Query 010205
Match_columns 515
No_of_seqs 294 out of 859
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 22:16:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010205.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010205hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2814 Transcription coactiva 100.0 4.1E-50 9E-55 402.3 15.9 338 60-508 2-345 (345)
2 PLN00108 unknown protein; Prov 100.0 4.4E-46 9.6E-51 368.1 22.5 224 227-510 33-256 (257)
3 PF10469 AKAP7_NLS: AKAP7 2'5' 100.0 8.6E-42 1.9E-46 331.1 21.4 207 230-508 1-209 (209)
4 COG1514 LigT 2'-5' RNA ligase 99.9 2.6E-26 5.6E-31 218.9 18.3 179 288-510 2-180 (180)
5 PRK15124 2'-5' RNA ligase; Pro 99.9 1.5E-24 3.2E-29 205.7 17.9 171 288-510 6-176 (176)
6 TIGR02258 2_5_ligase 2'-5' RNA 99.9 2.9E-24 6.3E-29 202.7 18.5 178 288-508 2-179 (179)
7 PRK13679 hypothetical protein; 99.7 4.6E-16 1E-20 146.5 16.2 167 288-509 2-168 (168)
8 PHA02574 57B hypothetical prot 99.7 3.9E-16 8.5E-21 144.5 9.6 109 288-448 10-118 (149)
9 PF13563 2_5_RNA_ligase2: 2'-5 99.2 2.8E-11 6.1E-16 110.1 9.6 129 337-492 21-150 (153)
10 cd02394 vigilin_like_KH K homo 99.2 1.3E-11 2.9E-16 97.3 6.0 60 156-216 2-62 (62)
11 cd02393 PNPase_KH Polynucleoti 99.2 1.6E-11 3.6E-16 97.3 6.4 59 155-216 3-61 (61)
12 PF00013 KH_1: KH domain syndr 99.2 2E-11 4.4E-16 95.6 4.0 60 155-215 1-60 (60)
13 PF05213 Corona_NS2A: Coronavi 99.0 7.1E-09 1.5E-13 100.0 13.4 127 343-506 45-177 (248)
14 cd00105 KH-I K homology RNA-bi 98.9 1.7E-09 3.6E-14 85.0 5.9 59 156-215 2-63 (64)
15 PF02834 LigT_PEase: LigT like 98.9 4.9E-10 1.1E-14 93.8 2.5 82 299-401 6-87 (87)
16 cd02396 PCBP_like_KH K homolog 98.8 1E-08 2.2E-13 82.0 6.1 59 156-215 2-64 (65)
17 smart00322 KH K homology RNA-b 98.7 3.9E-08 8.4E-13 76.7 8.0 66 153-219 2-68 (69)
18 PF13014 KH_3: KH domain 98.7 1.2E-08 2.6E-13 75.1 4.0 39 164-202 1-43 (43)
19 cd02395 SF1_like-KH Splicing f 98.7 3E-08 6.6E-13 89.0 6.7 60 162-221 14-95 (120)
20 KOG1676 K-homology type RNA bi 98.6 1.4E-07 3.1E-12 102.4 8.1 107 151-258 227-346 (600)
21 PRK13763 putative RNA-processi 98.4 6.6E-07 1.4E-11 85.8 6.9 65 154-220 3-70 (180)
22 TIGR03665 arCOG04150 arCOG0415 98.3 6E-07 1.3E-11 85.4 5.3 61 158-220 2-64 (172)
23 KOG0119 Splicing factor 1/bran 98.2 1.8E-06 3.9E-11 92.2 6.8 72 153-224 137-233 (554)
24 PRK13763 putative RNA-processi 98.0 7.9E-06 1.7E-10 78.4 5.8 54 163-221 104-157 (180)
25 TIGR03665 arCOG04150 arCOG0415 97.9 1.3E-05 2.8E-10 76.3 5.5 54 163-221 98-151 (172)
26 TIGR02696 pppGpp_PNP guanosine 97.9 2E-05 4.4E-10 89.1 6.9 66 153-221 577-642 (719)
27 COG5176 MSL5 Splicing factor ( 97.9 1.8E-05 4E-10 76.4 5.1 76 146-221 140-221 (269)
28 KOG2191 RNA-binding protein NO 97.8 0.00012 2.7E-09 75.1 11.0 107 151-258 36-160 (402)
29 KOG2208 Vigilin [Lipid transpo 97.8 3.4E-05 7.3E-10 88.5 7.2 104 152-259 345-449 (753)
30 KOG2193 IGF-II mRNA-binding pr 97.8 2E-05 4.3E-10 82.9 4.3 104 151-258 196-308 (584)
31 TIGR03591 polynuc_phos polyrib 97.7 3.8E-05 8.2E-10 87.5 6.1 65 154-221 551-615 (684)
32 KOG2193 IGF-II mRNA-binding pr 97.5 9.1E-05 2E-09 78.0 4.7 61 161-222 287-353 (584)
33 KOG1588 RNA-binding protein Sa 97.5 0.00023 5E-09 71.4 7.2 70 153-224 91-187 (259)
34 KOG1676 K-homology type RNA bi 97.4 0.00016 3.5E-09 79.2 5.2 110 150-260 50-169 (600)
35 COG1094 Predicted RNA-binding 97.4 0.00035 7.5E-09 67.4 6.4 67 152-220 6-76 (194)
36 PRK04163 exosome complex RNA-b 97.3 0.00044 9.6E-09 69.1 6.6 63 156-221 147-209 (235)
37 KOG2191 RNA-binding protein NO 97.3 0.0005 1.1E-08 70.8 6.3 67 154-221 132-204 (402)
38 PLN00207 polyribonucleotide nu 97.2 0.00035 7.6E-09 81.0 5.5 66 153-221 684-750 (891)
39 KOG2113 Predicted RNA binding 97.2 0.00034 7.5E-09 71.4 4.8 66 151-217 23-88 (394)
40 KOG2190 PolyC-binding proteins 97.1 0.0014 3.1E-08 71.8 8.3 67 154-221 138-208 (485)
41 COG1185 Pnp Polyribonucleotide 97.1 0.0008 1.7E-08 75.3 6.3 69 153-224 551-619 (692)
42 PRK11824 polynucleotide phosph 96.9 0.00079 1.7E-08 77.0 4.5 64 155-221 555-618 (693)
43 KOG2192 PolyC-binding hnRNP-K 96.7 0.0035 7.6E-08 63.0 6.8 68 153-221 314-384 (390)
44 TIGR03319 YmdA_YtgF conserved 96.5 0.0054 1.2E-07 67.9 7.1 69 151-221 201-270 (514)
45 PRK00106 hypothetical protein; 96.4 0.0069 1.5E-07 67.2 7.1 69 151-221 222-291 (535)
46 PRK12704 phosphodiesterase; Pr 96.3 0.0067 1.5E-07 67.3 6.6 68 152-221 208-276 (520)
47 KOG0336 ATP-dependent RNA heli 96.3 0.0031 6.8E-08 67.0 3.5 69 152-221 45-113 (629)
48 COG1094 Predicted RNA-binding 96.2 0.0074 1.6E-07 58.4 5.4 54 163-221 111-164 (194)
49 PF09749 HVSL: Uncharacterised 96.2 0.039 8.5E-07 55.1 10.7 104 338-451 86-191 (239)
50 PF02834 LigT_PEase: LigT like 95.8 0.0096 2.1E-07 49.5 3.6 76 410-500 8-87 (87)
51 PF07823 CPDase: Cyclic phosph 95.2 0.14 2.9E-06 49.9 10.0 142 343-508 40-196 (196)
52 cd02134 NusA_KH NusA_K homolog 95.1 0.024 5.2E-07 44.9 3.5 37 153-189 24-60 (61)
53 COG1097 RRP4 RNA-binding prote 95.0 0.04 8.7E-07 55.0 5.6 63 156-221 148-210 (239)
54 KOG2814 Transcription coactiva 94.9 0.0018 3.9E-08 66.9 -4.2 150 340-504 128-280 (345)
55 PRK12705 hypothetical protein; 94.9 0.031 6.8E-07 61.8 5.1 68 152-221 196-264 (508)
56 KOG2279 Kinase anchor protein 94.3 0.031 6.7E-07 61.3 3.1 103 150-257 64-167 (608)
57 KOG1067 Predicted RNA-binding 94.0 0.047 1E-06 60.1 3.6 64 154-221 597-660 (760)
58 KOG2192 PolyC-binding hnRNP-K 93.2 0.25 5.4E-06 50.1 6.9 70 151-221 45-115 (390)
59 KOG2190 PolyC-binding proteins 92.8 0.17 3.8E-06 55.7 5.8 103 156-258 45-166 (485)
60 KOG2208 Vigilin [Lipid transpo 91.2 0.15 3.2E-06 59.2 3.0 42 150-191 705-746 (753)
61 TIGR03223 Phn_opern_protn puta 91.1 3.5 7.6E-05 41.3 12.2 141 342-510 58-228 (228)
62 PF14611 SLS: Mitochondrial in 87.5 2.5 5.4E-05 41.1 8.1 73 156-238 28-100 (210)
63 COG1855 ATPase (PilT family) [ 86.3 0.5 1.1E-05 51.6 2.7 43 152-194 484-526 (604)
64 cd02409 KH-II KH-II (K homolo 85.3 1.1 2.3E-05 34.7 3.5 35 153-187 24-58 (68)
65 KOG3273 Predicted RNA-binding 85.3 0.61 1.3E-05 45.5 2.5 54 163-221 178-231 (252)
66 KOG2113 Predicted RNA binding 84.6 0.79 1.7E-05 47.5 3.1 68 151-218 112-180 (394)
67 PRK02821 hypothetical protein; 84.5 0.78 1.7E-05 38.3 2.5 32 152-183 29-60 (77)
68 PF13083 KH_4: KH domain; PDB: 84.2 0.55 1.2E-05 38.1 1.4 34 151-184 26-59 (73)
69 PRK08406 transcription elongat 83.8 1 2.2E-05 41.7 3.3 38 153-190 98-135 (140)
70 PRK00468 hypothetical protein; 83.4 1.1 2.4E-05 37.2 3.0 30 152-181 28-57 (75)
71 COG1837 Predicted RNA-binding 83.0 1.2 2.6E-05 37.2 2.9 31 151-181 27-57 (76)
72 COG5166 Uncharacterized conser 83.0 1.4 3.1E-05 48.5 4.3 68 153-220 448-523 (657)
73 PF10469 AKAP7_NLS: AKAP7 2'5' 82.8 0.61 1.3E-05 45.3 1.4 25 287-311 1-25 (209)
74 PRK13764 ATPase; Provisional 82.6 0.93 2E-05 51.4 2.9 43 152-194 479-521 (602)
75 PRK01064 hypothetical protein; 79.2 1.8 3.9E-05 36.3 2.8 32 151-182 27-58 (78)
76 PHA02977 hypothetical protein; 79.0 9.8 0.00021 35.6 7.7 112 343-475 71-192 (201)
77 PF07650 KH_2: KH domain syndr 76.9 1.4 3.1E-05 36.0 1.6 36 153-188 24-59 (78)
78 TIGR01952 nusA_arch NusA famil 75.7 2.5 5.3E-05 39.3 2.9 39 152-190 98-136 (141)
79 PRK08406 transcription elongat 74.1 3.3 7.2E-05 38.3 3.4 37 155-191 33-69 (140)
80 cd02414 jag_KH jag_K homology 73.9 2.7 5.9E-05 34.6 2.5 35 155-189 25-59 (77)
81 PLN00108 unknown protein; Prov 73.0 1.9 4E-05 44.0 1.5 29 283-311 32-61 (257)
82 PF13184 KH_5: NusA-like KH do 72.0 3.7 8E-05 33.5 2.8 26 165-190 19-45 (69)
83 KOG3102 Uncharacterized conser 71.5 14 0.00031 36.6 7.1 101 337-449 117-218 (269)
84 KOG2874 rRNA processing protei 67.6 9.9 0.00021 39.2 5.3 54 162-224 157-210 (356)
85 cd02413 40S_S3_KH K homology R 67.1 3.7 7.9E-05 34.5 1.8 37 155-191 31-67 (81)
86 TIGR01953 NusA transcription t 62.9 7.4 0.00016 41.3 3.6 39 153-191 300-338 (341)
87 PRK12328 nusA transcription el 60.5 9.1 0.0002 41.1 3.7 42 153-194 307-348 (374)
88 TIGR01952 nusA_arch NusA famil 59.2 11 0.00023 35.1 3.6 36 155-190 34-69 (141)
89 COG0195 NusA Transcription elo 57.2 11 0.00024 36.7 3.5 37 155-191 143-179 (190)
90 KOG2279 Kinase anchor protein 56.0 7.4 0.00016 43.4 2.2 68 150-218 136-206 (608)
91 PRK06418 transcription elongat 54.4 13 0.00028 35.5 3.3 33 156-189 63-95 (166)
92 PRK12327 nusA transcription el 52.6 14 0.00031 39.5 3.7 40 153-192 302-341 (362)
93 PRK10334 mechanosensitive chan 51.5 80 0.0017 32.6 8.8 91 341-447 185-276 (286)
94 cd02412 30S_S3_KH K homology R 51.1 12 0.00026 33.0 2.4 32 156-187 63-94 (109)
95 PRK09202 nusA transcription el 51.1 14 0.0003 40.9 3.4 39 153-191 301-339 (470)
96 COG5255 Uncharacterized protei 45.3 43 0.00093 33.2 5.3 33 417-452 156-189 (239)
97 PF07823 CPDase: Cyclic phosph 43.6 23 0.00051 34.3 3.3 42 399-449 4-46 (196)
98 PRK12329 nusA transcription el 42.6 24 0.00052 38.8 3.5 39 153-191 334-372 (449)
99 PF00352 TBP: Transcription fa 38.4 70 0.0015 26.7 5.0 35 184-221 49-84 (86)
100 COG1702 PhoH Phosphate starvat 38.0 75 0.0016 33.9 6.2 55 162-221 23-79 (348)
101 COG0799 Uncharacterized homolo 37.9 1.3E+02 0.0029 27.1 6.9 61 356-431 6-66 (115)
102 COG0195 NusA Transcription elo 36.3 33 0.00071 33.5 3.0 36 154-189 76-111 (190)
103 PRK11538 ribosome-associated p 34.1 1.8E+02 0.0039 25.6 7.1 60 357-431 7-66 (105)
104 cd02410 archeal_CPSF_KH The ar 34.1 34 0.00074 32.0 2.6 33 157-189 79-111 (145)
105 TIGR00436 era GTP-binding prot 33.2 27 0.00057 35.2 2.0 29 154-182 221-250 (270)
106 cd02411 archeal_30S_S3_KH K ho 31.9 39 0.00085 28.3 2.5 32 153-186 39-70 (85)
107 PRK11281 hypothetical protein; 31.0 1.6E+02 0.0036 36.2 8.3 76 354-432 1005-1080(1113)
108 PRK15494 era GTPase Era; Provi 30.7 30 0.00065 36.4 2.0 36 154-189 273-317 (339)
109 PF09749 HVSL: Uncharacterised 30.0 91 0.002 31.1 5.2 66 288-367 141-208 (239)
110 COG0092 RpsC Ribosomal protein 29.9 39 0.00084 34.1 2.4 37 154-190 51-87 (233)
111 PF06299 DUF1045: Protein of u 29.8 1.4E+02 0.0031 28.4 6.1 78 404-490 47-150 (160)
112 PRK00089 era GTPase Era; Revie 29.7 33 0.00072 34.7 2.0 36 154-189 226-270 (292)
113 COG1782 Predicted metal-depend 28.2 39 0.00084 37.8 2.2 36 156-191 101-136 (637)
114 COG5255 Uncharacterized protei 27.6 1E+02 0.0022 30.7 4.7 34 339-372 176-210 (239)
115 TIGR00090 iojap_ybeB iojap-lik 27.0 2.5E+02 0.0054 24.3 6.7 46 378-431 16-61 (99)
116 COG1908 FrhD Coenzyme F420-red 25.7 2.4E+02 0.0052 25.9 6.4 35 393-430 93-127 (132)
117 PF08302 tRNA_lig_CPD: Fungal 25.7 3.9E+02 0.0084 27.2 8.8 61 340-406 114-183 (257)
118 COG1847 Jag Predicted RNA-bind 25.3 1.2E+02 0.0026 30.1 4.8 74 146-222 83-156 (208)
119 COG1159 Era GTPase [General fu 23.5 39 0.00084 35.3 1.2 27 153-179 228-255 (298)
120 smart00411 BHL bacterial (prok 23.2 91 0.002 25.8 3.2 35 353-391 17-51 (90)
121 cd00591 HU_IHF Integration hos 22.8 1E+02 0.0022 25.2 3.4 35 353-391 16-50 (87)
122 KOG4369 RTK signaling protein 21.6 37 0.00081 41.4 0.6 64 157-221 1343-1410(2131)
123 PF08975 2H-phosphodiest: Doma 21.2 39 0.00085 30.5 0.6 47 288-349 14-61 (118)
No 1
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=100.00 E-value=4.1e-50 Score=402.33 Aligned_cols=338 Identities=36% Similarity=0.564 Sum_probs=289.1
Q ss_pred ccccccccCCceeeeccccccccccccccccCCCCCceEEe-eeccCCcccccccceeeeecccccccccCCcccccccc
Q 010205 60 YGDKKQKIINPVWRPVSTQASVNEESLVKDVSEDGSQIQEM-HCSTSSNVSDAQLGVEVAEAVNEGTDLTLSSSVSLDDI 138 (515)
Q Consensus 60 ~~~~~~k~~~~~wrp~~t~a~~~~~~~~~~~~~~~~~~~e~-~~~~s~~~s~~~~~~~~~~~~~~~~~~~~ss~~~~~~~ 138 (515)
+..++++..|.+|+|++|+.++.. .+++...|++ .|+++...+. ++
T Consensus 2 ~~~~~~~~~n~~~~~~~~~t~~~~-------~~~~~e~~~~~~c~d~p~~~~--------------------------dv 48 (345)
T KOG2814|consen 2 YRKTRYNLVNDVSFDLNTDTTFAD-------MSEEFEAQTSAECVDMPGDTV--------------------------DV 48 (345)
T ss_pred cchhhhhhhhhcccCccccccccc-------CchhhHHHhHhhcccCCCChH--------------------------Hh
Confidence 456789999999999999988763 3345556665 6666643322 11
Q ss_pred cccccCCCCccCCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHH
Q 010205 139 KDETLEGEPVPSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQA 217 (515)
Q Consensus 139 ~~~~~~~~~~~~~~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~~ 217 (515)
+.-+ -.++|+.++.|++.|+++|||++|.|+++||+||+|+|.+|++++ .+.|+|+|.++.+|.+|.+||..
T Consensus 49 ~~~~-------~~~~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~ 121 (345)
T KOG2814|consen 49 EDDA-------GAKDFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAK 121 (345)
T ss_pred hhcc-------ccccchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHH
Confidence 1110 122889999999999999999999999999999999999999995 78999999999999999999999
Q ss_pred HHHHhhhCCCCCceEEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCccccchHHhhhcccCCceEEEEccC
Q 010205 218 IIAEAVESPSLDYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNI 297 (515)
Q Consensus 218 iv~e~~~~~k~~~tHFIsIPl~~hp~I~~~~~~f~~~Il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rpn~FVAv~l~~ 297 (515)
++++.++ +++.|||+.+|++ ...+.++|..|+...+..
