Query 010498
Match_columns 509
No_of_seqs 323 out of 937
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 01:13:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010498.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010498hhsearch_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 8.1E-49 1.7E-53 392.1 16.1 338 55-502 2-345 (345)
2 PLN00108 unknown protein; Prov 100.0 7.9E-45 1.7E-49 358.4 23.0 224 222-504 33-256 (257)
3 PF10469 AKAP7_NLS: AKAP7 2'5' 100.0 3.6E-41 7.7E-46 326.4 21.6 207 225-502 1-209 (209)
4 COG1514 LigT 2'-5' RNA ligase 100.0 3.5E-28 7.6E-33 231.2 18.9 178 283-504 2-180 (180)
5 PRK15124 2'-5' RNA ligase; Pro 99.9 2.4E-26 5.1E-31 217.6 17.3 171 283-504 6-176 (176)
6 TIGR02258 2_5_ligase 2'-5' RNA 99.9 9.6E-26 2.1E-30 212.6 18.3 178 283-502 2-179 (179)
7 PRK13679 hypothetical protein; 99.8 2.5E-17 5.4E-22 154.8 16.0 167 283-503 2-168 (168)
8 PHA02574 57B hypothetical prot 99.7 2.9E-17 6.3E-22 151.7 9.7 109 283-442 10-118 (149)
9 PF13563 2_5_RNA_ligase2: 2'-5 99.3 5.5E-12 1.2E-16 114.7 10.3 130 331-486 20-150 (153)
10 cd02394 vigilin_like_KH K homo 99.2 1.2E-11 2.5E-16 97.4 6.1 60 151-211 2-62 (62)
11 cd02393 PNPase_KH Polynucleoti 99.2 1.6E-11 3.4E-16 97.1 6.4 59 150-211 3-61 (61)
12 PF00013 KH_1: KH domain syndr 99.2 2E-11 4.3E-16 95.5 3.9 60 150-210 1-60 (60)
13 PF02834 LigT_PEase: LigT like 99.1 7.9E-11 1.7E-15 98.4 2.9 82 294-396 6-87 (87)
14 PF05213 Corona_NS2A: Coronavi 99.0 5.7E-09 1.2E-13 100.3 11.5 167 280-500 4-177 (248)
15 cd00105 KH-I K homology RNA-bi 98.9 1.5E-09 3.3E-14 85.1 5.9 59 151-210 2-63 (64)
16 cd02396 PCBP_like_KH K homolog 98.8 7.8E-09 1.7E-13 82.5 6.1 59 151-210 2-64 (65)
17 smart00322 KH K homology RNA-b 98.7 3.4E-08 7.4E-13 76.9 7.6 66 148-214 2-68 (69)
18 cd02395 SF1_like-KH Splicing f 98.7 1.9E-08 4.2E-13 90.1 6.8 59 158-216 15-95 (120)
19 PF13014 KH_3: KH domain 98.7 1.1E-08 2.3E-13 75.2 4.0 39 159-197 1-43 (43)
20 KOG1676 K-homology type RNA bi 98.6 1.2E-07 2.5E-12 102.9 8.1 107 146-253 227-346 (600)
21 KOG0119 Splicing factor 1/bran 98.4 6.2E-07 1.3E-11 95.4 6.8 72 148-219 137-233 (554)
22 PRK13763 putative RNA-processi 98.3 8.9E-07 1.9E-11 84.7 6.8 65 149-215 3-70 (180)
23 TIGR03665 arCOG04150 arCOG0415 98.3 7.8E-07 1.7E-11 84.5 5.3 61 153-215 2-64 (172)
24 PRK13763 putative RNA-processi 98.0 7.8E-06 1.7E-10 78.2 5.8 53 159-216 105-157 (180)
25 COG5176 MSL5 Splicing factor ( 97.9 9.9E-06 2.2E-10 78.0 5.0 76 141-216 140-221 (269)
26 TIGR03665 arCOG04150 arCOG0415 97.9 1.3E-05 2.7E-10 76.3 5.5 54 158-216 98-151 (172)
27 KOG2208 Vigilin [Lipid transpo 97.9 1.9E-05 4E-10 90.5 7.3 104 147-254 345-449 (753)
28 KOG2191 RNA-binding protein NO 97.9 8.8E-05 1.9E-09 75.9 10.9 107 146-253 36-160 (402)
29 TIGR02696 pppGpp_PNP guanosine 97.8 2.5E-05 5.5E-10 88.2 6.9 65 149-216 578-642 (719)
30 KOG2193 IGF-II mRNA-binding pr 97.8 1.6E-05 3.5E-10 83.3 4.3 104 146-253 196-308 (584)
31 TIGR03591 polynuc_phos polyrib 97.7 4.5E-05 9.8E-10 86.7 6.1 65 149-216 551-615 (684)
32 KOG1588 RNA-binding protein Sa 97.6 0.00017 3.6E-09 72.2 7.1 70 148-219 91-187 (259)
33 KOG1676 K-homology type RNA bi 97.5 0.00011 2.5E-09 80.2 6.0 112 145-258 50-171 (600)
34 KOG2193 IGF-II mRNA-binding pr 97.5 0.00012 2.7E-09 76.9 4.7 61 156-217 287-353 (584)
35 PRK04163 exosome complex RNA-b 97.3 0.00047 1E-08 68.7 6.6 64 150-216 146-209 (235)
36 COG1094 Predicted RNA-binding 97.3 0.00057 1.2E-08 65.8 6.4 67 147-215 6-76 (194)
37 KOG2113 Predicted RNA binding 97.2 0.0004 8.7E-09 70.7 5.1 106 146-252 23-142 (394)
38 KOG2190 PolyC-binding proteins 97.2 0.00094 2E-08 73.1 8.3 67 149-216 138-208 (485)
39 KOG2191 RNA-binding protein NO 97.2 0.00063 1.4E-08 69.8 6.3 66 150-216 133-204 (402)
40 PLN00207 polyribonucleotide nu 97.2 0.00043 9.2E-09 80.1 5.5 65 149-216 685-750 (891)
41 COG1185 Pnp Polyribonucleotide 97.0 0.00097 2.1E-08 74.5 6.3 69 148-219 551-619 (692)
42 KOG2192 PolyC-binding hnRNP-K 97.0 0.0015 3.2E-08 65.4 6.7 67 149-216 315-384 (390)
43 PRK11824 polynucleotide phosph 96.9 0.0009 2E-08 76.4 4.5 64 150-216 555-618 (693)
44 PF02834 LigT_PEase: LigT like 96.7 0.0017 3.7E-08 54.0 3.5 76 405-494 8-87 (87)
45 TIGR03319 YmdA_YtgF conserved 96.5 0.0048 1E-07 68.2 7.0 69 146-216 201-270 (514)
46 PF09749 HVSL: Uncharacterised 96.5 0.025 5.5E-07 56.4 11.2 104 333-445 86-191 (239)
47 PRK00106 hypothetical protein; 96.4 0.0061 1.3E-07 67.5 7.1 69 146-216 222-291 (535)
48 KOG0336 ATP-dependent RNA heli 96.4 0.0023 4.9E-08 67.9 3.5 69 147-216 45-113 (629)
49 PRK12704 phosphodiesterase; Pr 96.4 0.0058 1.3E-07 67.7 6.6 68 147-216 208-276 (520)
50 COG1094 Predicted RNA-binding 96.1 0.0089 1.9E-07 57.7 5.3 54 158-216 111-164 (194)
51 PF07823 CPDase: Cyclic phosph 95.8 0.074 1.6E-06 51.6 10.4 137 338-502 40-196 (196)
52 COG1097 RRP4 RNA-binding prote 95.3 0.031 6.7E-07 55.7 5.6 64 150-216 147-210 (239)
53 cd02134 NusA_KH NusA_K homolog 95.1 0.024 5.2E-07 44.7 3.4 37 148-184 24-60 (61)
54 PRK12705 hypothetical protein; 95.1 0.027 5.8E-07 62.1 5.0 68 147-216 196-264 (508)
55 KOG2279 Kinase anchor protein 94.9 0.019 4E-07 62.8 3.1 103 145-252 64-167 (608)
56 KOG1067 Predicted RNA-binding 94.2 0.04 8.6E-07 60.5 3.7 63 150-216 598-660 (760)
57 KOG2192 PolyC-binding hnRNP-K 93.9 0.16 3.4E-06 51.3 6.9 70 146-216 45-115 (390)
58 KOG2190 PolyC-binding proteins 93.3 0.15 3.3E-06 56.1 6.3 102 151-253 45-166 (485)
59 KOG2814 Transcription coactiva 93.0 0.017 3.6E-07 59.7 -1.5 150 335-498 128-280 (345)
60 TIGR03223 Phn_opern_protn puta 91.8 3.4 7.4E-05 41.3 12.9 143 335-504 56-228 (228)
61 KOG2208 Vigilin [Lipid transpo 90.8 0.17 3.6E-06 58.7 3.0 42 145-186 705-746 (753)
62 PF14611 SLS: Mitochondrial in 87.4 2.5 5.4E-05 41.0 8.1 73 151-233 28-100 (210)
63 COG1855 ATPase (PilT family) [ 86.2 0.51 1.1E-05 51.3 2.7 43 147-189 484-526 (604)
64 KOG2113 Predicted RNA binding 85.8 0.68 1.5E-05 47.9 3.2 69 146-214 112-181 (394)
65 KOG3273 Predicted RNA-binding 84.6 0.7 1.5E-05 45.0 2.5 54 158-216 178-231 (252)
66 cd02409 KH-II KH-II (K homolo 84.2 1.2 2.7E-05 34.3 3.4 35 148-182 24-58 (68)
67 PRK02821 hypothetical protein; 83.9 0.85 1.8E-05 38.0 2.4 33 147-179 29-61 (77)
68 PF13083 KH_4: KH domain; PDB: 82.9 0.66 1.4E-05 37.5 1.4 34 146-179 26-59 (73)
69 PRK08406 transcription elongat 82.5 1.2 2.7E-05 41.0 3.2 38 148-185 98-135 (140)
70 PRK00468 hypothetical protein; 82.4 1.3 2.7E-05 36.8 2.9 30 147-176 28-57 (75)
71 PRK13764 ATPase; Provisional 82.0 1 2.2E-05 51.0 2.9 41 147-187 479-519 (602)
72 PF10469 AKAP7_NLS: AKAP7 2'5' 81.9 0.73 1.6E-05 44.7 1.6 25 282-306 1-25 (209)
73 COG1837 Predicted RNA-binding 81.8 1.4 3E-05 36.7 2.9 31 146-176 27-57 (76)
74 COG5166 Uncharacterized conser 79.5 2.2 4.8E-05 46.9 4.3 69 148-216 448-524 (657)
75 PHA02977 hypothetical protein; 78.2 11 0.00024 35.1 7.8 94 338-445 71-174 (201)
76 PRK01064 hypothetical protein; 77.8 2 4.4E-05 35.8 2.7 31 147-177 28-58 (78)
77 PF07650 KH_2: KH domain syndr 76.9 1.4 3.1E-05 35.9 1.5 36 148-183 24-59 (78)
78 TIGR01952 nusA_arch NusA famil 74.6 2.7 5.9E-05 38.9 2.9 38 148-185 99-136 (141)
79 PRK08406 transcription elongat 73.9 3.3 7.2E-05 38.2 3.3 36 150-185 33-68 (140)
80 PF13184 KH_5: NusA-like KH do 72.1 3.6 7.8E-05 33.4 2.7 25 160-184 19-44 (69)
81 cd02414 jag_KH jag_K homology 71.5 3.3 7.2E-05 34.0 2.5 35 150-184 25-59 (77)
82 PLN00108 unknown protein; Prov 70.8 2.3 5.1E-05 43.1 1.7 29 279-307 33-62 (257)
83 KOG3102 Uncharacterized conser 69.1 18 0.00039 35.9 7.2 101 332-443 117-218 (269)
84 KOG2874 rRNA processing protei 68.9 8.8 0.00019 39.4 5.2 54 157-219 157-210 (356)
85 PF05213 Corona_NS2A: Coronavi 65.0 8.6 0.00019 38.1 4.2 62 225-305 6-68 (248)
86 cd02413 40S_S3_KH K homology R 64.2 4.4 9.6E-05 33.9 1.8 37 150-186 31-67 (81)
87 TIGR01953 NusA transcription t 62.8 7.4 0.00016 41.2 3.6 39 148-186 300-338 (341)
88 PRK12328 nusA transcription el 60.1 9.2 0.0002 40.9 3.7 42 148-189 307-348 (374)
89 KOG2279 Kinase anchor protein 59.8 5 0.00011 44.5 1.7 71 141-212 132-205 (608)
90 TIGR01952 nusA_arch NusA famil 58.0 11 0.00025 34.8 3.5 36 150-185 34-69 (141)
91 COG0195 NusA Transcription elo 57.5 11 0.00024 36.7 3.4 37 150-186 143-179 (190)
92 PRK06418 transcription elongat 51.7 15 0.00033 35.0 3.3 33 151-184 63-95 (166)
93 PRK12327 nusA transcription el 51.5 15 0.00032 39.3 3.5 40 148-187 302-341 (362)
94 PRK09202 nusA transcription el 50.2 15 0.00032 40.7 3.4 39 148-186 301-339 (470)
95 cd02412 30S_S3_KH K homology R 49.5 13 0.00029 32.6 2.4 32 151-182 63-94 (109)
96 PF09749 HVSL: Uncharacterised 49.4 28 0.00061 34.6 5.0 67 283-363 141-209 (239)
97 COG5255 Uncharacterized protei 47.9 45 0.00096 33.0 5.8 34 412-447 156-190 (239)
98 PRK12329 nusA transcription el 41.5 26 0.00055 38.4 3.5 39 148-186 334-372 (449)
99 PF00352 TBP: Transcription fa 41.4 59 0.0013 27.1 5.0 35 179-216 49-84 (86)
100 PF07823 CPDase: Cyclic phosph 40.4 30 0.00064 33.6 3.5 41 394-442 4-45 (196)
101 COG1702 PhoH Phosphate starvat 38.3 73 0.0016 33.9 6.2 55 157-216 23-79 (348)
102 PF08302 tRNA_lig_CPD: Fungal 36.7 2E+02 0.0044 29.2 8.9 88 335-443 114-210 (257)
103 PF06299 DUF1045: Protein of u 35.2 1.4E+02 0.0029 28.5 6.9 79 399-485 47-151 (160)
104 COG0195 NusA Transcription elo 34.4 36 0.00079 33.1 3.0 35 150-184 77-111 (190)
105 cd02411 archeal_30S_S3_KH K ho 31.7 39 0.00085 28.2 2.4 32 148-181 39-70 (85)
106 TIGR00436 era GTP-binding prot 31.6 29 0.00063 34.9 1.9 29 149-177 221-250 (270)
107 cd02410 archeal_CPSF_KH The ar 31.0 41 0.00089 31.4 2.6 33 152-184 79-111 (145)
108 COG0799 Uncharacterized homolo 29.9 2.4E+02 0.0052 25.4 7.2 62 350-426 5-66 (115)
109 PRK15494 era GTPase Era; Provi 29.7 32 0.00069 36.1 1.9 36 149-184 273-317 (339)
110 PRK10334 mechanosensitive chan 29.7 2.1E+02 0.0046 29.4 7.9 83 336-426 185-268 (286)
111 PRK00089 era GTPase Era; Revie 29.2 34 0.00074 34.5 2.0 36 149-184 226-270 (292)
112 PF07485 DUF1529: Domain of Un 27.7 2.6E+02 0.0056 25.4 7.1 55 349-420 67-121 (123)
113 PRK11538 ribosome-associated p 27.5 2.8E+02 0.0061 24.3 7.2 61 351-426 6-66 (105)
114 PF08975 2H-phosphodiest: Doma 27.5 28 0.0006 31.4 0.8 47 283-343 14-60 (118)
115 COG0092 RpsC Ribosomal protein 26.6 34 0.00075 34.3 1.4 37 149-185 51-87 (233)
116 COG1782 Predicted metal-depend 24.8 49 0.0011 37.0 2.3 34 151-184 101-134 (637)
117 COG1847 Jag Predicted RNA-bind 22.7 1.4E+02 0.003 29.6 4.8 75 141-218 83-157 (208)
118 COG1159 Era GTPase [General fu 22.6 41 0.00089 35.0 1.1 26 149-174 229-255 (298)
119 PF10105 DUF2344: Uncharacteri 22.0 1E+02 0.0022 29.8 3.6 30 409-440 18-47 (187)
120 smart00411 BHL bacterial (prok 20.8 1E+02 0.0022 25.5 3.0 35 348-386 17-51 (90)
121 COG1908 FrhD Coenzyme F420-red 20.2 3.6E+02 0.0078 24.7 6.4 36 388-426 93-128 (132)
122 KOG4369 RTK signaling protein 20.0 41 0.00088 41.0 0.5 64 152-216 1343-1410(2131)
No 1
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=100.00 E-value=8.1e-49 Score=392.14 Aligned_cols=338 Identities=36% Similarity=0.555 Sum_probs=289.5
Q ss_pred cccccccccCceeeeccccccccccccccccCCCCCceEEe-eeccCCcccccccceeeeecccccccccCCcccccccc
Q 010498 55 YGDKKQKIINPVWRPVSTQASVNEESLVKDVSEDGSQIQEM-HCSTSSNVSDAQLGVEVAEAVNEGTDLTLSSSVSLDDI 133 (509)
Q Consensus 55 ~~~~~~k~~~~~wrp~~t~a~~~~~~~~~~~~~~~~~~~e~-~~~~s~~~~~~~~~~~~~~~~~~~~~~~~ss~~~~~~~ 133 (509)
+..++++..|.+|+|++|+.++.. .+++...|++ .|+++...+.+ +
T Consensus 2 ~~~~~~~~~n~~~~~~~~~t~~~~-------~~~~~e~~~~~~c~d~p~~~~d--------------------------v 48 (345)
T KOG2814|consen 2 YRKTRYNLVNDVSFDLNTDTTFAD-------MSEEFEAQTSAECVDMPGDTVD--------------------------V 48 (345)
T ss_pred cchhhhhhhhhcccCccccccccc-------CchhhHHHhHhhcccCCCChHH--------------------------h
Confidence 456788999999999999988763 3345556666 66666533321 1
Q ss_pred cccccCCCCccCCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHH
Q 010498 134 KDETLEGEPVPSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQA 212 (509)
Q Consensus 134 ~~~~~~~~~~~~~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~~ 212 (509)
+.- .-.++|+.++.|+++|+++|||++|.|+++||+||+|+|.+|++++ .+.|+|+|.++.+|.+|.+||..
