Query 001639
Match_columns 1039
No_of_seqs 404 out of 576
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 05:46:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001639.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001639hhsearch_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 2E-216 5E-221 1883.6 75.1 929 78-1039 55-1024(1024)
2 COG5164 SPT5 Transcription elo 100.0 3.4E-79 7.4E-84 672.8 34.2 403 331-763 4-411 (607)
3 KOG1999 RNA polymerase II tran 100.0 1.2E-36 2.6E-41 361.5 41.7 414 326-835 315-848 (1024)
4 PRK08559 nusG transcription an 99.9 6.1E-22 1.3E-26 200.7 15.2 130 180-311 4-133 (153)
5 PF03439 Spt5-NGN: Early trans 99.9 2.3E-22 4.9E-27 184.2 9.0 82 183-264 1-84 (84)
6 TIGR00405 L26e_arch ribosomal 99.7 1.4E-17 3E-22 167.3 14.1 125 185-311 1-125 (145)
7 COG5164 SPT5 Transcription elo 99.7 1.9E-17 4E-22 185.1 15.9 352 170-636 28-389 (607)
8 COG0250 NusG Transcription ant 99.6 2.8E-15 6E-20 155.4 10.8 127 181-307 2-158 (178)
9 PF11942 Spt5_N: Spt5 transcri 99.3 3.7E-13 8.1E-18 126.7 3.0 88 90-177 1-97 (97)
10 PRK05609 nusG transcription an 99.3 2.4E-11 5.1E-16 126.3 13.6 125 181-307 5-161 (181)
11 TIGR00922 nusG transcription t 99.2 9.4E-11 2E-15 121.0 13.3 124 184-307 1-154 (172)
12 TIGR01956 NusG_myco NusG famil 99.2 8.8E-11 1.9E-15 126.9 12.5 125 183-307 1-240 (258)
13 PF12815 CTD: Spt5 C-terminal 99.0 4.9E-11 1.1E-15 116.6 0.0 56 764-821 3-68 (123)
14 PRK09014 rfaH transcriptional 98.9 4.9E-09 1.1E-13 107.4 7.9 123 183-306 3-142 (162)
15 smart00738 NGN In Spt5p, this 98.9 5E-09 1.1E-13 99.3 7.1 83 183-265 1-105 (106)
16 TIGR01955 RfaH transcriptional 98.8 1.2E-08 2.6E-13 104.0 7.8 122 184-306 1-141 (159)
17 KOG0260 RNA polymerase II, lar 98.5 3.6E-06 7.7E-11 104.2 18.6 12 705-716 1400-1411(1605)
18 KOG0260 RNA polymerase II, lar 98.4 1.2E-05 2.5E-10 99.8 19.0 16 738-753 1409-1424(1605)
19 PF12815 CTD: Spt5 C-terminal 98.2 2.4E-07 5.3E-12 90.9 0.0 44 764-807 14-68 (123)
20 KOG1832 HIV-1 Vpr-binding prot 98.0 3.2E-06 6.8E-11 102.1 2.5 21 2-22 1398-1418(1516)
21 KOG2837 Protein containing a U 97.9 4.6E-07 9.9E-12 97.5 -6.3 55 943-1005 254-309 (309)
22 PF00467 KOW: KOW motif; Inte 97.4 0.00021 4.6E-09 54.2 4.2 32 275-306 1-32 (32)
23 PF04931 DNA_pol_phi: DNA poly 97.2 0.00017 3.6E-09 91.3 2.7 12 145-156 739-750 (784)
24 PF02357 NusG: Transcription t 96.8 0.0041 9E-08 57.7 7.4 65 183-249 2-78 (92)
25 PF10446 DUF2457: Protein of u 96.7 0.00081 1.8E-08 77.7 2.7 11 194-204 207-217 (458)
26 PF00467 KOW: KOW motif; Inte 96.7 0.0014 3E-08 49.7 3.0 31 708-738 1-31 (32)
27 KOG4315 G-patch nucleic acid b 96.7 0.00056 1.2E-08 78.2 0.9 103 933-1036 332-445 (455)
28 PF04931 DNA_pol_phi: DNA poly 96.5 0.00061 1.3E-08 86.3 -0.3 9 147-155 737-745 (784)
29 PRK12281 rplX 50S ribosomal pr 95.9 0.0092 2E-07 54.3 4.2 33 600-632 6-40 (76)
30 smart00739 KOW KOW (Kyprides, 95.7 0.016 3.4E-07 42.0 3.9 28 424-451 1-28 (28)
31 smart00739 KOW KOW (Kyprides, 95.6 0.013 2.9E-07 42.3 3.3 27 476-502 1-27 (28)
32 TIGR00405 L26e_arch ribosomal 95.0 0.038 8.3E-07 55.9 5.4 58 424-481 86-145 (145)
33 CHL00141 rpl24 ribosomal prote 94.3 0.051 1.1E-06 50.3 4.2 28 600-627 8-35 (83)
34 PRK00004 rplX 50S ribosomal pr 94.2 0.062 1.3E-06 51.9 4.7 32 600-631 4-37 (105)
35 PF04147 Nop14: Nop14-like fam 93.9 0.041 8.9E-07 70.5 3.5 9 144-152 428-436 (840)
36 KOG0262 RNA polymerase I, larg 93.5 0.14 3.1E-06 65.5 7.2 84 183-266 1441-1548(1640)
37 CHL00141 rpl24 ribosomal prote 93.3 0.15 3.1E-06 47.4 5.2 39 270-308 6-44 (83)
38 KOG1708 Mitochondrial/chloropl 93.1 0.16 3.5E-06 53.6 5.7 62 422-502 70-131 (236)
39 PF04147 Nop14: Nop14-like fam 93.0 0.09 2E-06 67.4 4.6 10 147-156 446-455 (840)
40 PRK01191 rpl24p 50S ribosomal 92.9 0.2 4.3E-06 49.5 5.7 40 270-309 43-82 (120)
41 TIGR00922 nusG transcription t 92.8 0.17 3.6E-06 52.6 5.5 53 423-475 118-172 (172)
42 COG0250 NusG Transcription ant 92.8 0.2 4.3E-06 52.9 6.0 56 421-476 120-177 (178)
43 TIGR01079 rplX_bact ribosomal 92.7 0.15 3.3E-06 49.2 4.6 32 600-631 3-36 (104)
44 PRK09014 rfaH transcriptional 92.7 0.16 3.6E-06 52.2 5.2 52 424-475 109-161 (162)
45 PRK01191 rpl24p 50S ribosomal 92.5 0.18 4E-06 49.7 4.8 33 600-632 45-79 (120)
46 PRK12281 rplX 50S ribosomal pr 92.1 0.25 5.3E-06 45.2 4.9 38 271-308 5-42 (76)
47 PF02724 CDC45: CDC45-like pro 92.1 0.061 1.3E-06 66.8 1.3 18 225-242 356-373 (622)
48 PF02724 CDC45: CDC45-like pro 91.8 0.15 3.2E-06 63.4 4.2 31 234-264 235-266 (622)
49 PRK05609 nusG transcription an 91.8 0.28 6.1E-06 51.2 5.7 53 423-475 125-179 (181)
50 KOG2038 CAATT-binding transcri 91.4 0.14 3E-06 63.1 3.1 12 143-154 968-979 (988)
51 TIGR01080 rplX_A_E ribosomal p 91.0 0.34 7.3E-06 47.6 4.9 34 988-1021 43-76 (114)
52 PRK08559 nusG transcription an 90.6 0.48 1E-05 48.7 5.8 52 423-474 93-146 (153)
53 TIGR01955 RfaH transcriptional 90.4 0.41 9E-06 48.9 5.2 51 423-473 107-158 (159)
54 PTZ00194 60S ribosomal protein 90.0 0.36 7.7E-06 49.0 4.2 33 600-632 46-80 (143)
55 PRK00004 rplX 50S ribosomal pr 90.0 0.49 1.1E-05 45.8 5.0 37 272-308 4-40 (105)
56 PTZ00415 transmission-blocking 89.9 0.18 4E-06 66.1 2.5 19 175-193 366-384 (2849)
57 TIGR01956 NusG_myco NusG famil 89.6 0.54 1.2E-05 52.1 5.5 52 423-474 204-257 (258)
58 COG0198 RplX Ribosomal protein 89.5 0.47 1E-05 45.8 4.4 33 599-631 3-35 (104)
59 TIGR01080 rplX_A_E ribosomal p 89.4 0.7 1.5E-05 45.4 5.6 48 259-308 30-77 (114)
60 PTZ00194 60S ribosomal protein 89.2 0.71 1.5E-05 46.9 5.6 51 259-311 35-85 (143)
61 KOG0943 Predicted ubiquitin-pr 88.9 0.26 5.6E-06 62.6 2.7 14 182-195 1880-1893(3015)
62 PRK06763 F0F1 ATP synthase sub 87.4 4 8.6E-05 43.6 9.9 45 439-486 40-84 (213)
63 COG0198 RplX Ribosomal protein 87.3 0.8 1.7E-05 44.2 4.4 33 423-455 3-35 (104)
64 KOG0943 Predicted ubiquitin-pr 87.1 0.28 6E-06 62.4 1.4 11 496-506 2286-2296(3015)
65 TIGR01079 rplX_bact ribosomal 86.7 1 2.2E-05 43.6 4.8 36 272-307 3-38 (104)
66 PHA03378 EBNA-3B; Provisional 86.3 14 0.0003 45.7 14.7 10 981-990 915-924 (991)
67 KOG1991 Nuclear transport rece 85.7 0.41 8.8E-06 60.7 1.9 17 16-32 897-913 (1010)
68 PTZ00415 transmission-blocking 85.2 0.46 1E-05 62.7 2.1 17 180-196 312-328 (2849)
69 KOG0307 Vesicle coat complex C 84.1 24 0.00053 46.0 16.2 20 636-655 596-615 (1049)
70 KOG4156 Claspin, protein media 83.9 0.1 2.3E-06 62.4 -4.0 13 89-101 1052-1064(1329)
71 PF04006 Mpp10: Mpp10 protein; 83.2 0.98 2.1E-05 56.1 3.7 17 78-94 175-192 (600)
72 PF14632 SPT6_acidic: Acidic N 82.0 0.44 9.5E-06 45.1 0.0 8 45-52 20-27 (92)
73 KOG2141 Protein involved in hi 81.0 0.64 1.4E-05 57.3 1.0 16 142-157 333-348 (822)
74 KOG2773 Apoptosis antagonizing 80.5 0.78 1.7E-05 54.0 1.4 12 88-99 126-137 (483)
75 PF00524 PPV_E1_N: E1 Protein, 79.5 0.8 1.7E-05 46.0 1.0 65 87-159 14-86 (130)
76 cd04467 S1_aIF5A S1_aIF5A: Arc 79.3 3.9 8.5E-05 35.5 4.9 45 441-487 4-49 (57)
77 KOG1856 Transcription elongati 79.0 1.2 2.6E-05 57.4 2.4 34 422-455 586-632 (1299)
78 KOG2773 Apoptosis antagonizing 77.2 1.3 2.8E-05 52.2 1.8 15 176-193 214-228 (483)
79 PTZ00223 40S ribosomal protein 75.5 6.3 0.00014 44.3 6.5 26 477-502 172-197 (273)
80 PRK04313 30S ribosomal protein 73.2 8.1 0.00017 42.7 6.5 41 477-517 172-217 (237)
81 PRK12269 bifunctional cytidyla 73.2 92 0.002 40.8 16.9 56 423-504 709-767 (863)
82 KOG2051 Nonsense-mediated mRNA 73.0 1 2.2E-05 57.6 -0.3 6 94-99 965-970 (1128)
83 KOG2418 Microtubule-associated 72.6 13 0.00029 42.9 8.2 12 1025-1036 424-435 (448)
84 KOG1708 Mitochondrial/chloropl 71.9 3.9 8.4E-05 43.7 3.6 29 475-503 71-99 (236)
85 PF11623 DUF3252: Protein of u 71.6 13 0.00029 31.5 5.9 44 709-752 5-52 (53)
86 COG1471 RPS4A Ribosomal protei 70.9 8.8 0.00019 42.1 6.0 34 468-501 163-198 (241)
87 KOG2076 RNA polymerase III tra 70.3 2.5 5.4E-05 53.6 2.0 10 174-185 201-210 (895)
88 COG2933 Predicted SAM-dependen 70.1 5.6 0.00012 44.4 4.5 58 186-247 5-62 (358)
89 PTZ00118 40S ribosomal protein 70.0 11 0.00024 42.2 6.8 25 477-501 175-199 (262)
90 KOG0127 Nucleolar protein fibr 69.8 2.4 5.2E-05 51.0 1.7 24 221-244 331-354 (678)
91 KOG0307 Vesicle coat complex C 68.9 85 0.0018 41.3 14.9 7 305-311 302-308 (1049)
92 KOG3118 Disrupter of silencing 68.6 1.9 4.1E-05 51.1 0.6 6 90-95 129-134 (517)
93 PRK05886 yajC preprotein trans 67.4 13 0.00028 36.4 5.9 52 423-481 37-88 (109)
94 PLN00036 40S ribosomal protein 67.4 17 0.00037 40.8 7.5 25 477-501 175-199 (261)
95 smart00743 Agenet Tudor-like d 67.4 14 0.0003 31.7 5.5 54 424-477 2-57 (61)
96 KOG1984 Vesicle coat complex C 64.9 92 0.002 40.3 13.7 16 847-862 196-211 (1007)
97 PRK14635 hypothetical protein; 63.6 9.2 0.0002 39.9 4.4 49 705-753 95-154 (162)
98 PRK05585 yajC preprotein trans 63.1 14 0.0003 36.0 5.2 49 422-477 50-98 (106)
99 PRK14639 hypothetical protein; 62.2 15 0.00033 37.4 5.5 49 705-753 84-132 (140)
100 PF11746 DUF3303: Protein of u 61.6 43 0.00094 31.6 8.1 75 185-259 2-85 (91)
101 PRK05886 yajC preprotein trans 61.1 14 0.00031 36.2 4.9 41 709-754 42-82 (109)
102 PRK04333 50S ribosomal protein 61.0 15 0.00032 34.4 4.7 33 272-305 3-35 (84)
103 COG1862 YajC Preprotein transl 60.9 13 0.00027 35.8 4.4 53 423-482 42-94 (97)
104 CHL00010 infA translation init 60.6 47 0.001 30.5 7.9 63 552-627 10-73 (78)
105 PF11623 DUF3252: Protein of u 60.6 17 0.00037 30.9 4.5 50 425-474 2-53 (53)
106 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 60.4 37 0.00079 30.9 7.3 50 424-486 3-64 (86)
107 PRK03879 ribonuclease P protei 60.1 21 0.00046 34.2 5.7 48 704-753 10-60 (96)
108 PRK04333 50S ribosomal protein 59.5 14 0.00029 34.7 4.2 29 708-736 6-35 (84)
109 PF05793 TFIIF_alpha: Transcri 58.9 3.2 6.8E-05 51.0 0.0 8 109-116 281-288 (527)
110 PRK07400 30S ribosomal protein 58.7 1E+02 0.0023 35.5 12.2 156 423-610 74-249 (318)
111 KOG0127 Nucleolar protein fibr 58.6 4.9 0.00011 48.5 1.5 18 225-242 497-514 (678)
112 PF02736 Myosin_N: Myosin N-te 57.5 22 0.00047 28.8 4.6 28 723-751 15-42 (42)
113 KOG0262 RNA polymerase I, larg 57.2 7.3 0.00016 51.0 2.7 6 260-265 1561-1566(1640)
114 PRK00276 infA translation init 57.0 56 0.0012 29.4 7.7 62 552-626 10-72 (72)
115 cd04455 S1_NusA S1_NusA: N-uti 56.9 34 0.00073 30.0 6.2 42 441-486 7-50 (67)
116 PRK04313 30S ribosomal protein 56.8 61 0.0013 36.0 9.4 73 949-1021 129-210 (237)
117 KOG0526 Nucleosome-binding fac 55.4 9.3 0.0002 46.2 3.0 15 143-157 580-594 (615)
118 smart00652 eIF1a eukaryotic tr 55.2 67 0.0014 30.0 8.0 65 549-627 5-70 (83)
119 smart00361 RRM_1 RNA recogniti 55.1 36 0.00079 29.9 6.1 28 221-248 34-61 (70)
120 KOG2393 Transcription initiati 55.1 10 0.00022 45.9 3.3 12 91-102 279-290 (555)
121 KOG1980 Uncharacterized conser 54.9 3 6.5E-05 51.1 -1.0 9 234-242 535-543 (754)
122 COG1588 POP4 RNase P/RNase MRP 54.4 25 0.00053 33.6 5.0 50 703-754 11-63 (95)
123 KOG2600 U3 small nucleolar rib 53.7 5 0.00011 48.4 0.5 14 78-91 170-184 (596)
124 KOG0699 Serine/threonine prote 53.7 5.6 0.00012 45.9 0.9 10 142-151 372-381 (542)
125 cd05687 S1_RPS1_repeat_ec1_hs1 53.1 50 0.0011 28.7 6.6 43 441-486 4-54 (70)
126 PRK11760 putative 23S rRNA C24 52.7 23 0.00051 41.3 5.6 58 185-246 4-61 (357)
127 TIGR00739 yajC preprotein tran 52.3 31 0.00066 32.3 5.3 41 708-753 40-80 (84)
128 PF02576 DUF150: Uncharacteris 51.6 27 0.00058 35.3 5.3 49 705-753 83-137 (141)
129 PRK07899 rpsA 30S ribosomal pr 51.5 3.2E+02 0.007 33.6 15.2 46 252-308 60-105 (486)
130 PF04050 Upf2: Up-frameshift s 51.5 4.9 0.00011 42.1 0.0 12 145-156 67-78 (170)
131 TIGR00523 eIF-1A eukaryotic/ar 51.4 53 0.0011 31.7 6.9 64 548-627 18-85 (99)
132 cd04454 S1_Rrp4_like S1_Rrp4_l 51.3 48 0.001 30.0 6.4 47 426-485 5-59 (82)
133 PRK14638 hypothetical protein; 51.2 26 0.00057 36.1 5.2 48 705-754 96-143 (150)
134 PLN00208 translation initiatio 51.2 67 0.0014 33.1 7.9 76 538-627 20-97 (145)
135 PRK13709 conjugal transfer nic 50.8 69 0.0015 44.9 10.4 98 422-522 646-761 (1747)
136 PRK00092 ribosome maturation p 50.1 27 0.00059 36.0 5.1 50 705-754 94-147 (154)
137 KOG1856 Transcription elongati 49.7 6.6 0.00014 51.2 0.7 12 742-753 1041-1052(1299)
138 TIGR00739 yajC preprotein tran 49.7 26 0.00057 32.7 4.5 35 471-509 32-66 (84)
139 smart00743 Agenet Tudor-like d 49.4 45 0.00098 28.5 5.6 51 476-527 2-57 (61)
140 cd01734 YlxS_C YxlS is a Bacil 49.2 35 0.00075 31.5 5.2 50 705-754 21-76 (83)
141 PTZ00329 eukaryotic translatio 48.9 71 0.0015 33.3 7.8 75 539-627 21-97 (155)
142 PRK14644 hypothetical protein; 48.8 25 0.00055 35.7 4.6 49 705-753 81-135 (136)
143 cd01734 YlxS_C YxlS is a Bacil 48.5 38 0.00082 31.2 5.3 51 426-476 23-77 (83)
144 cd05793 S1_IF1A S1_IF1A: Trans 48.1 96 0.0021 28.5 7.8 63 551-627 2-65 (77)
145 PF09953 DUF2187: Uncharacteri 48.1 39 0.00084 29.5 4.8 29 426-458 5-33 (57)
146 TIGR02760 TraI_TIGR conjugativ 47.9 68 0.0015 45.7 9.9 95 422-523 1327-1439(1960)
147 COG2139 RPL21A Ribosomal prote 47.9 25 0.00055 33.6 4.0 56 470-525 26-93 (98)
148 PRK05585 yajC preprotein trans 47.7 36 0.00078 33.2 5.2 42 708-754 55-96 (106)
149 PRK14637 hypothetical protein; 47.5 38 0.00082 35.0 5.7 47 705-753 94-141 (151)
150 KOG0699 Serine/threonine prote 47.5 13 0.00027 43.2 2.4 14 77-90 239-252 (542)
151 PRK14643 hypothetical protein; 47.3 31 0.00068 36.1 5.1 50 705-754 100-157 (164)
152 PF01868 UPF0086: Domain of un 47.1 60 0.0013 30.6 6.5 49 705-754 10-61 (89)
153 COG2139 RPL21A Ribosomal prote 46.9 34 0.00074 32.8 4.7 53 423-475 31-93 (98)
154 TIGR00717 rpsA ribosomal prote 46.4 2.9E+02 0.0064 33.7 14.1 45 253-308 212-256 (516)
155 KOG2422 Uncharacterized conser 46.4 10 0.00023 46.3 1.6 12 94-105 104-115 (665)
156 COG1862 YajC Preprotein transl 46.1 22 0.00049 34.2 3.5 41 709-754 47-87 (97)
157 PRK00087 4-hydroxy-3-methylbut 46.0 2.1E+02 0.0045 36.4 12.9 100 473-610 517-616 (647)
158 PRK06676 rpsA 30S ribosomal pr 45.9 2.5E+02 0.0053 33.1 12.9 45 253-308 44-88 (390)
159 KOG2023 Nuclear transport rece 45.7 10 0.00022 47.1 1.4 9 89-97 377-385 (885)
160 PF11213 DUF3006: Protein of u 45.7 30 0.00064 31.2 4.0 42 442-485 1-42 (71)
161 PRK04914 ATP-dependent helicas 44.9 62 0.0014 42.8 8.3 65 950-1019 18-82 (956)
162 KOG0119 Splicing factor 1/bran 44.6 6.9E+02 0.015 30.8 16.4 14 389-402 57-70 (554)
163 COG4547 CobT Cobalamin biosynt 44.6 18 0.00039 43.2 3.1 13 197-209 360-372 (620)
164 PRK12269 bifunctional cytidyla 44.2 60 0.0013 42.5 8.0 52 422-486 316-367 (863)
165 cd05790 S1_Rrp40 S1_Rrp40: Rrp 44.0 27 0.00058 32.9 3.6 50 426-485 5-58 (86)
166 PRK14634 hypothetical protein; 43.2 37 0.00079 35.3 4.8 48 705-754 96-147 (155)
167 PF11515 Cul7: Mouse developme 43.1 25 0.00054 32.5 3.1 31 271-301 16-49 (78)
168 PTZ00223 40S ribosomal protein 42.2 85 0.0018 35.6 7.7 72 949-1021 130-209 (273)
169 PRK14645 hypothetical protein; 42.1 38 0.00083 35.1 4.8 46 705-753 98-143 (154)
170 TIGR02760 TraI_TIGR conjugativ 42.1 1.2E+02 0.0026 43.4 10.8 93 422-518 679-792 (1960)
171 PF14851 FAM176: FAM176 family 41.9 57 0.0012 33.9 5.9 13 144-156 118-130 (153)
172 PRK04012 translation initiatio 41.6 1.4E+02 0.0031 28.9 8.2 74 540-627 11-86 (100)
173 KOG0299 U3 snoRNP-associated p 41.5 5.3 0.00012 47.3 -1.7 23 210-233 141-163 (479)
174 cd05705 S1_Rrp5_repeat_hs14 S1 41.4 61 0.0013 29.1 5.4 22 471-502 45-66 (74)
175 PRK14640 hypothetical protein; 41.0 50 0.0011 34.2 5.4 47 705-753 93-143 (152)
176 PTZ00065 60S ribosomal protein 40.9 38 0.00082 34.3 4.3 33 272-305 7-39 (130)
177 cd04456 S1_IF1A_like S1_IF1A_l 40.9 1.5E+02 0.0033 27.3 7.9 64 550-627 1-66 (78)
178 PRK06531 yajC preprotein trans 40.6 33 0.00071 33.9 3.7 38 714-754 44-81 (113)
179 CHL00084 rpl19 ribosomal prote 40.4 98 0.0021 30.9 7.0 31 421-451 19-56 (117)
180 PRK07594 type III secretion sy 40.3 4.3E+02 0.0092 32.1 13.7 62 420-509 8-69 (433)
181 PF01287 eIF-5a: Eukaryotic el 40.2 22 0.00048 32.1 2.3 43 441-483 5-52 (69)
182 PLN00036 40S ribosomal protein 40.1 1.1E+02 0.0024 34.6 8.1 72 949-1021 133-212 (261)
183 cd05791 S1_CSL4 S1_CSL4: CSL4, 39.9 49 0.0011 31.2 4.8 14 472-485 56-69 (92)
184 PRK06299 rpsA 30S ribosomal pr 39.8 3.1E+02 0.0067 34.0 13.0 46 252-308 225-270 (565)
185 PF10842 DUF2642: Protein of u 39.6 77 0.0017 28.5 5.5 45 705-752 17-61 (66)
186 PTZ00118 40S ribosomal protein 38.9 1.2E+02 0.0027 34.1 8.3 72 949-1021 133-212 (262)
187 KOG2893 Zn finger protein [Gen 38.8 2.7E+02 0.0059 30.9 10.5 11 626-636 10-20 (341)
188 PF05641 Agenet: Agenet domain 38.7 90 0.002 27.6 6.0 34 425-458 1-39 (68)
189 PF14944 TCRP1: Tongue Cancer 38.4 96 0.0021 32.1 6.7 9 877-885 72-80 (195)
190 KOG0338 ATP-dependent RNA heli 38.1 9.2 0.0002 46.2 -0.5 18 191-208 229-246 (691)
191 PF09870 DUF2097: Uncharacteri 38.1 47 0.001 31.3 4.2 51 423-474 17-67 (86)
192 KOG4264 Nucleo-cytoplasmic pro 38.1 21 0.00046 43.0 2.4 90 3-105 60-172 (694)
193 PRK06531 yajC preprotein trans 37.9 48 0.001 32.8 4.5 47 423-477 35-83 (113)
194 PRK14630 hypothetical protein; 37.7 68 0.0015 32.9 5.7 46 705-753 93-138 (143)
195 KOG3118 Disrupter of silencing 37.5 9.9 0.00022 45.4 -0.4 6 488-493 497-502 (517)
196 COG5271 MDN1 AAA ATPase contai 37.3 22 0.00048 48.7 2.6 12 226-237 4204-4215(4600)
197 COG4547 CobT Cobalamin biosynt 36.7 30 0.00066 41.4 3.3 10 332-341 478-487 (620)
198 PF03896 TRAP_alpha: Transloco 36.3 14 0.00031 41.9 0.7 12 303-314 251-262 (285)
199 smart00538 POP4 A domain found 36.2 94 0.002 29.6 6.0 48 704-752 8-58 (92)
200 PRK14712 conjugal transfer nic 36.1 1.3E+02 0.0029 41.9 9.5 85 423-510 515-617 (1623)
201 CHL00125 psaE photosystem I su 36.1 58 0.0013 28.8 4.1 29 273-301 2-32 (64)
202 COG1471 RPS4A Ribosomal protei 35.5 97 0.0021 34.3 6.6 71 950-1021 133-212 (241)
203 PRK09838 periplasmic copper-bi 35.5 73 0.0016 31.6 5.3 59 440-501 44-112 (115)
204 PTZ00065 60S ribosomal protein 35.4 35 0.00076 34.5 3.1 33 708-741 10-42 (130)
205 KOG0608 Warts/lats-like serine 34.9 4.5E+02 0.0097 33.6 12.6 8 876-883 273-280 (1034)
206 PRK04950 ProP expression regul 34.6 62 0.0013 35.3 5.0 45 707-753 168-212 (213)
207 PF02427 PSI_PsaE: Photosystem 34.5 83 0.0018 27.7 4.7 28 273-300 1-30 (61)
208 KOG0970 DNA polymerase alpha, 34.5 23 0.00051 46.4 2.1 22 31-52 49-70 (1429)
209 PRK07899 rpsA 30S ribosomal pr 34.4 1E+02 0.0023 37.7 7.5 51 423-486 31-89 (486)
210 PF03831 PhnA: PhnA protein; 34.3 22 0.00048 30.8 1.3 20 592-611 1-20 (56)
211 PRK06763 F0F1 ATP synthase sub 34.2 3.5E+02 0.0076 29.5 10.3 27 493-519 42-68 (213)
212 KOG0066 eIF2-interacting prote 34.2 35 0.00077 40.8 3.3 15 77-91 117-131 (807)
213 KOG0132 RNA polymerase II C-te 33.7 1.3E+02 0.0027 38.6 7.9 27 704-730 479-505 (894)
214 TIGR01024 rplS_bact ribosomal 33.1 1.4E+02 0.003 29.7 6.7 38 421-458 15-63 (113)
215 PLN00045 photosystem I reactio 33.1 42 0.0009 32.0 3.0 39 982-1020 35-80 (101)
216 PHA02774 E1; Provisional 32.9 14 0.00031 45.8 -0.1 20 140-159 65-84 (613)
217 PRK02749 photosystem I reactio 32.5 59 0.0013 29.3 3.6 38 273-312 3-42 (71)
218 PRK14633 hypothetical protein; 32.3 78 0.0017 32.7 5.2 49 705-754 90-142 (150)
219 PF01176 eIF-1a: Translation i 32.1 2.2E+02 0.0048 25.1 7.3 61 550-624 4-65 (65)
220 PF11604 CusF_Ec: Copper bindi 32.1 1E+02 0.0023 27.6 5.3 45 443-487 1-53 (70)
221 COG0779 Uncharacterized protei 32.0 97 0.0021 32.3 5.8 48 705-754 95-146 (153)
222 PRK14632 hypothetical protein; 32.0 81 0.0018 33.3 5.3 50 705-754 94-156 (172)
223 TIGR01651 CobT cobaltochelatas 31.9 40 0.00086 41.9 3.4 10 146-155 338-347 (600)
224 KOG4849 mRNA cleavage factor I 31.8 3E+02 0.0065 32.2 9.9 23 731-753 142-165 (498)
225 COG4873 Uncharacterized protei 31.7 66 0.0014 28.9 3.8 47 426-476 25-71 (81)
226 PRK12288 GTPase RsgA; Reviewed 31.6 2.4E+02 0.0051 33.1 9.6 88 551-655 40-129 (347)
227 KOG2418 Microtubule-associated 31.3 1.1E+02 0.0024 35.7 6.6 6 992-997 375-380 (448)
228 PF13051 DUF3912: Protein of u 31.3 99 0.0022 27.0 4.7 49 706-756 3-54 (68)
229 PF08553 VID27: VID27 cytoplas 31.3 27 0.00058 45.0 1.9 15 486-500 649-663 (794)
230 PF02699 YajC: Preprotein tran 31.2 16 0.00035 33.8 0.0 35 471-509 31-65 (82)
231 PF14563 DUF4444: Domain of un 31.1 92 0.002 25.6 4.2 33 1000-1033 7-39 (42)
232 PRK05338 rplS 50S ribosomal pr 31.1 1.8E+02 0.0039 29.0 7.2 37 422-458 16-63 (116)
233 PF05470 eIF-3c_N: Eukaryotic 30.6 27 0.00058 43.7 1.8 6 307-312 336-341 (595)
234 COG5129 MAK16 Nuclear protein 30.2 20 0.00044 38.9 0.5 6 78-83 267-272 (303)
235 PF02699 YajC: Preprotein tran 30.1 17 0.00037 33.6 0.0 41 708-753 39-79 (82)
236 TIGR00037 eIF_5A translation i 30.0 68 0.0015 32.4 4.2 62 422-487 57-119 (130)
237 PRK14636 hypothetical protein; 30.0 84 0.0018 33.4 5.0 49 705-754 94-146 (176)
238 KOG2023 Nuclear transport rece 29.8 25 0.00054 43.9 1.3 23 221-244 459-481 (885)
239 PF09444 MRC1: MRC1-like domai 29.8 11 0.00024 38.6 -1.4 16 86-101 5-20 (145)
240 TIGR01622 SF-CC1 splicing fact 29.7 1.8E+02 0.0039 34.6 8.5 66 196-264 384-454 (457)
241 PRK02001 hypothetical protein; 29.7 1.1E+02 0.0023 31.9 5.6 49 705-753 86-146 (152)
242 PF09507 CDC27: DNA polymerase 29.5 18 0.00039 42.6 0.0 6 89-94 366-371 (430)
243 smart00333 TUDOR Tudor domain. 29.2 96 0.0021 25.8 4.4 51 424-476 2-53 (57)
244 COG0779 Uncharacterized protei 29.1 80 0.0017 32.9 4.6 48 425-476 96-147 (153)
245 cd00164 S1_like S1_like: Ribos 29.0 87 0.0019 25.7 4.1 42 442-486 2-51 (65)
246 PF07076 DUF1344: Protein of u 28.9 1.3E+02 0.0029 26.7 5.2 44 440-486 4-47 (61)
247 KOG0526 Nucleosome-binding fac 28.8 34 0.00073 41.7 2.1 17 142-158 559-575 (615)
248 KOG3130 Uncharacterized conser 28.8 33 0.00071 40.3 1.9 7 176-182 358-364 (514)
249 PRK12366 replication factor A; 28.7 1.3E+03 0.029 29.3 17.6 31 617-647 518-553 (637)
250 smart00316 S1 Ribosomal protei 28.5 2.1E+02 0.0046 23.8 6.6 42 442-486 7-56 (72)
251 COG2163 RPL14A Ribosomal prote 28.4 73 0.0016 32.1 4.0 37 474-510 2-38 (125)
252 PF00924 MS_channel: Mechanose 28.0 65 0.0014 33.9 3.9 46 422-475 58-103 (206)
253 PRK14646 hypothetical protein; 28.0 98 0.0021 32.2 5.0 47 705-753 96-146 (155)
254 PRK05807 hypothetical protein; 27.9 2.2E+02 0.0049 28.8 7.5 15 472-486 44-58 (136)
255 cd04451 S1_IF1 S1_IF1: Transla 27.9 2.5E+02 0.0055 24.4 6.9 58 553-623 5-63 (64)
256 KOG2055 WD40 repeat protein [G 27.9 28 0.00061 41.6 1.2 10 147-156 175-184 (514)
257 COG0355 AtpC F0F1-type ATP syn 27.3 2.9E+02 0.0063 28.1 8.2 83 430-525 5-92 (135)
258 PLN00045 photosystem I reactio 27.2 1.1E+02 0.0023 29.4 4.6 31 269-299 36-68 (101)
259 PF14001 YdfZ: YdfZ protein 26.9 65 0.0014 28.7 2.9 31 593-626 2-32 (64)
260 PF15455 Pro-rich_19: Proline- 26.8 3.9E+02 0.0085 30.3 9.5 8 606-613 61-68 (357)
261 KOG2475 CDC45 (cell division c 26.8 11 0.00025 45.4 -2.2 7 77-83 183-189 (587)
262 COG0335 RplS Ribosomal protein 26.4 2.1E+02 0.0045 28.5 6.6 30 422-451 18-54 (115)
263 PRK08582 hypothetical protein; 26.3 2E+02 0.0042 29.4 6.8 15 472-486 45-59 (139)
264 PRK14647 hypothetical protein; 26.2 1.2E+02 0.0025 31.7 5.3 48 705-753 95-151 (159)
265 KOG0772 Uncharacterized conser 26.2 38 0.00083 41.1 1.9 13 387-399 296-308 (641)
266 COG0361 InfA Translation initi 25.4 2.8E+02 0.0061 25.7 6.8 63 552-627 10-73 (75)
267 PRK00098 GTPase RsgA; Reviewed 25.4 3.8E+02 0.0082 30.5 9.7 87 553-655 3-89 (298)
268 PRK14638 hypothetical protein; 25.4 1.2E+02 0.0026 31.3 5.2 47 426-476 98-144 (150)
269 PRK00409 recombination and DNA 24.9 93 0.002 40.4 5.2 47 423-476 635-682 (782)
270 KOG0162 Myosin class I heavy c 24.7 1.2E+03 0.027 30.2 14.0 7 725-731 895-901 (1106)
271 PF11942 Spt5_N: Spt5 transcri 24.6 32 0.00069 32.8 0.7 9 48-56 1-9 (97)
272 cd05703 S1_Rrp5_repeat_hs12_sc 24.4 42 0.00092 30.0 1.5 52 441-502 4-62 (73)
273 PHA03247 large tegument protei 24.3 1.8E+03 0.038 33.2 16.5 7 394-400 2200-2206(3151)
274 KOG2147 Nucleolar protein invo 24.1 49 0.0011 41.8 2.4 13 40-52 307-319 (823)
275 PF00575 S1: S1 RNA binding do 24.0 2.3E+02 0.005 24.7 6.1 56 441-509 8-72 (74)
276 COG0056 AtpA F0F1-type ATP syn 23.7 1.9E+02 0.0041 35.1 6.9 49 492-566 26-74 (504)
277 PRK12442 translation initiatio 23.7 3.1E+02 0.0067 26.1 6.9 62 552-626 10-72 (87)
278 PF02576 DUF150: Uncharacteris 23.5 95 0.0021 31.4 4.0 51 426-476 85-139 (141)
279 PTZ00482 membrane-attack compl 23.5 69 0.0015 41.6 3.6 7 150-156 231-237 (844)
280 COG5593 Nucleic-acid-binding p 23.3 48 0.001 40.4 2.0 7 144-150 812-818 (821)
281 KOG3416 Predicted nucleic acid 23.2 2.8E+02 0.0061 28.1 6.9 47 465-512 49-106 (134)
282 smart00333 TUDOR Tudor domain. 23.1 1.1E+02 0.0025 25.3 3.8 39 948-988 18-56 (57)
283 cd04469 S1_Hex1 S1_Hex1: Hex1, 22.7 74 0.0016 29.3 2.6 38 444-481 6-48 (75)
284 cd01854 YjeQ_engC YjeQ/EngC. 22.7 4.4E+02 0.0095 29.8 9.5 86 553-655 1-87 (287)
285 CHL00010 infA translation init 22.6 3.1E+02 0.0068 25.2 6.7 56 441-499 9-69 (78)
286 KOG0066 eIF2-interacting prote 22.6 62 0.0014 38.9 2.7 17 68-84 144-160 (807)
287 PRK09521 exosome complex RNA-b 22.1 1.5E+02 0.0032 31.5 5.2 53 423-485 60-127 (189)
288 PF07133 Merozoite_SPAM: Meroz 22.0 30 0.00065 36.6 0.0 11 197-207 137-147 (173)
289 PRK04163 exosome complex RNA-b 21.9 1.3E+02 0.0028 33.2 4.9 50 426-485 62-120 (235)
290 TIGR03318 YdfZ_fam putative se 21.8 68 0.0015 28.5 2.1 31 593-626 3-33 (65)
291 COG3109 ProQ Activator of osmo 21.7 1.3E+02 0.0027 32.0 4.4 43 708-752 164-206 (208)
292 PF12059 DUF3540: Protein of u 21.5 3.3E+02 0.0072 29.6 7.8 67 950-1021 3-72 (202)
293 cd05692 S1_RPS1_repeat_hs4 S1_ 21.4 2.7E+02 0.0058 23.3 5.9 43 441-486 4-54 (69)
294 smart00357 CSP Cold shock prot 21.4 2.9E+02 0.0062 22.9 6.0 56 443-500 2-63 (64)
295 KOG2140 Uncharacterized conser 21.2 41 0.0009 41.0 0.9 9 223-231 576-584 (739)
296 PRK00092 ribosome maturation p 21.2 1.5E+02 0.0032 30.6 4.9 49 426-476 96-148 (154)
297 PRK14631 hypothetical protein; 21.0 1.7E+02 0.0036 31.1 5.3 48 705-753 113-166 (174)
298 KOG0270 WD40 repeat-containing 21.0 76 0.0016 38.0 3.0 10 306-315 214-223 (463)
299 PRK13709 conjugal transfer nic 21.0 3.9E+02 0.0084 38.0 10.0 79 423-509 1274-1372(1747)
300 PF13893 RRM_5: RNA recognitio 20.8 1.7E+02 0.0037 24.2 4.3 35 214-248 11-45 (56)
301 PRK13806 rpsA 30S ribosomal pr 20.8 4.3E+02 0.0093 32.4 9.5 58 424-504 31-93 (491)
302 TIGR00358 3_prime_RNase VacB a 20.5 4.5E+02 0.0098 33.5 9.9 75 427-502 71-149 (654)
303 PHA03169 hypothetical protein; 20.4 1.3E+02 0.0028 35.4 4.5 91 5-111 155-245 (413)
304 PRK04306 50S ribosomal protein 20.4 1.6E+02 0.0035 28.5 4.5 53 423-475 33-95 (98)
305 cd05697 S1_Rrp5_repeat_hs5 S1_ 20.1 3.6E+02 0.0077 23.3 6.4 43 441-486 4-54 (69)
306 COG1097 RRP4 RNA-binding prote 20.1 2.2E+02 0.0048 31.7 6.1 50 426-485 63-121 (239)
No 1
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=100.00 E-value=2.3e-216 Score=1883.62 Aligned_cols=929 Identities=50% Similarity=0.780 Sum_probs=796.3
Q ss_pred CCcccccCCCCCCcccccccCCcchhccc--cccCcc-----ccCCCCCCCCCCCCCccCCCCCCCCcchhhhHHHHHHH
Q 001639 78 RKPKAKRRSGSEFFDLEAQVDSDEEEDEE--EGEDDF-----IVDGGAELPDEDGGRGIHRRPLLPREDEQEDVEALERR 150 (1039)
Q Consensus 78 r~kkr~~~~~~~FiD~EAEVDDdeEeeee--e~e~df-----I~~~~~~l~~~~~~r~~~r~~~~~~~~~~~d~e~~~~~ 150 (1039)
-++|+|+.+...||+.|||||||.||||+ |+|+|+ |++.+.+++++.-++|.||.++... ++..|++++.