T Consensus 122 ~ids~r~--s~p~thflal~ln-e~eVqe~f~~fke~~~~~--------------------------------------- 159 (345)
T KOG2814|consen 122 LIDSDRK--SFPITHFLALPLN-EHEVQEGFLAFKELKPFI--------------------------------------- 159 (345)
T ss_pred HHHhhhh--cCchhhhhhhhcc-hHHHHHHHHHHHhhhhhH---------------------------------------
Confidence 9999887 7899999999998 588999999988322211
Q ss_pred CcchhHHHhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeecccCChhhHHHHHHHHHHhHHHhhhhcCC
Q 010205 298 GDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDN 377 (515)
Q Consensus 298 ~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gl~~~~fv~p~~LHLTL~fLgL~~eeei~~a~~aL~~i~~~i~~iL~~ 377 (515)
++ +-+.|++.+.|++|.++||||+|+.|++++++++|+++|+.+.+++..+.+.
T Consensus 160 -----------es---------------l~~~g~~~s~F~~p~~~HLTvgm~~L~~dd~vq~a~e~les~~~e~~~~~~~ 213 (345)
T KOG2814|consen 160 -----------ES---------------LLDGGIDKSLFQGPGTFHLTVGMLKLLNDDDVQKALEILESTFQEIRIDVGE 213 (345)
T ss_pred -----------HH---------------hhccchhhccccCCceeeEEEEEEEecChHHHHHHHHHHHHHHHHHHhccCC
Confidence 00 1246888999999999999999999999999999999999998888888889
Q ss_pred CCeEEEecccccCCCCCCCceEEEEeccccCchhHHHHHH-HHHHHHHHHCCccccccCCCCcccccEEeeeeccccccc
Q 010205 378 RPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHAC-QVIIDAFNEAGLVFHRDYNKKLKQLHATLMNIRHKKRRK 456 (515)
Q Consensus 378 ~pf~l~lkGLg~F~~dp~~~rVLyagV~~~~~~~~L~~L~-~~L~~~f~~~Gl~~e~d~~r~fk~PHiTLar~r~~~~~~ 456 (515)
.|+.+.++|+.+|++||..++||||+|++.+....|+..+ +.|..+|...|+...+ .++.+ +|+|+||++|++.+.
T Consensus 214 kp~~i~lkG~~~mnddP~~~kVLYAkv~~~~~e~~l~~~~~~~i~~~f~~~~li~k~--~~~~k-LH~TvmNsryrk~~~ 290 (345)
T KOG2814|consen 214 KPLFIDLKGLDKMNDDPSLTKVLYAKVEPDDYEKFLQHRCGERILERFVASGLIKKE--SSSLK-LHCTVMNSRYRKNGG 290 (345)
T ss_pred CceeeeccchhhhcCCHhHheeeeeeccCcchHHHHHHHHHHHHHHHHHHhcchhcc--ccccE-EEEEEehhhhhhcCC
Confidence 9999999999999999999999999999877788899999 9999999999998854 78999 999999999987543
Q ss_pred C---CCccccccHHHHHHHhCCCccccEEecEEEEEeeecCCCCCceeEeEEEeC
Q 010205 457 G---TRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPF 508 (515)
Q Consensus 457 g---~~~~~~fda~~il~~~~d~~fG~~~V~~I~Ls~l~~~~~~g~Y~~i~si~L 508 (515)
. .++...||+.++++.|++++||++.+.++|||.+...+.+|||.+++++||
T Consensus 291 ~~g~~K~~~~Fdar~ilk~fg~f~fg~~~~~eih~~~~~~~d~ng~y~~~gsi~f 345 (345)
T KOG2814|consen 291 EPGLVKESESFDAREILKAFGQFLFGELKLQEIHLSVRFAADQNGNYNECGSIPF 345 (345)
T ss_pred CcchhhHhhhccHHHHHHHHhhHhHhhcccceeeeeeeeccccccchhhhcCCCC
Confidence 1 145567999999999999999999999999999998889999999999987
No 2
>PLN00108 unknown protein; Provisional
Probab=100.00 E-value=4.4e-46 Score=368.09 Aligned_cols=224 Identities=56% Similarity=0.968 Sum_probs=198.2
Q ss_pred CCCceEEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCccccchHHhhhcccCCceEEEEccCCcchhHHHh
Q 010205 227 SLDYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKV 306 (515)
Q Consensus 227 k~~~tHFIsIPl~~hp~I~~~~~~f~~~Il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rpn~FVAv~l~~~~~~~~v~~ 306 (515)
|.+||||||||+..+|.|.+++..|++.||+..+ ..|.-|
T Consensus 33 ~~~~THFlavPL~~~p~i~~~~~~Fk~~Vl~~~~------------------------~~~~~f---------------- 72 (257)
T PLN00108 33 REVFTHFVSLPLAIYPDLKKNIEAFQNSVLGNND------------------------KDPLKF---------------- 72 (257)
T ss_pred CCCCCeEEEEEcCCCHHHHHHHHHHHHHHHhccc------------------------cccccc----------------
Confidence 5679999999996689999999999999997521 001000
Q ss_pred hhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeecccCChhhHHHHHHHHHHhHHHhhhhcCCCCeEEEecc
Q 010205 307 DRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKG 386 (515)
Q Consensus 307 ~q~~i~~~~~~~~~~r~~~~~~~Gl~~~~fv~p~~LHLTL~fLgL~~eeei~~a~~aL~~i~~~i~~iL~~~pf~l~lkG 386 (515)
| +.++++||++++|++|.+|||||+||.|.+++++++|.++|+++...+.++++++|+.|.|+|
T Consensus 73 -~---------------~~l~~~gid~siF~~p~~LHLTLgmL~L~~~eev~kA~~~L~s~~~~i~~~l~~~pl~I~lkG 136 (257)
T PLN00108 73 -Q---------------STLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNILKSICSNVRQALKDRPVFIRLRG 136 (257)
T ss_pred -c---------------ccccccCCCHHHcCCCCceEEEEEEEEcCCHHHHHHHHHHHHHHHHHHHHhhCCCCeEEEEEe
Confidence 0 013477999999999999999999999999999999999999999889899999999999999
Q ss_pred cccCCCCCCCceEEEEeccccCchhHHHHHHHHHHHHHHHCCccccccCCCCcccccEEeeeecccccccCCCccccccH
Q 010205 387 LDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKQLHATLMNIRHKKRRKGTRRVDYFDA 466 (515)
Q Consensus 387 Lg~F~~dp~~~rVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fk~PHiTLar~r~~~~~~g~~~~~~fda 466 (515)
|++||+||+.++||||+|++.++.++|+++|+.|.+.|.++||...+ .+++++ ||+||||++|++... +++.+|||
T Consensus 137 L~~Mnddps~~~VLYA~Ve~~~~~~rLq~~ad~i~~~F~~aGL~~~d-~~~~vK-LH~TlmNt~~rk~k~--~k~~sFDA 212 (257)
T PLN00108 137 LDCMNGSLDKTRVLYAPVEEVGHEGRLLNACHVIIDAFENAGFAGKD-AKSRLK-LHATLMNASYRKDKS--KKMDTFDA 212 (257)
T ss_pred ehhcCCCcccceEEEEeccccCchhHHHHHHHHHHHHHHHcCCcccc-cCccee-eEeEEechhhhhccc--CccccccH
Confidence 99999999999999999988777789999999999999999999753 246899 999999999976532 46788999
Q ss_pred HHHHHHhCCCccccEEecEEEEEeeecCCCCCceeEeEEEeCCC
Q 010205 467 RDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 510 (515)
Q Consensus 467 ~~il~~~~d~~fG~~~V~~I~Ls~l~~~~~~g~Y~~i~si~L~~ 510 (515)
++||++|++++||++.|++||||+++.++.+|||+|+++++|++
T Consensus 213 ~~Il~~f~d~~FG~~~i~~vhls~r~s~~~dGyY~~~~sl~~~~ 256 (257)
T PLN00108 213 REIHKEFENKDWGTYLIREAHISQRYKYDPNGYFHCCASLPFPH 256 (257)
T ss_pred HHHHHhccCcccceEEecEEEEEeecccCCCCCEEEEEEeecCC
Confidence 99999999999999999999999999988899999999999986
No 3
>PF10469 AKAP7_NLS: AKAP7 2'5' RNA ligase-like domain; InterPro: IPR019510 This entry represents the N-terminal nuclear localisation signal-containing domain found in the cyclic AMP-dependent protein kinase A (PKA) anchor protein, AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes []. This domain carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein []. Binding to the regulatory subunits RI and RII of PKA is mediated via the RI-RII subunit-binding domain at the C terminus.
Probab=100.00 E-value=8.6e-42 Score=331.12 Aligned_cols=207 Identities=37% Similarity=0.627 Sum_probs=178.4
Q ss_pred ceEEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCccccchHHhhhcccCCceEEEEccCCcchhHHHhhhc
Q 010205 230 YSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKVDRT 309 (515)
Q Consensus 230 ~tHFIsIPl~~hp~I~~~~~~f~~~Il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rpn~FVAv~l~~~~~~~~v~~~q~ 309 (515)
||||||||++ +|.|++.+..|++.|+..
T Consensus 1 pthFl~ipl~-~~~i~~~~~~fq~~v~~~--------------------------------------------------- 28 (209)
T PF10469_consen 1 PTHFLCIPLN-SPEIQEKFKEFQNEVLSK--------------------------------------------------- 28 (209)
T ss_pred CCeEEEEECC-CHHHHHHHHHHHHHHHhh---------------------------------------------------
Confidence 5888888884 788888888888888743
Q ss_pred cccccccccccCCCCCCCCCCCCcccccCCCCceEEeeecccCChhhHHHHHHHHHHhHHHhhhhcCC-CCeEEEecccc
Q 010205 310 SIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDN-RPLFIRLKGLD 388 (515)
Q Consensus 310 ~i~~~~~~~~~~r~~~~~~~Gl~~~~fv~p~~LHLTL~fLgL~~eeei~~a~~aL~~i~~~i~~iL~~-~pf~l~lkGLg 388 (515)
.+|+++++|++|++|||||+||+|.+++++++|.++|+++.+.+.+.+.. +|+.|+|+||+
T Consensus 29 ------------------~~~~~~~~~i~~~~lHlTL~vl~L~~~~~i~~a~~~L~~~~~~i~~~~~~~~~~~i~l~Gl~ 90 (209)
T PF10469_consen 29 ------------------DPGLDESAFIPPEKLHLTLGVLSLDTDEEIEKAKEALKSLKQEIKDQLQNPPPLKITLKGLG 90 (209)
T ss_pred ------------------cCCCCHHHcCCcccceEEEEEeeCCCHHHHHHHHHHHHHHHHHHhhhccCCCCceEEeeech
Confidence 34677889999999999999999999999999999999999888877654 99999999999
Q ss_pred cCCCCCCCceEEEEeccccCchhHHHHHHHHHHHHHHHCCccccccCCCCcccccEEeeeecccccccCCCccccccHHH
Q 010205 389 LMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKQLHATLMNIRHKKRRKGTRRVDYFDARD 468 (515)
Q Consensus 389 ~F~~dp~~~rVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fk~PHiTLar~r~~~~~~g~~~~~~fda~~ 468 (515)
+|++||+++|||||+|.++++...|+++++.|.+.|.++||...++.+.+|+ ||+||||++++.... .+....||+++
T Consensus 91 ~f~~d~~~~~VLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~~~~~~~-~H~Tl~n~~~~~~~~-~~~~~~~d~~~ 168 (209)
T PF10469_consen 91 YFNDDPSKARVLYAKVSEDSNSERLQELANKLRERFQEAGLLVTDDRRFSFK-PHITLMNTSYRKKKK-RRQGNKFDASE 168 (209)
T ss_pred hhCCCCCcceEEEEcccccchHHHHHHHHHHHHHHHHHcCCccccccCCCcc-eEEEEEecccccccc-ccccCccccHH
Confidence 9999999999999999986667999999999999999999998653223489 999999999852111 01125789999
Q ss_pred HHHHhCCCccccEEecEEEEEeeecCCC-CCceeEeEEEeC
Q 010205 469 IFKQFGSKEWGEYLIKEAHLSQRFVYDE-SGFYHCCASIPF 508 (515)
Q Consensus 469 il~~~~d~~fG~~~V~~I~Ls~l~~~~~-~g~Y~~i~si~L 508 (515)
++++|++++||.+.|++|+||+|+..++ +|||.++++|+|
T Consensus 169 ~~~~~~~~~fG~~~v~~i~Lc~m~~~~~~dg~Y~~~~~i~l 209 (209)
T PF10469_consen 169 LLEKYKDFDFGEQPVEEIQLCSMGSTKPSDGYYQCIASIPL 209 (209)
T ss_pred HHHHcCCCccceEEECEEEEEeCCCCCCCCCeEEEEEEecC
Confidence 9999999999999999999999976655 999999999987
No 4
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=2.6e-26 Score=218.86 Aligned_cols=179 Identities=19% Similarity=0.320 Sum_probs=151.8
Q ss_pred CceEEEEccCCcchhHHHhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeecccCChhhHHHHHHHHHHh
Q 010205 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 367 (515)
Q Consensus 288 n~FVAv~l~~~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gl~~~~fv~p~~LHLTL~fLgL~~eeei~~a~~aL~~i 367 (515)
-+|+||+++ +++.+++..+++.+. ..+ ...|++++++||||.|||+++++.++.+.++|.++
T Consensus 2 RlFiAl~~p-~~i~~~i~~~~~~~~---------------~~~--~~k~v~~en~HiTL~flGev~e~~~~~l~~~l~~i 63 (180)
T COG1514 2 RLFIALDPP-AEIAERLARIRARLK---------------GAR--AIKWVEPENLHITLKFLGEVDEDKADELIEALARI 63 (180)
T ss_pred eeEEEecCC-HHHHHHHHHHHHhcC---------------ccc--ccccccccCceEEEEccCCcCchHHHHHHHHHHHh
Confidence 479999994 599999999998763 111 34799999999999999999999999999999987
Q ss_pred HHHhhhhcCCCCeEEEecccccCCCCCCCceEEEEeccccCchhHHHHHHHHHHHHHHHCCccccccCCCCcccccEEee
Q 010205 368 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKQLHATLM 447 (515)
Q Consensus 368 ~~~i~~iL~~~pf~l~lkGLg~F~~dp~~~rVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fk~PHiTLa 447 (515)
.. +. ||.|+++|+|+|++ +.+|||+|+++.+ .+.|.+|++.|...+..+||..+ .++|+ ||+||+
T Consensus 64 ~~------~~-~f~i~l~g~g~F~~-~~~~rvi~~~v~~---~~~L~~L~~~l~~~~~~~g~~~~---~r~F~-PHvTl~ 128 (180)
T COG1514 64 AA------PE-PFPITLDGAGSFPN-PRRPRVIWVGVEE---TEELRALAEELERALARLGLRPE---ERPFV-PHVTLA 128 (180)
T ss_pred hc------CC-ceEEEEeeEcccCC-CCCCcEEEEcCCC---cHHHHHHHHHHHHHHHhcCCCCC---CCCcC-CCEEEE
Confidence 42 23 99999999999998 9999999999975 57899999999999999999987 58999 999999
Q ss_pred eecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeecCCCCCceeEeEEEeCCC
Q 010205 448 NIRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 510 (515)
Q Consensus 448 r~r~~~~~~g~~~~~~fda~~il~~~~d~~fG~~~V~~I~Ls~l~~~~~~g~Y~~i~si~L~~ 510 (515)
|.+. + .. ..+++..+.+..||++.|++|.|.....+..|+.|+++.+++|.+
T Consensus 129 r~k~-~------~~----~~~~~~~~~~~~~~~~~vd~~~L~~S~l~~~gp~Y~~~~~~~L~~ 180 (180)
T COG1514 129 RVKS-K------DK----LVEALGEFKNVEFGEMEVDRFSLYSSTLTPGGPIYETLKEFPLSG 180 (180)
T ss_pred eecc-c------ch----hhhhhhhhccccccceEeeEEEEEEEeeCCCCCEEEEEEEEecCC
Confidence 9875 1 11 237788899999999999999994433335689999999999964
No 5
>PRK15124 2'-5' RNA ligase; Provisional
Probab=99.92 E-value=1.5e-24 Score=205.69 Aligned_cols=171 Identities=13% Similarity=0.137 Sum_probs=136.5
Q ss_pred CceEEEEccCCcchhHHHhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeecccCChhhHHHHHHHHHHh
Q 010205 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 367 (515)
Q Consensus 288 n~FVAv~l~~~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gl~~~~fv~p~~LHLTL~fLgL~~eeei~~a~~aL~~i 367 (515)
-+|+|++++. ++.+.+.++++.+. +.....|++|++|||||.|||.+++++++.+.++|+.+
T Consensus 6 RlFiAl~~p~-~~~~~l~~~~~~~~-----------------~~~~~rwv~~~nlHiTL~FlG~v~~~~~~~l~~~l~~~ 67 (176)
T PRK15124 6 RLFFAIDLPD-EIRQQIIHWRATHF-----------------PPEAGRPVAAANLHLTLAFLGEVSAEKQQALSQLAGRI 67 (176)
T ss_pred EEEEEeCCCH-HHHHHHHHHHHHhc-----------------cccCcccccccccEEEEEecCCCCHHHHHHHHHHHHhc
Confidence 5899999985 88899999887652 11124799999999999999999999999888888765
Q ss_pred HHHhhhhcCCCCeEEEecccccCCCCCCCceEEEEeccccCchhHHHHHHHHHHHHHHHCCccccccCCCCcccccEEee
Q 010205 368 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKQLHATLM 447 (515)
Q Consensus 368 ~~~i~~iL~~~pf~l~lkGLg~F~~dp~~~rVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fk~PHiTLa 447 (515)
..+||.|.+.|+|+||+ |||||+++++ +...|..|++.|++.+..+|+..+ .++|+ |||||+
T Consensus 68 --------~~~pF~l~l~~~g~Fp~----prvlwlg~~~--~~~~L~~L~~~l~~~l~~~G~~~e---~r~f~-PHiTLa 129 (176)
T PRK15124 68 --------RQPGFTLTLDDAGQWPR----SRVVWLGMRQ--PPRGLLQLANMLRSQAARSGCYQS---PQPFH-PHITLL 129 (176)
T ss_pred --------ccCCeEEEECcccCcCC----CCEEEEEcCC--CCHHHHHHHHHHHHHHHHcCCCCC---CCCCC-CCEeec
Confidence 45899999999999973 6999999974 357899999999999999999876 69999 999999
Q ss_pred eecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeecCCCCCceeEeEEEeCCC
Q 010205 448 NIRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 510 (515)
Q Consensus 448 r~r~~~~~~g~~~~~~fda~~il~~~~d~~fG~~~V~~I~Ls~l~~~~~~g~Y~~i~si~L~~ 510 (515)
|.+... .... . ....| .+.|++|+|.+...++.|+.|+++++++|.+
T Consensus 130 R~~~~~------~~~~-------~--~~~~~-~~~v~~~~L~~S~l~~~g~~Y~~l~~~~L~~ 176 (176)
T PRK15124 130 RDASRP------VAIP-------P--PGFNW-SFPVTEFTLYASSFARGRTRYTPLQRWPLTQ 176 (176)
T ss_pred cCCCCc------cccc-------C--CCCCC-ceEcCEEEEEEEeccCCCCEEEEEEEEeCCC
Confidence 964211 1110 0 11234 5889999996555446789999999999863
No 6
>TIGR02258 2_5_ligase 2'-5' RNA ligase. This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles.