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 EDD-------AGAKDFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAK 121 (345)
T ss_pred hhc-------cccccchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHH
Confidence 111 1123889999999999999999999999999999999999999995 78999999999999999999999
Q ss_pred HHHHhhhCCCCCceEEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCccccchHHhhhcccCCceEEEEccC
Q 010498 213 IIAEAVESPSLDYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNI 292 (509)
Q Consensus 213 i~~~~~~~~k~~~tHFIsIPl~~hp~I~~~~~~f~~~Il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rp~~FVAv~l~~ 292 (509)
++++.++ +++.|||+.+|++ ...+.++|..|+...+..
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 578999999987322211
Q ss_pred CcchhHHHHhhccCcccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCC
Q 010498 293 GDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDN 372 (509)
Q Consensus 293 ~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gld~~~fv~p~~LHLTL~fLgl~dee~v~~a~~aL~~i~~~i~~~L~~ 372 (509)
++ +-+.|++.+.|++|..+||||+|+.+++++++++|+++|+.+.+++....+.
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 1256888999999999999999999999999999999999998888888888
Q ss_pred CCeEEEEceeccCCCCCCCceEEEEeeeccCChhHHHHHH-HHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccC
Q 010498 373 RPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHAC-QVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKG 451 (509)
Q Consensus 373 ~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~L~-~~L~~~f~~~Gl~~e~~~~r~fkPHiTLaR~k~~~~~~~ 451 (509)
.|+.+.++|+.+|+++|..++||||+|++.+....|+..+ +.|..+|...|+... +.++.++|+|+||++|++.++.
T Consensus 214 kp~~i~lkG~~~mnddP~~~kVLYAkv~~~~~e~~l~~~~~~~i~~~f~~~~li~k--~~~~~kLH~TvmNsryrk~~~~ 291 (345)
T KOG2814|consen 214 KPLFIDLKGLDKMNDDPSLTKVLYAKVEPDDYEKFLQHRCGERILERFVASGLIKK--ESSSLKLHCTVMNSRYRKNGGE 291 (345)
T ss_pred CceeeeccchhhhcCCHhHheeeeeeccCcchHHHHHHHHHHHHHHHHHHhcchhc--cccccEEEEEEehhhhhhcCCC
Confidence 9999999999999999999999999999877778899988 999999999999885 4789999999999999876431
Q ss_pred ---CCccccccHHHHHHHhCCCccccEEecEEEEEeeecCCCCCceeEEEEEeC
Q 010498 452 ---TRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPF 502 (509)
Q Consensus 452 ---~~~~~~fda~~il~~~~d~~fG~~~V~eI~Ls~l~~~~~~g~Y~~i~si~L 502 (509)
.+....||++++++.|+++.||++...++|||.+...+.+|||.+++++||
T Consensus 292 ~g~~K~~~~Fdar~ilk~fg~f~fg~~~~~eih~~~~~~~d~ng~y~~~gsi~f 345 (345)
T KOG2814|consen 292 PGLVKESESFDAREILKAFGQFLFGELKLQEIHLSVRFAADQNGNYNECGSIPF 345 (345)
T ss_pred cchhhHhhhccHHHHHHHHhhHhHhhcccceeeeeeeeccccccchhhhcCCCC
Confidence 245678999999999999999999999999999998889999999999986
No 2
>PLN00108 unknown protein; Provisional
Probab=100.00 E-value=7.9e-45 Score=358.40 Aligned_cols=224 Identities=56% Similarity=0.968 Sum_probs=198.0
Q ss_pred CCCceEEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCccccchHHhhhcccCCceEEEEccCCcchhHHHH
Q 010498 222 SLDYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKV 301 (509)
Q Consensus 222 k~~~tHFIsIPl~~hp~I~~~~~~f~~~Il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rp~~FVAv~l~~~~~~~~v~~ 301 (509)
|.++|||||||+.++|.|.+++..|++.|++..+. .|.-|
T Consensus 33 ~~~~THFlavPL~~~p~i~~~~~~Fk~~Vl~~~~~------------------------~~~~f---------------- 72 (257)
T PLN00108 33 REVFTHFVSLPLAIYPDLKKNIEAFQNSVLGNNDK------------------------DPLKF---------------- 72 (257)
T ss_pred CCCCCeEEEEEcCCCHHHHHHHHHHHHHHHhcccc------------------------ccccc----------------
Confidence 56799999999966899999999999999975210 01000
Q ss_pred hhccCcccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEEce
Q 010498 302 DRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKG 381 (509)
Q Consensus 302 ~q~~i~~~~~~~~~~r~~~~~~~Gld~~~fv~p~~LHLTL~fLgl~dee~v~~a~~aL~~i~~~i~~~L~~~pf~L~l~G 381 (509)
| +.++++||++++|++|.+|||||+||.|.+++++++|.++|+++...+.++++.+|+.|+|+|
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 013378999999999999999999999999999999999999999889999989999999999
Q ss_pred eccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHH
Q 010498 382 LDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDAR 461 (509)
Q Consensus 382 Lg~F~~dp~~pRVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~~~~r~fkPHiTLaR~k~~~~~~~~~~~~~fda~ 461 (509)
|++||+||..++||||+|++.+..++|+++|+.|.+.|.++||...+ ..++++||+||||+++++.+. +++.+|||+
T Consensus 137 L~~Mnddps~~~VLYA~Ve~~~~~~rLq~~ad~i~~~F~~aGL~~~d-~~~~vKLH~TlmNt~~rk~k~--~k~~sFDA~ 213 (257)
T PLN00108 137 LDCMNGSLDKTRVLYAPVEEVGHEGRLLNACHVIIDAFENAGFAGKD-AKSRLKLHATLMNASYRKDKS--KKMDTFDAR 213 (257)
T ss_pred ehhcCCCcccceEEEEeccccCchhHHHHHHHHHHHHHHHcCCcccc-cCcceeeEeEEechhhhhccc--CccccccHH
Confidence 99999999999999999998767789999999999999999998642 346899999999999876532 467789999
Q ss_pred HHHHHhCCCccccEEecEEEEEeeecCCCCCceeEEEEEeCCC
Q 010498 462 DIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 504 (509)
Q Consensus 462 ~il~~~~d~~fG~~~V~eI~Ls~l~~~~~~g~Y~~i~si~L~~ 504 (509)
+|+++|++++||++.|++||||+++.++.+|||++.++++|++
T Consensus 214 ~Il~~f~d~~FG~~~i~~vhls~r~s~~~dGyY~~~~sl~~~~ 256 (257)
T PLN00108 214 EIHKEFENKDWGTYLIREAHISQRYKYDPNGYFHCCASLPFPH 256 (257)
T ss_pred HHHHhccCcccceEEecEEEEEeecccCCCCCEEEEEEeecCC
Confidence 9999999999999999999999999988899999999999986
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=3.6e-41 Score=326.40 Aligned_cols=207 Identities=37% Similarity=0.626 Sum_probs=178.4
Q ss_pred ceEEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCccccchHHhhhcccCCceEEEEccCCcchhHHHHhhc
Q 010498 225 YSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKVDRT 304 (509)
Q Consensus 225 ~tHFIsIPl~~hp~I~~~~~~f~~~Il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rp~~FVAv~l~~~~~~~~v~~~q~ 304 (509)
||||||||++ +|.|+..+..|++.|+..
T Consensus 1 pthFl~ipl~-~~~i~~~~~~fq~~v~~~--------------------------------------------------- 28 (209)
T PF10469_consen 1 PTHFLCIPLN-SPEIQEKFKEFQNEVLSK--------------------------------------------------- 28 (209)
T ss_pred CCeEEEEECC-CHHHHHHHHHHHHHHHhh---------------------------------------------------
Confidence 5888888885 788888888888888743
Q ss_pred cCcccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCC-CCeEEEEceec
Q 010498 305 SIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDN-RPLFIRLKGLD 383 (509)
Q Consensus 305 ~i~~~~~~~~~~r~~~~~~~Gld~~~fv~p~~LHLTL~fLgl~dee~v~~a~~aL~~i~~~i~~~L~~-~pf~L~l~GLg 383 (509)
.+|+++++|++|++|||||+||++.+++++++|.++|+++.+.+.+.+.. +|+.|+|+||+
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 34667778999999999999999999999999999999999888877654 99999999999
Q ss_pred cCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHHHH
Q 010498 384 LMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDI 463 (509)
Q Consensus 384 ~F~~dp~~pRVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~~~~r~fkPHiTLaR~k~~~~~~~~~~~~~fda~~i 463 (509)
+|++||+++|||||+|.++++...|+++++.|.+.|.++||...++.+.+|+||+||||++++..... +...+||++++
T Consensus 91 ~f~~d~~~~~VLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~~~~~~~~H~Tl~n~~~~~~~~~-~~~~~~d~~~~ 169 (209)
T PF10469_consen 91 YFNDDPSKARVLYAKVSEDSNSERLQELANKLRERFQEAGLLVTDDRRFSFKPHITLMNTSYRKKKKR-RQGNKFDASEL 169 (209)
T ss_pred hhCCCCCcceEEEEcccccchHHHHHHHHHHHHHHHHHcCCccccccCCCcceEEEEEeccccccccc-cccCccccHHH
Confidence 99999999999999999866679999999999999999999985422224899999999998521111 11256899999
Q ss_pred HHHhCCCccccEEecEEEEEeeecCCC-CCceeEEEEEeC
Q 010498 464 FKQFGSKEWGEYLIKEAHLSQRFVYDE-SGFYHCCASIPF 502 (509)
Q Consensus 464 l~~~~d~~fG~~~V~eI~Ls~l~~~~~-~g~Y~~i~si~L 502 (509)
+++|.+++||.+.|++|+||+|+..++ +|||.++++|+|
T Consensus 170 ~~~~~~~~fG~~~v~~i~Lc~m~~~~~~dg~Y~~~~~i~l 209 (209)
T PF10469_consen 170 LEKYKDFDFGEQPVEEIQLCSMGSTKPSDGYYQCIASIPL 209 (209)
T ss_pred HHHcCCCccceEEECEEEEEeCCCCCCCCCeEEEEEEecC
Confidence 999999999999999999999976655 999999999987
No 4
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=3.5e-28 Score=231.24 Aligned_cols=178 Identities=19% Similarity=0.318 Sum_probs=153.7
Q ss_pred CceEEEEccCCcchhHHHHhhccCcccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHh
Q 010498 283 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 362 (509)
Q Consensus 283 ~~FVAv~l~~~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gld~~~fv~p~~LHLTL~fLgl~dee~v~~a~~aL~~i 362 (509)
-+|+||++ .+++.+++..+++.+. ..+ ..+|++++|+||||.|||+++++.++.+.++|.++
T Consensus 2 RlFiAl~~-p~~i~~~i~~~~~~~~---------------~~~--~~k~v~~en~HiTL~flGev~e~~~~~l~~~l~~i 63 (180)
T COG1514 2 RLFIALDP-PAEIAERLARIRARLK---------------GAR--AIKWVEPENLHITLKFLGEVDEDKADELIEALARI 63 (180)
T ss_pred eeEEEecC-CHHHHHHHHHHHHhcC---------------ccc--ccccccccCceEEEEccCCcCchHHHHHHHHHHHh
Confidence 47999999 5688999999998774 112 33799999999999999999999999999999998
Q ss_pred HHhhhhhcCCC-CeEEEEceeccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEee
Q 010498 363 SSKVMDALDNR-PLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLM 441 (509)
Q Consensus 363 ~~~i~~~L~~~-pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~~~~r~fkPHiTLa 441 (509)
. .+ ||.|+|+|+|+||+ +.+|||+|+++.+ .+.|.+|++.|+..+.++||..+ .++|.||+||+
T Consensus 64 ~--------~~~~f~i~l~g~g~F~~-~~~~rvi~~~v~~---~~~L~~L~~~l~~~~~~~g~~~~---~r~F~PHvTl~ 128 (180)
T COG1514 64 A--------APEPFPITLDGAGSFPN-PRRPRVIWVGVEE---TEELRALAEELERALARLGLRPE---ERPFVPHVTLA 128 (180)
T ss_pred h--------cCCceEEEEeeEcccCC-CCCCcEEEEcCCC---cHHHHHHHHHHHHHHHhcCCCCC---CCCcCCCEEEE
Confidence 5 24 99999999999998 9999999999985 47899999999999999999986 68999999999
Q ss_pred eecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeecCCCCCceeEEEEEeCCC
Q 010498 442 NIRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 504 (509)
Q Consensus 442 R~k~~~~~~~~~~~~~fda~~il~~~~d~~fG~~~V~eI~Ls~l~~~~~~g~Y~~i~si~L~~ 504 (509)
|.+. +. .+.+++..+.+..||++.|+++.|..+..+..+++|+++.+++|.+
T Consensus 129 r~k~-~~----------~~~~~~~~~~~~~~~~~~vd~~~L~~S~l~~~gp~Y~~~~~~~L~~ 180 (180)
T COG1514 129 RVKS-KD----------KLVEALGEFKNVEFGEMEVDRFSLYSSTLTPGGPIYETLKEFPLSG 180 (180)
T ss_pred eecc-cc----------hhhhhhhhhccccccceEeeEEEEEEEeeCCCCCEEEEEEEEecCC
Confidence 9875 11 1247788899999999999999996555545689999999999974
No 5
>PRK15124 2'-5' RNA ligase; Provisional
Probab=99.94 E-value=2.4e-26 Score=217.64 Aligned_cols=171 Identities=13% Similarity=0.150 Sum_probs=138.1
Q ss_pred CceEEEEccCCcchhHHHHhhccCcccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHh
Q 010498 283 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 362 (509)
Q Consensus 283 ~~FVAv~l~~~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gld~~~fv~p~~LHLTL~fLgl~dee~v~~a~~aL~~i 362 (509)
-+|+||++++ ++.+.+.++++.+. .. ....|++|+||||||.|||++++++++.+.++|.++
T Consensus 6 RlFiAl~~p~-~~~~~l~~~~~~~~--------------~~---~~~rwv~~~nlHiTL~FlG~v~~~~~~~l~~~l~~~ 67 (176)
T PRK15124 6 RLFFAIDLPD-EIRQQIIHWRATHF--------------PP---EAGRPVAAANLHLTLAFLGEVSAEKQQALSQLAGRI 67 (176)
T ss_pred EEEEEeCCCH-HHHHHHHHHHHHhc--------------cc---cCcccccccccEEEEEecCCCCHHHHHHHHHHHHhc
Confidence 5899999985 77888999887663 01 123799999999999999999999999998888876
Q ss_pred HHhhhhhcCCCCeEEEEceeccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeee
Q 010498 363 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 442 (509)
Q Consensus 363 ~~~i~~~L~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~~~~r~fkPHiTLaR 442 (509)
. .+||.|.+.|+|+||+ |||||+++++ +...|..|++.|++.+..+|+..+ .|+|+|||||+|
T Consensus 68 ~--------~~pF~l~l~~~g~Fp~----prvlwlg~~~--~~~~L~~L~~~l~~~l~~~G~~~e---~r~f~PHiTLaR 130 (176)
T PRK15124 68 R--------QPGFTLTLDDAGQWPR----SRVVWLGMRQ--PPRGLLQLANMLRSQAARSGCYQS---PQPFHPHITLLR 130 (176)
T ss_pred c--------cCCeEEEECcccCcCC----CCEEEEEcCC--CCHHHHHHHHHHHHHHHHcCCCCC---CCCCCCCEeecc
Confidence 2 5899999999999974 6999999974 357899999999999999999876 689999999999
Q ss_pred ecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeecCCCCCceeEEEEEeCCC
Q 010498 443 IRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 504 (509)
Q Consensus 443 ~k~~~~~~~~~~~~~fda~~il~~~~d~~fG~~~V~eI~Ls~l~~~~~~g~Y~~i~si~L~~ 504 (509)
.+.... .. . . ..+.+ .|.|++|+|.++..++.|+.|+++++++|.+
T Consensus 131 ~~~~~~------~~--~------~-~~~~~-~~~v~~~~L~~S~l~~~g~~Y~~l~~~~L~~ 176 (176)
T PRK15124 131 DASRPV------AI--P------P-PGFNW-SFPVTEFTLYASSFARGRTRYTPLQRWPLTQ 176 (176)