T Consensus 55 ~~~~~k~~s~~gf~~~e~dvDdeveddd~~~edEed~~~~~~ie~~e~~~~d~~~~~R~~~~~~~~~---~~~~e~~~~r 131 (1024)
T KOG1999|consen 55 PDEKDKKESGGGFIDREADVDDEVEDDDDDEEDEEDIELHNDIEESEEDLPDERGDRRLRRYWDRQL---NELEEELAKR 131 (1024)
T ss_pred hhhhccccccccccccccccccccccccchhccCcchhhcccchhcccccccccccccchhhhhhhh---hHHHHHHHHH
Confidence 45566778889999999999998887766 334443 5544555555555555555533322 2255667777
Q ss_pred HHHHhccCC-cc-cccccccchhhhhcCCCCCCCcEEEEEccCchHHHHHHHHHHHHHhhC---CCcceEEEEeecCCcc
Q 001639 151 IQARYARSS-HT-EYDEETTDVEQQALLPSVRDPKLWMVKCAIGREREAAVCLMQKCIDKG---SELQIRSVIALDHLKN 225 (1039)
Q Consensus 151 l~eRY~~~~-~~-~~~~~~~~v~q~~LlPsv~Dp~lw~Vkc~~G~Er~vv~~Lm~K~~~~~---~~l~I~Svf~~~~lkG 225 (1039)
+++||.... +. ..+++.++|+||+||||++||+||+|||++|+||++|+|||+||+++. .+|+|+|||+++||||
T Consensus 132 ~aee~~~~~~~~~~~~~~~d~I~Q~~LLPsvkDP~LW~VKC~iG~Er~~a~~LMrK~i~~~~t~~plqI~Sv~a~D~lkG 211 (1024)
T KOG1999|consen 132 YAEEYIEKYGFEDGDDEDSDDIPQQALLPSVKDPNLWIVKCKIGREREVAFCLMRKFIELDKTDTPLQIKSVFAKDHLKG 211 (1024)
T ss_pred HHHhhcccccccccchhcccchhHHhhCCCCCCCCeeEEEeccccHHHHHHHHHHHHHhhcccCCCceEEEEEeccccce
Confidence 777775332 33 233567899999999999999999999999999999999999999985 8999999999999999
Q ss_pred EEEEEecchHHHHHHHhcCcccceeeeeeeChhhhhhccccccccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEE
Q 001639 226 YIYIEADKEAHVKEACKGLRNIYSQKVMLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTV 305 (1039)
Q Consensus 226 YIYVEA~~~~~V~~ai~gl~~v~~~~~~lVpi~Em~~vL~~~k~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~V 305 (1039)
||||||++|+||++||+||++||.+++.||||+||++||++.|+.+.|++|+|||||+|+||||||||+.|++++++|+|
T Consensus 212 yIYIEA~KqshV~~Ai~gv~niy~~~~~lVPikEM~dvLkV~K~~v~L~~gswVRiKrG~YKgDLAqVd~Vd~~~n~v~l 291 (1024)
T KOG1999|consen 212 YIYIEADKQSHVKEAIEGVRNIYANRILLVPIKEMPDVLKVVKKVVQLSEGSWVRIKRGKYKGDLAQVDDVDENRNRVRL 291 (1024)
T ss_pred eEEEEechhHHHHHHHhhhhhheeccEEEEehhHhhhhhhhhhhhhccCccceEEEeccccccceeeeeeecccCCEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeccchhhhhhhccccccccCCCCCCCCCCCCHHHHHhccccEeeeccCCCCceEEEeCCceeccceEEEEEecccee
Q 001639 306 KLIPRIDLQALANKLEGREVAKKKPFVPPPRFMNVDEARELHIRVERRRDPMTGDYFENIGGMLFKDGFLYKTVSMKSIS 385 (1039)
Q Consensus 306 klvPRiD~~~~~~~~~~~~~~kkk~~RPp~rlFn~~e~~~~~~~v~~~r~~~~g~~~~~~~~~~y~dGfL~K~~~i~~l~ 385 (1039)
||||||||+++.+++. ...++|++||++||||..++++..++++.+|+..+|+||++++|++|+||||||.|+|++|+
T Consensus 292 KlIPRIDyq~~~~~~~--~~~~~ka~~p~~R~~~~~~~~~~~ir~~~~~~~~~Gd~l~~~gn~~~~dGFLyK~v~i~sI~ 369 (1024)
T KOG1999|consen 292 KLIPRIDYQKLLGKLE--ETTDKKAFRPAPRRPNQKEFDEEAIRSEGRRDHSRGDYLEFEGNELFKDGFLYKDVSISSII 369 (1024)
T ss_pred EEeccccHHhhhcccc--ccchhhccCCcccCCCccccchhhhhhccccccccCceEEecCCceeccceeeeeeecceee
Confidence 9999999999998877 33456777999999999999999999999999999999998888899999999999999999
Q ss_pred ccCCCCChHHhhcccCCCCCCcchhhhhhHHhhcccc-CccCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCc
Q 001639 386 AQNIQPTFDELEKFRTPGENGESDIASLSTLFANRKK-GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPK 464 (1039)
Q Consensus 386 ~~~V~PTleEL~~F~~~~~~~~~dl~~ls~~~~~~~~-~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~ 464 (1039)
+++|+|||+||+||+...+ ++||..++++++++.+ +.|++||+|+||.|||+|++|+|++|++.+|+|++++++|+.
T Consensus 370 t~gV~PT~dELekF~~~~e--~~Dl~~~st~~~~r~~~~~F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~ 447 (1024)
T KOG1999|consen 370 TDGVKPTLDELEKFNPSNE--EGDLEWVSTLKSNRKKKHLFSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKG 447 (1024)
T ss_pred ecCcccCHHHHHhhcCCCc--cccceeeeeeccccccccccCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCCC
Confidence 9999999999999998876 5678888766655554 459999999999999999999999999999999999999999
Q ss_pred ceeeccccceeeccCCCceEEecccccCceEEEEEEeCcEEEEEeCCCCceEEEeccccccccccccccccCCceEeeee
Q 001639 465 TLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDL 544 (1039)
Q Consensus 465 ~i~v~~~~LrK~F~~GDhVkVi~G~~~GetGlVv~Ve~~~v~llSD~t~~ei~V~~~dL~~~~e~~~g~~~~g~y~l~DL 544 (1039)
+|+|++++|||||++|||||||+|+|+|+|||||+|+++.|+||||++|+|++||++||++|++|+++++++|+|+||||
T Consensus 448 pl~~~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe~~~vi~~Sd~t~eel~Vf~~dlq~c~ev~~gv~~~ge~e~hdl 527 (1024)
T KOG1999|consen 448 PLEVPASELRKYFEPGDHVKVIAGRYEGDTGLVVRVEQGDVILLSDLTMEELKVFARDLQLCSEVTLGVEKSGEYELHDL 527 (1024)
T ss_pred ccccchHhhhhhccCCCeEEEEeccccCCcceEEEEeCCeEEEEecCccceeeEEehhcccchheeecccccccccccce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCceEEEEEEccceeEEeccCCCCCcEEEEechhhhhccc-CCcccccCCCCeecCCCEEEEecCCCCCceecEEE
Q 001639 545 VLLDNNSFGVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLE-KKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEH 623 (1039)
Q Consensus 545 VqLd~~tVGvIvrverd~~~VL~~~~~~g~v~~v~~~~I~~k~~-~~~~a~D~~gn~I~~~D~Vkv~~Gp~kgr~G~V~h 623 (1039)
||||.++||||++++++.|+||+++ |+|++|++++|.+|++ ++++|+|+++|+|+++|+|+++.||++||+|.|+|
T Consensus 528 VqLd~~~vgvI~rle~e~~~vl~~~---g~v~~i~~~~i~~kk~~r~~~~~D~~~n~I~~kD~Vkvi~Gp~~g~~G~v~~ 604 (1024)
T KOG1999|consen 528 VQLDNQNVGVIVRLERETFQVLGMN---GKVVTIRKSSITKKKDNRKAVAVDRNGNEIRVKDTVKVIGGPSKGREGEVLH 604 (1024)
T ss_pred eecCCCcEEEEEEecchheeeecCc---CceEEEeechhhhhhhhhhheeecccCCeecccceEEEecCCCCCccCccce
Confidence 9999999999999999999999985 7999999999999986 56999999999999999999999999999999999
Q ss_pred EECCEEEEEeCceeeeceEEEEeCCceEEecccCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 001639 624 IYRGILFIHDRHHLEHAGFICAKSSSCVVVGGSRANGDRNGDAYSRFNSLRTPPRIPQSPGRYSRGGPPAGGRNRGGRGG 703 (1039)
Q Consensus 624 I~r~~lFl~~~~~~EN~Gifv~~a~~~~~~g~~~~~~~~~~~~~~~~~~~~~p~~~~~sp~~~~~~~~~~gg~~~~~~~~ 703 (1039)
|||+++|||||+++||+||||||++||.++|++++. ..+....+.|++|+ |.++ ++|+.++.+ +.++|++.++|||
T Consensus 605 i~r~~~F~h~r~~~En~Gv~vck~k~~~~~g~~~st-~~~~~~~~~l~~ms-P~r~-~sp~~~~~~-~ga~g~~gggrGg 680 (1024)
T KOG1999|consen 605 IYRPFVFLHSRKNLENGGVFVCKEKNLILAGGKKST-NSLAFNKGALAPMS-PGRI-QSPMGPSGG-PGAFGGHGGGRGG 680 (1024)
T ss_pred eecceeeeeehhhcccCCeEEEecCCceeccccCcc-cchhhcccccCCCC-cccc-cCCcCCCCC-CCCcCcCccCccC
Confidence 999999999999999999999999999999997642 11111223444443 4322 344332211 1122333344444
Q ss_pred --CccccCcEEEEeecCCCCceeEEEeecCCeEEEEecCCceEEEEecCccccccc-----cccCCC-CC-------CC-
Q 001639 704 --HDALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISDNVV-----VSTPYR-DT-------PR- 767 (1039)
Q Consensus 704 --~d~liGktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~~~~~-----~~~py~-~~-------p~- 767 (1039)
++.+|||||+|+.||||||+|+|||+|+++||||||++|+||+|++.++..++. ..++|+ ++ |+
T Consensus 681 ~rd~~l~GktVrI~~Gp~KG~~GivkD~~~~~arVELhs~~~ti~vd~~~~~~v~~~~~~g~~~sYg~~~~~~g~~~~~~ 760 (1024)
T KOG1999|consen 681 NRDDSLLGKTVRIRLGPKKGYLGIVKDVNGDTARVELHSKCVTIKVDRLKRKIVGSTRDGGETSSYGERTPGYGRVTPAR 760 (1024)
T ss_pred cCcchhcCcEEEEecCCcccccceeEeccCCeeEEEEEeccEEEEechhhceEEeeccCCCCccccccccccccccCccc
Confidence 459999999999999999999999999999999999999999999999988755 356676 23 33
Q ss_pred CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCC
Q 001639 768 YGMGSETPMHPSRTPLHP-YMTPMRDAGATPIHDGMRTPMRDRAWNPYTPMSPPR--DNWEDGNPGSWGTSPQYQPGSPP 844 (1039)
Q Consensus 768 y~~g~~tp~~~~~TP~~~-~~TP~~~g~~TP~h~g~~TP~~~~aW~p~~p~tp~~--~~~~~~~p~~~~~tp~y~p~tp~ 844 (1039)
|++||+|||||++||+|+ ++||++++++||+|||+|||||++||+|++++||++ ++|+++.+++|+.+|+|.
T Consensus 761 ~~~Gs~tp~~~s~tpl~~~s~tp~~~~~~Tp~~dG~rTP~r~~aW~~~~~~tPa~~~~~~~~g~~g~~g~sp~~~----- 835 (1024)
T KOG1999|consen 761 YGMGSSTPMYGSNTPLWGGSRTPARDGGATPSHDGSRTPARGRAWNPYNGKTPARNFDNREPGFEGSGGRSPQGY----- 835 (1024)
T ss_pred cCCCCcCccCCCCCCCCCcccCccccCCCCcCCCCCcCCCCCCCcCCCCCCCCccccCCcccCCCCCCCCCCCCC-----
Confidence 357999999999999998 999999999999999999999999999999999999 678888888888877653
Q ss_pred CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCc----CCCCCCCCCCCCC-CCCCCCCCCCCCCCCCC-CCCCCCCC
Q 001639 845 SRAYEAPTPGSGWASTPG-GNYSDAGTPRDSSSTYV----NAPSPYLPSTPGG-QPMTPNSASYLPGTPGG-QPMTPGTG 917 (1039)
Q Consensus 845 ~~~y~~~TPg~~~~~tP~-~~~~~~~tP~~~~~~y~----~~pspy~p~tp~~-~p~tp~~~~y~P~tPg~-~p~tp~~~ 917 (1039)
|.|+|||+.|+++++ +.|+.+.||....|+|. ++|+| +++++ ++||||+++|.|+|||+ +|||||++
T Consensus 836 ---~~a~Tpg~~~~~~~~~~~~~~~g~~~~~gsa~~~~~~~sps~---sp~~~~~~~tpss~s~~p~tpgg~~~~Tpgs~ 909 (1024)
T KOG1999|consen 836 ---YSAPTPGSNWGSTGGGGAPAWPGTPNGNGSAWGPSGQNSPSP---SPWGYQNNPTPSSSSYGPKTPGGGNPMTPGSG 909 (1024)
T ss_pred ---cCCCCCCCCCCcCCCCCCcCCCCCCCCCccccccccCCCCCC---CCccCccCCCCcccccCCCCCCCCCCCCCCcc
Confidence 678999999887754 56777788866666774 34443 44444 48899999999999998 89999994
Q ss_pred CCCCCCCccCCCCCCCcccCcEEE-EcCCCcccEEEEEEeCCCCeEEEEeccCCCCceEEecCCCeeecCCCCCCcEEEE
Q 001639 918 GLDAMSPVIGADNEGPWFMPDILV-RRSGEESVVGVIREVLPDGSCRVVLGSSGNGDTITALPNEIEIVPPRKTDKIKIM 996 (1039)
Q Consensus 918 g~~~~~p~~~~~~~~~W~~~~I~V-~~~g~~~~~GvV~~V~~~g~~~V~l~~~~~g~~v~v~~~~Le~V~P~kgd~VkVi 996 (1039)
++.++... ++....| .++..+ +.. -+|.++||+|.+ |.|+|+|.++ +++++++++||+++.|.+||.+||+
T Consensus 910 -~d~~~~~~-~~~~~~~-~~d~~~~~~~--~G~~~~ir~v~~-G~~sv~~~de--~~~~~~s~~~~a~~~p~~~d~~k~~ 981 (1024)
T KOG1999|consen 910 -LDSGSGNG-GDGNSSW-GPDTSLDTQL--VGQTGIIRSVAD-GGCSVWLGDE--GETISNSKPHLAPAPPCKGDDVKSI 981 (1024)
T ss_pred -ccccCCCC-CccceEe-ccccccccee--cccccceeeccC-CceeeecCCC--CcccccccccCccCCCCCCCCcccc
Confidence 55554322 1122223 334333 110 166889999977 9999999985 7899999999999999999999999
Q ss_pred cCCCCCceEEEEEEeCCCcEEEecCCCceEEEeccccccccCC
Q 001639 997 GGPHRGATGKLIGVDGTDGIVKVDVSLDVKILDMAILAKLAQP 1039 (1039)
Q Consensus 997 ~G~~rG~tG~LisiD~~dgiVk~d~~~~~kil~~~~L~Kl~~~ 1039 (1039)
.|.+||.+|+|+++|+.+||||+|.+.++|||++.+||||++|
T Consensus 982 ~g~~~g~~~~~~~~dg~~g~~~~d~~~~~k~l~~~~~~k~~~~ 1024 (1024)
T KOG1999|consen 982 WGDDRGSTGKLVGNDGWDGIVRIDETSDIKILNLGLLCKMVSP 1024 (1024)
T ss_pred ccccccccccccCCCcccceecccccccchhhhhhhhhhccCC
Confidence 9999999999999999999999999999999999999999875
No 2
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=100.00 E-value=3.4e-79 Score=672.84 Aligned_cols=403 Identities=23% Similarity=0.266 Sum_probs=352.8
Q ss_pred CCCCCCCCCHHHHHhccccEeeeccCCCCceEEEeCCceeccceEEEEEeccceeccCCCCChHHhhcccCCCCCCcchh
Q 001639 331 FVPPPRFMNVDEARELHIRVERRRDPMTGDYFENIGGMLFKDGFLYKTVSMKSISAQNIQPTFDELEKFRTPGENGESDI 410 (1039)
Q Consensus 331 ~RPp~rlFn~~e~~~~~~~v~~~r~~~~g~~~~~~~~~~y~dGfL~K~~~i~~l~~~~V~PTleEL~~F~~~~~~~~~dl 410 (1039)
.|||+||||+.|+.++......+|++. .| .|.|+.|.||||+|.|+++++++++++||+||+.+|....++ +||
T Consensus 4 ~r~~~~lfn~t~a~~~~~~~~~kr~~r---~f-~~~ne~~~dgflvk~~Ris~~et~~~~pt~de~~~F~~~~~d--ldl 77 (607)
T COG5164 4 HRAPPQLFNPTMALRLDQANLYKRDDR---HF-TYKNEDYIDGFLVKVKRISERETLMRIPTNDEKNVFSIICKD--LDL 77 (607)
T ss_pred ccCchhhcCchhhhhcChhhhhccCch---hc-cccCcccccceEEEEeeeceeeecccccccchhhhcCccccc--cch
Confidence 499999999999999988777777654 34 589999999999999999999999999999999999876444 788
Q ss_pred hhhhHHhhccccCccCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCceEEecccc
Q 001639 411 ASLSTLFANRKKGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVVSGTQ 490 (1039)
Q Consensus 411 ~~ls~~~~~~~~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi~G~~ 490 (1039)
.+++.++++.. ..|||||+|||+.|+|++..|.|.++.+++.+|... +.++|+||.+-|||.|..|||||||.|.|
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 88888876554 459999999999999999999999999999998864 46789999999999999999999999999
Q ss_pred cCceEEEEEEeCcEEEEEeCCCCceEEEeccccccccccccccccCCceEeeeeEEecCCceEEEEEEccceeEEeccCC
Q 001639 491 AGATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDNNSFGVIIRVESEAFQVLKGVP 570 (1039)
Q Consensus 491 ~GetGlVv~Ve~~~v~llSD~t~~ei~V~~~dL~~~~e~~~g~~~~g~y~l~DLVqLd~~tVGvIvrverd~~~VL~~~~ 570 (1039)
.+++|||++|+++.|+++|+++|.|++||+++|.++.+.+. ....|+|||||+|+..+|.||..|++|.++|+++
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 2368999999999999999999999999999997
Q ss_pred CCCcEEEEechhhhhccc-CC--cccccCCCCeecCCCEEEEecCCCCCceecEEEEECCEEEEEeCceeeeceEEEEeC
Q 001639 571 DRPEVALVKLREIKCKLE-KK--SNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRGILFIHDRHHLEHAGFICAKS 647 (1039)
Q Consensus 571 ~~g~v~~v~~~~I~~k~~-~~--~~a~D~~gn~I~~~D~Vkv~~Gp~kgr~G~V~hI~r~~lFl~~~~~~EN~Gifv~~a 647 (1039)
.|+|+++.+.+|..|++ +| .+++|+||++|++||.|+++-|- +++|+|+||++.|+|++++++.||+|+||++.
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 58999999999999986 45 59999999999999999999985 79999999999999999999999999999999
Q ss_pred CceEEecccCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcEEEEeecCCCCceeEEE
Q 001639 648 SSCVVVGGSRANGDRNGDAYSRFNSLRTPPRIPQSPGRYSRGGPPAGGRNRGGRGGHDALVGTTVKVRLGPYKGYRGRVV 727 (1039)
Q Consensus 648 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~p~~~~~sp~~~~~~~~~~gg~~~~~~~~~d~liGktV~I~~GpyKG~~G~Vk 727 (1039)
+|+.+++++... -. .-.+|++|| |+.+ ..+. .+...- -....+|||.+|||||+|+.|+|||++|+||
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 GNVCIVATKDFT-ES---LKVDLDKMN-PPVT-VNLQ-----NPKTNE-LERKIVGRDPAIGKTVRIRCGEYKGHLGVVK 373 (607)
T ss_pred CceeEEEeccch-hh---hcccHhhcC-chhh-cCCC-----CCcchh-hhccccccccccCceEEEeecccccccceee
Confidence 999999985322 11 225788998 5432 1111 111000 0112358999999999999999999999999
Q ss_pred eecCCeEEEEecCCceEEEEecCccccccc--cccCCC
Q 001639 728 DVKGQSVRVELESQMKVVTVDRSMISDNVV--VSTPYR 763 (1039)
Q Consensus 728 d~t~~~arVELhs~~k~I~V~r~~l~~~~~--~~~py~ 763 (1039)
|+++..|||||||+||.|||+|++|++.++ ..++|.
T Consensus 374 dv~~~~arVeLhs~nK~VTI~K~~l~y~~reGe~ity~ 411 (607)
T COG5164 374 DVDRNIARVELHSNNKFVTIEKSRLAYLGREGEGITYD 411 (607)
T ss_pred eccCceEEEEEecCCceEEeehhheEEecccccccchh
Confidence 999999999999999999999999999877 456775
No 3
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=100.00 E-value=1.2e-36 Score=361.52 Aligned_cols=414 Identities=21% Similarity=0.311 Sum_probs=263.9
Q ss_pred ccCCCCCCCCCCCCHHHHHhccccEeeeccC---CCCceEEEeCCceeccceEEEEEecccee-----ccCCCCChHH--
Q 001639 326 AKKKPFVPPPRFMNVDEARELHIRVERRRDP---MTGDYFENIGGMLFKDGFLYKTVSMKSIS-----AQNIQPTFDE-- 395 (1039)
Q Consensus 326 ~kkk~~RPp~rlFn~~e~~~~~~~v~~~r~~---~~g~~~~~~~~~~y~dGfL~K~~~i~~l~-----~~~V~PTleE-- 395 (1039)
++++..||+|++|.+..++..+.++-.+=+. -.+.+| -+|..|+ =|.++.+...-++ ++--+|.-+|
T Consensus 315 ~~p~~R~~~~~~~~~~~ir~~~~~~~~~Gd~l~~~gn~~~--~dGFLyK-~v~i~sI~t~gV~PT~dELekF~~~~e~~D 391 (1024)
T KOG1999|consen 315 FRPAPRRPNQKEFDEEAIRSEGRRDHSRGDYLEFEGNELF--KDGFLYK-DVSISSIITDGVKPTLDELEKFNPSNEEGD 391 (1024)
T ss_pred cCCcccCCCccccchhhhhhccccccccCceEEecCCcee--ccceeee-eeecceeeecCcccCHHHHHhhcCCCcccc
Confidence 3445559999999999999887765432111 112233 2444444 4788888777554 2233343331
Q ss_pred hhc-------------ccCCCCC--Ccchhhhh---------------------hHHh---hccccCccCCCCEEEEecc
Q 001639 396 LEK-------------FRTPGEN--GESDIASL---------------------STLF---ANRKKGHFMKGDAVIVIKG 436 (1039)
Q Consensus 396 L~~-------------F~~~~~~--~~~dl~~l---------------------s~~~---~~~~~~~F~~GD~V~V~~G 436 (1039)
|+. |+.+..- ...||.-| ...| +..++++|++||||+|+.|
T Consensus 392 l~~~st~~~~r~~~~~F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eLrKyF~~GDhVKVi~G 471 (1024)
T KOG1999|consen 392 LEWVSTLKSNRKKKHLFSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASELRKYFEPGDHVKVIAG 471 (1024)
T ss_pred ceeeeeeccccccccccCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCCCccccchHhhhhhccCCCeEEEEec
Confidence 111 5543210 01111111 1111 3456899999999999999
Q ss_pred cccCceeEEEEEcCCeEEEeecCCCCCcceeecccccee------------eccCCCceEEecccccCceEEEEEEeCcE
Q 001639 437 DLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK------------YFEPGNHVKVVSGTQAGATGMVLKVEQHV 504 (1039)
Q Consensus 437 el~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK------------~F~~GDhVkVi~G~~~GetGlVv~Ve~~~ 504 (1039)
.++|-+|+|++|+...|+|+++. .+++|+|.+++|++ .|+++|.|..-. . ..|+|++++.+.
T Consensus 472 ~~eG~tGlVvrVe~~~vi~~Sd~--t~eel~Vf~~dlq~c~ev~~gv~~~ge~e~hdlVqLd~---~-~vgvI~rle~e~ 545 (1024)
T KOG1999|consen 472 RYEGDTGLVVRVEQGDVILLSDL--TMEELKVFARDLQLCSEVTLGVEKSGEYELHDLVQLDN---Q-NVGVIVRLERET 545 (1024)
T ss_pred cccCCcceEEEEeCCeEEEEecC--ccceeeEEehhcccchheeecccccccccccceeecCC---C-cEEEEEEecchh
Confidence 99999999999999999999875 37789999999994 488999988753 3 899999999999
Q ss_pred EEEEeCCCCceEEEeccccccccccccc--ccc-CCceEeeeeEEe----cCCceEEEEEEccceeEEec-cCCCCCcEE
Q 001639 505 LIILSDTTKEDIRVFADDVVESSEVTTG--ITK-IGDYELRDLVLL----DNNSFGVIIRVESEAFQVLK-GVPDRPEVA 576 (1039)
Q Consensus 505 v~llSD~t~~ei~V~~~dL~~~~e~~~g--~~~-~g~y~l~DLVqL----d~~tVGvIvrverd~~~VL~-~~~~~g~v~ 576 (1039)
+.+|- +....++|....+..+.+.... ++. .+.....|+|.. ..+..|=|.+|-+-.+++-+ .+.+++-|.
T Consensus 546 ~~vl~-~~g~v~~i~~~~i~~kk~~r~~~~~D~~~n~I~~kD~Vkvi~Gp~~g~~G~v~~i~r~~~F~h~r~~~En~Gv~ 624 (1024)
T KOG1999|consen 546 FQVLG-MNGKVVTIRKSSITKKKDNRKAVAVDRNGNEIRVKDTVKVIGGPSKGREGEVLHIYRPFVFLHSRKNLENGGVF 624 (1024)
T ss_pred eeeec-CcCceEEEeechhhhhhhhhhheeecccCCeecccceEEEecCCCCCccCccceeecceeeeeehhhcccCCeE
Confidence 99985 5669999999998877665332 333 578899999987 23566999999999877766 345677788
Q ss_pred EEechhhhhc---ccC-------Ccccc------------cCC--------------CCeecCCCEEEEecCCCCCceec
Q 001639 577 LVKLREIKCK---LEK-------KSNVQ------------DRN--------------KNTVAVKDVVRIVEGPCKGKQGP 620 (1039)
Q Consensus 577 ~v~~~~I~~k---~~~-------~~~a~------------D~~--------------gn~I~~~D~Vkv~~Gp~kgr~G~ 620 (1039)
.|++..+.-. .++ -+.+. +.+ +..-..|.+|+|..||+||..|.
T Consensus 625 vck~k~~~~~g~~~st~~~~~~~~~l~~msP~r~~sp~~~~~~~ga~g~~gggrGg~rd~~l~GktVrI~~Gp~KG~~Gi 704 (1024)
T KOG1999|consen 625 VCKEKNLILAGGKKSTNSLAFNKGALAPMSPGRIQSPMGPSGGPGAFGGHGGGRGGNRDDSLLGKTVRIRLGPKKGYLGI 704 (1024)
T ss_pred EEecCCceeccccCcccchhhcccccCCCCcccccCCcCCCCCCCCcCcCccCccCcCcchhcCcEEEEecCCcccccce
Confidence 8876554211 100 00010 000 11245688999999999999999
Q ss_pred EEEEECCE--EEEEeCceeeeceEEEEeCCceEEecccCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 001639 621 VEHIYRGI--LFIHDRHHLEHAGFICAKSSSCVVVGGSRANGDRNGDAYSRFNSLRTPPRIPQSPGRYSRGGPPAGGRNR 698 (1039)
Q Consensus 621 V~hI~r~~--lFl~~~~~~EN~Gifv~~a~~~~~~g~~~~~~~~~~~~~~~~~~~~~p~~~~~sp~~~~~~~~~~gg~~~ 698 (1039)
|+.+--++ +-||+...+ + -+...++..++..+.++.. +..+.+ -| +- |+..
T Consensus 705 vkD~~~~~arVELhs~~~t----i-~vd~~~~~~v~~~~~~g~~-----~sYg~~--------~~--------~~-g~~~ 757 (1024)
T KOG1999|consen 705 VKDVNGDTARVELHSKCVT----I-KVDRLKRKIVGSTRDGGET-----SSYGER--------TP--------GY-GRVT 757 (1024)
T ss_pred eEeccCCeeEEEEEeccEE----E-EechhhceEEeeccCCCCc-----cccccc--------cc--------cc-cccC
Confidence 99999886 677765543 1 1344444444442111100 000000 00 00 0001
Q ss_pred CCCCCCccccCcEEEEeecCCCCceeEEEeecCCeEEEEecCCceEEEEecCccccccccccCCCCCCCCCCCCCCCCCC
Q 001639 699 GGRGGHDALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISDNVVVSTPYRDTPRYGMGSETPMHP 778 (1039)
Q Consensus 699 ~~~~~~d~liGktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~~~~~~~~py~~~p~y~~g~~tp~~~ 778 (1039)
+. |+ .++ ..||+| +|+||.|+
T Consensus 758 ~~------------------~~---------------------------------~~G------s~tp~~--~s~tpl~~ 778 (1024)
T KOG1999|consen 758 PA------------------RY---------------------------------GMG------SSTPMY--GSNTPLWG 778 (1024)
T ss_pred cc------------------cc---------------------------------CCC------CcCccC--CCCCCCCC
Confidence 10 11 111 246776 79999998
Q ss_pred -CCCCC-CCCCCCCCCCCCCCCCCCCC------CCCC-CCCCCCCCCCCCCCCC---CCCCCCCC-CCCC
Q 001639 779 -SRTPL-HPYMTPMRDAGATPIHDGMR------TPMR-DRAWNPYTPMSPPRDN---WEDGNPGS-WGTS 835 (1039)
Q Consensus 779 -~~TP~-~~~~TP~~~g~~TP~h~g~~------TP~~-~~aW~p~~p~tp~~~~---~~~~~p~~-~~~t 835 (1039)
++||+ |+++||.|||+|||++.++| ||++ .+.|.+..+..|.+.+ |.+++|++ |+++
T Consensus 779 ~s~tp~~~~~~Tp~~dG~rTP~r~~aW~~~~~~tPa~~~~~~~~g~~g~~g~sp~~~~~a~Tpg~~~~~~ 848 (1024)
T KOG1999|consen 779 GSRTPARDGGATPSHDGSRTPARGRAWNPYNGKTPARNFDNREPGFEGSGGRSPQGYYSAPTPGSNWGST 848 (1024)
T ss_pred cccCccccCCCCcCCCCCcCCCCCCCcCCCCCCCCccccCCcccCCCCCCCCCCCCCcCCCCCCCCCCcC
Confidence 99999 79999999999999766544 6766 3566776665554444 45666655 6654
No 4
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=99.88 E-value=6.1e-22 Score=200.66 Aligned_cols=130 Identities=26% Similarity=0.426 Sum_probs=118.9
Q ss_pred CCCcEEEEEccCchHHHHHHHHHHHHHhhCCCcceEEEEeecCCccEEEEEecchHHHHHHHhcCcccceeeeeeeChhh
Q 001639 180 RDPKLWMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIRE 259 (1039)
Q Consensus 180 ~Dp~lw~Vkc~~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~~~lkGYIYVEA~~~~~V~~ai~gl~~v~~~~~~lVpi~E 259 (1039)
+||+||.|+|++|+|+.|+.+|++|+.. .++.|++||++..++|||||||...++++++|++++++++.-..++|.+|
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 7899999999999999999999999765 35569999999999999999999999999999999999975445799999
Q ss_pred hhhccccccccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEEeecc
Q 001639 260 MTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLIPRI 311 (1039)
Q Consensus 260 m~~vL~~~k~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~VklvPRi 311 (1039)
|..+|...+....+++|+||||+.|+|+|+.|+|.+++..+..|+|+|+-|-
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=2.3e-22 Score=184.17 Aligned_cols=82 Identities=51% Similarity=0.835 Sum_probs=69.6
Q ss_pred cEEEEEccCchHHHHHHHHHHHHHhh--CCCcceEEEEeecCCccEEEEEecchHHHHHHHhcCcccceeeeeeeChhhh
Q 001639 183 KLWMVKCAIGREREAAVCLMQKCIDK--GSELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIREM 260 (1039)
Q Consensus 183 ~lw~Vkc~~G~Er~vv~~Lm~K~~~~--~~~l~I~Svf~~~~lkGYIYVEA~~~~~V~~ai~gl~~v~~~~~~lVpi~Em 260 (1039)
+||+|||++|+|+++|.+||+|+++. ...++|+|||+++++||||||||+++.+|.+||+|++++++..+.+||++||
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 001639 261 TDVL 264 (1039)
Q Consensus 261 ~~vL 264 (1039)
+++|
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
>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=1.4e-17 Score=167.29 Aligned_cols=125 Identities=26% Similarity=0.430 Sum_probs=110.7
Q ss_pred EEEEccCchHHHHHHHHHHHHHhhCCCcceEEEEeecCCccEEEEEecchHHHHHHHhcCcccceeeeeeeChhhhhhcc
Q 001639 185 WMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIREMTDVL 264 (1039)
Q Consensus 185 w~Vkc~~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~~~lkGYIYVEA~~~~~V~~ai~gl~~v~~~~~~lVpi~Em~~vL 264 (1039)
|+|+|++|+|+.++..|.+|+-. ..+.|+++|.+..++||||||+....+++.+|++++|+.+.-...||.+||..++
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 89999999999999888888633 5677999999999999999999999999999999999997544679999999999
Q ss_pred ccccccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEEeecc
Q 001639 265 AVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLIPRI 311 (1039)
Q Consensus 265 ~~~k~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~VklvPRi 311 (1039)
........+++|+||||++|||+|..|+|..++..+..|+|.|+-+-
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 7
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=99.74 E-value=1.9e-17 Score=185.15 Aligned_cols=352 Identities=25% Similarity=0.332 Sum_probs=247.4
Q ss_pred hhhhhcCCCCCCCcEEEEEccCchHHHHHHHHHHHHHhhCCCcceEEEEeecCCccEEEEEecchHHHH----HHHhcCc
Q 001639 170 VEQQALLPSVRDPKLWMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHVK----EACKGLR 245 (1039)
Q Consensus 170 v~q~~LlPsv~Dp~lw~Vkc~~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~~~lkGYIYVEA~~~~~V~----~ai~gl~ 245 (1039)
.+|.+|.|.-.-+..|+||.+.+.|+++.. +... ..++..|++.+.+ |++|-|+|+.+..|+. ++|+-++
T Consensus 28 ~~r~f~~~ne~~~dgflvk~~Ris~~et~~----~~pt-~de~~~F~~~~~d-ldl~s~~~s~kk~ha~fqpgD~~Evl~ 101 (607)
T COG5164 28 DDRHFTYKNEDYIDGFLVKVKRISERETLM----RIPT-NDEKNVFSIICKD-LDLYSYVESFKKQHAVFQPGDALEVLR 101 (607)
T ss_pred CchhccccCcccccceEEEEeeeceeeecc----cccc-cchhhhcCccccc-cchhHHHHHHhhcccccCCCCeeeeec
Confidence 367888888888999999999999997742 2222 2567778877766 9999999999999999 8888888
Q ss_pred ccceeeeeeeC-hhhhhhccccccccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEEeeccchhhhhhhccccc
Q 001639 246 NIYSQKVMLVP-IREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLIPRIDLQALANKLEGRE 324 (1039)
Q Consensus 246 ~v~~~~~~lVp-i~Em~~vL~~~k~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~VklvPRiD~~~~~~~~~~~~ 324 (1039)
+.-......|| .+||...|...- ..---+-|=||+.+.|+||+++|++ .+.++.+-+|||||-..
T Consensus 102 Geqrg~~gVV~~~~~~I~tm~~~~--~~rl~~p~~~lRk~f~~gD~vkVI~---g~~~~d~g~V~rI~~~~--------- 167 (607)
T COG5164 102 GEQRGRVGVVPRQKEMIETMTYHF--EQRLCGPWGRLRKGFYKGDLVKVIE---GGEMVDIGTVPRIDGEK--------- 167 (607)
T ss_pred ceecccceeecccccceeeeeecc--CceeecchhhhhcccccCCeEEEec---cccccccceEEEecCce---------
Confidence 88766777888 788877776541 1112478999999999999999975 47889999999998321
Q ss_pred cccCCCCCCCCCCCCHHHHHhccccEeeeccC---CCCceEEEeCCceeccceEEEEEeccceeccCCCCChHHhhcccC
Q 001639 325 VAKKKPFVPPPRFMNVDEARELHIRVERRRDP---MTGDYFENIGGMLFKDGFLYKTVSMKSISAQNIQPTFDELEKFRT 401 (1039)
Q Consensus 325 ~~kkk~~RPp~rlFn~~e~~~~~~~v~~~r~~---~~g~~~~~~~~~~y~dGfL~K~~~i~~l~~~~V~PTleEL~~F~~ 401 (1039)
.+|+++.... ..-|.++-.. ++.-.-.+|.-+.|.++||.|..-+.++. .+|-|++||+.+|..
T Consensus 168 -----------vtF~s~~~~~-e~tI~sr~l~ks~~tta~ss~Y~lhd~V~l~~~~vaci~sid-~Dv~kvide~g~v~t 234 (607)
T COG5164 168 -----------VTFNSENFKS-ESTIKSRGLSKSIDTTATSSIYKLHDYVDLFLEKVACINSID-FDVEKVIDELGEVHT 234 (607)
T ss_pred -----------eEEccccccc-cceEEeccccccccccchhhhhhhhhhhhhhhcceeEEeecc-cchhhhhhhcCceeE
Confidence 2455444321 1111111000 01111125677889999999988777776 579999999999964
Q ss_pred CCCCCcchhhhhhHHhhccccCccCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCC
Q 001639 402 PGENGESDIASLSTLFANRKKGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGN 481 (1039)
Q Consensus 402 ~~~~~~~dl~~ls~~~~~~~~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GD 481 (1039)
. ...++||+|.+.+|+|.++.|.+-+|......+... ....+.....|.|+|-.|-
T Consensus 235 ~--------------------~~~sI~~kv~~~Rg~~i~~d~ng~eI~igd~VvE~~----g~~~egq~l~i~~~f~f~~ 290 (607)
T COG5164 235 A--------------------CPISIGDKVRVTRGELIGMDGNGREISIGDAVVESR----GGKFEGQSLGIVKHFDFGE 290 (607)
T ss_pred e--------------------cchhhhhhhecccceeEeeccccceEeeceeEEEec----CCceeeEEEEEEEEEeeee
Confidence 2 346789999999999998888887776543333322 3457778889999999988
Q ss_pred ceEEecccccCceEEEEEEeCcEEEEEeCCCCceEEEeccccccccccccccccCCceEeeeeEEecCCceEEEEEEccc
Q 001639 482 HVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDNNSFGVIIRVESE 561 (1039)
Q Consensus 482 hVkVi~G~~~GetGlVv~Ve~~~v~llSD~t~~ei~V~~~dL~~~~e~~~g~~~~g~y~l~DLVqLd~~tVGvIvrverd 561 (1039)
.|++. ++.|++|+++.+.++|.+--.+.+++|- |=.+++ -|++.+
T Consensus 291 t~~i~-----ennGVfv~~~~nv~~VAtkd~~~s~k~d------------------------l~kmnp---~v~~~~--- 335 (607)
T COG5164 291 TVSIK-----ENNGVFVKIEGNVCIVATKDFTESLKVD------------------------LDKMNP---PVTVNL--- 335 (607)
T ss_pred eeeee-----ccCceEEEecCceeEEEeccchhhhccc------------------------HhhcCc---hhhcCC---
Confidence 88765 5899999999999998764333333321 111111 111111
Q ss_pred eeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCCCCceecEEEEECCE--EEEEeCce
Q 001639 562 AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRGI--LFIHDRHH 636 (1039)
Q Consensus 562 ~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~kgr~G~V~hI~r~~--lFl~~~~~ 636 (1039)
|+ +.+ ..+++++ -|....+|-+|+|.-|+|||.-|.||.+-++. +-||++..
