins (gp32, gp2.5, gpV), cold shock proteins, DNA ligases, RNA-capping enzymes, DNA replication initiators and RNA polymerase subunit RBP8 []. This entry represents the RNA-binding domain of translation elongation factor IF5A [].; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0043022 ribosome binding, 0006452 translational frameshifting, 0045901 positive regulation of translational elongation, 0045905 positive regulation of translational termination; PDB: 1IZ6_B 3CPF_A 1KHI_A 1BKB_A 1XTD_A 3ER0_A 3HKS_B 1X6O_A 2EIF_A 1EIF_A.
Probab=43.65 E-value=18 Score=32.73 Aligned_cols=43 Identities=19% Similarity=0.210 Sum_probs=33.0
Q ss_pred ceeEEEEEcCC-eEEEeecCCCCCcceeec----cccceeeccCCCcE
Q 001506 441 LKGWVEKVDEE-NVHIRPEMKGLPKTLAVN----SKELCKYFEPGNHV 483 (1065)
Q Consensus 441 l~G~V~~V~~d-~V~i~~~~~~l~~~l~v~----~~~LrK~F~~GDhV 483 (1065)
-.+.|++|++| .+++|-+..+..+-|.+| ..+++..|+.|..+
T Consensus 5 ~eyqli~I~~Dg~lsLMde~get~eDl~lP~~el~~ei~~~~~~g~~~ 52 (69)
T PF01287_consen 5 KEYQLIDIDGDGFLSLMDEDGETREDLKLPDGELGEEIKAKFEEGKEV 52 (69)
T ss_dssp EEEEEEEEETTTEEEEEETTS-EEEEEECCSHHHHHHHHHHHHTTCEE
T ss_pred EEEEEEEEccCcEEEEEcCCCCeeccEEecccchhHHHHhhccCCCeE
Confidence 35789999877 899998655555558898 56778899999884
No 167
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=43.28 E-value=2.2e+02 Score=33.02 Aligned_cols=64 Identities=8% Similarity=0.104 Sum_probs=36.3
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcCC--eEEEeecCCCCCcceeeccccceeeccCCCcEEEe-ccccCCceeEEEE
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVV-SGTQAGATGMVLK 499 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d--~V~i~~~~~~l~~~l~v~~~~LrK~F~~GDhVkVi-~G~~~getGlVVk 499 (1065)
..|++||.|+|+ |++++.+ .+++.... +. ..-+...|+..++.|+-|++. .+. ..-|++|.
T Consensus 74 ~~~~~G~~v~~~----------Vi~~~~~~~~i~lS~k~--~~--~~~~w~~l~~~~~~~~~V~g~V~~~--~~~G~~V~ 137 (318)
T PRK07400 74 EVLQPNETREFF----------ILSDENEDGQLTLSIRR--IE--YMRAWERVRQLQKEDATVRSEVFAT--NRGGALVR 137 (318)
T ss_pred HccCCCCEEEEE----------EEEEeCCCCeEEEehhh--hh--hhhHHHHHHHhccCCCEEEEEEEEE--ECCeEEEE
Confidence 469999999987 5555543 34443221 10 011345666677788877552 222 23488888
Q ss_pred EeC
Q 001506 500 VEQ 502 (1065)
Q Consensus 500 Ve~ 502 (1065)
+++
T Consensus 138 l~G 140 (318)
T PRK07400 138 IEG 140 (318)
T ss_pred ECC
Confidence 853
No 168
>COG4873 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.98 E-value=34 Score=30.74 Aligned_cols=32 Identities=28% Similarity=0.309 Sum_probs=25.4
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcCCeEEEeec
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPE 458 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~ 458 (1065)
+.-.+||.|+.. -||+|.|.+++++.|.+--.
T Consensus 22 ~~a~vgniief~----dgl~g~vek~nensvivdlt 53 (81)
T COG4873 22 KIAKVGNIIEFK----DGLTGVVEKVNENSVIVDLT 53 (81)
T ss_pred eeeeccceEEEc----ccceeeeeeecCCcEEEEEE
Confidence 345789999987 57999999999997766443
No 169
>KOG0299 consensus U3 snoRNP-associated protein (contains WD40 repeats) [RNA processing and modification]
Probab=42.44 E-value=5 Score=47.63 Aligned_cols=23 Identities=13% Similarity=0.260 Sum_probs=13.5
Q ss_pred CCcceEEEEeeCCCccEEEEEecc
Q 001506 210 SELQIRSVIALDHLKNYIYIEADK 233 (1065)
Q Consensus 210 ~~l~I~Svf~~~~lkGYIYIEA~~ 233 (1065)
..+.|.+++..+. --|+|=.+..
T Consensus 141 H~~s~~~vals~d-~~~~fsask~ 163 (479)
T KOG0299|consen 141 HQLSVTSVALSPD-DKRVFSASKD 163 (479)
T ss_pred ccCcceEEEeecc-ccceeecCCC
Confidence 4466778766543 3466655543
No 170
>PRK14634 hypothetical protein; Provisional
Probab=42.14 E-value=38 Score=35.31 Aligned_cols=49 Identities=10% Similarity=0.264 Sum_probs=39.0
Q ss_pred CccccCcEEEEe-eCC---CCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 704 HDALVGTTVKVR-LGP---YKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 704 ~d~liGktV~I~-~Gp---yKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
..+++|+.|+|+ ..+ -|=+.|++++++++.+++++ ..++++++.+.|+-
T Consensus 95 f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~v~l~~--~~~~~~i~~~~I~k 147 (155)
T PRK14634 95 FQTFRGFPVEVSHRDDDGSEQRLEGLLLERNEDHLQINI--RGRIKRIPRDSVIS 147 (155)
T ss_pred HHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCCEEEEEE--CCEEEEEEHHHeee
Confidence 357899999996 343 36789999999999999886 46778888877764
No 171
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=42.08 E-value=67 Score=42.13 Aligned_cols=52 Identities=19% Similarity=0.103 Sum_probs=40.5
Q ss_pred ccCcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCcEEEe
Q 001506 422 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVV 486 (1065)
Q Consensus 422 ~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~F~~GDhVkVi 486 (1065)
...|++||.|+ |+|++|+++.|.|-.. .+.+=-+|.+++.+-+++||.|+|.
T Consensus 316 ~~~~~~G~iV~----------G~Vv~i~~~~v~VdiG---~K~eGiI~~~E~~~~~kvGd~i~~~ 367 (863)
T PRK12269 316 FEAPEPGSVRM----------GTVVQVNAGTVFVDIG---GKSEGRVPVEEFEAPPKAGDGVRVY 367 (863)
T ss_pred cccCCCCCEEE----------EEEEEEECCEEEEEeC---CCceEEeEHHHhccCCCCCCEEEEE
Confidence 46788998874 8999999998888663 2334457788888888999999874
No 172
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=42.03 E-value=1.2e+02 Score=43.46 Aligned_cols=93 Identities=12% Similarity=0.231 Sum_probs=65.1
Q ss_pred ccCcCCCCEEEEeccc-ccCceeEEEEEcC--CeEEEeecCCCCCcceeeccccce-------------eeccCCCcEEE
Q 001506 422 KGHFMKGDAVIVIKGD-LKNLKGWVEKVDE--ENVHIRPEMKGLPKTLAVNSKELC-------------KYFEPGNHVKV 485 (1065)
Q Consensus 422 ~~~F~~GD~V~V~~Ge-l~gl~G~V~~V~~--d~V~i~~~~~~l~~~l~v~~~~Lr-------------K~F~~GDhVkV 485 (1065)
...|++||.|+-+.-. +.+-.++|+.|+. +.++|.... ++.+.|.+++|. .-+-.||.+++
T Consensus 679 ~~~Yr~Gdvv~~y~~~~~~~~~y~V~~V~~~~n~L~l~~~d---G~~~~~~p~~l~~~~~~~svy~~~~l~ia~Gdrl~~ 755 (1960)
T TIGR02760 679 AAHYKQGMVIRFWQKGKIPHDDYVVTNVNKHNNTLTLKDAQ---GKTQKFKPSSLKDLERPFSVYRPEQLEVAAGERLQV 755 (1960)
T ss_pred HhhcCCCCEEEeecccCccCCcEEEEEEeCCCCEEEEEcCC---CCEEEECHHHhcccccceeeeccccccccCCCEEEE
Confidence 4689999999975433 3455689999986 567766532 345666666662 24788999988
Q ss_pred ecc-----ccCCceeEEEEEeCcEEEEEeCCCCceEEE
Q 001506 486 VSG-----TQAGATGMVLKVEQHVLIILSDTTKEDIRV 518 (1065)
Q Consensus 486 i~G-----~~~getGlVVkVe~~~v~vlSD~t~~ei~V 518 (1065)
... ...|+...|+.++...++|-.+.. +.+++
T Consensus 756 trn~~~~gl~ng~~~tV~~i~~~~i~l~~~~g-~~~~L 792 (1960)
T TIGR02760 756 TGNHFHSRVRNGELLTVSSINNEGITLITEDG-QTLHL 792 (1960)
T ss_pred ccCCcccCccCCCEEEEEEEcCCeEEEEeCCC-ceEEc
Confidence 743 245799999999998888776533 45555
No 173
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=41.93 E-value=85 Score=35.71 Aligned_cols=72 Identities=18% Similarity=0.366 Sum_probs=49.6
Q ss_pred cEEEEEEeCCCCeEEEEecc--CCCCceEEec---CCCeeecCCCCCCcEEEEcCCCCCceEEEEEEeCC---CcEEEec
Q 001506 975 VVGVIREVLPDGSCRVVLGS--SGNGDTITAL---PNEIEIVPPRKTDKIKIMGGPHRGATGKLIGVDGT---DGIVKVD 1046 (1065)
Q Consensus 975 ~~GvI~~V~~~g~~~V~l~~--~~~g~~v~v~---~~~LE~V~P~kgd~VkVi~G~~rG~tG~LisiD~~---dgiVk~d 1046 (1065)
+.|++.=++-||.+ +...+ -..+++|.|+ +.=++.+.-..|..+.|+.|.+.|.+|+++.|... .-+|.+.
T Consensus 130 ~gG~~ql~~hDGrn-I~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~ 208 (273)
T PTZ00223 130 TGRIPVAVTHDGHR-IRYPDPRTSRGDTLVYNVKEKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLK 208 (273)
T ss_pred cCCeeEEEecCCce-eccCCccccCCCEEEEECCCCeeeEEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEE
Confidence 35566656667777 33222 1125677776 33366777799999999999999999999999543 3477776
Q ss_pred C
Q 001506 1047 V 1047 (1065)
Q Consensus 1047 ~ 1047 (1065)
+
T Consensus 209 d 209 (273)
T PTZ00223 209 D 209 (273)
T ss_pred e
Confidence 3
No 174
>KOG0772 consensus Uncharacterized conserved protein, contains WD40 repeat [Function unknown]
Probab=41.67 E-value=13 Score=45.00 Aligned_cols=10 Identities=20% Similarity=0.242 Sum_probs=4.0
Q ss_pred ccccCcEEEE
Q 001506 705 DALVGTTVKV 714 (1065)
Q Consensus 705 d~liGktV~I 714 (1065)
+..++.+|.|
T Consensus 508 ~e~~~~~~ii 517 (641)
T KOG0772|consen 508 DEDLSEDVII 517 (641)
T ss_pred hhhcCcceEE
Confidence 3334444433
No 175
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=41.08 E-value=33 Score=32.39 Aligned_cols=49 Identities=27% Similarity=0.224 Sum_probs=31.2
Q ss_pred CCCCEEEEecccccCceeEEEEEcCC--eEEEeecCCCCCcceeec--cccceeeccCCCcEE
Q 001506 426 MKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVN--SKELCKYFEPGNHVK 484 (1065)
Q Consensus 426 ~~GD~V~V~~Gel~gl~G~V~~V~~d--~V~i~~~~~~l~~~l~v~--~~~LrK~F~~GDhVk 484 (1065)
++||.| .|+|+.+..+ .|-|.+....+-..+.|+ .+..|.+|++||.|-
T Consensus 5 ~~gD~V----------IG~V~~~~~~~~~VdI~s~~~a~L~~~~f~gatk~~rp~L~~GDlV~ 57 (86)
T cd05790 5 AKGDHV----------IGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVY 57 (86)
T ss_pred CCCCEE----------EEEEEEEcCCeEEEEcCCCcceEechHHcccccccccccCCCCCEEE
Confidence 567776 4888888877 455544432221123332 567799999999984
No 176
>COG5129 MAK16 Nuclear protein with HMG-like acidic region [General function prediction only]
Probab=41.03 E-value=12 Score=40.69 Aligned_cols=9 Identities=44% Similarity=0.704 Sum_probs=3.5
Q ss_pred CccccCCCC
Q 001506 66 DDEDYGGGG 74 (1065)
Q Consensus 66 ~~~~~~~~~ 74 (1065)
.|+|++..+
T Consensus 258 ~d~dednk~ 266 (303)
T COG5129 258 EDEDEDNKG 266 (303)
T ss_pred ccccccccc
Confidence 333444333
No 177
>KOG2897 consensus DNA-binding protein YL1 and related proteins [General function prediction only]
Probab=40.40 E-value=11 Score=43.94 Aligned_cols=7 Identities=29% Similarity=0.994 Sum_probs=2.9
Q ss_pred CCCCCCH
Q 001506 334 PPRFMNV 340 (1065)
Q Consensus 334 p~rlFn~ 340 (1065)
|+|-|+|
T Consensus 302 PA~Y~DP 308 (390)
T KOG2897|consen 302 PARYLDP 308 (390)
T ss_pred cccccCc
Confidence 3444443
No 178
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=40.15 E-value=44 Score=29.18 Aligned_cols=49 Identities=18% Similarity=0.251 Sum_probs=35.5
Q ss_pred cccCcEEEEeeCCCCCceeEEEeec---CCeEEEEecCCCeEEEEecCCccccc
Q 001506 706 ALVGTTVKVRLGPYKGYRGRVVDVK---GQSVRVELESQMKVVTVDRSMISDNV 756 (1065)
Q Consensus 706 ~liGktV~I~~GpyKG~~G~Vkd~t---~~~~rVELhs~~k~I~V~r~~l~~~~ 756 (1065)
.++||..-|..|||.--+|+||.-. +.++-+-+. .+.|.|.-.+|..++
T Consensus 3 di~gqkayikdgp~rnrigivk~~e~q~~~~f~ivi~--~q~i~velkdivlvg 54 (68)
T PF13051_consen 3 DIVGQKAYIKDGPYRNRIGIVKKNEKQLESHFAIVIG--EQSIDVELKDIVLVG 54 (68)
T ss_pred cccccEeeeccCCccceeEEEecchhhcCCcEEEEEC--CeEEEEEeeeEEEEE
Confidence 4689999999999999999999754 334444443 455667666776654
No 179
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=39.74 E-value=78 Score=28.16 Aligned_cols=34 Identities=24% Similarity=0.351 Sum_probs=23.0
Q ss_pred cCCCCEEEEeccc--ccC--ceeEEEEEcCC-eEEEeec
Q 001506 425 FMKGDAVIVIKGD--LKN--LKGWVEKVDEE-NVHIRPE 458 (1065)
Q Consensus 425 F~~GD~V~V~~Ge--l~g--l~G~V~~V~~d-~V~i~~~ 458 (1065)
|++||.|||..-+ +.+ ..|+|++..++ .+.|.-+
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~~~~V~Y~ 39 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDDKYLVEYD 39 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT-EEEEEET
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCcEEEEEEC
Confidence 8999999998754 222 67899999988 7777764
No 180
>PHA02774 E1; Provisional
Probab=39.70 E-value=9.9 Score=47.23 Aligned_cols=20 Identities=25% Similarity=0.371 Sum_probs=14.3
Q ss_pred chhhHHHHHHHHHHHhcCCC
Q 001506 140 EQEDVEALERRIQARYARSS 159 (1065)
Q Consensus 140 ~~~d~ee~~~~l~eRY~~~~ 159 (1065)
+.++-++....||+||..+.
T Consensus 65 ~~~~~~~~i~~LKRKy~~sp 84 (613)
T PHA02774 65 EAEEDEQQIQALKRKYLSSP 84 (613)
T ss_pred HHHHHHHHHHHhccccCCCC
Confidence 34445677789999998654
No 181
>PRK14645 hypothetical protein; Provisional
Probab=39.66 E-value=41 Score=35.04 Aligned_cols=46 Identities=22% Similarity=0.315 Sum_probs=37.9
Q ss_pred ccccCcEEEEeeCCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCcc
Q 001506 705 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 753 (1065)
Q Consensus 705 d~liGktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~ 753 (1065)
..++|+.|+|+.| -|=+.|+++++++..+++++ ..+++.++.+.|.
T Consensus 98 ~r~~G~~v~v~~~-~k~~~G~L~~~~d~~i~l~~--~~~~~~i~~~~I~ 143 (154)
T PRK14645 98 ERFAGLKAKVRGP-GENFTGRIKAVSGDQVTFDV--GGEDRTLRIGTFQ 143 (154)
T ss_pred HHhCCCEEEEEcC-CeEEEEEEEEEeCCEEEEEE--CCeEEEEEHHHhh
Confidence 5789999999864 47888999999999988776 4677888887775
No 182
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=39.52 E-value=1.5e+02 Score=26.27 Aligned_cols=61 Identities=18% Similarity=0.213 Sum_probs=40.2
Q ss_pred CceEEEEEEccc-eEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCCceeeEEEE
Q 001506 550 NSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHI 624 (1065)
Q Consensus 550 ~tVGvIv~verd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~HI 624 (1065)
+..|+|+++-.+ .|.|... +|..+.+... .|+.++ =-|+.||.|.|---|+....|.|.|.
T Consensus 4 e~~~~V~~~lG~~~~~V~~~---dg~~~l~~i~---gK~r~~--------iwI~~GD~V~V~~~~~d~~kG~Ii~r 65 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECE---DGEERLARIP---GKFRKR--------IWIKRGDFVLVEPSPYDKVKGRIIYR 65 (65)
T ss_dssp EEEEEEEEEESSSEEEEEET---TSEEEEEEE----HHHHTC--------C---TTEEEEEEESTTCTTEEEEEEE
T ss_pred EEEEEEEEECCCCEEEEEeC---CCCEEEEEec---cceeee--------EecCCCCEEEEEecccCCCeEEEEEC
Confidence 457899998876 5788775 4666655533 332211 24999999999878887788999874
No 183
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=39.48 E-value=52 Score=31.16 Aligned_cols=14 Identities=43% Similarity=0.866 Sum_probs=12.1
Q ss_pred cceeeccCCCcEEE
Q 001506 472 ELCKYFEPGNHVKV 485 (1065)
Q Consensus 472 ~LrK~F~~GDhVkV 485 (1065)
+++++|++||.|+.