Probab=99.92 E-value=2.9e-24 Score=202.73 Aligned_cols=178 Identities=19% Similarity=0.367 Sum_probs=147.3
Q ss_pred CceEEEEccCCcchhHHHhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeecccCChhhHHHHHHHHHHh
Q 010205 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 367 (515)
Q Consensus 288 n~FVAv~l~~~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gl~~~~fv~p~~LHLTL~fLgL~~eeei~~a~~aL~~i 367 (515)
-+||||.++. ++.+.+.++|..+. + . .....|++++++||||.|+|+.++++++.+.++|+++
T Consensus 2 R~FiAl~~p~-~~~~~l~~~~~~l~---------~----~---~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~ 64 (179)
T TIGR02258 2 RLFIAIDLPP-EIREQLSRIQRKLK---------S----P---LDGIKWVPPENLHITLKFLGEVDEEQVEELEDALAKI 64 (179)
T ss_pred eEEEEecCCH-HHHHHHHHHHHHhh---------c----c---CCCcEECChHHCEEEEEEccCCCHHHHHHHHHHHHHh
Confidence 4799999986 69999999998762 0 0 1234799999999999999999999999888888775
Q ss_pred HHHhhhhcCCCCeEEEecccccCCCCCCCceEEEEeccccCchhHHHHHHHHHHHHHHHCCccccccCCCCcccccEEee
Q 010205 368 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKQLHATLM 447 (515)
Q Consensus 368 ~~~i~~iL~~~pf~l~lkGLg~F~~dp~~~rVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fk~PHiTLa 447 (515)
. .++|.+.+.|+|+|++ +..++|||++++. ...|.+|++.|.+.+...|+..+ .++|+ |||||+
T Consensus 65 ~--------~~~f~l~l~~~~~F~~-~~~~~vl~l~~~~---~~~L~~L~~~l~~~~~~~g~~~~---~~~f~-PHiTla 128 (179)
T TIGR02258 65 A--------EPPFTLKLEGIGVFGN-PKRPRVLWAGVEQ---SEELTQLHADLERELAKLGFSKE---ERPFT-PHITLA 128 (179)
T ss_pred c--------CCCeEEEEeeeeeCCC-CCCCeEEEEeeCC---CHHHHHHHHHHHHHHHHcCCCCC---CCCcC-CCEEEE
Confidence 2 3679999999999987 7889999999975 34899999999999999999865 57899 999999
Q ss_pred eecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeecCCCCCceeEeEEEeC
Q 010205 448 NIRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPF 508 (515)
Q Consensus 448 r~r~~~~~~g~~~~~~fda~~il~~~~d~~fG~~~V~~I~Ls~l~~~~~~g~Y~~i~si~L 508 (515)
|..... .++.++++.+....++.+.|++|+|.+......|+.|+++++++|
T Consensus 129 r~~~~~----------~~~~~~~~~~~~~~~~~~~v~~i~L~~S~~~~~g~~Y~~l~~~~l 179 (179)
T TIGR02258 129 RKKSGK----------PGVPEFLQEFANEEFGSFHVDEFHLYSSTLTPGGPIYEPLARFQL 179 (179)
T ss_pred EecCCc----------HhHHHHHHHhCCCCCCceEeeEEEEEEeeccCCCCcceEEEEEcC
Confidence 865321 124467888888889999999999976655456789999999987
No 7
>PRK13679 hypothetical protein; Provisional
Probab=99.70 E-value=4.6e-16 Score=146.48 Aligned_cols=167 Identities=14% Similarity=0.138 Sum_probs=125.6
Q ss_pred CceEEEEccCCcchhHHHhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeecccCChhhHHHHHHHHHHh
Q 010205 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 367 (515)
Q Consensus 288 n~FVAv~l~~~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gl~~~~fv~p~~LHLTL~fLgL~~eeei~~a~~aL~~i 367 (515)
.|||||.++. ++++.+..+|+.+. .+ ..|++| ||||.|++..++++++++.++|+++
T Consensus 2 ~~~iai~~p~-~~~~~l~~~~~~~~----------------~~---~~~v~p---HITL~f~g~~~~~~~~~l~~~l~~~ 58 (168)
T PRK13679 2 KYGIVLFPSK-KIQDFANSYRKRYD----------------PH---YALIPP---HITLKEPFEISDEQLDSIVEELRAI 58 (168)
T ss_pred eeEEEEcCCH-HHHHHHHHHHHhhC----------------cc---cccCCC---ceEEecCCCCCHHHHHHHHHHHHHH
Confidence 4899999986 68999999987652 11 247777 9999999999999999888888876
Q ss_pred HHHhhhhcCCCCeEEEecccccCCCCCCCceEEEEeccccCchhHHHHHHHHHHHHHHHCCccccccCCCCcccccEEee
Q 010205 368 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKQLHATLM 447 (515)
Q Consensus 368 ~~~i~~iL~~~pf~l~lkGLg~F~~dp~~~rVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fk~PHiTLa 447 (515)
.. ...||.+++.|+++|++ + ++|||+++++ .+.|.+|++.|...+. + ..+ .++|. |||||+
T Consensus 59 ~~------~~~pf~l~l~~~~~F~~-~--~~vl~l~~~~---~~~L~~L~~~l~~~~~--~-~~~---~~~f~-PHiTla 119 (168)
T PRK13679 59 AS------ETKPFTLHVTKVSSFAP-T--NNVIYFKVEK---TEELEELHERLHSGDF--Y-GEA---EYAFV-PHITIG 119 (168)
T ss_pred Hh------cCCCEEEEEeccccCCC-C--CCEEEEEccC---CHHHHHHHHHHHhccc--c-ccc---CCCCC-CeEEee
Confidence 42 34899999999999975 2 4899999975 4689999999987653 2 222 47899 999999
Q ss_pred eecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeecCCCCCceeEeEEEeCC
Q 010205 448 NIRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFP 509 (515)
Q Consensus 448 r~r~~~~~~g~~~~~~fda~~il~~~~d~~fG~~~V~~I~Ls~l~~~~~~g~Y~~i~si~L~ 509 (515)
|..... ..-++.+.++. .+..+ .+.|++|+|.... .|+-|..+.++.|+
T Consensus 120 r~~~~~--------~~~~~~~~l~~-~~~~~-~~~v~~i~L~~~~---~~~~w~~~~~~~~~ 168 (168)
T PRK13679 120 QGLSDD--------EHEDVLGQLKM-ADVDH-EETIDRFHLLYQL---ENGSWTVYETFRLG 168 (168)
T ss_pred CCCCcH--------HHHHHHHHHhc-CCcce-eEEECeEEEEEEC---CCCeEEEEEEeeCC
Confidence 764321 11123344433 55556 7889999997553 37899999999875
No 8
>PHA02574 57B hypothetical protein; Provisional
Probab=99.65 E-value=3.9e-16 Score=144.54 Aligned_cols=109 Identities=11% Similarity=0.040 Sum_probs=88.4
Q ss_pred CceEEEEccCCcchhHHHhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeecccCChhhHHHHHHHHHHh
Q 010205 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 367 (515)
Q Consensus 288 n~FVAv~l~~~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gl~~~~fv~p~~LHLTL~fLgL~~eeei~~a~~aL~~i 367 (515)
-.|||+++++ ++++++..+|+.+. ...||++++|||||.| +++.++.+..
T Consensus 10 RlF~Al~~~~-~~r~~L~~lq~~l~--------------------~~r~V~~enLHlTL~F----~~~~v~~l~~----- 59 (149)
T PHA02574 10 GTYVAAKFSE-ATLDALERLQRTLR--------------------IPNPVPRDKLHSTIVY----SRVYVPFIPA----- 59 (149)
T ss_pred eEEEEEcCCH-HHHHHHHHHHHhcc--------------------CCcccCHHHCEEEEec----CHHHhHHHhc-----
Confidence 4799999977 89999999998642 1369999999999999 3555544311
Q ss_pred HHHhhhhcCCCCeEEEecccccCCCCCCCceEEEEeccccCchhHHHHHHHHHHHHHHHCCccccccCCCCcccccEEee
Q 010205 368 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKQLHATLM 447 (515)
Q Consensus 368 ~~~i~~iL~~~pf~l~lkGLg~F~~dp~~~rVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fk~PHiTLa 447 (515)
..+||.+.+.|+|+|++ + ++||||+|++ .+.|..|++.+++.+.. .+ .++|+ |||||+
T Consensus 60 --------~~~~F~l~l~glG~F~~-~-~~rvlWlg~~----~~~L~~L~~~l~~~l~~----~~---~r~F~-PHITLa 117 (149)
T PHA02574 60 --------SGSTEVASSGHLEVWET-Q-DKNALVLVLE----SEYLQCRHKYARALGAT----HD---FDDYT-PHITLS 117 (149)
T ss_pred --------cCCCeEEEeccccccCC-C-CCCEEEEEeC----CHHHHHHHHHHHHHhhc----CC---CCCcC-CcEEEe
Confidence 45999999999999964 2 3699999996 47899999999999887 22 35899 999999
Q ss_pred e
Q 010205 448 N 448 (515)
Q Consensus 448 r 448 (515)
|
T Consensus 118 R 118 (149)
T PHA02574 118 Y 118 (149)
T ss_pred e
Confidence 9
No 9
>PF13563 2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB: 1IUH_A.
Probab=99.25 E-value=2.8e-11 Score=110.13 Aligned_cols=129 Identities=16% Similarity=0.216 Sum_probs=78.4
Q ss_pred cCCCCceEEeeecccCChhhHHHHHHHHHHhHHHhhhhcCCCCeEEEecccccCCCCCCCceEEEEeccccCchhHHHHH
Q 010205 337 IKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHA 416 (515)
Q Consensus 337 v~p~~LHLTL~fLgL~~eeei~~a~~aL~~i~~~i~~iL~~~pf~l~lkGLg~F~~dp~~~rVLyagV~~~~~~~~L~~L 416 (515)
......||||.+.+..++.. +.+.+.|..+.. ..+||.|+|.|+++|++ +.+|||+.+.. ...|.+|
T Consensus 21 ~~~~~pHITL~~~~~~~~~~-~~~~~~l~~~~~------~~~~f~l~l~~~~~F~~---~~~vi~l~~~~---~~~L~~L 87 (153)
T PF13563_consen 21 YPRWPPHITLAFPFDIDDSL-DELVEALARLAA------GFPPFELRLDGFGSFPG---KGRVIFLNVEP---SPELEAL 87 (153)
T ss_dssp --GGG-EEEEEEEEE--GGG-HHHHHHHHHHHH------HS--EEEEEEEEEEESS---SSSSEEEEEEE----HHHHHH
T ss_pred CCCCCCEeEEEecCcccccH-HHHHHHHHHHHc------cCCCeEEEEccEEEcCC---CCCEEEEEcCC---CHHHHHH
Confidence 44455899999999887644 555566665532 34899999999999974 23599999964 6899999
Q ss_pred HHHHHHHHHHCCccccccCCCCcccccEEeeeecccccccCCCccccccHHHHHHHh-CCCccccEEecEEEEEeee
Q 010205 417 CQVIIDAFNEAGLVFHRDYNKKLKQLHATLMNIRHKKRRKGTRRVDYFDARDIFKQF-GSKEWGEYLIKEAHLSQRF 492 (515)
Q Consensus 417 ~~~L~~~f~~~Gl~~e~d~~r~fk~PHiTLar~r~~~~~~g~~~~~~fda~~il~~~-~d~~fG~~~V~~I~Ls~l~ 492 (515)
++.|.+.|...|...+. .++|. |||||++...... ...+++.+ .......+.|++|.|....
T Consensus 88 ~~~l~~~~~~~~~~~~~--~~~~~-PHiTia~~~~~~~-----------~~~~~~~~~~~~~~~~~~v~~l~L~~~~ 150 (153)
T PF13563_consen 88 HRALREALRPFGFKQDS--YRPFR-PHITIARRLSPKQ-----------AAEAIEKLQSEFPPISFTVDELALVRSD 150 (153)
T ss_dssp HHHHHHHHHHHHGGGGG--GS-----EEEEEEESS----------------------------EEEEE-EEEEEEEE
T ss_pred HHHHHHHHHHcCCcccc--CCCcc-eEEEEeccCCcch-----------hHHHHHHHhCcCCCcEEEEeEEEEEEEC
Confidence 99999999999887752 27899 9999999754321 11344444 2223347899999996553
No 10
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.24 E-value=1.3e-11 Score=97.30 Aligned_cols=60 Identities=42% Similarity=0.612 Sum_probs=55.0
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHH
Q 010205 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQ 216 (515)
Q Consensus 156 ~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~ 216 (515)
..+.||..+|++|||++|+++++|+++|||+|+||+.+. ++.|+|+|+ .++|..|+++|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP-KENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC-HHHHHHHHHHhC
Confidence 578999999999999999999999999999999998654 678999997 799999999873
No 11
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.23 E-value=1.6e-11 Score=97.25 Aligned_cols=59 Identities=27% Similarity=0.402 Sum_probs=54.5
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHH
Q 010205 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQ 216 (515)
Q Consensus 155 ~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~ 216 (515)
...+.||.+++++|||++|+++|+|+++|||+|+|+. ++.|.|+|.++++++.|++.|+
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---CCEEEEEeCCHHHHHHHHHHhC
Confidence 4679999999999999999999999999999999997 4679999988899999999873
No 12
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.17 E-value=2e-11 Score=95.62 Aligned_cols=60 Identities=40% Similarity=0.598 Sum_probs=54.1
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHH
Q 010205 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKI 215 (515)
Q Consensus 155 ~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I 215 (515)
+..+.||..++++|||++|+++++||++|||+|.||..++...|+|+| ++++|++|++.|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G-~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISG-SPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEE-SHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEe-CHHHHHHHHhhC
Confidence 468999999999999999999999999999999999764345799999 689999999876
No 13
>PF05213 Corona_NS2A: Coronavirus NS2A protein; InterPro: IPR007878 This entry is represented by Coronavirus non-structural protein 2A (32kDa); it is a family of uncharacterised viral proteins. Members have a phosphoesterase module (2H) [] and are predicted to be involved in RNA modification. The viral group of 2H phosphoesterases contains proteins from two unrelated virus types: the type C rotaviruses (VP3 protein, IPR011181 from INTERPRO) that are double stranded multipartite RNA viruses and the coronaviruses (NS2 protein, this group) that are positive strand RNA viruses. Given that these viruses have vertebrate hosts, it is likely that the 2H phosphoesterase domain was derived from the host by one of virus groups followed by rapid sequence divergence []. Subsequently, it may have been exchanged between the viral families. Although the direction of the exchange is not clear, it is possible that a double stranded replicative form of a subgenomic RNA transcript of the coronavirus NS2 was stabilised by a rotavirus and incorporated into its multiple double stranded RNA genome []. These proteins can be utilised as novel drug targets because of their predicted RNA modification role.
Probab=98.98 E-value=7.1e-09 Score=99.95 Aligned_cols=127 Identities=17% Similarity=0.295 Sum_probs=89.4
Q ss_pred eEEeeecccCChhhHHHHHHHHHHhHHHhhhhcCCCCeEEEecccccCCCCCCCceEEEEeccccCchhHHHHHHHHHHH
Q 010205 343 HLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIID 422 (515)
Q Consensus 343 HLTL~fLgL~~eeei~~a~~aL~~i~~~i~~iL~~~pf~l~lkGLg~F~~dp~~~rVLyagV~~~~~~~~L~~L~~~L~~ 422 (515)
||||+||.+ .++++..+..+|+++... +.- .-..+++..-..++ |.+-+.|+ .+.+++..|..
T Consensus 45 HlSl~mL~I-sd~~i~~V~~~iq~Vidd---M~~-~~~~it~tnp~MLg------~~yV~nV~------Gv~slh~ki~n 107 (248)
T PF05213_consen 45 HLSLGMLDI-SDEDIPDVETAIQKVIDD---MVW-FEGDITFTNPHMLG------RCYVANVK------GVLSLHDKIVN 107 (248)
T ss_pred eeEEEEEEc-ChhhhhhHHHHHHHHHHH---hhc-ccceEEecCceeec------cEEEEecc------cHHHHHHHHHH
Confidence 999999986 578899998888877442 211 12267777666663 44445664 37788999999
Q ss_pred HHHHCCccccccCCCCcccccEEeeeecccccccCCCccccccHHHHHHHhCCCccc-cEEe-----cEEEEEeeecCCC
Q 010205 423 AFNEAGLVFHRDYNKKLKQLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGSKEWG-EYLI-----KEAHLSQRFVYDE 496 (515)
Q Consensus 423 ~f~~~Gl~~e~d~~r~fk~PHiTLar~r~~~~~~g~~~~~~fda~~il~~~~d~~fG-~~~V-----~~I~Ls~l~~~~~ 496 (515)
.|.+.|+..++ .|.|. ||+||+.+....-+ . ...+|+ +.++ .++.|-.++....
T Consensus 108 ~~~~kgit~gQ--SRmwI-PHiTia~~~~~av~-----I------------~~~qFny~~~~n~~~~~rle~VKlGa~K~ 167 (248)
T PF05213_consen 108 VFRKKGITFGQ--SRMWI-PHITIAQLNDAAVR-----I------------KEKQFNYKITINPSSPARLEFVKLGAEKK 167 (248)
T ss_pred HHHHhCcCcCc--ccccc-cceehhhhhchheE-----e------------ccceeeeEeeccCCChhcCeEEEcCCccc
Confidence 99999999975 89999 99999987543211 0 012333 3334 7777888887677
Q ss_pred CCceeEeEEE
Q 010205 497 SGFYHCCASI 506 (515)
Q Consensus 497 ~g~Y~~i~si 506 (515)
+|+|+.+.+.
T Consensus 168 dgfYe~i~s~ 177 (248)
T PF05213_consen 168 DGFYESIVSH 177 (248)
T ss_pred Cceeeeehhh
Confidence 9999988763
No 14
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.93 E-value=1.7e-09 Score=85.02 Aligned_cols=59 Identities=41% Similarity=0.516 Sum_probs=53.0
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEccChhHHHHHHHHH
Q 010205 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKI 215 (515)
Q Consensus 156 ~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~---~~~I~I~G~s~~~v~~A~~~I 215 (515)
..+.||..++++|||++|+++++|+++|||+|.||..++ .+.|.|.|. .+++..|...|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~-~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT-PEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcC-HHHHHHHHHHh
Confidence 578999999999999999999999999999999998643 567999997 78999998876
No 15
>PF02834 LigT_PEase: LigT like Phosphoesterase; InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases. These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.
Probab=98.92 E-value=4.9e-10 Score=93.75 Aligned_cols=82 Identities=20% Similarity=0.367 Sum_probs=64.5
Q ss_pred cchhHHHhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeecccCChhhHHHHHHHHHHhHHHhhhhcCCC
Q 010205 299 DNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNR 378 (515)
Q Consensus 299 ~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gl~~~~fv~p~~LHLTL~fLgL~~eeei~~a~~aL~~i~~~i~~iL~~~ 378 (515)
++.+.+..+++.+.- .....|+ .|++|.++||||.|||..+++.++.+.+.|.++.. ...
T Consensus 6 ~~~~~L~~l~~~l~~-----------~~~~~~~---r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~------~~~ 65 (87)
T PF02834_consen 6 EIKEQLNQLQERLRQ-----------ALPPLGI---RWVRPFNPHITLAFLGEVPPDQLPELIEALANIAS------RFP 65 (87)
T ss_dssp HHHHHHHHHHHHHHH-----------HCCSCTE---EEGSCGGSEEEEEEEEEESHHHHHHHHHHHHHHHC------CCB
T ss_pred HHHHHHHHHHHHHhh-----------hccccCC---cccCCCCCeEEEEeCCCCCHHHHHHHHHHHHhhhc------cCC
Confidence 567778888877620 0123444 79999999999999999999999988888887631 458
Q ss_pred CeEEEecccccCCCCCCCceEEE
Q 010205 379 PLFIRLKGLDLMRGSKDKARILY 401 (515)
Q Consensus 379 pf~l~lkGLg~F~~dp~~~rVLy 401 (515)
||.+++.|+++|++ ..++||+|
T Consensus 66 ~f~~~~~~~~~f~s-~~~~rvi~ 87 (87)
T PF02834_consen 66 PFTLTVDGFGLFPS-RLRPRVIW 87 (87)
T ss_dssp -EEEEEEEEEEEEE-EETCEEEE
T ss_pred CeEEEEeEEEEeCC-CCCCCCcC
Confidence 99999999999997 55889999
No 16
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=98.79 E-value=1e-08 Score=81.99 Aligned_cols=59 Identities=37% Similarity=0.387 Sum_probs=52.6
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHH
Q 010205 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKI 215 (515)
Q Consensus 156 ~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~----~~~I~I~G~s~~~v~~A~~~I 215 (515)
..+.||...++.|||++|+++++|+++|||+|+|++... ...|+|+|. .+++.+|...|
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~-~~~v~~A~~~I 64 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK-PSAVQKALLLI 64 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeC-HHHHHHHHHhh
Confidence 578999999999999999999999999999999987643 356899996 79999999877
No 17
>smart00322 KH K homology RNA-binding domain.