T Consensus 336 ------~~---p~~-----~~l~r~i---------~gRd~aigktVrIr~g~yKG~lGVVKdv~~~~arVeLhs~nK 389 (607)
T COG5164 336 ------QN---PKT-----NELERKI---------VGRDPAIGKTVRIRCGEYKGHLGVVKDVDRNIARVELHSNNK 389 (607)
T ss_pred ------CC---Ccc-----hhhhccc---------cccccccCceEEEeecccccccceeeeccCceEEEEEecCCc
Confidence 21 211 2333343 34466789999999999999999999999996 67777653
No 8
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=99.60 E-value=2.8e-15 Score=155.38 Aligned_cols=127 Identities=19% Similarity=0.288 Sum_probs=109.3
Q ss_pred CCcEEEEEccCchHHHHHHHHHHHHHhhCCC-----------------cceEEEEeecCCccEEEEEecchHHHHHHHhc
Q 001639 181 DPKLWMVKCAIGREREAAVCLMQKCIDKGSE-----------------LQIRSVIALDHLKNYIYIEADKEAHVKEACKG 243 (1039)
Q Consensus 181 Dp~lw~Vkc~~G~Er~vv~~Lm~K~~~~~~~-----------------l~I~Svf~~~~lkGYIYVEA~~~~~V~~ai~g 243 (1039)
.++||+|+|.+|+|+.|+..|++|+...+-+ -+.+.+..++.++|||||||.....+|..|++
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 5899999999999999999999998775421 13566689999999999999999999999999
Q ss_pred Ccccce------eeeeeeChhhhhhcccc-------ccccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEE
Q 001639 244 LRNIYS------QKVMLVPIREMTDVLAV-------ESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 307 (1039)
Q Consensus 244 l~~v~~------~~~~lVpi~Em~~vL~~-------~k~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vkl 307 (1039)
+++|.+ .++.+++.+|+.+.|.. .+....+++|+.|||..|+|+|..|+|.+||.++.+++|.|
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 36788999999994432 22357899999999999999999999999999998888876
No 9
>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=99.34 E-value=3.7e-13 Score=126.75 Aligned_cols=88 Identities=44% Similarity=0.588 Sum_probs=60.8
Q ss_pred CcccccccCCcchhccccc-cCccccCCCCCCCC--CCCCCccCCCCCCC-CcchhhhHHHHHHHHH--HHhccCC---c
Q 001639 90 FFDLEAQVDSDEEEDEEEG-EDDFIVDGGAELPD--EDGGRGIHRRPLLP-REDEQEDVEALERRIQ--ARYARSS---H 160 (1039)
Q Consensus 90 FiD~EAEVDDdeEeeeee~-e~dfI~~~~~~l~~--~~~~r~~~r~~~~~-~~~~~~d~e~~~~~l~--eRY~~~~---~ 160 (1039)
|||+||+||||+||+|+++ +.++|......+.+ ...+.++||++++. +....+++++||++|+ +||++++ .
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 9999999999988776522 23344322222211 12334577877655 4566789999999999 9999864 2
Q ss_pred ccccccccchhhhhcCC
Q 001639 161 TEYDEETTDVEQQALLP 177 (1039)
Q Consensus 161 ~~~~~~~~~v~q~~LlP 177 (1039)
..+.+.++.|+||+|||
T Consensus 81 ~~~~~~~~~v~q~~LLP 97 (97)
T PF11942_consen 81 DGDDEDSDEVPQQLLLP 97 (97)
T ss_pred cccccccccchHhccCc
Confidence 34555778999999999
No 10
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=99.30 E-value=2.4e-11 Score=126.29 Aligned_cols=125 Identities=15% Similarity=0.231 Sum_probs=98.7
Q ss_pred CCcEEEEEccCchHHHHHHHHHHHHHhhCCCcc--eEEEEee-----------------cCCccEEEEEecchHHHHHHH
Q 001639 181 DPKLWMVKCAIGREREAAVCLMQKCIDKGSELQ--IRSVIAL-----------------DHLKNYIYIEADKEAHVKEAC 241 (1039)
Q Consensus 181 Dp~lw~Vkc~~G~Er~vv~~Lm~K~~~~~~~l~--I~Svf~~-----------------~~lkGYIYVEA~~~~~V~~ai 241 (1039)
..+||+++|++|+|+.++..|.+++...+ +. ++.+|.| +.++|||||++......+..|
T Consensus 5 ~~~WYvl~~~~~~E~~v~~~L~~~~~~~~--i~~~~~~~~~P~~~~~~~~~g~~~~~~~plfpgYvFv~~~~~~~~~~~i 82 (181)
T PRK05609 5 KKRWYVVQTYSGYEKKVKENLENRIETLG--MEDLIGEVLVPTEEVVEVKNGKKKKVERKFFPGYVLVKMVMTDESWHLV 82 (181)
T ss_pred CCeEEEEEeECCcHHHHHHHHHHHHHHCC--CcceeeEEEeeeEEEEEccCCEEEEEEEecCCcEEEEEEEeCccHhHHh
Confidence 46899999999999999999998864322 22 3344444 459999999999877889999
Q ss_pred hcCcccce------eeeeeeChhhhhhccccc-------cccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEE
Q 001639 242 KGLRNIYS------QKVMLVPIREMTDVLAVE-------SKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 307 (1039)
Q Consensus 242 ~gl~~v~~------~~~~lVpi~Em~~vL~~~-------k~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vkl 307 (1039)
+.++++.+ ..+.+||..||..++... .....+++|+.|||+.|||+|-.|.|..++..+.+|+|.|
T Consensus 83 ~~~~gv~~~v~~~g~~p~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l 161 (181)
T PRK05609 83 RNTPGVTGFVGSTGSKPTPLSEKEVEKILKQLQEGVEKPKPKVDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLV 161 (181)
T ss_pred hcCCCeEEEecCCCCCcccCCHHHHHHHHHHhhcccccCccccCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEE
Confidence 99998753 356789999999987621 1134688999999999999999999999997777766654
No 11
>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=9.4e-11 Score=121.02 Aligned_cols=124 Identities=17% Similarity=0.203 Sum_probs=95.9
Q ss_pred EEEEEccCchHHHHHHHHHHHHHhhCC---------Cc--------ceEEEEeecCCccEEEEEecchHHHHHHHhcCcc
Q 001639 184 LWMVKCAIGREREAAVCLMQKCIDKGS---------EL--------QIRSVIALDHLKNYIYIEADKEAHVKEACKGLRN 246 (1039)
Q Consensus 184 lw~Vkc~~G~Er~vv~~Lm~K~~~~~~---------~l--------~I~Svf~~~~lkGYIYVEA~~~~~V~~ai~gl~~ 246 (1039)
||+|+|++|+|+.++..|.+++...+- |+ +.........++|||||++......+..|+.+++
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 899999999999999999888533221 00 1122333467899999999877788999999988
Q ss_pred cce-----eeeeeeCh-hhhhhcccccc-------ccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEE
Q 001639 247 IYS-----QKVMLVPI-REMTDVLAVES-------KAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 307 (1039)
Q Consensus 247 v~~-----~~~~lVpi-~Em~~vL~~~k-------~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vkl 307 (1039)
|.+ ..+..||. +||..++.... ....+++|+.|||..|||+|..|.|..++..+.+|+|.|
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 873 36888999 99999875421 123488999999999999999999999997776776654
No 12
>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=99.21 E-value=8.8e-11 Score=126.95 Aligned_cols=125 Identities=17% Similarity=0.257 Sum_probs=98.4
Q ss_pred cEEEEEccCchHHHHHHHHHHHHHhhC--CC---cce----------------------------------------EEE
Q 001639 183 KLWMVKCAIGREREAAVCLMQKCIDKG--SE---LQI----------------------------------------RSV 217 (1039)
Q Consensus 183 ~lw~Vkc~~G~Er~vv~~Lm~K~~~~~--~~---l~I----------------------------------------~Sv 217 (1039)
+||.|+|.+|+|..|...|.+|+.+.+ .. +.| +.+
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 599999999999999999999987754 10 000 234
Q ss_pred EeecCCccEEEEEecchHHHHHHHhcCcccce---e-----eeeeeChhhh-hhcccccc--------------------
Q 001639 218 IALDHLKNYIYIEADKEAHVKEACKGLRNIYS---Q-----KVMLVPIREM-TDVLAVES-------------------- 268 (1039)
Q Consensus 218 f~~~~lkGYIYVEA~~~~~V~~ai~gl~~v~~---~-----~~~lVpi~Em-~~vL~~~k-------------------- 268 (1039)
..++.++|||||+|.+.+++|.+|+++++|.| + +|.+++.+|. .++|....
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 44567999999999999999999999999984 2 5778887777 56654211
Q ss_pred -----------------------------------------ccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEE
Q 001639 269 -----------------------------------------KAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 307 (1039)
Q Consensus 269 -----------------------------------------~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vkl 307 (1039)
....+.+|+.|||..|+|+|..|+|.+++..+.+|+|.|
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 123578999999999999999999999997777766654
No 13
>PF12815 CTD: Spt5 C-terminal nonapeptide repeat binding Spt4; PDB: 2E70_A.
Probab=99.01 E-value=4.9e-11 Score=116.62 Aligned_cols=56 Identities=43% Similarity=0.627 Sum_probs=0.0
Q ss_pred CCCCCCC--CCCCCCC---CCCCCCC---CCCCCCCC-CCCCCC-CCCCCCCCCCCCCCCCCCCCCCC
Q 001639 764 DTPRYGM--GSETPMH---PSRTPLH---PYMTPMRD-AGATPI-HDGMRTPMRDRAWNPYTPMSPPR 821 (1039)
Q Consensus 764 ~~p~y~~--g~~tp~~---~~~TP~~---~~~TP~~~-g~~TP~-h~g~~TP~~~~aW~p~~p~tp~~ 821 (1039)
|||+|+. |++||+| ++|||++ ++.||.+. +++||+ |+|+|||+....|++ ..||..
T Consensus 3 rTPa~~~~~g~rTPa~~~~gsrTP~~~~~g~rTPa~~~gsrTP~~~~gsrTPa~~~~~~~--~~TPa~ 68 (123)
T PF12815_consen 3 RTPAYGSASGSRTPAWGNDGSRTPAPGADGSRTPAWGSGSRTPAFHDGSRTPAYGGSSSP--SRTPAY 68 (123)
T ss_dssp --------------------------------------------------------------------
T ss_pred CCCcCcCCCCCCCcccccCCCCCcCCcCCCCcCcccccCCcCcccCCCCCCCccCCCCCC--CCCccC
Confidence 6899987 8999999 7999997 68899997 679999 999999976555543 445543
No 14
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=98.86 E-value=4.9e-09 Score=107.44 Aligned_cols=123 Identities=15% Similarity=0.221 Sum_probs=90.6
Q ss_pred cEEEEEccCchHHHHHHHHHHHHHhhCCCc--------ceEEEEeecCCccEEEEEecchHHHHHHHhcCcccc-----e
Q 001639 183 KLWMVKCAIGREREAAVCLMQKCIDKGSEL--------QIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIY-----S 249 (1039)
Q Consensus 183 ~lw~Vkc~~G~Er~vv~~Lm~K~~~~~~~l--------~I~Svf~~~~lkGYIYVEA~~~~~V~~ai~gl~~v~-----~ 249 (1039)
+||+++|++|+|+.++..|.++-+..=-|+ +-........++|||||.+..+...+..|+.++++. +
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 122234457899999999987666666677777764 2
Q ss_pred eeeeeeChhhhhhcccccc----ccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEE
Q 001639 250 QKVMLVPIREMTDVLAVES----KAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 306 (1039)
Q Consensus 250 ~~~~lVpi~Em~~vL~~~k----~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vk 306 (1039)
..+.+||-.||..++.... ....+++|+.|||+.|||+|-.|.|..++ .+.++.|.
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 5688899889998875422 12347899999999999999999999998 55565543
No 15
>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=98.85 E-value=5e-09 Score=99.31 Aligned_cols=83 Identities=29% Similarity=0.389 Sum_probs=69.5
Q ss_pred cEEEEEccCchHHHHHHHHHHHHHhhCCCcceEEEEee-----------------cCCccEEEEEecchHHHHHHHhcCc
Q 001639 183 KLWMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIAL-----------------DHLKNYIYIEADKEAHVKEACKGLR 245 (1039)
Q Consensus 183 ~lw~Vkc~~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~-----------------~~lkGYIYVEA~~~~~V~~ai~gl~ 245 (1039)
+||+|+|++|+|+.++..|.+++.+.+-+..++++|+| ..++|||||++....+++.+|++++
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 59999999999999999999998665433346677777 3355999999999999999999999
Q ss_pred ccce-----eeeeeeChhhhhhccc
Q 001639 246 NIYS-----QKVMLVPIREMTDVLA 265 (1039)
Q Consensus 246 ~v~~-----~~~~lVpi~Em~~vL~ 265 (1039)
++++ .++.+||.+||..+++
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 16
>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=98.78 E-value=1.2e-08 Score=104.02 Aligned_cols=122 Identities=18% Similarity=0.241 Sum_probs=88.5
Q ss_pred EEEEEccCchHHHHHHHHHHHHHhhCCCc--------ceEEEEeecCCccEEEEEecchHHHHHHHhcCcccc-----ee
Q 001639 184 LWMVKCAIGREREAAVCLMQKCIDKGSEL--------QIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIY-----SQ 250 (1039)
Q Consensus 184 lw~Vkc~~G~Er~vv~~Lm~K~~~~~~~l--------~I~Svf~~~~lkGYIYVEA~~~~~V~~ai~gl~~v~-----~~ 250 (1039)
||+|+|++|+|+.++..|.++-+..=-|+ .-........++|||||.+....+.+..|..++++. +.
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 112335557899999999987666666666666665 24
Q ss_pred eeeeeChhhhhhcccccc------ccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEE
Q 001639 251 KVMLVPIREMTDVLAVES------KAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 306 (1039)
Q Consensus 251 ~~~lVpi~Em~~vL~~~k------~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vk 306 (1039)
.+.+||-.||..++.... ....+++|+.|||+.|||+|-.|.|..++. +.+|.|.
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 688899988887764321 123588999999999999999999999984 4466554
No 17
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=98.49 E-value=3.6e-06 Score=104.18 Aligned_cols=12 Identities=8% Similarity=0.282 Sum_probs=5.4
Q ss_pred ccccCcEEEEee
Q 001639 705 DALVGTTVKVRL 716 (1039)
Q Consensus 705 d~liGktV~I~~ 716 (1039)
+-++||+..+-.
T Consensus 1400 nImlgqlap~gT 1411 (1605)
T KOG0260|consen 1400 NIMLGQLAPMGT 1411 (1605)
T ss_pred eeeecccccCCC
Confidence 334555544433
No 18
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=98.38 E-value=1.2e-05 Score=99.85 Aligned_cols=16 Identities=6% Similarity=0.090 Sum_probs=8.4
Q ss_pred ecCCceEEEEecCccc
Q 001639 738 LESQMKVVTVDRSMIS 753 (1039)
Q Consensus 738 Lhs~~k~I~V~r~~l~ 753 (1039)
.-|.|+-|-.+-+.|.
T Consensus 1409 ~gTg~~d~~ld~e~l~ 1424 (1605)
T KOG0260|consen 1409 MGTGCFDLMLDAEKLK 1424 (1605)
T ss_pred CCCcceeeeccHHhhh
Confidence 3455555555555554
No 19
>PF12815 CTD: Spt5 C-terminal nonapeptide repeat binding Spt4; PDB: 2E70_A.
Probab=98.22 E-value=2.4e-07 Score=90.94 Aligned_cols=44 Identities=43% Similarity=0.577 Sum_probs=0.0
Q ss_pred CCCCC-CCCCCCCCC---CCCCCCC--CCCCCC-CCCCCCCCCCC----CCCCCC
Q 001639 764 DTPRY-GMGSETPMH---PSRTPLH--PYMTPM-RDAGATPIHDG----MRTPMR 807 (1039)
Q Consensus 764 ~~p~y-~~g~~tp~~---~~~TP~~--~~~TP~-~~g~~TP~h~g----~~TP~~ 807 (1039)
+||+| ..|++||++ ++|||.+ ++.||+ ++|++||+|.+ ++||+.
T Consensus 14 rTPa~~~~gsrTP~~~~~g~rTPa~~~gsrTP~~~~gsrTPa~~~~~~~~~TPa~ 68 (123)
T PF12815_consen 14 RTPAWGNDGSRTPAPGADGSRTPAWGSGSRTPAFHDGSRTPAYGGSSSPSRTPAY 68 (123)
T ss_dssp -------------------------------------------------------
T ss_pred CCcccccCCCCCcCCcCCCCcCcccccCCcCcccCCCCCCCccCCCCCCCCCccC
Confidence 68888 558899987 6899987 788998 78889999865 478843
No 20
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=97.96 E-value=3.2e-06 Score=102.11 Aligned_cols=21 Identities=43% Similarity=0.724 Sum_probs=11.6
Q ss_pred CCCCCCCccccccccchhhhh
Q 001639 2 PRRRDDDDDEMDAEEDEYDEQ 22 (1039)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~ 22 (1039)
.|+++-+||+|+|||+|+|++
T Consensus 1398 GR~r~~~dd~DeeeD~e~Ed~ 1418 (1516)
T KOG1832|consen 1398 GRRRPTDDDSDEEEDDETEDE 1418 (1516)
T ss_pred cccCCCccccCccccchhhcc
Confidence 466665555555555554443
No 21
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=97.86 E-value=4.6e-07 Score=97.48 Aligned_cols=55 Identities=27% Similarity=0.452 Sum_probs=49.2
Q ss_pred cCCCc-ccEEEEEEeCCCCeEEEEeccCCCCceEEecCCCeeecCCCCCCcEEEEcCCCCCceE
Q 001639 943 RSGEE-SVVGVIREVLPDGSCRVVLGSSGNGDTITALPNEIEIVPPRKTDKIKIMGGPHRGATG 1005 (1039)
Q Consensus 943 ~~g~~-~~~GvV~~V~~~g~~~V~l~~~~~g~~v~v~~~~Le~V~P~kgd~VkVi~G~~rG~tG 1005 (1039)
.+|.+ +++|||+.|+++++..|+ +++ |.+|++||.|||||||+ +||||+|||..+
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 45666 999999999999999999 555 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=97.41 E-value=0.00021 Score=54.18 Aligned_cols=32 Identities=34% Similarity=0.612 Sum_probs=30.0
Q ss_pred CCcEEEEecCCCCCCeeEEEEeeCCCCEEEEE
Q 001639 275 RDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 306 (1039)
Q Consensus 275 ~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vk 306 (1039)
+|++|+|++|+|+|..|+|.+++.++.+|+|+
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=97.20 E-value=0.00017 Score=91.33 Aligned_cols=12 Identities=25% Similarity=0.266 Sum_probs=9.8
Q ss_pred HHHHHHHHHHhc
Q 001639 145 EALERRIQARYA 156 (1039)
Q Consensus 145 e~~~~~l~eRY~ 156 (1039)
+.||+.|++|-.
T Consensus 739 ~~La~~Fk~r~~ 750 (784)
T PF04931_consen 739 EQLAAIFKERKE 750 (784)
T ss_pred HHHHHHHHHHHh
Confidence 578999999965
No 24
>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=96.79 E-value=0.0041 Score=57.68 Aligned_cols=65 Identities=12% Similarity=0.329 Sum_probs=46.1
Q ss_pred cEEEEEccCchHHHHHHHHHHHHHhh--C------C-C-c--ceEEEEeecCCccEEEEEecchHHHHHHHhcCcccce
Q 001639 183 KLWMVKCAIGREREAAVCLMQKCIDK--G------S-E-L--QIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYS 249 (1039)
Q Consensus 183 ~lw~Vkc~~G~Er~vv~~Lm~K~~~~--~------~-~-l--~I~Svf~~~~lkGYIYVEA~~~~~V~~ai~gl~~v~~ 249 (1039)
+||+|+|++|+|+.++..|.+.-+.. . . . - .+.. .....++|||||.+...+.++.+ +.+.++++
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 69999999999999999985554431 0 1 0 1 2333 56678999999999998555444 88888774
No 25
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=96.73 E-value=0.00081 Score=77.75 Aligned_cols=11 Identities=27% Similarity=0.456 Sum_probs=5.1
Q ss_pred HHHHHHHHHHH
Q 001639 194 EREAAVCLMQK 204 (1039)
Q Consensus 194 Er~vv~~Lm~K 204 (1039)
|-.-+.||..|
T Consensus 207 E~AY~Scle~R 217 (458)
T PF10446_consen 207 EAAYISCLEAR 217 (458)
T ss_pred HHHHHHHHHHH
Confidence 44444455544
No 26
>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=96.72 E-value=0.0014 Score=49.74 Aligned_cols=31 Identities=48% Similarity=0.830 Sum_probs=27.6
Q ss_pred cCcEEEEeecCCCCceeEEEeecCCeEEEEe
Q 001639 708 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVEL 738 (1039)
Q Consensus 708 iGktV~I~~GpyKG~~G~Vkd~t~~~arVEL 738 (1039)
.|.+|+|+.|||||..|.|+++.....+|.+
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 3789999999999999999999988877655
No 27
>KOG4315 consensus G-patch nucleic acid binding protein [General function prediction only]
Probab=96.67 E-value=0.00056 Score=78.16 Aligned_cols=103 Identities=21% Similarity=0.368 Sum_probs=83.0
Q ss_pred CcccCcEEE--E----cCCCc-ccEEEEEEeCCCCeEEEEeccCCCCceE-EecCCCeeecCCC-CCCcEEEEcCCCCCc
Q 001639 933 PWFMPDILV--R----RSGEE-SVVGVIREVLPDGSCRVVLGSSGNGDTI-TALPNEIEIVPPR-KTDKIKIMGGPHRGA 1003 (1039)
Q Consensus 933 ~W~~~~I~V--~----~~g~~-~~~GvV~~V~~~g~~~V~l~~~~~g~~v-~v~~~~Le~V~P~-kgd~VkVi~G~~rG~ 1003 (1039)
.|+..+|.| + +.|.. .++.+|..|.+--+|.+.+.+.. +.+- .|+|+-|||++|. -|++|.|+.|.+.|.
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 78999999966568999987653 2233 3899999999996 677799999999999
Q ss_pred eEEEEEEeCC--CcEEEecCCCceEEEeccccccc
Q 001639 1004 TGKLIGVDGT--DGIVKVDVSLDVKILDMAILAKL 1036 (1039)
Q Consensus 1004 tG~LisiD~~--dgiVk~d~~~~~kil~~~~L~Kl 1036 (1039)
.|.|++=|-. .++|++-.+.++..+-+..+|-.
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 89999877777777777777754
No 28
>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=96.50 E-value=0.00061 Score=86.34 Aligned_cols=9 Identities=22% Similarity=0.604 Sum_probs=3.5
Q ss_pred HHHHHHHHh
Q 001639 147 LERRIQARY 155 (1039)
Q Consensus 147 ~~~~l~eRY 155 (1039)
|-++|.+=+
T Consensus 737 lD~~La~~F 745 (784)
T PF04931_consen 737 LDEQLAAIF 745 (784)
T ss_pred HHHHHHHHH
Confidence 333343333
No 29
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=95.92 E-value=0.0092 Score=54.33 Aligned_cols=33 Identities=27% Similarity=0.460 Sum_probs=28.7
Q ss_pred eecCCCEEEEecCCCCCceecEEEEECC--EEEEE
Q 001639 600 TVAVKDVVRIVEGPCKGKQGPVEHIYRG--ILFIH 632 (1039)
Q Consensus 600 ~I~~~D~Vkv~~Gp~kgr~G~V~hI~r~--~lFl~ 632 (1039)
.|+.||.|.|+.|+.||++|+|+.|++. .+++.
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 5899999999999999999999999854 45553
No 30
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=95.68 E-value=0.016 Score=41.96 Aligned_cols=28 Identities=46% Similarity=0.564 Sum_probs=25.6
Q ss_pred ccCCCCEEEEecccccCceeEEEEEcCC
Q 001639 424 HFMKGDAVIVIKGDLKNLKGWVEKVDEE 451 (1039)
Q Consensus 424 ~F~~GD~V~V~~Gel~gl~G~V~~V~~d 451 (1039)
.|++||.|+|+.|.+.|..|.|++++.+
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~~ 28 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcCC
Confidence 4889999999999999999999999753
No 31
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=95.62 E-value=0.013 Score=42.28 Aligned_cols=27 Identities=41% Similarity=0.712 Sum_probs=24.9
Q ss_pred eccCCCceEEecccccCceEEEEEEeC
Q 001639 476 YFEPGNHVKVVSGTQAGATGMVLKVEQ 502 (1039)
Q Consensus 476 ~F~~GDhVkVi~G~~~GetGlVv~Ve~ 502 (1039)
.|++||.|+|++|.|+|.+|.|++++.
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 32
>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=94.95 E-value=0.038 Score=55.90 Aligned_cols=58 Identities=24% Similarity=0.341 Sum_probs=44.3
Q ss_pred ccCCCCEEEEecccccCceeEEEEEcCCe--EEEeecCCCCCcceeeccccceeeccCCC
Q 001639 424 HFMKGDAVIVIKGDLKNLKGWVEKVDEEN--VHIRPEMKGLPKTLAVNSKELCKYFEPGN 481 (1039)
Q Consensus 424 ~F~~GD~V~V~~Gel~gl~G~V~~V~~d~--V~i~~~~~~l~~~i~v~~~~LrK~F~~GD 481 (1039)
.|++||.|+|++|=++|+.|.|++++++. |+|.-......-+++++.++|+|.=+.||
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 49999999999999999999999998764 33333222333349999999988665554
No 33
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=94.34 E-value=0.051 Score=50.34 Aligned_cols=28 Identities=39% Similarity=0.595 Sum_probs=26.5
Q ss_pred eecCCCEEEEecCCCCCceecEEEEECC
Q 001639 600 TVAVKDVVRIVEGPCKGKQGPVEHIYRG 627 (1039)
Q Consensus 600 ~I~~~D~Vkv~~Gp~kgr~G~V~hI~r~ 627 (1039)
.|+.||.|.|+.|+.||++|+|++|++.
T Consensus 8 ~I~~GD~V~Vi~G~dKGK~G~V~~V~~~ 35 (83)
T CHL00141 8 HVKIGDTVKIISGSDKGKIGEVLKIIKK 35 (83)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 5899999999999999999999999875
No 34
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=94.25 E-value=0.062 Score=51.93 Aligned_cols=32 Identities=25% Similarity=0.431 Sum_probs=28.3
Q ss_pred eecCCCEEEEecCCCCCceecEEEEECC--EEEE
Q 001639 600 TVAVKDVVRIVEGPCKGKQGPVEHIYRG--ILFI 631 (1039)
Q Consensus 600 ~I~~~D~Vkv~~Gp~kgr~G~V~hI~r~--~lFl 631 (1039)
.|+.||+|.|+.|++||++|+|+.|++. .+++
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~V 37 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIV 37 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEE
Confidence 5899999999999999999999999954 4555
No 35
>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=93.88 E-value=0.041 Score=70.47 Aligned_cols=9 Identities=22% Similarity=0.176 Sum_probs=3.6
Q ss_pred HHHHHHHHH
Q 001639 144 VEALERRIQ 152 (1039)
Q Consensus 144 ~e~~~~~l~ 152 (1039)
-+++.+.|.
T Consensus 428 ~eel~~lL~ 436 (840)
T PF04147_consen 428 HEELLELLD 436 (840)
T ss_pred HHHHHHHHh
Confidence 344444433
No 36
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=93.52 E-value=0.14 Score=65.47 Aligned_cols=84 Identities=14% Similarity=0.236 Sum_probs=45.3
Q ss_pred cEEEEEc--cCchHHHHHHHHHHHHHhhC---CCcceEEEEeecC-----CccEEEEEecchHHHHHHHh--cCccccee
Q 001639 183 KLWMVKC--AIGREREAAVCLMQKCIDKG---SELQIRSVIALDH-----LKNYIYIEADKEAHVKEACK--GLRNIYSQ 250 (1039)
Q Consensus 183 ~lw~Vkc--~~G~Er~vv~~Lm~K~~~~~---~~l~I~Svf~~~~-----lkGYIYVEA~~~~~V~~ai~--gl~~v~~~ 250 (1039)
+|..|+. -.++|+..+.+|..++...- .--.|.-++..+. -+-++--|.-+-.+.|+... .+.++|.+
T Consensus 1441 ~wcev~~~lp~~~~k~~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~~~k~~~~l~TeGVnl~a~~~~~d~LDv~~lySN 1520 (1640)
T KOG0262|consen 1441 KWCEVELKLPLDKEKLDMSSIVESIAPKSVIHQVPGIERCVVSEPQDDVKEKSVLLTEGVNLPALFDHADILDVNRLYSN 1520 (1640)
T ss_pred cEEEEEEEecCCCcchHHHHHHHHHhcceeeeccCCceeeeccCCcccccccceehhcCccHHHHHHHHhhhhhhhhccc
Confidence 4444554 35788888888888865431 1123433433321 11255555555566665433 66667765
Q ss_pred eeeee------------Chhhhhhcccc
Q 001639 251 KVMLV------------PIREMTDVLAV 266 (1039)
Q Consensus 251 ~~~lV------------pi~Em~~vL~~ 266 (1039)
.+..| =++||.+||.+
T Consensus 1521 DI~ail~tyGVEAar~~Iv~Ev~~VF~v 1548 (1640)
T KOG0262|consen 1521 DIHAILNTYGVEAARNAIVNEVNNVFKV 1548 (1640)
T ss_pred hHHHHHHHhhHHHHHHHHHHHHHHhhhh
Confidence 43222 25677777765
No 37
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=93.32 E-value=0.15 Score=47.39 Aligned_cols=39 Identities=23% Similarity=0.336 Sum_probs=35.4
Q ss_pred cccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEEe
Q 001639 270 AIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLI 308 (1039)
Q Consensus 270 ~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vklv 308 (1039)
...|.+||-|.|.+|+|||-.|.|..|+..+++|+|+=+
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegv 44 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGI 44 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCc
Confidence 457999999999999999999999999999999988643
No 38
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=93.10 E-value=0.16 Score=53.62 Aligned_cols=62 Identities=27% Similarity=0.402 Sum_probs=46.9
Q ss_pred cCccCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCceEEecccccCceEEEEEEe
Q 001639 422 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLKVE 501 (1039)
Q Consensus 422 ~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi~G~~~GetGlVv~Ve 501 (1039)
.++|..||.|+|+.|.-+|-+|.|+.|.-+.-.|..+ +|+- |-+-+.+.-+|+-|.||+.|
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 5899999999999999999999999997654333322 3321 11345667889999999998
Q ss_pred C
Q 001639 502 Q 502 (1039)
Q Consensus 502 ~ 502 (1039)
.
T Consensus 131 a 131 (236)
T KOG1708|consen 131 A 131 (236)
T ss_pred C
Confidence 5
No 39
>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=93.03 E-value=0.09 Score=67.45 Aligned_cols=10 Identities=30% Similarity=0.541 Sum_probs=4.3
Q ss_pred HHHHHHHHhc
Q 001639 147 LERRIQARYA 156 (1039)
Q Consensus 147 ~~~~l~eRY~ 156 (1039)
|.+.|+.-|.
T Consensus 446 iI~RIrk~~h 455 (840)
T PF04147_consen 446 IIQRIRKCYH 455 (840)
T ss_pred HHHHHHHhCC
Confidence 3444444443
No 40
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=92.91 E-value=0.2 Score=49.48 Aligned_cols=40 Identities=30% Similarity=0.511 Sum_probs=36.1
Q ss_pred cccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEEee
Q 001639 270 AIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLIP 309 (1039)
Q Consensus 270 ~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~VklvP 309 (1039)
...|+.||.|.|.+|+|||-.|+|..|+...++|+|+=|=
T Consensus 43 ~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn 82 (120)
T PRK01191 43 SLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVT 82 (120)
T ss_pred cceEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcE
Confidence 3578999999999999999999999999999999987543
No 41
>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=92.83 E-value=0.17 Score=52.56 Aligned_cols=53 Identities=25% Similarity=0.347 Sum_probs=41.4
Q ss_pred CccCCCCEEEEecccccCceeEEEEEcC-C-eEEEeecCCCCCcceeecccccee
Q 001639 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDE-E-NVHIRPEMKGLPKTLAVNSKELCK 475 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~-d-~V~i~~~~~~l~~~i~v~~~~LrK 475 (1039)
..|++||.|+|++|-++|+.|.|++++. . .++|..+.=+....+++...+|+|
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 4599999999999999999999999983 3 677776643334457777777754
No 42
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=92.81 E-value=0.2 Score=52.86 Aligned_cols=56 Identities=30% Similarity=0.478 Sum_probs=45.2
Q ss_pred ccCccCCCCEEEEecccccCceeEEEEEcCC--eEEEeecCCCCCcceeeccccceee
Q 001639 421 KKGHFMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCKY 476 (1039)
Q Consensus 421 ~~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d--~V~i~~~~~~l~~~i~v~~~~LrK~ 476 (1039)
....|.+||.|+|+.|-++|..|+|..|+.+ .++++...-+..-++++..++++|.
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 3478999999999999999999999999998 5666655544455788877777763
No 43
>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=92.74 E-value=0.15 Score=49.21 Aligned_cols=32 Identities=25% Similarity=0.486 Sum_probs=28.0
Q ss_pred eecCCCEEEEecCCCCCceecEEEEECC--EEEE
Q 001639 600 TVAVKDVVRIVEGPCKGKQGPVEHIYRG--ILFI 631 (1039)
Q Consensus 600 ~I~~~D~Vkv~~Gp~kgr~G~V~hI~r~--~lFl 631 (1039)
-|+.||.|.|+.|+.||++|+|+.|++. .+++
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 4889999999999999999999999864 4554
No 44
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=92.74 E-value=0.16 Score=52.19 Aligned_cols=52 Identities=19% Similarity=0.256 Sum_probs=41.1
Q ss_pred ccCCCCEEEEecccccCceeEEEEEcCC-eEEEeecCCCCCcceeecccccee
Q 001639 424 HFMKGDAVIVIKGDLKNLKGWVEKVDEE-NVHIRPEMKGLPKTLAVNSKELCK 475 (1039)
Q Consensus 424 ~F~~GD~V~V~~Gel~gl~G~V~~V~~d-~V~i~~~~~~l~~~i~v~~~~LrK 475 (1039)
.|++||+|+|++|-++|+.|.|..+++. .+.|..+.=+..-+++++..+|.|
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 455555432334568888888765
No 45
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=92.45 E-value=0.18 Score=49.71 Aligned_cols=33 Identities=24% Similarity=0.483 Sum_probs=29.3
Q ss_pred eecCCCEEEEecCCCCCceecEEEEECC--EEEEE
Q 001639 600 TVAVKDVVRIVEGPCKGKQGPVEHIYRG--ILFIH 632 (1039)
Q Consensus 600 ~I~~~D~Vkv~~Gp~kgr~G~V~hI~r~--~lFl~ 632 (1039)
.|+.||.|+|+.|++||++|+|+.|.+. .+++.
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 46
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=92.12 E-value=0.25 Score=45.16 Aligned_cols=38 Identities=26% Similarity=0.408 Sum_probs=34.7
Q ss_pred ccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEEe
Q 001639 271 IDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLI 308 (1039)
Q Consensus 271 ~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vklv 308 (1039)
..|+.||-|.|.+|++||-.|.|..|+..+++|+|+=|
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegv 42 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGV 42 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCc
Confidence 36889999999999999999999999999999998743
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=92.07 E-value=0.061 Score=66.76 Aligned_cols=18 Identities=17% Similarity=0.521 Sum_probs=7.8
Q ss_pred cEEEEEecchHHHHHHHh
Q 001639 225 NYIYIEADKEAHVKEACK 242 (1039)
Q Consensus 225 GYIYVEA~~~~~V~~ai~ 242 (1039)
-|.|+...-+..+...+.
T Consensus 356 ~y~~Md~~~K~~L~~~l~ 373 (622)
T PF02724_consen 356 KYSYMDMELKRELREKLE 373 (622)
T ss_pred CchhCCHHHHHHHHHHHH
Confidence 444544444444444443
No 48
>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=91.83 E-value=0.15 Score=63.44 Aligned_cols=31 Identities=16% Similarity=0.174 Sum_probs=16.6
Q ss_pred hHHHHHHHhcCcccce-eeeeeeChhhhhhcc
Q 001639 234 EAHVKEACKGLRNIYS-QKVMLVPIREMTDVL 264 (1039)
Q Consensus 234 ~~~V~~ai~gl~~v~~-~~~~lVpi~Em~~vL 264 (1039)
.+.+|-||=|+...|. .++..--...+...|
T Consensus 235 ~d~LW~AIvGlT~q~i~~~i~~~~Y~~~~~~L 266 (622)
T PF02724_consen 235 NDLLWLAIVGLTDQYIHERISSERYDRYVPLL 266 (622)
T ss_pred hHHHHHHHHhhhHHhhhcccchhhHHHHHHHH
Confidence 3567777777777663 344333333333333
No 49
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=91.82 E-value=0.28 Score=51.18 Aligned_cols=53 Identities=25% Similarity=0.376 Sum_probs=41.4
Q ss_pred CccCCCCEEEEecccccCceeEEEEEcC-C-eEEEeecCCCCCcceeecccccee
Q 001639 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDE-E-NVHIRPEMKGLPKTLAVNSKELCK 475 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~-d-~V~i~~~~~~l~~~i~v~~~~LrK 475 (1039)
..|++||.|+|++|-++|+.|.|++++. . .++|....=+-.-.+++...+|.|
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 50
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=91.36 E-value=0.14 Score=63.12 Aligned_cols=12 Identities=8% Similarity=0.163 Sum_probs=6.9
Q ss_pred hHHHHHHHHHHH
Q 001639 143 DVEALERRIQAR 154 (1039)
Q Consensus 143 d~e~~~~~l~eR 154 (1039)
++|+.+..|.+.
T Consensus 968 saeey~hllD~d 979 (988)
T KOG2038|consen 968 SAEEYAHLLDQD 979 (988)
T ss_pred hHHHHHHHhhcc
Confidence 556666666543
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=91.04 E-value=0.34 Score=47.59 Aligned_cols=34 Identities=38% Similarity=0.507 Sum_probs=31.1
Q ss_pred CCCCcEEEEcCCCCCceEEEEEEeCCCcEEEecC
Q 001639 988 RKTDKIKIMGGPHRGATGKLIGVDGTDGIVKVDV 1021 (1039)
Q Consensus 988 ~kgd~VkVi~G~~rG~tG~LisiD~~dgiVk~d~ 1021 (1039)
.+||.|+||.|.+.|.+|+++.|+..++.|-+++
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
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=90.62 E-value=0.48 Score=48.69 Aligned_cols=52 Identities=27% Similarity=0.374 Sum_probs=38.6
Q ss_pred CccCCCCEEEEecccccCceeEEEEEcCCe--EEEeecCCCCCcceeeccccce
Q 001639 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEEN--VHIRPEMKGLPKTLAVNSKELC 474 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~--V~i~~~~~~l~~~i~v~~~~Lr 474 (1039)
..|++||.|+|++|-++|..|+|++++.+. ++|..-.....-+++++.++|+
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~~ 146 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQVR 146 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEEE
Confidence 469999999999999999999999998774 3333222222234888888874
No 53
>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=90.45 E-value=0.41 Score=48.89 Aligned_cols=51 Identities=20% Similarity=0.234 Sum_probs=37.9
Q ss_pred CccCCCCEEEEecccccCceeEEEEEcCC-eEEEeecCCCCCcceeeccccc
Q 001639 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEE-NVHIRPEMKGLPKTLAVNSKEL 473 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d-~V~i~~~~~~l~~~i~v~~~~L 473 (1039)
..|++||.|+|++|-++|+.|.|+.+++. .+.|..+.=+..-.++++.++|
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 4666655322223466655544
No 54
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=90.05 E-value=0.36 Score=49.02 Aligned_cols=33 Identities=36% Similarity=0.602 Sum_probs=28.9
Q ss_pred eecCCCEEEEecCCCCCceecEEEEECCE--EEEE
Q 001639 600 TVAVKDVVRIVEGPCKGKQGPVEHIYRGI--LFIH 632 (1039)
Q Consensus 600 ~I~~~D~Vkv~~Gp~kgr~G~V~hI~r~~--lFl~ 632 (1039)
.|+.||+|+|+.|.++|++|.|+.|++.. ++|.