T Consensus 56 ~~~~~f~~GDiV~A 69 (92)
T cd05791 56 EMYKCFRPGDIVRA 69 (92)
T ss_pred HHHhhcCCCCEEEE
Confidence 67899999999965
No 184
>CHL00084 rpl19 ribosomal protein L19
Probab=39.39 E-value=1e+02 Score=30.92 Aligned_cols=38 Identities=21% Similarity=0.294 Sum_probs=26.9
Q ss_pred cccCcCCCCEEEE----eccc---ccCceeEEEEEcCC----eEEEeec
Q 001506 421 KKGHFMKGDAVIV----IKGD---LKNLKGWVEKVDEE----NVHIRPE 458 (1065)
Q Consensus 421 ~~~~F~~GD~V~V----~~Ge---l~gl~G~V~~V~~d----~V~i~~~ 458 (1065)
.-..|++||.|+| .+|+ .....|.|+++.+. ++||.--
T Consensus 19 ~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki 67 (117)
T CHL00084 19 NLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKV 67 (117)
T ss_pred CCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEe
Confidence 3468999999998 4565 45688999998754 4555443
No 185
>smart00538 POP4 A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins.
Probab=39.14 E-value=77 Score=30.29 Aligned_cols=50 Identities=26% Similarity=0.335 Sum_probs=40.6
Q ss_pred CccccCcEEEEeeCC---CCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 704 HDALVGTTVKVRLGP---YKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 704 ~d~liGktV~I~~Gp---yKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
+.+|+|-.|+|.+=+ |-|..|+|.+-|..++.|+-.. ++..+|+|..-.+
T Consensus 8 ~~el~G~~v~Vv~s~~ps~vGi~GiVv~ET~nt~~I~t~~-~~~~~IpK~~~vF 60 (92)
T smart00538 8 RHELIGLKVRVVASKNPSLVGIEGIVVDETRNTLKIETKE-GRVKTVPKDGAVF 60 (92)
T ss_pred hhhhcCCEEEEEEcCCCCccCcEEEEEEeeeeEEEEEeCC-CcEEEEECCCeEE
Confidence 467899999998765 6799999999999999988654 5778888887443
No 186
>COG4547 CobT Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]
Probab=39.09 E-value=24 Score=42.38 Aligned_cols=9 Identities=22% Similarity=0.401 Sum_probs=5.0
Q ss_pred CCCCCCCCH
Q 001506 332 VPPPRFMNV 340 (1065)
Q Consensus 332 RPp~rlFn~ 340 (1065)
+-|.||-+-
T Consensus 478 ~~pgrlndl 486 (620)
T COG4547 478 AFPGRLNDL 486 (620)
T ss_pred CCchhhhhH
Confidence 556666543
No 187
>PRK04950 ProP expression regulator; Provisional
Probab=39.05 E-value=49 Score=36.25 Aligned_cols=45 Identities=29% Similarity=0.496 Sum_probs=37.0
Q ss_pred ccCcEEEEeeCCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCcc
Q 001506 707 LVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 753 (1065)
Q Consensus 707 liGktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~ 753 (1065)
-+||.|+|.-|. --.-|.|.+++-+.|||+|.+... |.|.-+||.
T Consensus 168 ~~gq~v~vk~g~-~~~~a~i~ei~kd~v~vql~~Gl~-~~v~ae~l~ 212 (213)
T PRK04950 168 TVGQAVKVKAGK-SAMDATVLEITKDDVRVQLDSGLS-MIVRAEHLV 212 (213)
T ss_pred ccCCEEEEeccC-CCCceEEEEEecCcEEEEcCCCcE-EEEeHhhhc
Confidence 379999999883 346689999999999999999876 677777764
No 188
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=38.69 E-value=43 Score=34.03 Aligned_cols=34 Identities=24% Similarity=0.290 Sum_probs=28.3
Q ss_pred cCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEE
Q 001506 272 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 306 (1065)
Q Consensus 272 ~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~Vk 306 (1065)
.+++|=.|.|..|+|+|-||.|++|-. +++|.|-
T Consensus 7 fVEiGRVvli~~Gp~~GKL~vIVDIID-~nRvLVD 40 (130)
T PTZ00065 7 FVEPGRLCLIQYGPDAGKLCFIVDIVT-PTRVLVD 40 (130)
T ss_pred ceeeceEEEEecCCCCCCEEEEEEEEc-CCeEEEe
Confidence 468899999999999999999999864 5666553
No 189
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=38.11 E-value=6.8e+02 Score=30.95 Aligned_cols=45 Identities=18% Similarity=0.175 Sum_probs=30.5
Q ss_pred eeeeChhhhhhccccccccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEEE
Q 001506 252 VMLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 307 (1065)
Q Consensus 252 ~~lVpi~Em~~vL~v~~~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~VkL 307 (1065)
-..||..||..-..... ...+++|+-|+ +.|+.++..+.++.|-+
T Consensus 60 eG~Ip~~Els~~~~~~~-~~~~~vGd~Ie----------~~V~~~~~~~g~liLS~ 104 (486)
T PRK07899 60 EGVIPSRELSIKHDVDP-NEVVEVGDEVE----------ALVLQKEDKEGRLILSK 104 (486)
T ss_pred EEEEEHHHhcccccCCh-hhcCCCCCEEE----------EEEEEEECCCCeEEEEe
Confidence 46889999987433222 22478999986 45888887777776653
No 190
>PF09870 DUF2097: Uncharacterized protein conserved in archaea (DUF2097); InterPro: IPR019208 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=37.96 E-value=47 Score=31.46 Aligned_cols=51 Identities=16% Similarity=0.246 Sum_probs=41.7
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccce
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELC 474 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~Lr 474 (1065)
..++.||.+++.=|. ...-|.|++++.-.+.|..+..-+++.++|...++.
T Consensus 17 ~nV~e~D~lEisygR-v~vpG~V~~~~~~~~~l~~~~~~~~g~ve~DleeI~ 67 (86)
T PF09870_consen 17 NNVKEGDYLEISYGR-VHVPGEVLSIEDGFLRLQLDGELINGTVEVDLEEIK 67 (86)
T ss_pred hcCCCCCEEEEEeeE-EEeeeEEEEeeeeEEEEEEcCccccCcEEEEHHHHH
Confidence 479999999999888 478899999999888888776555677888766654
No 191
>PRK14640 hypothetical protein; Provisional
Probab=37.75 E-value=57 Score=33.84 Aligned_cols=48 Identities=19% Similarity=0.343 Sum_probs=37.1
Q ss_pred ccccCcEEEEee----CCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 705 DALVGTTVKVRL----GPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 705 d~liGktV~I~~----GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
..++|+.|+|+- +.-|=+.|++++++++.+++++. .+++.++.+.|.-
T Consensus 93 ~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~v~l~~~--~~~~~i~~~~I~k 144 (152)
T PRK14640 93 EKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVD--GKDEVLAFTNIQK 144 (152)
T ss_pred HHhCCCeEEEEEecccCCceEEEEEEEEEeCCEEEEEEC--CeEEEEEhHHeee
Confidence 578999999974 23477889999999999998864 5667777666653
No 192
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=37.69 E-value=79 Score=28.57 Aligned_cols=45 Identities=27% Similarity=0.316 Sum_probs=33.7
Q ss_pred ccccCcEEEEeeCCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCc
Q 001506 705 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMI 752 (1065)
Q Consensus 705 d~liGktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l 752 (1065)
..+|||.|.|..- .--+.|+++|+..+++.||-+ .+..-|.-.+|
T Consensus 17 q~liG~~vvV~T~-~g~v~G~L~~V~pDhIvl~~~--~~~~~IR~~~I 61 (66)
T PF10842_consen 17 QSLIGQRVVVQTT-RGSVRGILVDVKPDHIVLEEN--GTPFFIRIAQI 61 (66)
T ss_pred HHhcCCEEEEEEc-CCcEEEEEEeecCCEEEEEeC--CcEEEEEeeeE
Confidence 5689999999763 334689999999999999988 55555544443
No 193
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=37.55 E-value=3.5e+02 Score=33.12 Aligned_cols=46 Identities=22% Similarity=0.230 Sum_probs=30.1
Q ss_pred eeeeChhhhhhccccccccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEEEe
Q 001506 252 VMLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLI 308 (1065)
Q Consensus 252 ~~lVpi~Em~~vL~v~~~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~VkLv 308 (1065)
..++|..||..-. .......+++|+.|+ ++|..+|..++++.|-+-
T Consensus 211 ~g~lp~~e~s~~~-~~~~~~~~~vG~~v~----------v~Vl~~d~~~~~i~lS~k 256 (516)
T TIGR00717 211 DGLLHITDMSWKR-VKHPSEYVKVGQEVK----------VKVIKFDKEKGRISLSLK 256 (516)
T ss_pred EEEEEHHHcCCCC-CCCHHHhccCCCEEE----------EEEEEEECCCCcEEEEEE
Confidence 3578888887521 111123478899886 468889988887777543
No 194
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=37.44 E-value=53 Score=29.16 Aligned_cols=29 Identities=21% Similarity=0.291 Sum_probs=24.5
Q ss_pred CCCCcEEEeecC--CCCCCeeEEEEeeCCCC
Q 001506 273 LSRDTWVRMKIG--NYKGDLAKVVDVDNVRQ 301 (1065)
Q Consensus 273 l~~G~wVRIk~G--~YkGDlAqV~~Vd~~~~ 301 (1065)
++.|+.|||+|- -+=+|.|.|..||..+-
T Consensus 2 i~rGskVrIlR~ESYWyn~vGtV~svd~~gi 32 (64)
T CHL00125 2 VKRGSKVRILRKESYWYNEIGTVATVDQSGI 32 (64)
T ss_pred cccCCEEEEccccceeecCcceEEEEcCCCC
Confidence 578999999984 57799999999998753
No 195
>PRK14630 hypothetical protein; Provisional
Probab=37.38 E-value=66 Score=33.11 Aligned_cols=47 Identities=21% Similarity=0.191 Sum_probs=36.3
Q ss_pred ccccCcEEEEeeCCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 705 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 705 d~liGktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
..++|+.|+|+-..- -..|++++++++.++++. ..+++.++.+.|.-
T Consensus 93 ~r~~G~~v~V~l~~~-~~~G~L~~~~d~~i~l~~--~~~~~~i~~~~I~k 139 (143)
T PRK14630 93 KIFEGKKIKLMLDND-FEEGFILEAKADSFIFKT--DSKEVNVLYSDVKK 139 (143)
T ss_pred HHhCCCEEEEEEcCc-ceEEEEEEEeCCEEEEEE--CCEEEEEEhHhcce
Confidence 578999999975332 248999999999999886 45778888777653
No 196
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=37.19 E-value=30 Score=35.07 Aligned_cols=33 Identities=24% Similarity=0.372 Sum_probs=27.4
Q ss_pred cCcEEEEeeCCCCCceeEEEeecCCeEEEEecCC
Q 001506 708 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQ 741 (1065)
Q Consensus 708 iGktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~ 741 (1065)
||.-|.|..|||+|-++.|+|+-+.. ||.++..
T Consensus 10 iGRVvli~~Gp~~GKL~vIVDIID~n-RvLVDGP 42 (130)
T PTZ00065 10 PGRLCLIQYGPDAGKLCFIVDIVTPT-RVLVDGA 42 (130)
T ss_pred eceEEEEecCCCCCCEEEEEEEEcCC-eEEEeCC
Confidence 78899999999999999999998653 5555555
No 197
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=37.05 E-value=1.7e+02 Score=25.61 Aligned_cols=58 Identities=19% Similarity=0.230 Sum_probs=35.4
Q ss_pred EEEEEEcc-ceEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCCceeeEEE
Q 001506 553 GVIIRVES-EAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEH 623 (1065)
Q Consensus 553 GvIv~ver-d~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~H 623 (1065)
|.|++.-. ..+.|.+. .|.+..+++.. |+.+ +.+.+.+||.|.+---++...+|.|.|
T Consensus 5 G~Vi~~~~g~~~~V~~~---~g~~~~c~~rG---klr~-------~~~~~~vGD~V~~~~~~~~~~~g~I~~ 63 (64)
T cd04451 5 GVVTEALPNAMFRVELE---NGHEVLAHISG---KMRM-------NYIRILPGDRVKVELSPYDLTKGRIVY 63 (64)
T ss_pred EEEEEEeCCCEEEEEeC---CCCEEEEEECc---eeec-------CCcccCCCCEEEEEEeecCCCEEEEEE
Confidence 78887774 66777653 35566655332 2211 344589999998874433344687766
No 198
>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=36.97 E-value=25 Score=48.49 Aligned_cols=12 Identities=17% Similarity=0.595 Sum_probs=6.4
Q ss_pred EEEEEecchHHH
Q 001506 226 YIYIEADKEAHV 237 (1065)
Q Consensus 226 YIYIEA~~~~~V 237 (1065)
|--||++.+.+.
T Consensus 4204 f~hv~~d~e~d~ 4215 (4600)
T COG5271 4204 FMHVKEDEEEDL 4215 (4600)
T ss_pred heeecccchhHH
Confidence 556665554443
No 199
>TIGR01651 CobT cobaltochelatase, CobT subunit. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model.
Probab=36.95 E-value=23 Score=44.01 Aligned_cols=10 Identities=40% Similarity=0.600 Sum_probs=4.5
Q ss_pred HHHHHHHHHh
Q 001506 146 ALERRIQARY 155 (1065)
Q Consensus 146 e~~~~l~eRY 155 (1065)
.|++.|+.+-
T Consensus 338 rLA~~Lqr~L 347 (600)
T TIGR01651 338 RLANRLQRRL 347 (600)
T ss_pred HHHHHHHHHH
Confidence 3444444443
No 200
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=36.87 E-value=1.3e+02 Score=42.15 Aligned_cols=85 Identities=14% Similarity=0.174 Sum_probs=63.7
Q ss_pred cCcCCCCEEEEecccc-cCceeEEEEEcCC--eEEEeecCCCCCcceeecccccee----------eccCCCcEEEeccc
Q 001506 423 GHFMKGDAVIVIKGDL-KNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCK----------YFEPGNHVKVVSGT 489 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel-~gl~G~V~~V~~d--~V~i~~~~~~l~~~l~v~~~~LrK----------~F~~GDhVkVi~G~ 489 (1065)
.+|++|+.|+.+..++ ++..-.|++|+.+ .++|.... ++..+|.++.+-+ .+..||.+++....
T Consensus 515 ~~Y~~GmVl~~~~r~~k~~~~y~V~~V~~~~n~LtL~~~d---G~~~~~~p~~~~~~~~vy~~e~lelA~GDrlr~t~nd 591 (1623)
T PRK14712 515 DMYRPGMVMEQWNPETRSHDRYVTERVTAQSHSLTLRNAQ---GETQVVRISSLDSSWSLFRPEKMPVADGERLRVTGKI 591 (1623)
T ss_pred hcCCCCCEEEecccCcCcCceEEEEEEcCCCceEEEEcCC---CcEEEechHHcccceeeecccccccCCCCEEEEccCC
Confidence 6899999999766654 4566699999876 45554332 3456777777632 36789999998653
Q ss_pred -----cCCceeEEEEEeCcEEEEEeC
Q 001506 490 -----QAGATGMVLKVEQHVLIILSD 510 (1065)
Q Consensus 490 -----~~getGlVVkVe~~~v~vlSD 510 (1065)
..|+...|++++++.++|..+
T Consensus 592 ~~~~L~ngd~~tV~~i~~~~itl~~~ 617 (1623)
T PRK14712 592 PGLRVSGGDRLQVASVSEDAMTVVVP 617 (1623)
T ss_pred cccCccCCCEEEEEEecCCeEEEEEC
Confidence 357999999999999999877
No 201
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=36.78 E-value=2.9e+02 Score=30.22 Aligned_cols=26 Identities=31% Similarity=0.566 Sum_probs=20.6
Q ss_pred eeEEEEEeCcEEEEEeCCCCceEEEe
Q 001506 494 TGMVLKVEQHVLIILSDTTKEDIRVF 519 (1065)
Q Consensus 494 tGlVVkVe~~~v~vlSD~t~~ei~V~ 519 (1065)
-|-||.|..+.+.|=|.+-.+.++|.
T Consensus 43 EGrVvEV~~~~i~iesk~yn~~v~i~ 68 (213)
T PRK06763 43 EGRVVEVDNGVIVIKSKQYEEPVSVY 68 (213)
T ss_pred eeEEEEEeCCEEEEEeccCCCceEEE
Confidence 47788888888888888777777774
No 202
>PF14851 FAM176: FAM176 family
Probab=36.59 E-value=74 Score=33.26 Aligned_cols=11 Identities=18% Similarity=0.235 Sum_probs=6.2
Q ss_pred HHHHHHHHHHh
Q 001506 145 EALERRIQARY 155 (1065)
Q Consensus 145 ee~~~~l~eRY 155 (1065)
-|+|+.|++|=
T Consensus 119 ~e~A~rlEeRe 129 (153)
T PF14851_consen 119 LERAQRLEERE 129 (153)
T ss_pred HHHHHHHHHHH
Confidence 35566666654
No 203
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=35.94 E-value=53 Score=32.63 Aligned_cols=46 Identities=26% Similarity=0.380 Sum_probs=30.9
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcCC--eEEEeecCCCCCcceeeccccceee
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCKY 476 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d--~V~i~~~~~~l~~~l~v~~~~LrK~ 476 (1065)
..+++||.|.-+ -|+.|+|++|+++ .|.|..+ +-.++|.-+.+...