T ss_pred CCCCcc------cc--c------C-CCCCC-ceEcCEEEEEEEeccCCCCEEEEEEEEeCCC
Confidence 643210 00 0 0 11244 5899999997777666789999999999863
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=99.94 E-value=9.6e-26 Score=212.56 Aligned_cols=178 Identities=19% Similarity=0.355 Sum_probs=149.2
Q ss_pred CceEEEEccCCcchhHHHHhhccCcccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHh
Q 010498 283 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 362 (509)
Q Consensus 283 ~~FVAv~l~~~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gld~~~fv~p~~LHLTL~fLgl~dee~v~~a~~aL~~i 362 (509)
-+||||.+++ ++.+.+.++|+.+. + .. ....|++++++||||.|+|++++++++.+.++|.++
T Consensus 2 R~FiAl~~p~-~~~~~l~~~~~~l~---------~----~~---~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~ 64 (179)
T TIGR02258 2 RLFIAIDLPP-EIREQLSRIQRKLK---------S----PL---DGIKWVPPENLHITLKFLGEVDEEQVEELEDALAKI 64 (179)
T ss_pred eEEEEecCCH-HHHHHHHHHHHHhh---------c----cC---CCcEECChHHCEEEEEEccCCCHHHHHHHHHHHHHh
Confidence 3799999987 58999999998773 0 01 123799999999999999999999999999888876
Q ss_pred HHhhhhhcCCCCeEEEEceeccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeee
Q 010498 363 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 442 (509)
Q Consensus 363 ~~~i~~~L~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~~~~r~fkPHiTLaR 442 (509)
. ..+|.++|.|+|+|++ +.+++|||+++.+ ...|.+|++.|.+.+...|+..+ .++|+|||||+|
T Consensus 65 ~--------~~~f~l~l~~~~~F~~-~~~~~vl~l~~~~---~~~L~~L~~~l~~~~~~~g~~~~---~~~f~PHiTlar 129 (179)
T TIGR02258 65 A--------EPPFTLKLEGIGVFGN-PKRPRVLWAGVEQ---SEELTQLHADLERELAKLGFSKE---ERPFTPHITLAR 129 (179)
T ss_pred c--------CCCeEEEEeeeeeCCC-CCCCeEEEEeeCC---CHHHHHHHHHHHHHHHHcCCCCC---CCCcCCCEEEEE
Confidence 3 3679999999999997 7889999999985 25899999999999999999865 578999999999
Q ss_pred ecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeecCCCCCceeEEEEEeC
Q 010498 443 IRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPF 502 (509)
Q Consensus 443 ~k~~~~~~~~~~~~~fda~~il~~~~d~~fG~~~V~eI~Ls~l~~~~~~g~Y~~i~si~L 502 (509)
.+... .++.++++.+....++.|.|++|+|.++.....|+.|+++++++|
T Consensus 130 ~~~~~----------~~~~~~~~~~~~~~~~~~~v~~i~L~~S~~~~~g~~Y~~l~~~~l 179 (179)
T TIGR02258 130 KKSGK----------PGVPEFLQEFANEEFGSFHVDEFHLYSSTLTPGGPIYEPLARFQL 179 (179)
T ss_pred ecCCc----------HhHHHHHHHhCCCCCCceEeeEEEEEEeeccCCCCcceEEEEEcC
Confidence 64321 234567888888889999999999987776566799999999987
No 7
>PRK13679 hypothetical protein; Provisional
Probab=99.75 E-value=2.5e-17 Score=154.84 Aligned_cols=167 Identities=14% Similarity=0.138 Sum_probs=126.5
Q ss_pred CceEEEEccCCcchhHHHHhhccCcccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHh
Q 010498 283 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 362 (509)
Q Consensus 283 ~~FVAv~l~~~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gld~~~fv~p~~LHLTL~fLgl~dee~v~~a~~aL~~i 362 (509)
.+||||.++. ++.+.+..+|+.+. .+ ..|++| ||||.|+|++++++++++.++|+++
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 4799999986 58899999987652 11 137777 9999999999999999999999887
Q ss_pred HHhhhhhcCCCCeEEEEceeccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeee
Q 010498 363 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 442 (509)
Q Consensus 363 ~~~i~~~L~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~~~~r~fkPHiTLaR 442 (509)
.. ...||.+++.|+++|++ + ++|||+++++ .+.|.+|++.|...+. + ..+ .++|.|||||+|
T Consensus 59 ~~------~~~pf~l~l~~~~~F~~-~--~~vl~l~~~~---~~~L~~L~~~l~~~~~--~-~~~---~~~f~PHiTlar 120 (168)
T PRK13679 59 AS------ETKPFTLHVTKVSSFAP-T--NNVIYFKVEK---TEELEELHERLHSGDF--Y-GEA---EYAFVPHITIGQ 120 (168)
T ss_pred Hh------cCCCEEEEEeccccCCC-C--CCEEEEEccC---CHHHHHHHHHHHhccc--c-ccc---CCCCCCeEEeeC
Confidence 42 24899999999999975 2 4899999985 4689999999987553 1 222 578999999998
Q ss_pred ecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeecCCCCCceeEEEEEeCC
Q 010498 443 IRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFP 503 (509)
Q Consensus 443 ~k~~~~~~~~~~~~~fda~~il~~~~d~~fG~~~V~eI~Ls~l~~~~~~g~Y~~i~si~L~ 503 (509)
..... ...++.+.++. .+..+ .+.|++|+|.... .++.|..+.+++|+
T Consensus 121 ~~~~~--------~~~~~~~~l~~-~~~~~-~~~v~~i~L~~~~---~~~~w~~~~~~~~~ 168 (168)
T PRK13679 121 GLSDD--------EHEDVLGQLKM-ADVDH-EETIDRFHLLYQL---ENGSWTVYETFRLG 168 (168)
T ss_pred CCCcH--------HHHHHHHHHhc-CCcce-eEEECeEEEEEEC---CCCeEEEEEEeeCC
Confidence 64321 11233344433 55666 7899999997553 36899999999885
No 8
>PHA02574 57B hypothetical protein; Provisional
Probab=99.71 E-value=2.9e-17 Score=151.69 Aligned_cols=109 Identities=12% Similarity=0.059 Sum_probs=89.4
Q ss_pred CceEEEEccCCcchhHHHHhhccCcccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHh
Q 010498 283 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 362 (509)
Q Consensus 283 ~~FVAv~l~~~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gld~~~fv~p~~LHLTL~fLgl~dee~v~~a~~aL~~i 362 (509)
-.|||+++++ .+++++.++|+.+. . .+||+++||||||+| ++++++.+..
T Consensus 10 RlF~Al~~~~-~~r~~L~~lq~~l~------------------~--~r~V~~enLHlTL~F----~~~~v~~l~~----- 59 (149)
T PHA02574 10 GTYVAAKFSE-ATLDALERLQRTLR------------------I--PNPVPRDKLHSTIVY----SRVYVPFIPA----- 59 (149)
T ss_pred eEEEEEcCCH-HHHHHHHHHHHhcc------------------C--CcccCHHHCEEEEec----CHHHhHHHhc-----
Confidence 4799999987 88999999998652 1 379999999999999 4666654421
Q ss_pred HHhhhhhcCCCCeEEEEceeccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeee
Q 010498 363 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 442 (509)
Q Consensus 363 ~~~i~~~L~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~~~~r~fkPHiTLaR 442 (509)
..+||.+++.|+|+|++ + ++||||+|++ .+.|..|++.+++.+.. .+ .++|+|||||+|
T Consensus 60 --------~~~~F~l~l~glG~F~~-~-~~rvlWlg~~----~~~L~~L~~~l~~~l~~----~~---~r~F~PHITLaR 118 (149)
T PHA02574 60 --------SGSTEVASSGHLEVWET-Q-DKNALVLVLE----SEYLQCRHKYARALGAT----HD---FDDYTPHITLSY 118 (149)
T ss_pred --------cCCCeEEEeccccccCC-C-CCCEEEEEeC----CHHHHHHHHHHHHHhhc----CC---CCCcCCcEEEee
Confidence 25899999999999974 2 3699999996 37899999999999988 22 358999999999
No 9
>PF13563 2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB: 1IUH_A.
Probab=99.34 E-value=5.5e-12 Score=114.66 Aligned_cols=130 Identities=16% Similarity=0.206 Sum_probs=78.8
Q ss_pred ccCCCCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEEceeccCCCCCCCceEEEEeeeccCChhHHHH
Q 010498 331 FIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLH 410 (509)
Q Consensus 331 fv~p~~LHLTL~fLgl~dee~v~~a~~aL~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~ 410 (509)
......+||||.+.+..++.. +.+.++|..+.. ..+||.|+|.|+++|++ +.+|||+.+.. ...|.+
T Consensus 20 ~~~~~~pHITL~~~~~~~~~~-~~~~~~l~~~~~------~~~~f~l~l~~~~~F~~---~~~vi~l~~~~---~~~L~~ 86 (153)
T PF13563_consen 20 RYPRWPPHITLAFPFDIDDSL-DELVEALARLAA------GFPPFELRLDGFGSFPG---KGRVIFLNVEP---SPELEA 86 (153)
T ss_dssp E--GGG-EEEEEEEEE--GGG-HHHHHHHHHHHH------HS--EEEEEEEEEEESS---SSSSEEEEEEE----HHHHH
T ss_pred CCCCCCCEeEEEecCcccccH-HHHHHHHHHHHc------cCCCeEEEEccEEEcCC---CCCEEEEEcCC---CHHHHH
Confidence 344556899999999987744 455555555432 25899999999999975 22599999964 589999
Q ss_pred HHHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHHHHHHHh-CCCccccEEecEEEEEeee
Q 010498 411 ACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQF-GSKEWGEYLIKEAHLSQRF 486 (509)
Q Consensus 411 L~~~L~~~f~~~Gl~~e~~~~r~fkPHiTLaR~k~~~~~~~~~~~~~fda~~il~~~-~d~~fG~~~V~eI~Ls~l~ 486 (509)
|++.|.+.|...|...+. .++|+|||||++...... +..+++.+ .......+.|++|.|....
T Consensus 87 L~~~l~~~~~~~~~~~~~--~~~~~PHiTia~~~~~~~-----------~~~~~~~~~~~~~~~~~~v~~l~L~~~~ 150 (153)
T PF13563_consen 87 LHRALREALRPFGFKQDS--YRPFRPHITIARRLSPKQ-----------AAEAIEKLQSEFPPISFTVDELALVRSD 150 (153)
T ss_dssp HHHHHHHHHHHHHGGGGG--GS----EEEEEEESS----------------------------EEEEE-EEEEEEEE
T ss_pred HHHHHHHHHHHcCCcccc--CCCcceEEEEeccCCcch-----------hHHHHHHHhCcCCCcEEEEeEEEEEEEC
Confidence 999999999999887751 279999999999654321 12344444 2223347899999996654
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=99.25 E-value=1.2e-11 Score=97.42 Aligned_cols=60 Identities=42% Similarity=0.612 Sum_probs=55.0
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHH
Q 010498 151 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQ 211 (509)
Q Consensus 151 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~ 211 (509)
.++.||..+|++|||++|+++++|+++|||+|+||..+. ++.|+|+|+ .++|..|+++|+
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 678999998 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=99.24 E-value=1.6e-11 Score=97.15 Aligned_cols=59 Identities=27% Similarity=0.402 Sum_probs=54.5
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHH
Q 010498 150 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQ 211 (509)
Q Consensus 150 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~ 211 (509)
...+.||.+++++|||++|+|+|+|+++|||+|+|+. ++.|.|+|.++++++.|++.|+
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 4679999988999999999873
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=95.47 Aligned_cols=60 Identities=40% Similarity=0.598 Sum_probs=54.0
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHH
Q 010498 150 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKI 210 (509)
Q Consensus 150 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I 210 (509)
+..+.||..++++|||++|+++++||++|||+|.||..++...|.|+| +.++|.+|++.|
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 468999999999999999999999999999999998764345799999 689999999886
No 13
>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=99.05 E-value=7.9e-11 Score=98.39 Aligned_cols=82 Identities=20% Similarity=0.367 Sum_probs=65.1
Q ss_pred cchhHHHHhhccCcccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCC
Q 010498 294 DNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNR 373 (509)
Q Consensus 294 ~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gld~~~fv~p~~LHLTL~fLgl~dee~v~~a~~aL~~i~~~i~~~L~~~ 373 (509)
++.+.|..+++.+.- .+...|+ .|++|.++||||+|+|++++++++.+++.|.++.. ...
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 456778888877630 0123444 79999999999999999999999999999988741 358
Q ss_pred CeEEEEceeccCCCCCCCceEEE
Q 010498 374 PLFIRLKGLDLMRGSKDKARILY 396 (509)
Q Consensus 374 pf~L~l~GLg~F~~dp~~pRVLy 396 (509)
||.+++.|+++|++ ..++||+|
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 14
>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=98.95 E-value=5.7e-09 Score=100.32 Aligned_cols=167 Identities=17% Similarity=0.239 Sum_probs=119.2
Q ss_pred ccCCceEEEEccC-CcchhHHHHhhccCcccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHH
Q 010498 280 VDQEHKVAVELNI-GDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNV 358 (509)
Q Consensus 280 ~rp~~FVAv~l~~-~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gld~~~fv~p~~LHLTL~fLgl~dee~v~~a~~a 358 (509)
.+||||+...|.. ..+....+.+|-+|. +.|+|-.+=.-| ||||+||-. +++++..+..+
T Consensus 4 D~P~HFin~Pl~~f~~f~~~~~~LQ~~~~---------------~eG~d~k~QkaP---HlSl~mL~I-sd~~i~~V~~~ 64 (248)
T PF05213_consen 4 DKPTHFINFPLVQFEGFMLNFKDLQFQLL---------------EEGVDCKLQKAP---HLSLGMLDI-SDEDIPDVETA 64 (248)
T ss_pred CCCCceeeccchhhhhHHHHHHHHHHHHH---------------HcCCCccccccC---eeEEEEEEc-ChhhhhhHHHH
Confidence 5899999999998 889999999997663 445554333333 999999976 57889988888
Q ss_pred HHHhHHhhhhhcCCCCeEEEEceeccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeE
Q 010498 359 LKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHA 438 (509)
Q Consensus 359 L~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~~~~r~fkPHi 438 (509)
|+++...+. + ....+++..--.++ |.+-+.|+ .+..|+..|...|.+.|+..+ ..|.|.||+
T Consensus 65 iq~ViddM~-~---~~~~it~tnp~MLg------~~yV~nV~------Gv~slh~ki~n~~~~kgit~g--QSRmwIPHi 126 (248)
T PF05213_consen 65 IQKVIDDMV-W---FEGDITFTNPHMLG------RCYVANVK------GVLSLHDKIVNVFRKKGITFG--QSRMWIPHI 126 (248)
T ss_pred HHHHHHHhh-c---ccceEEecCceeec------cEEEEecc------cHHHHHHHHHHHHHHhCcCcC--cccccccce
Confidence 887753321 1 12267777666663 45556675 478889999999999999997 489999999
Q ss_pred EeeeecccccccCCCccccccHHHHHHHhCCCccc-cEEe-----cEEEEEeeecCCCCCceeEEEEE
Q 010498 439 TLMNIRHKKRRKGTRRVDYFDARDIFKQFGSKEWG-EYLI-----KEAHLSQRFVYDESGFYHCCASI 500 (509)
Q Consensus 439 TLaR~k~~~~~~~~~~~~~fda~~il~~~~d~~fG-~~~V-----~eI~Ls~l~~~~~~g~Y~~i~si 500 (509)
||+......-+ . +. .+|+ +.++ .++.|-.++....+|+|+.+.+.