Probab=98.75 E-value=3.9e-08 Score=76.67 Aligned_cols=66 Identities=39% Similarity=0.530 Sum_probs=58.2
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHH
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAII 219 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~~iv 219 (515)
..+..+.||..+++++||++|.++++|+++||++|.++.... ...|.|.|+ .+++..|...|...+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~-~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGP-PENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcC-HHHHHHHHHHHHHHh
Confidence 457789999999999999999999999999999999987653 567999997 799999999987653
No 18
>PF13014 KH_3: KH domain
Probab=98.72 E-value=1.2e-08 Score=75.08 Aligned_cols=39 Identities=38% Similarity=0.572 Sum_probs=34.3
Q ss_pred ccccccCCCchhHHHHHHHhCcEEEcCC---CCC-CCcEEEEc
Q 010205 164 VIRFIKGKEGSTQKKFEKEMGVKIILPS---SKK-EDSIIIEG 202 (515)
Q Consensus 164 ~~~~IIGk~G~t~k~iE~eT~~~I~iP~---~~~-~~~I~I~G 202 (515)
+|++|||++|+++++|+++|+|+|+||+ ++. +..|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5899999999999999999999999999 333 56788887
No 19
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.70 E-value=3e-08 Score=89.05 Aligned_cols=60 Identities=28% Similarity=0.466 Sum_probs=53.4
Q ss_pred ccccccccCCCchhHHHHHHHhCcEEEcCCCCC--------------------CCcEEEEccC--hhHHHHHHHHHHHHH
Q 010205 162 ASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK--------------------EDSIIIEGNS--TDSVAKASEKIQAII 219 (515)
Q Consensus 162 ~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~--------------------~~~I~I~G~s--~~~v~~A~~~I~~iv 219 (515)
..|+|.|||++|.|+|+||++|||+|.|...++ ...|.|+|.+ .+++.+|++.|+.|+
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 378899999999999999999999999987642 2789999998 899999999999887
Q ss_pred HH
Q 010205 220 AE 221 (515)
Q Consensus 220 ~e 221 (515)
..
T Consensus 94 ~~ 95 (120)
T cd02395 94 KP 95 (120)
T ss_pred cc
Confidence 64
No 20
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.56 E-value=1.4e-07 Score=102.44 Aligned_cols=107 Identities=26% Similarity=0.305 Sum_probs=87.0
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHHHHHHHHhhhCC
Q 010205 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIAEAVESP 226 (515)
Q Consensus 151 ~~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~----~~~I~I~G~s~~~v~~A~~~I~~iv~e~~~~~ 226 (515)
..+.+..|.||..-+|.||||+|+|||+|..|||+||+|-+.++ .+...|.|. ++.|+.|.+.|..|+.++...+
T Consensus 227 g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~-~d~ie~Aa~lI~eii~~~~~~~ 305 (600)
T KOG1676|consen 227 GGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGT-VDQIEHAAELINEIIAEAEAGA 305 (600)
T ss_pred cccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecC-HHHHHHHHHHHHHHHHHHhccC
Confidence 34558999999999999999999999999999999999944433 567899996 7999999999999999876631
Q ss_pred ---------CCCceEEEEeccccchhhhccHHHHHHHHhcc
Q 010205 227 ---------SLDYSHFVSLPLAVHPELVDKLVNFQNTILGI 258 (515)
Q Consensus 227 ---------k~~~tHFIsIPl~~hp~I~~~~~~f~~~Il~~ 258 (515)
-..-.-++.||-.----++|+..+-++.|-.+
T Consensus 306 ~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~q 346 (600)
T KOG1676|consen 306 GGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQ 346 (600)
T ss_pred CCCcCCCCccceeeEEEeccccccccccCCCccchhhhccc
Confidence 11114456699765566889999999988765
No 21
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.38 E-value=6.6e-07 Score=85.78 Aligned_cols=65 Identities=32% Similarity=0.439 Sum_probs=59.4
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEE---ccChhHHHHHHHHHHHHHH
Q 010205 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIE---GNSTDSVAKASEKIQAIIA 220 (515)
Q Consensus 154 ~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~---G~s~~~v~~A~~~I~~iv~ 220 (515)
...++.||++.++.|||++|++++.|+++||++|+|.. +.+.|.|. +.+++.+.+|++.|++|+.
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~--~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS--ETGEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC--CCCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 45789999999999999999999999999999999985 34789998 7789999999999999986
No 22
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.33 E-value=6e-07 Score=85.43 Aligned_cols=61 Identities=33% Similarity=0.432 Sum_probs=55.2
Q ss_pred EeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEE--EccChhHHHHHHHHHHHHHH
Q 010205 158 VEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIII--EGNSTDSVAKASEKIQAIIA 220 (515)
Q Consensus 158 v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I--~G~s~~~v~~A~~~I~~iv~ 220 (515)
+.||++.++.|||+||+++|+|+++||++|+|.. +.+.|.| .+.+++.+.+|++.|.+|..
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~--~~g~V~I~~~t~d~~~i~kA~~~I~~i~~ 64 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS--ETGEVKIEEEDEDPLAVMKAREVVKAIGR 64 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc--CCceEEEecCCCCHHHHHHHHHHHHHHHc
Confidence 6899999999999999999999999999999975 3467999 56678999999999999876
No 23
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.23 E-value=1.8e-06 Score=92.17 Aligned_cols=72 Identities=26% Similarity=0.409 Sum_probs=62.6
Q ss_pred CeEEEEeccc------cccccccCCCchhHHHHHHHhCcEEEcCCCCC-------------------CCcEEEEccChhH
Q 010205 153 RHSLSVEVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-------------------EDSIIIEGNSTDS 207 (515)
Q Consensus 153 ~~~~~v~Ip~------~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-------------------~~~I~I~G~s~~~ 207 (515)
++...|.||. .|+|+|||..|.|+|+||+|||+||.|-..+. .-.+-|++.+.+.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 7788888885 79999999999999999999999999987432 1258899999999
Q ss_pred HHHHHHHHHHHHHHhhh
Q 010205 208 VAKASEKIQAIIAEAVE 224 (515)
Q Consensus 208 v~~A~~~I~~iv~e~~~ 224 (515)
|.+|...|+.|+.++.-
T Consensus 217 i~~Ai~vienli~~av~ 233 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSAVS 233 (554)
T ss_pred HHHHHHHHHHHHHhhcc
Confidence 99999999999988544
No 24
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.02 E-value=7.9e-06 Score=78.38 Aligned_cols=54 Identities=28% Similarity=0.409 Sum_probs=49.0
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 163 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 163 ~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
..+|.|||++|+|+|.||+.|||+|+|+. +.|.|.|. .++++.|++.|..|++.
T Consensus 104 r~~griIG~~G~~~k~ie~~t~~~i~i~~----~~v~i~G~-~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 104 RIKGRIIGEGGKTRRIIEELTGVDISVYG----KTVAIIGD-PEQVEIAREAIEMLIEG 157 (180)
T ss_pred HHhhheeCCCcHHHHHHHHHHCcEEEEcC----CEEEEEeC-HHHHHHHHHHHHHHHcC
Confidence 36999999999999999999999999985 45999995 89999999999999954
No 25
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=97.93 E-value=1.3e-05 Score=76.33 Aligned_cols=54 Identities=28% Similarity=0.372 Sum_probs=49.8
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 163 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 163 ~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
...|.|||++|+|++.||..|||+|.|+. ..|.|.| +.++++.|++.|+.|++.
T Consensus 98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~----~~v~i~G-~~~~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEELTGVSISVYG----KTVGIIG-DPEQVQIAREAIEMLIEG 151 (172)
T ss_pred HHHhhhcCCCcHHHHHHHHHHCCeEEEcC----CEEEEEC-CHHHHHHHHHHHHHHHcC
Confidence 36899999999999999999999999985 6799999 489999999999999965
No 26
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.88 E-value=2e-05 Score=89.13 Aligned_cols=66 Identities=20% Similarity=0.310 Sum_probs=60.5
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
--..++.||++.++-|||+||.++|.|.++||++|+|-. ++.|.|.|.+.+.+++|++.|+.|+..
T Consensus 577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 346788999999999999999999999999999999974 688999999999999999999988873
No 27
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=97.85 E-value=1.8e-05 Score=76.42 Aligned_cols=76 Identities=17% Similarity=0.249 Sum_probs=62.3
Q ss_pred CCccCCCCeEEEEeccc------cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHH
Q 010205 146 EPVPSAERHSLSVEVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAII 219 (515)
Q Consensus 146 ~~~~~~~~~~~~v~Ip~------~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv 219 (515)
.-+.+.++|+..++||. .|+|+|||+.|.|+|+||+.++|+|-|-..++..+..|....++....|.+-|.-++
T Consensus 140 ~dy~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI 219 (269)
T COG5176 140 NDYIRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLI 219 (269)
T ss_pred ccccCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHh
Confidence 44557788888999984 799999999999999999999999999988876566676666777777777777666
Q ss_pred HH
Q 010205 220 AE 221 (515)
Q Consensus 220 ~e 221 (515)
..
T Consensus 220 ~a 221 (269)
T COG5176 220 EA 221 (269)
T ss_pred hc
Confidence 54
No 28
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.84 E-value=0.00012 Score=75.08 Aligned_cols=107 Identities=23% Similarity=0.234 Sum_probs=82.3
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEccChhHHHHHHHHHHHHHHHhhh
Q 010205 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAEAVE 224 (515)
Q Consensus 151 ~~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~------~~~I~I~G~s~~~v~~A~~~I~~iv~e~~~ 224 (515)
..+|.+.|.||.-..|-||||||.|+.+|++||||||++.+..+ ++.|.|.|. -+.++.-.+-|..-+.|.-+
T Consensus 36 ~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt-~eai~av~efI~dKire~p~ 114 (402)
T KOG2191|consen 36 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGT-VEALNAVHEFIADKIREKPQ 114 (402)
T ss_pred CCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEecc-HHHHHHHHHHHHHHHHHhHH
Confidence 44699999999999999999999999999999999999988766 356889995 57777776666555544211
Q ss_pred ---------CCCC---CceEEEEeccccchhhhccHHHHHHHHhcc
Q 010205 225 ---------SPSL---DYSHFVSLPLAVHPELVDKLVNFQNTILGI 258 (515)
Q Consensus 225 ---------~~k~---~~tHFIsIPl~~hp~I~~~~~~f~~~Il~~ 258 (515)
.|+. ....-|.+|-..---|+++...+++.|+++
T Consensus 115 ~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eq 160 (402)
T KOG2191|consen 115 AVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQ 160 (402)
T ss_pred hhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHh
Confidence 1110 112456688776678999999999999986
No 29
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=97.81 E-value=3.4e-05 Score=88.55 Aligned_cols=104 Identities=27% Similarity=0.414 Sum_probs=93.2
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCCCc
Q 010205 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDY 230 (515)
Q Consensus 152 ~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~~iv~e~~~~~k~~~ 230 (515)
..+.+.+.|.++++.+++||+|.++.+|+++++|.|++|.+++ ...|+++|. ..++.+|.+.++.+..+...+ ..
T Consensus 345 nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~-~~~~~ka~~~v~~~~~ei~n~---~~ 420 (753)
T KOG2208|consen 345 NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGV-SANDEKAVEDVEKIIAEILNS---IV 420 (753)
T ss_pred cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEecc-ccchhHHHHHHHHHHHhhhcc---cc
Confidence 4478899999999999999999999999999999999999766 678999997 589999999999999997763 34
Q ss_pred eEEEEeccccchhhhccHHHHHHHHhccc
Q 010205 231 SHFVSLPLAVHPELVDKLVNFQNTILGIT 259 (515)
Q Consensus 231 tHFIsIPl~~hp~I~~~~~~f~~~Il~~~ 259 (515)
.+.+.||-..|.+|.|......+.|+.+.
T Consensus 421 ~~~~~iP~k~~~~iig~~g~~i~~I~~k~ 449 (753)
T KOG2208|consen 421 KEEVQIPTKSHKRIIGTKGALINYIMGKH 449 (753)
T ss_pred cceeecCccchhhhhccccccHHHHHhhc
Confidence 67777999999999999999999999873
No 30
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.78 E-value=2e-05 Score=82.85 Aligned_cols=104 Identities=25% Similarity=0.289 Sum_probs=75.0
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHHHHHHH-HhhhC
Q 010205 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIA-EAVES 225 (515)
Q Consensus 151 ~~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~----~~~I~I~G~s~~~v~~A~~~I~~iv~-e~~~~ 225 (515)
...|-+.+-||..||+.||||.|+|+|.|-..|.|||+|-+..+ +..|+|-|. +++..+|+.+|..|+. |+.+-
T Consensus 196 ~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~t-pEg~s~Ac~~ILeimqkEA~~~ 274 (584)
T KOG2193|consen 196 LKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHST-PEGTSKACKMILEIMQKEAVDD 274 (584)
T ss_pred ccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecC-ccchHHHHHHHHHHHHHhhhcc
Confidence 35577888999999999999999999999999999999977644 457899995 6999999999998864 44432
Q ss_pred CCCCceEEEEeccccchhhhc----cHHHHHHHHhcc
Q 010205 226 PSLDYSHFVSLPLAVHPELVD----KLVNFQNTILGI 258 (515)
Q Consensus 226 ~k~~~tHFIsIPl~~hp~I~~----~~~~f~~~Il~~ 258 (515)
| .+.-+-+.+--|..++| .-++-.+.|+++
T Consensus 275 -k--~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~ 308 (584)
T KOG2193|consen 275 -K--VAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQD 308 (584)
T ss_pred -c--hhhhcchhhhhhcchhhhhhhhccccHHHHHhh
Confidence 2 33333233223554443 334455555554
No 31
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.74 E-value=3.8e-05 Score=87.48 Aligned_cols=65 Identities=22% Similarity=0.366 Sum_probs=59.1
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 154 ~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
-..++.||++.++.|||+||.++|+|+++||++|+|-. ++.|.|.+.+.+.+.+|.+.|..+..+
T Consensus 551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d---dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED---DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 35678999999999999999999999999999999964 688999999999999999999988654
No 32
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.52 E-value=9.1e-05 Score=78.04 Aligned_cols=61 Identities=28% Similarity=0.480 Sum_probs=53.2
Q ss_pred cccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEccChhHHHHHHHHHHHHHHHh
Q 010205 161 GASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAEA 222 (515)
Q Consensus 161 p~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~------~~~I~I~G~s~~~v~~A~~~I~~iv~e~ 222 (515)
-..|.|.||||.|+++|+||++|||+|.|.+--+ +.+|++.| +-+++.+|-..|.+-+.++
T Consensus 287 HN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkG-siEac~~AE~eImkKlre~ 353 (584)
T KOG2193|consen 287 HNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKG-SIEACVQAEAEIMKKLREC 353 (584)
T ss_pred hcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecc-cHHHHHHHHHHHHHHHHHH
Confidence 3689999999999999999999999999987644 57899999 6899999999998777663
No 33
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.51 E-value=0.00023 Score=71.37 Aligned_cols=70 Identities=23% Similarity=0.335 Sum_probs=53.3
Q ss_pred CeEEEEeccc------cccccccCCCchhHHHHHHHhCcEEEcCCCCC-C--------------------CcEEEEccCh
Q 010205 153 RHSLSVEVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-E--------------------DSIIIEGNST 205 (515)
Q Consensus 153 ~~~~~v~Ip~------~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~--------------------~~I~I~G~s~ 205 (515)
+.+..|.||. .|+|.|+|++|.|+|+||++|||||-|-..++ . =.|.|+-.
T Consensus 91 k~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~-- 168 (259)
T KOG1588|consen 91 KLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETE-- 168 (259)
T ss_pred eEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEe--
Confidence 4566677775 59999999999999999999999999988765 1 14666653
Q ss_pred hHHHHHHHHHHHHHHHhhh
Q 010205 206 DSVAKASEKIQAIIAEAVE 224 (515)
Q Consensus 206 ~~v~~A~~~I~~iv~e~~~ 224 (515)
.--..|..+|...+++..+
T Consensus 169 ~p~~ea~~rl~~AleeI~k 187 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKK 187 (259)
T ss_pred CCHHHHHHHHHHHHHHHHH
Confidence 3456677777777777554
No 34
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=97.42 E-value=0.00016 Score=79.22 Aligned_cols=110 Identities=13% Similarity=0.222 Sum_probs=89.7
Q ss_pred CCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEccChhHHHHHHHHHHHHHHHhhhC-
Q 010205 150 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKIQAIIAEAVES- 225 (515)
Q Consensus 150 ~~~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~---~~~I~I~G~s~~~v~~A~~~I~~iv~e~~~~- 225 (515)
+.+.-+...+||.+..++|||++|+-++.|.++.||+++||+... .+.+.|+|. .+.|+.|++.|..+++.-+-.
T Consensus 50 s~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~-pe~v~~aK~li~evv~r~~~~~ 128 (600)
T KOG1676|consen 50 SDTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGS-PENVEVAKQLIGEVVSRGRPPG 128 (600)
T ss_pred cccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCC-cccHHHHHHhhhhhhhccCCCC
Confidence 445667788999999999999999999999999999999988655 578999996 599999999999998874300
Q ss_pred --C-CCC---ceEEEEeccccchhhhccHHHHHHHHhcccc
Q 010205 226 --P-SLD---YSHFVSLPLAVHPELVDKLVNFQNTILGITD 260 (515)
Q Consensus 226 --~-k~~---~tHFIsIPl~~hp~I~~~~~~f~~~Il~~~~ 260 (515)
+ ... .|.-|.||-+---.|+|..++-++.+-+...
T Consensus 129 ~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg 169 (600)
T KOG1676|consen 129 GFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSG 169 (600)
T ss_pred CccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcC
Confidence 0 111 4777888877678899999999998877644
No 35
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.38 E-value=0.00035 Score=67.44 Aligned_cols=67 Identities=30% Similarity=0.388 Sum_probs=59.4
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEcc----ChhHHHHHHHHHHHHHH
Q 010205 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGN----STDSVAKASEKIQAIIA 220 (515)
Q Consensus 152 ~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~----s~~~v~~A~~~I~~iv~ 220 (515)
...+..+.||+...+.+||+.|++.+.||+.|+|+|.|.. +++.|.|+.. ++-.+++|++-|++|..