T Consensus 35 ~sLk~GD~VvT~----GGi~G~V~~I~~~~~~v~le~~----gv~i~v~r~AI~~V 82 (113)
T PRK06531 35 NAIQKGDEVVTI----GGLYGTVDEVDTEAKTIVLDVD----GVYLTFELAAIKRV 82 (113)
T ss_pred HhcCCCCEEEEC----CCcEEEEEEEecCCCEEEEEEC----CEEEEEEhhHhhhh
Confidence 579999999988 4678999999875 4555431 23455554444443
No 204
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=35.63 E-value=3e+02 Score=35.07 Aligned_cols=156 Identities=15% Similarity=0.244 Sum_probs=73.6
Q ss_pred CcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeecccc--------ceeeccCCCcEEEeccccCCcee
Q 001506 424 HFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKE--------LCKYFEPGNHVKVVSGTQAGATG 495 (1065)
Q Consensus 424 ~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~--------LrK~F~~GDhVkVi~G~~~getG 495 (1065)
.|++|+.|. |+|.+|....+.|... .+ .--++.++ ..+.|++||.|++
T Consensus 474 ~l~~G~iV~----------g~V~~v~~~G~fV~l~--gv--~Gll~~sels~~~~~~~~~~~~vGd~V~v---------- 529 (647)
T PRK00087 474 SLEEGDVVE----------GEVKRLTDFGAFVDIG--GV--DGLLHVSEISWGRVEKPSDVLKVGDEIKV---------- 529 (647)
T ss_pred hCCCCCEEE----------EEEEEEeCCcEEEEEC--CE--EEEEEHHHcCccccCCHHHhcCCCCEEEE----------
Confidence 578898885 4455555443333221 11 12233333 4468999999977
Q ss_pred EEEEEeCcEEEEEeCCCCceEEEecccccccccccccccccCceeeeeeEEeCCCceEEEEEEccceEEEeccCCCCCcE
Q 001506 496 MVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDNNSFGVIIRVESEAFQVLKGVPDRPEV 575 (1065)
Q Consensus 496 lVVkVe~~~v~vlSD~t~~ei~V~~~dL~~~~e~~~g~~~~g~y~l~DLVqLd~~tVGvIv~verd~~~VL~~~~~~g~v 575 (1065)
.|+.++. ....+.+..+.+....-. .-...|..++.| -|.|+++..-.+.|--.. +-.
T Consensus 530 kV~~id~---------~~~~I~lS~K~~~~~p~~----~~~~~~~~G~~v------~g~V~~i~~~G~fV~l~~---~i~ 587 (647)
T PRK00087 530 YILDIDK---------ENKKLSLSLKKLLPDPWE----NVEEKYPVGSIV------LGKVVRIAPFGAFVELEP---GVD 587 (647)
T ss_pred EEEEEEC---------CCCEEEEEeeccccChhh----hhhhhccCCeEE------EEEEEEEECCeEEEEECC---CCE
Confidence 3556642 122233333333222110 011234444443 366666666544332211 222
Q ss_pred EEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCCceeeEEEEE--CCEEEEEecceeccce
Q 001506 576 ALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIY--RGILFIHDRHHLEHAG 641 (1065)
Q Consensus 576 ~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~HI~--r~~lFl~~~~~~EN~G 641 (1065)
-.+..+++.... .......+++||.|++. |+.|- +..+-|..+...+|-|
T Consensus 588 Gli~~sel~~~~------~~~~~~~~kvGd~V~vk----------V~~id~e~~rI~lslk~~~~~~~ 639 (647)
T PRK00087 588 GLVHISQISWKR------IDKPEDVLSEGEEVKAK----------ILEVDPEEKRIRLSIKEVEEEPG 639 (647)
T ss_pred EEEEhhhcCccc------cCCHhhcCCCCCEEEEE----------EEEEeCCCCEEEEEEeecccCcc
Confidence 234445554221 11223568999999874 44443 2345555555555543
No 205
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=35.62 E-value=95 Score=34.49 Aligned_cols=71 Identities=24% Similarity=0.383 Sum_probs=48.0
Q ss_pred EEEEEEeCCCCeEEEEecc--CCCCceEEecCC--C-eeecCCCCCCcEEEEcCCCCCceEEEEEEeCCC----cEEEec
Q 001506 976 VGVIREVLPDGSCRVVLGS--SGNGDTITALPN--E-IEIVPPRKTDKIKIMGGPHRGATGKLIGVDGTD----GIVKVD 1046 (1065)
Q Consensus 976 ~GvI~~V~~~g~~~V~l~~--~~~g~~v~v~~~--~-LE~V~P~kgd~VkVi~G~~rG~tG~LisiD~~d----giVk~d 1046 (1065)
.|.|.=+.-||+- |.+.+ ...|+++.++-. + ++.....+|..|.|+.|.+.|.+|++..|.-.. -+|.++
T Consensus 133 gG~~QLn~hDGrn-i~~~d~~~k~~Dtv~i~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e 211 (241)
T COG1471 133 GGRIQLNLHDGRN-IRLEDDNYKTGDTVKISLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVE 211 (241)
T ss_pred CCEEEEEecCCce-eeccCCccccccEEEEeCCChhheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEe
Confidence 3445544455553 33333 112455555433 3 677778999999999999999999999998764 577777
Q ss_pred C
Q 001506 1047 V 1047 (1065)
Q Consensus 1047 ~ 1047 (1065)
+
T Consensus 212 ~ 212 (241)
T COG1471 212 D 212 (241)
T ss_pred c
Confidence 5
No 206
>PF02427 PSI_PsaE: Photosystem I reaction centre subunit IV / PsaE; InterPro: IPR003375 PsaE is a 69 amino acid polypeptide from photosystem I present on the stromal side of the thylakoid membrane. The structure is comprised of a well-defined five-stranded beta-sheet similar to SH3 domains []. This subunit may form complexes with ferredoxin and ferredoxin-oxidoreductase in the photosystem I reaction centre.; GO: 0015979 photosynthesis, 0009522 photosystem I, 0009538 photosystem I reaction center; PDB: 1PSF_A 1PSE_A 2WSF_E 2WSC_E 2O01_E 2WSE_E 1GXI_E 1JB0_E 3PCQ_E 1QP2_A ....
Probab=35.53 E-value=77 Score=28.06 Aligned_cols=29 Identities=21% Similarity=0.297 Sum_probs=23.2
Q ss_pred CCCCcEEEeecC--CCCCCeeEEEEeeCCCC
Q 001506 273 LSRDTWVRMKIG--NYKGDLAKVVDVDNVRQ 301 (1065)
Q Consensus 273 l~~G~wVRIk~G--~YkGDlAqV~~Vd~~~~ 301 (1065)
++.|+.|||+|- -+=+|+|.|..||..+-
T Consensus 1 i~rgskVrIlR~ESYWyn~vGtV~svdqs~i 31 (61)
T PF02427_consen 1 IKRGSKVRILRKESYWYNEVGTVASVDQSGI 31 (61)
T ss_dssp S-TTSEEEE-SSSSTTTTSEEEEEEETTSSS
T ss_pred CCCCCEEEEccccceeecccceEEEEccCCc
Confidence 467999999984 57899999999998863
No 207
>PF03831 PhnA: PhnA protein; InterPro: IPR013988 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the C-terminal domain of PhnA.; PDB: 2AKK_A 2AKL_A.
Probab=35.18 E-value=20 Score=31.19 Aligned_cols=20 Identities=30% Similarity=0.421 Sum_probs=13.2
Q ss_pred ccccCCCCeecCCCEEEEEc
Q 001506 592 NVQDRNKNTVAVKDVVRIVE 611 (1065)
Q Consensus 592 ~a~D~~gn~I~~~D~Vkvv~ 611 (1065)
+..|+|||.+.-||.|.++.
T Consensus 1 vv~DsnGn~L~dGDsV~~iK 20 (56)
T PF03831_consen 1 VVKDSNGNELQDGDSVTLIK 20 (56)
T ss_dssp S-B-TTS-B--TTEEEEESS
T ss_pred CeEcCCCCCccCCCEEEEEe
Confidence 46899999999999999964
No 208
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=34.26 E-value=81 Score=31.40 Aligned_cols=59 Identities=17% Similarity=0.305 Sum_probs=37.8
Q ss_pred CceeEEEEEcCCe--EEEeecCCCCCc--------ceeeccccceeeccCCCcEEEeccccCCceeEEEEEe
Q 001506 440 NLKGWVEKVDEEN--VHIRPEMKGLPK--------TLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLKVE 501 (1065)
Q Consensus 440 gl~G~V~~V~~d~--V~i~~~~~~l~~--------~l~v~~~~LrK~F~~GDhVkVi~G~~~getGlVVkVe 501 (1065)
-..|+|.+|+.+. |+|. |+.+.. .+.+....+.+.+++||.|..-== ..++.-+|++|+
T Consensus 44 ~~~G~V~~vd~~~~~iti~--H~pIp~l~wPaMTM~F~v~~~~~l~~lk~G~~V~F~~~-~~~~~~~i~~i~ 112 (115)
T PRK09838 44 SGTGVVKGIDLESKKITIH--HEPIPAVNWPEMTMRFTITPQTKMSEIKTGDKVAFNFV-QQGNLSLLQDIK 112 (115)
T ss_pred EEEEEEEEEeCCCCEEEEe--ecccccCCCCCccccccCCChhhhccCCCCCEEEEEEE-EcCCcEEEEEEe
Confidence 3579999998875 6654 443322 367777777788999999977311 122333666664
No 209
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=34.24 E-value=52 Score=29.75 Aligned_cols=38 Identities=26% Similarity=0.385 Sum_probs=29.1
Q ss_pred CCCCcEEEeecC--CCCCCeeEEEEeeCCCCEEEEEEeeccc
Q 001506 273 LSRDTWVRMKIG--NYKGDLAKVVDVDNVRQRVTVKLIPRID 312 (1065)
Q Consensus 273 l~~G~wVRIk~G--~YkGDlAqV~~Vd~~~~~V~VkLvPRiD 312 (1065)
++.|+.|||+|- -+=+|.|.|..||..+ +.--++=|+|
T Consensus 3 i~rGskVrIlR~ESYWyn~vGtV~svD~sg--i~YPV~VRF~ 42 (71)
T PRK02749 3 ISRGDKVRILRPESYWYNEVGTVASVDKSG--IKYPVIVRFD 42 (71)
T ss_pred cccCCEEEEccccceeecCcceEEEEccCC--CeeeEEEEee
Confidence 678999999985 5789999999999886 3334444554
No 210
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=33.66 E-value=2.5e+02 Score=31.92 Aligned_cols=86 Identities=20% Similarity=0.178 Sum_probs=55.5
Q ss_pred EEEEEEccceEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCCceeeEEEEE-CCEEEE
Q 001506 553 GVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIY-RGILFI 631 (1065)
Q Consensus 553 GvIv~verd~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~HI~-r~~lFl 631 (1065)
|.|+++.++.+.|++. +.+..++.... +.. ..+.+-+||.|.+..-. +.+|.|..|+ |..+|.
T Consensus 1 g~v~~~~~~~~~v~~~----~~~~~~~~~g~---~~~-------~~~~~~vGD~V~~~~~~--~~~~~i~~i~~R~~~l~ 64 (287)
T cd01854 1 GRVIAVHGGFYDVETE----GGELRCRARGK---LRK-------KGIKPVVGDWVEVEPDD--DGEGVIVRVLPRKNLLS 64 (287)
T ss_pred CEEEEEECCEEEEEEC----CeEEEEEeccc---ccc-------CCCCccCCCEEEEEecC--CCcEEEEEEECCCceEE
Confidence 6788999999988873 34444443321 111 14569999999885322 4579999999 555555
Q ss_pred EecceeccceEEEEeCCceEEeec
Q 001506 632 HDRHHLEHAGFICAKSSSCVVVGG 655 (1065)
Q Consensus 632 ~~~~~~EN~Gifv~~a~~~~~~g~ 655 (1065)
+-..... .-+++.++..++++-+
T Consensus 65 R~~~~~~-~~~i~anvD~vllV~d 87 (287)
T cd01854 65 RPAAGGR-EQVIAANVDQLVIVVS 87 (287)
T ss_pred ccCCCCc-ceeEEEeCCEEEEEEE
Confidence 5332222 4577888888777765
No 211
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=33.00 E-value=42 Score=32.13 Aligned_cols=39 Identities=26% Similarity=0.494 Sum_probs=31.8
Q ss_pred eeecCCCCCCcEEEEcCC--CCCceEEEEEEeCCCc-----EEEec
Q 001506 1008 IEIVPPRKTDKIKIMGGP--HRGATGKLIGVDGTDG-----IVKVD 1046 (1065)
Q Consensus 1008 LE~V~P~kgd~VkVi~G~--~rG~tG~LisiD~~dg-----iVk~d 1046 (1065)
-.++-|++|++|+|+.=+ +-..+|++.+||.+.| +||++
T Consensus 35 pp~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~~girYPVvVRF~ 80 (101)
T PLN00045 35 PPPIGPKRGSKVKILRPESYWFNDVGKVVAVDQDPGVRYPVVVRFE 80 (101)
T ss_pred CCCcccCCCCEEEEccccceeecCcceEEEEeCCCCcccceEEEee
Confidence 456778999999999977 4678999999999877 46654
No 212
>PF09507 CDC27: DNA polymerase subunit Cdc27; InterPro: IPR019038 This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterised by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. ; GO: 0006260 DNA replication, 0005634 nucleus; PDB: 1U76_B 3E0J_B.
Probab=32.87 E-value=14 Score=43.51 Aligned_cols=6 Identities=33% Similarity=0.645 Sum_probs=0.0
Q ss_pred CCcccc
Q 001506 89 EFFDLE 94 (1065)
Q Consensus 89 ~FlD~E 94 (1065)
.|+|++
T Consensus 366 t~~Ded 371 (430)
T PF09507_consen 366 TFVDED 371 (430)
T ss_dssp ------
T ss_pred EEEcCC
Confidence 677655
No 213
>PF03896 TRAP_alpha: Translocon-associated protein (TRAP), alpha subunit; InterPro: IPR005595 The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane [].; GO: 0005783 endoplasmic reticulum
Probab=32.70 E-value=17 Score=41.41 Aligned_cols=13 Identities=31% Similarity=0.465 Sum_probs=6.2
Q ss_pred EEEEEeeccchhh
Q 001506 303 VTVKLIPRIDLQA 315 (1065)
Q Consensus 303 V~VkLvPRiD~~~ 315 (1065)
+--.-||+-=+.+
T Consensus 251 ~D~eWIp~~~l~~ 263 (285)
T PF03896_consen 251 VDEEWIPKEHLNR 263 (285)
T ss_pred CCcccCCHHHhhh
Confidence 3444556554433
No 214
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=32.62 E-value=1.2e+02 Score=37.41 Aligned_cols=51 Identities=31% Similarity=0.388 Sum_probs=33.6
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccc--------eeeccCCCcEEEe
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKEL--------CKYFEPGNHVKVV 486 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~L--------rK~F~~GDhVkVi 486 (1065)
..|++||.|+ |+|++|+.+.|.|.... +-+=.+|.++| .+.|++||.|++.
T Consensus 31 ~~~~~GdiV~----------G~V~~v~~~gv~VdIg~---k~eG~Ip~~Els~~~~~~~~~~~~vGd~Ie~~ 89 (486)
T PRK07899 31 KYFNDGDIVE----------GTVVKVDRDEVLLDIGY---KTEGVIPSRELSIKHDVDPNEVVEVGDEVEAL 89 (486)
T ss_pred hcCCCCCEEE----------EEEEEEECCcEEEEECC---CcEEEEEHHHhcccccCChhhcCCCCCEEEEE
Confidence 4699999885 78999988876665421 11122344443 4579999999764
No 215
>PF14001 YdfZ: YdfZ protein
Probab=32.39 E-value=48 Score=29.64 Aligned_cols=31 Identities=29% Similarity=0.437 Sum_probs=26.5
Q ss_pred cccCCCCeecCCCEEEEEcCCCCCceeeEEEEEC
Q 001506 593 VQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYR 626 (1065)
Q Consensus 593 a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~HI~r 626 (1065)
+-|+|.|.|..|..|.|-. .|..|+|+-|+-
T Consensus 2 tYDRnRN~i~~G~rVMiag---tG~~gvikAih~ 32 (64)
T PF14001_consen 2 TYDRNRNAITTGSRVMIAG---TGATGVIKAIHA 32 (64)
T ss_pred ccccccCcCCCCCEEEEcC---CCcccEEeeeec
Confidence 5699999999999999864 478999998874
No 216
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=32.23 E-value=1.4e+02 Score=29.76 Aligned_cols=38 Identities=24% Similarity=0.297 Sum_probs=26.2
Q ss_pred cccCcCCCCEEEEe----ccc---ccCceeEEEEEcCC----eEEEeec
Q 001506 421 KKGHFMKGDAVIVI----KGD---LKNLKGWVEKVDEE----NVHIRPE 458 (1065)
Q Consensus 421 ~~~~F~~GD~V~V~----~Ge---l~gl~G~V~~V~~d----~V~i~~~ 458 (1065)
.-..|.+||.|+|. +|. .....|.|+++.+. +++|...
T Consensus 15 ~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i 63 (113)
T TIGR01024 15 DLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKI 63 (113)
T ss_pred CCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEe
Confidence 34689999999983 332 45688999998743 4555544
No 217
>PF09444 MRC1: MRC1-like domain; InterPro: IPR018564 This putative domain is found in the most conserved region in mediator of replication checkpoint protein 1. This protein is a component of the replisome and is required for Rad3-dependent activation of the checkpoint kinase Cds1 in response to replication fork arrest [].