T Consensus 127 Tia~~~~~av~-----I----------~~--~qFny~~~~n~~~~~rle~VKlGa~K~dgfYe~i~s~ 177 (248)
T PF05213_consen 127 TIAQLNDAAVR-----I----------KE--KQFNYKITINPSSPARLEFVKLGAEKKDGFYESIVSH 177 (248)
T ss_pred ehhhhhchheE-----e----------cc--ceeeeEeeccCCChhcCeEEEcCCcccCceeeeehhh
Confidence 99987543210 0 00 2233 2334 67777778776678999988763
No 15
>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=98.94 E-value=1.5e-09 Score=85.11 Aligned_cols=59 Identities=41% Similarity=0.516 Sum_probs=53.0
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEccChhHHHHHHHHH
Q 010498 151 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKI 210 (509)
Q Consensus 151 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~---~~~I~I~G~s~~~v~~A~~~I 210 (509)
..+.||..++++|||++|+++++|+++|||+|.||..+. .+.|.|.|. .+++..|...|
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 578999999999999999999999999999999988642 567999997 78999998876
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=98.82 E-value=7.8e-09 Score=82.46 Aligned_cols=59 Identities=37% Similarity=0.387 Sum_probs=52.5
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHH
Q 010498 151 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKI 210 (509)
Q Consensus 151 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~----~~~I~I~G~s~~~v~~A~~~I 210 (509)
..+.||...++.|||++|+++++|+++|||+|+|++... ...|+|+|. .+++.+|..+|
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 578999999999999999999999999999999987543 356899996 79999999877
No 17
>smart00322 KH K homology RNA-binding domain.
Probab=98.75 E-value=3.4e-08 Score=76.89 Aligned_cols=66 Identities=39% Similarity=0.536 Sum_probs=58.1
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCC-CCCcEEEEccChhHHHHHHHHHHHHH
Q 010498 148 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSK-KEDSIIIEGNSTDSVAKASEKIQAII 214 (509)
Q Consensus 148 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~-~~~~I~I~G~s~~~v~~A~~~I~~i~ 214 (509)
.....+.||..+++++||++|.++++|+++||++|.++... ....|.|.|+ .+++..|...|...+
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 45678999999999999999999999999999999998765 3567899998 799999999987654
No 18
>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=98.74 E-value=1.9e-08 Score=90.08 Aligned_cols=59 Identities=29% Similarity=0.486 Sum_probs=53.0
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCC--------------------CCcEEEEccC--hhHHHHHHHHHHHHHH
Q 010498 158 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK--------------------EDSIIIEGNS--TDSVAKASEKIQAIIA 215 (509)
Q Consensus 158 ~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~--------------------~~~I~I~G~s--~~~v~~A~~~I~~i~~ 215 (509)
.|+|.|||++|.|+|+||++|||+|.|...++ ..+|.|+|.+ .+++.+|++.|+.|+.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 67899999999999999999999999987642 2789999998 8999999999998876
Q ss_pred H
Q 010498 216 E 216 (509)
Q Consensus 216 ~ 216 (509)
.
T Consensus 95 ~ 95 (120)
T cd02395 95 P 95 (120)
T ss_pred c
Confidence 4
No 19
>PF13014 KH_3: KH domain
Probab=98.73 E-value=1.1e-08 Score=75.15 Aligned_cols=39 Identities=38% Similarity=0.572 Sum_probs=34.3
Q ss_pred ccccccCCCchhHHHHHHHhCcEEEcCC---CCC-CCcEEEEc
Q 010498 159 VIRFIKGKEGSTQKKFEKEMGVKIILPS---SKK-EDSIIIEG 197 (509)
Q Consensus 159 ~~~~IIGk~G~t~k~iE~eT~~~I~iP~---~~~-~~~I~I~G 197 (509)
+|++|||++|+++++|+++|+|+|+||+ .+. +..|+|+|
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 20
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.58 E-value=1.2e-07 Score=102.92 Aligned_cols=107 Identities=27% Similarity=0.329 Sum_probs=86.8
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEc-CCCC-C--CCcEEEEccChhHHHHHHHHHHHHHHHhhhCC
Q 010498 146 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL-PSSK-K--EDSIIIEGNSTDSVAKASEKIQAIIAEAVESP 221 (509)
Q Consensus 146 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~i-P~~~-~--~~~I~I~G~s~~~v~~A~~~I~~i~~~~~~~~ 221 (509)
..+.+..|+||..-+|.||||+|+|||+|..|||+||+| |..+ . .+...|.|. ++.|+.|.+.|..|+.++...+
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 344589999999999999999999999999999999999 4433 1 567899996 8999999999999999876631
Q ss_pred ---------CCCceEEEEeccccchhhhccHHHHHHHHhcc
Q 010498 222 ---------SLDYSHFVSLPLAVHPELVDKLVNFQNTILGI 253 (509)
Q Consensus 222 ---------k~~~tHFIsIPl~~hp~I~~~~~~f~~~Il~~ 253 (509)
-..-.-.+.||-.----++|+.++-++.|-.+
T Consensus 306 ~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~q 346 (600)
T KOG1676|consen 306 GGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQ 346 (600)
T ss_pred CCCcCCCCccceeeEEEeccccccccccCCCccchhhhccc
Confidence 11114456699865677899999999988765
No 21
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.36 E-value=6.2e-07 Score=95.36 Aligned_cols=72 Identities=26% Similarity=0.409 Sum_probs=62.7
Q ss_pred CeEEEEeccc------cccccccCCCchhHHHHHHHhCcEEEcCCCCC-------------------CCcEEEEccChhH
Q 010498 148 RHSLSVEVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-------------------EDSIIIEGNSTDS 202 (509)
Q Consensus 148 ~~~~~v~Vp~------~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-------------------~~~I~I~G~s~~~ 202 (509)
++...|.||. .|+|+|||.+|.|+|+||+|||+||.|-..++ .-++-|++.+.+.
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 7778888885 68999999999999999999999999987432 1268999999999
Q ss_pred HHHHHHHHHHHHHHhhh
Q 010498 203 VAKASEKIQAIIAEAVE 219 (509)
Q Consensus 203 v~~A~~~I~~i~~~~~~ 219 (509)
|.+|...|+.|+.+++-
T Consensus 217 i~~Ai~vienli~~av~ 233 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSAVS 233 (554)
T ss_pred HHHHHHHHHHHHHhhcc
Confidence 99999999999988544
No 22
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.34 E-value=8.9e-07 Score=84.72 Aligned_cols=65 Identities=32% Similarity=0.439 Sum_probs=59.2
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEE---ccChhHHHHHHHHHHHHHH
Q 010498 149 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIE---GNSTDSVAKASEKIQAIIA 215 (509)
Q Consensus 149 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~---G~s~~~v~~A~~~I~~i~~ 215 (509)
....+.||++.++.|||++|.++|.|+++||++|+|.. +.+.|.|. +.+++++.+|++.|++|..
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 45789999999999999999999999999999999975 34789998 7789999999999999986
No 23
>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=98.30 E-value=7.8e-07 Score=84.47 Aligned_cols=61 Identities=33% Similarity=0.432 Sum_probs=55.0
Q ss_pred EeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEE--EccChhHHHHHHHHHHHHHH
Q 010498 153 VEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIII--EGNSTDSVAKASEKIQAIIA 215 (509)
Q Consensus 153 v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I--~G~s~~~v~~A~~~I~~i~~ 215 (509)
+.||++.++.|||+||+++|+|+++||++|+|.. +.+.|.| .+.++.++.+|++.|++|..
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 24
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.02 E-value=7.8e-06 Score=78.24 Aligned_cols=53 Identities=28% Similarity=0.418 Sum_probs=48.6
Q ss_pred ccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 159 VIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 159 ~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
.+|.|||++|+|+|.||+.|||+|+|+. +.|.|.|. .++++.|++.|+.|++.
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~----~~v~i~G~-~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYG----KTVAIIGD-PEQVEIAREAIEMLIEG 157 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcC----CEEEEEeC-HHHHHHHHHHHHHHHcC
Confidence 6999999999999999999999999985 45999995 89999999999999954
No 25
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=97.95 E-value=9.9e-06 Score=77.99 Aligned_cols=76 Identities=17% Similarity=0.249 Sum_probs=61.6
Q ss_pred CCccCCCCeEEEEeccc------cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHH
Q 010498 141 EPVPSAERHSLSVEVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAII 214 (509)
Q Consensus 141 ~~~~~~~~~~~~v~Vp~------~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~ 214 (509)
.-+.+.++|+..+.||. .|+|+|||+.|.|+|+||+.++|+|.|...++..+..|....++....|.+-|.-++
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 44557788888888884 689999999999999999999999999988876666676666677777777776666
Q ss_pred HH
Q 010498 215 AE 216 (509)
Q Consensus 215 ~~ 216 (509)
..
T Consensus 220 ~a 221 (269)
T COG5176 220 EA 221 (269)
T ss_pred hc
Confidence 44
No 26
>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=76.27 Aligned_cols=54 Identities=28% Similarity=0.383 Sum_probs=49.7
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 158 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 158 ~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
...|.|||++|+|++.||..|||+|.|+. ..|.|.|. .++++.|++.|+.|++.
T Consensus 98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~----~~v~i~G~-~~~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEELTGVSISVYG----KTVGIIGD-PEQVQIAREAIEMLIEG 151 (172)
T ss_pred HHHhhhcCCCcHHHHHHHHHHCCeEEEcC----CEEEEECC-HHHHHHHHHHHHHHHcC
Confidence 36899999999999999999999999985 67999994 89999999999999965
No 27
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=97.91 E-value=1.9e-05 Score=90.48 Aligned_cols=104 Identities=27% Similarity=0.414 Sum_probs=93.7
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCCCc
Q 010498 147 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDY 225 (509)
Q Consensus 147 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~~i~~~~~~~~k~~~ 225 (509)
..+.+.+.|.++++.+++||+|.++.+|+++++|.|++|.+++ ...++++|. ..++.+|.+.++.+..+...+ ..
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 4588899999999999999999999999999999999999766 678999997 589999999999999997763 34
Q ss_pred eEEEEeccccchhhhccHHHHHHHHhccc
Q 010498 226 SHFVSLPLAVHPELVDKLVNFQNTILGIT 254 (509)
Q Consensus 226 tHFIsIPl~~hp~I~~~~~~f~~~Il~~~ 254 (509)
.+.+.||-..|.+|.|.....++.|+.+.
T Consensus 421 ~~~~~iP~k~~~~iig~~g~~i~~I~~k~ 449 (753)
T KOG2208|consen 421 KEEVQIPTKSHKRIIGTKGALINYIMGKH 449 (753)
T ss_pred cceeecCccchhhhhccccccHHHHHhhc
Confidence 67777999999999999999999999874
No 28
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.89 E-value=8.8e-05 Score=75.94 Aligned_cols=107 Identities=23% Similarity=0.232 Sum_probs=82.0
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEccChhHHHHHHHHHHHHHHHhhh
Q 010498 146 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAEAVE 219 (509)
Q Consensus 146 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~------~~~I~I~G~s~~~v~~A~~~I~~i~~~~~~ 219 (509)
..+|.+.|.||.-..|-||||||.|+.+|+.||||||++-+..+ ++.|-|.|. -+.++...+-|..-++|.-+
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 34699999999999999999999999999999999999988665 456889995 57777766665554444211
Q ss_pred ---------CCC---CCceEEEEeccccchhhhccHHHHHHHHhcc
Q 010498 220 ---------SPS---LDYSHFVSLPLAVHPELVDKLVNFQNTILGI 253 (509)
Q Consensus 220 ---------~~k---~~~tHFIsIPl~~hp~I~~~~~~f~~~Il~~ 253 (509)
.|+ +....-|.+|-..---|+|+...+++.|+++
T Consensus 115 ~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eq 160 (402)
T KOG2191|consen 115 AVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQ 160 (402)
T ss_pred hhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHh
Confidence 111 0122456688776788999999999999987
No 29
>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=97.85 E-value=2.5e-05 Score=88.19 Aligned_cols=65 Identities=20% Similarity=0.319 Sum_probs=59.9
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 149 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 149 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
-..++.||++.++-|||+||.++|.|.++||++|+|-. ++.|.|.|.+.+.+++|++.|+.|+..
T Consensus 578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 46788999999999999999999999999999999974 688999999999999999999988873
No 30
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.82 E-value=1.6e-05 Score=83.33 Aligned_cols=104 Identities=25% Similarity=0.289 Sum_probs=76.2
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHHHHHHH-HhhhC
Q 010498 146 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIA-EAVES 220 (509)
Q Consensus 146 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~----~~~I~I~G~s~~~v~~A~~~I~~i~~-~~~~~ 220 (509)
...|-+.+-||..||+.||||.|+|+|.|-..|.|||+|-+..+ +..|+|-|. .++..+|+.+|..|+. |+.+-
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 35677889999999999999999999999999999999976544 467899996 6899999999998874 43332
Q ss_pred CCCCceEEEEeccccchhhh----ccHHHHHHHHhcc
Q 010498 221 PSLDYSHFVSLPLAVHPELV----DKLVNFQNTILGI 253 (509)
Q Consensus 221 ~k~~~tHFIsIPl~~hp~I~----~~~~~f~~~Il~~ 253 (509)
+ .+.-+-+.+--|..++ |.-++-.+.|+++
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 3333333332355444 4445556666665
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=97.70 E-value=4.5e-05 Score=86.71 Aligned_cols=65 Identities=22% Similarity=0.366 Sum_probs=58.9
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 149 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 149 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
-..++.||++.++.|||+||.|+|+|+++||++|+|-. ++.|.|.+.+.+.+.+|.+.|..+...
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 588999999999999999999988654
No 32
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.57 E-value=0.00017 Score=72.17 Aligned_cols=70 Identities=23% Similarity=0.335 Sum_probs=53.3
Q ss_pred CeEEEEeccc------cccccccCCCchhHHHHHHHhCcEEEcCCCCC-C--------------------CcEEEEccCh
Q 010498 148 RHSLSVEVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-E--------------------DSIIIEGNST 200 (509)
Q Consensus 148 ~~~~~v~Vp~------~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~--------------------~~I~I~G~s~ 200 (509)
+-+..|.||. .|+|.|+|++|.|+|+||++|||||-|-..++ . -+|.|+-.
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 58999999999999999999999999988765 1 14666653
Q ss_pred hHHHHHHHHHHHHHHHhhh
Q 010498 201 DSVAKASEKIQAIIAEAVE 219 (509)
Q Consensus 201 ~~v~~A~~~I~~i~~~~~~ 219 (509)
.--..|..||...+++..+
T Consensus 169 ~p~~ea~~rl~~AleeI~k 187 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKK 187 (259)
T ss_pred CCHHHHHHHHHHHHHHHHH
Confidence 2456677777777777554
No 33
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=97.54 E-value=0.00011 Score=80.18 Aligned_cols=112 Identities=13% Similarity=0.212 Sum_probs=91.0
Q ss_pred CCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEccChhHHHHHHHHHHHHHHHhhhC-
Q 010498 145 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKIQAIIAEAVES- 220 (509)
Q Consensus 145 ~~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~---~~~I~I~G~s~~~v~~A~~~I~~i~~~~~~~- 220 (509)
+.+--+...+||.+..++||||+|+-++.|.++.||+++||+... .+.|.|+|. .+.|+.|+..|..+++.-+-.