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~--~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgr 76 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS--KTGSVTIRTTRKTEDPLALLKARDVVKAIGR 76 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC--CCCeEEEEecCCCCChHHHHHHHHHHHHHhc
Confidence 3556789999999999999999999999999999999987 5678888764 78999999999999863
No 36
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.31 E-value=0.00044 Score=69.07 Aligned_cols=63 Identities=29% Similarity=0.377 Sum_probs=58.1
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 156 ~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
..+.||..+.+.+||++|.+++.|.++|+++|.|- .++.|.|.|++.+.+.+|.+.|+.+-.+
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig---~NG~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG---QNGRIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc---CCcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 56889999999999999999999999999999994 4689999999999999999999988765
No 37
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.26 E-value=0.0005 Score=70.76 Aligned_cols=67 Identities=27% Similarity=0.361 Sum_probs=57.3
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 154 ~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~------~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
..+.+-||..--+.||||+|+|+|.+.++.++-|+|-.+.+ +..|++.|+ .+..++|..+|..-+.|
T Consensus 132 kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge-~e~~~~A~~~IL~Ki~e 204 (402)
T KOG2191|consen 132 KQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGE-PEQNMKAVSLILQKIQE 204 (402)
T ss_pred ceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCC-HHHHHHHHHHHHHHhhc
Confidence 34788999999999999999999999999999999964444 346788996 78999999998877666
No 38
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.23 E-value=0.00035 Score=80.95 Aligned_cols=66 Identities=20% Similarity=0.261 Sum_probs=59.8
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcE-EEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVK-IILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~-I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
--...+.||++.++-|||+||.|+|.|.++||++ |+|-. ++.|.|.|.+.+.+++|++.|+.|..+
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 3467889999999999999999999999999999 88864 688999999999999999999988764
No 39
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.23 E-value=0.00034 Score=71.37 Aligned_cols=66 Identities=24% Similarity=0.332 Sum_probs=61.4
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHH
Q 010205 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQA 217 (515)
Q Consensus 151 ~~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~ 217 (515)
..+.+.+++||.++.+.|.|++|.++|.|.++|+++|.-|++++.....++|. .+.|..||..|..
T Consensus 23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~-~edv~~aRrei~s 88 (394)
T KOG2113|consen 23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGR-HEDVRRARREIPS 88 (394)
T ss_pred CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCCcceeccC-chhHHHHhhcCcc
Confidence 37888999999999999999999999999999999999999999877889997 6899999999986
No 40
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.10 E-value=0.0014 Score=71.81 Aligned_cols=67 Identities=31% Similarity=0.393 Sum_probs=58.8
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCC---C-CCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSK---K-EDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 154 ~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~---~-~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
.++.+-||....|-||||+|..+|+|.++||++|.|-+.. . ...|+|.|. .+.|.+|...|-.++.+
T Consensus 138 v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~-~~av~~al~~Is~~L~~ 208 (485)
T KOG2190|consen 138 VTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGE-PDAVKKALVQISSRLLE 208 (485)
T ss_pred eEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCc-hHHHHHHHHHHHHHHHh
Confidence 5788999999999999999999999999999999985541 1 356999997 69999999999988877
No 41
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.09 E-value=0.0008 Score=75.27 Aligned_cols=69 Identities=29% Similarity=0.400 Sum_probs=62.6
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhhh
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVE 224 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e~~~ 224 (515)
-...++.|+++-++-+||+||.++++|-++||++|+|- +.+.|.|.+.+.+.+.+|+++|+.|+.+..-
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie---ddGtv~i~~s~~~~~~~ak~~I~~i~~e~ev 619 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE---DDGTVKIAASDGESAKKAKERIEAITREVEV 619 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec---CCCcEEEEecchHHHHHHHHHHHHHHhhccc
Confidence 34678889999999999999999999999999999997 5688999998899999999999999987544
No 42
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.92 E-value=0.00079 Score=77.03 Aligned_cols=64 Identities=25% Similarity=0.413 Sum_probs=58.0
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 155 ~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
...+.||++.++-+||+||.|+|.|.++||++|+|- +++.|.|.+.+.+.+++|++.|+.+..+
T Consensus 555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~---d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE---DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC---CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 457889999999999999999999999999999983 4688999999999999999999988854
No 43
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=96.73 E-value=0.0035 Score=62.99 Aligned_cols=68 Identities=22% Similarity=0.296 Sum_probs=56.3
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC--CCC-CCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS--SKK-EDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~--~~~-~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
-.+..|.||+++-|-||||||..+++|.+|.|..|.|.. .+. ...|+|+|. .+.+..|.--++.-|+.
T Consensus 314 itTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGT-qdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 314 ITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT-QDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred eeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEecc-HHHHhhHHHHHHHHHHh
Confidence 346788999999999999999999999999999999955 344 456789995 78899988777766653
No 44
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.49 E-value=0.0054 Score=67.95 Aligned_cols=69 Identities=22% Similarity=0.335 Sum_probs=59.7
Q ss_pred CCCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 151 AERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 151 ~~~~~~~v~Ip~-~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
.......|.+|. ++-|.|||+.|.++|-+|.-||+-|.|.. .++.|+|+|-++-.-+-|+.-++.++.+
T Consensus 201 ~e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd--tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 201 AETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred hhheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC--CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 345566788998 78899999999999999999999999975 3568999997788889999999999877
No 45
>PRK00106 hypothetical protein; Provisional
Probab=96.40 E-value=0.0069 Score=67.23 Aligned_cols=69 Identities=17% Similarity=0.340 Sum_probs=59.1
Q ss_pred CCCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 151 AERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 151 ~~~~~~~v~Ip~-~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
.......|.+|. ++-|.|||+.|.++|.+|.-|||-|.|.. .++.|+|+|-++-.-+-|+.-++.++.+
T Consensus 222 ~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 222 TEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD--TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred hhheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC--CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 345566788998 78899999999999999999999999975 4568999997788888888888888876
No 46
>PRK12704 phosphodiesterase; Provisional
Probab=96.33 E-value=0.0067 Score=67.31 Aligned_cols=68 Identities=19% Similarity=0.315 Sum_probs=57.7
Q ss_pred CCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 152 ERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 152 ~~~~~~v~Ip~-~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
......|.+|. ++-|.|||+.|.++|.||.-||+-|.|.. .++.|+|+|-++..-+.|+.-++.++.+
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd--tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC--CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 45566788998 78899999999999999999999999975 3568999997666767888888888776
No 47
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.29 E-value=0.0031 Score=67.04 Aligned_cols=69 Identities=17% Similarity=0.238 Sum_probs=60.5
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 152 ~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
+.+...+.|-.+++|.+||++|+++++|+..|+|+|+|-.....-.|+|-|. +..-.+|+.-|...++.
T Consensus 45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~-~~m~~kaka~id~~~~k 113 (629)
T KOG0336|consen 45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGI-NHMRKKAKASIDRGQDK 113 (629)
T ss_pred CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCceeEEEEech-HHHHHHHHhhHhhhhhh
Confidence 4567788899999999999999999999999999999998666677899995 67888899999888865
No 48
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.21 E-value=0.0074 Score=58.42 Aligned_cols=54 Identities=28% Similarity=0.407 Sum_probs=48.6
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 163 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 163 ~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
...|.|||++|.|++.||+=|||.|.+=. ..|-|.|. .++|+-|++-|..++..
T Consensus 111 R~kgRIIG~~GkTr~~IE~lt~~~I~V~g----~tVaiiG~-~~~v~iAr~AVemli~G 164 (194)
T COG1094 111 RIKGRIIGREGKTRRAIEELTGVYISVYG----KTVAIIGG-FEQVEIAREAVEMLING 164 (194)
T ss_pred HhhceeeCCCchHHHHHHHHhCCeEEEeC----cEEEEecC-hhhhHHHHHHHHHHHcC
Confidence 35689999999999999999999999954 68999997 69999999999999876
No 49
>PF09749 HVSL: Uncharacterised conserved protein; InterPro: IPR019146 This entry is of proteins of approximately 300 residues conserved from plants to humans. It contains two conserved motifs, HxSL and FHVSL. The function is unknown.
Probab=96.20 E-value=0.039 Score=55.15 Aligned_cols=104 Identities=19% Similarity=0.347 Sum_probs=75.3
Q ss_pred CCCCceEEeeecccCChhhHHHHHHHHHHhHHHhhhhcCCCCeEEEecccccCCCCCCCceEEEE-eccccCchhHHHHH
Q 010205 338 KPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYA-PVEEIGDGDRLLHA 416 (515)
Q Consensus 338 ~p~~LHLTL~fLgL~~eeei~~a~~aL~~i~~~i~~iL~~~pf~l~lkGLg~F~~dp~~~rVLya-gV~~~~~~~~L~~L 416 (515)
.+.-|||+|.=---....+++.-.+.|+.. +.. ....+|.+.+.++.+|.+ .++.|...+ .|.. +....|..|
T Consensus 86 ~~~~lHISLSr~~~lr~~~id~f~~~lr~~---l~~-~~~~~F~v~f~~~~~~~N-~e~TR~FL~l~V~~-~~~~~l~~l 159 (239)
T PF09749_consen 86 SPDPLHISLSRTFPLRTHQIDPFVDSLRQA---LRS-SNIRPFYVSFSGLDVYTN-DEKTRSFLALRVSE-GSNNELKRL 159 (239)
T ss_pred CCCCeEEEeCCCccccHHHHHHHHHHHHHH---Hhh-cCCceEEEEeCceEEEec-CCCCeEEEEEEecc-cccHHHHHH
Confidence 678899999754444556676665555543 211 245999999999999997 677786443 5554 223339999
Q ss_pred HHHHHHHHHHCCccccccCC-CCcccccEEeeeecc
Q 010205 417 CQVIIDAFNEAGLVFHRDYN-KKLKQLHATLMNIRH 451 (515)
Q Consensus 417 ~~~L~~~f~~~Gl~~e~d~~-r~fk~PHiTLar~r~ 451 (515)
.+.|.+.+.+.|+..= . .... +||.||-+-.
T Consensus 160 ~~~i~~~l~~~~lp~~---Y~~~~~-fHvSIAw~~~ 191 (239)
T PF09749_consen 160 LDRINEVLKEFGLPPF---YDEDPS-FHVSIAWTLG 191 (239)
T ss_pred HHHHHHHHHHhCCCcc---cCCCCC-CEEEEEEECC
Confidence 9999999999999764 4 5677 9999998753
No 50
>PF02834 LigT_PEase: LigT like Phosphoesterase; InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases. These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.
Probab=95.78 E-value=0.0096 Score=49.50 Aligned_cols=76 Identities=9% Similarity=0.118 Sum_probs=50.5
Q ss_pred hhHHHHHHHHHHHHHHHCCccccccCCCCcccccEEeeeecccccccCCCccccccHHHHHHHhCCC--ccc--cEEecE
Q 010205 410 GDRLLHACQVIIDAFNEAGLVFHRDYNKKLKQLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGSK--EWG--EYLIKE 485 (515)
Q Consensus 410 ~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fk~PHiTLar~r~~~~~~g~~~~~~fda~~il~~~~d~--~fG--~~~V~~ 485 (515)
.+.|.++++.+.+.+...|+..+ +++. |||||+++..... -.+..+.+..... .+. ++.+++
T Consensus 8 ~~~L~~l~~~l~~~~~~~~~r~~----~~~~-~HiTL~flg~~~~---------~~~~~l~~~l~~~~~~~~~f~~~~~~ 73 (87)
T PF02834_consen 8 KEQLNQLQERLRQALPPLGIRWV----RPFN-PHITLAFLGEVPP---------DQLPELIEALANIASRFPPFTLTVDG 73 (87)
T ss_dssp HHHHHHHHHHHHHHCCSCTEEEG----SCGG-SEEEEEEEEEESH---------HHHHHHHHHHHHHHCCCB-EEEEEEE
T ss_pred HHHHHHHHHHHhhhccccCCccc----CCCC-CeEEEEeCCCCCH---------HHHHHHHHHHHhhhccCCCeEEEEeE
Confidence 46788899999988888999885 6898 9999999875321 1123444444333 233 478999
Q ss_pred EEEEeeecCCCCCce
Q 010205 486 AHLSQRFVYDESGFY 500 (515)
Q Consensus 486 I~Ls~l~~~~~~g~Y 500 (515)
+.+..... ..+..|
T Consensus 74 ~~~f~s~~-~~rvi~ 87 (87)
T PF02834_consen 74 FGLFPSRL-RPRVIW 87 (87)
T ss_dssp EEEEEEEE-TCEEEE
T ss_pred EEEeCCCC-CCCCcC
Confidence 99954332 334555
No 51
>PF07823 CPDase: Cyclic phosphodiesterase-like protein; InterPro: IPR012386 2',3' Cyclic nucleotide phosphodiesterases (CPDases) are enzymes that catalyse at least two distinct steps in the splicing of tRNA introns in eukaryotes. The active site is characterised by two conserved histidine residues []. The enzyme has six cysteine residues, four of which are involved in forming two intra-molecular disulphide bridges. One of these bridges is involved in the catalytic activity of the enzyme as it opens when CPDase is semi-reduced []. Proteins in this entryand belong to 3.1.4.37 from EC and catalyse the reaction Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate. ; GO: 0004112 cyclic-nucleotide phosphodiesterase activity; PDB: 1JH7_A 1JH6_B 1FSI_B.
Probab=95.24 E-value=0.14 Score=49.89 Aligned_cols=142 Identities=17% Similarity=0.162 Sum_probs=66.0
Q ss_pred eEEeee-cccCChhhHHHHHHHHHHhHHHhhhhcCCCCeEEEecccccCCCCCCCceEEEEeccccCchhHHHHHHHHHH
Q 010205 343 HLTVLM-LKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVII 421 (515)
Q Consensus 343 HLTL~f-LgL~~eeei~~a~~aL~~i~~~i~~iL~~~pf~l~lkGLg~F~~dp~~~rVLyagV~~~~~~~~L~~L~~~L~ 421 (515)
||||.- +.+...+++ .+.|+.+...+..+ ....+.++|.++.+= ...=+=+|+.++. ...|..+++.++
T Consensus 40 HiTL~s~i~~~~~~~~---~~~L~~~~~~~~~~-~~~~~~v~~~~v~~g---~~yfq~vyl~v~~---t~~L~~l~~~~r 109 (196)
T PF07823_consen 40 HITLTSGISLDSSDDV---QKVLDSAAAALKPL-PKNHFTVRFDKVASG---DKYFQCVYLEVEK---TPELMSLAQIAR 109 (196)
T ss_dssp -EEEEEEEEE--HHHH---HHHHHHHHHH-B-E------EEEEEEEEEE---EETTEEEEEEE------HHHHHHHCHHH
T ss_pred eEEEeCCCccCCHHHH---HHHHHHHHHhccCc-ccceeEEEeeeEeeC---CeEEEEEEEEecC---ChhHHHHHHHHH
Confidence 999987 333334444 44555554322211 111138888877541 1233679999986 578999999999
Q ss_pred HHHHHC-------CccccccCCCCcccccEEeeeecccccccCCCccccccHHHHHHHhCCC-------ccccEEecEEE
Q 010205 422 DAFNEA-------GLVFHRDYNKKLKQLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGSK-------EWGEYLIKEAH 487 (515)
Q Consensus 422 ~~f~~~-------Gl~~e~d~~r~fk~PHiTLar~r~~~~~~g~~~~~~fda~~il~~~~d~-------~fG~~~V~~I~ 487 (515)
+.|... |-.. ..+|. ||+.|+-.--.... + -.+..+.....+. ..+.|.+.+|.
T Consensus 110 ~~~~~~~~~~~~~~~~~----~~~y~-PHlSLlY~d~~~~e----~---~~~~~~~~~i~~~l~~~~~~~~~~~~~~~l~ 177 (196)
T PF07823_consen 110 ELFVEGPPDEVKAAEWP----REPYM-PHLSLLYGDLPPEE----K---AEAAEIAQRIDDALGVDSGISGLGWEGGELK 177 (196)
T ss_dssp HCT----------T--------S-----EEEEE-----HHH----H---HHHHHHHHHH-TT------GTT-EEEEEEEE
T ss_pred HHhhhcccccccccccc----CCCCC-CeEEEEEcCCCccc----H---HHHHHHHHHhcccccccccCCCCCEeccEEE
Confidence 988532 2221 46899 99999974311100 0 0112333333333 34577899999
Q ss_pred EEeeecCCCCCceeEeEEEeC
Q 010205 488 LSQRFVYDESGFYHCCASIPF 508 (515)
Q Consensus 488 Ls~l~~~~~~g~Y~~i~si~L 508 (515)
|.... ++=.-.+++++++|
T Consensus 178 lv~t~--g~v~~W~~l~~~~l 196 (196)
T PF07823_consen 178 LVRTD--GPVEEWEVLASVDL 196 (196)
T ss_dssp EEE----TT-TT-EEEEEEE-
T ss_pred EEEcC--CCCCcEEEEEEEeC
Confidence 95543 22356788888765
No 52
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=95.09 E-value=0.024 Score=44.88 Aligned_cols=37 Identities=24% Similarity=0.269 Sum_probs=34.2
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~i 189 (515)
.....+.||.+-.+..|||+|.+++.+++.+|.+|+|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3678899999999999999999999999999988876
No 53
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=95.04 E-value=0.04 Score=55.02 Aligned_cols=63 Identities=25% Similarity=0.360 Sum_probs=54.4
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 156 ~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
.-+.||+.+++.+||++|+.++.|.++|+|+|.+= .++-|.|.|+......-|...|..|-.+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG---~NG~IWV~~~~~~~e~~~~~aI~~ie~e 210 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVG---QNGRIWVDGENESLEELAIEAIRKIERE 210 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEe---cCCEEEecCCCcchHHHHHHHHHHHhhh
Confidence 46889999999999999999999999999999994 5789999998655677787778777655
No 54
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=94.94 E-value=0.0018 Score=66.89 Aligned_cols=150 Identities=15% Similarity=0.132 Sum_probs=103.2
Q ss_pred CCceEEeeecccCChhhHHHHHHHHHHhHHHhhhhcCCCCeEEEecccccCCCCCCCceEEEEeccccCchhHHHHHHHH
Q 010205 340 KTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQV 419 (515)
Q Consensus 340 ~~LHLTL~fLgL~~eeei~~a~~aL~~i~~~i~~iL~~~pf~l~lkGLg~F~~dp~~~rVLyagV~~~~~~~~L~~L~~~ 419 (515)
.++|+|+...-..++.+++.-...+++....+..++..+-...-|.|.++|+. .|-.+++-+ .+.+++.++.
T Consensus 128 ~s~p~thflal~lne~eVqe~f~~fke~~~~~esl~~~g~~~s~F~~p~~~HL-----Tvgm~~L~~---dd~vq~a~e~ 199 (345)
T KOG2814|consen 128 KSFPITHFLALPLNEHEVQEGFLAFKELKPFIESLLDGGIDKSLFQGPGTFHL-----TVGMLKLLN---DDDVQKALEI 199 (345)
T ss_pred hcCchhhhhhhhcchHHHHHHHHHHHhhhhhHHHhhccchhhccccCCceeeE-----EEEEEEecC---hHHHHHHHHH
Confidence 47899999888889999998888888766655555565666677899999987 788888864 4788999999
Q ss_pred HHHHHHHCCccccccCCCCcccccEEeeeecccc--cccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeecCCC-
Q 010205 420 IIDAFNEAGLVFHRDYNKKLKQLHATLMNIRHKK--RRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDE- 496 (515)
Q Consensus 420 L~~~f~~~Gl~~e~d~~r~fk~PHiTLar~r~~~--~~~g~~~~~~fda~~il~~~~d~~fG~~~V~~I~Ls~l~~~~~- 496 (515)
+...|.+.++...+ ++-|. +|-+++.+.... .+-.+.+..+-+. +++-..-+|++....+..|.+...+.