Probab=32.17 E-value=9.6 Score=39.27 Aligned_cols=17 Identities=41% Similarity=0.556 Sum_probs=13.6
Q ss_pred CCCCCCcccccccCCch
Q 001506 85 RSGSEFFDLEAQVDSDE 101 (1065)
Q Consensus 85 ~~~~~FlD~EAeVddde 101 (1065)
+.++.||+.|||++|||
T Consensus 4 ~~~~~~vE~EAEESeDE 20 (145)
T PF09444_consen 4 SGASEFVEEEAEESEDE 20 (145)
T ss_pred hhHHHHHHHHHhcchhh
Confidence 34578999999998865
No 218
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.06 E-value=94 Score=32.48 Aligned_cols=48 Identities=33% Similarity=0.532 Sum_probs=40.1
Q ss_pred ccccCcEEEEee----CCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 705 DALVGTTVKVRL----GPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 705 d~liGktV~I~~----GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
..++|+.|+|.- .-=|=+.|++..+.++++.++. ..|.|.|+.+.|+-
T Consensus 95 ~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~v~~~~--~~k~v~Ip~~~i~k 146 (153)
T COG0779 95 ARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGETVTLEV--DGKEVEIPFSDIAK 146 (153)
T ss_pred HHhcCcEEEEEEecccCCceEEEEEEEEEcCCeEEEEE--CCEEEEEEcccchh
Confidence 578999999998 5568899999999999988884 46668888887764
No 219
>PRK12366 replication factor A; Reviewed
Probab=31.82 E-value=1.2e+03 Score=29.83 Aligned_cols=16 Identities=25% Similarity=0.463 Sum_probs=13.6
Q ss_pred CcCCCCEEEEeccccc
Q 001506 424 HFMKGDAVIVIKGDLK 439 (1065)
Q Consensus 424 ~F~~GD~V~V~~Gel~ 439 (1065)
.+++||.|+|-.|..+
T Consensus 344 ~l~~G~vy~is~~~vk 359 (637)
T PRK12366 344 NLKEGDAVKIENCKVR 359 (637)
T ss_pred ccCCCCEEEEecCEEe
Confidence 4568999999999887
No 220
>PRK12288 GTPase RsgA; Reviewed
Probab=31.52 E-value=2.6e+02 Score=32.83 Aligned_cols=87 Identities=20% Similarity=0.227 Sum_probs=56.4
Q ss_pred ceEEEEEEccceEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcC--CCCCceeeEEEEECCE
Q 001506 551 SFGVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEG--PCKGKQGPVEHIYRGI 628 (1065)
Q Consensus 551 tVGvIv~verd~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~G--p~~gr~G~V~HI~r~~ 628 (1065)
..|.|+++.+..+.|++. .|.+..++... ++ ..+-+||.|.+-.. ......|.|.+|+--+
T Consensus 40 ~~g~Vi~~~~~~~~v~~~---~g~~~~~~~~g---~~-----------~~~~vGD~V~~~~~~~~~~~~~~~I~~il~R~ 102 (347)
T PRK12288 40 QEGIVISRFGQHADVEAA---DGEVHRCNIRR---TI-----------RSLVTGDRVVWRPGKEALEGVSGVVEAVHPRT 102 (347)
T ss_pred cceEEEEEECCEEEEEeC---CCcEEEEEecc---cC-----------CCCCCCcEEEEEeCCCcccccceEEEEEeccc
Confidence 469999999999999873 36655544222 11 12899999998521 1101249999999554
Q ss_pred -EEEEecceeccceEEEEeCCceEEeec
Q 001506 629 -LFIHDRHHLEHAGFICAKSSSCVVVGG 655 (1065)
Q Consensus 629 -lFl~~~~~~EN~Gifv~~a~~~~~~g~ 655 (1065)
.|.. +......-+++++...+.++-+
T Consensus 103 n~L~R-~~~~~~~q~iaANvD~vlIV~s 129 (347)
T PRK12288 103 SVLTR-PDYYDGVKPIAANIDQIVIVSA 129 (347)
T ss_pred ceEEC-CCcccccceEEEEccEEEEEEe
Confidence 4443 3333333578899999888866
No 221
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=31.37 E-value=1.7e+02 Score=37.54 Aligned_cols=27 Identities=19% Similarity=0.160 Sum_probs=19.8
Q ss_pred CccccCcEEEEeeCCCCCceeEEEeec
Q 001506 704 HDALVGTTVKVRLGPYKGYRGRVVDVK 730 (1065)
Q Consensus 704 ~d~liGktV~I~~GpyKG~~G~Vkd~t 730 (1065)
...+..|+|||.=|.=||-.---||.-
T Consensus 479 n~kv~~k~Iki~Wa~g~G~kse~k~~w 505 (894)
T KOG0132|consen 479 NVKVADKTIKIAWAVGKGPKSEYKDYW 505 (894)
T ss_pred cccccceeeEEeeeccCCcchhhhhhh
Confidence 467788999999998888765444443
No 222
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=31.23 E-value=91 Score=25.75 Aligned_cols=33 Identities=24% Similarity=0.450 Sum_probs=22.2
Q ss_pred CCCceEEEEEEeCCCcEEEecCCCceEEEeccch
Q 001506 1026 HRGATGKLIGVDGTDGIVKVDVSLDVKILDMAIL 1059 (1065)
Q Consensus 1026 ~rG~tG~LisiD~~dgiVk~d~~~d~kil~~~~L 1059 (1065)
.+|.+|+.+++|+.=|.+ |..+.+-.++++..|
T Consensus 7 ~~g~tGtFlGvDE~FGmL-Lr~~~~T~LIPLT~l 39 (42)
T PF14563_consen 7 VAGLTGTFLGVDEDFGML-LRDDDTTHLIPLTTL 39 (42)
T ss_dssp ETTEEEEEEEE-TT--EE-EE-SS-EEEE-GGGG
T ss_pred EcCcceeEEeeccccceE-EEeCCccEEEEchHh
Confidence 578999999999998887 555667888988765
No 223
>PLN00036 40S ribosomal protein S4; Provisional
Probab=31.20 E-value=69 Score=36.20 Aligned_cols=54 Identities=17% Similarity=0.292 Sum_probs=41.4
Q ss_pred eecCCCEEEEEcCCCCCceeeEEEEECC---EEEEEecceeccceEEEEeCCceEEeec
Q 001506 600 TVAVKDVVRIVEGPCKGKQGPVEHIYRG---ILFIHDRHHLEHAGFICAKSSSCVVVGG 655 (1065)
Q Consensus 600 ~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~---~lFl~~~~~~EN~Gifv~~a~~~~~~g~ 655 (1065)
.+..|.+|.|+.|.+.|+.|+|.||-+. +=-+|.+ ..++.-|-++..||.++|.
T Consensus 174 kfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~--d~~g~~F~T~~~~vfvIG~ 230 (261)
T PLN00036 174 KFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVK--DATGHEFATRLGNVFVIGK 230 (261)
T ss_pred ecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEE--eCCCCeEEEEeeeEEEEcc
Confidence 4778999999999999999999999843 1122221 1345589999999999985
No 224
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=31.12 E-value=1.1e+02 Score=27.46 Aligned_cols=44 Identities=25% Similarity=0.362 Sum_probs=28.0
Q ss_pred eEEEEEc--CCeEEEeec-CCCCC-----cceeeccccceeeccCCCcEEEe
Q 001506 443 GWVEKVD--EENVHIRPE-MKGLP-----KTLAVNSKELCKYFEPGNHVKVV 486 (1065)
Q Consensus 443 G~V~~V~--~d~V~i~~~-~~~l~-----~~l~v~~~~LrK~F~~GDhVkVi 486 (1065)
|.|.+|+ ...|+|.-. ..+|. -.+.+....+-.-|++||.|...
T Consensus 1 G~V~~vd~~~~~iti~H~pIp~l~wpaMTM~F~v~~~~~l~~l~~Gd~V~F~ 52 (70)
T PF11604_consen 1 GVVKSVDPEAGTITISHEPIPELGWPAMTMDFPVADPVDLAGLKPGDKVRFT 52 (70)
T ss_dssp EEEEEEETTTTEEEEEE--BCCCTB-SEEEEEE--TTSEESS-STT-EEEEE
T ss_pred CEEEEEecCCCEEEEecCccccCCCCCeEEEEEcCChhhhhcCCCCCEEEEE
Confidence 7899999 557777643 22331 14777777888999999999875
No 225
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=30.98 E-value=16 Score=33.93 Aligned_cols=42 Identities=31% Similarity=0.480 Sum_probs=0.0
Q ss_pred cCcEEEEeeCCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 708 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 708 iGktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
.|..|.-. | |+.|+|++++++++.||+.. +-.+++.|+.|+-
T Consensus 39 ~Gd~VvT~-g---Gi~G~V~~i~~~~v~lei~~-g~~i~v~k~aI~~ 80 (82)
T PF02699_consen 39 PGDEVVTI-G---GIYGTVVEIDDDTVVLEIAP-GVEITVEKSAIAR 80 (82)
T ss_dssp -----------------------------------------------
T ss_pred CCCEEEEC-C---cEEEEEEEEeCCEEEEEECC-CeEEEEEHHHhHh
Confidence 35555443 3 79999999999999999988 4568999987763
No 226
>KOG4553 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.97 E-value=25 Score=45.88 Aligned_cols=9 Identities=33% Similarity=0.291 Sum_probs=4.4
Q ss_pred cccccccCC
Q 001506 91 FDLEAQVDS 99 (1065)
Q Consensus 91 lD~EAeVdd 99 (1065)
.|-|-.|.-
T Consensus 1370 rd~~~tv~a 1378 (1398)
T KOG4553|consen 1370 RDQENTVGA 1378 (1398)
T ss_pred hhhhhhhcc
Confidence 454555553
No 227
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=30.96 E-value=63 Score=32.72 Aligned_cols=63 Identities=17% Similarity=0.049 Sum_probs=47.5
Q ss_pred cccCcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCC-cceeeccccceeeccCCCcEEEec
Q 001506 421 KKGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLP-KTLAVNSKELCKYFEPGNHVKVVS 487 (1065)
Q Consensus 421 ~~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~-~~l~v~~~~LrK~F~~GDhVkVi~ 487 (1065)
....|..+|.|++. .+.--....+-++++..++|-... .. -.|..+. ++.++++.|..|.|++
T Consensus 56 ~e~~f~s~~~ve~~--~ve~~~~qylY~dg~~~~fMd~et-yeq~~i~~~~-~~~~~Lke~~~V~v~~ 119 (130)
T TIGR00037 56 LEFVSPSTSKVEVP--IVDRREYQVLAIMGGMVQLMDLDT-YETDELPIPE-ELGDSLEPGFEVEYIE 119 (130)
T ss_pred EEEEECCCCEEEEe--EEEEEEEEEEEecCCEEEEEcCCC-cEEEEecCCh-hHHHHhhcCCEEEEEe
Confidence 34689999999987 555566678888999988886532 22 2355555 8999999999999886
No 228
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=30.83 E-value=1.5e+02 Score=29.57 Aligned_cols=30 Identities=27% Similarity=0.405 Sum_probs=22.8
Q ss_pred ccCcCCCCEEEE----eccc---ccCceeEEEEEcCC
Q 001506 422 KGHFMKGDAVIV----IKGD---LKNLKGWVEKVDEE 451 (1065)
Q Consensus 422 ~~~F~~GD~V~V----~~Ge---l~gl~G~V~~V~~d 451 (1065)
-..|.|||+|+| ++|. ++...|.|+++.+.
T Consensus 18 iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~ 54 (115)
T COG0335 18 IPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGR 54 (115)
T ss_pred CCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCC
Confidence 568999998764 6775 56677888888764
No 229
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=30.80 E-value=17 Score=33.88 Aligned_cols=36 Identities=19% Similarity=0.518 Sum_probs=3.0
Q ss_pred ccceeeccCCCcEEEeccccCCceeEEEEEeCcEEEEEeC
Q 001506 471 KELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSD 510 (1065)
Q Consensus 471 ~~LrK~F~~GDhVkVi~G~~~getGlVVkVe~~~v~vlSD 510 (1065)
.+++...++||.|.-++|-| |.|++++++.++|=.+
T Consensus 31 ~~m~~~Lk~Gd~VvT~gGi~----G~V~~i~~~~v~lei~ 66 (82)
T PF02699_consen 31 QEMLASLKPGDEVVTIGGIY----GTVVEIDDDTVVLEIA 66 (82)
T ss_dssp TTGGG-----------------------------------
T ss_pred HHHHHcCCCCCEEEECCcEE----EEEEEEeCCEEEEEEC
Confidence 45667789999999988866 9999999998887443
No 230
>KOG1248 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.60 E-value=44 Score=44.30 Aligned_cols=70 Identities=19% Similarity=0.202 Sum_probs=32.0
Q ss_pred hhhhhhhhccccccccccccccccccchhhccc-CCCccccCCCCCCCCCccc-ccCCCCCCcccccccCCc
Q 001506 31 EEEEEDDRSSRKRRRSQFIDDVAEEDDEEEEED-YDDDEDYGGGGGAARKPKA-KRRSGSEFFDLEAQVDSD 100 (1065)
Q Consensus 31 ~d~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~kr-k~~~~~~FlD~EAeVddd 100 (1065)
+|+|+.+.++++++..++.+....+.-.+.=|+ +|+--+.-....+.+++|+ +++...++.|.+...++|
T Consensus 970 ~D~e~n~~~~~~~~~~~~k~~s~r~~p~dllD~s~~~~~~~l~~~~~~~~~k~q~~~~R~q~~d~~fk~s~d 1041 (1176)
T KOG1248|consen 970 EDMEANDAGERRKKASTLKSTSSRDQPRDLLDESDDEPLNTLTPKSAQRALKKQKRTYRKQKPDSGFKFSRD 1041 (1176)
T ss_pred chhhhhhhhhccccchhccCccccCCcHHHHhhcccchhhhhchhhccchhhhhhhhhhccCCccccccCCC
Confidence 555555555666666666644443332111111 1222222222222333333 222345788888877765
No 231
>COG5593 Nucleic-acid-binding protein possibly involved in ribosomal biogenesis [Translation, ribosomal structure and biogenesis]
Probab=30.19 E-value=13 Score=45.20 Aligned_cols=9 Identities=22% Similarity=0.257 Sum_probs=3.9
Q ss_pred CcccccccC
Q 001506 90 FFDLEAQVD 98 (1065)
Q Consensus 90 FlD~EAeVd 98 (1065)
||.++.|.+
T Consensus 766 ~f~e~~e~~ 774 (821)
T COG5593 766 SFAESSEED 774 (821)
T ss_pred hhhhccccC
Confidence 444444444
No 232
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.11 E-value=76 Score=33.18 Aligned_cols=48 Identities=23% Similarity=0.282 Sum_probs=39.3
Q ss_pred cCCCCEEEEec----ccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceee
Q 001506 425 FMKGDAVIVIK----GDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 476 (1065)
Q Consensus 425 F~~GD~V~V~~----Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~ 476 (1065)
...|-.|+|.- ...+..+|+|+.++++.|++..+. +++.+|-+.+.|.
T Consensus 96 r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~v~~~~~~----k~v~Ip~~~i~kA 147 (153)
T COG0779 96 RFIGEKVKVKLRLPIEGRKKFEGKIVAVDGETVTLEVDG----KEVEIPFSDIAKA 147 (153)
T ss_pred HhcCcEEEEEEecccCCceEEEEEEEEEcCCeEEEEECC----EEEEEEcccchhh
Confidence 35799999987 677899999999999999998664 3488888777764
No 233
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=30.11 E-value=1.9e+02 Score=29.05 Aligned_cols=37 Identities=24% Similarity=0.354 Sum_probs=27.2
Q ss_pred ccCcCCCCEEEEe----ccc---ccCceeEEEEEcCC----eEEEeec
Q 001506 422 KGHFMKGDAVIVI----KGD---LKNLKGWVEKVDEE----NVHIRPE 458 (1065)
Q Consensus 422 ~~~F~~GD~V~V~----~Ge---l~gl~G~V~~V~~d----~V~i~~~ 458 (1065)
-..|.+||.|+|. +|+ .....|.|+++.+. +++|.--
T Consensus 16 ~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki 63 (116)
T PRK05338 16 IPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKI 63 (116)
T ss_pred CCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEc
Confidence 5689999999983 564 45789999999754 4555544
No 234
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=30.02 E-value=88 Score=30.05 Aligned_cols=32 Identities=28% Similarity=0.311 Sum_probs=27.4
Q ss_pred cccccCCCCcEEEeecC--CCCCCeeEEEEeeCC
Q 001506 268 SKAIDLSRDTWVRMKIG--NYKGDLAKVVDVDNV 299 (1065)
Q Consensus 268 ~~~~~l~~G~wVRIk~G--~YkGDlAqV~~Vd~~ 299 (1065)
+..+.++.|+.|||+|- -+=+|.|.|..||..
T Consensus 35 pp~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~ 68 (101)
T PLN00045 35 PPPIGPKRGSKVKILRPESYWFNDVGKVVAVDQD 68 (101)
T ss_pred CCCcccCCCCEEEEccccceeecCcceEEEEeCC
Confidence 34668999999999984 578999999999986
No 235
>PF04050 Upf2: Up-frameshift suppressor 2 ; InterPro: IPR007193 This entry represents Up-frameshift suppressor 2 (also known as Nonsense-mediated mRNA decay protein 2). Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay [].; PDB: 2WJV_D.
Probab=30.01 E-value=17 Score=38.17 Aligned_cols=8 Identities=38% Similarity=0.571 Sum_probs=3.4
Q ss_pred HHHHHHHH
Q 001506 146 ALERRIQA 153 (1065)
Q Consensus 146 e~~~~l~e 153 (1065)
++.+.|.+
T Consensus 64 dFeref~k 71 (170)
T PF04050_consen 64 DFEREFQK 71 (170)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 44444433
No 236
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=29.84 E-value=1.3e+02 Score=25.20 Aligned_cols=51 Identities=20% Similarity=0.105 Sum_probs=36.9
Q ss_pred CcCCCCEEEEecccccCceeEEEEEcC-CeEEEeecCCCCCcceeeccccceee
Q 001506 424 HFMKGDAVIVIKGDLKNLKGWVEKVDE-ENVHIRPEMKGLPKTLAVNSKELCKY 476 (1065)
Q Consensus 424 ~F~~GD~V~V~~Gel~gl~G~V~~V~~-d~V~i~~~~~~l~~~l~v~~~~LrK~ 476 (1065)
.|++|+.|.+.--+-.=-+|+|+++++ ..+.|.-. |.+....|+..+||..
T Consensus 2 ~~~~G~~~~a~~~d~~wyra~I~~~~~~~~~~V~f~--D~G~~~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARWEDGEWYRARIIKVDGEQLYEVFFI--DYGNEEVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEeCCCCEEEEEEEEECCCCEEEEEEE--CCCccEEEeHHHeecC
Confidence 588999999986444568999999998 45555433 4556677888777753
No 237
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=29.82 E-value=1.3e+02 Score=26.92 Aligned_cols=44 Identities=20% Similarity=0.311 Sum_probs=29.8
Q ss_pred CceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCcEEEe
Q 001506 440 NLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVV 486 (1065)
Q Consensus 440 gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~F~~GDhVkVi 486 (1065)
...|+|.+|+.+..+|.-+.+ +.+.+|..-=--..++|.-|.|.