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 445566788999999999999999999999999999999988655 578999996 599999999999998864300
Q ss_pred --C-CCC---ceEEEEeccccchhhhccHHHHHHHHhccccccc
Q 010498 221 --P-SLD---YSHFVSLPLAVHPELVDKLVNFQNTILGITDVCL 258 (509)
Q Consensus 221 --~-k~~---~tHFIsIPl~~hp~I~~~~~~f~~~Il~~~~~~~ 258 (509)
+ ... .|.-|.||-+----|+|..++-++.+-+... |+
T Consensus 129 ~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg-~k 171 (600)
T KOG1676|consen 129 GFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSG-VK 171 (600)
T ss_pred CccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcC-Cc
Confidence 0 111 4777889987678899999999998887644 44
No 34
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.45 E-value=0.00012 Score=76.86 Aligned_cols=61 Identities=28% Similarity=0.480 Sum_probs=52.5
Q ss_pred cccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEccChhHHHHHHHHHHHHHHHh
Q 010498 156 GASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAEA 217 (509)
Q Consensus 156 p~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~------~~~I~I~G~s~~~v~~A~~~I~~i~~~~ 217 (509)
-..|.|.||||.|+++|+||++|||+|.|.+--+ +..|++.| +-+++.+|-..|-+-++++
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 3689999999999999999999999999977544 57899999 5899999999887776653
No 35
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.29 E-value=0.00047 Score=68.72 Aligned_cols=64 Identities=28% Similarity=0.374 Sum_probs=58.7
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 150 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 150 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
-..+.||..+.+.+||++|.+++.|.++|+++|.|- .++.|.|.|++.+.+.+|.+.|+.+-++
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig---~NG~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG---QNGRIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc---CCcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 457899999999999999999999999999999994 4689999999999999999999988766
No 36
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.26 E-value=0.00057 Score=65.80 Aligned_cols=67 Identities=30% Similarity=0.388 Sum_probs=59.3
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEcc----ChhHHHHHHHHHHHHHH
Q 010498 147 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGN----STDSVAKASEKIQAIIA 215 (509)
Q Consensus 147 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~----s~~~v~~A~~~I~~i~~ 215 (509)
...+..+.||+...+.+||+.|.+.+.||+.|+|+|.+.. ..+.|.|+.. ++-.+.+|++-|++|..
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 3566789999999999999999999999999999999987 4577888775 78999999999999864
No 37
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.22 E-value=0.0004 Score=70.71 Aligned_cols=106 Identities=24% Similarity=0.234 Sum_probs=78.7
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhhh---C--
Q 010498 146 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVE---S-- 220 (509)
Q Consensus 146 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~~~~---~-- 220 (509)
..+-..+++||.++.+.|.|++|.++|.|.++|+++|.-|++++.....++|. .+.|..||..|....+.... .
T Consensus 23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~-~edv~~aRrei~saaeH~~l~~~s~s 101 (394)
T KOG2113|consen 23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGR-HEDVRRARREIPSAAEHFGLIRASRS 101 (394)
T ss_pred CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCCcceeccC-chhHHHHhhcCccccceeeeeeeccc
Confidence 36788999999999999999999999999999999999999999877789997 68999999999862211000 0
Q ss_pred ---------CCCCceEEEEeccccchhhhccHHHHHHHHhc
Q 010498 221 ---------PSLDYSHFVSLPLAVHPELVDKLVNFQNTILG 252 (509)
Q Consensus 221 ---------~k~~~tHFIsIPl~~hp~I~~~~~~f~~~Il~ 252 (509)
..-..+.++++|+..-.-+++++.+-+..|.+
T Consensus 102 ~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq 142 (394)
T KOG2113|consen 102 FSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQ 142 (394)
T ss_pred ccCCCccccccCCCceeeeccceeeeeccccccCccchhee
Confidence 01124567777754444555555555555543
No 38
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.21 E-value=0.00094 Score=73.07 Aligned_cols=67 Identities=31% Similarity=0.404 Sum_probs=58.7
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCC---CC-CCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 149 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS---KK-EDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 149 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~---~~-~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
....+-||....|-||||+|..+|+|.++||++|.+=+. .. ...|.|.|. .+.|.+|...|-.++.+
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 578899999999999999999999999999999998443 11 456999997 69999999999998877
No 39
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.20 E-value=0.00063 Score=69.83 Aligned_cols=66 Identities=27% Similarity=0.363 Sum_probs=56.2
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 150 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 150 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~------~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
.+.+-||..--+.||||+|+|+|.+.++.+|-|+|-.+.+ +..|++.|. .+..++|..+|..-+.|
T Consensus 133 qikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge-~e~~~~A~~~IL~Ki~e 204 (402)
T KOG2191|consen 133 QIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGE-PEQNMKAVSLILQKIQE 204 (402)
T ss_pred eeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCC-HHHHHHHHHHHHHHhhc
Confidence 4788899999999999999999999999999999954433 356788896 78999999988766665
No 40
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.18 E-value=0.00043 Score=80.11 Aligned_cols=65 Identities=20% Similarity=0.269 Sum_probs=59.2
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcE-EEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 149 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVK-IILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 149 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~-I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
-...+.||++.++-|||+||.|+|.|.++||++ |+|-. ++.|.|.|.+.+.+++|++.|+.|..+
T Consensus 685 ~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 685 LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 467889999999999999999999999999999 88854 588999999999999999999988764
No 41
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.04 E-value=0.00097 Score=74.46 Aligned_cols=69 Identities=29% Similarity=0.400 Sum_probs=62.4
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhhh
Q 010498 148 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVE 219 (509)
Q Consensus 148 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~~~~ 219 (509)
-...++.|+++-++-+||+||.++++|-++||++|+|- +.+.|.|.+.+.+.+.+|+++|+.|+++..-
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 34677889999999999999999999999999999997 5688999999899999999999999987544
No 42
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=97.01 E-value=0.0015 Score=65.40 Aligned_cols=67 Identities=22% Similarity=0.312 Sum_probs=55.8
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC--CCC-CCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 149 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS--SKK-EDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 149 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~--~~~-~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
.+..|-||+++-|-||||||..+++|.+|.|+.|.|.. .++ ...|+|+|. ++.+..|.--++.-|..
T Consensus 315 tTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGT-qdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 315 TTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT-QDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred eeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEecc-HHHHhhHHHHHHHHHHh
Confidence 46788999999999999999999999999999999954 444 456789996 78899888777666553
No 43
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.88 E-value=0.0009 Score=76.42 Aligned_cols=64 Identities=25% Similarity=0.413 Sum_probs=57.9
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 150 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 150 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
...+.||++.++-+||+||.|+|.|.++||++|+|- +++.|.|.+.+.+.+++|++.|+.+..+
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 357889999999999999999999999999999983 3688999999999999999999988854
No 44
>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=96.66 E-value=0.0017 Score=53.98 Aligned_cols=76 Identities=9% Similarity=0.118 Sum_probs=52.5
Q ss_pred hhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHHHHHHHhCCC--ccc--cEEecEE
Q 010498 405 GDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGSK--EWG--EYLIKEA 480 (509)
Q Consensus 405 ~~~L~~L~~~L~~~f~~~Gl~~e~~~~r~fkPHiTLaR~k~~~~~~~~~~~~~fda~~il~~~~d~--~fG--~~~V~eI 480 (509)
.+.|.++++.+.+.+...|+..+ +++.|||||+++..... -.+..+.+.+... .+. ++.++++
T Consensus 8 ~~~L~~l~~~l~~~~~~~~~r~~----~~~~~HiTL~flg~~~~---------~~~~~l~~~l~~~~~~~~~f~~~~~~~ 74 (87)
T PF02834_consen 8 KEQLNQLQERLRQALPPLGIRWV----RPFNPHITLAFLGEVPP---------DQLPELIEALANIASRFPPFTLTVDGF 74 (87)
T ss_dssp HHHHHHHHHHHHHHCCSCTEEEG----SCGGSEEEEEEEEEESH---------HHHHHHHHHHHHHHCCCB-EEEEEEEE
T ss_pred HHHHHHHHHHHhhhccccCCccc----CCCCCeEEEEeCCCCCH---------HHHHHHHHHHHhhhccCCCeEEEEeEE
Confidence 46788999999988888999884 68999999999864321 1234455555443 333 3789999
Q ss_pred EEEeeecCCCCCce
Q 010498 481 HLSQRFVYDESGFY 494 (509)
Q Consensus 481 ~Ls~l~~~~~~g~Y 494 (509)
.+..... ..+.+|
T Consensus 75 ~~f~s~~-~~rvi~ 87 (87)
T PF02834_consen 75 GLFPSRL-RPRVIW 87 (87)
T ss_dssp EEEEEEE-TCEEEE
T ss_pred EEeCCCC-CCCCcC
Confidence 9966543 344555
No 45
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.54 E-value=0.0048 Score=68.24 Aligned_cols=69 Identities=22% Similarity=0.335 Sum_probs=59.8
Q ss_pred CCCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 146 AERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 146 ~~~~~~~v~Vp~-~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
.......|.+|. ++-|.|||+.|.|+|.+|.-||+-|.|.. ..+.|+|+|-++-.-+-|+.-++.++.+
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 345566789998 78899999999999999999999999975 3568999997788889999999999887
No 46
>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=96.48 E-value=0.025 Score=56.38 Aligned_cols=104 Identities=19% Similarity=0.347 Sum_probs=77.6
Q ss_pred CCCCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEEceeccCCCCCCCceEEEE-eeeccCChhHHHHH
Q 010498 333 KPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYA-PVEEIGDGDRLLHA 411 (509)
Q Consensus 333 ~p~~LHLTL~fLgl~dee~v~~a~~aL~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~pRVLya-gV~~~~~~~~L~~L 411 (509)
.+.-|||+|.=-=-+...+++.-.+.|+.. +.. ....+|.+.|.++.+|.| .++.|...+ .|.. +....|..|
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 678899999765555667777666666553 210 135899999999999998 677786444 5554 223339999
Q ss_pred HHHHHHHHHHCCCccccCCC-CCceeeEEeeeecc
Q 010498 412 CQVIIDAFNEAGLVFHRDYN-KKLKLHATLMNIRH 445 (509)
Q Consensus 412 ~~~L~~~f~~~Gl~~e~~~~-r~fkPHiTLaR~k~ 445 (509)
.+.|.+.+.+.|++.- . .+-.+||.||-+-.
T Consensus 160 ~~~i~~~l~~~~lp~~---Y~~~~~fHvSIAw~~~ 191 (239)
T PF09749_consen 160 LDRINEVLKEFGLPPF---YDEDPSFHVSIAWTLG 191 (239)
T ss_pred HHHHHHHHHHhCCCcc---cCCCCCCEEEEEEECC
Confidence 9999999999999874 4 67899999998743
No 47
>PRK00106 hypothetical protein; Provisional
Probab=96.45 E-value=0.0061 Score=67.49 Aligned_cols=69 Identities=17% Similarity=0.340 Sum_probs=59.4
Q ss_pred CCCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 146 AERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 146 ~~~~~~~v~Vp~-~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
+......|.+|. ++-|.|||+.|.++|.+|.-||+-|.|.. ..+.|+|+|-++-.-+-|+.-++.++.+
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 345566889998 78899999999999999999999999975 4568999997788888899888888876
No 48
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.45 E-value=0.0023 Score=67.88 Aligned_cols=69 Identities=17% Similarity=0.238 Sum_probs=60.0
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 147 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 147 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
+.+...+.|-.+++|.+||++|+++++|+..|+|+|+|-..+..-.|+|-|. +..-.+|+.-|...++.
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 4566788899999999999999999999999999999998766777899996 67778888888888765
No 49
>PRK12704 phosphodiesterase; Provisional
Probab=96.40 E-value=0.0058 Score=67.66 Aligned_cols=68 Identities=19% Similarity=0.315 Sum_probs=57.7
Q ss_pred CCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 147 ERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 147 ~~~~~~v~Vp~-~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
......|.+|. ++-|.|||+.|.|+|.||.-||+-|.|.. ..+.|+|+|-++..-+-|+.-++.++.+
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 44566788998 78899999999999999999999999975 3568999997666667899989888876
No 50
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.11 E-value=0.0089 Score=57.74 Aligned_cols=54 Identities=28% Similarity=0.407 Sum_probs=48.5
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 158 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 158 ~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
-..|.|||++|.|++.||+=|||.|.+-. ..|-|.|. .++|+-|++.|..+++.
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 34689999999999999999999999954 68999997 68999999999999876
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=95.83 E-value=0.074 Score=51.61 Aligned_cols=137 Identities=19% Similarity=0.191 Sum_probs=66.4
Q ss_pred eEEeec-cccCCHHHHHHHHHHHHHhHHhhhhhcCCCCe-----EEEEceeccCCCCCCCceEEEEeeeccCChhHHHHH
Q 010498 338 HLTVLM-LKLWNKDRVNAATNVLKSISSKVMDALDNRPL-----FIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHA 411 (509)
Q Consensus 338 HLTL~f-Lgl~dee~v~~a~~aL~~i~~~i~~~L~~~pf-----~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~L 411 (509)
||||.- +...+.+++. +.|+.+... ..++ .++|.++.+= ...=+=+|+.++. ...|..|
T Consensus 40 HiTL~s~i~~~~~~~~~---~~L~~~~~~------~~~~~~~~~~v~~~~v~~g---~~yfq~vyl~v~~---t~~L~~l 104 (196)
T PF07823_consen 40 HITLTSGISLDSSDDVQ---KVLDSAAAA------LKPLPKNHFTVRFDKVASG---DKYFQCVYLEVEK---TPELMSL 104 (196)
T ss_dssp -EEEEEEEEE--HHHHH---HHHHHHHHH-------B-E-----EEEEEEEEEE---EETTEEEEEEE------HHHHHH
T ss_pred eEEEeCCCccCCHHHHH---HHHHHHHHh------ccCcccceeEEEeeeEeeC---CeEEEEEEEEecC---ChhHHHH
Confidence 999987 3333455554 444444322 2444 8888877541 1222668999986 4789999
Q ss_pred HHHHHHHHHHC-------CCccccCCCCCceeeEEeeeecccccccCCCccccccHHHHHHHhCCC-------ccccEEe
Q 010498 412 CQVIIDAFNEA-------GLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGSK-------EWGEYLI 477 (509)
Q Consensus 412 ~~~L~~~f~~~-------Gl~~e~~~~r~fkPHiTLaR~k~~~~~~~~~~~~~fda~~il~~~~d~-------~fG~~~V 477 (509)
++.+++.|... +.- ...+|.||+.|+..--.... + -.++.+.....+. ..+.|.+
T Consensus 105 ~~~~r~~~~~~~~~~~~~~~~----~~~~y~PHlSLlY~d~~~~e----~---~~~~~~~~~i~~~l~~~~~~~~~~~~~ 173 (196)
T PF07823_consen 105 AQIARELFVEGPPDEVKAAEW----PREPYMPHLSLLYGDLPPEE----K---AEAAEIAQRIDDALGVDSGISGLGWEG 173 (196)
T ss_dssp HCHHHHCT----------T--------S----EEEEE-----HHH----H---HHHHHHHHHH-TT------GTT-EEEE
T ss_pred HHHHHHHhhhccccccccccc----cCCCCCCeEEEEEcCCCccc----H---HHHHHHHHHhcccccccccCCCCCEec
Confidence 99999988532 222 24689999999974211100 0 0122344444443 3457889
Q ss_pred cEEEEEeeecCCCCCceeEEEEEeC
Q 010498 478 KEAHLSQRFVYDESGFYHCCASIPF 502 (509)
Q Consensus 478 ~eI~Ls~l~~~~~~g~Y~~i~si~L 502 (509)
.+|.|..... +=.-.+.+++++|
T Consensus 174 ~~l~lv~t~g--~v~~W~~l~~~~l 196 (196)
T PF07823_consen 174 GELKLVRTDG--PVEEWEVLASVDL 196 (196)
T ss_dssp EEEEEEE--T--T-TT-EEEEEEE-
T ss_pred cEEEEEEcCC--CCCcEEEEEEEeC
Confidence 9999954321 2356778887765
No 52
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=95.27 E-value=0.031 Score=55.67 Aligned_cols=64 Identities=25% Similarity=0.356 Sum_probs=55.4
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 150 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 150 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
-.-++||+.+++.+||++|++++.|.++|+|+|.+= .++-|.|.|+......-|...|..|-.+
T Consensus 147 G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG---~NG~IWV~~~~~~~e~~~~~aI~~ie~e 210 (239)
T COG1097 147 GQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVG---QNGRIWVDGENESLEELAIEAIRKIERE 210 (239)
T ss_pred CEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEe---cCCEEEecCCCcchHHHHHHHHHHHhhh
Confidence 346899999999999999999999999999999994 5789999998665677888888777665
No 53
>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=95.07 E-value=0.024 Score=44.74 Aligned_cols=37 Identities=24% Similarity=0.269 Sum_probs=34.1
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010498 148 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 184 (509)
Q Consensus 148 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~i 184 (509)
.....+.||..-.+..|||+|.+++.++..+|.+|++
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3678899999999999999999999999999988875
No 54
>PRK12705 hypothetical protein; Provisional
Probab=95.07 E-value=0.027 Score=62.12 Aligned_cols=68 Identities=19% Similarity=0.318 Sum_probs=56.6
Q ss_pred CCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 147 ERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 147 ~~~~~~v~Vp~-~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
......|.+|. ++-|.|||+.|.++|.+|..||+-|.|+. ....|+|.+-++..-+.|+..++.++.+
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 44556778887 77899999999999999999999999975 3456888887777888888888888765
No 55
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=94.90 E-value=0.019 Score=62.77 Aligned_cols=103 Identities=20% Similarity=0.317 Sum_probs=81.8
Q ss_pred CCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCC
Q 010498 145 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSL 223 (509)
Q Consensus 145 ~~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~~i~~~~~~~~k~ 223 (509)
-+++..+++-||.+++..|+|++|++++.|+..|+.||.+...+. ...+-+.+..+..+..|+..|-.++.+ ..