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 69999999999999999999999998663 5553
No 55
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=90.01 E-value=0.49 Score=45.82 Aligned_cols=37 Identities=24% Similarity=0.303 Sum_probs=34.2
Q ss_pred cCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEEe
Q 001639 272 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLI 308 (1039)
Q Consensus 272 ~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vklv 308 (1039)
.|.+||.|.|.+|++||-.|.|..|+..+++|.|+=|
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegv 40 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGV 40 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCc
Confidence 6889999999999999999999999999999998643
No 56
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=89.88 E-value=0.18 Score=66.05 Aligned_cols=19 Identities=26% Similarity=0.595 Sum_probs=10.3
Q ss_pred cCCCCCCCcEEEEEccCch
Q 001639 175 LLPSVRDPKLWMVKCAIGR 193 (1039)
Q Consensus 175 LlPsv~Dp~lw~Vkc~~G~ 193 (1039)
|-|-|..++-|-+=|-.|+
T Consensus 366 lppv~~~~~~~y~icdn~k 384 (2849)
T PTZ00415 366 LPPVLHEAKKFYFICDNGK 384 (2849)
T ss_pred cCCeeeccceEEEEeCCCc
Confidence 3444555555555565554
No 57
>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=89.60 E-value=0.54 Score=52.11 Aligned_cols=52 Identities=25% Similarity=0.448 Sum_probs=41.1
Q ss_pred CccCCCCEEEEecccccCceeEEEEEcC--CeEEEeecCCCCCcceeeccccce
Q 001639 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDE--ENVHIRPEMKGLPKTLAVNSKELC 474 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~--d~V~i~~~~~~l~~~i~v~~~~Lr 474 (1039)
..|.+||.|+|++|-+.|+.|.|..++. ..+.|+...-+...+++++..+|.
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 467777665333446777766664
No 58
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=89.55 E-value=0.47 Score=45.78 Aligned_cols=33 Identities=27% Similarity=0.443 Sum_probs=28.6
Q ss_pred CeecCCCEEEEecCCCCCceecEEEEECCEEEE
Q 001639 599 NTVAVKDVVRIVEGPCKGKQGPVEHIYRGILFI 631 (1039)
Q Consensus 599 n~I~~~D~Vkv~~Gp~kgr~G~V~hI~r~~lFl 631 (1039)
.-|+.||+|+|+.|..||++|.|+-++.-.+++
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 358999999999999999999999998766443
No 59
>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=89.43 E-value=0.7 Score=45.43 Aligned_cols=48 Identities=29% Similarity=0.448 Sum_probs=38.4
Q ss_pred hhhhccccccccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEEe
Q 001639 259 EMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLI 308 (1039)
Q Consensus 259 Em~~vL~~~k~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vklv 308 (1039)
|+...+.. ....|+.||-|+|.+|.|||-.|.|..|+..++.|+|+=|
T Consensus 30 elr~~y~~--r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegv 77 (114)
T TIGR01080 30 ELREKYGK--RALPVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGV 77 (114)
T ss_pred HHHHHcCc--ccceeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCe
Confidence 44444432 2347899999999999999999999999998988887644
No 60
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=89.22 E-value=0.71 Score=46.93 Aligned_cols=51 Identities=24% Similarity=0.276 Sum_probs=42.0
Q ss_pred hhhhccccccccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEEeecc
Q 001639 259 EMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLIPRI 311 (1039)
Q Consensus 259 Em~~vL~~~k~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~VklvPRi 311 (1039)
|+..-..+. ...|+.||-|.|.+|.|||-.|+|+.|+...++|+|+=|.+.
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 347899999999999999999999999999999999877665
No 61
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=88.95 E-value=0.26 Score=62.62 Aligned_cols=14 Identities=21% Similarity=0.233 Sum_probs=9.9
Q ss_pred CcEEEEEccCchHH
Q 001639 182 PKLWMVKCAIGRER 195 (1039)
Q Consensus 182 p~lw~Vkc~~G~Er 195 (1039)
|.+|+++.....-|
T Consensus 1880 p~imAsiaaqsaaR 1893 (3015)
T KOG0943|consen 1880 PMIMASIAAQSAAR 1893 (3015)
T ss_pred hhHHHHHhhHHHHH
Confidence 88999988654433
No 62
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=87.45 E-value=4 Score=43.61 Aligned_cols=45 Identities=20% Similarity=0.324 Sum_probs=36.3
Q ss_pred cCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCceEEe
Q 001639 439 KNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVV 486 (1039)
Q Consensus 439 ~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi 486 (1039)
.-..|+|+.|..+.+.|.++ ...+++.+- -+....+++||.||+.
T Consensus 40 ~tiEGrVvEV~~~~i~iesk--~yn~~v~i~-~d~~~nvKVGD~VKaT 84 (213)
T PRK06763 40 STIEGRVVEVDNGVIVIKSK--QYEEPVSVY-IDSLSNVKVGDEVKAT 84 (213)
T ss_pred ceeeeEEEEEeCCEEEEEec--cCCCceEEE-ecCCCCcccCcEEEEc
Confidence 45689999999999999887 356677774 5566778999999998
No 63
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=87.29 E-value=0.8 Score=44.25 Aligned_cols=33 Identities=39% Similarity=0.378 Sum_probs=28.9
Q ss_pred CccCCCCEEEEecccccCceeEEEEEcCCeEEE
Q 001639 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHI 455 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i 455 (1039)
..++.||.|.|+.|..+|-.|+|++|....|+|
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 64
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=87.06 E-value=0.28 Score=62.39 Aligned_cols=11 Identities=9% Similarity=0.247 Sum_probs=5.7
Q ss_pred EEEEEeCcEEE
Q 001639 496 MVLKVEQHVLI 506 (1039)
Q Consensus 496 lVv~Ve~~~v~ 506 (1039)
+=|+++++.+.
T Consensus 2286 fE~rn~g~~La 2296 (3015)
T KOG0943|consen 2286 FEVRNDGNCLA 2296 (3015)
T ss_pred EEEecCCceee
Confidence 55555555443
No 65
>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=86.68 E-value=1 Score=43.56 Aligned_cols=36 Identities=25% Similarity=0.294 Sum_probs=33.3
Q ss_pred cCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEE
Q 001639 272 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 307 (1039)
Q Consensus 272 ~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vkl 307 (1039)
.|+.||-|.|.+|++||-.|.|..|+..+++|.|+=
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg 38 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEG 38 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECC
Confidence 478999999999999999999999999999998863
No 66
>PHA03378 EBNA-3B; Provisional
Probab=86.25 E-value=14 Score=45.75 Aligned_cols=10 Identities=30% Similarity=0.501 Sum_probs=4.5
Q ss_pred CeeecCCCCC
Q 001639 981 EIEIVPPRKT 990 (1039)
Q Consensus 981 ~Le~V~P~kg 990 (1039)
|-+-+.|+|.
T Consensus 915 ~~~~i~p~kr 924 (991)
T PHA03378 915 HPTDIPPSKR 924 (991)
T ss_pred ChhhCCCchh
Confidence 4444445443
No 67
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=85.66 E-value=0.41 Score=60.74 Aligned_cols=17 Identities=24% Similarity=0.446 Sum_probs=6.4
Q ss_pred cchhhhhccCccchhhh
Q 001639 16 EDEYDEQVMDDEIDEEE 32 (1039)
Q Consensus 16 ~~~~~~~~~~~~~~eed 32 (1039)
++++|+-.++|+|.+++
T Consensus 897 ~~~~e~~~~d~dD~d~~ 913 (1010)
T KOG1991|consen 897 DDEEEDFIDDEDDIDED 913 (1010)
T ss_pred CcchhhccCcccccccc
Confidence 33333333333333333
No 68
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=85.24 E-value=0.46 Score=62.67 Aligned_cols=17 Identities=24% Similarity=0.419 Sum_probs=11.6
Q ss_pred CCCcEEEEEccCchHHH
Q 001639 180 RDPKLWMVKCAIGRERE 196 (1039)
Q Consensus 180 ~Dp~lw~Vkc~~G~Er~ 196 (1039)
+-|=+-.++.+.|.|..
T Consensus 312 kapyv~l~~~~~~~~e~ 328 (2849)
T PTZ00415 312 KAPYVTLTKANEGSEEK 328 (2849)
T ss_pred CCceEEEEccCCcchhh
Confidence 44777888887776443
No 69
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=84.07 E-value=24 Score=46.01 Aligned_cols=20 Identities=30% Similarity=0.579 Sum_probs=8.3
Q ss_pred eeeeceEEEEeCCceEEecc
Q 001639 636 HLEHAGFICAKSSSCVVVGG 655 (1039)
Q Consensus 636 ~~EN~Gifv~~a~~~~~~g~ 655 (1039)
.++|+|-+-..+.-|-+..|
T Consensus 596 rl~~~g~~~~~a~lcYi~ag 615 (1049)
T KOG0307|consen 596 RLENAGDLTSAAILCYICAG 615 (1049)
T ss_pred HHhhccchhhhhhHHhhhcc
Confidence 34555543333333433333
No 70
>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=83.93 E-value=0.1 Score=62.38 Aligned_cols=13 Identities=23% Similarity=0.570 Sum_probs=10.8
Q ss_pred CCcccccccCCcc
Q 001639 89 EFFDLEAQVDSDE 101 (1039)
Q Consensus 89 ~FiD~EAEVDDde 101 (1039)
.+|++||+|.-+|
T Consensus 1052 k~~eDEAevSGsD 1064 (1329)
T KOG4156|consen 1052 KYLEDEAEVSGSD 1064 (1329)
T ss_pred HhhcchhhcccCc
Confidence 6999999997555
No 71
>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=83.17 E-value=0.98 Score=56.14 Aligned_cols=17 Identities=18% Similarity=0.458 Sum_probs=9.7
Q ss_pred CCcccccCCCC-CCcccc
Q 001639 78 RKPKAKRRSGS-EFFDLE 94 (1039)
Q Consensus 78 r~kkr~~~~~~-~FiD~E 94 (1039)
..++.++..++ .||+++
T Consensus 175 ~~~~~d~~glnD~FFsid 192 (600)
T PF04006_consen 175 EEKKEDKSGLNDGFFSID 192 (600)
T ss_pred ccccccCCCcCCCcCCHH
Confidence 33444555555 688773
No 72
>PF14632 SPT6_acidic: Acidic N-terminal SPT6
Probab=82.02 E-value=0.44 Score=45.08 Aligned_cols=8 Identities=50% Similarity=0.576 Sum_probs=4.8
Q ss_pred ccccccCc
Q 001639 45 RSQFIDDV 52 (1039)
Q Consensus 45 ~~~~~~d~ 52 (1039)
..-||-|+
T Consensus 20 ~eGFIvDd 27 (92)
T PF14632_consen 20 REGFIVDD 27 (92)
T ss_pred hcCCccCC
Confidence 34577665
No 73
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=81.03 E-value=0.64 Score=57.29 Aligned_cols=16 Identities=13% Similarity=0.204 Sum_probs=10.3
Q ss_pred hhHHHHHHHHHHHhcc
Q 001639 142 EDVEALERRIQARYAR 157 (1039)
Q Consensus 142 ~d~e~~~~~l~eRY~~ 157 (1039)
.....|+.-|.+=|..
T Consensus 333 aNi~~I~~~i~~Ly~~ 348 (822)
T KOG2141|consen 333 ANIIKIIAGIAELYMN 348 (822)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 3455666777777763
No 74
>KOG2773 consensus Apoptosis antagonizing transcription factor/protein transport protein [Transcription; Intracellular trafficking, secretion, and vesicular transport]
Probab=80.47 E-value=0.78 Score=53.98 Aligned_cols=12 Identities=25% Similarity=0.044 Sum_probs=7.6
Q ss_pred CCCcccccccCC
Q 001639 88 SEFFDLEAQVDS 99 (1039)
Q Consensus 88 ~~FiD~EAEVDD 99 (1039)
..+.|.||++.+
T Consensus 126 e~~~deEes~~s 137 (483)
T KOG2773|consen 126 EDKSDEEESDRS 137 (483)
T ss_pred ccccchhhcccc
Confidence 356667776666
No 75
>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=79.52 E-value=0.8 Score=46.01 Aligned_cols=65 Identities=25% Similarity=0.375 Sum_probs=33.6
Q ss_pred CCCCcccccccCCc----chhccc-c---ccCccccCCCCCCCCCCCCCccCCCCCCCCcchhhhHHHHHHHHHHHhccC
Q 001639 87 GSEFFDLEAQVDSD----EEEDEE-E---GEDDFIVDGGAELPDEDGGRGIHRRPLLPREDEQEDVEALERRIQARYARS 158 (1039)
Q Consensus 87 ~~~FiD~EAEVDDd----eEeeee-e---~e~dfI~~~~~~l~~~~~~r~~~r~~~~~~~~~~~d~e~~~~~l~eRY~~~ 158 (1039)
.+.|+.+||++++| +|.|+. + +..+||++.... .+..++.|...+ +.++-++....||+||..+
T Consensus 14 ~~gw~~vEAec~dd~~s~de~E~~~d~~sd~~dfIDd~~~~------~qgnslaLf~~Q--~~~~d~~~v~~LKRK~~~S 85 (130)
T PF00524_consen 14 CGGWFIVEAECSDDDISEDEDEDLFDSGSDISDFIDDSEVS------EQGNSLALFNQQ--EAEDDERAVQALKRKYLGS 85 (130)
T ss_pred cCcEEEEEEEEcCCCCCCCcccccccCCccccccccCCCcc------cccHHHHHHHHH--HHHHHHHHHHHHHHHHcCC
Confidence 34566669999982 221111 1 124788754321 222344432222 2233345556999999865
Q ss_pred C
Q 001639 159 S 159 (1039)
Q Consensus 159 ~ 159 (1039)
.
T Consensus 86 P 86 (130)
T PF00524_consen 86 P 86 (130)
T ss_pred c
Confidence 3
No 76
>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=79.33 E-value=3.9 Score=35.51 Aligned_cols=45 Identities=22% Similarity=0.338 Sum_probs=34.4
Q ss_pred ceeEEEEEcCCeEEEeecCCCCCcceeecc-ccceeeccCCCceEEec
Q 001639 441 LKGWVEKVDEENVHIRPEMKGLPKTLAVNS-KELCKYFEPGNHVKVVS 487 (1039)
Q Consensus 441 l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~-~~LrK~F~~GDhVkVi~ 487 (1039)
-+|.|++|.++.|.|| +.+.. ++++++. .+++-.+++|+.|.++.
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 4689999999999999 55433 4666665 35556699999999875
No 77
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=79.04 E-value=1.2 Score=57.44 Aligned_cols=34 Identities=9% Similarity=0.170 Sum_probs=21.2
Q ss_pred cCccCC--CC--------EEEEecccccC---ceeEEEEEcCCeEEE
Q 001639 422 KGHFMK--GD--------AVIVIKGDLKN---LKGWVEKVDEENVHI 455 (1039)
Q Consensus 422 ~~~F~~--GD--------~V~V~~Gel~g---l~G~V~~V~~d~V~i 455 (1039)
...|.| ++ .|..|.|.-.+ +.++.++.+|+.|-.
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 456777 55 66676665433 566677777776643
No 78
>KOG2773 consensus Apoptosis antagonizing transcription factor/protein transport protein [Transcription; Intracellular trafficking, secretion, and vesicular transport]
Probab=77.21 E-value=1.3 Score=52.25 Aligned_cols=15 Identities=20% Similarity=0.308 Sum_probs=8.6
Q ss_pred CCCCCCCcEEEEEccCch
Q 001639 176 LPSVRDPKLWMVKCAIGR 193 (1039)
Q Consensus 176 lPsv~Dp~lw~Vkc~~G~ 193 (1039)
||+ |-+|..-|-.+.
T Consensus 214 LP~---~ev~~lf~sd~~ 228 (483)
T KOG2773|consen 214 LPQ---PEVLSLFKSDDE 228 (483)
T ss_pred CCC---hhhHHHhhcccc
Confidence 555 356666665554
No 79
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=75.49 E-value=6.3 Score=44.27 Aligned_cols=26 Identities=27% Similarity=0.489 Sum_probs=24.0
Q ss_pred ccCCCceEEecccccCceEEEEEEeC
Q 001639 477 FEPGNHVKVVSGTQAGATGMVLKVEQ 502 (1039)
Q Consensus 477 F~~GDhVkVi~G~~~GetGlVv~Ve~ 502 (1039)
|++|..|-|++|+|.|.+|.|+.++.
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 80
>PRK04313 30S ribosomal protein S4e; Validated
Probab=73.18 E-value=8.1 Score=42.69 Aligned_cols=41 Identities=27% Similarity=0.512 Sum_probs=31.2
Q ss_pred ccCCCceEEecccccCceEEEEEEeCc-----EEEEEeCCCCceEE
Q 001639 477 FEPGNHVKVVSGTQAGATGMVLKVEQH-----VLIILSDTTKEDIR 517 (1039)
Q Consensus 477 F~~GDhVkVi~G~~~GetGlVv~Ve~~-----~v~llSD~t~~ei~ 517 (1039)
|++|..|-|++|+|.|++|.|+.++.. ..+.+.|...+++.
T Consensus 172 fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~ 217 (237)
T PRK04313 172 FEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFE 217 (237)
T ss_pred cCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEE
Confidence 789999999999999999999999632 23444565555554
No 81
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=73.16 E-value=92 Score=40.80 Aligned_cols=56 Identities=16% Similarity=0.214 Sum_probs=34.3
Q ss_pred CccCCCCEEEEecccccCceeEEEEEcCCe--EEEeecCCCC-CcceeeccccceeeccCCCceEEecccccCceEEEEE
Q 001639 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEEN--VHIRPEMKGL-PKTLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLK 499 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~--V~i~~~~~~l-~~~i~v~~~~LrK~F~~GDhVkVi~G~~~GetGlVv~ 499 (1039)
..|++||.|+| +|+.|+.+. +.+..+ .+ .+ |...+.+.|++|+-| +|.|++
T Consensus 709 ~~~kvGq~Vkv----------kVl~ID~e~rrI~LS~K--~l~~d----pw~~~~~~~~vG~iV----------~GkV~~ 762 (863)
T PRK12269 709 HELEVGKEIEC----------MVIECDPQARRIRLGVK--QLSDN----PWQVFANAYGVGSTV----------EGEVSS 762 (863)
T ss_pred hccCCCCEEEE----------EEEEEeccCCEEEEEec--ccccC----hHHHHHhhCCCCCEE----------EEEEEE
Confidence 46999999997 588888653 444332 22 12 233345567889866 355666
Q ss_pred EeCcE
Q 001639 500 VEQHV 504 (1039)
Q Consensus 500 Ve~~~ 504 (1039)
|.+.-
T Consensus 763 v~~~G 767 (863)
T PRK12269 763 VTDFG 767 (863)
T ss_pred EecCe
Confidence 65544
No 82
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=73.00 E-value=1 Score=57.63 Aligned_cols=6 Identities=33% Similarity=0.523 Sum_probs=2.5
Q ss_pred ccccCC
Q 001639 94 EAQVDS 99 (1039)
Q Consensus 94 EAEVDD 99 (1039)
-++||+
T Consensus 965 ~~~v~~ 970 (1128)
T KOG2051|consen 965 TPDVDQ 970 (1128)
T ss_pred CCChhh
Confidence 334443
No 83
>KOG2418 consensus Microtubule-associated protein TAU [Cytoskeleton]
Probab=72.60 E-value=13 Score=42.87 Aligned_cols=12 Identities=42% Similarity=0.628 Sum_probs=5.9
Q ss_pred eEEEeccccccc
Q 001639 1025 VKILDMAILAKL 1036 (1039)
Q Consensus 1025 ~kil~~~~L~Kl 1036 (1039)
|-+|+-..||-|
T Consensus 424 idll~spqlatl 435 (448)
T KOG2418|consen 424 IDLLDSPQLATL 435 (448)
T ss_pred cccccCcccchh
Confidence 445555555444
No 84
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=71.89 E-value=3.9 Score=43.66 Aligned_cols=29 Identities=34% Similarity=0.469 Sum_probs=26.2
Q ss_pred eeccCCCceEEecccccCceEEEEEEeCc
Q 001639 475 KYFEPGNHVKVVSGTQAGATGMVLKVEQH 503 (1039)
Q Consensus 475 K~F~~GDhVkVi~G~~~GetGlVv~Ve~~ 503 (1039)
=+|..||.|+|+.|+-+|.-|.|++|-.+
T Consensus 71 w~ff~GDtVeVlvGkDkGkqG~Vtqv~r~ 99 (236)
T KOG1708|consen 71 WHFFFGDTVEVLVGKDKGKQGEVTQVIRH 99 (236)
T ss_pred eeEecCCEEEEEecccCCccceEEEEeec
Confidence 37889999999999999999999999654
No 85
>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=71.62 E-value=13 Score=31.49 Aligned_cols=44 Identities=36% Similarity=0.442 Sum_probs=34.6
Q ss_pred CcEEEEeec--CCCCceeEEEeecCCeEEEEecCCc--eEEEEecCcc
Q 001639 709 GTTVKVRLG--PYKGYRGRVVDVKGQSVRVELESQM--KVVTVDRSMI 752 (1039)
Q Consensus 709 GktV~I~~G--pyKG~~G~Vkd~t~~~arVELhs~~--k~I~V~r~~l 752 (1039)
|-+|++..- +|-||.|.|..+++..|-|...-.| |.||..-+.|
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 667887754 6999999999999999999999888 8888876655
No 86
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=70.87 E-value=8.8 Score=42.06 Aligned_cols=34 Identities=26% Similarity=0.566 Sum_probs=27.4
Q ss_pred eccccceee--ccCCCceEEecccccCceEEEEEEe
Q 001639 468 VNSKELCKY--FEPGNHVKVVSGTQAGATGMVLKVE 501 (1039)
Q Consensus 468 v~~~~LrK~--F~~GDhVkVi~G~~~GetGlVv~Ve 501 (1039)
+|.+++..+ |++|-.|-|++|+|.|++|.|+.|+
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 6899999999999999999999986
No 87
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=70.26 E-value=2.5 Score=53.59 Aligned_cols=10 Identities=50% Similarity=0.963 Sum_probs=5.2
Q ss_pred hcCCCCCCCcEE
Q 001639 174 ALLPSVRDPKLW 185 (1039)
Q Consensus 174 ~LlPsv~Dp~lw 185 (1039)
.|-|+ |+-+|
T Consensus 201 HL~p~--d~e~W 210 (895)
T KOG2076|consen 201 HLNPK--DYELW 210 (895)
T ss_pred hcCCC--ChHHH
Confidence 44553 45666
No 88
>COG2933 Predicted SAM-dependent methyltransferase [General function prediction only]
Probab=70.12 E-value=5.6 Score=44.40 Aligned_cols=58 Identities=19% Similarity=0.261 Sum_probs=48.3
Q ss_pred EEEccCchHHHHHHHHHHHHHhhCCCcceEEEEeecCCccEEEEEecchHHHHHHHhcCccc
Q 001639 186 MVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNI 247 (1039)
Q Consensus 186 ~Vkc~~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~~~lkGYIYVEA~~~~~V~~ai~gl~~v 247 (1039)
+.-|++|.|++++.-|-.|+.. |.|+.-.-...-.|||..|.+..+++...++.|+.-
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 5679999999999999988754 567764444566899999999999999999998763
No 89
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=70.05 E-value=11 Score=42.18 Aligned_cols=25 Identities=36% Similarity=0.651 Sum_probs=23.2
Q ss_pred ccCCCceEEecccccCceEEEEEEe
Q 001639 477 FEPGNHVKVVSGTQAGATGMVLKVE 501 (1039)
Q Consensus 477 F~~GDhVkVi~G~~~GetGlVv~Ve 501 (1039)
|++|..|-|++|+|.|.+|.|+.++
T Consensus 175 fe~G~l~~vtgG~n~GriG~I~~~~ 199 (262)
T PTZ00118 175 FEVGNLVMITGGHNVGRVGTIVSKE 199 (262)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEE
Confidence 7899999999999999999998865
No 90
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=69.75 E-value=2.4 Score=50.97 Aligned_cols=24 Identities=8% Similarity=0.212 Sum_probs=17.3
Q ss_pred cCCccEEEEEecchHHHHHHHhcC
Q 001639 221 DHLKNYIYIEADKEAHVKEACKGL 244 (1039)
Q Consensus 221 ~~lkGYIYVEA~~~~~V~~ai~gl 244 (1039)
.+-+|--||--..+.+...+|.+.
T Consensus 331 ~~skGtAFv~Fkt~~~~~~ci~~A 354 (678)
T KOG0127|consen 331 GHSKGTAFVKFKTQIAAQNCIEAA 354 (678)
T ss_pred CCcccceEEEeccHHHHHHHHHhc
Confidence 456777777777777777777665
No 91
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=68.89 E-value=85 Score=41.35 Aligned_cols=7 Identities=43% Similarity=0.601 Sum_probs=2.8
Q ss_pred EEEeecc
Q 001639 305 VKLIPRI 311 (1039)
Q Consensus 305 VklvPRi 311 (1039)
|+.=||.
T Consensus 302 v~w~pr~ 308 (1049)
T KOG0307|consen 302 VQWCPRN 308 (1049)
T ss_pred eeecCCC
Confidence 3344443
No 92
>KOG3118 consensus Disrupter of silencing SAS10 [Chromatin structure and dynamics]
Probab=68.58 E-value=1.9 Score=51.14 Aligned_cols=6 Identities=17% Similarity=-0.119 Sum_probs=2.3
Q ss_pred Cccccc
Q 001639 90 FFDLEA 95 (1039)
Q Consensus 90 FiD~EA 95 (1039)
|-|+++
T Consensus 129 ~dddd~ 134 (517)
T KOG3118|consen 129 VDDDDL 134 (517)
T ss_pred ccchhh
Confidence 333333
No 93
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=67.44 E-value=13 Score=36.43 Aligned_cols=52 Identities=12% Similarity=0.133 Sum_probs=37.9
Q ss_pred CccCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCC
Q 001639 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGN 481 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GD 481 (1039)
..+++||.|.-+ -|+.|+|++|+++.|+|.... +-.++|.-+.+.+...+.+
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 457899999999988887531 2346666666665555444
No 94
>PLN00036 40S ribosomal protein S4; Provisional
Probab=67.42 E-value=17 Score=40.76 Aligned_cols=25 Identities=36% Similarity=0.618 Sum_probs=23.7
Q ss_pred ccCCCceEEecccccCceEEEEEEe
Q 001639 477 FEPGNHVKVVSGTQAGATGMVLKVE 501 (1039)
Q Consensus 477 F~~GDhVkVi~G~~~GetGlVv~Ve 501 (1039)
|++|..|-|++|+|.|.+|.|+.++
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 95
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=67.41 E-value=14 Score=31.69 Aligned_cols=54 Identities=24% Similarity=0.147 Sum_probs=38.9
Q ss_pred ccCCCCEEEEeccc-ccCceeEEEEEcC-CeEEEeecCCCCCcceeeccccceeec
Q 001639 424 HFMKGDAVIVIKGD-LKNLKGWVEKVDE-ENVHIRPEMKGLPKTLAVNSKELCKYF 477 (1039)
Q Consensus 424 ~F~~GD~V~V~~Ge-l~gl~G~V~~V~~-d~V~i~~~~~~l~~~i~v~~~~LrK~F 477 (1039)
.|++||.|+|..=+ -.=-.|+|+++.+ +...|.-.........+|+.++||-+.
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 69999999999633 2236799999998 555555444224567888999988654
No 96
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=64.90 E-value=92 Score=40.25 Aligned_cols=16 Identities=38% Similarity=0.771 Sum_probs=7.0
Q ss_pred CCCCCCCCCCCCCCCC
Q 001639 847 AYEAPTPGSGWASTPG 862 (1039)
Q Consensus 847 ~y~~~TPg~~~~~tP~ 862 (1039)
.|.+++||.+.+++||
T Consensus 196 ~~~~p~p~~p~p~~pg 211 (1007)
T KOG1984|consen 196 QMQPPPPGAPRPSGPG 211 (1007)
T ss_pred CCCCCCCCCCCCCCCC
Confidence 3444445544434444
No 97
>PRK14635 hypothetical protein; Provisional
Probab=63.62 E-value=9.2 Score=39.86 Aligned_cols=49 Identities=22% Similarity=0.251 Sum_probs=38.4
Q ss_pred ccccCcEEEEee-----cCCCCceeEEEeecCCeEEEEecCC------ceEEEEecCccc
Q 001639 705 DALVGTTVKVRL-----GPYKGYRGRVVDVKGQSVRVELESQ------MKVVTVDRSMIS 753 (1039)
Q Consensus 705 d~liGktV~I~~-----GpyKG~~G~Vkd~t~~~arVELhs~------~k~I~V~r~~l~ 753 (1039)
..++|+.|+|+- ..|+|++|++++++++.+++++..+ .++++++.+.|.
T Consensus 95 ~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~~v~l~~~~k~~~~~~~~~~~ip~~~I~ 154 (162)
T PRK14635 95 DRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGDQVELEKFQKGKKSKVKKQTTLNLKDIL 154 (162)
T ss_pred HHhCCCEEEEEEecCCCcEEEecceEEEEEcCCEEEEEEecccccccCCeEEEEEhHHee
Confidence 568899988862 2567888899999999999988543 667888877765
No 98
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=63.08 E-value=14 Score=36.03 Aligned_cols=49 Identities=22% Similarity=0.308 Sum_probs=35.4
Q ss_pred cCccCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeec
Q 001639 422 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYF 477 (1039)
Q Consensus 422 ~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F 477 (1039)
...+++||.|.-+ -|+.|+|++|++++|+|.... +-.++|.-+.+....
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 4689999999998 467899999999988887532 134666555554443
No 99
>PRK14639 hypothetical protein; Provisional
Probab=62.20 E-value=15 Score=37.42 Aligned_cols=49 Identities=18% Similarity=0.329 Sum_probs=40.6
Q ss_pred ccccCcEEEEeecCCCCceeEEEeecCCeEEEEecCCceEEEEecCccc
Q 001639 705 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 753 (1039)
Q Consensus 705 d~liGktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~ 753 (1039)
..++|+.|+|+-..-|-+.|++++++++.+++++-.+.++++++.+.|.
T Consensus 84 ~r~~G~~v~v~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I~ 132 (140)
T PRK14639 84 AKSIGELVKITTNEKEKFEGKIVSVDDENITLENLENKEKTTINFNDIK 132 (140)
T ss_pred HHhCCCEEEEEECCCcEEEEEEEEEeCCEEEEEEccCCcEEEEEhHHee
Confidence 5789999999875568899999999999999987545567888887765
No 100
>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=61.59 E-value=43 Score=31.65 Aligned_cols=75 Identities=12% Similarity=0.273 Sum_probs=53.9
Q ss_pred EEEEc--cCchHHHHHHHHHHHHHhhC------CCcc-eEEEEeecCCccEEEEEecchHHHHHHHhcCcccceeeeeee
Q 001639 185 WMVKC--AIGREREAAVCLMQKCIDKG------SELQ-IRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLV 255 (1039)
Q Consensus 185 w~Vkc--~~G~Er~vv~~Lm~K~~~~~------~~l~-I~Svf~~~~lkGYIYVEA~~~~~V~~ai~gl~~v~~~~~~lV 255 (1039)
|+|.+ +++....-....+.++++.+ ..+. |-..+.+.+..||+.+||++...+.+.+.--+.++|.....+
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 34555544456677777765 2233 555677889999999999999999999999999987766666
Q ss_pred Chhh
Q 001639 256 PIRE 259 (1039)
Q Consensus 256 pi~E 259 (1039)
|+=+
T Consensus 82 Pv~~ 85 (91)
T PF11746_consen 82 PVMT 85 (91)
T ss_pred eccc
Confidence 6543
No 101
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=61.07 E-value=14 Score=36.18 Aligned_cols=41 Identities=22% Similarity=0.336 Sum_probs=32.6
Q ss_pred CcEEEEeecCCCCceeEEEeecCCeEEEEecCCceEEEEecCcccc
Q 001639 709 GTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1039)
Q Consensus 709 GktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~~ 754 (1039)
|..| |+.| |+.|+|+++++.++.||+. .+-.|++.|..|+-
T Consensus 42 GD~V-vT~g---Gi~G~V~~I~d~~v~leia-~gv~i~~~r~AI~~ 82 (109)
T PRK05886 42 GDRV-HTTS---GLQATIVGITDDTVDLEIA-PGVVTTWMKLAVRD 82 (109)
T ss_pred CCEE-EECC---CeEEEEEEEeCCEEEEEEC-CCeEEEEEhhheee
Confidence 4455 4444 7999999999999999995 45669999999873
No 102
>PRK04333 50S ribosomal protein L14e; Validated
Probab=60.96 E-value=15 Score=34.44 Aligned_cols=33 Identities=18% Similarity=0.195 Sum_probs=27.9
Q ss_pred cCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEE
Q 001639 272 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTV 305 (1039)
Q Consensus 272 ~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~V 305 (1039)
.+++|..|.+..|.|+|-+|.|+++.. .++|.|
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 355555
No 103
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=60.91 E-value=13 Score=35.81 Aligned_cols=53 Identities=25% Similarity=0.409 Sum_probs=38.1
Q ss_pred CccCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCc
Q 001639 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNH 482 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDh 482 (1039)
..+++||.|.-+ -|+.|+|++|.++.++|.... +-.++|.-+.+......|+.
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 23566655555544444443
No 104
>CHL00010 infA translation initiation factor 1
Probab=60.62 E-value=47 Score=30.52 Aligned_cols=63 Identities=17% Similarity=0.174 Sum_probs=41.6
Q ss_pred eEEEEEEc-cceeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCCCCceecEEEEECC
Q 001639 552 FGVIIRVE-SEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRG 627 (1039)
Q Consensus 552 VGvIvrve-rd~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~kgr~G~V~hI~r~ 627 (1039)
.|+|+++- ...|.|... .|+++.++. ..|+.+ +..-|.+||.|.+---++....|.|.|=|++
T Consensus 10 ~G~Vik~lg~~~y~V~~~---~g~~~~c~~---rGklr~-------~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~ 73 (78)
T CHL00010 10 EGLVTESLPNGMFRVRLD---NGCQVLGYI---SGKIRR-------NSIRILPGDRVKVELSPYDLTKGRIIYRLRN 73 (78)
T ss_pred EEEEEEEcCCCEEEEEeC---CCCEEEEEe---ccceec-------CCcccCCCCEEEEEEcccCCCeEEEEEEecC
Confidence 59999998 577888542 356666553 222221 2344889999999744544567899888775
No 105
>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=60.59 E-value=17 Score=30.92 Aligned_cols=50 Identities=20% Similarity=0.271 Sum_probs=37.0
Q ss_pred cCCCCEEEEeccc--ccCceeEEEEEcCCeEEEeecCCCCCcceeeccccce
Q 001639 425 FMKGDAVIVIKGD--LKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELC 474 (1039)
Q Consensus 425 F~~GD~V~V~~Ge--l~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~Lr 474 (1039)
+.||-.|+|..-. +-+..|.|.+|.++.+-|+-.-....+.++|+.++|.
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 5689999998875 4779999999999999888776666678999988873
No 106
>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=60.36 E-value=37 Score=30.92 Aligned_cols=50 Identities=18% Similarity=0.205 Sum_probs=30.4
Q ss_pred ccCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeecc------------ccceeeccCCCceEEe
Q 001639 424 HFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNS------------KELCKYFEPGNHVKVV 486 (1039)
Q Consensus 424 ~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~------------~~LrK~F~~GDhVkVi 486 (1039)
.+++||.|+ |+|++|..+.+.+....+ -+--++. .++.+.|++||.|++-
T Consensus 3 ~p~~GdiV~----------g~V~~i~~~g~~v~i~~~---~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~ 64 (86)
T cd05789 3 IPEVGDVVI----------GRVTEVGFKRWKVDINSP---YDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAE 64 (86)
T ss_pred cCCCCCEEE----------EEEEEECCCEEEEECCCC---eEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEE
Confidence 346788774 778888887665543211 1122233 3445579999999763
No 107
>PRK03879 ribonuclease P protein component 1; Validated
Probab=60.13 E-value=21 Score=34.20 Aligned_cols=48 Identities=27% Similarity=0.360 Sum_probs=41.2
Q ss_pred CccccCcEEEEeecC---CCCceeEEEeecCCeEEEEecCCceEEEEecCccc
Q 001639 704 HDALVGTTVKVRLGP---YKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 753 (1039)
Q Consensus 704 ~d~liGktV~I~~Gp---yKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~ 753 (1039)
+..|+|-.|+|.+=+ |-|..|+|++-|..++.|+ +.++..+|+|+.-.
T Consensus 10 ~~eliGl~v~Vv~S~npslvGi~GiVv~ETknt~~I~--~~~~~~~VPK~~~i 60 (96)
T PRK03879 10 RHELIGLKVEVVDSTNPSLVGIKGRVVDETRNTLVIE--TDGKEWMVPKDGAT 60 (96)
T ss_pred HHHhcCCEEEEEEcCCCCcccceEEEEEeceeEEEEE--cCCcEEEEeCCCeE
Confidence 367999999998765 5689999999999999999 77888899998843
No 108
>PRK04333 50S ribosomal protein L14e; Validated
Probab=59.46 E-value=14 Score=34.68 Aligned_cols=29 Identities=28% Similarity=0.286 Sum_probs=25.0
Q ss_pred cCcEEEEeecCCCCceeEEEeec-CCeEEE
Q 001639 708 VGTTVKVRLGPYKGYRGRVVDVK-GQSVRV 736 (1039)
Q Consensus 708 iGktV~I~~GpyKG~~G~Vkd~t-~~~arV 736 (1039)
+|+-|.+..|+|+|-+++|.++- +..|-|
T Consensus 6 ~GrvV~~~~Grd~gk~~vIv~i~d~~~vlV 35 (84)
T PRK04333 6 VGRVCVKTAGREAGRKCVIVDIIDKNFVLV 35 (84)
T ss_pred ccEEEEEeccCCCCCEEEEEEEecCCEEEE
Confidence 78999999999999999999994 555555
No 109
>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=58.86 E-value=3.2 Score=50.97 Aligned_cols=8 Identities=38% Similarity=0.713 Sum_probs=0.0
Q ss_pred cCccccCC
Q 001639 109 EDDFIVDG 116 (1039)
Q Consensus 109 e~dfI~~~ 116 (1039)
+.+|+++.
T Consensus 281 E~dY~SD~ 288 (527)
T PF05793_consen 281 EVDYMSDS 288 (527)
T ss_dssp --------
T ss_pred cccccccc
Confidence 34566543
No 110
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=58.74 E-value=1e+02 Score=35.53 Aligned_cols=156 Identities=13% Similarity=0.137 Sum_probs=74.4
Q ss_pred CccCCCCEEEEecccccCceeEEEEEcCC--eEEEeecCCCCCcceeeccccceeeccCCCceEEe-cccccCceEEEEE
Q 001639 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVV-SGTQAGATGMVLK 499 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d--~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi-~G~~~GetGlVv~ 499 (1039)
..|++||.|+|+ |++++.+ .+++.... +. ..-+...|+..++.|+-|++. .+.. .-|++|.
T Consensus 74 ~~~~~G~~v~~~----------Vi~~~~~~~~i~lS~k~--~~--~~~~w~~l~~~~~~~~~V~g~V~~~~--~~G~~V~ 137 (318)
T PRK07400 74 EVLQPNETREFF----------ILSDENEDGQLTLSIRR--IE--YMRAWERVRQLQKEDATVRSEVFATN--RGGALVR 137 (318)
T ss_pred HccCCCCEEEEE----------EEEEeCCCCeEEEehhh--hh--hhhHHHHHHHhccCCCEEEEEEEEEE--CCeEEEE
Confidence 469999999987 5555543 34433221 10 011244566677778776652 2222 3478887
Q ss_pred EeCcEEEE-EeCCC---------CceEEEeccccc-------cccccccccccCCceEeeeeEEecCCceEEEEEEccce
Q 001639 500 VEQHVLII-LSDTT---------KEDIRVFADDVV-------ESSEVTTGITKIGDYELRDLVLLDNNSFGVIIRVESEA 562 (1039)
Q Consensus 500 Ve~~~v~l-lSD~t---------~~ei~V~~~dL~-------~~~e~~~g~~~~g~y~l~DLVqLd~~tVGvIvrverd~ 562 (1039)
+++=...| +|.++ .++|+|.--.+. .|.-.+.--..+..|..+++|. |.|++|..-.
T Consensus 138 l~Gv~gfip~s~ls~~~~~~~~vG~~i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~------G~V~~I~~~G 211 (318)
T PRK07400 138 IEGLRGFIPGSHISTRKPKEELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVV------GTVRGIKPYG 211 (318)
T ss_pred ECCEEEEEEHHHcCccCCccccCCCEEEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEE------EEEEEEECCe
Confidence 75321111 12222 233333221111 1110000001234455555554 8888887766
Q ss_pred eEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEe
Q 001639 563 FQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIV 610 (1039)
Q Consensus 563 ~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~ 610 (1039)
+.|--. |-.-.+..++|..... ..-.+.+++||.|++.