T Consensus 4 ~veG~I~~id~~~~titLdDG---ksy~lp~ef~~~~L~~G~kV~V~ 47 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDG---KSYKLPEEFDFDGLKPGMKVVVF 47 (61)
T ss_pred cceEEEEEEcCCceEEEecCC---CEEECCCcccccccCCCCEEEEE
Confidence 467999999999888876643 34444433333456788888775
No 238
>PRK14633 hypothetical protein; Provisional
Probab=29.71 E-value=87 Score=32.46 Aligned_cols=49 Identities=29% Similarity=0.407 Sum_probs=38.3
Q ss_pred ccccCcEEEEee-C---CCCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 705 DALVGTTVKVRL-G---PYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 705 d~liGktV~I~~-G---pyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
..++|+.|+|+- . .-|=+.|+.+.++++.+++++.. .+++.++.++|.-
T Consensus 90 ~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~~i~l~~~~-~~~~~i~~~~I~k 142 (150)
T PRK14633 90 QALVGFNVKAVTLAPVGSQTKFKGVLERVEGNNVILNLED-GKEISFDFDELKK 142 (150)
T ss_pred HHhCCCeEEEEEecccCCcEEEEEEEEEEeCCEEEEEEcC-CcEEEEEhHHeee
Confidence 578999999964 3 34667899999999999988743 4677888877764
No 239
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=29.48 E-value=31 Score=45.49 Aligned_cols=12 Identities=17% Similarity=0.235 Sum_probs=6.6
Q ss_pred CCEEEEEEeecc
Q 001506 300 RQRVTVKLIPRI 311 (1065)
Q Consensus 300 ~~~V~VkLvPRi 311 (1065)
+-.=+|-++||.
T Consensus 373 ni~R~lyflPR~ 384 (1429)
T KOG0970|consen 373 NICRVLYFLPRP 384 (1429)
T ss_pred CeeeEEEecccc
Confidence 334455667764
No 240
>PF04889 Cwf_Cwc_15: Cwf15/Cwc15 cell cycle control protein; InterPro: IPR006973 This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing [].; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=29.38 E-value=26 Score=39.10 Aligned_cols=7 Identities=14% Similarity=0.714 Sum_probs=2.7
Q ss_pred HHHHHHh
Q 001506 149 RRIQARY 155 (1065)
Q Consensus 149 ~~l~eRY 155 (1065)
+.|..||
T Consensus 236 ~kFl~Ky 242 (244)
T PF04889_consen 236 KKFLNKY 242 (244)
T ss_pred HHHHHHh
Confidence 3333333
No 241
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=29.35 E-value=1.9e+02 Score=34.59 Aligned_cols=67 Identities=13% Similarity=0.119 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHhhCCCcceEEEEee-CCCccEEEEEecchHHHHHHHhcCcccc--e--eeeeeeChhhhhhcc
Q 001506 195 REAAVCLMQKCIDKGSELQIRSVIAL-DHLKNYIYIEADKEAHVKEACKGLRNIY--S--QKVMLVPIREMTDVL 264 (1065)
Q Consensus 195 r~vv~~Lm~K~~~~~~~l~I~Svf~~-~~lkGYIYIEA~~~~~V~~ai~Gl~~v~--~--~~~~lVpi~Em~~vL 264 (1065)
.++..-|..-|...| .|.+|+.. ....|++||+-.+..+...|++.|.|-+ + ..+..+|.+.+...+
T Consensus 383 ~~~~~dv~~e~~k~G---~v~~v~v~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~~~~~~~ 454 (457)
T TIGR01622 383 NEILDDVKEECSKYG---GVVHIYVDTKNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVNDVYDMSC 454 (457)
T ss_pred HHHHHHHHHHHHhcC---CeeEEEEeCCCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHHHHHhhc
Confidence 344444555554444 36666554 6778999999999999999999999976 3 355677777766554
No 242
>PRK14632 hypothetical protein; Provisional
Probab=29.06 E-value=92 Score=33.04 Aligned_cols=51 Identities=20% Similarity=0.438 Sum_probs=39.5
Q ss_pred ccccCcEEEEe-eCC------CCCceeEEEeecCCeEEEEecCC------CeEEEEecCCcccc
Q 001506 705 DALVGTTVKVR-LGP------YKGYRGRVVDVKGQSVRVELESQ------MKVVTVDRSMISDN 755 (1065)
Q Consensus 705 d~liGktV~I~-~Gp------yKG~~G~Vkd~t~~~~rVELhs~------~k~I~V~r~~l~~~ 755 (1065)
..++|+.|+|+ ..+ -|=+.|+++.++++.+++++..+ ..++.++.+.|.-.
T Consensus 94 ~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~~i~l~~~~~~~~~~~~~~~~i~~~~I~ka 157 (172)
T PRK14632 94 SPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGDTVVLRPEGAPAPEAEEAVLRTSWQGVRKA 157 (172)
T ss_pred HHhCCCEEEEEEeccccccCCceEEEEEEEEEeCCEEEEEEcCcccccCCceeEEEEhHHccEE
Confidence 57899999995 343 36688999999999999998643 24688888887753
No 243
>PF11942 Spt5_N: Spt5 transcription elongation factor, acidic N-terminal; InterPro: IPR022581 This is the very acidic N-terminal domain of the early transcription elongation factor Spt5 []. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4 [], nor is it essential for RNA polymerase II binding [].
Probab=29.02 E-value=22 Score=34.01 Aligned_cols=12 Identities=75% Similarity=1.063 Sum_probs=6.4
Q ss_pred cccccccccchh
Q 001506 48 FIDDVAEEDDEE 59 (1065)
Q Consensus 48 ~~~~~~~~~~~~ 59 (1065)
|++++|+-+|++
T Consensus 1 Fid~EAeVDdde 12 (97)
T PF11942_consen 1 FIDDEAEVDDDE 12 (97)
T ss_pred CchhhcccCCcc
Confidence 566666644333
No 244
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=28.72 E-value=83 Score=35.61 Aligned_cols=54 Identities=20% Similarity=0.250 Sum_probs=40.9
Q ss_pred eecCCCEEEEEcCCCCCceeeEEEEECCE---EEEEecceeccceEEEEeCCceEEeec
Q 001506 600 TVAVKDVVRIVEGPCKGKQGPVEHIYRGI---LFIHDRHHLEHAGFICAKSSSCVVVGG 655 (1065)
Q Consensus 600 ~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~~---lFl~~~~~~EN~Gifv~~a~~~~~~g~ 655 (1065)
.+..|.+|.|+.|.+.|+.|+|.|+-+.. =-+|.+ ..++.-|-++..||.++|.
T Consensus 174 kfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~--d~~g~~F~T~~~~vfvIG~ 230 (262)
T PTZ00118 174 KFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVK--DSRGKTFATRLSNVFVIGV 230 (262)
T ss_pred ecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEE--eCCCCeEEEEeeeEEEEcc
Confidence 47889999999999999999999966431 122221 1355589999999999984
No 245
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=28.52 E-value=73 Score=32.23 Aligned_cols=37 Identities=22% Similarity=0.372 Sum_probs=29.7
Q ss_pred eeeccCCCcEEEeccccCCceeEEEEEeCcEEEEEeC
Q 001506 474 CKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSD 510 (1065)
Q Consensus 474 rK~F~~GDhVkVi~G~~~getGlVVkVe~~~v~vlSD 510 (1065)
++.+++|--|.+++|+++|.--+||++=++.+.+.++
T Consensus 2 ~~~l~~GrVvvv~~GR~aGkk~VIv~~iDd~~v~i~g 38 (125)
T COG2163 2 RASLEVGRVVVVTAGRFAGKKVVIVKIIDDNFVLITG 38 (125)
T ss_pred CccccCCeEEEEecceeCCceEEEEEEccCCEEEEeC
Confidence 5678999999999999999999999985554444443
No 246
>KOG0066 consensus eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]
Probab=28.46 E-value=49 Score=39.85 Aligned_cols=7 Identities=14% Similarity=0.463 Sum_probs=3.6
Q ss_pred EEEEecc
Q 001506 988 CRVVLGS 994 (1065)
Q Consensus 988 ~~V~l~~ 994 (1065)
|.+++.+
T Consensus 769 C~LwVvE 775 (807)
T KOG0066|consen 769 CNLWVVE 775 (807)
T ss_pred ceEEEEc
Confidence 5555543
No 247
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.36 E-value=47 Score=35.23 Aligned_cols=8 Identities=25% Similarity=0.393 Sum_probs=4.3
Q ss_pred ccccccCC
Q 001506 92 DLEAQVDS 99 (1065)
Q Consensus 92 D~EAeVdd 99 (1065)
|.|++.+|
T Consensus 209 D~e~~~ed 216 (227)
T KOG3241|consen 209 DDEHDLED 216 (227)
T ss_pred cccccccc
Confidence 56665533
No 248
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=28.28 E-value=92 Score=25.62 Aligned_cols=42 Identities=24% Similarity=0.228 Sum_probs=26.2
Q ss_pred eeEEEEEcCCeEEEeecCCCCCcceeecccc--------ceeeccCCCcEEEe
Q 001506 442 KGWVEKVDEENVHIRPEMKGLPKTLAVNSKE--------LCKYFEPGNHVKVV 486 (1065)
Q Consensus 442 ~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~--------LrK~F~~GDhVkVi 486 (1065)
.|+|++|....+.+..... ..--++.++ ..++|++||.|++.
T Consensus 2 ~g~V~~v~~~g~~v~l~~~---~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~ 51 (65)
T cd00164 2 TGKVVSITKFGVFVELEDG---VEGLVHISELSDKFVKDPSEVFKVGDEVEVK 51 (65)
T ss_pred EEEEEEEEeeeEEEEecCC---CEEEEEHHHCCCccccCHhhEeCCCCEEEEE
Confidence 5888888877666654411 122333333 35679999999773
No 249
>PRK14636 hypothetical protein; Provisional
Probab=27.97 E-value=90 Score=33.27 Aligned_cols=49 Identities=18% Similarity=0.356 Sum_probs=37.2
Q ss_pred ccccCcEEEEe-eCCC---CCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 705 DALVGTTVKVR-LGPY---KGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 705 d~liGktV~I~-~Gpy---KG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
.+++|+.|+|+ ..+. |=+.|+++++++..+++++.. .++++|+.+.|.-
T Consensus 94 ~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~~v~l~~~~-~~~~~i~~~~I~k 146 (176)
T PRK14636 94 ADWAGHEARIALSEPLDGRKQFRGELKGIDGDTVTIADNK-AGEVILPFAAIES 146 (176)
T ss_pred HHhCCCeEEEEEecccCCeEEEEEEEEEEeCCEEEEEEcC-CcEEEEEhHHcce
Confidence 57899999996 3443 456899999999999988742 4567888777764
No 250
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=27.79 E-value=66 Score=33.97 Aligned_cols=46 Identities=17% Similarity=0.286 Sum_probs=32.2
Q ss_pred ccCcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeecccccee
Q 001506 422 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK 475 (1065)
Q Consensus 422 ~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK 475 (1065)
...|++||.|+|- +..|+|++|.--.+++.... ++.+.+|-+.|..
T Consensus 58 ~~pf~vGD~I~i~-----~~~G~V~~I~l~~t~l~~~~---g~~v~IPNs~l~~ 103 (206)
T PF00924_consen 58 ERPFKVGDRIEIG-----GVEGRVEEIGLRSTRLRTWD---GEIVIIPNSKLIS 103 (206)
T ss_dssp C-SS-TT-EEESS-----S-EEEEEEE-SSEEEEEETT---S-EEEEEHHHHHC
T ss_pred cCCccCCCEEEEE-----EeehHHHhcCcceeeeecCC---CCEEEEEchheee
Confidence 4699999999987 99999999999888887643 3568888777663
No 251
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=27.65 E-value=6.3e+02 Score=31.41 Aligned_cols=46 Identities=22% Similarity=0.245 Sum_probs=30.4
Q ss_pred eeeeChhhhhhccccccccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEEEe
Q 001506 252 VMLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLI 308 (1065)
Q Consensus 252 ~~lVpi~Em~~vL~v~~~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~VkLv 308 (1065)
..+||+.||..- ++......+++|+.|++ +|..+|.+++++.|-+-
T Consensus 225 ~glv~~se~s~~-~~~~~~~~~kvG~~v~v----------~V~~~d~~~~~i~lS~k 270 (565)
T PRK06299 225 DGLLHITDISWK-RVNHPSEVVNVGDEVKV----------KVLKFDKEKKRVSLGLK 270 (565)
T ss_pred EEEEEHHHhccc-ccCCHhhcCCCCCEEEE----------EEEEEeCCCCeEEEEEE
Confidence 357888888542 11111234789999964 68899988888777654
No 252
>PRK05807 hypothetical protein; Provisional
Probab=27.58 E-value=2.3e+02 Score=28.77 Aligned_cols=15 Identities=20% Similarity=0.337 Sum_probs=11.7
Q ss_pred cceeeccCCCcEEEe
Q 001506 472 ELCKYFEPGNHVKVV 486 (1065)
Q Consensus 472 ~LrK~F~~GDhVkVi 486 (1065)
++..+|++||.|+|.
T Consensus 44 ~~~~~~kvGd~V~Vk 58 (136)
T PRK05807 44 DIREHLKEQDKVKVK 58 (136)
T ss_pred CccccCCCCCEEEEE
Confidence 336789999999874
No 253
>PRK02001 hypothetical protein; Validated
Probab=27.40 E-value=1.2e+02 Score=31.71 Aligned_cols=50 Identities=16% Similarity=0.191 Sum_probs=37.9
Q ss_pred CccccCcEEEEeeCCCCCceeEEEeecCCeEEEEecCC------------CeEEEEecCCcc
Q 001506 704 HDALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQ------------MKVVTVDRSMIS 753 (1065)
Q Consensus 704 ~d~liGktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~------------~k~I~V~r~~l~ 753 (1065)
...++|+.|+|+-..-|-+.|+++++++..+.+++..+ .+.++++.+.|.
T Consensus 85 f~r~~G~~v~V~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~k~~~~~~~~~~i~~~~I~ 146 (152)
T PRK02001 85 YKKNIGRELEVLTKNGKKIEGELKSADENDITLEVKAREPKEGGKGKVTVEKEETITYDDIK 146 (152)
T ss_pred HHHhCCCEEEEEECCCCEEEEEEEEEeCCEEEEEEcccccccccccccccceeEEEEhHhee
Confidence 35789999999863348899999999999999998743 235666665554
No 254
>PRK00098 GTPase RsgA; Reviewed
Probab=27.10 E-value=3.8e+02 Score=30.57 Aligned_cols=87 Identities=23% Similarity=0.234 Sum_probs=55.5
Q ss_pred EEEEEEccceEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCCceeeEEEEECCEEEEE
Q 001506 553 GVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRGILFIH 632 (1065)
Q Consensus 553 GvIv~verd~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~~lFl~ 632 (1065)
|.|+++.+..+.|++. .|.+..+++.. ++.. ..+.+-+||.|.+-. + ....|.|.+|..-.-+|.
T Consensus 3 g~v~~~~~~~~~v~~~---~~~~~~~~~~g---~~~~-------~~~~~~vGD~V~~~~-~-~~~~g~i~~i~~R~~~l~ 67 (298)
T PRK00098 3 GLIIKALGGFYYVESE---DGQVYQCRARG---KFRK-------KTNTPAVGDRVEFSA-E-NNDEGVILEIHERKNLLV 67 (298)
T ss_pred EEEEEEECCEEEEEEC---CCCEEEEEecc---cccc-------CCCCcCCCCEEEEEE-C-CCCcEEEEEEeCCCceEE
Confidence 8899999999999873 24455544322 1110 235678999998842 1 224699999997766665
Q ss_pred ecceeccceEEEEeCCceEEeec
Q 001506 633 DRHHLEHAGFICAKSSSCVVVGG 655 (1065)
Q Consensus 633 ~~~~~EN~Gifv~~a~~~~~~g~ 655 (1065)
.+.. ...-+++.++..+.++-.
T Consensus 68 R~~~-~~~q~iaaniD~vllV~d 89 (298)
T PRK00098 68 RPPI-FKSKLIAANVDQAVLVFA 89 (298)
T ss_pred CCCC-ccccceeecCCEEEEEEE
Confidence 5554 222356777777666654
No 255
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=27.06 E-value=33 Score=45.34 Aligned_cols=9 Identities=33% Similarity=0.652 Sum_probs=4.6
Q ss_pred hHHhhhccC
Q 001506 393 FDELEKFRT 401 (1065)
Q Consensus 393 leEL~kF~~ 401 (1065)
++||..|..
T Consensus 517 ~e~l~~~y~ 525 (1299)
T KOG1856|consen 517 IEELKEFYL 525 (1299)
T ss_pred HHHHHHHHH
Confidence 455555543
No 256
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.85 E-value=31 Score=40.66 Aligned_cols=8 Identities=50% Similarity=1.169 Sum_probs=4.8
Q ss_pred CCCCCCCc
Q 001506 176 LPSVRDPK 183 (1065)
Q Consensus 176 lPsv~DP~ 183 (1065)
||+++.|.