T Consensus 200 les~~~e~~~~~~~--kp~~i-~lkG~~~mnddP~~~kVLYAkv~~~~~----e~~l~~~~~~~i~~~f~~~~li~k~~~ 272 (345)
T KOG2814|consen 200 LESTFQEIRIDVGE--KPLFI-DLKGLDKMNDDPSLTKVLYAKVEPDDY----EKFLQHRCGERILERFVASGLIKKESS 272 (345)
T ss_pred HHHHHHHHHhccCC--Cceee-eccchhhhcCCHhHheeeeeeccCcch----HHHHHHHHHHHHHHHHHHhcchhcccc
Confidence 99999998888763 44455 999999886531 1112233333232 33333345677777777776654332
Q ss_pred CCceeEeE
Q 010205 497 SGFYHCCA 504 (515)
Q Consensus 497 ~g~Y~~i~ 504 (515)
..+|+|.-
T Consensus 273 ~~kLH~Tv 280 (345)
T KOG2814|consen 273 SLKLHCTV 280 (345)
T ss_pred ccEEEEEE
Confidence 35666544
No 55
>PRK12705 hypothetical protein; Provisional
Probab=94.94 E-value=0.031 Score=61.75 Aligned_cols=68 Identities=19% Similarity=0.318 Sum_probs=56.7
Q ss_pred CCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 152 ERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 152 ~~~~~~v~Ip~-~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
......|.+|. ++-|.|||+.|.++|.+|..||+-|.|+. ....|+|.+-++..-+.|+..++.++..
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--tp~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD--TPEAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC--CccchhhcccCccchHHHHHHHHHHHhc
Confidence 34556778887 78899999999999999999999999975 3456888887778888888888888765
No 56
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=94.33 E-value=0.031 Score=61.26 Aligned_cols=103 Identities=20% Similarity=0.317 Sum_probs=81.4
Q ss_pred CCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCC
Q 010205 150 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSL 228 (515)
Q Consensus 150 ~~~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~~iv~e~~~~~k~ 228 (515)
-+++..+++.||.+++..|+|++|++++.|+..|+.||.+..... ...+-+.+..+..+..|+..|-.++-+ ..
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~~--~~--- 138 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTE--NT--- 138 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHhc--CC---
Confidence 456788899999999999999999999999999999999976443 233444443456788888887777665 32
Q ss_pred CceEEEEeccccchhhhccHHHHHHHHhc
Q 010205 229 DYSHFVSLPLAVHPELVDKLVNFQNTILG 257 (515)
Q Consensus 229 ~~tHFIsIPl~~hp~I~~~~~~f~~~Il~ 257 (515)
++..-.+.|...|+.|.+.+...+++|-.
T Consensus 139 pvk~~lsvpqr~~~~i~grgget~~si~~ 167 (608)
T KOG2279|consen 139 PVSEQLSVPQRSVGRIIGRGGETIRSICK 167 (608)
T ss_pred cccccccchhhhcccccccchhhhcchhc
Confidence 46677888988899999999998887754
No 57
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=93.97 E-value=0.047 Score=60.12 Aligned_cols=64 Identities=25% Similarity=0.266 Sum_probs=56.3
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 154 ~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
....+.|+.+-...+||++|-.+|+|+.|||+.-++. ++++.|-.+++...++|++.|.-|...
T Consensus 597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD----e~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD----EGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred eeeEEeecchhhheeecCccceeeeEeeeccceeeec----CceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 3677889999999999999999999999999666664 488999999999999999999887654
No 58
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=93.18 E-value=0.25 Score=50.05 Aligned_cols=70 Identities=19% Similarity=0.321 Sum_probs=53.1
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 151 ~~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
.+++.+.+.+...--|.||||||.++|+|..+.+..|++|.++. ...++|+.. .+.|-.-...|.-.+++
T Consensus 45 ~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad-~~ti~~ilk~iip~lee 115 (390)
T KOG2192|consen 45 RSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISAD-IETIGEILKKIIPTLEE 115 (390)
T ss_pred hcceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCCCceeEEEecc-HHHHHHHHHHHhhhhhh
Confidence 35677788888889999999999999999999999999998655 556788874 45554444444444444
No 59
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=92.84 E-value=0.17 Score=55.74 Aligned_cols=103 Identities=24% Similarity=0.212 Sum_probs=76.5
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCC--CC-CCcEEEEc--------cChhHHHHHHHHHHHHHH----
Q 010205 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS--KK-EDSIIIEG--------NSTDSVAKASEKIQAIIA---- 220 (515)
Q Consensus 156 ~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~--~~-~~~I~I~G--------~s~~~v~~A~~~I~~iv~---- 220 (515)
..+-.+....|.||||+|.++++|.++|+.+|.|-.. +. ...|+|+| +..+++.+|-++|-...+
T Consensus 45 ~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~ 124 (485)
T KOG2190|consen 45 YRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDE 124 (485)
T ss_pred EEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccccccc
Confidence 6777888999999999999999999888888877443 33 56788999 136899999999876421
Q ss_pred Hhhh----CCCCCceEEEEeccccchhhhccHHHHHHHHhcc
Q 010205 221 EAVE----SPSLDYSHFVSLPLAVHPELVDKLVNFQNTILGI 258 (515)
Q Consensus 221 e~~~----~~k~~~tHFIsIPl~~hp~I~~~~~~f~~~Il~~ 258 (515)
+... ..+...+-.+-+|-..--.|+|..+..++.|.++
T Consensus 125 ~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~ 166 (485)
T KOG2190|consen 125 AAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREE 166 (485)
T ss_pred ccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHh
Confidence 0000 0012235556688875688999999999999876
No 60
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=91.17 E-value=0.15 Score=59.22 Aligned_cols=42 Identities=29% Similarity=0.572 Sum_probs=38.4
Q ss_pred CCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010205 150 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (515)
Q Consensus 150 ~~~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 191 (515)
.....+.++.||.++|+.|||++|++.|+++.++++.|.+|.
T Consensus 705 ~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 705 AKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred cccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence 345567889999999999999999999999999999999998
No 61
>TIGR03223 Phn_opern_protn putative phosphonate metabolism protein. This family of proteins is observed in the vicinity of other caharacterized genes involved in the catabolism of phosphonates via the3 C-P lyase system (GenProp0232), its function is unknown. These proteins are members of the somewhat broader pfam06299 model "Protein of unknown function (DUF1045)" which contains proteins found in a different genomic context as well.
Probab=91.12 E-value=3.5 Score=41.31 Aligned_cols=141 Identities=12% Similarity=0.135 Sum_probs=77.7
Q ss_pred ceEEeee-cccCChhhHHHHHHHHHHhHHHhhhhcCCCCeEE---EecccccCCCCCCCceEEEEeccccCchhHHHHHH
Q 010205 342 FHLTVLM-LKLWNKDRVNAATNVLKSISSKVMDALDNRPLFI---RLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHAC 417 (515)
Q Consensus 342 LHLTL~f-LgL~~eeei~~a~~aL~~i~~~i~~iL~~~pf~l---~lkGLg~F~~dp~~~rVLyagV~~~~~~~~L~~L~ 417 (515)
||.||+- +.|..........++++.+.. ...||.| .+.-||-|-- ++.+ .....|+.|+
T Consensus 58 fHaTLKaPFrLa~g~~~a~L~~al~~fA~------~~~pf~i~~L~l~~Lg~FlA--------L~P~---~~~~~L~~LA 120 (228)
T TIGR03223 58 FHATLKAPFRLAPGVTEAELLAAVAAFAA------TRAPFALPPLRVALLGGFLA--------LRPA---APCPALQALA 120 (228)
T ss_pred cceeecCCcccCCCCCHHHHHHHHHHHHh------cCCCccCCcceeeeeCCEEE--------EeeC---CCCHHHHHHH
Confidence 4999984 344433334444445555432 2355554 3444443321 2222 3468899999
Q ss_pred HHHHHHHHH---------------CCccccccC----------CCCcccccEEeeeecccccccCCCccccccHHHHHHH
Q 010205 418 QVIIDAFNE---------------AGLVFHRDY----------NKKLKQLHATLMNIRHKKRRKGTRRVDYFDARDIFKQ 472 (515)
Q Consensus 418 ~~L~~~f~~---------------~Gl~~e~d~----------~r~fk~PHiTLar~r~~~~~~g~~~~~~fda~~il~~ 472 (515)
..+.+.|.. .||...++. -..|. .||||-.--.... .. .+...++.
T Consensus 121 a~~V~~~d~fRAPls~aelaRRr~~~Ls~~Q~~~L~~WGYPYV~deFr-FHmTLTg~l~~~~----~~----~~~~~l~~ 191 (228)
T TIGR03223 121 AACVRELDPFRAPLTEAELARRRPDQLTPRQRALLERWGYPYVLEEFR-FHMTLTGRLDEEE----RA----AVLARLEA 191 (228)
T ss_pred HHHHHhhhhccCCCCHHHHhhcCccCCCHHHHHHHHHcCCCceecceE-EEEEecCCCChHH----HH----HHHHHHHH
Confidence 999998843 233222100 13689 9999975321110 00 11233433
Q ss_pred -hCCCccccEEecEEEEEeeecCCCCCceeEeEEEeCCC
Q 010205 473 -FGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 510 (515)
Q Consensus 473 -~~d~~fG~~~V~~I~Ls~l~~~~~~g~Y~~i~si~L~~ 510 (515)
|....-..+.|+.|.|+.-. ..|.-++.+..++|.+
T Consensus 192 ~~~~~l~~p~~id~laLf~e~--~~g~pF~~~~~~~l~~ 228 (228)
T TIGR03223 192 RFAPLLADPLAVDGLALFVEP--EPGAPFRLIARVALAG 228 (228)
T ss_pred HhhhccCCCeeeeeEEEEecc--CCCCCcEEEEeecCCC
Confidence 44443457789999996432 3456699999999864
No 62
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=87.46 E-value=2.5 Score=41.13 Aligned_cols=73 Identities=18% Similarity=0.249 Sum_probs=59.0
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCCCceEEEE
Q 010205 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDYSHFVS 235 (515)
Q Consensus 156 ~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e~~~~~k~~~tHFIs 235 (515)
..+.+++..+-+|...+|..++.|-...|++|.+-. +.+.|.|+|. +..++.+...|..++... .+..|.
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~--~~~~i~I~g~-k~~~~~i~~~i~~~l~~i-------~~~~i~ 97 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR--SENRIRITGT-KSTAEYIEASINEILSNI-------RTEEID 97 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEec--CCcEEEEEcc-HHHHHHHHHHHHHHHhhc-------EEEEEe
Confidence 356666899999999999999999888899999976 4568999995 788888888888888762 355565
Q ss_pred ecc
Q 010205 236 LPL 238 (515)
Q Consensus 236 IPl 238 (515)
+|.
T Consensus 98 l~~ 100 (210)
T PF14611_consen 98 LSP 100 (210)
T ss_pred cch
Confidence 664
No 63
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=86.31 E-value=0.5 Score=51.56 Aligned_cols=43 Identities=28% Similarity=0.359 Sum_probs=37.6
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC
Q 010205 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 194 (515)
Q Consensus 152 ~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~ 194 (515)
+.....|.||...++.+|||+|.++++||+..|.+|.+-..++
T Consensus 484 gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 484 GDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred cCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 3456789999999999999999999999999999999955433
No 64
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=85.26 E-value=1.1 Score=34.74 Aligned_cols=35 Identities=17% Similarity=0.288 Sum_probs=28.4
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEE
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKI 187 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I 187 (515)
.....+.+...-.+.+||++|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35556666666689999999999999999999665
No 65
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=85.26 E-value=0.61 Score=45.53 Aligned_cols=54 Identities=26% Similarity=0.352 Sum_probs=45.7
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 163 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 163 ~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
-.+|.|+||+|.|+=.||+-|.|||.+-. ..|-|-|. -+++.-|++-|-.++-.
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad----~kIHiLG~-~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLAD----SKIHILGA-FQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecC----ceEEEeec-chhhHHHHHhhHhhhcc
Confidence 45899999999999999999999999964 56888885 57899999888766643
No 66
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=84.61 E-value=0.79 Score=47.50 Aligned_cols=68 Identities=21% Similarity=0.299 Sum_probs=58.3
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHH-HHHHHH
Q 010205 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKAS-EKIQAI 218 (515)
Q Consensus 151 ~~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~-~~I~~i 218 (515)
..+....+.+|...++.+.|.+|++++++++-|++-|.-|.+......-++|-+.-++++|+ ..|+..
T Consensus 112 s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~~~~Vf~Vtg~~~nC~kra~s~eie~t 180 (394)
T KOG2113|consen 112 SGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRCGEPVFCVTGAPKNCVKRARSCEIEQT 180 (394)
T ss_pred cCCCceeeeccceeeeeccccccCccchheecccceEeeeccCCCceEEEecCCcchhhhccccchhhh
Confidence 56777788999999999999999999999999999999998777777889997666688888 666544
No 67
>PRK02821 hypothetical protein; Provisional
Probab=84.52 E-value=0.78 Score=38.32 Aligned_cols=32 Identities=19% Similarity=0.293 Sum_probs=27.3
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHh
Q 010205 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEM 183 (515)
Q Consensus 152 ~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT 183 (515)
......+.+.++-.|.||||+|.+++.|..=.
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 34678999999999999999999999886543
No 68
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=84.19 E-value=0.55 Score=38.14 Aligned_cols=34 Identities=15% Similarity=0.251 Sum_probs=28.7
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhC
Q 010205 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMG 184 (515)
Q Consensus 151 ~~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~ 184 (515)
.......+.|..+-.|.||||+|.|++.|+.=++
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 4466778889999999999999999999986544
No 69
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=83.84 E-value=1 Score=41.67 Aligned_cols=38 Identities=16% Similarity=0.110 Sum_probs=34.5
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP 190 (515)
+....+.|+.+-++..|||+|.+++.++.=++-.|+|-
T Consensus 98 ~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 98 DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred cEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 45678899999999999999999999999999998874
No 70
>PRK00468 hypothetical protein; Provisional
Probab=83.39 E-value=1.1 Score=37.17 Aligned_cols=30 Identities=20% Similarity=0.302 Sum_probs=26.0
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHH
Q 010205 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEK 181 (515)
Q Consensus 152 ~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~ 181 (515)
......+.+.++-.|.||||+|.|++.|..
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRt 57 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRT 57 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHH
Confidence 346778999999999999999999998854
No 71
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=83.01 E-value=1.2 Score=37.19 Aligned_cols=31 Identities=16% Similarity=0.297 Sum_probs=26.8
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHH
Q 010205 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEK 181 (515)
Q Consensus 151 ~~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~ 181 (515)
.+.....+.+-++-.|.+|||+|.|++.|..
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHH
Confidence 4456788999999999999999999998853
No 72
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=82.98 E-value=1.4 Score=48.48 Aligned_cols=68 Identities=16% Similarity=0.194 Sum_probs=46.5
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEcc--ChhHHHHHHHHHHHHHH
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGN--STDSVAKASEKIQAIIA 220 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~------~~~I~I~G~--s~~~v~~A~~~I~~iv~ 220 (515)
-...++-||...|+.|||.||..+++....-++-|++-..-+ .+.|.|+.+ +++++..|+.-...+|.
T Consensus 448 pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~ 523 (657)
T COG5166 448 PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVK 523 (657)
T ss_pred chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHh
Confidence 456788999999999999999999999999999888754322 234555553 33344444444444443
No 73
>PF10469 AKAP7_NLS: AKAP7 2'5' RNA ligase-like domain; InterPro: IPR019510 This entry represents the N-terminal nuclear localisation signal-containing domain found in the cyclic AMP-dependent protein kinase A (PKA) anchor protein, AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes []. This domain carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein []. Binding to the regulatory subunits RI and RII of PKA is mediated via the RI-RII subunit-binding domain at the C terminus.
Probab=82.82 E-value=0.61 Score=45.30 Aligned_cols=25 Identities=20% Similarity=0.272 Sum_probs=23.3
Q ss_pred CCceEEEEccCCcchhHHHhhhccc
Q 010205 287 QEHKVAVELNIGDNSERVKVDRTSI 311 (515)
Q Consensus 287 pn~FVAv~l~~~~~~~~v~~~q~~i 311 (515)
|||||||+|+.+++.++++.+|+.|
T Consensus 1 pthFl~ipl~~~~i~~~~~~fq~~v 25 (209)
T PF10469_consen 1 PTHFLCIPLNSPEIQEKFKEFQNEV 25 (209)
T ss_pred CCeEEEEECCCHHHHHHHHHHHHHH
Confidence 8999999999999999999999754
No 74
>PRK13764 ATPase; Provisional
Probab=82.63 E-value=0.93 Score=51.40 Aligned_cols=43 Identities=28% Similarity=0.332 Sum_probs=38.0
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC
Q 010205 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 194 (515)
Q Consensus 152 ~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~ 194 (515)
+.....|.||...++.+|||+|.++++||+..|..|+|-...+
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence 5667789999999999999999999999999999999954433
No 75
>PRK01064 hypothetical protein; Provisional
Probab=79.17 E-value=1.8 Score=36.26 Aligned_cols=32 Identities=28% Similarity=0.243 Sum_probs=27.3
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHH
Q 010205 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKE 182 (515)
Q Consensus 151 ~~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~e 182 (515)
.......+.|.++-.|.+|||+|.|++.|..=
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 34567889999999999999999999988653
No 76
>PHA02977 hypothetical protein; Provisional
Probab=79.03 E-value=9.8 Score=35.60 Aligned_cols=112 Identities=17% Similarity=0.204 Sum_probs=61.8
Q ss_pred eEEeeecccCChhhHHHHHHHHHHhHHHhhhhcCCCCeEEEecccccCCCCC------CCceEEEEeccccCchhHHHHH
Q 010205 343 HLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSK------DKARILYAPVEEIGDGDRLLHA 416 (515)
Q Consensus 343 HLTL~fLgL~~eeei~~a~~aL~~i~~~i~~iL~~~pf~l~lkGLg~F~~dp------~~~rVLyagV~~~~~~~~L~~L 416 (515)
|+||+.- +.++-+ .+++.++.+.++ +-..+.++-+..-+||.+. .+-+-+-++++. ++.|..|
T Consensus 71 hitlgia---n~dq~~----~f~~fk~~~~d~-dl~sis~~cke~icfpqs~askelga~g~avvmkle~---sddlkal 139 (201)
T PHA02977 71 HITLGIA---NKDQCD----NFENFKELIKDI-DLQSISFTCKEEICFPQSNASKELGAKGCAVVMKLEA---SDDLKAL 139 (201)
T ss_pred ceeeecc---CccHhH----HHHHHHHHhhcc-cceeEEEEeeeeEeccccchhhhhCcCccEEEEEEEe---chHHHHH
Confidence 9999885 333322 233333333332 4467778888888998531 122445556654 4567666
Q ss_pred HHHHHHHHH----HCCccccccCCCCcccccEEeeeecccccccCCCccccccHHHHHHHhCC
Q 010205 417 CQVIIDAFN----EAGLVFHRDYNKKLKQLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGS 475 (515)
Q Consensus 417 ~~~L~~~f~----~~Gl~~e~d~~r~fk~PHiTLar~r~~~~~~g~~~~~~fda~~il~~~~d 475 (515)
.+.|-.+.- -.|=... ..++- ||+|+.-++.-.. .+++++. +..+.|..
T Consensus 140 rnvl~n~vp~pkdifg~i~~---d~~w~-phitigyv~~dd~--dnk~r~i----e~~~~frg 192 (201)
T PHA02977 140 RNVLFNAVPCPKDIFGDILS---DNPWC-PHITIGYVKADDE--DNKKRFI----ECAEAFRG 192 (201)
T ss_pred HHHhhcccCCcHHhhccccc---CCCCC-CceEEEeecccch--hhHHHHH----HHHHHhCC
Confidence 666654321 0232222 25788 9999999875321 1234432 66666664
No 77
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=76.87 E-value=1.4 Score=36.00 Aligned_cols=36 Identities=25% Similarity=0.351 Sum_probs=31.0
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEE
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKII 188 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~ 188 (515)
.....+.|-...-+.+||++|+++++|.++.+-.+.