T Consensus 212 ~fV~i~----gv~Gllhisels~~~~------~~~~~~~~vGd~Vkvk 249 (318)
T PRK07400 212 AFIDIG----GVSGLLHISEISHEHI------ETPHSVFNVNDEMKVM 249 (318)
T ss_pred EEEEEC----CEEEEEEHHHcccccc------cChhhccCCCCEEEEE
Confidence 555321 2122344455543321 1234668999999884
No 111
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=58.60 E-value=4.9 Score=48.51 Aligned_cols=18 Identities=22% Similarity=0.434 Sum_probs=7.2
Q ss_pred cEEEEEecchHHHHHHHh
Q 001639 225 NYIYIEADKEAHVKEACK 242 (1039)
Q Consensus 225 GYIYVEA~~~~~V~~ai~ 242 (1039)
||-|+|-.--.|...|++
T Consensus 497 g~aF~~f~EhEhalkalk 514 (678)
T KOG0127|consen 497 GYAFVGFTEHEHALKALK 514 (678)
T ss_pred cccccCccHHHHHHHhhh
Confidence 444444433333333333
No 112
>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=57.50 E-value=22 Score=28.79 Aligned_cols=28 Identities=32% Similarity=0.523 Sum_probs=25.3
Q ss_pred eeEEEeecCCeEEEEecCCceEEEEecCc
Q 001639 723 RGRVVDVKGQSVRVELESQMKVVTVDRSM 751 (1039)
Q Consensus 723 ~G~Vkd~t~~~arVELhs~~k~I~V~r~~ 751 (1039)
+|.|++..+..++|++.. .++++|.+++
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 689999999999999999 8899998763
No 113
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=57.22 E-value=7.3 Score=50.98 Aligned_cols=6 Identities=17% Similarity=0.562 Sum_probs=2.6
Q ss_pred hhhccc
Q 001639 260 MTDVLA 265 (1039)
Q Consensus 260 m~~vL~ 265 (1039)
++|+++
T Consensus 1561 iADYMT 1566 (1640)
T KOG0262|consen 1561 IADYMT 1566 (1640)
T ss_pred HHHHHh
Confidence 344443
No 114
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=56.96 E-value=56 Score=29.45 Aligned_cols=62 Identities=18% Similarity=0.205 Sum_probs=39.8
Q ss_pred eEEEEEEccc-eeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCCCCceecEEEEEC
Q 001639 552 FGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYR 626 (1039)
Q Consensus 552 VGvIvrverd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~kgr~G~V~hI~r 626 (1039)
.|.|+++-.+ .|.|.+. .|.++.++.. .|+.+ +...+.+||.|.+---++....|.|.|=||
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 3666665532 22221 233489999999985555455688877654
No 115
>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=56.91 E-value=34 Score=29.97 Aligned_cols=42 Identities=26% Similarity=0.427 Sum_probs=29.0
Q ss_pred ceeEEEEEcCCeEEEeecCCCCCcceeeccccce--eeccCCCceEEe
Q 001639 441 LKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELC--KYFEPGNHVKVV 486 (1039)
Q Consensus 441 l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~Lr--K~F~~GDhVkVi 486 (1039)
++|+|++++.+.+.|... . -+--+|.+++. ..|++||+|++.
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 579999999885
No 116
>PRK04313 30S ribosomal protein S4e; Validated
Probab=56.77 E-value=61 Score=35.99 Aligned_cols=73 Identities=26% Similarity=0.396 Sum_probs=50.5
Q ss_pred cEEEEEEeCCCCeEEEEe--ccCCCCceEEec-CCC--eeecCCCCCCcEEEEcCCCCCceEEEEEEeC----CCcEEEe
Q 001639 949 VVGVIREVLPDGSCRVVL--GSSGNGDTITAL-PNE--IEIVPPRKTDKIKIMGGPHRGATGKLIGVDG----TDGIVKV 1019 (1039)
Q Consensus 949 ~~GvV~~V~~~g~~~V~l--~~~~~g~~v~v~-~~~--Le~V~P~kgd~VkVi~G~~rG~tG~LisiD~----~dgiVk~ 1019 (1039)
+.|++.=++-||.+-++- ..-..+++|.++ .++ ++.+.-..|..+.|+.|.+.|.+|++.+|.. ..-+|.+
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 455666566677764442 121125666666 233 6666679999999999999999999999973 4567887
Q ss_pred cC
Q 001639 1020 DV 1021 (1039)
Q Consensus 1020 d~ 1021 (1039)
.+
T Consensus 209 ~d 210 (237)
T PRK04313 209 ED 210 (237)
T ss_pred Ec
Confidence 74
No 117
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=55.40 E-value=9.3 Score=46.17 Aligned_cols=15 Identities=20% Similarity=0.189 Sum_probs=8.5
Q ss_pred hHHHHHHHHHHHhcc
Q 001639 143 DVEALERRIQARYAR 157 (1039)
Q Consensus 143 d~e~~~~~l~eRY~~ 157 (1039)
-+|+-|+.=++||..
T Consensus 580 ~we~ka~~dk~ry~~ 594 (615)
T KOG0526|consen 580 EWEDKAAVDKQRYED 594 (615)
T ss_pred hhhHHHHHHHHHHHH
Confidence 345555566666653
No 118
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=55.20 E-value=67 Score=29.99 Aligned_cols=65 Identities=14% Similarity=0.192 Sum_probs=45.7
Q ss_pred CCceEEEEEEccc-eeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCCCCceecEEEEECC
Q 001639 549 NNSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRG 627 (1039)
Q Consensus 549 ~~tVGvIvrverd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~kgr~G~V~hI~r~ 627 (1039)
.+.+|.|+++-.+ .|.|.+. +|..+.+. |..|+.++. =|+.||.|.|---|+.-..|.|.|+|..
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~---dG~~~la~---ipgK~Rk~i--------wI~~GD~VlVe~~~~~~~kg~Iv~r~~~ 70 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCA---DGKERLAR---IPGKMRKKV--------WIRRGDIVLVDPWDFQDVKADIIYKYTK 70 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEEC---CCCEEEEE---EchhhcccE--------EEcCCCEEEEEecCCCCCEEEEEEEeCH
Confidence 4678999999855 5888874 46665543 344443321 4899999999876776678999998863
No 119
>smart00361 RRM_1 RNA recognition motif.
Probab=55.07 E-value=36 Score=29.87 Aligned_cols=28 Identities=21% Similarity=0.432 Sum_probs=25.2
Q ss_pred cCCccEEEEEecchHHHHHHHhcCcccc
Q 001639 221 DHLKNYIYIEADKEAHVKEACKGLRNIY 248 (1039)
Q Consensus 221 ~~lkGYIYVEA~~~~~V~~ai~gl~~v~ 248 (1039)
.+.+||.||+-.+..++..||+.|.+-.
T Consensus 34 ~~~rG~~fV~f~~~~dA~~A~~~l~g~~ 61 (70)
T smart00361 34 NHKRGNVYITFERSEDAARAIVDLNGRY 61 (70)
T ss_pred CCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence 4579999999999999999999998865
No 120
>KOG2393 consensus Transcription initiation factor IIF, large subunit (RAP74) [Transcription]
Probab=55.06 E-value=10 Score=45.93 Aligned_cols=12 Identities=42% Similarity=0.385 Sum_probs=7.2
Q ss_pred cccccccCCcch
Q 001639 91 FDLEAQVDSDEE 102 (1039)
Q Consensus 91 iD~EAEVDDdeE 102 (1039)
.|++|-+++|+-
T Consensus 279 ~Dd~a~eesdd~ 290 (555)
T KOG2393|consen 279 VDDEAFEESDDG 290 (555)
T ss_pred CcccccccCCCc
Confidence 477776655443
No 121
>KOG1980 consensus Uncharacterized conserved protein [Function unknown]
Probab=54.93 E-value=3 Score=51.10 Aligned_cols=9 Identities=33% Similarity=0.316 Sum_probs=4.9
Q ss_pred hHHHHHHHh
Q 001639 234 EAHVKEACK 242 (1039)
Q Consensus 234 ~~~V~~ai~ 242 (1039)
+-.|+++++
T Consensus 535 P~~i~E~~~ 543 (754)
T KOG1980|consen 535 PVSILEAIK 543 (754)
T ss_pred cHHHHHHHh
Confidence 345556655
No 122
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=54.38 E-value=25 Score=33.62 Aligned_cols=50 Identities=26% Similarity=0.335 Sum_probs=40.8
Q ss_pred CCccccCcEEEEeecC---CCCceeEEEeecCCeEEEEecCCceEEEEecCcccc
Q 001639 703 GHDALVGTTVKVRLGP---YKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1039)
Q Consensus 703 ~~d~liGktV~I~~Gp---yKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~~ 754 (1039)
=+..|||..|+|..-+ |-|.-|.|+|-|-++..++-.+ +.+.|+|....+
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 3578999999999876 5677889999999999888776 777888877544
No 123
>KOG2600 consensus U3 small nucleolar ribonucleoprotein (snoRNP) subunit - Mpp10p [RNA processing and modification]
Probab=53.72 E-value=5 Score=48.38 Aligned_cols=14 Identities=21% Similarity=0.387 Sum_probs=9.1
Q ss_pred CCcccccCCCC-CCc
Q 001639 78 RKPKAKRRSGS-EFF 91 (1039)
Q Consensus 78 r~kkr~~~~~~-~Fi 91 (1039)
..|+.++...+ +||
T Consensus 170 q~K~~d~~gi~DkFF 184 (596)
T KOG2600|consen 170 QPKKFDKSGINDKFF 184 (596)
T ss_pred ccCcccccccccccc
Confidence 45556666666 788
No 124
>KOG0699 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=53.71 E-value=5.6 Score=45.88 Aligned_cols=10 Identities=30% Similarity=0.142 Sum_probs=5.0
Q ss_pred hhHHHHHHHH
Q 001639 142 EDVEALERRI 151 (1039)
Q Consensus 142 ~d~e~~~~~l 151 (1039)
+|..++++.+
T Consensus 372 EDevE~~RI~ 381 (542)
T KOG0699|consen 372 EDEVETNRIH 381 (542)
T ss_pred ccHHHHHHHH
Confidence 4555555443
No 125
>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=53.07 E-value=50 Score=28.70 Aligned_cols=43 Identities=23% Similarity=0.301 Sum_probs=27.7
Q ss_pred ceeEEEEEcCCeEEEeecCCCCCcceeeccccce--------eeccCCCceEEe
Q 001639 441 LKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELC--------KYFEPGNHVKVV 486 (1039)
Q Consensus 441 l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~Lr--------K~F~~GDhVkVi 486 (1039)
.+|+|++|....+.|.-.. ..+-.++.+++. ..|++||.+++.
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 4689999988866655421 122334445553 569999999875
No 126
>PRK11760 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional
Probab=52.75 E-value=23 Score=41.29 Aligned_cols=58 Identities=16% Similarity=0.248 Sum_probs=46.7
Q ss_pred EEEEccCchHHHHHHHHHHHHHhhCCCcceEEEEeecCCccEEEEEecchHHHHHHHhcCcc
Q 001639 185 WMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRN 246 (1039)
Q Consensus 185 w~Vkc~~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~~~lkGYIYVEA~~~~~V~~ai~gl~~ 246 (1039)
|..-|++|.|++.+.-|..|+... +++.-.-...-.|||..|.+...+....++.++-
T Consensus 4 l~lyCR~GFE~e~aaEi~~~a~~~----~~~G~~~~~~~sgyv~f~~~~~~~~~~l~~~l~~ 61 (357)
T PRK11760 4 LLLYCRPGFEKECAAEITDKAAEL----GVFGYARVKENSGYVIFECYQPDDADRLARELPF 61 (357)
T ss_pred EEEEeCCCchHHHHHHHHHHHHhc----CCcccccccCCCeEEEEEecCcchHHHHHhhCCc
Confidence 889999999999999999998654 4555443445579999999998999988887654
No 127
>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=52.31 E-value=31 Score=32.26 Aligned_cols=41 Identities=22% Similarity=0.319 Sum_probs=32.6
Q ss_pred cCcEEEEeecCCCCceeEEEeecCCeEEEEecCCceEEEEecCccc
Q 001639 708 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 753 (1039)
Q Consensus 708 iGktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~ 753 (1039)
.|..|.-.. |..|+|+++.++++.||+. .+-.|+++|..|+
T Consensus 40 ~Gd~VvT~g----Gi~G~V~~i~d~~v~vei~-~g~~i~~~r~aI~ 80 (84)
T TIGR00739 40 KGDKVLTIG----GIIGTVTKIAENTIVIELN-DNTEITFSKNAIV 80 (84)
T ss_pred CCCEEEECC----CeEEEEEEEeCCEEEEEEC-CCeEEEEEhHHhh
Confidence 455665444 6999999999999999995 5566999998876
No 128
>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=51.61 E-value=27 Score=35.33 Aligned_cols=49 Identities=31% Similarity=0.573 Sum_probs=35.0
Q ss_pred ccccCcEEEEee-cC---CCCceeEEEeecCCeEEEEecCC--ceEEEEecCccc
Q 001639 705 DALVGTTVKVRL-GP---YKGYRGRVVDVKGQSVRVELESQ--MKVVTVDRSMIS 753 (1039)
Q Consensus 705 d~liGktV~I~~-Gp---yKG~~G~Vkd~t~~~arVELhs~--~k~I~V~r~~l~ 753 (1039)
..++|+.|+|+- -+ -|=+.|++.++++..+++++..+ .++++|+.++|.
T Consensus 83 ~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~~I~~~~I~ 137 (141)
T PF02576_consen 83 ERFIGRKVKVKLKQPVNGRKEFEGKLLEVDEDEITLEVEGKGKKKEVEIPFSDIK 137 (141)
T ss_dssp HHH-SEEEEEE-SS-SSS-SEEEEEEEEEETTEEEEEEE-SS-EEEEEE-SS--S
T ss_pred HHhcCCeEEEEEeccCCCcEEEEEEEEEEeCCEEEEEECCccceEEEEEEHHHCc
Confidence 468999999995 33 34479999999999999999888 468888888775
No 129
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=51.53 E-value=3.2e+02 Score=33.61 Aligned_cols=46 Identities=17% Similarity=0.156 Sum_probs=30.3
Q ss_pred eeeeChhhhhhccccccccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEEe
Q 001639 252 VMLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLI 308 (1039)
Q Consensus 252 ~~lVpi~Em~~vL~~~k~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vklv 308 (1039)
-..||..||..-..... ...+++|+-|+ +.|+.++..+.++.|-+-
T Consensus 60 eG~Ip~~Els~~~~~~~-~~~~~vGd~Ie----------~~V~~~~~~~g~liLS~k 105 (486)
T PRK07899 60 EGVIPSRELSIKHDVDP-NEVVEVGDEVE----------ALVLQKEDKEGRLILSKK 105 (486)
T ss_pred EEEEEHHHhcccccCCh-hhcCCCCCEEE----------EEEEEEECCCCeEEEEeh
Confidence 46889999987332221 22478999986 458888877766666443
No 130
>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=51.45 E-value=4.9 Score=42.07 Aligned_cols=12 Identities=0% Similarity=0.202 Sum_probs=7.4
Q ss_pred HHHHHHHHHHhc
Q 001639 145 EALERRIQARYA 156 (1039)
Q Consensus 145 e~~~~~l~eRY~ 156 (1039)
.++++++.+=|.
T Consensus 67 ref~kmm~eS~~ 78 (170)
T PF04050_consen 67 REFQKMMAESLE 78 (170)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 456666666664
No 131
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=51.38 E-value=53 Score=31.74 Aligned_cols=64 Identities=22% Similarity=0.207 Sum_probs=42.4
Q ss_pred cCCceEEEEEEccc-eeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCCCCc---eecEEE
Q 001639 548 DNNSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGK---QGPVEH 623 (1039)
Q Consensus 548 d~~tVGvIvrverd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~kgr---~G~V~h 623 (1039)
+.+..|.|+++-.+ .|.|... +|..+.+ .|..|+.++. =|..||.|.| .|+.-- .|.|.|
T Consensus 18 e~e~~g~V~~~lG~~~~~V~~~---dG~~~la---~i~GK~Rk~i--------wI~~GD~VlV--sp~d~~~~~kg~Iv~ 81 (99)
T TIGR00523 18 EGEILGVIEQMLGAGRVKVRCL---DGKTRLG---RIPGKLKKRI--------WIREGDVVIV--KPWEFQGDDKCDIVW 81 (99)
T ss_pred CCEEEEEEEEEcCCCEEEEEeC---CCCEEEE---EEchhhcccE--------EecCCCEEEE--EEccCCCCccEEEEE
Confidence 34678999999755 5888874 3555543 3444544322 4899999999 455433 699999
Q ss_pred EECC
Q 001639 624 IYRG 627 (1039)
Q Consensus 624 I~r~ 627 (1039)
.|..
T Consensus 82 r~~~ 85 (99)
T TIGR00523 82 RYTK 85 (99)
T ss_pred EcCH
Confidence 8864
No 132
>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=51.33 E-value=48 Score=29.98 Aligned_cols=47 Identities=28% Similarity=0.375 Sum_probs=30.9
Q ss_pred CCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeec--------cccceeeccCCCceEE
Q 001639 426 MKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVN--------SKELCKYFEPGNHVKV 485 (1039)
Q Consensus 426 ~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~--------~~~LrK~F~~GDhVkV 485 (1039)
++||.|. |+|++|.++.+.|..... -+-.++ .+++...|++||.+++
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 5677664 889999999777655321 111222 4455677999999976
No 133
>PRK14638 hypothetical protein; Provisional
Probab=51.25 E-value=26 Score=36.13 Aligned_cols=48 Identities=10% Similarity=0.155 Sum_probs=38.9
Q ss_pred ccccCcEEEEeecCCCCceeEEEeecCCeEEEEecCCceEEEEecCcccc
Q 001639 705 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1039)
Q Consensus 705 d~liGktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~~ 754 (1039)
..++|+.|+|+-..-|-+.|+++++++..++++. ..+++.++.+.|.-
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 5789999999763358899999999999999874 56778888777653
No 134
>PLN00208 translation initiation factor (eIF); Provisional
Probab=51.17 E-value=67 Score=33.15 Aligned_cols=76 Identities=20% Similarity=0.271 Sum_probs=54.4
Q ss_pred ceEeeeeEEecC-CceEEEEEEccc-eeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCCC
Q 001639 538 DYELRDLVLLDN-NSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCK 615 (1039)
Q Consensus 538 ~y~l~DLVqLd~-~tVGvIvrverd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~k 615 (1039)
.-+..+|+..+. +.+|.|+++-.+ .|.|.+. .|..+.+. |..|+.++. =|+.||.|.|---++.
T Consensus 20 ~~~~~el~~p~egq~~g~V~~~lGn~~~~V~c~---dG~~rLa~---IpGKmRKrI--------WI~~GD~VlVel~~~d 85 (145)
T PLN00208 20 DDEKRELIFKEDGQEYAQVLRMLGNGRCEALCI---DGTKRLCH---IRGKMRKKV--------WIAAGDIILVGLRDYQ 85 (145)
T ss_pred ccceeecccCCCCcEEEEEEEEcCCCEEEEEEC---CCCEEEEE---EeccceeeE--------EecCCCEEEEEccCCC
Confidence 456677887754 668999999855 6888875 35555443 444544322 4899999999877887
Q ss_pred CceecEEEEECC
Q 001639 616 GKQGPVEHIYRG 627 (1039)
Q Consensus 616 gr~G~V~hI~r~ 627 (1039)
--.|.|.|.|..
T Consensus 86 ~~KgdIv~ry~~ 97 (145)
T PLN00208 86 DDKADVILKYMP 97 (145)
T ss_pred CCEEEEEEEcCH
Confidence 788999998865
No 135
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=50.80 E-value=69 Score=44.93 Aligned_cols=98 Identities=15% Similarity=0.194 Sum_probs=69.9
Q ss_pred cCccCCCCEEEEeccc-ccCceeEEEEEcCC--eEEEeecCCCCCcceeecccccee----------eccCCCceEEecc
Q 001639 422 KGHFMKGDAVIVIKGD-LKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCK----------YFEPGNHVKVVSG 488 (1039)
Q Consensus 422 ~~~F~~GD~V~V~~Ge-l~gl~G~V~~V~~d--~V~i~~~~~~l~~~i~v~~~~LrK----------~F~~GDhVkVi~G 488 (1039)
..+|++|+.|+-.... +++...+|+.|+.+ .++|.... +..+.|+++.+.+ -|..||.+++...
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 24556799999876 45554432 3456777776632 3668999999854
Q ss_pred -----cccCceEEEEEEeCcEEEEEeCCCCceEEEeccc
Q 001639 489 -----TQAGATGMVLKVEQHVLIILSDTTKEDIRVFADD 522 (1039)
Q Consensus 489 -----~~~GetGlVv~Ve~~~v~llSD~t~~ei~V~~~d 522 (1039)
...|+.+.|+.|+++.++|-.+-..+++++-.+.
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 3468999999999999999876455666664443
No 136
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=50.13 E-value=27 Score=35.97 Aligned_cols=50 Identities=28% Similarity=0.502 Sum_probs=39.0
Q ss_pred ccccCcEEEEe----ecCCCCceeEEEeecCCeEEEEecCCceEEEEecCcccc
Q 001639 705 DALVGTTVKVR----LGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1039)
Q Consensus 705 d~liGktV~I~----~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~~ 754 (1039)
..++|+.|+|+ .+.-|=+.|++++++++.+.++...+.|+++++.+.|.-
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 244466789999999999988876543488888887763
No 137
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=49.70 E-value=6.6 Score=51.15 Aligned_cols=12 Identities=33% Similarity=0.587 Sum_probs=7.2
Q ss_pred ceEEEEecCccc
Q 001639 742 MKVVTVDRSMIS 753 (1039)
Q Consensus 742 ~k~I~V~r~~l~ 753 (1039)
||+|+++++.++
T Consensus 1041 ~kvi~id~e~f~ 1052 (1299)
T KOG1856|consen 1041 CKVIKIDKERFS 1052 (1299)
T ss_pred EEeeeeeHhhhh
Confidence 556666666654
No 138
>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=49.67 E-value=26 Score=32.66 Aligned_cols=35 Identities=26% Similarity=0.475 Sum_probs=28.5
Q ss_pred ccceeeccCCCceEEecccccCceEEEEEEeCcEEEEEe
Q 001639 471 KELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILS 509 (1039)
Q Consensus 471 ~~LrK~F~~GDhVkVi~G~~~GetGlVv~Ve~~~v~llS 509 (1039)
++++...++||.|..++|-| |.|+.++++.++|-.
T Consensus 32 ~~m~~~L~~Gd~VvT~gGi~----G~V~~i~d~~v~vei 66 (84)
T TIGR00739 32 KKLIESLKKGDKVLTIGGII----GTVTKIAENTIVIEL 66 (84)
T ss_pred HHHHHhCCCCCEEEECCCeE----EEEEEEeCCEEEEEE
Confidence 45667789999999988754 999999999887643
No 139
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=49.35 E-value=45 Score=28.49 Aligned_cols=51 Identities=22% Similarity=0.120 Sum_probs=37.5
Q ss_pred eccCCCceEEecccccC--ceEEEEEEeC-cEEEEEeCC--CCceEEEecccccccc
Q 001639 476 YFEPGNHVKVVSGTQAG--ATGMVLKVEQ-HVLIILSDT--TKEDIRVFADDVVESS 527 (1039)
Q Consensus 476 ~F~~GDhVkVi~G~~~G--etGlVv~Ve~-~~v~llSD~--t~~ei~V~~~dL~~~~ 527 (1039)
.|++||.|-+-.=. .| -.|.|+++.+ +.+.|.-+. +..+.+|-..+|+-+.
T Consensus 2 ~~~~G~~Ve~~~~~-~~~W~~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LRp~~ 57 (61)
T smart00743 2 DFKKGDRVEVFSKE-EDSWWEAVVTKVLGDGKYLVRYLTESEPLKETVDWSDLRPHP 57 (61)
T ss_pred CcCCCCEEEEEECC-CCEEEEEEEEEECCCCEEEEEECCCCcccEEEEeHHHcccCC
Confidence 58899999887311 22 4799999987 666666666 7778888888887653
No 140
>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=49.18 E-value=35 Score=31.50 Aligned_cols=50 Identities=26% Similarity=0.435 Sum_probs=38.2
Q ss_pred ccccCcEEEEee----cCCCCceeEEEeecCCeEEEEecCC--ceEEEEecCcccc
Q 001639 705 DALVGTTVKVRL----GPYKGYRGRVVDVKGQSVRVELESQ--MKVVTVDRSMISD 754 (1039)
Q Consensus 705 d~liGktV~I~~----GpyKG~~G~Vkd~t~~~arVELhs~--~k~I~V~r~~l~~ 754 (1039)
..++|+.|+|.- +.-|-+.|++.+++++.+++++..+ .++++++.++|.-
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 578999999963 3335689999999999999887643 5678888777653
No 141
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=48.90 E-value=71 Score=33.31 Aligned_cols=75 Identities=16% Similarity=0.237 Sum_probs=52.7
Q ss_pred eEeeeeEEec-CCceEEEEEEccc-eeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCCCC
Q 001639 539 YELRDLVLLD-NNSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKG 616 (1039)
Q Consensus 539 y~l~DLVqLd-~~tVGvIvrverd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~kg 616 (1039)
-+..+|+.=. .+.+|+|+++-.+ .|+|.+. .|..+.+ .|..|+.++. -|..||.|.|---||.-
T Consensus 21 ~~~rel~~~eegq~~g~V~~~LGn~~f~V~c~---dG~~rLa---~I~GKmRK~I--------WI~~GD~VlVel~~yd~ 86 (155)
T PTZ00329 21 GEKRELVFKEEGQEYAQVLRMLGNGRLEAYCF---DGVKRLC---HIRGKMRKRV--------WINIGDIILVSLRDFQD 86 (155)
T ss_pred cceeeeccCCCCcEEEEEEEEcCCCEEEEEEC---CCCEEEE---EeeccceeeE--------EecCCCEEEEeccCCCC
Confidence 3445555543 4678999999855 6888875 3555443 3445554432 48999999998888877
Q ss_pred ceecEEEEECC
Q 001639 617 KQGPVEHIYRG 627 (1039)
Q Consensus 617 r~G~V~hI~r~ 627 (1039)
-.|.|.|.|..
T Consensus 87 ~KgdIi~Ry~~ 97 (155)
T PTZ00329 87 SKADVILKYTP 97 (155)
T ss_pred CEEEEEEEcCH
Confidence 88999998875
No 142
>PRK14644 hypothetical protein; Provisional
Probab=48.79 E-value=25 Score=35.68 Aligned_cols=49 Identities=14% Similarity=0.343 Sum_probs=36.9
Q ss_pred ccccCcEEEEee-cC---CCCceeEEEeecCCeEEEEe--cCCceEEEEecCccc
Q 001639 705 DALVGTTVKVRL-GP---YKGYRGRVVDVKGQSVRVEL--ESQMKVVTVDRSMIS 753 (1039)
Q Consensus 705 d~liGktV~I~~-Gp---yKG~~G~Vkd~t~~~arVEL--hs~~k~I~V~r~~l~ 753 (1039)
..++|+.|+|+- .+ -|-+.|+++++.+..++++. ..+-++|++++++|+
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 467999999963 22 36788999999999999864 444567777777764
No 143
>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=48.49 E-value=38 Score=31.24 Aligned_cols=51 Identities=24% Similarity=0.298 Sum_probs=37.6
Q ss_pred CCCCEEEEec----ccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceee
Q 001639 426 MKGDAVIVIK----GDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 476 (1039)
Q Consensus 426 ~~GD~V~V~~----Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~ 476 (1039)
..|-.|+|.- +..+...|.+.+++++.|+|..+.+.-.+++.++-.+++|.
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 44567899999999999998875333345788888888774
No 144
>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=48.15 E-value=96 Score=28.54 Aligned_cols=63 Identities=14% Similarity=0.175 Sum_probs=44.7
Q ss_pred ceEEEEEEccc-eeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCCCCceecEEEEECC
Q 001639 551 SFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRG 627 (1039)
Q Consensus 551 tVGvIvrverd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~kgr~G~V~hI~r~ 627 (1039)
..|.|+++-.+ .|+|...+ |..+.+ .|..|+.++. -|..||.|.|---|+.-..|.|.|.|..
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~---g~~~la---~i~gK~rk~i--------wI~~GD~V~Ve~~~~d~~kg~Iv~r~~~ 65 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFD---GKKRLC---RIRGKMRKRV--------WINEGDIVLVAPWDFQDDKADIIYKYTP 65 (77)
T ss_pred EEEEEEEEcCCCEEEEEECC---CCEEEE---EEchhhcccE--------EEcCCCEEEEEeccccCCEEEEEEEcCH
Confidence 46888888755 58888753 555443 3444544322 4899999999877887889999999863
No 145
>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=48.12 E-value=39 Score=29.51 Aligned_cols=29 Identities=31% Similarity=0.359 Sum_probs=23.2
Q ss_pred CCCCEEEEecccccCceeEEEEEcCCeEEEeec
Q 001639 426 MKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPE 458 (1039)
Q Consensus 426 ~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~ 458 (1039)
.+||.++.- .|++|+|++|..+.|.+.-.
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 689999963 57999999999997766543
No 146
>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=47.89 E-value=68 Score=45.70 Aligned_cols=95 Identities=16% Similarity=0.187 Sum_probs=65.5
Q ss_pred cCccCCCCEEEEecccccCceeEEEEEcCC--eEEEeecCCCCCcceeecccccee-----------eccCCCceEEec-
Q 001639 422 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCK-----------YFEPGNHVKVVS- 487 (1039)
Q Consensus 422 ~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d--~V~i~~~~~~l~~~i~v~~~~LrK-----------~F~~GDhVkVi~- 487 (1039)
...|++|+.|+.-.| ....|+.|+.+ .|++..-.. +....|.++.+.+ -|..||.++...
T Consensus 1327 ~~~Y~~G~vv~~~~~----~y~~V~~vd~~~~~v~l~~~~~--G~~~~~~p~~~~~~~~~~y~~~~~~l~~GDri~~t~~ 1400 (1960)
T TIGR02760 1327 MMPFEKGAVLRLKKD----AYLTIADIDREHGKLTVADIKT--GSERDILPRQLDHTFTSLYSDSELPLAKGDKIRLRAT 1400 (1960)
T ss_pred ccccCCCcEEEecCC----cEEEEEEecCCCCEEEEEecCC--CCeEeeChhhcCcccceeeccccccccCCCEEEEeec
Confidence 357999999996554 45778888754 555543111 3345565665542 578999999874
Q ss_pred ----ccccCceEEEEEEeCcEEEEEeCCCCceEEEecccc
Q 001639 488 ----GTQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDV 523 (1039)
Q Consensus 488 ----G~~~GetGlVv~Ve~~~v~llSD~t~~ei~V~~~dL 523 (1039)
|.-.|+.+.|+.|+.+.+++++|. .+++++.+.+.
T Consensus 1401 d~~~g~~n~~~~~V~~v~~~~~~~~~~~-~~~~~l~~~~~ 1439 (1960)
T TIGR02760 1401 DKNRGIKANEVYTVTQVVNGLSVQLSKV-KNSLSLKPIQA 1439 (1960)
T ss_pred CcccccccCCeEEEEEEcCCcEEEEcCC-CceEEecCchh
Confidence 334679999999988888888876 46787766543
No 147
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=47.89 E-value=25 Score=33.62 Aligned_cols=56 Identities=16% Similarity=0.287 Sum_probs=40.6
Q ss_pred cccceeeccCCCceEEe------cc----cccCceEEEEEEeCcEEEE--EeCCCCceEEEecccccc
Q 001639 470 SKELCKYFEPGNHVKVV------SG----TQAGATGMVLKVEQHVLII--LSDTTKEDIRVFADDVVE 525 (1039)
Q Consensus 470 ~~~LrK~F~~GDhVkVi------~G----~~~GetGlVv~Ve~~~v~l--lSD~t~~ei~V~~~dL~~ 525 (1039)
.+-+-+-|++||.|-++ .| +|.|-||.|+-+-++.+.| ......+.|-|.+.+|+-
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 34444569999999765 34 5789999999999886544 334556777888888864
No 148
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=47.68 E-value=36 Score=33.21 Aligned_cols=42 Identities=26% Similarity=0.357 Sum_probs=34.3
Q ss_pred cCcEEEEeecCCCCceeEEEeecCCeEEEEecCCceEEEEecCcccc
Q 001639 708 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1039)
Q Consensus 708 iGktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~~ 754 (1039)
.|..|.-.. |..|+|+++.++++.||+ +.+-.|+++|..|.-
T Consensus 55 ~Gd~VvT~g----Gi~G~Vv~i~~~~v~lei-~~g~~i~~~r~aI~~ 96 (106)
T PRK05585 55 KGDEVVTNG----GIIGKVTKVSEDFVIIEL-NDDTEIKIQKSAIAA 96 (106)
T ss_pred CCCEEEECC----CeEEEEEEEeCCEEEEEE-CCCeEEEEEhHHhhh
Confidence 566665554 699999999999999999 456779999998874
No 149
>PRK14637 hypothetical protein; Provisional
Probab=47.53 E-value=38 Score=35.04 Aligned_cols=47 Identities=21% Similarity=0.244 Sum_probs=37.2
Q ss_pred ccccCcEEEEeecCCCCc-eeEEEeecCCeEEEEecCCceEEEEecCccc
Q 001639 705 DALVGTTVKVRLGPYKGY-RGRVVDVKGQSVRVELESQMKVVTVDRSMIS 753 (1039)
Q Consensus 705 d~liGktV~I~~GpyKG~-~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~ 753 (1039)
..++|+.|+|+-..-|.+ .|++++++++.++++. ..+++.++.+.|.
T Consensus 94 ~r~~G~~V~V~l~~~~~~~~G~L~~~~d~~v~l~~--~~~~~~i~~~~I~ 141 (151)
T PRK14637 94 SIFVGETVKVWFECTGQWQVGTIAEADETCLVLTS--DGVPVTIPYVQIT 141 (151)
T ss_pred HHhCCCEEEEEECCCCcEEEEEEEEEeCCEEEEEE--CCEEEEEEHHHee
Confidence 578999999986323567 5999999999998885 5677888877765
No 150
>KOG0699 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=47.52 E-value=13 Score=43.17 Aligned_cols=14 Identities=36% Similarity=0.453 Sum_probs=7.9
Q ss_pred CCCcccccCCCCCC
Q 001639 77 ARKPKAKRRSGSEF 90 (1039)
Q Consensus 77 ~r~kkr~~~~~~~F 90 (1039)
+-.+|-.+.+.+.|
T Consensus 239 S~s~Kl~q~sKsef 252 (542)
T KOG0699|consen 239 SESKKLNQSSKSEF 252 (542)
T ss_pred hhhhhccccccccc
Confidence 44555555555666
No 151
>PRK14643 hypothetical protein; Provisional
Probab=47.35 E-value=31 Score=36.14 Aligned_cols=50 Identities=20% Similarity=0.167 Sum_probs=39.3
Q ss_pred ccccCcEEEEee-cCC---CCceeEEEeecCCeEEEEec----CCceEEEEecCcccc
Q 001639 705 DALVGTTVKVRL-GPY---KGYRGRVVDVKGQSVRVELE----SQMKVVTVDRSMISD 754 (1039)
Q Consensus 705 d~liGktV~I~~-Gpy---KG~~G~Vkd~t~~~arVELh----s~~k~I~V~r~~l~~ 754 (1039)
..++|+.|+|+- .|+ |-+.|+++++.+..++++|+ ...+++.++++.|.-
T Consensus 100 ~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l~~~~~~~~~~~~ip~~~I~k 157 (164)
T PRK14643 100 VKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRFTFFIKGQKKKLDVKYEQIKF 157 (164)
T ss_pred HHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEEEeeccCcCcEEEEeHHHhhh
Confidence 478999999963 444 44899999999998888864 446789999888764
No 152
>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=47.13 E-value=60 Score=30.56 Aligned_cols=49 Identities=22% Similarity=0.249 Sum_probs=38.2
Q ss_pred ccccCcEEEEeecC---CCCceeEEEeecCCeEEEEecCCceEEEEecCcccc
Q 001639 705 DALVGTTVKVRLGP---YKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1039)
Q Consensus 705 d~liGktV~I~~Gp---yKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~~ 754 (1039)
..|+|-.|+|.+=+ |-|..|+|++=|..+++|. ...+|+.+|+|..-.+
T Consensus 10 ~dl~G~~i~V~~s~~pslvG~~GiVV~ETknt~~I~-t~~~~~~~IpK~~~vF 61 (89)
T PF01868_consen 10 ADLIGAKIEVVRSKNPSLVGIEGIVVDETKNTFVIV-TEDGKVKTIPKAGSVF 61 (89)
T ss_dssp S--TT-EEEEEEESSCCCTTEEEEEEEEETTEEEEE-ETTEEEEEEESTTEEE
T ss_pred hhhcCCEEEEEEcCCCCccCCEEEEEEcccceEEEE-ecCCcEEEEecCCEEE
Confidence 57899999998765 7799999999999999986 4455789999988553
No 153
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=46.93 E-value=34 Score=32.80 Aligned_cols=53 Identities=23% Similarity=0.204 Sum_probs=39.7
Q ss_pred CccCCCCEEEEec------c----cccCceeEEEEEcCCeEEEeecCCCCCcceeecccccee
Q 001639 423 GHFMKGDAVIVIK------G----DLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK 475 (1039)
Q Consensus 423 ~~F~~GD~V~V~~------G----el~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK 475 (1039)
..|.+||.|-|.- | .+.|.+|+|+.+.++-..|.....+..+.|-+.+..|+.
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 4689999987742 2 467899999999999776666666666667777666654
No 154
>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=46.40 E-value=2.9e+02 Score=33.68 Aligned_cols=45 Identities=22% Similarity=0.268 Sum_probs=29.4
Q ss_pred eeeChhhhhhccccccccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEEe
Q 001639 253 MLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLI 308 (1039)
Q Consensus 253 ~lVpi~Em~~vL~~~k~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vklv 308 (1039)
.++|..||..-. .......+++|+.|++ +|..+|..++++.|-+-
T Consensus 212 g~lp~~e~s~~~-~~~~~~~~~vG~~v~v----------~Vl~~d~~~~~i~lS~k 256 (516)
T TIGR00717 212 GLLHITDMSWKR-VKHPSEYVKVGQEVKV----------KVIKFDKEKGRISLSLK 256 (516)
T ss_pred EEEEHHHcCCCC-CCCHHHhccCCCEEEE----------EEEEEECCCCcEEEEEE
Confidence 578888887521 1111234788988864 58889988887777543
No 155
>KOG2422 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.39 E-value=10 Score=46.31 Aligned_cols=12 Identities=50% Similarity=0.759 Sum_probs=6.8
Q ss_pred ccccCCcchhcc
Q 001639 94 EAQVDSDEEEDE 105 (1039)
Q Consensus 94 EAEVDDdeEeee 105 (1039)
-++||+++.-++
T Consensus 104 ~~~~d~~e~s~d 115 (665)
T KOG2422|consen 104 TAEVDKDEGSDD 115 (665)
T ss_pred cCccccccCCch
Confidence 356666665444
No 156
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=46.10 E-value=22 Score=34.15 Aligned_cols=41 Identities=27% Similarity=0.442 Sum_probs=34.1
Q ss_pred CcEEEEeecCCCCceeEEEeecCCeEEEEecCCceEEEEecCcccc
Q 001639 709 GTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1039)
Q Consensus 709 GktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~~ 754 (1039)
|..|.-. | |+.|+|..+.++.+.|+|. .+-.|++.|+.++.
T Consensus 47 GD~VvT~-g---Gi~G~V~~v~d~~v~I~l~-~~~~i~~~k~aI~~ 87 (97)
T COG1862 47 GDEVVTI-G---GIVGTVTKVGDDTVEIELG-DGTKIKFEKEAIAT 87 (97)
T ss_pred CCEEEEc-C---CeEEEEEEEecCcEEEEEC-CCeEEEEEHHHHHh
Confidence 5555444 3 7999999999999999999 88889999998874
No 157
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=45.95 E-value=2.1e+02 Score=36.38 Aligned_cols=100 Identities=16% Similarity=0.264 Sum_probs=48.6
Q ss_pred ceeeccCCCceEEecccccCceEEEEEEeCcEEEEEeCCCCceEEEeccccccccccccccccCCceEeeeeEEecCCce
Q 001639 473 LCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDNNSF 552 (1039)
Q Consensus 473 LrK~F~~GDhVkVi~G~~~GetGlVv~Ve~~~v~llSD~t~~ei~V~~~dL~~~~e~~~g~~~~g~y~l~DLVqLd~~tV 552 (1039)
..+.|++||.|++ .|+.++.. ...|.+..+.+....-. .-...|..++.|+
T Consensus 517 ~~~~~~vGd~V~v----------kV~~id~~---------~~~I~lS~K~~~~~p~~----~~~~~~~~G~~v~------ 567 (647)
T PRK00087 517 PSDVLKVGDEIKV----------YILDIDKE---------NKKLSLSLKKLLPDPWE----NVEEKYPVGSIVL------ 567 (647)
T ss_pred HHHhcCCCCEEEE----------EEEEEECC---------CCEEEEEeeccccChhh----hhhhhccCCeEEE------
Confidence 4468999999987 36666431 22233333333221110 0113455555544
Q ss_pred EEEEEEccceeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEe
Q 001639 553 GVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIV 610 (1039)
Q Consensus 553 GvIvrverd~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~ 610 (1039)
|.|+++.+-.+.|--.. +-.-.+..+++.... .......+++||.|++.