T Consensus 358 lp~i~~p~ 365 (514)
T KOG3130|consen 358 LPTIRTPA 365 (514)
T ss_pred CCccCCcc
Confidence 67766443
No 257
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=26.70 E-value=6.3e+02 Score=29.78 Aligned_cols=45 Identities=13% Similarity=0.135 Sum_probs=31.5
Q ss_pred eeeChhhhhhccccccccccCCCCcEEEeecCCCCCCeeEEEEeeCCCCEEEEEEe
Q 001506 253 MLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLI 308 (1065)
Q Consensus 253 ~lVpi~Em~~vL~v~~~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~VkLv 308 (1065)
..+|..||.+-.- ......+++|+.|++ .|+.++..+.++.|-+-
T Consensus 44 g~lp~~e~~~~~~-~~~~~~~~vGd~v~~----------~V~~v~~~~~~i~lS~k 88 (390)
T PRK06676 44 GVIPISELSNDHI-EDINDVVKVGDELEV----------YVLKVEDGEGNLLLSKR 88 (390)
T ss_pred EEEEHHHhccccc-cCcccccCCCCEEEE----------EEEEEECCCCCEEEEHH
Confidence 5789999976422 222335789999974 79999988877776644
No 258
>PF05470 eIF-3c_N: Eukaryotic translation initiation factor 3 subunit 8 N-terminus; InterPro: IPR008905 The largest of the mammalian translation initiation factors, eIF3, consists of at least eight subunits ranging in mass from 35 to 170 kDa. eIF3 binds to the 40 S ribosome in an early step of translation initiation and promotes the binding of methionyl-tRNAi and mRNA [].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation, 0005852 eukaryotic translation initiation factor 3 complex
Probab=26.60 E-value=36 Score=42.77 Aligned_cols=7 Identities=29% Similarity=0.805 Sum_probs=3.5
Q ss_pred EEeeccc
Q 001506 306 KLIPRID 312 (1065)
Q Consensus 306 kLvPRiD 312 (1065)
-+|=|||
T Consensus 335 s~verLd 341 (595)
T PF05470_consen 335 SFVERLD 341 (595)
T ss_pred HHHHHHH
Confidence 3455555
No 259
>PHA03247 large tegument protein UL36; Provisional
Probab=26.28 E-value=1.5e+03 Score=34.07 Aligned_cols=31 Identities=13% Similarity=0.067 Sum_probs=14.5
Q ss_pred EEeCCCCceEEEeccccc-------ccccccccccccC
Q 001506 507 ILSDTTKEDIRVFADDVV-------ESSEVTTGITKIG 537 (1065)
Q Consensus 507 vlSD~t~~ei~V~~~dL~-------~~~e~~~g~~~~g 537 (1065)
+||.-++=+++|..=|-+ ..+-|++.+.+.|
T Consensus 2322 ~fS~~SgL~Lc~~LFDSR~g~~d~~l~~aVSsD~~SWg 2359 (3151)
T PHA03247 2322 AFSRGSELELCVTLFDSRARGADAALREVVSSDVETWA 2359 (3151)
T ss_pred ccCCCCcceehhhhhcCCCCCcccchHHHhcccHHHHH
Confidence 455555545555444444 2233455454544
No 260
>PRK14638 hypothetical protein; Provisional
Probab=26.22 E-value=1.1e+02 Score=31.62 Aligned_cols=47 Identities=17% Similarity=0.314 Sum_probs=38.1
Q ss_pred CCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceee
Q 001506 426 MKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 476 (1065)
Q Consensus 426 ~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~ 476 (1065)
..|-.|+|.-...+..+|++.+++++.|+|..+ ++.++++.++++|+
T Consensus 98 ~~G~~v~V~~~~~k~~~G~L~~~~~~~i~l~~~----~~~~~i~~~~I~~a 144 (150)
T PRK14638 98 FTGKLAKIVTKDGKTFIGRIESFVDGTITISDE----KEKYEINIDDVKRA 144 (150)
T ss_pred hCCCEEEEEECCCcEEEEEEEEEeCCEEEEEEC----CcEEEEEhHHcceE
Confidence 579999996555688999999999999998743 35688888888774
No 261
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=26.20 E-value=2.5e+02 Score=23.39 Aligned_cols=42 Identities=19% Similarity=0.189 Sum_probs=24.4
Q ss_pred eeEEEEEcCCeEEEeecCCCCCcceeeccccce--------eeccCCCcEEEe
Q 001506 442 KGWVEKVDEENVHIRPEMKGLPKTLAVNSKELC--------KYFEPGNHVKVV 486 (1065)
Q Consensus 442 ~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~Lr--------K~F~~GDhVkVi 486 (1065)
.|+|+++....+.+.... .-.--++.+++. +.|++||.|++.
T Consensus 7 ~g~V~~v~~~g~~v~i~~---~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~ 56 (72)
T smart00316 7 EGTVTEITPFGAFVDLGN---GVEGLIPISELSDKRVKDPEEVLKVGDEVKVK 56 (72)
T ss_pred EEEEEEEEccEEEEEeCC---CCEEEEEHHHCCccccCCHHHeecCCCEEEEE
Confidence 577888877655544321 112233444444 459999999873
No 262
>TIGR03318 YdfZ_fam putative selenium-binding protein YdfZ. This small protein has a very limited distribution, being found so far only among some gamma-Proteobacteria. The member from Escherichia coli was shown to bind selenium in the absence of a working SelD-dependent selenium incorporation system. Note that while the E. coli member contains a single Cys residue, a likely selenium binding site, some other members of this protein family contain two Cys residues or none.
Probab=26.03 E-value=53 Score=29.35 Aligned_cols=31 Identities=29% Similarity=0.452 Sum_probs=26.5
Q ss_pred cccCCCCeecCCCEEEEEcCCCCCceeeEEEEEC
Q 001506 593 VQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYR 626 (1065)
Q Consensus 593 a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~HI~r 626 (1065)
+-|+|.|.|..|+.|.|.. .|+.|.|+-|+-
T Consensus 3 ~YDRnRNait~G~rVMia~---tG~tgvikaIh~ 33 (65)
T TIGR03318 3 TYDRNRNAITTGSRVMIAG---TGHTGVIKAIHT 33 (65)
T ss_pred cccccccccCCCcEEEEec---CCccceeehhhh
Confidence 5699999999999999864 478999998874
No 263
>cd04469 S1_Hex1 S1_Hex1: Hex1, S1-like RNA-binding domain. Hex1 protein is the major component of the Woronin body in filamentous fungi. The Woronin body is a dense vesicle and plays a vital role in filamentous fungi cell integrity. When cell damage occurs, Woronin bodies seal the septal pore to prevent further cytoplasmic bleeding. Hex1 protein self-assembles to form the solid core of the Woronin body vesicle. The Hex1 sequence and structure are similar to eukaryotic initiation factor 5A (eIF5A), suggesting they share a common ancestor during evolution. All members of the EF superfamily to which Hex1 belongs, contain an S1 domain, which has been shown to bind RNA or single-stranded DNA and often interacts with the ribosome.
Probab=25.98 E-value=58 Score=30.11 Aligned_cols=38 Identities=21% Similarity=0.245 Sum_probs=30.4
Q ss_pred EEEEEcCCeEEEeecCCCCCcceeec-----cccceeeccCCC
Q 001506 444 WVEKVDEENVHIRPEMKGLPKTLAVN-----SKELCKYFEPGN 481 (1065)
Q Consensus 444 ~V~~V~~d~V~i~~~~~~l~~~l~v~-----~~~LrK~F~~GD 481 (1065)
.++.|++..+++|.+..+.++.|.+| ..+|+..|+.|.
T Consensus 6 qLidI~DG~lsLM~e~G~~kdDl~lP~~~~l~~~I~~~f~~gk 48 (75)
T cd04469 6 RVLDIQDGSIVAMTETGDVKQGLPVIDQSNLWTRLKTAFESGR 48 (75)
T ss_pred EEEEecCCeEEEEcCCCCcccCccCCCcchHHHHHHHHHHCCC
Confidence 46778667899998888888889999 455667888888
No 264
>COG3343 RpoE DNA-directed RNA polymerase, delta subunit [Transcription]
Probab=25.57 E-value=28 Score=36.79 Aligned_cols=9 Identities=56% Similarity=1.051 Sum_probs=4.6
Q ss_pred ccCCchhhh
Q 001506 96 QVDSDEEED 104 (1065)
Q Consensus 96 eVdddeEee 104 (1065)
+||++++++
T Consensus 158 ~~Dede~d~ 166 (175)
T COG3343 158 EVDEDEDDD 166 (175)
T ss_pred ccccccccc
Confidence 555555443
No 265
>PRK14646 hypothetical protein; Provisional
Probab=25.17 E-value=1.1e+02 Score=31.92 Aligned_cols=48 Identities=15% Similarity=0.193 Sum_probs=37.6
Q ss_pred ccccCcEEEEee-CCC---CCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 705 DALVGTTVKVRL-GPY---KGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 705 d~liGktV~I~~-Gpy---KG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
..++|+.|+|+- .+. |=+.|+++.+.++.+.+++ ..+++.++.+.|.-
T Consensus 96 ~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~~v~l~~--~g~~~~i~~~~I~k 147 (155)
T PRK14646 96 KTFKGFPVNVELNQKNSKIKFLNGLLYEKSKDYLAINI--KGKIKKIPFNEVLK 147 (155)
T ss_pred HHhCCCEEEEEEecCcCCeEEEEEEEEEEeCCEEEEEE--CCEEEEEEHHHeee
Confidence 578999999973 333 4567999999999999886 46778888777764
No 266
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=25.16 E-value=3.4e+02 Score=25.95 Aligned_cols=61 Identities=15% Similarity=0.177 Sum_probs=41.7
Q ss_pred EEEEEEccc-eEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCCceeeEEEEEC
Q 001506 553 GVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYR 626 (1065)
Q Consensus 553 GvIv~verd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~HI~r 626 (1065)
|+|+.+-.+ .|+|... +|..+. --|..|+.++ -=-|..||.|+|---||.=..|.|.|=|+
T Consensus 11 G~V~e~Lp~~~frV~Le---nG~~vl---a~isGKmR~~-------rIrIl~GD~V~VE~spYDltkGRIiyR~~ 72 (87)
T PRK12442 11 GIVDEVLPDSRFRVTLE---NGVEVG---AYASGRMRKH-------RIRILAGDRVTLELSPYDLTKGRINFRHK 72 (87)
T ss_pred EEEEEECCCCEEEEEeC---CCCEEE---EEeccceeee-------eEEecCCCEEEEEECcccCCceeEEEEec
Confidence 899998876 5787764 355443 3344554431 12488999999988898777788876654
No 267
>KOG4264 consensus Nucleo-cytoplasmic protein MLN51 [General function prediction only]
Probab=25.15 E-value=49 Score=40.33 Aligned_cols=90 Identities=23% Similarity=0.426 Sum_probs=0.0
Q ss_pred CCCCCCCcccccccchh----------hhhccCccchhhhhhhhhhccccccccccccccccccchhhcccCCCccccCC
Q 001506 3 RRRDDDDDEMDAEEDEY----------DEQVMDDEIDEEEEEEDDRSSRKRRRSQFIDDVAEEDDEEEEEDYDDDEDYGG 72 (1065)
Q Consensus 3 ~~~~~~~~~~~~~~~~~----------~~~~~~~e~~~~d~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 (1065)
|+-+...+.+-+||++| -+.+|.||.+.||.|++++-.|--.++..-|-.+|-..+|-.|++=+---|.-
T Consensus 60 rrvesa~~~e~~Ed~deE~~~~g~asgsdsEe~ed~~~Edge~~eEnskgE~ks~~ddaVndStkeeKgde~~~np~yIp 139 (694)
T KOG4264|consen 60 RRVESAKPAESVEDDDEEPAPAGKASGSDSEEKEDEAAEDGEEDEENSKGEEKSNLDDAVNDSTKEEKGDENVENPAYIP 139 (694)
T ss_pred hcccccCccccccccccccccccccccCCcccccccccccCccccccccchhhhhhhhhhcchhhhhhcccCccCccccc
Q ss_pred CCCCCCCcccccCCCCCCccccc-------------ccCCchhhhc
Q 001506 73 GGGAARKPKAKRRSGSEFFDLEA-------------QVDSDEEEDE 105 (1065)
Q Consensus 73 ~~~~~~~~krk~~~~~~FlD~EA-------------eVdddeEeee 105 (1065)
..+ +|-+-.. ++.+|+.+|+
T Consensus 140 k~g-------------~fy~hddsTe~~eg~v~~~g~~~~dd~~dr 172 (694)
T KOG4264|consen 140 KTG-------------RFYMHDDSTENREGDVNNSGQVQDDDSDDR 172 (694)
T ss_pred ccc-------------cccccccccccccccccccccccccchhhc
No 268
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=25.01 E-value=86 Score=31.81 Aligned_cols=51 Identities=25% Similarity=0.326 Sum_probs=33.7
Q ss_pred CCCCEEEEec----ccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceee
Q 001506 426 MKGDAVIVIK----GDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 476 (1065)
Q Consensus 426 ~~GD~V~V~~----Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~ 476 (1065)
..|-.|+|.- ...+...|++.+++++.|+|....+..++.++++.+++.|+
T Consensus 85 ~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~~I~~~~I~ka 139 (141)
T PF02576_consen 85 FIGRKVKVKLKQPVNGRKEFEGKLLEVDEDEITLEVEGKGKKKEVEIPFSDIKKA 139 (141)
T ss_dssp H-SEEEEEE-SS-SSS-SEEEEEEEEEETTEEEEEEE-SS-EEEEEE-SS--SS-
T ss_pred hcCCeEEEEEeccCCCcEEEEEEEEEEeCCEEEEEECCccceEEEEEEHHHCceE
Confidence 4788999985 23355799999999999999776554445788988888764
No 269
>COG3109 ProQ Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]
Probab=24.97 E-value=99 Score=32.89 Aligned_cols=44 Identities=27% Similarity=0.499 Sum_probs=35.9
Q ss_pred cCcEEEEeeCCCCCceeEEEeecCCeEEEEecCCCeEEEEecCCcc
Q 001506 708 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 753 (1065)
Q Consensus 708 iGktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~ 753 (1065)
+|+.|++..|. -..-.+|.+++-+.|||+|.+... +.|.-+||-
T Consensus 164 ~g~~~kVk~G~-~a~~AtvlEv~Kd~vRVqL~~Gl~-m~V~AehL~ 207 (208)
T COG3109 164 VGQALKVKAGQ-NAMDATVLEITKDGVRVQLNSGLS-MIVRAEHLV 207 (208)
T ss_pred ccceeeecccc-ccccceEEEEeccceEEeecCCce-EEEehhhhc
Confidence 89999999994 456789999999999999998765 566666653
No 270
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=24.69 E-value=3e+02 Score=39.12 Aligned_cols=89 Identities=15% Similarity=0.222 Sum_probs=58.0
Q ss_pred cCcCC--CCEEEEecccccCceeEEEEEcCC--eEEEeecCCCCCcceeeccccc-----------eeeccCCCcEEEec
Q 001506 423 GHFMK--GDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKEL-----------CKYFEPGNHVKVVS 487 (1065)
Q Consensus 423 ~~F~~--GD~V~V~~Gel~gl~G~V~~V~~d--~V~i~~~~~~l~~~l~v~~~~L-----------rK~F~~GDhVkVi~ 487 (1065)
..|++ ||.|.. .+ ....|+.|+.+ .|+|.... ++.+.|.++.+ ..-|.+||.|+...
T Consensus 1274 ~~Y~~~~G~vv~~-~~----~y~~V~~vd~~~~~ltl~~~~---G~~~~~~P~~~~~~~~~vy~~~~~ela~GDrIr~Tr 1345 (1747)
T PRK13709 1274 STWEAHRGALALV-DN----VYHRIAGIDKDDGLITLRDAE---GNTRLISPREAVAEGVTLYTPDTIRVGTGDRMRFTK 1345 (1747)
T ss_pred hhcccCCCcEEEe-cC----ceEEEEEEcCCCCEEEEEcCC---CCEEEeChhhcccccccccccccccccCCCEEEEcc
Confidence 46777 888875 33 34678888754 56665432 44566666554 23588999998873
Q ss_pred -----cccCCceeEEEEEeCcEEEEEeCCCCceEEEecc
Q 001506 488 -----GTQAGATGMVLKVEQHVLIILSDTTKEDIRVFAD 521 (1065)
Q Consensus 488 -----G~~~getGlVVkVe~~~v~vlSD~t~~ei~V~~~ 521 (1065)
|...|+.+.|+.|+++.++| .|-.. ++++.+.
T Consensus 1346 nDk~~G~~Ng~~~tV~~I~~~~I~l-~~~~~-~~~l~~~ 1382 (1747)
T PRK13709 1346 SDRERGYVANSVWTVTAVSGDSVTL-SDGQQ-TRVIRPG 1382 (1747)
T ss_pred cCcccccccCCEEEEEEEcCCeEEE-EcCCc-eEEeccc
Confidence 44568999999999988654 44332 3555443
No 271
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=24.53 E-value=95 Score=40.39 Aligned_cols=47 Identities=19% Similarity=0.232 Sum_probs=35.4
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcC-CeEEEeecCCCCCcceeeccccceee
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDE-ENVHIRPEMKGLPKTLAVNSKELCKY 476 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~-d~V~i~~~~~~l~~~l~v~~~~LrK~ 476 (1065)
..|++||.|+|.. -|..|+|++|.+ +.++|... .+ .+.|+.++|++.
T Consensus 635 ~~~~~Gd~V~v~~---~~~~g~v~~i~~~~~~~V~~g--~~--k~~v~~~~l~~~ 682 (782)
T PRK00409 635 EELKVGDEVKYLS---LGQKGEVLSIPDDKEAIVQAG--IM--KMKVPLSDLEKI 682 (782)
T ss_pred cCCCCCCEEEEcc---CCceEEEEEEcCCCeEEEEEC--CE--EEEEeHHHceeC
Confidence 4599999999986 455799999964 56777653 22 478888888754
No 272
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=24.44 E-value=3.4e+02 Score=25.25 Aligned_cols=63 Identities=24% Similarity=0.293 Sum_probs=44.8
Q ss_pred eEEEEEEccc-eEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCCceeeEEEEECC
Q 001506 552 FGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRG 627 (1065)
Q Consensus 552 VGvIv~verd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~HI~r~ 627 (1065)
.|+|+.+-.+ .|+|... +|.++. .-|..|..+ |.=-|..||.|.|---||.-..|.|.+=|+.
T Consensus 10 ~g~V~e~L~~~~f~v~~e---dg~~~~---ahI~GKmr~-------~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~~ 73 (75)
T COG0361 10 EGTVIEMLPNGRFRVELE---NGHERL---AHISGKMRK-------NRIRILPGDVVLVELSPYDLTKGRIVYRYKK 73 (75)
T ss_pred EEEEEEecCCCEEEEEec---CCcEEE---EEccCcchh-------eeEEeCCCCEEEEEecccccccccEEEEecC
Confidence 4888888876 5899985 466554 335555433 1124899999999988887788988877653
No 273
>PRK08582 hypothetical protein; Provisional
Probab=24.37 E-value=2.3e+02 Score=28.99 Aligned_cols=15 Identities=20% Similarity=0.421 Sum_probs=11.6
Q ss_pred cceeeccCCCcEEEe
Q 001506 472 ELCKYFEPGNHVKVV 486 (1065)
Q Consensus 472 ~LrK~F~~GDhVkVi 486 (1065)
++.++|++||.|+|.
T Consensus 45 ~~~~~l~vGD~Vkvk 59 (139)
T PRK08582 45 DINDHLKVGDEVEVK 59 (139)
T ss_pred ccccccCCCCEEEEE
Confidence 344789999999874
No 274
>PRK14647 hypothetical protein; Provisional
Probab=24.18 E-value=1.3e+02 Score=31.56 Aligned_cols=49 Identities=20% Similarity=0.287 Sum_probs=38.1
Q ss_pred ccccCcEEEEee-C--------CCCCceeEEEeecCCeEEEEecCCCeEEEEecCCccc
Q 001506 705 DALVGTTVKVRL-G--------PYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1065)
Q Consensus 705 d~liGktV~I~~-G--------pyKG~~G~Vkd~t~~~~rVELhs~~k~I~V~r~~l~~ 754 (1065)
..++|+.|+|+- . .-|=+.|++++++++.+++++.. .+++.++.+.|.-
T Consensus 95 ~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~-~~~~~i~~~~I~k 152 (159)
T PRK14647 95 ERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADGVVTIALKE-GQQARIPLDKIAK 152 (159)
T ss_pred HHhCCcEEEEEEeccccccccCCceEEEEEEEeecCCEEEEEEcC-CcEEEEEHHHCCE
Confidence 578999999973 2 23778999999999999998742 4567888777764
No 275
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=24.07 E-value=46 Score=29.89 Aligned_cols=46 Identities=26% Similarity=0.311 Sum_probs=26.2
Q ss_pred ceeEEEEEcCCeEEEeec--CCCCCcceee-----ccccceeeccCCCcEEEe
Q 001506 441 LKGWVEKVDEENVHIRPE--MKGLPKTLAV-----NSKELCKYFEPGNHVKVV 486 (1065)
Q Consensus 441 l~G~V~~V~~d~V~i~~~--~~~l~~~l~v-----~~~~LrK~F~~GDhVkVi 486 (1065)
..|+|.+|.+.-+.|... ...+-.-..+ ..+++.+.|++||.|++.