T Consensus 24 ~~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 24 PDQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SSEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CCeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 466778888999999999999999999988877664
No 78
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=75.74 E-value=2.5 Score=39.33 Aligned_cols=39 Identities=15% Similarity=0.071 Sum_probs=35.0
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 010205 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (515)
Q Consensus 152 ~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP 190 (515)
++....+.||.+-++..|||+|.+.+...+=|+-+|+|-
T Consensus 98 ~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 98 GKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 356788999999999999999999999999999888774
No 79
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=74.07 E-value=3.3 Score=38.32 Aligned_cols=37 Identities=24% Similarity=0.362 Sum_probs=31.9
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010205 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (515)
Q Consensus 155 ~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 191 (515)
.+-+-|+....|..||++|+.++.|++..|-+|+|=.
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 4566778889999999999999999999998888743
No 80
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=73.88 E-value=2.7 Score=34.56 Aligned_cols=35 Identities=17% Similarity=0.282 Sum_probs=28.8
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010205 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (515)
Q Consensus 155 ~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~i 189 (515)
.+.+.|..+-.+.||||+|.|+..|+-=++.-++-
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 45677778889999999999999998877755553
No 81
>PLN00108 unknown protein; Provisional
Probab=72.95 E-value=1.9 Score=43.95 Aligned_cols=29 Identities=17% Similarity=0.181 Sum_probs=26.4
Q ss_pred hcccCCceEEEEcc-CCcchhHHHhhhccc
Q 010205 283 QQVDQEHKVAVELN-IGDNSERVKVDRTSI 311 (515)
Q Consensus 283 ~~~rpn~FVAv~l~-~~~~~~~v~~~q~~i 311 (515)
.+..+||||||+|. .|++.++++++|+.|
T Consensus 32 ~~~~~THFlavPL~~~p~i~~~~~~Fk~~V 61 (257)
T PLN00108 32 HREVFTHFVSLPLAIYPDLKKNIEAFQNSV 61 (257)
T ss_pred cCCCCCeEEEEEcCCCHHHHHHHHHHHHHH
Confidence 36789999999996 899999999999987
No 82
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=71.98 E-value=3.7 Score=33.48 Aligned_cols=26 Identities=35% Similarity=0.437 Sum_probs=21.9
Q ss_pred cccccCCCchhHHHHHHHh-CcEEEcC
Q 010205 165 IRFIKGKEGSTQKKFEKEM-GVKIILP 190 (515)
Q Consensus 165 ~~~IIGk~G~t~k~iE~eT-~~~I~iP 190 (515)
.|..||++|..++.|+++. |-+|+|=
T Consensus 19 vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 19 VGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp HHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred ceecCccccHHHHHHHHHhCCCeEEEE
Confidence 8999999999999999999 8888763
No 83
>KOG3102 consensus Uncharacterized conserved protein [Function unknown]
Probab=71.52 E-value=14 Score=36.63 Aligned_cols=101 Identities=11% Similarity=0.199 Sum_probs=67.9
Q ss_pred cCCCCceEEeeecccCChhhHHHHHHHHHHhHHHhhhhcCCCCeEEEecccccCCCCCCCceE-EEEeccccCchhHHHH
Q 010205 337 IKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARI-LYAPVEEIGDGDRLLH 415 (515)
Q Consensus 337 v~p~~LHLTL~fLgL~~eeei~~a~~aL~~i~~~i~~iL~~~pf~l~lkGLg~F~~dp~~~rV-LyagV~~~~~~~~L~~ 415 (515)
+--.-|||.|.=-.-.---+|.....+|+.- +. ....|-+++.++.+|-+ .++.|. |-+.+.. .+...+.+
T Consensus 117 ~~~~~fHlSLsr~VvLr~HqI~~fi~~L~~~---l~---s~~rf~~t~n~~~iytN-~e~TRtFi~leitt-~~~~~~~~ 188 (269)
T KOG3102|consen 117 ALGREFHLSLSRNVVLRVHQINSFISMLRQK---LQ---SQKRFLITFNKWEIYTN-DEHTRTFISLEITT-SGLSEISK 188 (269)
T ss_pred hccceEEEeeccceEEEeehhhHHHHHHHHH---Hh---hhhhheEeecceEEEec-cccceeEEEEEech-hhHHHHHH
Confidence 3356789998743333344566555555542 21 34788999999999987 566666 3345543 46677888
Q ss_pred HHHHHHHHHHHCCccccccCCCCcccccEEeeee
Q 010205 416 ACQVIIDAFNEAGLVFHRDYNKKLKQLHATLMNI 449 (515)
Q Consensus 416 L~~~L~~~f~~~Gl~~e~d~~r~fk~PHiTLar~ 449 (515)
+.+.+.+.+....|..= .+.-. +|+.|+=.
T Consensus 189 ~i~~vd~Vm~~~nL~~F---Y~DPs-fHiSL~Wc 218 (269)
T KOG3102|consen 189 QIDAVDEVMKLHNLPEF---YKDPS-FHISLVWC 218 (269)
T ss_pred HHHHHHHHHHHcCchhh---hcCCC-CCceEEEE
Confidence 88889999888887643 33347 99999865
No 84
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=67.55 E-value=9.9 Score=39.16 Aligned_cols=54 Identities=17% Similarity=0.264 Sum_probs=41.2
Q ss_pred ccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhhh
Q 010205 162 ASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVE 224 (515)
Q Consensus 162 ~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e~~~ 224 (515)
....-.|||++|+|++.||--|+|-|-+-. ++|.+.|+ -.++..++ .||.+..+
T Consensus 157 vKRRqRLiGpng~TLKAlelLT~CYilVqG----~TVsaiGp-fkGlkevr----~IV~DcM~ 210 (356)
T KOG2874|consen 157 VKRRQRLIGPNGSTLKALELLTNCYILVQG----NTVSAIGP-FKGLKEVR----KIVEDCMK 210 (356)
T ss_pred HHHHHHhcCCCchhHHHHHHHhhcEEEeeC----cEEEeecC-cchHHHHH----HHHHHHHh
Confidence 345668999999999999999999999854 68888887 35665544 45556443
No 85
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=67.08 E-value=3.7 Score=34.50 Aligned_cols=37 Identities=11% Similarity=0.253 Sum_probs=30.3
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010205 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (515)
Q Consensus 155 ~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 191 (515)
.+.|.|-...=|.+||++|+++++|.++..-.+.++.
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~ 67 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE 67 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence 3566666677799999999999999999888887754
No 86
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=62.91 E-value=7.4 Score=41.26 Aligned_cols=39 Identities=26% Similarity=0.296 Sum_probs=36.3
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 191 (515)
.....+.||.+-.+.-|||+|.+.|.--.=||.+|+|=+
T Consensus 300 ~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 300 KHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred CcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 367899999999999999999999999999999999854
No 87
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=60.46 E-value=9.1 Score=41.08 Aligned_cols=42 Identities=17% Similarity=0.056 Sum_probs=38.1
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 194 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~ 194 (515)
.....+.||.+.++.-|||+|.+.|.--+=||.+|+|-+-++
T Consensus 307 ~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 307 EKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred CcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 467899999999999999999999999999999999976544
No 88
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=59.21 E-value=11 Score=35.11 Aligned_cols=36 Identities=25% Similarity=0.287 Sum_probs=32.3
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 010205 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (515)
Q Consensus 155 ~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP 190 (515)
.+-+-|.+...|..||++|..++.|++..|-+|+|=
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV 69 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI 69 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE
Confidence 677888899999999999999999999999888874
No 89
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=57.16 E-value=11 Score=36.72 Aligned_cols=37 Identities=19% Similarity=0.190 Sum_probs=34.8
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010205 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (515)
Q Consensus 155 ~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 191 (515)
...+.||.+-.+..|||+|.+.+...+=||-+|+|-.
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 7889999999999999999999999999999999854
No 90
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=55.95 E-value=7.4 Score=43.38 Aligned_cols=68 Identities=25% Similarity=0.249 Sum_probs=52.7
Q ss_pred CCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEccChhHHHHHHHHHHHH
Q 010205 150 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKIQAI 218 (515)
Q Consensus 150 ~~~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~---~~~I~I~G~s~~~v~~A~~~I~~i 218 (515)
.++-++....+|...++.|+|++|.+++.|+.--+.+|.+...|. ...+.|.|. +.-++.|+..|..=
T Consensus 136 ~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~q-qk~~~~a~~~~~~~ 206 (608)
T KOG2279|consen 136 ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQ-QKEVAAAKHLILEK 206 (608)
T ss_pred cCCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccc-cchHHHHHhhhhcc
Confidence 345677788999999999999999999999999999999987655 335566664 45555666665443
No 91
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=54.39 E-value=13 Score=35.53 Aligned_cols=33 Identities=24% Similarity=0.397 Sum_probs=26.9
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010205 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (515)
Q Consensus 156 ~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~i 189 (515)
+-+-|.+-. |.-|||+|.++|+|++..|-+|.+
T Consensus 63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~Vev 95 (166)
T PRK06418 63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRV 95 (166)
T ss_pred EEEEEeCCC-cccccccchHHHHHHHHhCCcEEE
Confidence 344455555 999999999999999999988776
No 92
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=52.59 E-value=14 Score=39.46 Aligned_cols=40 Identities=25% Similarity=0.269 Sum_probs=36.7
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCC
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS 192 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~ 192 (515)
.....+.||.+.++.-|||+|.+.|.--.=||.+|+|=+.
T Consensus 302 ~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 302 EKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred CcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 4578999999999999999999999999999999999653
No 93
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=51.51 E-value=80 Score=32.61 Aligned_cols=91 Identities=13% Similarity=0.185 Sum_probs=55.5
Q ss_pred CceEEeeecccCChhhHHHHHHHHHHhHHHhhhhcCCCCeEEEecccccCCCCCCCceE-EEEeccccCchhHHHHHHHH
Q 010205 341 TFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARI-LYAPVEEIGDGDRLLHACQV 419 (515)
Q Consensus 341 ~LHLTL~fLgL~~eeei~~a~~aL~~i~~~i~~iL~~~pf~l~lkGLg~F~~dp~~~rV-LyagV~~~~~~~~L~~L~~~ 419 (515)
+.++++++= -+.++++|.+.|.++.+....++..++..+.+.+++-..= .-.| .|+... +-...-.++...
T Consensus 185 r~~~~v~V~---y~~d~~~~~~il~~~~~~~~~vl~~p~p~v~~~~~~dssi---~~~v~~wv~~~--~~~~~~~~~~~~ 256 (286)
T PRK10334 185 RNEFIIGVA---YDSDIDQVKQILTNIIQSEDRILKDREMTVRLNELGASSI---NFVVRVWSNSG--DLQNVYWDVLER 256 (286)
T ss_pred EEEEEEEec---CCCCHHHHHHHHHHHHHhCCceecCCCCEEEEEeeeCceE---EEEEEEEEecc--hhHHHHHHHHHH
Confidence 456776653 3455777888887776554455666666777776554321 1122 455432 222334577888
Q ss_pred HHHHHHHCCccccccCCCCcccccEEee
Q 010205 420 IIDAFNEAGLVFHRDYNKKLKQLHATLM 447 (515)
Q Consensus 420 L~~~f~~~Gl~~e~d~~r~fk~PHiTLa 447 (515)
|.++|.++|+... | |+.|+.
T Consensus 257 I~~~f~~~gI~ip------~--p~~~v~ 276 (286)
T PRK10334 257 IKREFDAAGISFP------Y--PQMDVN 276 (286)
T ss_pred HHHHHHHCCCcCC------C--CCeEEE
Confidence 9999999999874 3 666654
No 94
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=51.12 E-value=12 Score=32.96 Aligned_cols=32 Identities=25% Similarity=0.377 Sum_probs=26.1
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEE
Q 010205 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKI 187 (515)
Q Consensus 156 ~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I 187 (515)
+.|.|-..+-|+|||++|+++++|.+.....+
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~~ 94 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQKLL 94 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHHHh
Confidence 55666666779999999999999988877654
No 95
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=51.12 E-value=14 Score=40.94 Aligned_cols=39 Identities=28% Similarity=0.307 Sum_probs=36.0
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 191 (515)
.....+.||...++.-|||+|.+.|...+=||.+|+|=+
T Consensus 301 ~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 458899999999999999999999999999999999854
No 96
>COG5255 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.34 E-value=43 Score=33.21 Aligned_cols=33 Identities=18% Similarity=0.153 Sum_probs=23.9
Q ss_pred HHHHHHHHH-HCCccccccCCCCcccccEEeeeeccc
Q 010205 417 CQVIIDAFN-EAGLVFHRDYNKKLKQLHATLMNIRHK 452 (515)
Q Consensus 417 ~~~L~~~f~-~~Gl~~e~d~~r~fk~PHiTLar~r~~ 452 (515)
...+++.|. .+|+...+ ...+. .||||+-+..+
T Consensus 156 l~~~Rd~ls~~~g~r~P~--HDaY~-FHITlgYl~~w 189 (239)
T COG5255 156 LEEWRDYLSEKFGYRHPD--HDAYQ-FHITLGYLRIW 189 (239)
T ss_pred HHHHHHHHhhhhcccCCC--CcceE-EEEEeeeEeee
Confidence 345555554 57998764 56788 99999998754
No 97
>PF07823 CPDase: Cyclic phosphodiesterase-like protein; InterPro: IPR012386 2',3' Cyclic nucleotide phosphodiesterases (CPDases) are enzymes that catalyse at least two distinct steps in the splicing of tRNA introns in eukaryotes. The active site is characterised by two conserved histidine residues []. The enzyme has six cysteine residues, four of which are involved in forming two intra-molecular disulphide bridges. One of these bridges is involved in the catalytic activity of the enzyme as it opens when CPDase is semi-reduced []. Proteins in this entryand belong to 3.1.4.37 from EC and catalyse the reaction Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate. ; GO: 0004112 cyclic-nucleotide phosphodiesterase activity; PDB: 1JH7_A 1JH6_B 1FSI_B.
Probab=43.58 E-value=23 Score=34.34 Aligned_cols=42 Identities=17% Similarity=0.074 Sum_probs=20.3
Q ss_pred EEEEeccc-cCchhHHHHHHHHHHHHHHHCCccccccCCCCcccccEEeeee
Q 010205 399 ILYAPVEE-IGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKQLHATLMNI 449 (515)
Q Consensus 399 VLyagV~~-~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fk~PHiTLar~ 449 (515)
-||+-+.. ++....|+.+...|...|-.. ...|- |||||.--
T Consensus 4 SlWl~P~~~~~~~~~L~~lI~~L~~~~~~~--------~p~F~-PHiTL~s~ 46 (196)
T PF07823_consen 4 SLWLVPPPGSPLYERLKTLISSLASLFPGS--------PPPFE-PHITLTSG 46 (196)
T ss_dssp EEEEEE-T--TTHHHHHHHHHHHHHHST------------------EEEEEE
T ss_pred EEEEcCCCCccHHHHHHHHHHHHHHHCCCC--------CCCcC-CeEEEeCC
Confidence 37776643 234567777766666654311 14799 99999963
No 98
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=42.64 E-value=24 Score=38.77 Aligned_cols=39 Identities=23% Similarity=0.244 Sum_probs=35.9
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 191 (515)
.....+.||.+.++.-|||+|.+.|---.=||.+|+|-+
T Consensus 334 ~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 334 GRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred CcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 356789999999999999999999999999999999965
No 99
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=38.45 E-value=70 Score=26.74 Aligned_cols=35 Identities=31% Similarity=0.485 Sum_probs=27.6
Q ss_pred CcEEEcCCCCCCCcEEEEc-cChhHHHHHHHHHHHHHHH
Q 010205 184 GVKIILPSSKKEDSIIIEG-NSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 184 ~~~I~iP~~~~~~~I~I~G-~s~~~v~~A~~~I~~iv~e 221 (515)
++.+.|=+ +|-|+|+| .+.+.+..|.++|..++.+
T Consensus 49 ~~t~~IF~---sGki~itGaks~~~~~~a~~~i~~~L~~ 84 (86)
T PF00352_consen 49 KATVLIFS---SGKIVITGAKSEEEAKKAIEKILPILQK 84 (86)
T ss_dssp TEEEEEET---TSEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred cEEEEEEc---CCEEEEEecCCHHHHHHHHHHHHHHHHH
Confidence 56666654 47799999 4889999999999888875
No 100
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=38.00 E-value=75 Score=33.88 Aligned_cols=55 Identities=20% Similarity=0.297 Sum_probs=45.5
Q ss_pred ccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHH--HHHHH
Q 010205 162 ASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQ--AIIAE 221 (515)
Q Consensus 162 ~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~--~iv~e 221 (515)
....--|.|..|.+++.||+.+|+.|.-+. ..+.|+|. +..|..|...++ .+...
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG----~~~~i~g~-~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVARG----EAVRIIGA-RPLVDVATRVLLTLELLAE 79 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEeCC----ceEEEEec-hHHHHHHHHHHhHHHHHHH
Confidence 556677899999999999999999998765 57899996 459999999999 44444
No 101
>COG0799 Uncharacterized homolog of plant Iojap protein [Function unknown]
Probab=37.92 E-value=1.3e+02 Score=27.10 Aligned_cols=61 Identities=11% Similarity=0.168 Sum_probs=44.3
Q ss_pred hHHHHHHHHHHhHHHhhhhcCCCCeEEEecccccCCCCCCCceEEEEeccccCchhHHHHHHHHHHHHHHHCCccc
Q 010205 356 RVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 431 (515)
Q Consensus 356 ei~~a~~aL~~i~~~i~~iL~~~pf~l~lkGLg~F~~dp~~~rVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~ 431 (515)
.++.+.++|.+.+ ......|.++|...+-+ |+-+....+......+++.|.+.++++|+.+
T Consensus 6 l~~~i~~alddkK-------AeDIv~lDv~~~s~~tD--------yfVIatg~s~rhv~Aiad~i~~~~k~~g~~~ 66 (115)
T COG0799 6 LLEVIVEALDDKK-------AEDIVVLDVSGKSSLTD--------YFVIATGNSSRHVKAIADNVKEELKEAGEVP 66 (115)
T ss_pred HHHHHHHHHHhcc-------CCCeEEEEccCCccccc--------EEEEEEeCchHHHHHHHHHHHHHHHHcCCCc
Confidence 3445555555543 34677899999999987 4434333346789999999999999999876
No 102
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=36.29 E-value=33 Score=33.53 Aligned_cols=36 Identities=31% Similarity=0.305 Sum_probs=29.9
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010205 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (515)
Q Consensus 154 ~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~i 189 (515)
......+-..-.|..||++|..++.|.++.|-+|+|
T Consensus 76 av~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdV 111 (190)
T COG0195 76 AVVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDV 111 (190)
T ss_pred ceEEeecCcCchhhhccCCChHHHHHHHHhCCceEE
Confidence 345555666778999999999999999999977766
No 103
>PRK11538 ribosome-associated protein; Provisional
Probab=34.15 E-value=1.8e+02 Score=25.64 Aligned_cols=60 Identities=7% Similarity=0.141 Sum_probs=39.9
Q ss_pred HHHHHHHHHHhHHHhhhhcCCCCeEEEecccccCCCCCCCceEEEEeccccCchhHHHHHHHHHHHHHHHCCccc
Q 010205 357 VNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 431 (515)
Q Consensus 357 i~~a~~aL~~i~~~i~~iL~~~pf~l~lkGLg~F~~dp~~~rVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~ 431 (515)
+..+.++|.+.+ ...-..+.++++..|-+ |.-+....+...++.+++.|.+.+.+.|+.+
T Consensus 7 ~~~i~~~l~dkK-------a~DI~vlDv~~~~~~~D--------y~VIatg~S~rh~~aia~~v~~~~k~~~~~~ 66 (105)
T PRK11538 7 QDFVIDKIDDLK-------GQDIIALDVQGKSSITD--------CMIICTGTSSRHVMSIADHVVQESRAAGLLP 66 (105)
T ss_pred HHHHHHHHHHcC-------CCCeEEEECCCCCcccC--------EEEEEEeCCHHHHHHHHHHHHHHHHHcCCCC
Confidence 344555555432 23556788889887766 4434333446889999999999998887753
No 104
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=34.13 E-value=34 Score=32.03 Aligned_cols=33 Identities=27% Similarity=0.339 Sum_probs=28.7
Q ss_pred EEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010205 157 SVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (515)
Q Consensus 157 ~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~i 189 (515)
.|.|-.+.=|.+||++|.++++|-.+||-+-.+
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~v 111 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKV 111 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEE
Confidence 566667778999999999999999999988666
No 105
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=33.19 E-value=27 Score=35.23 Aligned_cols=29 Identities=24% Similarity=0.236 Sum_probs=21.1
Q ss_pred eEEEEecccccc-ccccCCCchhHHHHHHH
Q 010205 154 HSLSVEVGASVI-RFIKGKEGSTQKKFEKE 182 (515)
Q Consensus 154 ~~~~v~Ip~~~~-~~IIGk~G~t~k~iE~e 182 (515)
....|.|.++-| +.|||++|+++|+|-.+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 456667776555 67889999999986443
No 106
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=31.88 E-value=39 Score=28.28 Aligned_cols=32 Identities=9% Similarity=0.254 Sum_probs=23.6
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcE
Q 010205 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVK 186 (515)
Q Consensus 153 ~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~ 186 (515)
+..+.+++ .+-|.+||++|.++++|.+...-.