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 356788899999999999999999999999999999999966444 334444443456788888887777665 22
Q ss_pred CceEEEEeccccchhhhccHHHHHHHHhc
Q 010498 224 DYSHFVSLPLAVHPELVDKLVNFQNTILG 252 (509)
Q Consensus 224 ~~tHFIsIPl~~hp~I~~~~~~f~~~Il~ 252 (509)
.+..-.+.|...|+.|.+.++..+++|-.
T Consensus 139 pvk~~lsvpqr~~~~i~grgget~~si~~ 167 (608)
T KOG2279|consen 139 PVSEQLSVPQRSVGRIIGRGGETIRSICK 167 (608)
T ss_pred cccccccchhhhcccccccchhhhcchhc
Confidence 46677889988899999999999888754
No 56
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=94.24 E-value=0.04 Score=60.54 Aligned_cols=63 Identities=25% Similarity=0.280 Sum_probs=55.8
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 150 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 150 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
...++|+.+-...+||++|-.+|+|+.|||+.-++. ++.+.|-.+++...++|++.|.-|...
T Consensus 598 ~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD----e~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 598 LETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD----EGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred eeEEeecchhhheeecCccceeeeEeeeccceeeec----CceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 567889999999999999999999999999766664 488999999999999999999877654
No 57
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=93.95 E-value=0.16 Score=51.33 Aligned_cols=70 Identities=19% Similarity=0.321 Sum_probs=53.0
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 146 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 146 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
.+++.+.+.+...--|.||||||.++|+|..+.++.|++|.++. ...++|+.. .+.|-.-...|.-.+++
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 34677777888888999999999999999999999999998665 566788875 45555444444444444
No 58
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=93.32 E-value=0.15 Score=56.06 Aligned_cols=102 Identities=25% Similarity=0.212 Sum_probs=76.4
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCC--CC-CCcEEEEc---------cChhHHHHHHHHHHHHHH---
Q 010498 151 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS--KK-EDSIIIEG---------NSTDSVAKASEKIQAIIA--- 215 (509)
Q Consensus 151 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~--~~-~~~I~I~G---------~s~~~v~~A~~~I~~i~~--- 215 (509)
..+..+....|.||||+|.++++|..+|+.+|.|-.. +. ...|+|+| . .+++.+|-++|-...+
T Consensus 45 ~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~-~~al~ka~~~iv~~~~~d~ 123 (485)
T KOG2190|consen 45 YRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPA-TDALFKAFDMIVFKLEEDD 123 (485)
T ss_pred EEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCch-HHHHHHHHHHHhhcccccc
Confidence 6778888999999999999999999888888877443 33 56788999 5 6899999999876421
Q ss_pred -HhhhC----CCCCceEEEEeccccchhhhccHHHHHHHHhcc
Q 010498 216 -EAVES----PSLDYSHFVSLPLAVHPELVDKLVNFQNTILGI 253 (509)
Q Consensus 216 -~~~~~----~k~~~tHFIsIPl~~hp~I~~~~~~f~~~Il~~ 253 (509)
+.... .+...+-.+-+|-..--.|+|+.+..+++|.++
T Consensus 124 ~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~ 166 (485)
T KOG2190|consen 124 EAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREE 166 (485)
T ss_pred cccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHh
Confidence 10010 011234556688775588999999999999976
No 59
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=93.05 E-value=0.017 Score=59.75 Aligned_cols=150 Identities=15% Similarity=0.122 Sum_probs=102.6
Q ss_pred CCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEEceeccCCCCCCCceEEEEeeeccCChhHHHHHHHH
Q 010498 335 KTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQV 414 (509)
Q Consensus 335 ~~LHLTL~fLgl~dee~v~~a~~aL~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~L~~~ 414 (509)
..+|+|+...-.+++.+++.-..++++....+..++...-.+.-|.|.++|+. .|-.+.+.+ .+.+++.++.
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 47899999999999999999998888765555454555555666799999987 788888875 4788999999
Q ss_pred HHHHHHHCCCccccCCCCCceeeEEeeeeccccc--ccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeecCCC-C
Q 010498 415 IIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKR--RKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDE-S 491 (509)
Q Consensus 415 L~~~f~~~Gl~~e~~~~r~fkPHiTLaR~k~~~~--~~~~~~~~~fda~~il~~~~d~~fG~~~V~eI~Ls~l~~~~~-~ 491 (509)
++..|.+.+...+ +++-|.+|-+++....... +-...+..+.+..+.+ +..+|++..+.+..|.+...+. .
T Consensus 200 les~~~e~~~~~~--~kp~~i~lkG~~~mnddP~~~kVLYAkv~~~~~e~~l----~~~~~~~i~~~f~~~~li~k~~~~ 273 (345)
T KOG2814|consen 200 LESTFQEIRIDVG--EKPLFIDLKGLDKMNDDPSLTKVLYAKVEPDDYEKFL----QHRCGERILERFVASGLIKKESSS 273 (345)
T ss_pred HHHHHHHHHhccC--CCceeeeccchhhhcCCHhHheeeeeeccCcchHHHH----HHHHHHHHHHHHHHhcchhccccc
Confidence 9999999888876 3667999999988754211 1112233333333333 3345666677777766654332 3
Q ss_pred CceeEEE
Q 010498 492 GFYHCCA 498 (509)
Q Consensus 492 g~Y~~i~ 498 (509)
.+|++..
T Consensus 274 ~kLH~Tv 280 (345)
T KOG2814|consen 274 LKLHCTV 280 (345)
T ss_pred cEEEEEE
Confidence 4555443
No 60
>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=91.77 E-value=3.4 Score=41.28 Aligned_cols=143 Identities=11% Similarity=0.104 Sum_probs=78.4
Q ss_pred CCceEEeec-cccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEE---EEceeccCCCCCCCceEEEEeeeccCChhHHHH
Q 010498 335 KTFHLTVLM-LKLWNKDRVNAATNVLKSISSKVMDALDNRPLFI---RLKGLDLMRGSKDKARILYAPVEEIGDGDRLLH 410 (509)
Q Consensus 335 ~~LHLTL~f-Lgl~dee~v~~a~~aL~~i~~~i~~~L~~~pf~L---~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~ 410 (509)
.-||.||+- +.+.+........++++.+... ..||.| .+.-||-|-- +..+ +....|..
T Consensus 56 YGfHaTLKaPFrLa~g~~~a~L~~al~~fA~~------~~pf~i~~L~l~~Lg~FlA--------L~P~---~~~~~L~~ 118 (228)
T TIGR03223 56 YGFHATLKAPFRLAPGVTEAELLAAVAAFAAT------RAPFALPPLRVALLGGFLA--------LRPA---APCPALQA 118 (228)
T ss_pred cccceeecCCcccCCCCCHHHHHHHHHHHHhc------CCCccCCcceeeeeCCEEE--------EeeC---CCCHHHHH
Confidence 346999984 3443333344444455554321 355554 4455544421 2222 34578999
Q ss_pred HHHHHHHHHHHC---------------CCccccC----------CCCCceeeEEeeeecccccccCCCccccccHHHHHH
Q 010498 411 ACQVIIDAFNEA---------------GLVFHRD----------YNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFK 465 (509)
Q Consensus 411 L~~~L~~~f~~~---------------Gl~~e~~----------~~r~fkPHiTLaR~k~~~~~~~~~~~~~fda~~il~ 465 (509)
|+..+.+.|... ||...++ --..|..||||-.---... . -.+...++
T Consensus 119 LAa~~V~~~d~fRAPls~aelaRRr~~~Ls~~Q~~~L~~WGYPYV~deFrFHmTLTg~l~~~~------~--~~~~~~l~ 190 (228)
T TIGR03223 119 LAAACVRELDPFRAPLTEAELARRRPDQLTPRQRALLERWGYPYVLEEFRFHMTLTGRLDEEE------R--AAVLARLE 190 (228)
T ss_pred HHHHHHHhhhhccCCCCHHHHhhcCccCCCHHHHHHHHHcCCCceecceEEEEEecCCCChHH------H--HHHHHHHH
Confidence 999999888432 2221100 0246999999985321100 0 01122333
Q ss_pred H-hCCCccccEEecEEEEEeeecCCCCCceeEEEEEeCCC
Q 010498 466 Q-FGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 504 (509)
Q Consensus 466 ~-~~d~~fG~~~V~eI~Ls~l~~~~~~g~Y~~i~si~L~~ 504 (509)
. |...--..+.|+.|.|+.-. ..|.-+..+..++|++
T Consensus 191 ~~~~~~l~~p~~id~laLf~e~--~~g~pF~~~~~~~l~~ 228 (228)
T TIGR03223 191 ARFAPLLADPLAVDGLALFVEP--EPGAPFRLIARVALAG 228 (228)
T ss_pred HHhhhccCCCeeeeeEEEEecc--CCCCCcEEEEeecCCC
Confidence 3 33443457889999996542 2346699999999864
No 61
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=90.81 E-value=0.17 Score=58.68 Aligned_cols=42 Identities=29% Similarity=0.572 Sum_probs=38.3
Q ss_pred CCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010498 145 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 186 (509)
Q Consensus 145 ~~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 186 (509)
....-+.++.||.++|+.|||++|++.|+++.++++.|.+|.
T Consensus 705 ~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 705 AKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred cccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence 345567888999999999999999999999999999999997
No 62
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=87.39 E-value=2.5 Score=41.03 Aligned_cols=73 Identities=18% Similarity=0.249 Sum_probs=59.0
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCCCceEEEE
Q 010498 151 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDYSHFVS 230 (509)
Q Consensus 151 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~~~~~~k~~~tHFIs 230 (509)
..+.+++..+-+|...+|..++.|-...|++|.+-. +.+.|.|+|. +..++.+...|..++... .+..|.
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 356666889999999999999999888899999976 4568999996 788888888888888762 355565
Q ss_pred ecc
Q 010498 231 LPL 233 (509)
Q Consensus 231 IPl 233 (509)
+|.
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=86.16 E-value=0.51 Score=51.34 Aligned_cols=43 Identities=28% Similarity=0.359 Sum_probs=37.4
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC
Q 010498 147 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 189 (509)
Q Consensus 147 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~ 189 (509)
+.....|.||...++.+|||+|.++++||...|.+|.+-..++
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 3456789999999999999999999999999999999944333
No 64
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=85.78 E-value=0.68 Score=47.85 Aligned_cols=69 Identities=20% Similarity=0.290 Sum_probs=59.0
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHH-HHHHHHH
Q 010498 146 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKAS-EKIQAII 214 (509)
Q Consensus 146 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~-~~I~~i~ 214 (509)
..+....+.+|...++.+.|.+|++++++.+-|++-|.-|.+......-++|-...++.+|+ ..|+...
T Consensus 112 s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~~~~Vf~Vtg~~~nC~kra~s~eie~ta 181 (394)
T KOG2113|consen 112 SGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRCGEPVFCVTGAPKNCVKRARSCEIEQTA 181 (394)
T ss_pred cCCCceeeeccceeeeeccccccCccchheecccceEeeeccCCCceEEEecCCcchhhhccccchhhhh
Confidence 56677788899999999999999999999999999999998777777889997667788888 6666543
No 65
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=84.57 E-value=0.7 Score=45.03 Aligned_cols=54 Identities=26% Similarity=0.352 Sum_probs=45.6
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 158 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 158 ~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
-.+|.|+||+|.|+=.||+-|.|||.+-. ..|-|-|. -+++.-|++-|-.++-.
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 35899999999999999999999999964 56888885 57899999888766643
No 66
>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=84.19 E-value=1.2 Score=34.28 Aligned_cols=35 Identities=17% Similarity=0.288 Sum_probs=28.2
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEE
Q 010498 148 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKI 182 (509)
Q Consensus 148 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I 182 (509)
.....+.+...-.+.+||++|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 34555666665689999999999999999999665
No 67
>PRK02821 hypothetical protein; Provisional
Probab=83.88 E-value=0.85 Score=37.99 Aligned_cols=33 Identities=18% Similarity=0.289 Sum_probs=27.6
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhC
Q 010498 147 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMG 179 (509)
Q Consensus 147 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~ 179 (509)
......+.+.++-.|.||||+|.+++.|..=..
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 346788999999999999999999998865433
No 68
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=82.91 E-value=0.66 Score=37.55 Aligned_cols=34 Identities=15% Similarity=0.251 Sum_probs=28.7
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhC
Q 010498 146 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMG 179 (509)
Q Consensus 146 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~ 179 (509)
.......+.|..+-.|.||||+|.|++.|+.=++
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=82.54 E-value=1.2 Score=41.04 Aligned_cols=38 Identities=16% Similarity=0.110 Sum_probs=34.3
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 010498 148 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 185 (509)
Q Consensus 148 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP 185 (509)
+....+.|+..-++..|||+|.|++.++.=++-.|+|-
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=82.38 E-value=1.3 Score=36.75 Aligned_cols=30 Identities=20% Similarity=0.302 Sum_probs=25.9
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHH
Q 010498 147 ERHSLSVEVGASVIRFIKGKEGSTQKKFEK 176 (509)
Q Consensus 147 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~ 176 (509)
......+.+.++-.|.||||+|.|++.|..
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRt 57 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRT 57 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHH
Confidence 346678999999999999999999998854
No 71
>PRK13764 ATPase; Provisional
Probab=82.04 E-value=1 Score=51.02 Aligned_cols=41 Identities=29% Similarity=0.334 Sum_probs=37.3
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCC
Q 010498 147 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS 187 (509)
Q Consensus 147 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~ 187 (509)
+.....|.||...++.+|||+|.++++||+..|.+|++-..
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 56677899999999999999999999999999999999443
No 72
>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=81.91 E-value=0.73 Score=44.69 Aligned_cols=25 Identities=20% Similarity=0.272 Sum_probs=23.2
Q ss_pred CCceEEEEccCCcchhHHHHhhccC
Q 010498 282 QEHKVAVELNIGDNSERVKVDRTSI 306 (509)
Q Consensus 282 p~~FVAv~l~~~~~~~~v~~~q~~i 306 (509)
|||||||+|..+++.++++.+|+.|
T Consensus 1 pthFl~ipl~~~~i~~~~~~fq~~v 25 (209)
T PF10469_consen 1 PTHFLCIPLNSPEIQEKFKEFQNEV 25 (209)
T ss_pred CCeEEEEECCCHHHHHHHHHHHHHH
Confidence 8999999999999999999999754
No 73
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=81.79 E-value=1.4 Score=36.70 Aligned_cols=31 Identities=16% Similarity=0.297 Sum_probs=26.5
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHH
Q 010498 146 AERHSLSVEVGASVIRFIKGKEGSTQKKFEK 176 (509)
Q Consensus 146 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~ 176 (509)
.+.....+.+-++-.|.+|||+|.|++.|..
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHH
Confidence 3455678999999999999999999999853
No 74
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=79.53 E-value=2.2 Score=46.92 Aligned_cols=69 Identities=16% Similarity=0.199 Sum_probs=49.5
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEcc--ChhHHHHHHHHHHHHHHH
Q 010498 148 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGN--STDSVAKASEKIQAIIAE 216 (509)
Q Consensus 148 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~------~~~I~I~G~--s~~~v~~A~~~I~~i~~~ 216 (509)
-....+-||...|+.|||.||..+++....-++-|++-..-+ .+.|.|+.+ +++++..|+.-...++.+
T Consensus 448 pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~ 524 (657)
T COG5166 448 PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ 524 (657)
T ss_pred chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhh
Confidence 456788999999999999999999999999999888754222 244666663 344555555555555543
No 75
>PHA02977 hypothetical protein; Provisional
Probab=78.21 E-value=11 Score=35.10 Aligned_cols=94 Identities=17% Similarity=0.152 Sum_probs=53.6
Q ss_pred eEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEEceeccCCCCC------CCceEEEEeeeccCChhHHHHH
Q 010498 338 HLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSK------DKARILYAPVEEIGDGDRLLHA 411 (509)
Q Consensus 338 HLTL~fLgl~dee~v~~a~~aL~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp------~~pRVLyagV~~~~~~~~L~~L 411 (509)
|+||+.-.-...+..+.-++. +.++ +-..++++-+..-+||.+. .+-+-+.++++- ++.|..|
T Consensus 71 hitlgian~dq~~~f~~fk~~-------~~d~-dl~sis~~cke~icfpqs~askelga~g~avvmkle~---sddlkal 139 (201)
T PHA02977 71 HITLGIANKDQCDNFENFKEL-------IKDI-DLQSISFTCKEEICFPQSNASKELGAKGCAVVMKLEA---SDDLKAL 139 (201)
T ss_pred ceeeeccCccHhHHHHHHHHH-------hhcc-cceeEEEEeeeeEeccccchhhhhCcCccEEEEEEEe---chHHHHH
Confidence 999977543322333332222 2222 2366778888888998521 133556667764 3567666
Q ss_pred HHHHHHHHH----HCCCccccCCCCCceeeEEeeeecc
Q 010498 412 CQVIIDAFN----EAGLVFHRDYNKKLKLHATLMNIRH 445 (509)
Q Consensus 412 ~~~L~~~f~----~~Gl~~e~~~~r~fkPHiTLaR~k~ 445 (509)
.+.|-.+.- -.|=... ..++.||+|++.++.