T Consensus 568 g~V~~i~~~G~fV~l~~---~i~Gli~~sel~~~~------~~~~~~~~kvGd~V~vk 616 (647)
T PRK00087 568 GKVVRIAPFGAFVELEP---GVDGLVHISQISWKR------IDKPEDVLSEGEEVKAK 616 (647)
T ss_pred EEEEEEECCeEEEEECC---CCEEEEEhhhcCccc------cCCHhhcCCCCCEEEEE
Confidence 66676665544332211 222234444543221 11234568999999875
No 158
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=45.89 E-value=2.5e+02 Score=33.09 Aligned_cols=45 Identities=13% Similarity=0.135 Sum_probs=31.3
Q ss_pred eeeChhhhhhccccccccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEEe
Q 001639 253 MLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLI 308 (1039)
Q Consensus 253 ~lVpi~Em~~vL~~~k~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vklv 308 (1039)
..+|..||..-.- ......+++|+.|++ .|+.++..+.++.|-+-
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 222335789999975 79999988877766554
No 159
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=45.68 E-value=10 Score=47.06 Aligned_cols=9 Identities=33% Similarity=0.368 Sum_probs=5.9
Q ss_pred CCccccccc
Q 001639 89 EFFDLEAQV 97 (1039)
Q Consensus 89 ~FiD~EAEV 97 (1039)
++||+-|-|
T Consensus 377 AaLDVLanv 385 (885)
T KOG2023|consen 377 AALDVLANV 385 (885)
T ss_pred HHHHHHHHh
Confidence 577776655
No 160
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=45.68 E-value=30 Score=31.16 Aligned_cols=42 Identities=17% Similarity=0.260 Sum_probs=35.1
Q ss_pred eeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCceEE
Q 001639 442 KGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKV 485 (1039)
Q Consensus 442 ~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkV 485 (1039)
++.|-+++++.+.+...... +.+.||.+.|-.-.++||.+.+
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 46899999998888876543 5799999999999999998776
No 161
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=44.88 E-value=62 Score=42.77 Aligned_cols=65 Identities=14% Similarity=0.161 Sum_probs=55.3
Q ss_pred EEEEEEeCCCCeEEEEeccCCCCceEEecCCCeeecCCCCCCcEEEEcCCCCCceEEEEEEeCCCcEEEe
Q 001639 950 VGVIREVLPDGSCRVVLGSSGNGDTITALPNEIEIVPPRKTDKIKIMGGPHRGATGKLIGVDGTDGIVKV 1019 (1039)
Q Consensus 950 ~GvV~~V~~~g~~~V~l~~~~~g~~v~v~~~~Le~V~P~kgd~VkVi~G~~rG~tG~LisiD~~dgiVk~ 1019 (1039)
-|+|.+|.+ ++++|..+.+++.+...+...-|.-|++.+|++|.+..| ...++..|...+|++..
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 889999999987788889999999999999999997655 56777778778887775
No 162
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=44.63 E-value=6.9e+02 Score=30.79 Aligned_cols=14 Identities=7% Similarity=0.195 Sum_probs=8.4
Q ss_pred CCCChHHhhcccCC
Q 001639 389 IQPTFDELEKFRTP 402 (1039)
Q Consensus 389 V~PTleEL~~F~~~ 402 (1039)
+++.++|+.+|-..
T Consensus 57 l~~~iee~t~kLrt 70 (554)
T KOG0119|consen 57 LNLRIEEITRKLRT 70 (554)
T ss_pred HHHHHHHhhhhhcc
Confidence 45666666666543
No 163
>COG4547 CobT Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]
Probab=44.61 E-value=18 Score=43.19 Aligned_cols=13 Identities=15% Similarity=0.135 Sum_probs=7.5
Q ss_pred HHHHHHHHHHhhC
Q 001639 197 AAVCLMQKCIDKG 209 (1039)
Q Consensus 197 vv~~Lm~K~~~~~ 209 (1039)
++..|.+|+++.+
T Consensus 360 lanrlqrRlmAqq 372 (620)
T COG4547 360 LANRLQRRLMAQQ 372 (620)
T ss_pred HHHHHHHHHHHhh
Confidence 4456666666653
No 164
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=44.23 E-value=60 Score=42.45 Aligned_cols=52 Identities=19% Similarity=0.103 Sum_probs=40.3
Q ss_pred cCccCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCceEEe
Q 001639 422 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVV 486 (1039)
Q Consensus 422 ~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi 486 (1039)
...|++|+.|+ |+|++|+.+.|.|-.. .+.+=-+|.+++.+-+++||.|+|.
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 8999999998888653 2334457788888888999999874
No 165
>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=44.02 E-value=27 Score=32.86 Aligned_cols=50 Identities=28% Similarity=0.260 Sum_probs=31.8
Q ss_pred CCCCEEEEecccccCceeEEEEEcCC--eEEEeecCCCCCcceeec--cccceeeccCCCceEE
Q 001639 426 MKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVN--SKELCKYFEPGNHVKV 485 (1039)
Q Consensus 426 ~~GD~V~V~~Gel~gl~G~V~~V~~d--~V~i~~~~~~l~~~i~v~--~~~LrK~F~~GDhVkV 485 (1039)
++||.|. |+|+.+..+ .|-|.+....+-..+.|+ .+..|.+|++||.|-.
T Consensus 5 ~~gD~VI----------G~V~~~~~~~~~VdI~s~~~a~L~~~~f~gatk~~rp~L~~GDlV~A 58 (86)
T cd05790 5 AKGDHVI----------GIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYA 58 (86)
T ss_pred CCCCEEE----------EEEEEEcCCeEEEEcCCCcceEechHHcccccccccccCCCCCEEEE
Confidence 5778764 888888877 455544432221123333 5667999999999843
No 166
>PRK14634 hypothetical protein; Provisional
Probab=43.19 E-value=37 Score=35.27 Aligned_cols=48 Identities=10% Similarity=0.270 Sum_probs=38.2
Q ss_pred ccccCcEEEEe-ecC---CCCceeEEEeecCCeEEEEecCCceEEEEecCcccc
Q 001639 705 DALVGTTVKVR-LGP---YKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1039)
Q Consensus 705 d~liGktV~I~-~Gp---yKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~~ 754 (1039)
..++|+.|+|+ ..+ -|=+.|++++++++.+++++ ..++++++.+.|+-
T Consensus 96 ~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~v~l~~--~~~~~~i~~~~I~k 147 (155)
T PRK14634 96 QTFRGFPVEVSHRDDDGSEQRLEGLLLERNEDHLQINI--RGRIKRIPRDSVIS 147 (155)
T ss_pred HHhCCCeEEEEEecCCCCeEEEEEEEEEEeCCEEEEEE--CCEEEEEEHHHeee
Confidence 57899999996 443 36789999999999999886 46778888777653
No 167
>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=43.05 E-value=25 Score=32.48 Aligned_cols=31 Identities=19% Similarity=0.082 Sum_probs=19.8
Q ss_pred ccCCCCcEEEEec---CCCCCCeeEEEEeeCCCC
Q 001639 271 IDLSRDTWVRMKI---GNYKGDLAKVVDVDNVRQ 301 (1039)
Q Consensus 271 ~~l~~G~wVRIk~---G~YkGDlAqV~~Vd~~~~ 301 (1039)
..|++|+.||+.+ ...+||.|+|..++.++.
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 4689999999986 589999999998886553
No 168
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=42.23 E-value=85 Score=35.59 Aligned_cols=72 Identities=18% Similarity=0.366 Sum_probs=49.8
Q ss_pred cEEEEEEeCCCCeEEEEecc--CCCCceEEec---CCCeeecCCCCCCcEEEEcCCCCCceEEEEEEeCC---CcEEEec
Q 001639 949 VVGVIREVLPDGSCRVVLGS--SGNGDTITAL---PNEIEIVPPRKTDKIKIMGGPHRGATGKLIGVDGT---DGIVKVD 1020 (1039)
Q Consensus 949 ~~GvV~~V~~~g~~~V~l~~--~~~g~~v~v~---~~~Le~V~P~kgd~VkVi~G~~rG~tG~LisiD~~---dgiVk~d 1020 (1039)
+.|++.=++-||.+ +...+ -..+++|.++ +.=++.+.-..|..+.|+.|.+.|.+|+++.|... .-+|.+.
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 45566666667777 33222 1125677776 33366777799999999999999999999999543 3477776
Q ss_pred C
Q 001639 1021 V 1021 (1039)
Q Consensus 1021 ~ 1021 (1039)
+
T Consensus 209 d 209 (273)
T PTZ00223 209 D 209 (273)
T ss_pred e
Confidence 3
No 169
>PRK14645 hypothetical protein; Provisional
Probab=42.10 E-value=38 Score=35.12 Aligned_cols=46 Identities=22% Similarity=0.315 Sum_probs=37.9
Q ss_pred ccccCcEEEEeecCCCCceeEEEeecCCeEEEEecCCceEEEEecCccc
Q 001639 705 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 753 (1039)
Q Consensus 705 d~liGktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~ 753 (1039)
..++|+.|+|+.| -|=+.|+++++++..++++. ..+++.++.+.|.
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 5689999999864 47889999999999988876 5677888888775
No 170
>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=42.09 E-value=1.2e+02 Score=43.44 Aligned_cols=93 Identities=12% Similarity=0.231 Sum_probs=64.8
Q ss_pred cCccCCCCEEEEeccc-ccCceeEEEEEcC--CeEEEeecCCCCCcceeeccccce-------------eeccCCCceEE
Q 001639 422 KGHFMKGDAVIVIKGD-LKNLKGWVEKVDE--ENVHIRPEMKGLPKTLAVNSKELC-------------KYFEPGNHVKV 485 (1039)
Q Consensus 422 ~~~F~~GD~V~V~~Ge-l~gl~G~V~~V~~--d~V~i~~~~~~l~~~i~v~~~~Lr-------------K~F~~GDhVkV 485 (1039)
..+|++||.|+-+.-. +.+-.++|+.|+. +.++|.... ++.+.|.+++|. .-|-.||.+++
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 4689999999975432 3455589999986 567766532 345666666662 24668999988
Q ss_pred ecc-----cccCceEEEEEEeCcEEEEEeCCCCceEEE
Q 001639 486 VSG-----TQAGATGMVLKVEQHVLIILSDTTKEDIRV 518 (1039)
Q Consensus 486 i~G-----~~~GetGlVv~Ve~~~v~llSD~t~~ei~V 518 (1039)
... ...|+...|+.++...++|-.+.. +.+++
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 346789999999998888876543 35554
No 171
>PF14851 FAM176: FAM176 family
Probab=41.93 E-value=57 Score=33.93 Aligned_cols=13 Identities=15% Similarity=0.136 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHhc
Q 001639 144 VEALERRIQARYA 156 (1039)
Q Consensus 144 ~e~~~~~l~eRY~ 156 (1039)
+-|+|+.|++|=+
T Consensus 118 ~~e~A~rlEeRe~ 130 (153)
T PF14851_consen 118 ELERAQRLEERER 130 (153)
T ss_pred HHHHHHHHHHHHH
Confidence 3456677776644
No 172
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=41.57 E-value=1.4e+02 Score=28.86 Aligned_cols=74 Identities=16% Similarity=0.158 Sum_probs=50.1
Q ss_pred EeeeeEEecC-CceEEEEEEccc-eeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCCCCc
Q 001639 540 ELRDLVLLDN-NSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGK 617 (1039)
Q Consensus 540 ~l~DLVqLd~-~tVGvIvrverd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~kgr 617 (1039)
..++|+..+. +..|.|+++-.+ .|.|... +|..+.+. |..|+.++. -|..||.|.|---|+.--
T Consensus 11 ~~~~~~~p~e~e~~g~V~~~lG~~~~~V~~~---dG~~~la~---i~GK~Rk~I--------wI~~GD~VlVe~~~~~~~ 76 (100)
T PRK04012 11 TRVRLPMPEEGEVFGVVEQMLGANRVRVRCM---DGVERMGR---IPGKMKKRM--------WIREGDVVIVAPWDFQDE 76 (100)
T ss_pred eeEEccCCCCCEEEEEEEEEcCCCEEEEEeC---CCCEEEEE---EchhhcccE--------EecCCCEEEEEecccCCC
Confidence 4456777754 557999998755 5888874 35555443 334443322 488999999976666656
Q ss_pred eecEEEEECC
Q 001639 618 QGPVEHIYRG 627 (1039)
Q Consensus 618 ~G~V~hI~r~ 627 (1039)
.|.|.|.|..
T Consensus 77 kg~Iv~r~~~ 86 (100)
T PRK04012 77 KADIIWRYTK 86 (100)
T ss_pred EEEEEEEcCH
Confidence 8999998863
No 173
>KOG0299 consensus U3 snoRNP-associated protein (contains WD40 repeats) [RNA processing and modification]
Probab=41.52 E-value=5.3 Score=47.27 Aligned_cols=23 Identities=13% Similarity=0.260 Sum_probs=14.8
Q ss_pred CCcceEEEEeecCCccEEEEEecc
Q 001639 210 SELQIRSVIALDHLKNYIYIEADK 233 (1039)
Q Consensus 210 ~~l~I~Svf~~~~lkGYIYVEA~~ 233 (1039)
..+.|.+++..+. --|+|=.+..
T Consensus 141 H~~s~~~vals~d-~~~~fsask~ 163 (479)
T KOG0299|consen 141 HQLSVTSVALSPD-DKRVFSASKD 163 (479)
T ss_pred ccCcceEEEeecc-ccceeecCCC
Confidence 5577888877654 3567766544
No 174
>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=41.40 E-value=61 Score=29.12 Aligned_cols=22 Identities=27% Similarity=0.389 Sum_probs=16.9
Q ss_pred ccceeeccCCCceEEecccccCceEEEEEEeC
Q 001639 471 KELCKYFEPGNHVKVVSGTQAGATGMVLKVEQ 502 (1039)
Q Consensus 471 ~~LrK~F~~GDhVkVi~G~~~GetGlVv~Ve~ 502 (1039)
+++.++|++||.|++ .|+.|+.
T Consensus 45 ~~~~~~~~~G~~v~~----------kVl~id~ 66 (74)
T cd05705 45 SLYNKYLPEGKLLTA----------KVLSVNS 66 (74)
T ss_pred hhHhcccCCCCEEEE----------EEEEEEC
Confidence 446789999999976 4777764
No 175
>PRK14640 hypothetical protein; Provisional
Probab=40.99 E-value=50 Score=34.15 Aligned_cols=47 Identities=19% Similarity=0.347 Sum_probs=36.6
Q ss_pred ccccCcEEEEee----cCCCCceeEEEeecCCeEEEEecCCceEEEEecCccc
Q 001639 705 DALVGTTVKVRL----GPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 753 (1039)
Q Consensus 705 d~liGktV~I~~----GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~ 753 (1039)
..++|+.|+|+- +.-|=+.|++++++++.+++++. .+++.++.+.|.
T Consensus 93 ~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~v~l~~~--~~~~~i~~~~I~ 143 (152)
T PRK14640 93 EKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVD--GKDEVLAFTNIQ 143 (152)
T ss_pred HHhCCCeEEEEEecccCCceEEEEEEEEEeCCEEEEEEC--CeEEEEEhHHee
Confidence 578999999974 33477899999999999998864 566777766654
No 176
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=40.95 E-value=38 Score=34.26 Aligned_cols=33 Identities=24% Similarity=0.293 Sum_probs=27.6
Q ss_pred cCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEE
Q 001639 272 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTV 305 (1039)
Q Consensus 272 ~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~V 305 (1039)
.+++|=.|.|..|+|+|-||.|++|-. +++|.|
T Consensus 7 fVEiGRVvli~~Gp~~GKL~vIVDIID-~nRvLV 39 (130)
T PTZ00065 7 FVEPGRLCLIQYGPDAGKLCFIVDIVT-PTRVLV 39 (130)
T ss_pred ceeeceEEEEecCCCCCCEEEEEEEEc-CCeEEE
Confidence 467899999999999999999999854 455554
No 177
>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=40.86 E-value=1.5e+02 Score=27.34 Aligned_cols=64 Identities=16% Similarity=0.118 Sum_probs=44.5
Q ss_pred CceEEEEEEccc-eeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCC-CCceecEEEEECC
Q 001639 550 NSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPC-KGKQGPVEHIYRG 627 (1039)
Q Consensus 550 ~tVGvIvrverd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~-kgr~G~V~hI~r~ 627 (1039)
+.+|.|+++-.+ .|+|... +|..+.+. |..|+.++ + =|+.||.|.|---|+ .--.|.|.|.|+.
T Consensus 1 q~i~~V~~~lG~~~~~V~~~---dg~~~l~~---i~gK~Rk~-i-------wI~~GD~VlV~~~~~~~~~kg~Iv~r~~~ 66 (78)
T cd04456 1 QQIVRVLRMLGNNRHEVECA---DGQRRLVS---IPGKLRKN-I-------WIKRGDFLIVDPIEEGEDVKADIIFVYCK 66 (78)
T ss_pred CeEEEEEEECCCCEEEEEEC---CCCEEEEE---EchhhccC-E-------EEcCCCEEEEEecccCCCceEEEEEEeCH
Confidence 357888888755 5788874 36655543 34454432 2 489999999987676 4578999999864
No 178
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=40.56 E-value=33 Score=33.94 Aligned_cols=38 Identities=24% Similarity=0.364 Sum_probs=27.6
Q ss_pred EeecCCCCceeEEEeecCCeEEEEecCCceEEEEecCcccc
Q 001639 714 VRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1039)
Q Consensus 714 I~~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~~ 754 (1039)
|+.| |+.|+|.++.++..+|.|...+-.|+|.|..|+-
T Consensus 44 vT~G---Gi~G~V~~I~~~~~~v~le~~gv~i~v~r~AI~~ 81 (113)
T PRK06531 44 VTIG---GLYGTVDEVDTEAKTIVLDVDGVYLTFELAAIKR 81 (113)
T ss_pred EECC---CcEEEEEEEecCCCEEEEEECCEEEEEEhhHhhh
Confidence 4555 8999999998754444443356789999998874
No 179
>CHL00084 rpl19 ribosomal protein L19
Probab=40.45 E-value=98 Score=30.88 Aligned_cols=31 Identities=23% Similarity=0.267 Sum_probs=23.2
Q ss_pred ccCccCCCCEEEE----eccc---ccCceeEEEEEcCC
Q 001639 421 KKGHFMKGDAVIV----IKGD---LKNLKGWVEKVDEE 451 (1039)
Q Consensus 421 ~~~~F~~GD~V~V----~~Ge---l~gl~G~V~~V~~d 451 (1039)
.-..|++||.|+| .+|+ .....|.|+++.+.
T Consensus 19 ~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~ 56 (117)
T CHL00084 19 NLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNS 56 (117)
T ss_pred CCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCC
Confidence 3468999999998 3464 34678999988654
No 180
>PRK07594 type III secretion system ATPase SsaN; Validated
Probab=40.30 E-value=4.3e+02 Score=32.12 Aligned_cols=62 Identities=10% Similarity=0.052 Sum_probs=44.3
Q ss_pred cccCccCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCceEEecccccCceEEEEE
Q 001639 420 RKKGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLK 499 (1039)
Q Consensus 420 ~~~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi~G~~~GetGlVv~ 499 (1039)
+.+-.|-||+.+..+ |+|++|.+..|.+... ....|+.|.+-. .+..|.|+.
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 345567788777665 9999999998887622 135678887722 346899999
Q ss_pred EeCcEEEEEe
Q 001639 500 VEQHVLIILS 509 (1039)
Q Consensus 500 Ve~~~v~llS 509 (1039)
++++.+.+..
T Consensus 60 ~~~~~~~l~~ 69 (433)
T PRK07594 60 INGSKALLSP 69 (433)
T ss_pred EcCCeEEEEE
Confidence 9998877643
No 181
>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=40.23 E-value=22 Score=32.07 Aligned_cols=43 Identities=19% Similarity=0.210 Sum_probs=32.5
Q ss_pred ceeEEEEEcCC-eEEEeecCCCCCcceeec----cccceeeccCCCce
Q 001639 441 LKGWVEKVDEE-NVHIRPEMKGLPKTLAVN----SKELCKYFEPGNHV 483 (1039)
Q Consensus 441 l~G~V~~V~~d-~V~i~~~~~~l~~~i~v~----~~~LrK~F~~GDhV 483 (1039)
-.+.|++|++| .+++|-...+..+-|.+| ..+++..|+.|..+
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 899998655555558888 56778899999884
No 182
>PLN00036 40S ribosomal protein S4; Provisional
Probab=40.09 E-value=1.1e+02 Score=34.56 Aligned_cols=72 Identities=19% Similarity=0.241 Sum_probs=49.3
Q ss_pred cEEEEEEeCCCCeEEEEecc--CCCCceEEec--CC-CeeecCCCCCCcEEEEcCCCCCceEEEEEEeC---CCcEEEec
Q 001639 949 VVGVIREVLPDGSCRVVLGS--SGNGDTITAL--PN-EIEIVPPRKTDKIKIMGGPHRGATGKLIGVDG---TDGIVKVD 1020 (1039)
Q Consensus 949 ~~GvV~~V~~~g~~~V~l~~--~~~g~~v~v~--~~-~Le~V~P~kgd~VkVi~G~~rG~tG~LisiD~---~dgiVk~d 1020 (1039)
+.|++.=++-||.+ +...+ -..+++|.++ .. =++.+.-..|..+.|+.|.+.|.+|+++.|.. ..-+|.+.
T Consensus 133 ~gG~~ql~~hDGrn-i~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~ 211 (261)
T PLN00036 133 QKGIPYLNTHDGRT-IRYPDPLIKANDTIKIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVK 211 (261)
T ss_pred cCCeEEEEecCCce-eccCCCccccCCEEEEeCCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEE
Confidence 45566656667777 33222 1125677665 22 25666668999999999999999999999983 23478776
Q ss_pred C
Q 001639 1021 V 1021 (1039)
Q Consensus 1021 ~ 1021 (1039)
+
T Consensus 212 d 212 (261)
T PLN00036 212 D 212 (261)
T ss_pred e
Confidence 4
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=39.92 E-value=49 Score=31.16 Aligned_cols=14 Identities=43% Similarity=0.866 Sum_probs=12.2
Q ss_pred cceeeccCCCceEE
Q 001639 472 ELCKYFEPGNHVKV 485 (1039)
Q Consensus 472 ~LrK~F~~GDhVkV 485 (1039)
+++++|++||.|+.
T Consensus 56 ~~~~~f~~GDiV~A 69 (92)
T cd05791 56 EMYKCFRPGDIVRA 69 (92)
T ss_pred HHHhhcCCCCEEEE
Confidence 67899999999875
No 184
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=39.84 E-value=3.1e+02 Score=34.02 Aligned_cols=46 Identities=22% Similarity=0.245 Sum_probs=30.0
Q ss_pred eeeeChhhhhhccccccccccCCCCcEEEEecCCCCCCeeEEEEeeCCCCEEEEEEe
Q 001639 252 VMLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLI 308 (1039)
Q Consensus 252 ~~lVpi~Em~~vL~~~k~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~v~Vklv 308 (1039)
..+||+.||..- ++......+++|+.|++ +|..++.++.++.|-+-
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 357788888542 11111234788999864 58899988887776654
No 185
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=39.55 E-value=77 Score=28.53 Aligned_cols=45 Identities=27% Similarity=0.316 Sum_probs=34.1
Q ss_pred ccccCcEEEEeecCCCCceeEEEeecCCeEEEEecCCceEEEEecCcc
Q 001639 705 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMI 752 (1039)
Q Consensus 705 d~liGktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l 752 (1039)
..+|||.|.|..- .--+.|+++++..+++.||-+ .+..-|.-.+|
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 4689999999873 334689999999999999988 55555554444
No 186
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=38.95 E-value=1.2e+02 Score=34.15 Aligned_cols=72 Identities=18% Similarity=0.238 Sum_probs=49.2
Q ss_pred cEEEEEEeCCCCeEEEEecc--CCCCceEEec--CC-CeeecCCCCCCcEEEEcCCCCCceEEEEEEeC---CCcEEEec
Q 001639 949 VVGVIREVLPDGSCRVVLGS--SGNGDTITAL--PN-EIEIVPPRKTDKIKIMGGPHRGATGKLIGVDG---TDGIVKVD 1020 (1039)
Q Consensus 949 ~~GvV~~V~~~g~~~V~l~~--~~~g~~v~v~--~~-~Le~V~P~kgd~VkVi~G~~rG~tG~LisiD~---~dgiVk~d 1020 (1039)
+.|++.=++-||.+ +...+ -..+++|.++ .. =++.+.-..|..+.|+.|.+.|.+|+++.+.. +.-+|.+.
T Consensus 133 ~gg~~~l~~hDGrn-i~~~d~~ik~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~ 211 (262)
T PTZ00118 133 PKEVSIAVTHDGRT-IRYVHPDVKVGDSLRLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVK 211 (262)
T ss_pred CCCeEEEEecCcce-eccCCCcccCCCEEEEECCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEE
Confidence 45566656667777 33222 1125677765 22 25666669999999999999999999998774 34578776
Q ss_pred C
Q 001639 1021 V 1021 (1039)
Q Consensus 1021 ~ 1021 (1039)
+
T Consensus 212 d 212 (262)
T PTZ00118 212 D 212 (262)
T ss_pred e
Confidence 4
No 187
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=38.78 E-value=2.7e+02 Score=30.93 Aligned_cols=11 Identities=9% Similarity=0.202 Sum_probs=6.1
Q ss_pred CCEEEEEeCce
Q 001639 626 RGILFIHDRHH 636 (1039)
Q Consensus 626 r~~lFl~~~~~ 636 (1039)
+-|+|.+||++
T Consensus 10 kpwcwycnref 20 (341)
T KOG2893|consen 10 KPWCWYCNREF 20 (341)
T ss_pred Cceeeeccccc
Confidence 44566666653
No 188
>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=38.70 E-value=90 Score=27.64 Aligned_cols=34 Identities=24% Similarity=0.293 Sum_probs=22.9
Q ss_pred cCCCCEEEEecccc--cC--ceeEEEEEcCC-eEEEeec
Q 001639 425 FMKGDAVIVIKGDL--KN--LKGWVEKVDEE-NVHIRPE 458 (1039)
Q Consensus 425 F~~GD~V~V~~Gel--~g--l~G~V~~V~~d-~V~i~~~ 458 (1039)
|++||.|||..-+- .| ..|+|++..++ .+.|.-.
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 89999999987542 22 67899999988 7777754
No 189
>PF14944 TCRP1: Tongue Cancer Chemotherapy Resistant Protein 1
Probab=38.41 E-value=96 Score=32.14 Aligned_cols=9 Identities=44% Similarity=1.147 Sum_probs=4.2
Q ss_pred CCcCCCCCC
Q 001639 877 TYVNAPSPY 885 (1039)
Q Consensus 877 ~y~~~pspy 885 (1039)
+|+++|.||
T Consensus 72 pys~sPnPY 80 (195)
T PF14944_consen 72 PYSPSPNPY 80 (195)
T ss_pred CCCCCCCcc
Confidence 444444444
No 190
>KOG0338 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=38.12 E-value=9.2 Score=46.24 Aligned_cols=18 Identities=11% Similarity=0.312 Sum_probs=10.5
Q ss_pred CchHHHHHHHHHHHHHhh
Q 001639 191 IGREREAAVCLMQKCIDK 208 (1039)
Q Consensus 191 ~G~Er~vv~~Lm~K~~~~ 208 (1039)
.|+--..+.-++.|++.+
T Consensus 229 sGKTAAF~lPiLERLlYr 246 (691)
T KOG0338|consen 229 SGKTAAFALPILERLLYR 246 (691)
T ss_pred CCchhhhHHHHHHHHhcC
Confidence 456555555566666654
No 191
>PF09870 DUF2097: Uncharacterized protein conserved in archaea (DUF2097); InterPro: IPR019208 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=38.11 E-value=47 Score=31.33 Aligned_cols=51 Identities=16% Similarity=0.246 Sum_probs=41.4
Q ss_pred CccCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccce
Q 001639 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELC 474 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~Lr 474 (1039)
..++.||.+++.=|. ...-|.|++++.-.+.|..+..-+++.++|...++.
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 478899999999888888766545677888766654
No 192
>KOG4264 consensus Nucleo-cytoplasmic protein MLN51 [General function prediction only]
Probab=38.06 E-value=21 Score=43.04 Aligned_cols=90 Identities=23% Similarity=0.422 Sum_probs=0.0
Q ss_pred CCCCCCccccccccchhhh----------hccCccchhhhhhhhchhhccccccccccCccccccccccccCCCccccCC
Q 001639 3 RRRDDDDDEMDAEEDEYDE----------QVMDDEIDEEEEEEDDRSSRKRRRSQFIDDVAEEDDEEEEEDYDDDEDYGG 72 (1039)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~----------~~~~~~~~eedeee~~~~~~~~~~~~~~~d~~~~~d~~~~~~~~~~~~~~~ 72 (1039)
|+-+-.-+.+-+||++||+ .+|.||.+.||.|+.++-.+-..++...|-.+|-+.+|-.||+=+---|.-
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-------------ccCCcchhcc
Q 001639 73 GGGAARKPKAKRRSGSEFFDLEA-------------QVDSDEEEDE 105 (1039)
Q Consensus 73 ~~~~~r~kkr~~~~~~~FiD~EA-------------EVDDdeEeee 105 (1039)
+.+ +|-+-.. ++-+|+.+|+
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 193
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=37.92 E-value=48 Score=32.77 Aligned_cols=47 Identities=26% Similarity=0.373 Sum_probs=31.7
Q ss_pred CccCCCCEEEEecccccCceeEEEEEcCC--eEEEeecCCCCCcceeeccccceeec
Q 001639 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCKYF 477 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d--~V~i~~~~~~l~~~i~v~~~~LrK~F 477 (1039)
..+++||.|.-+ -|+.|+|++|+++ .|.|..+ +-.++|.-+.+....
T Consensus 35 ~sLk~GD~VvT~----GGi~G~V~~I~~~~~~v~le~~----gv~i~v~r~AI~~Vv 83 (113)
T PRK06531 35 NAIQKGDEVVTI----GGLYGTVDEVDTEAKTIVLDVD----GVYLTFELAAIKRVV 83 (113)
T ss_pred HhcCCCCEEEEC----CCcEEEEEEEecCCCEEEEEEC----CEEEEEEhhHhhhhc
Confidence 579999999988 4678999999875 4555431 234555555444433
No 194
>PRK14630 hypothetical protein; Provisional
Probab=37.71 E-value=68 Score=32.89 Aligned_cols=46 Identities=22% Similarity=0.205 Sum_probs=35.7
Q ss_pred ccccCcEEEEeecCCCCceeEEEeecCCeEEEEecCCceEEEEecCccc
Q 001639 705 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 753 (1039)
Q Consensus 705 d~liGktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~ 753 (1039)
..++|+.|+|+-..- -..|++++++++.++++.. .+++.++.+.|.
T Consensus 93 ~r~~G~~v~V~l~~~-~~~G~L~~~~d~~i~l~~~--~~~~~i~~~~I~ 138 (143)
T PRK14630 93 KIFEGKKIKLMLDND-FEEGFILEAKADSFIFKTD--SKEVNVLYSDVK 138 (143)
T ss_pred HHhCCCEEEEEEcCc-ceEEEEEEEeCCEEEEEEC--CEEEEEEhHhcc
Confidence 578999999975332 2489999999999998864 567888777765
No 195
>KOG3118 consensus Disrupter of silencing SAS10 [Chromatin structure and dynamics]
Probab=37.46 E-value=9.9 Score=45.41 Aligned_cols=6 Identities=33% Similarity=0.700 Sum_probs=2.5
Q ss_pred ccccCc
Q 001639 488 GTQAGA 493 (1039)
Q Consensus 488 G~~~Ge 493 (1039)
|+|+|+
T Consensus 497 g~Y~GE 502 (517)
T KOG3118|consen 497 GQYSGE 502 (517)
T ss_pred ccccch
Confidence 344443
No 196
>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=37.28 E-value=22 Score=48.74 Aligned_cols=12 Identities=17% Similarity=0.595 Sum_probs=6.9
Q ss_pred EEEEEecchHHH
Q 001639 226 YIYIEADKEAHV 237 (1039)
Q Consensus 226 YIYVEA~~~~~V 237 (1039)
|--|+++.+.+.
T Consensus 4204 f~hv~~d~e~d~ 4215 (4600)
T COG5271 4204 FMHVKEDEEEDL 4215 (4600)
T ss_pred heeecccchhHH
Confidence 666666555443
No 197
>COG4547 CobT Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]
Probab=36.67 E-value=30 Score=41.36 Aligned_cols=10 Identities=20% Similarity=0.351 Sum_probs=5.7
Q ss_pred CCCCCCCCHH
Q 001639 332 VPPPRFMNVD 341 (1039)
Q Consensus 332 RPp~rlFn~~ 341 (1039)
+-|.||-+.-
T Consensus 478 ~~pgrlndlr 487 (620)
T COG4547 478 AFPGRLNDLR 487 (620)
T ss_pred CCchhhhhHH
Confidence 5566665543
No 198
>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=36.32 E-value=14 Score=41.91 Aligned_cols=12 Identities=33% Similarity=0.520 Sum_probs=5.8
Q ss_pred EEEEEeeccchh
Q 001639 303 VTVKLIPRIDLQ 314 (1039)
Q Consensus 303 v~VklvPRiD~~ 314 (1039)
+--.-||+-=+.
T Consensus 251 ~D~eWIp~~~l~ 262 (285)
T PF03896_consen 251 VDEEWIPKEHLN 262 (285)
T ss_pred CCcccCCHHHhh
Confidence 334455655443
No 199
>smart00538 POP4 A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins.
Probab=36.17 E-value=94 Score=29.58 Aligned_cols=48 Identities=27% Similarity=0.387 Sum_probs=39.4
Q ss_pred CccccCcEEEEeecC---CCCceeEEEeecCCeEEEEecCCceEEEEecCcc
Q 001639 704 HDALVGTTVKVRLGP---YKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMI 752 (1039)
Q Consensus 704 ~d~liGktV~I~~Gp---yKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l 752 (1039)
+..|+|-.|+|.+=+ |-|..|+|++-|..++.|+-.. ++..+|+|..-
T Consensus 8 ~~el~G~~v~Vv~s~~ps~vGi~GiVv~ET~nt~~I~t~~-~~~~~IpK~~~ 58 (92)
T smart00538 8 RHELIGLKVRVVASKNPSLVGIEGIVVDETRNTLKIETKE-GRVKTVPKDGA 58 (92)
T ss_pred hhhhcCCEEEEEEcCCCCccCcEEEEEEeeeeEEEEEeCC-CcEEEEECCCe
Confidence 357899999998765 6799999999999999988654 57788888873
No 200
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=36.09 E-value=1.3e+02 Score=41.88 Aligned_cols=85 Identities=14% Similarity=0.174 Sum_probs=63.5
Q ss_pred CccCCCCEEEEecccc-cCceeEEEEEcCC--eEEEeecCCCCCcceeecccccee----------eccCCCceEEeccc
Q 001639 423 GHFMKGDAVIVIKGDL-KNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCK----------YFEPGNHVKVVSGT 489 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel-~gl~G~V~~V~~d--~V~i~~~~~~l~~~i~v~~~~LrK----------~F~~GDhVkVi~G~ 489 (1039)
.+|++|+.|+.+..+. ++..-.|++|+.+ .++|.... ++..+|+++.+-+ -+..||.+++....
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 6899999999666654 4666699999876 45544332 4457777777632 35689999998653
Q ss_pred -----ccCceEEEEEEeCcEEEEEeC
Q 001639 490 -----QAGATGMVLKVEQHVLIILSD 510 (1039)
Q Consensus 490 -----~~GetGlVv~Ve~~~v~llSD 510 (1039)
..|+...|++++++.++|..+
T Consensus 592 ~~~~L~ngd~~tV~~i~~~~itl~~~ 617 (1623)
T PRK14712 592 PGLRVSGGDRLQVASVSEDAMTVVVP 617 (1623)
T ss_pred cccCccCCCEEEEEEecCCeEEEEEC
Confidence 357999999999999999877
No 201
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=36.08 E-value=58 Score=28.79 Aligned_cols=29 Identities=21% Similarity=0.291 Sum_probs=24.4
Q ss_pred CCCCcEEEEecC--CCCCCeeEEEEeeCCCC
Q 001639 273 LSRDTWVRMKIG--NYKGDLAKVVDVDNVRQ 301 (1039)
Q Consensus 273 l~~G~wVRIk~G--~YkGDlAqV~~Vd~~~~ 301 (1039)
++.|+.|||+|- -+=+|.|.|..||..+-
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 202
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=35.50 E-value=97 Score=34.30 Aligned_cols=71 Identities=24% Similarity=0.383 Sum_probs=48.2
Q ss_pred EEEEEEeCCCCeEEEEecc--CCCCceEEecCC--C-eeecCCCCCCcEEEEcCCCCCceEEEEEEeCCC----cEEEec
Q 001639 950 VGVIREVLPDGSCRVVLGS--SGNGDTITALPN--E-IEIVPPRKTDKIKIMGGPHRGATGKLIGVDGTD----GIVKVD 1020 (1039)
Q Consensus 950 ~GvV~~V~~~g~~~V~l~~--~~~g~~v~v~~~--~-Le~V~P~kgd~VkVi~G~~rG~tG~LisiD~~d----giVk~d 1020 (1039)
.|.|.=+.-||+- |.+.+ ...|+++.++-. + ++.....+|..|.|+.|.+.|.+|++..|.-.. -+|.++
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 3455545555553 33333 112456655433 3 677778999999999999999999999998763 577777
Q ss_pred C
Q 001639 1021 V 1021 (1039)
Q Consensus 1021 ~ 1021 (1039)
+
T Consensus 212 ~ 212 (241)
T COG1471 212 D 212 (241)
T ss_pred c
Confidence 5
No 203
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=35.49 E-value=73 Score=31.59 Aligned_cols=59 Identities=15% Similarity=0.290 Sum_probs=37.9
Q ss_pred CceeEEEEEcCCe--EEEeecCCCCCc--------ceeeccccceeeccCCCceEEecccccCceEEEEEEe
Q 001639 440 NLKGWVEKVDEEN--VHIRPEMKGLPK--------TLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLKVE 501 (1039)
Q Consensus 440 gl~G~V~~V~~d~--V~i~~~~~~l~~--------~i~v~~~~LrK~F~~GDhVkVi~G~~~GetGlVv~Ve 501 (1039)
-.+|+|.+|+.+. |+|. |+.+.. .+.+....+.+.+++||.|..-==+ .++.-+|++|+
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--HEPIPAVNWPEMTMRFTITPQTKMSEIKTGDKVAFNFVQ-QGNLSLLQDIK 112 (115)
T ss_pred EEEEEEEEEeCCCCEEEEe--ecccccCCCCCccccccCCChhhhccCCCCCEEEEEEEE-cCCcEEEEEEe
Confidence 3579999998875 6654 443322 3667777777889999999874212 22333666664
No 204
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=35.41 E-value=35 Score=34.50 Aligned_cols=33 Identities=24% Similarity=0.372 Sum_probs=26.3
Q ss_pred cCcEEEEeecCCCCceeEEEeecCCeEEEEecCC
Q 001639 708 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQ 741 (1039)
Q Consensus 708 iGktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~ 741 (1039)
||.-|.|..|||+|-++.|+|+=+.. ||.++..
T Consensus 10 iGRVvli~~Gp~~GKL~vIVDIID~n-RvLVDGP 42 (130)
T PTZ00065 10 PGRLCLIQYGPDAGKLCFIVDIVTPT-RVLVDGA 42 (130)
T ss_pred eceEEEEecCCCCCCEEEEEEEEcCC-eEEEeCC
Confidence 78899999999999999999998643 4444433
No 205
>KOG0608 consensus Warts/lats-like serine threonine kinases [Cell cycle control, cell division, chromosome partitioning]
Probab=34.88 E-value=4.5e+02 Score=33.64 Aligned_cols=8 Identities=50% Similarity=0.812 Sum_probs=3.7
Q ss_pred CCCcCCCC
Q 001639 876 STYVNAPS 883 (1039)
Q Consensus 876 ~~y~~~ps 883 (1039)
++|..+|+
T Consensus 273 s~y~ssPs 280 (1034)
T KOG0608|consen 273 SAYDSSPS 280 (1034)
T ss_pred cccccCCC
Confidence 44554443
No 206
>PRK04950 ProP expression regulator; Provisional
Probab=34.59 E-value=62 Score=35.34 Aligned_cols=45 Identities=29% Similarity=0.496 Sum_probs=36.7
Q ss_pred ccCcEEEEeecCCCCceeEEEeecCCeEEEEecCCceEEEEecCccc
Q 001639 707 LVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 753 (1039)
Q Consensus 707 liGktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~ 753 (1039)
-+||.|+|.-|. --.-|.|.+++-+.|||+|.+... |.|.-+||.