T Consensus 39 ~i~V~I~t--~~pg~iIGk~G~~I~~l~~~l~k~ 70 (85)
T cd02411 39 GTQITIYA--ERPGMVIGRGGKNIRELTEILETK 70 (85)
T ss_pred cEEEEEEE--CCCCceECCCchhHHHHHHHHHHH
Confidence 44445554 677999999999999987766543
No 107
>PRK11281 hypothetical protein; Provisional
Probab=31.02 E-value=1.6e+02 Score=36.21 Aligned_cols=76 Identities=9% Similarity=0.020 Sum_probs=48.8
Q ss_pred hhhHHHHHHHHHHhHHHhhhhcCCCCeEEEecccccCCCCCCCceEEEEeccccCchhHHHHHHHHHHHHHHHCCcccc
Q 010205 354 KDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFH 432 (515)
Q Consensus 354 eeei~~a~~aL~~i~~~i~~iL~~~pf~l~lkGLg~F~~dp~~~rVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e 432 (515)
+.++++|.+.|.++......++..++..+.+.++|.+.= ..-=..|+.-. .+....-.++...|.++|.+.|+...
T Consensus 1005 ~sDi~~v~~iL~eaa~~~p~Vl~~P~P~V~~~~fgdssi--~~~lr~wv~~~-~~~~~v~s~L~~~I~~~f~e~GIeIp 1080 (1113)
T PRK11281 1005 GSDLEKVRELLLQAATENPRVMKEPEPQVFFLNFGASTL--DHELRLYVREL-GDRSPTVDELNRRIDRLFRENDINIA 1080 (1113)
T ss_pred CCCHHHHHHHHHHHHHcCcccccCCCCEEEEEeccCceE--EEEEEEEEcCH-hhHHHHHHHHHHHHHHHHHHCCCcCC
Confidence 456888888888776554456666666788887765532 11011355421 12334456788999999999999863
No 108
>PRK15494 era GTPase Era; Provisional
Probab=30.74 E-value=30 Score=36.35 Aligned_cols=36 Identities=28% Similarity=0.375 Sum_probs=25.8
Q ss_pred eEEEEecccccc-ccccCCCchhHHH--------HHHHhCcEEEc
Q 010205 154 HSLSVEVGASVI-RFIKGKEGSTQKK--------FEKEMGVKIIL 189 (515)
Q Consensus 154 ~~~~v~Ip~~~~-~~IIGk~G~t~k~--------iE~eT~~~I~i 189 (515)
....|.|+++-| +.|||++|.++|+ ||+-+|+++.+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 446677887555 6789999999987 45556666554
No 109
>PF09749 HVSL: Uncharacterised conserved protein; InterPro: IPR019146 This entry is of proteins of approximately 300 residues conserved from plants to humans. It contains two conserved motifs, HxSL and FHVSL. The function is unknown.
Probab=30.02 E-value=91 Score=31.09 Aligned_cols=66 Identities=17% Similarity=0.269 Sum_probs=40.2
Q ss_pred CceEEEEccCCcchhHHHhhhccccccccccccCCCCCCCCCCCCccccc-CCCCceEEeeecccCChhhHHHH-HHHHH
Q 010205 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFI-KPKTFHLTVLMLKLWNKDRVNAA-TNVLK 365 (515)
Q Consensus 288 n~FVAv~l~~~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gl~~~~fv-~p~~LHLTL~fLgL~~eeei~~a-~~aL~ 365 (515)
..|+++++..+.... ++.+.+.+- .++..+|+++ |. ....+|+.|+..-....+++.+. .+.+.
T Consensus 141 R~FL~l~V~~~~~~~-l~~l~~~i~-----------~~l~~~~lp~--~Y~~~~~fHvSIAw~~~~~~~~l~~~~~~~~~ 206 (239)
T PF09749_consen 141 RSFLALRVSEGSNNE-LKRLLDRIN-----------EVLKEFGLPP--FYDEDPSFHVSIAWTLGDPSEELKESSLKILQ 206 (239)
T ss_pred eEEEEEEecccccHH-HHHHHHHHH-----------HHHHHhCCCc--ccCCCCCCEEEEEEECCCchHHHHHHHHHHHH
Confidence 489999999865432 555544441 1234566643 55 89999999998744444444443 34454
Q ss_pred Hh
Q 010205 366 SI 367 (515)
Q Consensus 366 ~i 367 (515)
..
T Consensus 207 ~~ 208 (239)
T PF09749_consen 207 EP 208 (239)
T ss_pred HH
Confidence 44
No 110
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=29.88 E-value=39 Score=34.07 Aligned_cols=37 Identities=24% Similarity=0.267 Sum_probs=28.3
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 010205 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (515)
Q Consensus 154 ~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP 190 (515)
..+.|.|-...=|.+||++|+.+++|.++....+..+
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~ 87 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKE 87 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCC
Confidence 3445666677789999999999999888777665553
No 111
>PF06299 DUF1045: Protein of unknown function (DUF1045); InterPro: IPR009389 This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
Probab=29.80 E-value=1.4e+02 Score=28.38 Aligned_cols=78 Identities=17% Similarity=0.176 Sum_probs=43.6
Q ss_pred ccccCchhHHHHHHHHHHHHHHHC---------------Ccccccc-----C-----CCCcccccEEeeeecccccccCC
Q 010205 404 VEEIGDGDRLLHACQVIIDAFNEA---------------GLVFHRD-----Y-----NKKLKQLHATLMNIRHKKRRKGT 458 (515)
Q Consensus 404 V~~~~~~~~L~~L~~~L~~~f~~~---------------Gl~~e~d-----~-----~r~fk~PHiTLar~r~~~~~~g~ 458 (515)
+.+.+....|+.|+..+...|-.. |+...++ + -..|. .||||-.--.....
T Consensus 47 Lvp~~~~~~L~~LAa~cV~~~d~fRAPls~aelaRR~~~~Ls~~Q~~~L~rWGYPYV~deFR-FHmTLTg~l~~~~~--- 122 (160)
T PF06299_consen 47 LVPAGPCPALQALAAACVRAFDPFRAPLSEAELARRRPAGLSPRQRANLERWGYPYVMDEFR-FHMTLTGRLDPAER--- 122 (160)
T ss_pred EeeCCCCHHHHHHHHHHHHhhhhccCCCChHHHhhcCcccCCHHHHHHHHHhCCCceeCcCE-eeEEeCCCCCHHHH---
Confidence 334345689999999999888642 2222110 0 13699 99999853211100
Q ss_pred CccccccHHHHHHH-hCCCccccEEecEEEEEe
Q 010205 459 RRVDYFDARDIFKQ-FGSKEWGEYLIKEAHLSQ 490 (515)
Q Consensus 459 ~~~~~fda~~il~~-~~d~~fG~~~V~~I~Ls~ 490 (515)
. .+...++. |....-..+.|+.|.|+.
T Consensus 123 -~----~~~~~l~~~f~~~l~~p~~id~laLf~ 150 (160)
T PF06299_consen 123 -A----RVEAALEAHFAPLLPEPLRIDSLALFG 150 (160)
T ss_pred -H----HHHHHHHHHHHhhcCCCeeecceEEEe
Confidence 1 11233333 444434678899999964
No 112
>PRK00089 era GTPase Era; Reviewed
Probab=29.70 E-value=33 Score=34.68 Aligned_cols=36 Identities=33% Similarity=0.419 Sum_probs=24.8
Q ss_pred eEEEEecccccc-ccccCCCchhHHH--------HHHHhCcEEEc
Q 010205 154 HSLSVEVGASVI-RFIKGKEGSTQKK--------FEKEMGVKIIL 189 (515)
Q Consensus 154 ~~~~v~Ip~~~~-~~IIGk~G~t~k~--------iE~eT~~~I~i 189 (515)
....|.|.++-+ +.|||++|+++|+ ||+-++++|.+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 345566665444 6789999999987 55556666655
No 113
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=28.24 E-value=39 Score=37.84 Aligned_cols=36 Identities=25% Similarity=0.231 Sum_probs=30.3
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010205 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (515)
Q Consensus 156 ~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 191 (515)
-+|-|-.+.=|.+|||+|++.++|-++||-+-.|=+
T Consensus 101 GEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 101 GEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred ceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 466777778899999999999999999998866633
No 114
>COG5255 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.61 E-value=1e+02 Score=30.72 Aligned_cols=34 Identities=18% Similarity=0.270 Sum_probs=24.0
Q ss_pred CCCceEEeeeccc-CChhhHHHHHHHHHHhHHHhh
Q 010205 339 PKTFHLTVLMLKL-WNKDRVNAATNVLKSISSKVM 372 (515)
Q Consensus 339 p~~LHLTL~fLgL-~~eeei~~a~~aL~~i~~~i~ 372 (515)
.-.|||||++|.- .++++...-..+|+++.+.+.
T Consensus 176 aY~FHITlgYl~~wltpee~a~~q~~l~e~~e~la 210 (239)
T COG5255 176 AYQFHITLGYLRIWLTPEEEAEWQAVLDELLEILA 210 (239)
T ss_pred ceEEEEEeeeEeeecChhhhHHHHHHHHHHHHHHH
Confidence 3579999999986 456666666677777755444
No 115
>TIGR00090 iojap_ybeB iojap-like ribosome-associated protein. This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown.
Probab=27.02 E-value=2.5e+02 Score=24.26 Aligned_cols=46 Identities=13% Similarity=0.203 Sum_probs=33.5
Q ss_pred CCeEEEecccccCCCCCCCceEEEEeccccCchhHHHHHHHHHHHHHHHCCccc
Q 010205 378 RPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 431 (515)
Q Consensus 378 ~pf~l~lkGLg~F~~dp~~~rVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~ 431 (515)
...-+.+++...+-+ |+-+....+...++.+++.|.+.+.+.|+.+
T Consensus 16 dI~vldv~~~~~~~d--------y~VI~Tg~S~rh~~aia~~v~~~~k~~~~~~ 61 (99)
T TIGR00090 16 DIVVLDVRGKSSIAD--------YFVIASGTSSRHVKAIADNVEEELKEAGLKP 61 (99)
T ss_pred CEEEEECCCCCcccC--------EEEEEEeCCHHHHHHHHHHHHHHHHHcCCCc
Confidence 455677788877765 4444433456889999999999999887754
No 116
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=25.67 E-value=2.4e+02 Score=25.86 Aligned_cols=35 Identities=17% Similarity=0.461 Sum_probs=27.3
Q ss_pred CCCCceEEEEeccccCchhHHHHHHHHHHHHHHHCCcc
Q 010205 393 SKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLV 430 (515)
Q Consensus 393 dp~~~rVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~ 430 (515)
+|++.|++|+...+ .+++.+..+...+.+.+.|=.
T Consensus 93 e~eRv~~~wiSa~E---~ekf~e~~~efv~~i~~lGpn 127 (132)
T COG1908 93 EPERVRVLWISAAE---GEKFAETINEFVERIKELGPN 127 (132)
T ss_pred CcceEEEEEEehhh---HHHHHHHHHHHHHHHHHhCCC
Confidence 47899999999976 477877777777777777743
No 117
>PF08302 tRNA_lig_CPD: Fungal tRNA ligase phosphodiesterase domain; InterPro: IPR015965 This entry represents a phosphodiesterase domain found in fungal tRNA ligases []. Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation
Probab=25.66 E-value=3.9e+02 Score=27.22 Aligned_cols=61 Identities=16% Similarity=0.104 Sum_probs=31.7
Q ss_pred CCceEEeeecccCChhhHHHHHHHHHH-hHHHhhhhc--------CCCCeEEEecccccCCCCCCCceEEEEeccc
Q 010205 340 KTFHLTVLMLKLWNKDRVNAATNVLKS-ISSKVMDAL--------DNRPLFIRLKGLDLMRGSKDKARILYAPVEE 406 (515)
Q Consensus 340 ~~LHLTL~fLgL~~eeei~~a~~aL~~-i~~~i~~iL--------~~~pf~l~lkGLg~F~~dp~~~rVLyagV~~ 406 (515)
..||+||.-..-..+.......+.+.. ......... ....+.++|.-|= +.+ ||+-+.|+-
T Consensus 114 ~~FHVTL~H~as~k~~~~k~lW~~y~~~~~~~~~~~~~~~~~~~~~~~~~~v~L~rlv-wd~-----rimai~V~~ 183 (257)
T PF08302_consen 114 PEFHVTLIHRASSKEQPAKELWKRYTKLYKSALKKNPKQEPTQTPTLGSCDVRLERLV-WDD-----RIMAIVVRI 183 (257)
T ss_pred CCCeEEEEecccCCcCcchHHHHHHHHHHHhhcccccccccccccccceEEEEEEEEE-ECC-----cEEEEEEEc
Confidence 568999998766544221112221111 111111110 0135788888886 776 887777653
No 118
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=25.27 E-value=1.2e+02 Score=30.14 Aligned_cols=74 Identities=15% Similarity=0.133 Sum_probs=47.4
Q ss_pred CCccCCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHh
Q 010205 146 EPVPSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEA 222 (515)
Q Consensus 146 ~~~~~~~~~~~~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~e~ 222 (515)
++..+...-.+.+.|..+-.+.|||+.|.|+..||-=++.-++- ..+....|++.-. .=.++=.+.+..+...+
T Consensus 83 ~i~v~~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~-~~g~~~~v~ldv~--~yRerR~e~L~~LA~~~ 156 (208)
T COG1847 83 TITVSEEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK-IGGKFKRVTLDVG--DYRERRKETLIKLAERA 156 (208)
T ss_pred EEEEeecCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh-hcCcceEEEEEhh--hHHHHHHHHHHHHHHHH
Confidence 34444456677888888889999999999999999998877765 2222334444321 23334444455554443
No 119
>COG1159 Era GTPase [General function prediction only]
Probab=23.49 E-value=39 Score=35.28 Aligned_cols=27 Identities=26% Similarity=0.308 Sum_probs=20.1
Q ss_pred CeEEEEecccc-ccccccCCCchhHHHH
Q 010205 153 RHSLSVEVGAS-VIRFIKGKEGSTQKKF 179 (515)
Q Consensus 153 ~~~~~v~Ip~~-~~~~IIGk~G~t~k~i 179 (515)
.....+.|+++ .-+.||||+|+++|+|
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~I 255 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKI 255 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHH
Confidence 33455677765 4467899999999987
No 120
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=23.15 E-value=91 Score=25.78 Aligned_cols=35 Identities=20% Similarity=0.341 Sum_probs=20.6
Q ss_pred ChhhHHHHHHHHHHhHHHhhhhcCCCCeEEEecccccCC
Q 010205 353 NKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMR 391 (515)
Q Consensus 353 ~eeei~~a~~aL~~i~~~i~~iL~~~pf~l~lkGLg~F~ 391 (515)
+..++..+.++| ...+.+.|... -.+.|.|+|.|.
T Consensus 17 ~~~~v~~vl~~l---~~~i~~~L~~g-~~V~i~g~G~F~ 51 (90)
T smart00411 17 SKKDAKAAVDAF---LEIITEALKKG-EKVELRGFGTFE 51 (90)
T ss_pred CHHHHHHHHHHH---HHHHHHHHhCC-CeEEEeCcEEEE
Confidence 455555554444 33455544322 278899999995
No 121
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=22.80 E-value=1e+02 Score=25.20 Aligned_cols=35 Identities=20% Similarity=0.311 Sum_probs=20.3
Q ss_pred ChhhHHHHHHHHHHhHHHhhhhcCCCCeEEEecccccCC
Q 010205 353 NKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMR 391 (515)
Q Consensus 353 ~eeei~~a~~aL~~i~~~i~~iL~~~pf~l~lkGLg~F~ 391 (515)
+..++..+ |+.+...+.+.|... -.+.|.|+|.|.
T Consensus 16 ~~~~v~~v---l~~~~~~i~~~L~~g-~~V~l~~~G~F~ 50 (87)
T cd00591 16 SKKDAEAA---VDAFLDVITEALAKG-EKVELPGFGTFE 50 (87)
T ss_pred CHHHHHHH---HHHHHHHHHHHHhCC-CeEEEeCCEEEE
Confidence 34454444 444444455444322 288999999995
No 122
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=21.56 E-value=37 Score=41.40 Aligned_cols=64 Identities=20% Similarity=0.106 Sum_probs=51.5
Q ss_pred EEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHHHHHHHH
Q 010205 157 SVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIAE 221 (515)
Q Consensus 157 ~v~Ip~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~----~~~I~I~G~s~~~v~~A~~~I~~iv~e 221 (515)
.+.||.-....+||+||.+++.+..-||+-|.|-+-.. ++.+.+.|. .+.+.-|.--|...+.+
T Consensus 1343 k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~-p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1343 KGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGR-PPSQRVATSPIGLPIID 1410 (2131)
T ss_pred ccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCC-Chhhhhhhccccceeec
Confidence 45688888999999999999999999999999987332 357788885 47788888777766654
No 123
>PF08975 2H-phosphodiest: Domain of unknown function (DUF1868); InterPro: IPR015069 This family consist of hypothetical bacterial proteins. ; PDB: 2FSQ_A.
Probab=21.19 E-value=39 Score=30.54 Aligned_cols=47 Identities=17% Similarity=0.224 Sum_probs=26.2
Q ss_pred CceEEEEccC-CcchhHHHhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeec
Q 010205 288 EHKVAVELNI-GDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLML 349 (515)
Q Consensus 288 n~FVAv~l~~-~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gl~~~~fv~p~~LHLTL~fL 349 (515)
|.||+ .|.. -+...++..+|+.+. ..+ ..+.=.|.||+.+|+|+.=.
T Consensus 14 NTvIc-hl~~~s~~~~al~~i~~~l~---------~~~-----~~~k~a~lP~sS~HMTVf~G 61 (118)
T PF08975_consen 14 NTVIC-HLPQDSPFYAALLAIQQRLR---------ESP-----FADKLAFLPPSSYHMTVFEG 61 (118)
T ss_dssp EEEEE-EB-TTSHHHHHHHHHHHHHH---------TSG-----GGGGEEE--GGG-EEEEEEE
T ss_pred CeEEe-ecCCCChHHHHHHHHHHHHH---------hCc-----cccceEecCcchhhhhhhcc
Confidence 44555 3333 355678888888774 111 12334799999999999754
Done!