T Consensus 140 rnvl~n~vp~pkdifg~i~~---d~~w~phitigyv~~ 174 (201)
T PHA02977 140 RNVLFNAVPCPKDIFGDILS---DNPWCPHITIGYVKA 174 (201)
T ss_pred HHHhhcccCCcHHhhccccc---CCCCCCceEEEeecc
Confidence 666644321 0222222 358999999999865
No 76
>PRK01064 hypothetical protein; Provisional
Probab=77.82 E-value=2 Score=35.85 Aligned_cols=31 Identities=29% Similarity=0.245 Sum_probs=26.8
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHH
Q 010498 147 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKE 177 (509)
Q Consensus 147 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~e 177 (509)
......+.|.++-.|.+|||+|.|++.|..=
T Consensus 28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 4567788999999999999999999998764
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=76.93 E-value=1.4 Score=35.94 Aligned_cols=36 Identities=25% Similarity=0.351 Sum_probs=30.9
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEE
Q 010498 148 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKII 183 (509)
Q Consensus 148 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~ 183 (509)
.....+.+-...-+.+||++|+++++|.++.+-.+.
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 466778888999999999999999999988876664
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=74.60 E-value=2.7 Score=38.93 Aligned_cols=38 Identities=16% Similarity=0.080 Sum_probs=34.5
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 010498 148 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 185 (509)
Q Consensus 148 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP 185 (509)
+....+.||.+-++..|||+|.+.+...+=|+-+++|-
T Consensus 99 ~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 99 KKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 46788999999999999999999999999999888774
No 79
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=73.85 E-value=3.3 Score=38.21 Aligned_cols=36 Identities=25% Similarity=0.370 Sum_probs=31.4
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 010498 150 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 185 (509)
Q Consensus 150 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP 185 (509)
..-+-|+....|..||++|+.++.|++..|-+|++=
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv 68 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV 68 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence 446667888999999999999999999999888874
No 80
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=72.09 E-value=3.6 Score=33.44 Aligned_cols=25 Identities=36% Similarity=0.478 Sum_probs=21.5
Q ss_pred cccccCCCchhHHHHHHHh-CcEEEc
Q 010498 160 IRFIKGKEGSTQKKFEKEM-GVKIIL 184 (509)
Q Consensus 160 ~~~IIGk~G~t~k~iE~eT-~~~I~i 184 (509)
+|..||++|..++.|+++. |-+|++
T Consensus 19 vG~~iG~~G~rik~i~~~L~gekIdv 44 (69)
T PF13184_consen 19 VGACIGKKGSRIKAISEELNGEKIDV 44 (69)
T ss_dssp HHHHH-CCCCCHHHHHHHTTT-EEEE
T ss_pred ceecCccccHHHHHHHHHhCCCeEEE
Confidence 7999999999999999999 888876
No 81
>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=71.48 E-value=3.3 Score=33.96 Aligned_cols=35 Identities=17% Similarity=0.282 Sum_probs=28.7
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010498 150 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 184 (509)
Q Consensus 150 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~i 184 (509)
...+.|..+-.+.||||+|.|+..|+-=++.-++-
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 45677778889999999999999999877755553
No 82
>PLN00108 unknown protein; Provisional
Probab=70.80 E-value=2.3 Score=43.12 Aligned_cols=29 Identities=17% Similarity=0.141 Sum_probs=26.5
Q ss_pred cccCCceEEEEcc-CCcchhHHHHhhccCc
Q 010498 279 QVDQEHKVAVELN-IGDNSERVKVDRTSIP 307 (509)
Q Consensus 279 ~~rp~~FVAv~l~-~~~~~~~v~~~q~~i~ 307 (509)
+..+||||||.|. .+++.++++++|+.+.
T Consensus 33 ~~~~THFlavPL~~~p~i~~~~~~Fk~~Vl 62 (257)
T PLN00108 33 REVFTHFVSLPLAIYPDLKKNIEAFQNSVL 62 (257)
T ss_pred CCCCCeEEEEEcCCCHHHHHHHHHHHHHHH
Confidence 6789999999996 8999999999999873
No 83
>KOG3102 consensus Uncharacterized conserved protein [Function unknown]
Probab=69.12 E-value=18 Score=35.88 Aligned_cols=101 Identities=11% Similarity=0.210 Sum_probs=69.0
Q ss_pred cCCCCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEEceeccCCCCCCCceEE-EEeeeccCChhHHHH
Q 010498 332 IKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARIL-YAPVEEIGDGDRLLH 410 (509)
Q Consensus 332 v~p~~LHLTL~fLgl~dee~v~~a~~aL~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~pRVL-yagV~~~~~~~~L~~ 410 (509)
+--.-|||.|.=---+.--+|.....+|+.-. . ....|-+++.++.+|-| .++.|-. -+.+. ..+...+.+
T Consensus 117 ~~~~~fHlSLsr~VvLr~HqI~~fi~~L~~~l---~---s~~rf~~t~n~~~iytN-~e~TRtFi~leit-t~~~~~~~~ 188 (269)
T KOG3102|consen 117 ALGREFHLSLSRNVVLRVHQINSFISMLRQKL---Q---SQKRFLITFNKWEIYTN-DEHTRTFISLEIT-TSGLSEISK 188 (269)
T ss_pred hccceEEEeeccceEEEeehhhHHHHHHHHHH---h---hhhhheEeecceEEEec-cccceeEEEEEec-hhhHHHHHH
Confidence 33577899987544444456666666665532 2 24778999999999988 4566653 33444 345677777
Q ss_pred HHHHHHHHHHHCCCccccCCCCCceeeEEeeee
Q 010498 411 ACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNI 443 (509)
Q Consensus 411 L~~~L~~~f~~~Gl~~e~~~~r~fkPHiTLaR~ 443 (509)
+.+.+.+.+....|..- .+.| .+|+.|+=.
T Consensus 189 ~i~~vd~Vm~~~nL~~F--Y~DP-sfHiSL~Wc 218 (269)
T KOG3102|consen 189 QIDAVDEVMKLHNLPEF--YKDP-SFHISLVWC 218 (269)
T ss_pred HHHHHHHHHHHcCchhh--hcCC-CCCceEEEE
Confidence 88899999999888752 1234 899999854
No 84
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=68.85 E-value=8.8 Score=39.37 Aligned_cols=54 Identities=17% Similarity=0.293 Sum_probs=41.4
Q ss_pred ccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhhh
Q 010498 157 ASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVE 219 (509)
Q Consensus 157 ~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~~~~ 219 (509)
....-.|||++|+|++.||--|+|-|-+-. +.|.+.|+ -.++.. ++.|+.+..+
T Consensus 157 vKRRqRLiGpng~TLKAlelLT~CYilVqG----~TVsaiGp-fkGlke----vr~IV~DcM~ 210 (356)
T KOG2874|consen 157 VKRRQRLIGPNGSTLKALELLTNCYILVQG----NTVSAIGP-FKGLKE----VRKIVEDCMK 210 (356)
T ss_pred HHHHHHhcCCCchhHHHHHHHhhcEEEeeC----cEEEeecC-cchHHH----HHHHHHHHHh
Confidence 345678999999999999999999999864 67888887 345554 4556666554
No 85
>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=65.02 E-value=8.6 Score=38.07 Aligned_cols=62 Identities=16% Similarity=0.192 Sum_probs=42.7
Q ss_pred ceEEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCccccchHHhhhcccCC-ceEEEEccCCcchhHHHHhh
Q 010498 225 YSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQE-HKVAVELNIGDNSERVKVDR 303 (509)
Q Consensus 225 ~tHFIsIPl~~hp~I~~~~~~f~~~Il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rp~-~FVAv~l~~~~~~~~v~~~q 303 (509)
|||||++|+..-.-..++|-.+|-.+++++=.| +- +.+|- .+..+.|+++++..-+..+|
T Consensus 6 P~HFin~Pl~~f~~f~~~~~~LQ~~~~~eG~d~------------------k~-QkaPHlSl~mL~Isd~~i~~V~~~iq 66 (248)
T PF05213_consen 6 PTHFINFPLVQFEGFMLNFKDLQFQLLEEGVDC------------------KL-QKAPHLSLGMLDISDEDIPDVETAIQ 66 (248)
T ss_pred CCceeeccchhhhhHHHHHHHHHHHHHHcCCCc------------------cc-cccCeeEEEEEEcChhhhhhHHHHHH
Confidence 899999999865888999999999999874222 11 23444 35556777777655554555
Q ss_pred cc
Q 010498 304 TS 305 (509)
Q Consensus 304 ~~ 305 (509)
+-
T Consensus 67 ~V 68 (248)
T PF05213_consen 67 KV 68 (248)
T ss_pred HH
Confidence 43
No 86
>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=64.16 E-value=4.4 Score=33.90 Aligned_cols=37 Identities=11% Similarity=0.253 Sum_probs=30.1
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010498 150 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 186 (509)
Q Consensus 150 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 186 (509)
.+.|.|-...=|.+||++|.++++|.++....+.++.
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 3556666666799999999999999999888887754
No 87
>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=62.84 E-value=7.4 Score=41.18 Aligned_cols=39 Identities=26% Similarity=0.296 Sum_probs=36.2
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010498 148 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 186 (509)
Q Consensus 148 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 186 (509)
.....+.||.+-.+.-|||+|.+.|.--.=||.+|+|=+
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 88
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=60.13 E-value=9.2 Score=40.94 Aligned_cols=42 Identities=17% Similarity=0.056 Sum_probs=37.9
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC
Q 010498 148 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 189 (509)
Q Consensus 148 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~ 189 (509)
.....+.||.+-++.-|||+|.+.|.-.+=||.+|+|-+-++
T Consensus 307 ~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 307 EKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred CcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 467899999999999999999999999999999999966544
No 89
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=59.81 E-value=5 Score=44.53 Aligned_cols=71 Identities=24% Similarity=0.253 Sum_probs=54.6
Q ss_pred CCccCCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEccChhHHHHHHHHHHH
Q 010498 141 EPVPSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKIQA 212 (509)
Q Consensus 141 ~~~~~~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~---~~~I~I~G~s~~~v~~A~~~I~~ 212 (509)
.+....+-.+....+|...++.|+|++|.+++.|+.-.+.+|.+...+. ...+.|.|. +.-++.|+..|..
T Consensus 132 ~~~~~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~q-qk~~~~a~~~~~~ 205 (608)
T KOG2279|consen 132 QILTENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQ-QKEVAAAKHLILE 205 (608)
T ss_pred HHHhcCCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccc-cchHHHHHhhhhc
Confidence 3344556677889999999999999999999999999999999987665 345556654 4555666666644
No 90
>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=58.00 E-value=11 Score=34.84 Aligned_cols=36 Identities=25% Similarity=0.287 Sum_probs=31.8
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 010498 150 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 185 (509)
Q Consensus 150 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP 185 (509)
.+-+-|.+...|..||++|+.++.|++..|-+|++=
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 667778888999999999999999999999888873
No 91
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=57.51 E-value=11 Score=36.71 Aligned_cols=37 Identities=19% Similarity=0.190 Sum_probs=34.7
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010498 150 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 186 (509)
Q Consensus 150 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 186 (509)
...+.||.+-.+..|||+|.+.+...+=||-+|+|-.
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 92
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=51.74 E-value=15 Score=35.02 Aligned_cols=33 Identities=24% Similarity=0.397 Sum_probs=27.0
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010498 151 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 184 (509)
Q Consensus 151 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~i 184 (509)
+-+-|.+-. |.-|||+|.++|+|++..|-+|.+
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 93
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=51.52 E-value=15 Score=39.30 Aligned_cols=40 Identities=25% Similarity=0.269 Sum_probs=36.6
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCC
Q 010498 148 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS 187 (509)
Q Consensus 148 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~ 187 (509)
.....+.||.+.++.-|||+|.+.+.--.=||.+|+|=+.
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 94
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=50.17 E-value=15 Score=40.69 Aligned_cols=39 Identities=28% Similarity=0.307 Sum_probs=35.9
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010498 148 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 186 (509)
Q Consensus 148 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 186 (509)
.....+-||...++.-|||+|.+.|...+=||.+|+|=+
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 95
>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=49.49 E-value=13 Score=32.63 Aligned_cols=32 Identities=25% Similarity=0.377 Sum_probs=26.0
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEE
Q 010498 151 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKI 182 (509)
Q Consensus 151 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I 182 (509)
+.|.|-...-|.|||++|+++++|.+.....+
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 55666666679999999999999988877654
No 96
>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=49.40 E-value=28 Score=34.64 Aligned_cols=67 Identities=16% Similarity=0.255 Sum_probs=42.7
Q ss_pred CceEEEEccCCcchhHHHHhhccCcccccccccCCCCCCCCCCCCccccc-CCCCceEEeeccccCCHHHHHHH-HHHHH
Q 010498 283 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFI-KPKTFHLTVLMLKLWNKDRVNAA-TNVLK 360 (509)
Q Consensus 283 ~~FVAv~l~~~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gld~~~fv-~p~~LHLTL~fLgl~dee~v~~a-~~aL~ 360 (509)
..|+|++|..+.-.. ++.+.+.+. .++..+|++. +- ....+|+.|+..-....+++... .+.+.
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 489999999866432 555554442 1234677765 66 99999999998744444454444 45555
Q ss_pred HhH
Q 010498 361 SIS 363 (509)
Q Consensus 361 ~i~ 363 (509)
...
T Consensus 207 ~~~ 209 (239)
T PF09749_consen 207 EPL 209 (239)
T ss_pred HHH
Confidence 543
No 97
>COG5255 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.89 E-value=45 Score=33.00 Aligned_cols=34 Identities=18% Similarity=0.128 Sum_probs=24.8
Q ss_pred HHHHHHHHH-HCCCccccCCCCCceeeEEeeeecccc
Q 010498 412 CQVIIDAFN-EAGLVFHRDYNKKLKLHATLMNIRHKK 447 (509)
Q Consensus 412 ~~~L~~~f~-~~Gl~~e~~~~r~fkPHiTLaR~k~~~ 447 (509)
...+++.|. .+|+...+ ...|..||||+....+-
T Consensus 156 l~~~Rd~ls~~~g~r~P~--HDaY~FHITlgYl~~wl 190 (239)
T COG5255 156 LEEWRDYLSEKFGYRHPD--HDAYQFHITLGYLRIWL 190 (239)
T ss_pred HHHHHHHHhhhhcccCCC--CcceEEEEEeeeEeeec
Confidence 445566665 57998763 67899999999987653
No 98
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=41.49 E-value=26 Score=38.44 Aligned_cols=39 Identities=23% Similarity=0.244 Sum_probs=35.8
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010498 148 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 186 (509)
Q Consensus 148 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 186 (509)
.....+.||..-++.-|||+|.+.|---.=||.+|+|-+
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=41.39 E-value=59 Score=27.10 Aligned_cols=35 Identities=31% Similarity=0.485 Sum_probs=27.5
Q ss_pred CcEEEcCCCCCCCcEEEEc-cChhHHHHHHHHHHHHHHH
Q 010498 179 GVKIILPSSKKEDSIIIEG-NSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 179 ~~~I~iP~~~~~~~I~I~G-~s~~~v~~A~~~I~~i~~~ 216 (509)
++.+.|=+ +|-|+|+| .+.+.+..|.++|..++.+
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 56666643 47899999 4889999999999888875
No 100
>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=40.41 E-value=30 Score=33.55 Aligned_cols=41 Identities=17% Similarity=0.112 Sum_probs=18.1
Q ss_pred EEEEeeec-cCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeee
Q 010498 394 ILYAPVEE-IGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 442 (509)
Q Consensus 394 VLyagV~~-~~~~~~L~~L~~~L~~~f~~~Gl~~e~~~~r~fkPHiTLaR 442 (509)
-||+-+.. ++..+.|+.|-..|...|-.. .-.|-|||||.-
T Consensus 4 SlWl~P~~~~~~~~~L~~lI~~L~~~~~~~--------~p~F~PHiTL~s 45 (196)
T PF07823_consen 4 SLWLVPPPGSPLYERLKTLISSLASLFPGS--------PPPFEPHITLTS 45 (196)
T ss_dssp EEEEEE-T--TTHHHHHHHHHHHHHHST-----------------EEEEE
T ss_pred EEEEcCCCCccHHHHHHHHHHHHHHHCCCC--------CCCcCCeEEEeC
Confidence 47887764 123455655555554443311 136999999996
No 101
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=38.35 E-value=73 Score=33.86 Aligned_cols=55 Identities=20% Similarity=0.297 Sum_probs=45.5
Q ss_pred ccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHH--HHHHH
Q 010498 157 ASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQ--AIIAE 216 (509)
Q Consensus 157 ~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~--~i~~~ 216 (509)
....--+.|+.|.+++.||+.+|+.|.-+. ..+.|+|. +..|..|...++ .+...