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 379999999884 346689999999999999999876 677776663
No 207
>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=34.48 E-value=83 Score=27.72 Aligned_cols=28 Identities=21% Similarity=0.330 Sum_probs=22.8
Q ss_pred CCCCcEEEEecC--CCCCCeeEEEEeeCCC
Q 001639 273 LSRDTWVRMKIG--NYKGDLAKVVDVDNVR 300 (1039)
Q Consensus 273 l~~G~wVRIk~G--~YkGDlAqV~~Vd~~~ 300 (1039)
++.|+.|||+|- -+=+|+|.|..||.++
T Consensus 1 i~rgskVrIlR~ESYWyn~vGtV~svdqs~ 30 (61)
T PF02427_consen 1 IKRGSKVRILRKESYWYNEVGTVASVDQSG 30 (61)
T ss_dssp S-TTSEEEE-SSSSTTTTSEEEEEEETTSS
T ss_pred CCCCCEEEEccccceeecccceEEEEccCC
Confidence 467999999984 5789999999999887
No 208
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=34.48 E-value=23 Score=46.35 Aligned_cols=22 Identities=32% Similarity=0.413 Sum_probs=11.4
Q ss_pred hhhhhhchhhccccccccccCc
Q 001639 31 EEEEEDDRSSRKRRRSQFIDDV 52 (1039)
Q Consensus 31 edeee~~~~~~~~~~~~~~~d~ 52 (1039)
-||||=....+.|..+.||-|+
T Consensus 49 VDeeEY~k~v~~r~~DdfvVdD 70 (1429)
T KOG0970|consen 49 VDEEEYRKIVRQRLDDDFVVDD 70 (1429)
T ss_pred cCHHHHHHHHHHHhcCCeEEeC
Confidence 3333333345555567885554
No 209
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=34.42 E-value=1e+02 Score=37.71 Aligned_cols=51 Identities=31% Similarity=0.388 Sum_probs=33.5
Q ss_pred CccCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccc--------eeeccCCCceEEe
Q 001639 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKEL--------CKYFEPGNHVKVV 486 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~L--------rK~F~~GDhVkVi 486 (1039)
..|++||.|+ |+|++|+.+.|.|.... +-.=.+|.++| .+.|++||.|++.
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 78999988876655421 11122344444 4579999999864
No 210
>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=34.35 E-value=22 Score=30.79 Aligned_cols=20 Identities=30% Similarity=0.421 Sum_probs=13.3
Q ss_pred ccccCCCCeecCCCEEEEec
Q 001639 592 NVQDRNKNTVAVKDVVRIVE 611 (1039)
Q Consensus 592 ~a~D~~gn~I~~~D~Vkv~~ 611 (1039)
+..|+|||.+.-||.|.++.
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 46899999999999999975
No 211
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=34.18 E-value=3.5e+02 Score=29.51 Aligned_cols=27 Identities=30% Similarity=0.535 Sum_probs=21.4
Q ss_pred ceEEEEEEeCcEEEEEeCCCCceEEEe
Q 001639 493 ATGMVLKVEQHVLIILSDTTKEDIRVF 519 (1039)
Q Consensus 493 etGlVv~Ve~~~v~llSD~t~~ei~V~ 519 (1039)
--|-||.|..+.+.|=|.+-.+.++|.
T Consensus 42 iEGrVvEV~~~~i~iesk~yn~~v~i~ 68 (213)
T PRK06763 42 IEGRVVEVDNGVIVIKSKQYEEPVSVY 68 (213)
T ss_pred eeeEEEEEeCCEEEEEeccCCCceEEE
Confidence 347788888888888888887777774
No 212
>KOG0066 consensus eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]
Probab=34.16 E-value=35 Score=40.81 Aligned_cols=15 Identities=20% Similarity=0.512 Sum_probs=6.9
Q ss_pred CCCcccccCCCCCCc
Q 001639 77 ARKPKAKRRSGSEFF 91 (1039)
Q Consensus 77 ~r~kkr~~~~~~~Fi 91 (1039)
++|-|+++...+.|-
T Consensus 117 ~~k~~k~~k~~d~fs 131 (807)
T KOG0066|consen 117 SKKNKKNKKKNDDFS 131 (807)
T ss_pred CccccccccCCCccc
Confidence 333344444455665
No 213
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=33.66 E-value=1.3e+02 Score=38.60 Aligned_cols=27 Identities=19% Similarity=0.160 Sum_probs=19.8
Q ss_pred CccccCcEEEEeecCCCCceeEEEeec
Q 001639 704 HDALVGTTVKVRLGPYKGYRGRVVDVK 730 (1039)
Q Consensus 704 ~d~liGktV~I~~GpyKG~~G~Vkd~t 730 (1039)
...+..|+|||.=|.=||-.---|+.-
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 467888999999998888765444443
No 214
>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=33.08 E-value=1.4e+02 Score=29.66 Aligned_cols=38 Identities=24% Similarity=0.290 Sum_probs=25.4
Q ss_pred ccCccCCCCEEEEe----cc---cccCceeEEEEEcCC----eEEEeec
Q 001639 421 KKGHFMKGDAVIVI----KG---DLKNLKGWVEKVDEE----NVHIRPE 458 (1039)
Q Consensus 421 ~~~~F~~GD~V~V~----~G---el~gl~G~V~~V~~d----~V~i~~~ 458 (1039)
.-..|.+||.|+|. +| ......|.|+++.+. +++|...
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 23 234578888888743 4455443
No 215
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=33.08 E-value=42 Score=32.00 Aligned_cols=39 Identities=26% Similarity=0.494 Sum_probs=31.7
Q ss_pred eeecCCCCCCcEEEEcCC--CCCceEEEEEEeCCCc-----EEEec
Q 001639 982 IEIVPPRKTDKIKIMGGP--HRGATGKLIGVDGTDG-----IVKVD 1020 (1039)
Q Consensus 982 Le~V~P~kgd~VkVi~G~--~rG~tG~LisiD~~dg-----iVk~d 1020 (1039)
-.++-|++|++|+|+.=+ +-..+|++.+||.+.| +||++
T Consensus 35 pp~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~~girYPVvVRF~ 80 (101)
T PLN00045 35 PPPIGPKRGSKVKILRPESYWFNDVGKVVAVDQDPGVRYPVVVRFE 80 (101)
T ss_pred CCCcccCCCCEEEEccccceeecCcceEEEEeCCCCcccceEEEee
Confidence 356778999999999977 4678999999999877 46655
No 216
>PHA02774 E1; Provisional
Probab=32.95 E-value=14 Score=45.77 Aligned_cols=20 Identities=25% Similarity=0.371 Sum_probs=14.3
Q ss_pred hhhhHHHHHHHHHHHhccCC
Q 001639 140 EQEDVEALERRIQARYARSS 159 (1039)
Q Consensus 140 ~~~d~e~~~~~l~eRY~~~~ 159 (1039)
+.++-++....||+||..+.
T Consensus 65 ~~~~~~~~i~~LKRKy~~sp 84 (613)
T PHA02774 65 EAEEDEQQIQALKRKYLSSP 84 (613)
T ss_pred HHHHHHHHHHHhccccCCCC
Confidence 34455667789999998653
No 217
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=32.47 E-value=59 Score=29.30 Aligned_cols=38 Identities=26% Similarity=0.385 Sum_probs=29.2
Q ss_pred CCCCcEEEEecC--CCCCCeeEEEEeeCCCCEEEEEEeeccc
Q 001639 273 LSRDTWVRMKIG--NYKGDLAKVVDVDNVRQRVTVKLIPRID 312 (1039)
Q Consensus 273 l~~G~wVRIk~G--~YkGDlAqV~~Vd~~~~~v~VklvPRiD 312 (1039)
++.|+.|||+|- -+=+|.|.|..||..+ +.--++=|+|
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 678999999984 5789999999999886 3444444554
No 218
>PRK14633 hypothetical protein; Provisional
Probab=32.30 E-value=78 Score=32.67 Aligned_cols=49 Identities=29% Similarity=0.407 Sum_probs=38.0
Q ss_pred ccccCcEEEEee-c---CCCCceeEEEeecCCeEEEEecCCceEEEEecCcccc
Q 001639 705 DALVGTTVKVRL-G---PYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1039)
Q Consensus 705 d~liGktV~I~~-G---pyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~~ 754 (1039)
..++|+.|+|+- . .-|=+.|+++.++++.+++++.. .+++.++.++|.-
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 34668899999999999988743 4677888877753
No 219
>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=32.07 E-value=2.2e+02 Score=25.09 Aligned_cols=61 Identities=18% Similarity=0.218 Sum_probs=39.6
Q ss_pred CceEEEEEEccc-eeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCCCCceecEEEE
Q 001639 550 NSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHI 624 (1039)
Q Consensus 550 ~tVGvIvrverd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~kgr~G~V~hI 624 (1039)
+.+|+|+++-.+ .|.|... +|..+.+... .|+.++. -|+.||.|.|---|+.-..|.|.|.
T Consensus 4 e~~~~V~~~lG~~~~~V~~~---dg~~~l~~i~---gK~r~~i--------wI~~GD~V~V~~~~~d~~kG~Ii~r 65 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECE---DGEERLARIP---GKFRKRI--------WIKRGDFVLVEPSPYDKVKGRIIYR 65 (65)
T ss_dssp EEEEEEEEEESSSEEEEEET---TSEEEEEEE----HHHHTCC-----------TTEEEEEEESTTCTTEEEEEEE
T ss_pred EEEEEEEEECCCCEEEEEeC---CCCEEEEEec---cceeeeE--------ecCCCCEEEEEecccCCCeEEEEEC
Confidence 457889998865 5788774 4666665543 3322212 4899999999877777778888773
No 220
>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=32.06 E-value=1e+02 Score=27.59 Aligned_cols=45 Identities=24% Similarity=0.333 Sum_probs=28.2
Q ss_pred eEEEEEc--CCeEEEeec-CCCCC-----cceeeccccceeeccCCCceEEec
Q 001639 443 GWVEKVD--EENVHIRPE-MKGLP-----KTLAVNSKELCKYFEPGNHVKVVS 487 (1039)
Q Consensus 443 G~V~~V~--~d~V~i~~~-~~~l~-----~~i~v~~~~LrK~F~~GDhVkVi~ 487 (1039)
|.|.+|+ ...|+|.-. .++|. =.+.+....+-.-|++||.|...-
T Consensus 1 G~V~~vd~~~~~iti~H~pIp~l~wpaMTM~F~v~~~~~l~~l~~Gd~V~F~~ 53 (70)
T PF11604_consen 1 GVVKSVDPEAGTITISHEPIPELGWPAMTMDFPVADPVDLAGLKPGDKVRFTF 53 (70)
T ss_dssp EEEEEEETTTTEEEEEE--BCCCTB-SEEEEEE--TTSEESS-STT-EEEEEE
T ss_pred CEEEEEecCCCEEEEecCccccCCCCCeEEEEEcCChhhhhcCCCCCEEEEEE
Confidence 7899999 557777633 12331 137777777889999999998753
No 221
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.99 E-value=97 Score=32.28 Aligned_cols=48 Identities=33% Similarity=0.544 Sum_probs=39.6
Q ss_pred ccccCcEEEEee----cCCCCceeEEEeecCCeEEEEecCCceEEEEecCcccc
Q 001639 705 DALVGTTVKVRL----GPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1039)
Q Consensus 705 d~liGktV~I~~----GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~~ 754 (1039)
..++|+.|+|.. ..=|=+.|+++.+.+++++++.. .|.|.|+...|+-
T Consensus 95 ~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~v~~~~~--~k~v~Ip~~~i~k 146 (153)
T COG0779 95 ARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGETVTLEVD--GKEVEIPFSDIAK 146 (153)
T ss_pred HHhcCcEEEEEEecccCCceEEEEEEEEEcCCeEEEEEC--CEEEEEEcccchh
Confidence 578999999998 55788999999999999888844 5668888877653
No 222
>PRK14632 hypothetical protein; Provisional
Probab=31.96 E-value=81 Score=33.33 Aligned_cols=50 Identities=20% Similarity=0.449 Sum_probs=39.1
Q ss_pred ccccCcEEEEe-ecC------CCCceeEEEeecCCeEEEEecCC------ceEEEEecCcccc
Q 001639 705 DALVGTTVKVR-LGP------YKGYRGRVVDVKGQSVRVELESQ------MKVVTVDRSMISD 754 (1039)
Q Consensus 705 d~liGktV~I~-~Gp------yKG~~G~Vkd~t~~~arVELhs~------~k~I~V~r~~l~~ 754 (1039)
..++|+.|+|+ ..+ -|=+.|+++.++++.+++++..+ ..++.++.+.|.-
T Consensus 94 ~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~~i~l~~~~~~~~~~~~~~~~i~~~~I~k 156 (172)
T PRK14632 94 SPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGDTVVLRPEGAPAPEAEEAVLRTSWQGVRK 156 (172)
T ss_pred HHhCCCEEEEEEeccccccCCceEEEEEEEEEeCCEEEEEEcCcccccCCceeEEEEhHHccE
Confidence 57899999995 343 36788999999999999998643 2478888888764
No 223
>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=31.90 E-value=40 Score=41.90 Aligned_cols=10 Identities=40% Similarity=0.600 Sum_probs=4.6
Q ss_pred HHHHHHHHHh
Q 001639 146 ALERRIQARY 155 (1039)
Q Consensus 146 ~~~~~l~eRY 155 (1039)
.|++.|+.+-
T Consensus 338 rLA~~Lqr~L 347 (600)
T TIGR01651 338 RLANRLQRRL 347 (600)
T ss_pred HHHHHHHHHH
Confidence 3444444443
No 224
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=31.80 E-value=3e+02 Score=32.22 Aligned_cols=23 Identities=9% Similarity=0.004 Sum_probs=14.7
Q ss_pred CCeEEEEecCCceEEE-EecCccc
Q 001639 731 GQSVRVELESQMKVVT-VDRSMIS 753 (1039)
Q Consensus 731 ~~~arVELhs~~k~I~-V~r~~l~ 753 (1039)
+-.-+-+||-++-+|+ -+|..++
T Consensus 142 eiLP~k~iHGQ~P~V~~~NK~~~a 165 (498)
T KOG4849|consen 142 EILPTKTIHGQSPTVLSYNKTNQA 165 (498)
T ss_pred HhcccceecCCCCeeeccchhhHH
Confidence 3344558898887765 4666654
No 225
>COG4873 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.70 E-value=66 Score=28.87 Aligned_cols=47 Identities=23% Similarity=0.306 Sum_probs=0.0
Q ss_pred CCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceee
Q 001639 426 MKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 476 (1039)
Q Consensus 426 ~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~ 476 (1039)
.+||.|+.. -|++|.|.+++++.|.+--..-+--..|.++.+.+.-+
T Consensus 25 ~vgniief~----dgl~g~vek~nensvivdlt~menf~dl~l~ektvvnh 71 (81)
T COG4873 25 KVGNIIEFK----DGLTGVVEKVNENSVIVDLTIMENFRDLELDEKTVVNH 71 (81)
T ss_pred eccceEEEc----ccceeeeeeecCCcEEEEEEeeccccccCCcceeeEcc
No 226
>PRK12288 GTPase RsgA; Reviewed
Probab=31.60 E-value=2.4e+02 Score=33.11 Aligned_cols=88 Identities=19% Similarity=0.211 Sum_probs=57.2
Q ss_pred ceEEEEEEccceeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecC--CCCCceecEEEEECCE
Q 001639 551 SFGVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEG--PCKGKQGPVEHIYRGI 628 (1039)
Q Consensus 551 tVGvIvrverd~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~G--p~kgr~G~V~hI~r~~ 628 (1039)
..|.|+++.+..+.|++. .|.+..++... ++ ..+-+||.|.+... ......|.|.+|+-.+
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 459999999999999873 46665544322 11 12889999998521 1101249999999666
Q ss_pred EEEEeCceeeeceEEEEeCCceEEecc
Q 001639 629 LFIHDRHHLEHAGFICAKSSSCVVVGG 655 (1039)
Q Consensus 629 lFl~~~~~~EN~Gifv~~a~~~~~~g~ 655 (1039)
=.|.-+......-+++++...+.++-+
T Consensus 103 n~L~R~~~~~~~q~iaANvD~vlIV~s 129 (347)
T PRK12288 103 SVLTRPDYYDGVKPIAANIDQIVIVSA 129 (347)
T ss_pred ceEECCCcccccceEEEEccEEEEEEe
Confidence 444433333333578888888888865
No 227
>KOG2418 consensus Microtubule-associated protein TAU [Cytoskeleton]
Probab=31.30 E-value=1.1e+02 Score=35.72 Aligned_cols=6 Identities=33% Similarity=0.728 Sum_probs=2.9
Q ss_pred cEEEEc
Q 001639 992 KIKIMG 997 (1039)
Q Consensus 992 ~VkVi~ 997 (1039)
.|||..
T Consensus 375 nvKI~S 380 (448)
T KOG2418|consen 375 NVKIVS 380 (448)
T ss_pred ceeeee
Confidence 355544
No 228
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=31.29 E-value=99 Score=26.97 Aligned_cols=49 Identities=18% Similarity=0.251 Sum_probs=34.6
Q ss_pred cccCcEEEEeecCCCCceeEEEeec---CCeEEEEecCCceEEEEecCcccccc
Q 001639 706 ALVGTTVKVRLGPYKGYRGRVVDVK---GQSVRVELESQMKVVTVDRSMISDNV 756 (1039)
Q Consensus 706 ~liGktV~I~~GpyKG~~G~Vkd~t---~~~arVELhs~~k~I~V~r~~l~~~~ 756 (1039)
.+.||..-|..|||.--+|+||.-. ++++-+-+. .+.|.|...+|..++
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 4789999999999999999999755 334444443 345566666665544
No 229
>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=31.25 E-value=27 Score=44.97 Aligned_cols=15 Identities=20% Similarity=0.370 Sum_probs=9.6
Q ss_pred ecccccCceEEEEEE
Q 001639 486 VSGTQAGATGMVLKV 500 (1039)
Q Consensus 486 i~G~~~GetGlVv~V 500 (1039)
..|+++|.+|..-+.
T Consensus 649 ~~g~~~g~~GF~~~~ 663 (794)
T PF08553_consen 649 KDGKNSGKLGFEKSF 663 (794)
T ss_pred ecCCccCcccccccc
Confidence 356777777765554
No 230
>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=31.18 E-value=16 Score=33.82 Aligned_cols=35 Identities=20% Similarity=0.536 Sum_probs=2.9
Q ss_pred ccceeeccCCCceEEecccccCceEEEEEEeCcEEEEEe
Q 001639 471 KELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILS 509 (1039)
Q Consensus 471 ~~LrK~F~~GDhVkVi~G~~~GetGlVv~Ve~~~v~llS 509 (1039)
.+++...++||.|..++|-| |.|++++++.++|=.
T Consensus 31 ~~m~~~Lk~Gd~VvT~gGi~----G~V~~i~~~~v~lei 65 (82)
T PF02699_consen 31 QEMLASLKPGDEVVTIGGIY----GTVVEIDDDTVVLEI 65 (82)
T ss_dssp TTGGG----------------------------------
T ss_pred HHHHHcCCCCCEEEECCcEE----EEEEEEeCCEEEEEE
Confidence 45667788999999998855 999999998887744
No 231
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=31.14 E-value=92 Score=25.58 Aligned_cols=33 Identities=24% Similarity=0.450 Sum_probs=22.1
Q ss_pred CCCceEEEEEEeCCCcEEEecCCCceEEEecccc
Q 001639 1000 HRGATGKLIGVDGTDGIVKVDVSLDVKILDMAIL 1033 (1039)
Q Consensus 1000 ~rG~tG~LisiD~~dgiVk~d~~~~~kil~~~~L 1033 (1039)
.+|.+|+.+++|+.=|.+ |..+.+-.++++..|
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 555667888888765
No 232
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=31.06 E-value=1.8e+02 Score=29.01 Aligned_cols=37 Identities=24% Similarity=0.354 Sum_probs=26.6
Q ss_pred cCccCCCCEEEEe----ccc---ccCceeEEEEEcCC----eEEEeec
Q 001639 422 KGHFMKGDAVIVI----KGD---LKNLKGWVEKVDEE----NVHIRPE 458 (1039)
Q Consensus 422 ~~~F~~GD~V~V~----~Ge---l~gl~G~V~~V~~d----~V~i~~~ 458 (1039)
-..|.+||.|+|. +|+ .....|.|+++.+. +++|.--
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 454 45688999998744 4555544
No 233
>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=30.62 E-value=27 Score=43.66 Aligned_cols=6 Identities=33% Similarity=0.933 Sum_probs=2.6
Q ss_pred Eeeccc
Q 001639 307 LIPRID 312 (1039)
Q Consensus 307 lvPRiD 312 (1039)
+|=|||
T Consensus 336 ~verLd 341 (595)
T PF05470_consen 336 FVERLD 341 (595)
T ss_pred HHHHHH
Confidence 344444
No 234
>COG5129 MAK16 Nuclear protein with HMG-like acidic region [General function prediction only]
Probab=30.24 E-value=20 Score=38.93 Aligned_cols=6 Identities=33% Similarity=0.307 Sum_probs=2.5
Q ss_pred CCcccc
Q 001639 78 RKPKAK 83 (1039)
Q Consensus 78 r~kkr~ 83 (1039)
+.||||
T Consensus 267 ~~rkrk 272 (303)
T COG5129 267 KIRKRK 272 (303)
T ss_pred chhhcc
Confidence 344443
No 235
>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=30.06 E-value=17 Score=33.63 Aligned_cols=41 Identities=29% Similarity=0.404 Sum_probs=0.0
Q ss_pred cCcEEEEeecCCCCceeEEEeecCCeEEEEecCCceEEEEecCccc
Q 001639 708 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 753 (1039)
Q Consensus 708 iGktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~ 753 (1039)
.|..|.-.. |+.|+|++++++++.||+.. +-.+++.|..|+
T Consensus 39 ~Gd~VvT~g----Gi~G~V~~i~~~~v~lei~~-g~~i~v~k~aI~ 79 (82)
T PF02699_consen 39 PGDEVVTIG----GIYGTVVEIDDDTVVLEIAP-GVEITVEKSAIA 79 (82)
T ss_dssp ----------------------------------------------
T ss_pred CCCEEEECC----cEEEEEEEEeCCEEEEEECC-CeEEEEEHHHhH
Confidence 355555444 69999999999999999998 456899988775
No 236
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=30.00 E-value=68 Score=32.35 Aligned_cols=62 Identities=18% Similarity=0.059 Sum_probs=47.0
Q ss_pred cCccCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCc-ceeeccccceeeccCCCceEEec
Q 001639 422 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPK-TLAVNSKELCKYFEPGNHVKVVS 487 (1039)
Q Consensus 422 ~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~-~i~v~~~~LrK~F~~GDhVkVi~ 487 (1039)
...|..+|.|++. .+.--....+-++++.+++|-... ..+ .|..+. ++.++++.|..|.|++
T Consensus 57 e~~f~s~~~ve~~--~ve~~~~qylY~dg~~~~fMd~et-yeq~~i~~~~-~~~~~Lke~~~V~v~~ 119 (130)
T TIGR00037 57 EFVSPSTSKVEVP--IVDRREYQVLAIMGGMVQLMDLDT-YETDELPIPE-ELGDSLEPGFEVEYIE 119 (130)
T ss_pred EEEECCCCEEEEe--EEEEEEEEEEEecCCEEEEEcCCC-cEEEEecCCh-hHHHHhhcCCEEEEEe
Confidence 4689999999987 555566678888999988886532 222 355555 8999999999999886
No 237
>PRK14636 hypothetical protein; Provisional
Probab=29.95 E-value=84 Score=33.38 Aligned_cols=49 Identities=20% Similarity=0.398 Sum_probs=37.0
Q ss_pred ccccCcEEEEee-cCC---CCceeEEEeecCCeEEEEecCCceEEEEecCcccc
Q 001639 705 DALVGTTVKVRL-GPY---KGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 754 (1039)
Q Consensus 705 d~liGktV~I~~-Gpy---KG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~~ 754 (1039)
..++|+.|+|+- .+. |=+.|+++++++..+++++.. .++++|+.+.|.-
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 578999999963 443 456899999999999988742 4567888777753
No 238
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=29.84 E-value=25 Score=43.86 Aligned_cols=23 Identities=13% Similarity=0.384 Sum_probs=11.3
Q ss_pred cCCccEEEEEecchHHHHHHHhcC
Q 001639 221 DHLKNYIYIEADKEAHVKEACKGL 244 (1039)
Q Consensus 221 ~~lkGYIYVEA~~~~~V~~ai~gl 244 (1039)
..+.-||.=+. .+...+..+.|+
T Consensus 459 sRys~wv~~~~-~~~~f~pvL~~l 481 (885)
T KOG2023|consen 459 SRYSKWVVQDS-RDEYFKPVLEGL 481 (885)
T ss_pred hhhhhhHhcCC-hHhhhHHHHHHH
Confidence 44555555544 334444455444
No 239
>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=29.81 E-value=11 Score=38.64 Aligned_cols=16 Identities=44% Similarity=0.594 Sum_probs=12.8
Q ss_pred CCCCCcccccccCCcc
Q 001639 86 SGSEFFDLEAQVDSDE 101 (1039)
Q Consensus 86 ~~~~FiD~EAEVDDde 101 (1039)
..+.||+.|||++|||
T Consensus 5 ~~~~~vE~EAEESeDE 20 (145)
T PF09444_consen 5 GASEFVEEEAEESEDE 20 (145)
T ss_pred hHHHHHHHHHhcchhh
Confidence 4568999999988865
No 240
>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=29.71 E-value=1.8e+02 Score=34.58 Aligned_cols=66 Identities=14% Similarity=0.119 Sum_probs=46.4
Q ss_pred HHHHHHHHHHHhhCCCcceEEEEee-cCCccEEEEEecchHHHHHHHhcCcccc--e--eeeeeeChhhhhhcc
Q 001639 196 EAAVCLMQKCIDKGSELQIRSVIAL-DHLKNYIYIEADKEAHVKEACKGLRNIY--S--QKVMLVPIREMTDVL 264 (1039)
Q Consensus 196 ~vv~~Lm~K~~~~~~~l~I~Svf~~-~~lkGYIYVEA~~~~~V~~ai~gl~~v~--~--~~~~lVpi~Em~~vL 264 (1039)
++..-|..-|...| .|.+|+.. ....|++||+-.+..+...|++.|.|-+ + ..+..+|.+.+...+
T Consensus 384 ~~~~dv~~e~~k~G---~v~~v~v~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~~~~~~~ 454 (457)
T TIGR01622 384 EILDDVKEECSKYG---GVVHIYVDTKNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVNDVYDMSC 454 (457)
T ss_pred HHHHHHHHHHHhcC---CeeEEEEeCCCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHHHHHhhc
Confidence 34444444444433 35566554 6778999999999999999999999976 3 355677777766554
No 241
>PRK02001 hypothetical protein; Validated
Probab=29.71 E-value=1.1e+02 Score=31.89 Aligned_cols=49 Identities=16% Similarity=0.209 Sum_probs=37.6
Q ss_pred ccccCcEEEEeecCCCCceeEEEeecCCeEEEEecCC------------ceEEEEecCccc
Q 001639 705 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQ------------MKVVTVDRSMIS 753 (1039)
Q Consensus 705 d~liGktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~------------~k~I~V~r~~l~ 753 (1039)
..++|+.|+|+-..-|-+.|+++++++..+.+++..+ .+.++++.+.|.
T Consensus 86 ~r~~G~~v~V~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~k~~~~~~~~~~i~~~~I~ 146 (152)
T PRK02001 86 KKNIGRELEVLTKNGKKIEGELKSADENDITLEVKAREPKEGGKGKVTVEKEETITYDDIK 146 (152)
T ss_pred HHhCCCEEEEEECCCCEEEEEEEEEeCCEEEEEEcccccccccccccccceeEEEEhHhee
Confidence 5789999999864348899999999999999998753 235666665554
No 242
>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=29.52 E-value=18 Score=42.65 Aligned_cols=6 Identities=33% Similarity=0.645 Sum_probs=0.0
Q ss_pred CCcccc
Q 001639 89 EFFDLE 94 (1039)
Q Consensus 89 ~FiD~E 94 (1039)
.|+|++
T Consensus 366 t~~Ded 371 (430)
T PF09507_consen 366 TFVDED 371 (430)
T ss_dssp ------
T ss_pred EEEcCC
Confidence 677655
No 243
>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=29.18 E-value=96 Score=25.82 Aligned_cols=51 Identities=20% Similarity=0.109 Sum_probs=36.6
Q ss_pred ccCCCCEEEEecccccCceeEEEEEcC-CeEEEeecCCCCCcceeeccccceee
Q 001639 424 HFMKGDAVIVIKGDLKNLKGWVEKVDE-ENVHIRPEMKGLPKTLAVNSKELCKY 476 (1039)
Q Consensus 424 ~F~~GD~V~V~~Gel~gl~G~V~~V~~-d~V~i~~~~~~l~~~i~v~~~~LrK~ 476 (1039)
.|++|+.|.+.--+-.=-+|+|+++++ ..+.|.- -|.+....|+..+||..
T Consensus 2 ~~~~G~~~~a~~~d~~wyra~I~~~~~~~~~~V~f--~D~G~~~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARWEDGEWYRARIIKVDGEQLYEVFF--IDYGNEEVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEeCCCCEEEEEEEEECCCCEEEEEE--ECCCccEEEeHHHeecC
Confidence 588999999986444568999999998 4455443 34556677777777753
No 244
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.07 E-value=80 Score=32.86 Aligned_cols=48 Identities=23% Similarity=0.282 Sum_probs=39.2
Q ss_pred cCCCCEEEEec----ccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceee
Q 001639 425 FMKGDAVIVIK----GDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 476 (1039)
Q Consensus 425 F~~GD~V~V~~----Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~ 476 (1039)
...|-.|+|.- ...+..+|+|+.++++.|++..+. +++.+|-+.+.|.
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 35799999988 777999999999999999998664 3488887777663
No 245
>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=28.97 E-value=87 Score=25.69 Aligned_cols=42 Identities=24% Similarity=0.228 Sum_probs=26.0
Q ss_pred eeEEEEEcCCeEEEeecCCCCCcceeecccc--------ceeeccCCCceEEe
Q 001639 442 KGWVEKVDEENVHIRPEMKGLPKTLAVNSKE--------LCKYFEPGNHVKVV 486 (1039)
Q Consensus 442 ~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~--------LrK~F~~GDhVkVi 486 (1039)
.|+|++|..+.+.+..... ..--++.++ ..++|++||.|++.
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 5888888877666654311 122233333 35679999999873
No 246
>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=28.93 E-value=1.3e+02 Score=26.66 Aligned_cols=44 Identities=20% Similarity=0.311 Sum_probs=29.7
Q ss_pred CceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCceEEe
Q 001639 440 NLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVV 486 (1039)
Q Consensus 440 gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi 486 (1039)
...|+|.+|+....+|.-+.+ +.+.+|..-=--..++|.-|.|.
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 367999999999888876543 34444443333456788888774
No 247
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=28.84 E-value=34 Score=41.67 Aligned_cols=17 Identities=6% Similarity=0.237 Sum_probs=10.3
Q ss_pred hhHHHHHHHHHHHhccC
Q 001639 142 EDVEALERRIQARYARS 158 (1039)
Q Consensus 142 ~d~e~~~~~l~eRY~~~ 158 (1039)
...-++|+..=++++..
T Consensus 559 i~~~dv~kk~g~~wk~m 575 (615)
T KOG0526|consen 559 ISVGDVAKKAGEKWKQM 575 (615)
T ss_pred chHHHHHHHHhHHHhhh
Confidence 34556777776666543
No 248
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.77 E-value=33 Score=40.32 Aligned_cols=7 Identities=57% Similarity=1.355 Sum_probs=4.1
Q ss_pred CCCCCCC
Q 001639 176 LPSVRDP 182 (1039)
Q Consensus 176 lPsv~Dp 182 (1039)
||+++-|
T Consensus 358 lp~i~~p 364 (514)
T KOG3130|consen 358 LPTIRTP 364 (514)
T ss_pred CCccCCc
Confidence 6666643
No 249
>PRK12366 replication factor A; Reviewed
Probab=28.67 E-value=1.3e+03 Score=29.35 Aligned_cols=31 Identities=16% Similarity=0.157 Sum_probs=19.9
Q ss_pred ceecEEEEECCEEEE-----EeCceeeeceEEEEeC
Q 001639 617 KQGPVEHIYRGILFI-----HDRHHLEHAGFICAKS 647 (1039)
Q Consensus 617 r~G~V~hI~r~~lFl-----~~~~~~EN~Gifv~~a 647 (1039)
-.|.|.||+..-.|. ++|++.++.|.+.|..
T Consensus 518 v~g~i~~i~~~~~~y~aCp~CnkKv~~~~g~~~C~~ 553 (637)
T PRK12366 518 IRGTVVDIRKQKIILYLCPNCRKRVEEVDGEYICEF 553 (637)
T ss_pred EEEEEEEEeCCCEEEecccccCeEeEcCCCcEECCC
Confidence 468999999764333 4455666666666644
No 250
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=28.47 E-value=2.1e+02 Score=23.75 Aligned_cols=42 Identities=21% Similarity=0.254 Sum_probs=24.2
Q ss_pred eeEEEEEcCCeEEEeecCCCCCcceeeccccce--------eeccCCCceEEe
Q 001639 442 KGWVEKVDEENVHIRPEMKGLPKTLAVNSKELC--------KYFEPGNHVKVV 486 (1039)
Q Consensus 442 ~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~Lr--------K~F~~GDhVkVi 486 (1039)
.|+|.++....+.+.... . -.--++.+++. +.|++||.|++.
T Consensus 7 ~g~V~~v~~~g~~v~i~~-~--~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~ 56 (72)
T smart00316 7 EGTVTEITPFGAFVDLGN-G--VEGLIPISELSDKRVKDPEEVLKVGDEVKVK 56 (72)
T ss_pred EEEEEEEEccEEEEEeCC-C--CEEEEEHHHCCccccCCHHHeecCCCEEEEE
Confidence 577777777655444321 1 12233444443 459999999873
No 251
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=28.35 E-value=73 Score=32.12 Aligned_cols=37 Identities=22% Similarity=0.372 Sum_probs=29.6
Q ss_pred eeeccCCCceEEecccccCceEEEEEEeCcEEEEEeC
Q 001639 474 CKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSD 510 (1039)
Q Consensus 474 rK~F~~GDhVkVi~G~~~GetGlVv~Ve~~~v~llSD 510 (1039)
++.+++|--|.+.+|+++|.--+||++=++.+.+.++
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 252
>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=28.01 E-value=65 Score=33.90 Aligned_cols=46 Identities=17% Similarity=0.286 Sum_probs=32.2
Q ss_pred cCccCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeecccccee
Q 001639 422 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK 475 (1039)
Q Consensus 422 ~~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK 475 (1039)
...|++||.|+|- +..|+|++|.--.+++.... ++.+.+|-+.|..
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 99999999998888887543 3568888777753
No 253
>PRK14646 hypothetical protein; Provisional
Probab=27.96 E-value=98 Score=32.18 Aligned_cols=47 Identities=15% Similarity=0.194 Sum_probs=36.9
Q ss_pred ccccCcEEEEee-cCC---CCceeEEEeecCCeEEEEecCCceEEEEecCccc
Q 001639 705 DALVGTTVKVRL-GPY---KGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 753 (1039)
Q Consensus 705 d~liGktV~I~~-Gpy---KG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~ 753 (1039)
..++|+.|+|+- .+. |=+.|+++.+.++.+++++ ..+++.++.+.|.
T Consensus 96 ~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~~v~l~~--~g~~~~i~~~~I~ 146 (155)
T PRK14646 96 KTFKGFPVNVELNQKNSKIKFLNGLLYEKSKDYLAINI--KGKIKKIPFNEVL 146 (155)
T ss_pred HHhCCCEEEEEEecCcCCeEEEEEEEEEEeCCEEEEEE--CCEEEEEEHHHee
Confidence 578999999973 333 4567999999999999986 4677888877765
No 254
>PRK05807 hypothetical protein; Provisional
Probab=27.92 E-value=2.2e+02 Score=28.79 Aligned_cols=15 Identities=20% Similarity=0.337 Sum_probs=11.8
Q ss_pred cceeeccCCCceEEe
Q 001639 472 ELCKYFEPGNHVKVV 486 (1039)
Q Consensus 472 ~LrK~F~~GDhVkVi 486 (1039)
++..+|++||.|+|.
T Consensus 44 ~~~~~~kvGd~V~Vk 58 (136)
T PRK05807 44 DIREHLKEQDKVKVK 58 (136)
T ss_pred CccccCCCCCEEEEE
Confidence 346789999999884
No 255
>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=27.91 E-value=2.5e+02 Score=24.38 Aligned_cols=58 Identities=19% Similarity=0.230 Sum_probs=34.2
Q ss_pred EEEEEEcc-ceeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCCCCceecEEE
Q 001639 553 GVIIRVES-EAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEH 623 (1039)
Q Consensus 553 GvIvrver-d~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~kgr~G~V~h 623 (1039)
|.|++.-. ..|.|.+. .|.+..+++.. |+.+ +.+.+.+||.|.+.--++...+|.|.|
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 77887774 66777552 35566655322 2211 344589999998874433334576654
No 256
>KOG2055 consensus WD40 repeat protein [General function prediction only]
Probab=27.88 E-value=28 Score=41.62 Aligned_cols=10 Identities=10% Similarity=0.278 Sum_probs=5.1
Q ss_pred HHHHHHHHhc
Q 001639 147 LERRIQARYA 156 (1039)
Q Consensus 147 ~~~~l~eRY~ 156 (1039)
+-+.|+.-|.
T Consensus 175 ~d~lL~tt~~ 184 (514)
T KOG2055|consen 175 LDDLLKTTVG 184 (514)
T ss_pred HHHHHHhhhc
Confidence 4455655543
No 257
>COG0355 AtpC F0F1-type ATP synthase, epsilon subunit (mitochondrial delta subunit) [Energy production and conversion]
Probab=27.25 E-value=2.9e+02 Score=28.13 Aligned_cols=83 Identities=23% Similarity=0.293 Sum_probs=47.5
Q ss_pred EEEEecccccCceeEEEEE----cCCeEEEeecCCCCCcceeeccccceeeccC-CCceEEecccccCceEEEEEEeCcE
Q 001639 430 AVIVIKGDLKNLKGWVEKV----DEENVHIRPEMKGLPKTLAVNSKELCKYFEP-GNHVKVVSGTQAGATGMVLKVEQHV 504 (1039)
Q Consensus 430 ~V~V~~Gel~gl~G~V~~V----~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~-GDhVkVi~G~~~GetGlVv~Ve~~~ 504 (1039)
+|+|+.-+..=..|.|..| ....+.|+|.|-.|-..| ...+.+.... |++...+ --+|=++-|..+.
T Consensus 5 ~l~IVsP~~~i~~g~v~~V~~~t~eGe~GILp~H~Plit~L---k~g~v~i~~~~~~~~~~i-----~VsgGfleV~~~~ 76 (135)
T COG0355 5 KLEIVSPEGIIYSGEVKSVVVPTTEGELGILPGHAPLITAL---KPGVVRIKTEDGDKEEKI-----AVSGGFLEVQPNE 76 (135)
T ss_pred EEEEEcCCceEEeeEEEEEEEecCCeeeecCCCCccceeee---cCcEEEEEEcCCCceEEE-----EEeccEEEEeCCE
Confidence 4566666666666666665 456789999987663332 2233333323 2221111 0234478888999
Q ss_pred EEEEeCCCCceEEEecccccc
Q 001639 505 LIILSDTTKEDIRVFADDVVE 525 (1039)
Q Consensus 505 v~llSD~t~~ei~V~~~dL~~ 525 (1039)
|+||.|. =+|..|+..
T Consensus 77 vtIlad~-----A~~~~did~ 92 (135)
T COG0355 77 VTILADS-----AERADDIDE 92 (135)
T ss_pred EEEEEce-----eEecccCCH
Confidence 9999875 356666653
No 258
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=27.16 E-value=1.1e+02 Score=29.36 Aligned_cols=31 Identities=29% Similarity=0.317 Sum_probs=26.8
Q ss_pred ccccCCCCcEEEEecC--CCCCCeeEEEEeeCC
Q 001639 269 KAIDLSRDTWVRMKIG--NYKGDLAKVVDVDNV 299 (1039)
Q Consensus 269 ~~~~l~~G~wVRIk~G--~YkGDlAqV~~Vd~~ 299 (1039)
..+.++.|+.|||+|- -+=+|.|.|..||..