T Consensus 4 V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~k 56 (73)
T cd05703 4 VTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAK 56 (73)
T ss_pred EEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEE
Confidence 468888888775544432 2211000111 133566789999999763
No 276
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=23.95 E-value=28 Score=45.13 Aligned_cols=24 Identities=21% Similarity=0.188 Sum_probs=13.0
Q ss_pred CCccEEEEEecchHHHHHHHhcCc
Q 001506 222 HLKNYIYIEADKEAHVKEACKGLR 245 (1065)
Q Consensus 222 ~lkGYIYIEA~~~~~V~~ai~Gl~ 245 (1065)
.++|-||.=.++.+--.--+..+.
T Consensus 477 lvpgI~~~l~DkSsss~~ki~~L~ 500 (1233)
T KOG1824|consen 477 LVPGIIYSLNDKSSSSNLKIDALV 500 (1233)
T ss_pred cchhhhhhcCCccchHHHHHHHHH
Confidence 466777776666544443333333
No 277
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=23.86 E-value=1e+03 Score=29.44 Aligned_cols=14 Identities=7% Similarity=0.195 Sum_probs=8.4
Q ss_pred CCCChHHhhhccCC
Q 001506 389 IQPTFDELEKFRTP 402 (1065)
Q Consensus 389 V~PTleEL~kF~~~ 402 (1065)
+++-|+|+++|-..
T Consensus 57 l~~~iee~t~kLrt 70 (554)
T KOG0119|consen 57 LNLRIEEITRKLRT 70 (554)
T ss_pred HHHHHHHhhhhhcc
Confidence 45666666666543
No 278
>PF01157 Ribosomal_L21e: Ribosomal protein L21e; InterPro: IPR001147 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 [, ]. L21E family contains proteins from a number of eukaryotic and archaebacterial organisms which include; mammalian L2, Entamoeba histolytica L21, Caenorhabditis elegans L21 (C14B9.7), Saccharomyces cerevisiae (Baker's yeast) L21E (URP1) and Haloarcula marismortui HL31.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_U 1S1I_Q 3O58_T 3IZS_U 3O5H_T 1Q82_R 1KQS_P 3CCJ_Q 3CCQ_Q 1VQ5_Q ....
Probab=23.68 E-value=97 Score=30.16 Aligned_cols=58 Identities=19% Similarity=0.258 Sum_probs=30.8
Q ss_pred ccccceeeccCCCcEEEe-cc---------ccCCceeEEEEEeCcEEEE-----EeC-CCCceEEEeccccccc
Q 001506 469 NSKELCKYFEPGNHVKVV-SG---------TQAGATGMVLKVEQHVLII-----LSD-TTKEDIRVFADDVVES 526 (1065)
Q Consensus 469 ~~~~LrK~F~~GDhVkVi-~G---------~~~getGlVVkVe~~~v~v-----lSD-~t~~ei~V~~~dL~~~ 526 (1065)
+.+.+-..|++||.|-+. .| .|.|-||.|+.|....+=+ +-| .-.+.|.|.+.+|+.+
T Consensus 25 ~ls~~l~~yk~GD~V~I~id~sv~kGmPh~~yHGkTG~V~~v~~~~~G~~~~~~v~~~~~~K~i~vr~eHlk~s 98 (99)
T PF01157_consen 25 PLSTYLQEYKVGDKVDIKIDPSVHKGMPHKRYHGKTGRVFNVTKGARGVAYNKQVKDRIKEKRIIVRPEHLKPS 98 (99)
T ss_dssp -CHHHH----TT-EEEE---TTSSSSS--GGGTTEEEEEEEE-SSCEEEEEEEECSSSCEEEEEEEEGGGEEE-
T ss_pred cHHHHHHHccCCCEEEEEecCccccCCCcceECCCceeEEEeCCCceEEEEEEEecCCcccEEEEECHHHcccC
Confidence 445555679999999765 22 2679999999998753311 222 2245667777776643
No 279
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=23.48 E-value=29 Score=40.90 Aligned_cols=12 Identities=8% Similarity=0.191 Sum_probs=7.2
Q ss_pred HHHHHHHHHHhc
Q 001506 145 EALERRIQARYA 156 (1065)
Q Consensus 145 ee~~~~l~eRY~ 156 (1065)
|+.++.|++|-+
T Consensus 568 e~~~~~lk~kkk 579 (591)
T COG5163 568 EEQAENLKKKKK 579 (591)
T ss_pred HHHHHHHHHHHH
Confidence 566666666543
No 280
>COG0056 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion]
Probab=23.38 E-value=2e+02 Score=35.10 Aligned_cols=49 Identities=14% Similarity=0.258 Sum_probs=39.8
Q ss_pred CceeEEEEEeCcEEEEEeCCCCceEEEecccccccccccccccccCceeeeeeEEeCCCceEEEEEEccceEEEe
Q 001506 492 GATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDNNSFGVIIRVESEAFQVL 566 (1065)
Q Consensus 492 getGlVVkVe~~~v~vlSD~t~~ei~V~~~dL~~~~e~~~g~~~~g~y~l~DLVqLd~~tVGvIv~verd~~~VL 566 (1065)
-++|.|+.|-+..+.|. .+-++.++.||++.++..|++..+|.+.+-++
T Consensus 26 ~~~g~V~sv~DgIa~v~--------------------------Gl~~~~~~E~~ef~~~v~G~alnle~d~VG~v 74 (504)
T COG0056 26 KEVGTVISVGDGIARVS--------------------------GLENVMAGELVEFPGGVKGMALNLEEDSVGAV 74 (504)
T ss_pred hccceEEEEecceEEEe--------------------------cCchhhcCceEEecCCcEEEEEeccccceeEE
Confidence 37899999988777653 24578899999999999999999999875444
No 281
>CHL00010 infA translation initiation factor 1
Probab=23.35 E-value=3e+02 Score=25.41 Aligned_cols=56 Identities=18% Similarity=0.216 Sum_probs=33.1
Q ss_pred ceeEEEEEcC-CeEEEeecCCCCCcce-eeccccceee---ccCCCcEEEeccccCCceeEEEE
Q 001506 441 LKGWVEKVDE-ENVHIRPEMKGLPKTL-AVNSKELCKY---FEPGNHVKVVSGTQAGATGMVLK 499 (1065)
Q Consensus 441 l~G~V~~V~~-d~V~i~~~~~~l~~~l-~v~~~~LrK~---F~~GDhVkVi~G~~~getGlVVk 499 (1065)
+.|+|+++-+ +...|.+... ..+ ....--||+. ..+||.|.|--=.+..+.|.||-
T Consensus 9 ~~G~Vik~lg~~~y~V~~~~g---~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~ 69 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDNG---CQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIY 69 (78)
T ss_pred EEEEEEEEcCCCEEEEEeCCC---CEEEEEeccceecCCcccCCCCEEEEEEcccCCCeEEEEE
Confidence 6789999884 6666654321 222 2223334432 46799998863344566788774
No 282
>KOG0608 consensus Warts/lats-like serine threonine kinases [Cell cycle control, cell division, chromosome partitioning]
Probab=23.19 E-value=9.4e+02 Score=31.08 Aligned_cols=8 Identities=50% Similarity=0.812 Sum_probs=3.6
Q ss_pred CCCcCCCC
Q 001506 902 STYVNAPS 909 (1065)
Q Consensus 902 ~~y~~~ps 909 (1065)
++|..+|+
T Consensus 273 s~y~ssPs 280 (1034)
T KOG0608|consen 273 SAYDSSPS 280 (1034)
T ss_pred cccccCCC
Confidence 34544443
No 283
>PF14944 TCRP1: Tongue Cancer Chemotherapy Resistant Protein 1
Probab=23.17 E-value=2.5e+02 Score=29.36 Aligned_cols=9 Identities=44% Similarity=1.147 Sum_probs=3.7
Q ss_pred CCcCCCCCC
Q 001506 903 TYVNAPSPY 911 (1065)
Q Consensus 903 ~y~~~pspy 911 (1065)
+|+++|.||
T Consensus 72 pys~sPnPY 80 (195)
T PF14944_consen 72 PYSPSPNPY 80 (195)
T ss_pred CCCCCCCcc
Confidence 344444443
No 284
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=23.13 E-value=1.4e+02 Score=31.82 Aligned_cols=53 Identities=28% Similarity=0.374 Sum_probs=31.7
Q ss_pred cCcCCCCEEEEecccccCceeEEEEEcCCeEEEeecC-----CCCC--cceeecccc--------ceeeccCCCcEEE
Q 001506 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEM-----KGLP--KTLAVNSKE--------LCKYFEPGNHVKV 485 (1065)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~-----~~l~--~~l~v~~~~--------LrK~F~~GDhVkV 485 (1065)
..+++||.|. |+|++|.++.+.|.... ..+. -+--++.++ +++.|++||.|++
T Consensus 60 ~~~~~GdiV~----------GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~a 127 (189)
T PRK09521 60 PLLKKGDIVY----------GRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRA 127 (189)
T ss_pred CCCCCCCEEE----------EEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEE
Confidence 4677888875 78999988865444210 0011 112223333 4678999999976
No 285
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=23.02 E-value=1.3e+02 Score=31.12 Aligned_cols=49 Identities=27% Similarity=0.303 Sum_probs=37.8
Q ss_pred CCCCEEEEe----cccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceee
Q 001506 426 MKGDAVIVI----KGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 476 (1065)
Q Consensus 426 ~~GD~V~V~----~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~ 476 (1065)
..|-.|+|. -+..+..+|.+.+++++.|+|....+. +.++++.++++|.
T Consensus 96 ~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~--~~~~i~~~~I~~a 148 (154)
T PRK00092 96 FIGREVKVKLYEPIDGRKKFQGILLAVDGETVTLEVEGKE--KEVEIPLDNIAKA 148 (154)
T ss_pred hCCCeEEEEEEcccCCceEEEEEEEEeeCCEEEEEECCCe--EEEEEEHHHcceE
Confidence 579999997 245577899999999999998865321 3688888888774
No 286
>COG5129 MAK16 Nuclear protein with HMG-like acidic region [General function prediction only]
Probab=22.99 E-value=34 Score=37.44 Aligned_cols=13 Identities=15% Similarity=0.120 Sum_probs=6.1
Q ss_pred CCCCCCCCCcccc
Q 001506 71 GGGGGAARKPKAK 83 (1065)
Q Consensus 71 ~~~~~~~~~~krk 83 (1065)
+...-+++.||||
T Consensus 260 ~dednk~~~rkrk 272 (303)
T COG5129 260 EDEDNKGKIRKRK 272 (303)
T ss_pred cccccccchhhcc
Confidence 3344555555543
No 287
>PF08553 VID27: VID27 cytoplasmic protein; InterPro: IPR013863 This entry represents fungal and plant proteins and contains many hypothetical proteins. Vid27p is a cytoplasmic protein of unknown function, possibly regulates import of fructose-1,6-bisphosphatase into Vacuolar Import and Degradation (Vid) vesicles and is not essential for proteasome-dependent degradation of fructose-1,6-bisphosphatase (FBPase) [, ].
Probab=22.90 E-value=41 Score=43.55 Aligned_cols=15 Identities=20% Similarity=0.370 Sum_probs=8.6
Q ss_pred eccccCCceeEEEEE
Q 001506 486 VSGTQAGATGMVLKV 500 (1065)
Q Consensus 486 i~G~~~getGlVVkV 500 (1065)
..|+++|.+|..-+.
T Consensus 649 ~~g~~~g~~GF~~~~ 663 (794)
T PF08553_consen 649 KDGKNSGKLGFEKSF 663 (794)
T ss_pred ecCCccCcccccccc
Confidence 346666666665444
No 288
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=22.65 E-value=1.2e+02 Score=25.37 Aligned_cols=39 Identities=15% Similarity=0.145 Sum_probs=31.4
Q ss_pred ccEEEEEEeCCCCeEEEEeccCCCCceEEecCCCeeecCCC
Q 001506 974 SVVGVIREVLPDGSCRVVLGSSGNGDTITALPNEIEIVPPR 1014 (1065)
Q Consensus 974 ~~~GvI~~V~~~g~~~V~l~~~~~g~~v~v~~~~LE~V~P~ 1014 (1065)
=..|.|.++.+++.|.|.+.|. |....|..++|-+..+.
T Consensus 18 wyra~I~~~~~~~~~~V~f~D~--G~~~~v~~~~l~~l~~~ 56 (57)
T smart00333 18 WYRARIIKVDGEQLYEVFFIDY--GNEEVVPPSDLRPLPEE 56 (57)
T ss_pred EEEEEEEEECCCCEEEEEEECC--CccEEEeHHHeecCCCC
Confidence 3488999998778899999987 57888888888776653
No 289
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=22.57 E-value=5.1e+02 Score=30.21 Aligned_cols=12 Identities=33% Similarity=0.653 Sum_probs=5.2
Q ss_pred eEEEEECCEEEE
Q 001506 620 PVEHIYRGILFI 631 (1065)
Q Consensus 620 ~V~HI~r~~lFl 631 (1065)
+|..|-++.||+
T Consensus 135 rIeq~~~g~iFm 146 (389)
T KOG2932|consen 135 RIEQIMMGGIFM 146 (389)
T ss_pred HHHHhcccceEE
Confidence 344444444444
No 290
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=22.47 E-value=2.9e+02 Score=28.17 Aligned_cols=48 Identities=21% Similarity=0.399 Sum_probs=30.9
Q ss_pred cceeeccc-cceeeccCCCcEEEeccc----------cCCceeEEEEEeCcEEEEEeCCC
Q 001506 464 KTLAVNSK-ELCKYFEPGNHVKVVSGT----------QAGATGMVLKVEQHVLIILSDTT 512 (1065)
Q Consensus 464 ~~l~v~~~-~LrK~F~~GDhVkVi~G~----------~~getGlVVkVe~~~v~vlSD~t 512 (1065)
..|.+..+ +..+.|++||-||...|- |.|..|.+-|| ++...+|+-.-
T Consensus 48 gsI~isvW~e~~~~~~PGDIirLt~Gy~Si~qg~LtL~~GK~Ge~~Ki-Gef~~vf~etp 106 (134)
T KOG3416|consen 48 GSINISVWDEEGCLIQPGDIIRLTGGYASIFQGCLTLYVGKGGEVQKI-GEFCMVFSETP 106 (134)
T ss_pred ceEEEEEecCcCcccCCccEEEecccchhhhcCceEEEecCCceEeEe-eeeEEeeecCC
Confidence 34555433 467889999999998772 33566666665 34666666543
No 291
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=22.28 E-value=1.4e+02 Score=29.12 Aligned_cols=53 Identities=23% Similarity=0.256 Sum_probs=36.1
Q ss_pred cCcCCCCEEEEe-ccc---------ccCceeEEEEEcCCeEEEeecCCCCCcceeecccccee
Q 001506 423 GHFMKGDAVIVI-KGD---------LKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK 475 (1065)
Q Consensus 423 ~~F~~GD~V~V~-~Ge---------l~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK 475 (1065)
..|++||.|-|. .|- +-|-+|+|.++.+.-+.|.....+..+.|-|.+..|++
T Consensus 33 ~~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v~vg~k~Kri~vr~eHlk~ 95 (98)
T PRK04306 33 QEFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEVKDGGKEKTLIVRPEHLRP 95 (98)
T ss_pred HhccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEEEECCceeEEEcCHHHcCc
Confidence 468899998774 222 35679999999999655444444445667777776665
No 292
>PF12059 DUF3540: Protein of unknown function (DUF3540); InterPro: IPR021927 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 212 to 238 amino acids in length. This protein has a conserved SCL sequence motif.
Probab=21.96 E-value=3.2e+02 Score=29.83 Aligned_cols=67 Identities=19% Similarity=0.164 Sum_probs=39.4
Q ss_pred EEEEEEeCCCCeEEEEeccCCCCceEEecCCCeeecCCCCCCcEEEEcCCCCC---ceEEEEEEeCCCcEEEecC
Q 001506 976 VGVIREVLPDGSCRVVLGSSGNGDTITALPNEIEIVPPRKTDKIKIMGGPHRG---ATGKLIGVDGTDGIVKVDV 1047 (1065)
Q Consensus 976 ~GvI~~V~~~g~~~V~l~~~~~g~~v~v~~~~LE~V~P~kgd~VkVi~G~~rG---~tG~LisiD~~dgiVk~d~ 1047 (1065)
.|.|....+++.+ |... . |. +.+-..-==++.|+.||+|.|....+-+ ..+.|.--++....+.+++
T Consensus 3 ~g~V~~~~~~~~~-v~~~-~--G~-~~arrAaSCLl~P~~GD~VLv~~~~d~~~~yILAVL~r~~~~~a~L~~~G 72 (202)
T PF12059_consen 3 SGTVVGREGDGLV-VVDD-D--GE-WRARRAASCLLEPAVGDTVLVSGVADEERVYILAVLERADPGPATLSVPG 72 (202)
T ss_pred eEEEEEEeCCeEE-EEcC-C--CE-EEEEeccccccCCCCCCEEEEeecCCCCcEEEEEEEecCCCCcceEecCC
Confidence 5778888775443 3322 2 54 5555555456789999999997733322 3455555555555444443
No 293
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=21.93 E-value=3.8e+02 Score=33.03 Aligned_cols=58 Identities=22% Similarity=0.312 Sum_probs=37.6
Q ss_pred CcCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeecccccee-----eccCCCcEEEeccccCCceeEEE
Q 001506 424 HFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK-----YFEPGNHVKVVSGTQAGATGMVL 498 (1065)
Q Consensus 424 ~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK-----~F~~GDhVkVi~G~~~getGlVV 498 (1065)
.|++|+.|+ |+|++|+.+.|.|... .+.+=.+|.+++.. .+++||.|.+ +|+
T Consensus 31 ~~~~G~~v~----------G~V~~v~~~~v~Vdig---~k~eg~ip~~e~~~~~~~~~~~~G~~i~~----------~Vi 87 (491)
T PRK13806 31 ELRVGDKIT----------GTVIAITEDSVFVDTG---SKVDGVVDRAELLDADGELTVAVGDEVEL----------YVV 87 (491)
T ss_pred cCCCCCEEE----------EEEEEEECCEEEEEEC---CCcEEEEEHHHhcCccccccccCCCEEEE----------EEE
Confidence 488888774 7899999998777653 12233456665532 3788888754 456
Q ss_pred EEeCcE
Q 001506 499 KVEQHV 504 (1065)
Q Consensus 499 kVe~~~ 504 (1065)
++++..