T Consensus 36 p~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~ 68 (101)
T PLN00045 36 PPIGPKRGSKVKILRPESYWFNDVGKVVAVDQD 68 (101)
T ss_pred CCcccCCCCEEEEccccceeecCcceEEEEeCC
Confidence 4568899999999984 578999999999986
No 259
>PF14001 YdfZ: YdfZ protein
Probab=26.86 E-value=65 Score=28.73 Aligned_cols=31 Identities=29% Similarity=0.437 Sum_probs=26.4
Q ss_pred cccCCCCeecCCCEEEEecCCCCCceecEEEEEC
Q 001639 593 VQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYR 626 (1039)
Q Consensus 593 a~D~~gn~I~~~D~Vkv~~Gp~kgr~G~V~hI~r 626 (1039)
+-|+|.|.|..|..|.+-. .|..|+|+-|+-
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 4699999999999999865 378999998874
No 260
>PF15455 Pro-rich_19: Proline-rich 19
Probab=26.77 E-value=3.9e+02 Score=30.31 Aligned_cols=8 Identities=38% Similarity=0.609 Sum_probs=3.7
Q ss_pred EEEEecCC
Q 001639 606 VVRIVEGP 613 (1039)
Q Consensus 606 ~Vkv~~Gp 613 (1039)
.|.|..|.
T Consensus 61 lVVITQGR 68 (357)
T PF15455_consen 61 LVVITQGR 68 (357)
T ss_pred ceEEeccc
Confidence 34454443
No 261
>KOG2475 consensus CDC45 (cell division cycle 45)-like protein [Replication, recombination and repair]
Probab=26.76 E-value=11 Score=45.43 Aligned_cols=7 Identities=0% Similarity=0.425 Sum_probs=3.2
Q ss_pred CCCcccc
Q 001639 77 ARKPKAK 83 (1039)
Q Consensus 77 ~r~kkr~ 83 (1039)
+|||+||
T Consensus 183 ~krr~rr 189 (587)
T KOG2475|consen 183 SKRRERR 189 (587)
T ss_pred HHHHHHH
Confidence 4444443
No 262
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=26.40 E-value=2.1e+02 Score=28.50 Aligned_cols=30 Identities=27% Similarity=0.405 Sum_probs=21.2
Q ss_pred cCccCCCCEEEE----eccc---ccCceeEEEEEcCC
Q 001639 422 KGHFMKGDAVIV----IKGD---LKNLKGWVEKVDEE 451 (1039)
Q Consensus 422 ~~~F~~GD~V~V----~~Ge---l~gl~G~V~~V~~d 451 (1039)
-..|.|||+|+| ++|. +....|.|+++.+.
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 568999998765 5664 34566777777654
No 263
>PRK08582 hypothetical protein; Provisional
Probab=26.28 E-value=2e+02 Score=29.36 Aligned_cols=15 Identities=20% Similarity=0.421 Sum_probs=11.7
Q ss_pred cceeeccCCCceEEe
Q 001639 472 ELCKYFEPGNHVKVV 486 (1039)
Q Consensus 472 ~LrK~F~~GDhVkVi 486 (1039)
++.++|++||.|+|.
T Consensus 45 ~~~~~l~vGD~Vkvk 59 (139)
T PRK08582 45 DINDHLKVGDEVEVK 59 (139)
T ss_pred ccccccCCCCEEEEE
Confidence 344789999999884
No 264
>PRK14647 hypothetical protein; Provisional
Probab=26.20 E-value=1.2e+02 Score=31.69 Aligned_cols=48 Identities=21% Similarity=0.290 Sum_probs=37.5
Q ss_pred ccccCcEEEEee-c--------CCCCceeEEEeecCCeEEEEecCCceEEEEecCccc
Q 001639 705 DALVGTTVKVRL-G--------PYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 753 (1039)
Q Consensus 705 d~liGktV~I~~-G--------pyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l~ 753 (1039)
..++|+.|+|+- . .-|=+.|++++++++.+++++.. .++++++.+.|.
T Consensus 95 ~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~-~~~~~i~~~~I~ 151 (159)
T PRK14647 95 ERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADGVVTIALKE-GQQARIPLDKIA 151 (159)
T ss_pred HHhCCcEEEEEEeccccccccCCceEEEEEEEeecCCEEEEEEcC-CcEEEEEHHHCC
Confidence 578999999974 2 23778999999999999998742 456888877765
No 265
>KOG0772 consensus Uncharacterized conserved protein, contains WD40 repeat [Function unknown]
Probab=26.19 E-value=38 Score=41.07 Aligned_cols=13 Identities=15% Similarity=0.227 Sum_probs=5.1
Q ss_pred cCCCCChHHhhcc
Q 001639 387 QNIQPTFDELEKF 399 (1039)
Q Consensus 387 ~~V~PTleEL~~F 399 (1039)
++|+=+.+.++-|
T Consensus 296 Wdv~~~k~q~qVi 308 (641)
T KOG0772|consen 296 WDVNNTKSQLQVI 308 (641)
T ss_pred EecCCchhheeEE
Confidence 3333333333333
No 266
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=25.45 E-value=2.8e+02 Score=25.66 Aligned_cols=63 Identities=22% Similarity=0.266 Sum_probs=44.1
Q ss_pred eEEEEEEccc-eeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCCCCceecEEEEECC
Q 001639 552 FGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRG 627 (1039)
Q Consensus 552 VGvIvrverd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~kgr~G~V~hI~r~ 627 (1039)
.|+|+.+-.+ .|+|... +|.++.. -|..|..+..+ -|..||.|.|.--||.-..|.|.+=|+.
T Consensus 10 ~g~V~e~L~~~~f~v~~e---dg~~~~a---hI~GKmr~~~i-------~I~~GD~V~Ve~~~~d~~kg~I~~Ry~~ 73 (75)
T COG0361 10 EGTVIEMLPNGRFRVELE---NGHERLA---HISGKMRKNRI-------RILPGDVVLVELSPYDLTKGRIVYRYKK 73 (75)
T ss_pred EEEEEEecCCCEEEEEec---CCcEEEE---EccCcchheeE-------EeCCCCEEEEEecccccccccEEEEecC
Confidence 4888888866 5899885 4665543 34455443111 4889999999988887778888876653
No 267
>PRK00098 GTPase RsgA; Reviewed
Probab=25.43 E-value=3.8e+02 Score=30.48 Aligned_cols=87 Identities=23% Similarity=0.234 Sum_probs=55.2
Q ss_pred EEEEEEccceeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCCCCceecEEEEECCEEEEE
Q 001639 553 GVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRGILFIH 632 (1039)
Q Consensus 553 GvIvrverd~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~kgr~G~V~hI~r~~lFl~ 632 (1039)
|.|+++.+..+.|++. .|.+..+++.. ++.. ..+.+-+||.|.+-. + ....|.|..|....-+|.
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 35555554322 1110 235678999998842 1 224689999998876776
Q ss_pred eCceeeeceEEEEeCCceEEecc
Q 001639 633 DRHHLEHAGFICAKSSSCVVVGG 655 (1039)
Q Consensus 633 ~~~~~EN~Gifv~~a~~~~~~g~ 655 (1039)
.+.. ...-+++.++..++++-.
T Consensus 68 R~~~-~~~q~iaaniD~vllV~d 89 (298)
T PRK00098 68 RPPI-FKSKLIAANVDQAVLVFA 89 (298)
T ss_pred CCCC-ccccceeecCCEEEEEEE
Confidence 6654 222356666666665544
No 268
>PRK14638 hypothetical protein; Provisional
Probab=25.40 E-value=1.2e+02 Score=31.33 Aligned_cols=47 Identities=17% Similarity=0.314 Sum_probs=38.0
Q ss_pred CCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceee
Q 001639 426 MKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 476 (1039)
Q Consensus 426 ~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~ 476 (1039)
..|-.|+|.-...+..+|++.+++++.|+|..+ ++++++|.++++|.
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 579999997655688999999999999998743 35688888888774
No 269
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=24.93 E-value=93 Score=40.35 Aligned_cols=47 Identities=19% Similarity=0.232 Sum_probs=35.4
Q ss_pred CccCCCCEEEEecccccCceeEEEEEcC-CeEEEeecCCCCCcceeeccccceee
Q 001639 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDE-ENVHIRPEMKGLPKTLAVNSKELCKY 476 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~-d~V~i~~~~~~l~~~i~v~~~~LrK~ 476 (1039)
..|++||.|+|.+ -|..|.|++|.+ +.++|... .+ .+.|+.++|.+.
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 270
>KOG0162 consensus Myosin class I heavy chain [Cytoskeleton]
Probab=24.74 E-value=1.2e+03 Score=30.18 Aligned_cols=7 Identities=14% Similarity=-0.382 Sum_probs=3.5
Q ss_pred EEEeecC
Q 001639 725 RVVDVKG 731 (1039)
Q Consensus 725 ~Vkd~t~ 731 (1039)
.|+-..+
T Consensus 895 tV~~~~~ 901 (1106)
T KOG0162|consen 895 TVQFGID 901 (1106)
T ss_pred eEEeccC
Confidence 5554444
No 271
>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=24.62 E-value=32 Score=32.85 Aligned_cols=9 Identities=78% Similarity=1.010 Sum_probs=4.9
Q ss_pred cccCccccc
Q 001639 48 FIDDVAEED 56 (1039)
Q Consensus 48 ~~~d~~~~~ 56 (1039)
|++++++=+
T Consensus 1 Fid~EAeVD 9 (97)
T PF11942_consen 1 FIDDEAEVD 9 (97)
T ss_pred CchhhcccC
Confidence 556666533
No 272
>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=24.45 E-value=42 Score=29.99 Aligned_cols=52 Identities=27% Similarity=0.388 Sum_probs=30.0
Q ss_pred ceeEEEEEcCCeEEEee--cCCCCCcceeec-----cccceeeccCCCceEEecccccCceEEEEEEeC
Q 001639 441 LKGWVEKVDEENVHIRP--EMKGLPKTLAVN-----SKELCKYFEPGNHVKVVSGTQAGATGMVLKVEQ 502 (1039)
Q Consensus 441 l~G~V~~V~~d~V~i~~--~~~~l~~~i~v~-----~~~LrK~F~~GDhVkVi~G~~~GetGlVv~Ve~ 502 (1039)
..|+|.+|...-+.|.. ...++-.-..+. .+++.+.|++||.|++ .|+.++.
T Consensus 4 V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~----------kV~~id~ 62 (73)
T cd05703 4 VTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKA----------KVVGVDK 62 (73)
T ss_pred EEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEE----------EEEEEeC
Confidence 46888888877554443 222211111111 3456678999999976 3677764
No 273
>PHA03247 large tegument protein UL36; Provisional
Probab=24.31 E-value=1.8e+03 Score=33.22 Aligned_cols=7 Identities=14% Similarity=0.173 Sum_probs=4.0
Q ss_pred HHhhccc
Q 001639 394 DELEKFR 400 (1039)
Q Consensus 394 eEL~~F~ 400 (1039)
..|.+|.
T Consensus 2200 ~~l~~l~ 2206 (3151)
T PHA03247 2200 AALGGLS 2206 (3151)
T ss_pred HHHhccC
Confidence 4566664
No 274
>KOG2147 consensus Nucleolar protein involved in 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=24.12 E-value=49 Score=41.79 Aligned_cols=13 Identities=23% Similarity=0.217 Sum_probs=6.5
Q ss_pred hccccccccccCc
Q 001639 40 SRKRRRSQFIDDV 52 (1039)
Q Consensus 40 ~~~~~~~~~~~d~ 52 (1039)
...+....|.|+.
T Consensus 307 ~~~r~~~~~ddgk 319 (823)
T KOG2147|consen 307 DDSRFEVDFDDGK 319 (823)
T ss_pred ccccccccccccc
Confidence 3445555555554
No 275
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 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 S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=23.97 E-value=2.3e+02 Score=24.65 Aligned_cols=56 Identities=29% Similarity=0.401 Sum_probs=0.0
Q ss_pred ceeEEEEEcCCeEEEeecCCCCCcceeeccccce--------eeccCCCceEEecccccCceEEEEEEeCcEE-EEEe
Q 001639 441 LKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELC--------KYFEPGNHVKVVSGTQAGATGMVLKVEQHVL-IILS 509 (1039)
Q Consensus 441 l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~Lr--------K~F~~GDhVkVi~G~~~GetGlVv~Ve~~~v-~llS 509 (1039)
+.|+|.+|+...+.|.-. ..+ .--+|.++|. +.|++||.|+|. |++++.+.= +.||
T Consensus 8 v~g~V~~v~~~g~~V~l~-~~~--~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~----------v~~vd~~~~~i~lS 72 (74)
T PF00575_consen 8 VEGKVTSVEDFGVFVDLG-NGI--EGFIPISELSDDRIDDPSEVYKIGQTVRVK----------VIKVDKEKGRIRLS 72 (74)
T ss_dssp EEEEEEEEETTEEEEEES-TSS--EEEEEGGGSSSSEESSSHGTCETTCEEEEE----------EEEEETTTTEEEEE
T ss_pred EEEEEEEEECCEEEEEEC-CcE--EEEEEeehhcCccccccccccCCCCEEEEE----------EEEEECCCCeEEEE
No 276
>COG0056 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion]
Probab=23.73 E-value=1.9e+02 Score=35.12 Aligned_cols=49 Identities=16% Similarity=0.310 Sum_probs=39.6
Q ss_pred CceEEEEEEeCcEEEEEeCCCCceEEEeccccccccccccccccCCceEeeeeEEecCCceEEEEEEccceeEEe
Q 001639 492 GATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDNNSFGVIIRVESEAFQVL 566 (1039)
Q Consensus 492 GetGlVv~Ve~~~v~llSD~t~~ei~V~~~dL~~~~e~~~g~~~~g~y~l~DLVqLd~~tVGvIvrverd~~~VL 566 (1039)
-++|.|+.|.+..+.+. | +.++.++.||++..+..|+...+|.+.+-++
T Consensus 26 ~~~g~V~sv~DgIa~v~-----------------------G---l~~~~~~E~~ef~~~v~G~alnle~d~VG~v 74 (504)
T COG0056 26 KEVGTVISVGDGIARVS-----------------------G---LENVMAGELVEFPGGVKGMALNLEEDSVGAV 74 (504)
T ss_pred hccceEEEEecceEEEe-----------------------c---CchhhcCceEEecCCcEEEEEeccccceeEE
Confidence 37899999988877652 2 4578889999999999999999998875444
No 277
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=23.72 E-value=3.1e+02 Score=26.12 Aligned_cols=62 Identities=15% Similarity=0.138 Sum_probs=41.2
Q ss_pred eEEEEEEccc-eeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCCCCceecEEEEEC
Q 001639 552 FGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYR 626 (1039)
Q Consensus 552 VGvIvrverd-~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~kgr~G~V~hI~r 626 (1039)
.|+|+.+-.+ .|+|... +|..+.. -|..|+.++.+ -|..||.|+|---||--..|.|.|=|+
T Consensus 10 ~G~V~e~Lp~~~frV~Le---nG~~vla---~isGKmR~~rI-------rIl~GD~V~VE~spYDltkGRIiyR~~ 72 (87)
T PRK12442 10 DGIVDEVLPDSRFRVTLE---NGVEVGA---YASGRMRKHRI-------RILAGDRVTLELSPYDLTKGRINFRHK 72 (87)
T ss_pred EEEEEEECCCCEEEEEeC---CCCEEEE---EeccceeeeeE-------EecCCCEEEEEECcccCCceeEEEEec
Confidence 3889988766 5787764 3554432 34455543222 488899999988898766787766554
No 278
>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=23.49 E-value=95 Score=31.38 Aligned_cols=51 Identities=25% Similarity=0.326 Sum_probs=33.6
Q ss_pred CCCCEEEEec----ccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceee
Q 001639 426 MKGDAVIVIK----GDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 476 (1039)
Q Consensus 426 ~~GD~V~V~~----Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~ 476 (1039)
..|-.|+|.- ...+...|++.+++++.|+|....+..+..++++-+++.|+
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 33356799999999999999776544445788888887763
No 279
>PTZ00482 membrane-attack complex/perforin (MACPF) Superfamily; Provisional
Probab=23.47 E-value=69 Score=41.56 Aligned_cols=7 Identities=29% Similarity=0.543 Sum_probs=3.1
Q ss_pred HHHHHhc
Q 001639 150 RIQARYA 156 (1039)
Q Consensus 150 ~l~eRY~ 156 (1039)
-+++-|-
T Consensus 231 ~~~~~~~ 237 (844)
T PTZ00482 231 NTRAAYT 237 (844)
T ss_pred cchhhhh
Confidence 3444443
No 280
>COG5593 Nucleic-acid-binding protein possibly involved in ribosomal biogenesis [Translation, ribosomal structure and biogenesis]
Probab=23.28 E-value=48 Score=40.41 Aligned_cols=7 Identities=0% Similarity=0.107 Sum_probs=2.7
Q ss_pred HHHHHHH
Q 001639 144 VEALERR 150 (1039)
Q Consensus 144 ~e~~~~~ 150 (1039)
|+..|.+
T Consensus 812 ad~ya~~ 818 (821)
T COG5593 812 ADDYAQY 818 (821)
T ss_pred hHHHHHH
Confidence 3333333
No 281
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=23.20 E-value=2.8e+02 Score=28.14 Aligned_cols=47 Identities=21% Similarity=0.444 Sum_probs=30.4
Q ss_pred ceeecc-ccceeeccCCCceEEeccc----------ccCceEEEEEEeCcEEEEEeCCC
Q 001639 465 TLAVNS-KELCKYFEPGNHVKVVSGT----------QAGATGMVLKVEQHVLIILSDTT 512 (1039)
Q Consensus 465 ~i~v~~-~~LrK~F~~GDhVkVi~G~----------~~GetGlVv~Ve~~~v~llSD~t 512 (1039)
.|.+.. .+..+.|++||-||...|- |.|..|-+-|| ++...+|+-.-
T Consensus 49 sI~isvW~e~~~~~~PGDIirLt~Gy~Si~qg~LtL~~GK~Ge~~Ki-Gef~~vf~etp 106 (134)
T KOG3416|consen 49 SINISVWDEEGCLIQPGDIIRLTGGYASIFQGCLTLYVGKGGEVQKI-GEFCMVFSETP 106 (134)
T ss_pred eEEEEEecCcCcccCCccEEEecccchhhhcCceEEEecCCceEeEe-eeeEEeeecCC
Confidence 344443 3577899999999998882 34555655555 34566666543
No 282
>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=23.14 E-value=1.1e+02 Score=25.35 Aligned_cols=39 Identities=15% Similarity=0.145 Sum_probs=31.5
Q ss_pred ccEEEEEEeCCCCeEEEEeccCCCCceEEecCCCeeecCCC
Q 001639 948 SVVGVIREVLPDGSCRVVLGSSGNGDTITALPNEIEIVPPR 988 (1039)
Q Consensus 948 ~~~GvV~~V~~~g~~~V~l~~~~~g~~v~v~~~~Le~V~P~ 988 (1039)
=..|.|.++.+++.|.|.+.|. |....|..++|-+..+.
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 3588999998778899999987 57888888888776653
No 283
>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=22.72 E-value=74 Score=29.31 Aligned_cols=38 Identities=21% Similarity=0.245 Sum_probs=30.0
Q ss_pred EEEEEcCCeEEEeecCCCCCcceeec-----cccceeeccCCC
Q 001639 444 WVEKVDEENVHIRPEMKGLPKTLAVN-----SKELCKYFEPGN 481 (1039)
Q Consensus 444 ~V~~V~~d~V~i~~~~~~l~~~i~v~-----~~~LrK~F~~GD 481 (1039)
.++.|++..+++|.+..+.++.|.+| ..+|+..|..|.
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 445567888888
No 284
>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=22.70 E-value=4.4e+02 Score=29.82 Aligned_cols=86 Identities=21% Similarity=0.198 Sum_probs=53.9
Q ss_pred EEEEEEccceeEEeccCCCCCcEEEEechhhhhcccCCcccccCCCCeecCCCEEEEecCCCCCceecEEEEE-CCEEEE
Q 001639 553 GVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIY-RGILFI 631 (1039)
Q Consensus 553 GvIvrverd~~~VL~~~~~~g~v~~v~~~~I~~k~~~~~~a~D~~gn~I~~~D~Vkv~~Gp~kgr~G~V~hI~-r~~lFl 631 (1039)
|.|++..+..+.|++. +.+..++... ++.. ..+.+-+||.|.+..-. +.+|.|..|+ |..+|.
T Consensus 1 g~v~~~~~~~~~v~~~----~~~~~~~~~g---~~~~-------~~~~~~vGD~V~~~~~~--~~~~~i~~i~~R~~~l~ 64 (287)
T cd01854 1 GRVIAVHGGFYDVETE----GGELRCRARG---KLRK-------KGIKPVVGDWVEVEPDD--DGEGVIVRVLPRKNLLS 64 (287)
T ss_pred CEEEEEECCEEEEEEC----CeEEEEEecc---cccc-------CCCCccCCCEEEEEecC--CCcEEEEEEECCCceEE
Confidence 5788999999988873 3444444322 1111 14569999999885322 4579999999 444555
Q ss_pred EeCceeeeceEEEEeCCceEEecc
Q 001639 632 HDRHHLEHAGFICAKSSSCVVVGG 655 (1039)
Q Consensus 632 ~~~~~~EN~Gifv~~a~~~~~~g~ 655 (1039)
+-..... .-+++.++..++++-+
T Consensus 65 R~~~~~~-~~~i~anvD~vllV~d 87 (287)
T cd01854 65 RPAAGGR-EQVIAANVDQLVIVVS 87 (287)
T ss_pred ccCCCCc-ceeEEEeCCEEEEEEE
Confidence 4332222 4567777777776655
No 285
>CHL00010 infA translation initiation factor 1
Probab=22.64 E-value=3.1e+02 Score=25.19 Aligned_cols=56 Identities=18% Similarity=0.216 Sum_probs=32.8
Q ss_pred ceeEEEEEcC-CeEEEeecCCCCCcce-eeccccceee---ccCCCceEEecccccCceEEEEE
Q 001639 441 LKGWVEKVDE-ENVHIRPEMKGLPKTL-AVNSKELCKY---FEPGNHVKVVSGTQAGATGMVLK 499 (1039)
Q Consensus 441 l~G~V~~V~~-d~V~i~~~~~~l~~~i-~v~~~~LrK~---F~~GDhVkVi~G~~~GetGlVv~ 499 (1039)
+.|+|+++-+ +...|.+... ..+ ....--||+. ..+||.|.|--=.+..+.|.|+-
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 6666654221 222 2223334432 46799999863344566787764
No 286
>KOG0066 consensus eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]
Probab=22.62 E-value=62 Score=38.87 Aligned_cols=17 Identities=24% Similarity=0.163 Sum_probs=8.7
Q ss_pred cccCCCCCCCCCccccc
Q 001639 68 EDYGGGGGAARKPKAKR 84 (1039)
Q Consensus 68 ~~~~~~~~~~r~kkr~~ 84 (1039)
++-++--++++++||+.
T Consensus 144 ~e~~~~kpa~~~~~k~~ 160 (807)
T KOG0066|consen 144 VEVVAVKPASKKSKKKQ 160 (807)
T ss_pred eeccCCCCCChhhhhhh
Confidence 34455555555555543
No 287
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=22.07 E-value=1.5e+02 Score=31.55 Aligned_cols=53 Identities=28% Similarity=0.365 Sum_probs=31.5
Q ss_pred CccCCCCEEEEecccccCceeEEEEEcCCeEEEeecC-----CCCC--cceeeccc--------cceeeccCCCceEE
Q 001639 423 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEM-----KGLP--KTLAVNSK--------ELCKYFEPGNHVKV 485 (1039)
Q Consensus 423 ~~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~-----~~l~--~~i~v~~~--------~LrK~F~~GDhVkV 485 (1039)
..+++||.|. |+|++|..+.+.|.... ..+. -+--++.+ ++++.|++||.|++
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 78999988855443210 0010 11222333 34678999999977
No 288
>PF07133 Merozoite_SPAM: Merozoite surface protein (SPAM); InterPro: IPR010784 This entry consists of several Plasmodium falciparum SPAM (secreted polymorphic antigen associated with merozoites) proteins, also know as merozoite surface proteins. Variation among SPAM alleles is the result of deletions and amino acid substitutions in non-repetitive sequences within and flanking the alanine heptad-repeat domain. Heptad repeats in which the a and d position contain hydrophobic residues generate amphipathic alpha-helices which give rise to helical bundles or coiled-coil structures in proteins. SPAM is an example of a P. falciparum antigen in which a repetitive sequence has features characteristic of a well-defined structural element [,].
Probab=22.05 E-value=30 Score=36.60 Aligned_cols=11 Identities=27% Similarity=0.344 Sum_probs=4.5
Q ss_pred HHHHHHHHHHh
Q 001639 197 AAVCLMQKCID 207 (1039)
Q Consensus 197 vv~~Lm~K~~~ 207 (1039)
++..|++.++.
T Consensus 137 ~ae~lvktLis 147 (173)
T PF07133_consen 137 VAEALVKTLIS 147 (173)
T ss_pred HHHHHHHHHHH
Confidence 34444444433
No 289
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=21.94 E-value=1.3e+02 Score=33.22 Aligned_cols=50 Identities=26% Similarity=0.374 Sum_probs=30.3
Q ss_pred CCCCEEEEecccccCceeEEEEEcCCeEEEeec--CCCC------C-cceeeccccceeeccCCCceEE
Q 001639 426 MKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPE--MKGL------P-KTLAVNSKELCKYFEPGNHVKV 485 (1039)
Q Consensus 426 ~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~--~~~l------~-~~i~v~~~~LrK~F~~GDhVkV 485 (1039)
++||.|. |+|++|..+...+... ...+ . ..++...+.++.+|++||.|++
T Consensus 62 ~vGDiVi----------G~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~a 120 (235)
T PRK04163 62 KVGDLVI----------GKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIA 120 (235)
T ss_pred CCCCEEE----------EEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEE
Confidence 7888875 7788887775433322 1111 0 1111223677888999999976
No 290
>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=21.80 E-value=68 Score=28.54 Aligned_cols=31 Identities=29% Similarity=0.452 Sum_probs=26.3
Q ss_pred cccCCCCeecCCCEEEEecCCCCCceecEEEEEC
Q 001639 593 VQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYR 626 (1039)
Q Consensus 593 a~D~~gn~I~~~D~Vkv~~Gp~kgr~G~V~hI~r 626 (1039)
+-|+|.|.|..|+.|.|.. .|..|.++-|+-
T Consensus 3 ~YDRnRNait~G~rVMia~---tG~tgvikaIh~ 33 (65)
T TIGR03318 3 TYDRNRNAITTGSRVMIAG---TGHTGVIKAIHT 33 (65)
T ss_pred cccccccccCCCcEEEEec---CCccceeehhhh
Confidence 5699999999999999864 378999988874
No 291
>COG3109 ProQ Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]
Probab=21.71 E-value=1.3e+02 Score=32.02 Aligned_cols=43 Identities=28% Similarity=0.518 Sum_probs=35.4
Q ss_pred cCcEEEEeecCCCCceeEEEeecCCeEEEEecCCceEEEEecCcc
Q 001639 708 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMI 752 (1039)
Q Consensus 708 iGktV~I~~GpyKG~~G~Vkd~t~~~arVELhs~~k~I~V~r~~l 752 (1039)
+|+.|++..|. -..-.+|.+++-+.|||+|.+... +.|.-+||
T Consensus 164 ~g~~~kVk~G~-~a~~AtvlEv~Kd~vRVqL~~Gl~-m~V~AehL 206 (208)
T COG3109 164 VGQALKVKAGQ-NAMDATVLEITKDGVRVQLNSGLS-MIVRAEHL 206 (208)
T ss_pred ccceeeecccc-ccccceEEEEeccceEEeecCCce-EEEehhhh
Confidence 79999999984 356789999999999999998765 55666665
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=21.49 E-value=3.3e+02 Score=29.58 Aligned_cols=67 Identities=19% Similarity=0.164 Sum_probs=39.3
Q ss_pred EEEEEEeCCCCeEEEEeccCCCCceEEecCCCeeecCCCCCCcEEEEcCCCCC---ceEEEEEEeCCCcEEEecC
Q 001639 950 VGVIREVLPDGSCRVVLGSSGNGDTITALPNEIEIVPPRKTDKIKIMGGPHRG---ATGKLIGVDGTDGIVKVDV 1021 (1039)
Q Consensus 950 ~GvV~~V~~~g~~~V~l~~~~~g~~v~v~~~~Le~V~P~kgd~VkVi~G~~rG---~tG~LisiD~~dgiVk~d~ 1021 (1039)
.|.|....+++.+ |... . |. +.+-..-==++.|+.||+|.|....+-+ ..+.|.--++....+.+++
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
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: 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 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=21.42 E-value=2.7e+02 Score=23.32 Aligned_cols=43 Identities=16% Similarity=0.217 Sum_probs=24.0
Q ss_pred ceeEEEEEcCCeEEEeecCCCCCcceeeccccce--------eeccCCCceEEe
Q 001639 441 LKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELC--------KYFEPGNHVKVV 486 (1039)
Q Consensus 441 l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~Lr--------K~F~~GDhVkVi 486 (1039)
..|+|+++....+.|.-... ..--++.++|. +.|++||.|+|.
T Consensus 4 ~~g~V~~i~~~g~~v~i~~~---~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~ 54 (69)
T cd05692 4 VEGTVTRLKPFGAFVELGGG---ISGLVHISQIAHKRVKDVKDVLKEGDKVKVK 54 (69)
T ss_pred EEEEEEEEEeeeEEEEECCC---CEEEEEhHHcCCcccCCHHHccCCCCEEEEE
Confidence 35777777766544443211 11223333333 678999999874
No 294
>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=21.40 E-value=2.9e+02 Score=22.94 Aligned_cols=56 Identities=18% Similarity=0.188 Sum_probs=32.2
Q ss_pred eEEEEEcCCeEEEeecCCCCCcceeeccccc---eeeccCCCceEEeccc---ccCceEEEEEE
Q 001639 443 GWVEKVDEENVHIRPEMKGLPKTLAVNSKEL---CKYFEPGNHVKVVSGT---QAGATGMVLKV 500 (1039)
Q Consensus 443 G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~L---rK~F~~GDhVkVi~G~---~~GetGlVv~V 500 (1039)
|.|...+...--|.++.. ...+-|+.+.+ ...+..||.|.+---. ..+..+.|++|
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 555555544444555432 24688888875 4556779999875321 23345566554
No 295
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=21.19 E-value=41 Score=40.98 Aligned_cols=9 Identities=22% Similarity=0.394 Sum_probs=4.3
Q ss_pred CccEEEEEe
Q 001639 223 LKNYIYIEA 231 (1039)
Q Consensus 223 lkGYIYVEA 231 (1039)
-.|-|||.-
T Consensus 576 sssRIfiKi 584 (739)
T KOG2140|consen 576 SSSRIFIKI 584 (739)
T ss_pred ccceehHHH
Confidence 345555443
No 296
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=21.19 E-value=1.5e+02 Score=30.59 Aligned_cols=49 Identities=27% Similarity=0.303 Sum_probs=37.5
Q ss_pred CCCCEEEEe----cccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceee
Q 001639 426 MKGDAVIVI----KGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 476 (1039)
Q Consensus 426 ~~GD~V~V~----~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~ 476 (1039)
..|-.|+|. -+..+..+|.+.+++++.|+|....+. ++++++-.+++|.
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 255577899999999999988865321 3688888887764
No 297
>PRK14631 hypothetical protein; Provisional
Probab=21.04 E-value=1.7e+02 Score=31.11 Aligned_cols=48 Identities=23% Similarity=0.539 Sum_probs=36.1
Q ss_pred ccccCcEEEEee----cCCCCceeEEEeec--CCeEEEEecCCceEEEEecCccc
Q 001639 705 DALVGTTVKVRL----GPYKGYRGRVVDVK--GQSVRVELESQMKVVTVDRSMIS 753 (1039)
Q Consensus 705 d~liGktV~I~~----GpyKG~~G~Vkd~t--~~~arVELhs~~k~I~V~r~~l~ 753 (1039)
..++|+.|+|+- +.-|-+.|++..++ ++.+++++.-+ +++.++.+.|.
T Consensus 113 ~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~~v~l~~~~~-~~~~i~~~~I~ 166 (174)
T PRK14631 113 QGYIGQQVALRLIAAVENRRKFQAKLLAVDLENEEIQVEVEGK-HVLDIDSNNID 166 (174)
T ss_pred HHhCCCeEEEEEecccCCceEEEEEEEEeecCCCEEEEEEcCC-cEEEEEhHHcc
Confidence 578999999985 22466889999999 99999887533 45777766654
No 298
>KOG0270 consensus WD40 repeat-containing protein [Function unknown]
Probab=21.03 E-value=76 Score=37.96 Aligned_cols=10 Identities=20% Similarity=0.561 Sum_probs=4.5
Q ss_pred EEeeccchhh
Q 001639 306 KLIPRIDLQA 315 (1039)
Q Consensus 306 klvPRiD~~~ 315 (1039)
.+.|-+=+++
T Consensus 214 ~v~P~~~LGs 223 (463)
T KOG0270|consen 214 AVLPCVTLGS 223 (463)
T ss_pred ccccceeech
Confidence 3445544443
No 299
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=20.97 E-value=3.9e+02 Score=38.01 Aligned_cols=79 Identities=14% Similarity=0.229 Sum_probs=53.8
Q ss_pred CccCC--CCEEEEecccccCceeEEEEEcCC--eEEEeecCCCCCcceeeccccc-----------eeeccCCCceEEec
Q 001639 423 GHFMK--GDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKEL-----------CKYFEPGNHVKVVS 487 (1039)
Q Consensus 423 ~~F~~--GD~V~V~~Gel~gl~G~V~~V~~d--~V~i~~~~~~l~~~i~v~~~~L-----------rK~F~~GDhVkVi~ 487 (1039)
..|++ ||.|.. .+ ....|+.|+.+ .|++.... ++.+.|.++.+ ..-|.+||.|+...
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 23578999999873
Q ss_pred -----ccccCceEEEEEEeCcEEEEEe
Q 001639 488 -----GTQAGATGMVLKVEQHVLIILS 509 (1039)
Q Consensus 488 -----G~~~GetGlVv~Ve~~~v~llS 509 (1039)
|...|+.+.|+.|+++.++|-+
T Consensus 1346 nDk~~G~~Ng~~~tV~~I~~~~I~l~~ 1372 (1747)
T PRK13709 1346 SDRERGYVANSVWTVTAVSGDSVTLSD 1372 (1747)
T ss_pred cCcccccccCCEEEEEEEcCCeEEEEc
Confidence 4456889999999998865543
No 300
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=20.81 E-value=1.7e+02 Score=24.16 Aligned_cols=35 Identities=9% Similarity=0.261 Sum_probs=27.3
Q ss_pred eEEEEeecCCccEEEEEecchHHHHHHHhcCcccc
Q 001639 214 IRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIY 248 (1039)
Q Consensus 214 I~Svf~~~~lkGYIYVEA~~~~~V~~ai~gl~~v~ 248 (1039)
|.++.....-+|+.|||..+..+...|++.+.+..
T Consensus 11 V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~ 45 (56)
T PF13893_consen 11 VKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQ 45 (56)
T ss_dssp EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSE
T ss_pred EEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCE
Confidence 55554444337999999999999999999887654
No 301
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=20.77 E-value=4.3e+02 Score=32.45 Aligned_cols=58 Identities=22% Similarity=0.312 Sum_probs=37.7
Q ss_pred ccCCCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeecccccee-----eccCCCceEEecccccCceEEEE
Q 001639 424 HFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK-----YFEPGNHVKVVSGTQAGATGMVL 498 (1039)
Q Consensus 424 ~F~~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK-----~F~~GDhVkVi~G~~~GetGlVv 498 (1039)
.|++|+.|+ |+|++|+.+.|.|... .+.+=.+|.+++.. .+++||.|.+ +|+
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 3788888764 466
Q ss_pred EEeCcE
Q 001639 499 KVEQHV 504 (1039)
Q Consensus 499 ~Ve~~~ 504 (1039)
++++..
T Consensus 88 ~~~~~~ 93 (491)
T PRK13806 88 SVNGQE 93 (491)
T ss_pred EEcCCE
Confidence 666543
No 302
>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=20.50 E-value=4.5e+02 Score=33.48 Aligned_cols=75 Identities=11% Similarity=0.102 Sum_probs=45.2
Q ss_pred CCCEEEEecccccCceeEEEEEcCCeEEEeecCCCCCcceeeccccceeeccCCCceEEecccc----cCceEEEEEEeC
Q 001639 427 KGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVVSGTQ----AGATGMVLKVEQ 502 (1039)
Q Consensus 427 ~GD~V~V~~Gel~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi~G~~----~GetGlVv~Ve~ 502 (1039)
.|-.|+|++=..+.+.|++.. .++...+.|+...+...|.++.+...+.++.||.|+|-==+| ..-.|-|+++=+
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 344455555555555554433 233455667766677778887776656788999998752222 123677777743
No 303
>PHA03169 hypothetical protein; Provisional
Probab=20.44 E-value=1.3e+02 Score=35.40 Aligned_cols=91 Identities=10% Similarity=0.098 Sum_probs=0.0
Q ss_pred CCCCccccccccchhhhhccCccchhhhhhhhchhhccccccccccCccccccccccccCCCccccCCCCCCCCCccccc
Q 001639 5 RDDDDDEMDAEEDEYDEQVMDDEIDEEEEEEDDRSSRKRRRSQFIDDVAEEDDEEEEEDYDDDEDYGGGGGAARKPKAKR 84 (1039)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~eedeee~~~~~~~~~~~~~~~d~~~~~d~~~~~~~~~~~~~~~~~~~~r~kkr~~ 84 (1039)
...+.++..++..+++.++.+||-++.++|.++++..--....-.+.....+..+++.++-.+.-+.+...
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 CCCCCCcccccccCCcchhccccccCc
Q 001639 85 RSGSEFFDLEAQVDSDEEEDEEEGEDD 111 (1039)
Q Consensus 85 ~~~~~FiD~EAEVDDdeEeeeee~e~d 111 (1039)
+..++|..++|.++++.+..
T Consensus 226 -------~~~~~~e~e~e~~e~e~e~~ 245 (413)
T PHA03169 226 -------NTQQAVEHEDEPTEPEREGP 245 (413)
T ss_pred -------cccccccccccccccccCCC
No 304
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=20.36 E-value=1.6e+02 Score=28.51 Aligned_cols=53 Identities=23% Similarity=0.251 Sum_probs=35.2
Q ss_pred CccCCCCEEEEe-cc---------cccCceeEEEEEcCCeEEEeecCCCCCcceeecccccee
Q 001639 423 GHFMKGDAVIVI-KG---------DLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK 475 (1039)
Q Consensus 423 ~~F~~GD~V~V~-~G---------el~gl~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK 475 (1039)
..|++||.|-|. .| .+-|-+|+|..+.+.-+.|.....+..+.|-+.+..|++
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 468899988763 23 234679999999999655544444445567666666654
No 305
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: 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 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.15 E-value=3.6e+02 Score=23.30 Aligned_cols=43 Identities=26% Similarity=0.330 Sum_probs=24.5
Q ss_pred ceeEEEEEcCCeEEEeecCCCCCcceeec--------cccceeeccCCCceEEe
Q 001639 441 LKGWVEKVDEENVHIRPEMKGLPKTLAVN--------SKELCKYFEPGNHVKVV 486 (1039)
Q Consensus 441 l~G~V~~V~~d~V~i~~~~~~l~~~i~v~--------~~~LrK~F~~GDhVkVi 486 (1039)
..|+|++|...-+.|..... + +--++ .....+.|++||.+++.
T Consensus 4 v~g~V~~v~~~Gv~V~l~~~-v--~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~ 54 (69)
T cd05697 4 VKGTIRKLRPSGIFVKLSDH-I--KGLVPPMHLADVRLKHPEKKFKPGLKVKCR 54 (69)
T ss_pred EEEEEEEEeccEEEEEecCC-c--EEEEEHHHCCCccccCHHHcCCCCCEEEEE
Confidence 45777777766555543211 1 11122 23345689999999873
No 306
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=20.09 E-value=2.2e+02 Score=31.74 Aligned_cols=50 Identities=26% Similarity=0.384 Sum_probs=33.0
Q ss_pred CCCCEEEEecccccCceeEEEEEcCC--eEEEeecCCCC-------CcceeeccccceeeccCCCceEE
Q 001639 426 MKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGL-------PKTLAVNSKELCKYFEPGNHVKV 485 (1039)
Q Consensus 426 ~~GD~V~V~~Gel~gl~G~V~~V~~d--~V~i~~~~~~l-------~~~i~v~~~~LrK~F~~GDhVkV 485 (1039)
++||.|. |+|+.|..+ .|-|.+....+ ...++--..++|.+|++||+|..
T Consensus 63 ~~gD~VI----------G~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~A 121 (239)
T COG1097 63 EVGDVVI----------GKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYA 121 (239)
T ss_pred CCCCEEE----------EEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEE
Confidence 5678763 888888766 45555543221 22234447899999999999854
Done!