T Consensus 88 ~~~~~~ 93 (491)
T PRK13806 88 SVNGQE 93 (491)
T ss_pred EEcCCE
Confidence 665543
No 294
>PF01157 Ribosomal_L21e: Ribosomal protein L21e; InterPro: IPR001147 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 [, ]. L21E family contains proteins from a number of eukaryotic and archaebacterial organisms which include; mammalian L2, Entamoeba histolytica L21, Caenorhabditis elegans L21 (C14B9.7), Saccharomyces cerevisiae (Baker's yeast) L21E (URP1) and Haloarcula marismortui HL31.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_U 1S1I_Q 3O58_T 3IZS_U 3O5H_T 1Q82_R 1KQS_P 3CCJ_Q 3CCQ_Q 1VQ5_Q ....
Probab=21.79 E-value=1.9e+02 Score=28.19 Aligned_cols=53 Identities=17% Similarity=0.125 Sum_probs=30.4
Q ss_pred cCcCCCCEEEEec-c---------cccCceeEEEEEcCCe----EEEeecCCCCCcceeecccccee
Q 001506 423 GHFMKGDAVIVIK-G---------DLKNLKGWVEKVDEEN----VHIRPEMKGLPKTLAVNSKELCK 475 (1065)
Q Consensus 423 ~~F~~GD~V~V~~-G---------el~gl~G~V~~V~~d~----V~i~~~~~~l~~~l~v~~~~LrK 475 (1065)
..|++||.|-|.- | -+-|-+|.|.+|.... +.+......+.+.|-+.+..|++
T Consensus 31 ~~yk~GD~V~I~id~sv~kGmPh~~yHGkTG~V~~v~~~~~G~~~~~~v~~~~~~K~i~vr~eHlk~ 97 (99)
T PF01157_consen 31 QEYKVGDKVDIKIDPSVHKGMPHKRYHGKTGRVFNVTKGARGVAYNKQVKDRIKEKRIIVRPEHLKP 97 (99)
T ss_dssp ----TT-EEEE---TTSSSSS--GGGTTEEEEEEEE-SSCEEEEEEEECSSSCEEEEEEEEGGGEEE
T ss_pred HHccCCCEEEEEecCccccCCCcceECCCceeEEEeCCCceEEEEEEEecCCcccEEEEECHHHccc
Confidence 5799999998842 2 2456799999998763 34444455555667777776664
No 295
>PF04006 Mpp10: Mpp10 protein; InterPro: IPR007151 This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites [].
Probab=21.68 E-value=49 Score=41.63 Aligned_cols=8 Identities=25% Similarity=0.285 Sum_probs=3.6
Q ss_pred HHHHHHHh
Q 001506 200 CLMQKCID 207 (1065)
Q Consensus 200 ~Lm~K~~~ 207 (1065)
.|.+||+.
T Consensus 397 ~Ik~RI~~ 404 (600)
T PF04006_consen 397 LIKQRIKD 404 (600)
T ss_pred HHHHHHHh
Confidence 34445444
No 296
>KOG2418 consensus Microtubule-associated protein TAU [Cytoskeleton]
Probab=21.58 E-value=2.4e+02 Score=33.32 Aligned_cols=9 Identities=22% Similarity=0.578 Sum_probs=4.2
Q ss_pred ccEEEEEEe
Q 001506 974 SVVGVIREV 982 (1065)
Q Consensus 974 ~~~GvI~~V 982 (1065)
.+.|-.+.+
T Consensus 327 SKcGSLkNi 335 (448)
T KOG2418|consen 327 SKCGSLKNI 335 (448)
T ss_pred hhhcccccc
Confidence 334555544
No 297
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=21.23 E-value=2.9e+02 Score=22.95 Aligned_cols=56 Identities=18% Similarity=0.173 Sum_probs=32.4
Q ss_pred eEEEEEcCCeEEEeecCCCCCcceeeccccc---eeeccCCCcEEEecc---ccCCceeEEEEE
Q 001506 443 GWVEKVDEENVHIRPEMKGLPKTLAVNSKEL---CKYFEPGNHVKVVSG---TQAGATGMVLKV 500 (1065)
Q Consensus 443 G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~L---rK~F~~GDhVkVi~G---~~~getGlVVkV 500 (1065)
|.|...+...--|.++.. ...+-|+.+.+ ...+..||.|.+--- ...+..+.|++|
T Consensus 2 G~i~~~~~g~gfv~~~~~--~~~i~v~~~~~~~~~~~~~~Gd~V~~~i~~~~~~~~~~a~~v~~ 63 (64)
T smart00357 2 GVVKWFNKGFGFIRPDDG--GKDVFVHPSQIQGGLKSLREGDEVEFKVVSPRGGGKPEAENVVK 63 (64)
T ss_pred eEEEEEcCCeeEEecCCC--CccEEEEhHHhhcCCCcCCCCCEEEEEEEEccCCCCcEEEEEEe
Confidence 555555544444455432 24688888875 455777999977422 123445666654
No 298
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=21.18 E-value=65 Score=31.75 Aligned_cols=21 Identities=33% Similarity=0.325 Sum_probs=18.5
Q ss_pred cccccCCCCeecCCCEEEEEc
Q 001506 591 SNVQDRNKNTVAVKDVVRIVE 611 (1065)
Q Consensus 591 ~~a~D~~gn~I~~~D~Vkvv~ 611 (1065)
.+..|+|||.+.-||.|.++.
T Consensus 41 ~~~kDsnG~~L~dGDsV~liK 61 (109)
T TIGR00686 41 LIVKDCNGNLLANGDSVILIK 61 (109)
T ss_pred ceEEcCCCCCccCCCEEEEEe
Confidence 357899999999999999974
No 299
>KOG3540 consensus Beta amyloid precursor protein [General function prediction only]
Probab=20.97 E-value=53 Score=39.70 Aligned_cols=39 Identities=38% Similarity=0.598 Sum_probs=0.0
Q ss_pred cchhhcccCCCccccCCCCCCCCCcccccCCCCCCcccccccCCchhhhcccccc
Q 001506 56 DDEEEEEDYDDDEDYGGGGGAARKPKAKRRSGSEFFDLEAQVDSDEEEDEEEGED 110 (1065)
Q Consensus 56 ~~~~~~~~~~~~~~~~~~~~~~~~~krk~~~~~~FlD~EAeVdddeEeeeee~~~ 110 (1065)
+-.+.++|++||+||+++-. |.+.|+.||+++||-+.++
T Consensus 198 ~~~~~eede~dd~d~~d~~e----------------de~~eesDd~deEep~sqe 236 (615)
T KOG3540|consen 198 DVAKTEEDEDDDDDYDDGYE----------------DEYSEESDDEDEEEPSSQE 236 (615)
T ss_pred cccccCcccCCccccccccc----------------cccccccccccccCCcccC
No 300
>PRK07218 replication factor A; Provisional
Probab=20.87 E-value=9.8e+02 Score=29.14 Aligned_cols=48 Identities=19% Similarity=0.234 Sum_probs=29.4
Q ss_pred ccCceeEEEEEcCCeEEEeec----------CCCCCcceeeccccceeeccCCCcEEEecc
Q 001506 438 LKNLKGWVEKVDEENVHIRPE----------MKGLPKTLAVNSKELCKYFEPGNHVKVVSG 488 (1065)
Q Consensus 438 l~gl~G~V~~V~~d~V~i~~~----------~~~l~~~l~v~~~~LrK~F~~GDhVkVi~G 488 (1065)
..+++|+|+++.. . ++..+ ..|=...+.|-.++ -+.+++||-|++..+
T Consensus 70 ~V~v~~kVl~i~~-r-t~r~dg~~g~v~~~~igDeTG~Ir~tlW~-~~~l~~Gdvv~I~na 127 (423)
T PRK07218 70 NVTVTGRVLTIGE-R-SIRYQGDDHVIYEGILADETGTISYTAWK-DFGLSPGDTVTIGNA 127 (423)
T ss_pred eeEEEEEEEEecc-e-eEecCCCceEEEEEEEECCCCeEEEEEEC-CCCCCCCCEEEEecc
Confidence 3456688888852 1 11111 11224458888887 445999999999865
No 301
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=20.80 E-value=5.1e+02 Score=23.68 Aligned_cols=59 Identities=17% Similarity=0.169 Sum_probs=39.5
Q ss_pred eEEEEEEccc-eEEEeccCCCCCcEEEEecchhhhcccCCcccccCCCCeecCCCEEEEEcCCCCCceeeEEE
Q 001506 552 FGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEH 623 (1065)
Q Consensus 552 VGvIv~verd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~r~~a~D~~gn~I~~~D~Vkvv~Gp~~gr~G~V~H 623 (1065)
.|+|+++-.+ .|+|... +|..+.. -|..|+.++ .=-|..||.|+|---||.--.|.|.|
T Consensus 8 ~G~V~e~L~~~~f~V~l~---ng~~vla---~i~GKmr~~-------rI~I~~GD~V~Ve~spyd~tkgrIi~ 67 (68)
T TIGR00008 8 EGKVTESLPNAMFRVELE---NGHEVLA---HISGKIRMH-------YIRILPGDKVKVELSPYDLTRGRITY 67 (68)
T ss_pred EEEEEEECCCCEEEEEEC---CCCEEEE---EecCcchhc-------cEEECCCCEEEEEECcccCCcEeEEe
Confidence 3899998876 5787764 3554433 344454321 12489999999988888766788764
No 302
>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=20.74 E-value=1.4e+02 Score=34.98 Aligned_cols=102 Identities=20% Similarity=0.249 Sum_probs=66.2
Q ss_pred cchhhHHHHHHHHHHHhcCCCCCCcccchhhhhhhhcCCCCCCCcEEEEEccCchHHHHHHHHHHHHHhhCCCcceEEE-
Q 001506 139 DEQEDVEALERRIQARYARSSHTEYDEETTDVEQQALLPSVRDPKLWMVKCAIGREREAAVCLMQKCIDKGSELQIRSV- 217 (1065)
Q Consensus 139 ~~~~d~ee~~~~l~eRY~~~~~~~~~~~~~~v~q~~LlPsv~DP~lw~Vkck~G~Er~vv~~Lm~K~~~~~~~l~I~Sv- 217 (1065)
++.+.||||++.|+||-+..++. .-+...++|..-..|- +--||..|..+=-+.+=+..|..+|= .|.|+
T Consensus 200 ~~g~saeel~e~~~e~ea~~~A~-iLEmvGDlpdAd~~PP--eNVLFVCKLNPVTtDeDLeiIFSrFG------~i~sce 270 (479)
T KOG0415|consen 200 DEGLSAEELEEVLAEKEAKAQAV-ILEMVGDLPDADVKPP--ENVLFVCKLNPVTTDEDLEIIFSRFG------KIVSCE 270 (479)
T ss_pred ccccCHHHHHHHHHHHHHHhhHh-HHHHhcCCcccccCCC--cceEEEEecCCcccccchhhHHhhcc------cceeee
Confidence 34678999999999998864321 1122333333333332 34577777777655555556666652 25565
Q ss_pred EeeCC----CccEEEEEecchHHHHHHHhcCcccce
Q 001506 218 IALDH----LKNYIYIEADKEAHVKEACKGLRNIYS 249 (1065)
Q Consensus 218 f~~~~----lkGYIYIEA~~~~~V~~ai~Gl~~v~~ 249 (1065)
+.++- .=-|-|||-.++..+.+|.=.|-||.-
T Consensus 271 VIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLI 306 (479)
T KOG0415|consen 271 VIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLI 306 (479)
T ss_pred EEecccccchhheeeeeecchhhHHHHHhhhcceee
Confidence 44432 234999999999999999999998873
No 303
>PRK14640 hypothetical protein; Provisional
Probab=20.66 E-value=1.6e+02 Score=30.52 Aligned_cols=47 Identities=15% Similarity=0.235 Sum_probs=37.2
Q ss_pred CCCCEEEEec----ccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceee
Q 001506 426 MKGDAVIVIK----GDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 476 (1065)
Q Consensus 426 ~~GD~V~V~~----Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~ 476 (1065)
..|-.|+|.- +..+..+|++.+++++.|++..+ .++++++-.++.|.
T Consensus 95 ~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~v~l~~~----~~~~~i~~~~I~ka 145 (152)
T PRK14640 95 YVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVD----GKDEVLAFTNIQKA 145 (152)
T ss_pred hCCCeEEEEEecccCCceEEEEEEEEEeCCEEEEEEC----CeEEEEEhHHeeeE
Confidence 5799999964 44588999999999999998764 34677887787774
No 304
>PF09122 DUF1930: Domain of unknown function (DUF1930); InterPro: IPR015206 This entry represents a domain found in 3-mercaptopyruvate sulphurtransferase which has no known function. This domain adopts a structure consisting of a four-stranded antiparallel beta-sheet and an alpha-helix, arranged in a beta(2)-alpha-beta(2) fashion, and bearing a remarkable structural similarity to the FK506-binding protein class of peptidylprolyl cis/trans-isomerase []. ; PDB: 1OKG_A.
Probab=20.58 E-value=1.1e+02 Score=27.50 Aligned_cols=25 Identities=28% Similarity=0.412 Sum_probs=15.8
Q ss_pred CCCCCeeEEEEeeCCCCEEEEEEeeccc
Q 001506 285 NYKGDLAKVVDVDNVRQRVTVKLIPRID 312 (1065)
Q Consensus 285 ~YkGDlAqV~~Vd~~~~~V~VkLvPRiD 312 (1065)
...|+.|||. -.++..|++++ ||||
T Consensus 44 lH~GEkA~V~--FkS~Rv~~iEv-P~i~ 68 (68)
T PF09122_consen 44 LHIGEKAQVF--FKSQRVAVIEV-PRID 68 (68)
T ss_dssp -BTT-EEEEE--ETTS-EEEEE---SS-
T ss_pred hhcCceeEEE--EecCcEEEEEc-cCCC
Confidence 5678899996 47788889998 9997
No 305
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=20.46 E-value=4.7e+02 Score=33.47 Aligned_cols=75 Identities=11% Similarity=0.102 Sum_probs=46.9
Q ss_pred CCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCcEEEecccc----CCceeEEEEEeC
Q 001506 427 KGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVVSGTQ----AGATGMVLKVEQ 502 (1065)
Q Consensus 427 ~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~l~v~~~~LrK~F~~GDhVkVi~G~~----~getGlVVkVe~ 502 (1065)
.|-.|+|++=..+.+.|++.. .++...+.|+...+...|.++.+...+.++.||.|.|-==+| ..-.|-|+++=+
T Consensus 71 ~g~v~~il~r~~~~~vG~~~~-~~~~~~v~p~~~~~~~~i~i~~~~~~~~~~~g~~V~v~i~~~p~~~~~~~g~i~~~lG 149 (654)
T TIGR00358 71 EAEVERILEPALTRFVGKFLG-ENDFGFVVPDDPRIYLDIIVPKASVKNELAEGDKVVVELTEYPLRRNLFYGEITQILG 149 (654)
T ss_pred eEEEEEEeccCCCEEEEEEEE-eCCeEEEEECCCCCCCcEEEcCCccccCCCCCCEEEEEEccCCCCCCCceEEEEEEEc
Confidence 455555555555555665443 334556777776677778888776656788999997742222 123678887743
No 306
>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=20.25 E-value=1.7e+03 Score=29.77 Aligned_cols=33 Identities=36% Similarity=0.472 Sum_probs=18.9
Q ss_pred cCcEEEEeeCCCCC---ceeEEEeecCCeEEEEecC
Q 001506 708 VGTTVKVRLGPYKG---YRGRVVDVKGQSVRVELES 740 (1065)
Q Consensus 708 iGktV~I~~GpyKG---~~G~Vkd~t~~~~rVELhs 740 (1065)
||+.|.++.+.+.| |.|.---|++.-+=|-|+.
T Consensus 8 vG~RVevtgknl~G~VayvG~T~FA~G~WvGVvLDe 43 (1243)
T KOG0971|consen 8 VGTRVEVTGKNLQGTVAYVGQTQFAEGKWVGVVLDE 43 (1243)
T ss_pred ccceEEeccCCccceEEEecccccccCceEEEEecc
Confidence 77888888764333 3333344555556666653
No 307
>PHA03169 hypothetical protein; Provisional
Probab=20.13 E-value=1.2e+02 Score=35.77 Aligned_cols=91 Identities=10% Similarity=0.098 Sum_probs=0.0
Q ss_pred CCCCCcccccccchhhhhccCccchhhhhhhhhhccccccccccccccccccchhhcccCCCccccCCCCCCCCCccccc
Q 001506 5 RDDDDDEMDAEEDEYDEQVMDDEIDEEEEEEDDRSSRKRRRSQFIDDVAEEDDEEEEEDYDDDEDYGGGGGAARKPKAKR 84 (1065)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~e~~~~d~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~krk~ 84 (1065)
...+.++..++..+++.++.+||-++.+++.++++..--.-..-.+.....+..+++.++-.+.=+.+...
T Consensus 155 ~~~s~~~~~~~~~~~~~ed~~ee~e~~~~e~e~d~~~~~~~e~~~~~~~~~~~~d~~ge~~~~~~~~~~~~--------- 225 (413)
T PHA03169 155 HNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPPQSPPDEPGEPQSPTPQQAPSP--------- 225 (413)
T ss_pred cCCCcccCccccccccccccccCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCc---------
Q ss_pred CCCCCCcccccccCCchhhhccccccc
Q 001506 85 RSGSEFFDLEAQVDSDEEEDEEEGEDD 111 (1065)
Q Consensus 85 ~~~~~FlD~EAeVdddeEeeeee~~~~ 111 (1065)
+..++|..++|.++++.+..
T Consensus 226 -------~~~~~~e~e~e~~e~e~e~~ 245 (413)
T PHA03169 226 -------NTQQAVEHEDEPTEPEREGP 245 (413)
T ss_pred -------cccccccccccccccccCCC
Done!