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 456677899999999999999999998765 57899996 459999999999 44444
No 102
>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=36.66 E-value=2e+02 Score=29.20 Aligned_cols=88 Identities=15% Similarity=0.052 Sum_probs=46.7
Q ss_pred CCceEEeeccccCCHHHHHHHHHHHHHh-HHhhhhhc--------CCCCeEEEEceeccCCCCCCCceEEEEeeeccCCh
Q 010498 335 KTFHLTVLMLKLWNKDRVNAATNVLKSI-SSKVMDAL--------DNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDG 405 (509)
Q Consensus 335 ~~LHLTL~fLgl~dee~v~~a~~aL~~i-~~~i~~~L--------~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~ 405 (509)
..||+||.-.....+..-.+..+.+..+ ........ ....+.++|..|- |.+ ||+-+.|.-.+..
T Consensus 114 ~~FHVTL~H~as~k~~~~k~lW~~y~~~~~~~~~~~~~~~~~~~~~~~~~~v~L~rlv-wd~-----rimai~V~~~~~~ 187 (257)
T PF08302_consen 114 PEFHVTLIHRASSKEQPAKELWKRYTKLYKSALKKNPKQEPTQTPTLGSCDVRLERLV-WDD-----RIMAIVVRIVPPE 187 (257)
T ss_pred CCCeEEEEecccCCcCcchHHHHHHHHHHHhhcccccccccccccccceEEEEEEEEE-ECC-----cEEEEEEEccCcc
Confidence 5689999998776653311222222221 11111100 0135888898886 776 8988887642110
Q ss_pred hHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeeee
Q 010498 406 DRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNI 443 (509)
Q Consensus 406 ~~L~~L~~~L~~~f~~~Gl~~e~~~~r~fkPHiTLaR~ 443 (509)
..-.. ..++..- .=.|||||+-.
T Consensus 188 ~~~~~----------~~~~~c~-----N~~~HITVGT~ 210 (257)
T PF08302_consen 188 DEEDE----------VPEWECT-----NKIPHITVGTR 210 (257)
T ss_pred ccccc----------cCCcccC-----CCCCEEEEEcC
Confidence 00000 2344332 34899999975
No 103
>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=35.17 E-value=1.4e+02 Score=28.46 Aligned_cols=79 Identities=13% Similarity=0.084 Sum_probs=43.5
Q ss_pred eeccCChhHHHHHHHHHHHHHHHCCCcccc---------------C----------CCCCceeeEEeeeecccccccCCC
Q 010498 399 VEEIGDGDRLLHACQVIIDAFNEAGLVFHR---------------D----------YNKKLKLHATLMNIRHKKRRKGTR 453 (509)
Q Consensus 399 V~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~---------------~----------~~r~fkPHiTLaR~k~~~~~~~~~ 453 (509)
+.+.+....|+.|+..+...|...-=+..+ + --..|..||||-.---...
T Consensus 47 Lvp~~~~~~L~~LAa~cV~~~d~fRAPls~aelaRR~~~~Ls~~Q~~~L~rWGYPYV~deFRFHmTLTg~l~~~~----- 121 (160)
T PF06299_consen 47 LVPAGPCPALQALAAACVRAFDPFRAPLSEAELARRRPAGLSPRQRANLERWGYPYVMDEFRFHMTLTGRLDPAE----- 121 (160)
T ss_pred EeeCCCCHHHHHHHHHHHHhhhhccCCCChHHHhhcCcccCCHHHHHHHHHhCCCceeCcCEeeEEeCCCCCHHH-----
Confidence 333344578999999988877653111110 0 0257999999986321100
Q ss_pred ccccccHHHHHH-HhCCCccccEEecEEEEEee
Q 010498 454 RVDYFDARDIFK-QFGSKEWGEYLIKEAHLSQR 485 (509)
Q Consensus 454 ~~~~fda~~il~-~~~d~~fG~~~V~eI~Ls~l 485 (509)
. -.+...++ .|...--..+.|+.|.|+.-
T Consensus 122 -~--~~~~~~l~~~f~~~l~~p~~id~laLf~e 151 (160)
T PF06299_consen 122 -R--ARVEAALEAHFAPLLPEPLRIDSLALFGE 151 (160)
T ss_pred -H--HHHHHHHHHHHHhhcCCCeeecceEEEec
Confidence 0 01112222 23444446788999999643
No 104
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=34.37 E-value=36 Score=33.13 Aligned_cols=35 Identities=31% Similarity=0.321 Sum_probs=28.6
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010498 150 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 184 (509)
Q Consensus 150 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~i 184 (509)
.....+-..-.|..||++|+.++.|.++.|-+|+|
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdV 111 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDV 111 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEE
Confidence 44445556668999999999999999999977765
No 105
>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=31.68 E-value=39 Score=28.19 Aligned_cols=32 Identities=9% Similarity=0.254 Sum_probs=23.3
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcE
Q 010498 148 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVK 181 (509)
Q Consensus 148 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~ 181 (509)
+..+.+.+ .+-|.+||++|.++++|.+...-.
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 44444444 677999999999999987765443
No 106
>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=31.57 E-value=29 Score=34.88 Aligned_cols=29 Identities=24% Similarity=0.236 Sum_probs=21.0
Q ss_pred eEEEEecccccc-ccccCCCchhHHHHHHH
Q 010498 149 HSLSVEVGASVI-RFIKGKEGSTQKKFEKE 177 (509)
Q Consensus 149 ~~~~v~Vp~~~~-~~IIGk~G~t~k~iE~e 177 (509)
....|.|.++-| +.|||++|+++|+|-.+
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 455667776554 67899999999986433
No 107
>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=31.05 E-value=41 Score=31.42 Aligned_cols=33 Identities=27% Similarity=0.339 Sum_probs=28.4
Q ss_pred EEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010498 152 SVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 184 (509)
Q Consensus 152 ~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~i 184 (509)
.|.|-.+.=|.+||++|.++++|-.+||-+-.+
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~v 111 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKV 111 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEE
Confidence 455666778999999999999999999988666
No 108
>COG0799 Uncharacterized homolog of plant Iojap protein [Function unknown]
Probab=29.90 E-value=2.4e+02 Score=25.40 Aligned_cols=62 Identities=11% Similarity=0.165 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHHhHHhhhhhcCCCCeEEEEceeccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcc
Q 010498 350 DRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 426 (509)
Q Consensus 350 e~v~~a~~aL~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~ 426 (509)
+.+..+.++|.+.+ ......|.++|...+-+ ..+.+.- .+...+..+++.|.+.+.++|+.+
T Consensus 5 ~l~~~i~~alddkK-------AeDIv~lDv~~~s~~tD-----yfVIatg---~s~rhv~Aiad~i~~~~k~~g~~~ 66 (115)
T COG0799 5 ELLEVIVEALDDKK-------AEDIVVLDVSGKSSLTD-----YFVIATG---NSSRHVKAIADNVKEELKEAGEVP 66 (115)
T ss_pred HHHHHHHHHHHhcc-------CCCeEEEEccCCccccc-----EEEEEEe---CchHHHHHHHHHHHHHHHHcCCCc
Confidence 34555566666554 24677899999999987 3444433 235789999999999999999976
No 109
>PRK15494 era GTPase Era; Provisional
Probab=29.69 E-value=32 Score=36.10 Aligned_cols=36 Identities=28% Similarity=0.357 Sum_probs=25.6
Q ss_pred eEEEEeccccc-cccccCCCchhHHHH--------HHHhCcEEEc
Q 010498 149 HSLSVEVGASV-IRFIKGKEGSTQKKF--------EKEMGVKIIL 184 (509)
Q Consensus 149 ~~~~v~Vp~~~-~~~IIGk~G~t~k~i--------E~eT~~~I~i 184 (509)
....|.|+++- -+.|||++|.++|+| |+-+|+++.+
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 44667777755 467899999999884 5556666554
No 110
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=29.68 E-value=2.1e+02 Score=29.43 Aligned_cols=83 Identities=14% Similarity=0.190 Sum_probs=48.2
Q ss_pred CceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEEceeccCCCCCCCceE-EEEeeeccCChhHHHHHHHH
Q 010498 336 TFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARI-LYAPVEEIGDGDRLLHACQV 414 (509)
Q Consensus 336 ~LHLTL~fLgl~dee~v~~a~~aL~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~pRV-LyagV~~~~~~~~L~~L~~~ 414 (509)
..++++.+=...| +++|.+.|.++.......+..++..+.+.+++-..= .-.| .|+... +-...-.++...
T Consensus 185 r~~~~v~V~y~~d---~~~~~~il~~~~~~~~~vl~~p~p~v~~~~~~dssi---~~~v~~wv~~~--~~~~~~~~~~~~ 256 (286)
T PRK10334 185 RNEFIIGVAYDSD---IDQVKQILTNIIQSEDRILKDREMTVRLNELGASSI---NFVVRVWSNSG--DLQNVYWDVLER 256 (286)
T ss_pred EEEEEEEecCCCC---HHHHHHHHHHHHHhCCceecCCCCEEEEEeeeCceE---EEEEEEEEecc--hhHHHHHHHHHH
Confidence 4567766555444 555666676664444445555555677766544321 1122 454432 222334577888
Q ss_pred HHHHHHHCCCcc
Q 010498 415 IIDAFNEAGLVF 426 (509)
Q Consensus 415 L~~~f~~~Gl~~ 426 (509)
|.++|.++|+..
T Consensus 257 I~~~f~~~gI~i 268 (286)
T PRK10334 257 IKREFDAAGISF 268 (286)
T ss_pred HHHHHHHCCCcC
Confidence 999999999987
No 111
>PRK00089 era GTPase Era; Reviewed
Probab=29.21 E-value=34 Score=34.55 Aligned_cols=36 Identities=33% Similarity=0.417 Sum_probs=24.6
Q ss_pred eEEEEeccccc-cccccCCCchhHHH--------HHHHhCcEEEc
Q 010498 149 HSLSVEVGASV-IRFIKGKEGSTQKK--------FEKEMGVKIIL 184 (509)
Q Consensus 149 ~~~~v~Vp~~~-~~~IIGk~G~t~k~--------iE~eT~~~I~i 184 (509)
....|.|.++- -+.|||++|+++|+ ||+-+|++|.+
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 34455666544 46789999999987 45556666655
No 112
>PF07485 DUF1529: Domain of Unknown Function (DUF1259); InterPro: IPR011094 This family is the lppY/lpqO homologue family. They are related to 'probable conserved lipoproteins' LppY and LpqO from Mycobacterium bovis.
Probab=27.67 E-value=2.6e+02 Score=25.36 Aligned_cols=55 Identities=16% Similarity=0.297 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHhHHhhhhhcCCCCeEEEEceeccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHH
Q 010498 349 KDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFN 420 (509)
Q Consensus 349 ee~v~~a~~aL~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~L~~~L~~~f~ 420 (509)
++|++.+..+|.+ ..+.++-=-=..+ .++||+.|+=+...++ -..||+.++++|.
T Consensus 67 ~~EV~pvi~aL~~-----------~GI~vtAlHNH~l---~e~Prl~ymH~~~~gd---p~~lA~~vr~Ald 121 (123)
T PF07485_consen 67 EDEVNPVISALRK-----------NGIEVTALHNHWL---FEQPRLFYMHIWGVGD---PAKLARKVRAALD 121 (123)
T ss_pred HHHHHHHHHHHHH-----------CCceEEEEecccc---cCCCCEEEEEEEecCC---HHHHHHHHHHHHh
Confidence 7899988888876 2333332222233 3467999999986544 4455888888764
No 113
>PRK11538 ribosome-associated protein; Provisional
Probab=27.53 E-value=2.8e+02 Score=24.32 Aligned_cols=61 Identities=7% Similarity=0.170 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHhHHhhhhhcCCCCeEEEEceeccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcc
Q 010498 351 RVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 426 (509)
Q Consensus 351 ~v~~a~~aL~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~ 426 (509)
.+..+.++|.+.+ ...-..+.++++..|-+ -.+-+.. .+...++.+++.|.+.+.+.|+.+
T Consensus 6 ~~~~i~~~l~dkK-------a~DI~vlDv~~~~~~~D-----y~VIatg---~S~rh~~aia~~v~~~~k~~~~~~ 66 (105)
T PRK11538 6 LQDFVIDKIDDLK-------GQDIIALDVQGKSSITD-----CMIICTG---TSSRHVMSIADHVVQESRAAGLLP 66 (105)
T ss_pred HHHHHHHHHHHcC-------CCCeEEEECCCCCcccC-----EEEEEEe---CCHHHHHHHHHHHHHHHHHcCCCC
Confidence 3445566666643 23455678888887765 3333332 346789999999999998888754
No 114
>PF08975 2H-phosphodiest: Domain of unknown function (DUF1868); InterPro: IPR015069 This family consist of hypothetical bacterial proteins. ; PDB: 2FSQ_A.
Probab=27.51 E-value=28 Score=31.43 Aligned_cols=47 Identities=15% Similarity=0.172 Sum_probs=27.4
Q ss_pred CceEEEEccCCcchhHHHHhhccCcccccccccCCCCCCCCCCCCcccccCCCCceEEeec
Q 010498 283 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLM 343 (509)
Q Consensus 283 ~~FVAv~l~~~~~~~~v~~~q~~i~~~~~~~~~~r~~~~~~~Gld~~~fv~p~~LHLTL~f 343 (509)
|.||+==-...+....+..+|+.|. ..+ ..+.=.|.||..+|+|+.=
T Consensus 14 NTvIchl~~~s~~~~al~~i~~~l~---------~~~-----~~~k~a~lP~sS~HMTVf~ 60 (118)
T PF08975_consen 14 NTVICHLPQDSPFYAALLAIQQRLR---------ESP-----FADKLAFLPPSSYHMTVFE 60 (118)
T ss_dssp EEEEEEB-TTSHHHHHHHHHHHHHH---------TSG-----GGGGEEE--GGG-EEEEEE
T ss_pred CeEEeecCCCChHHHHHHHHHHHHH---------hCc-----cccceEecCcchhhhhhhc
Confidence 5566643333455678888998875 111 1233369999999999854
No 115
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=26.61 E-value=34 Score=34.32 Aligned_cols=37 Identities=24% Similarity=0.267 Sum_probs=28.1
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 010498 149 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 185 (509)
Q Consensus 149 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP 185 (509)
..+.|-|=...=|.+||++|+.+++|.++....+..+
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 3445556667789999999999999888776665553
No 116
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=24.81 E-value=49 Score=36.96 Aligned_cols=34 Identities=26% Similarity=0.264 Sum_probs=29.3
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010498 151 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 184 (509)
Q Consensus 151 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~i 184 (509)
-+|-|-..-=|.+|||+|++.++|-++||-+-.|
T Consensus 101 GEViIea~KPGlvigk~g~~~reI~~~tgW~p~i 134 (637)
T COG1782 101 GEVIIEAKKPGLVIGKGGSTLREITAETGWAPKI 134 (637)
T ss_pred ceEEEEecCCceEEecCchHHHHHHHHhCCccee
Confidence 4566777778999999999999999999988666
No 117
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=22.74 E-value=1.4e+02 Score=29.57 Aligned_cols=75 Identities=15% Similarity=0.125 Sum_probs=47.8
Q ss_pred CCccCCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhh
Q 010498 141 EPVPSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAV 218 (509)
Q Consensus 141 ~~~~~~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i~~~~~ 218 (509)
++..+...-.+.+.|..+-.+.|||+.|.|+..||-=++.-+.- ..+....|++.- ..=.++=.+.+..+...+.
T Consensus 83 ~i~v~~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~-~~g~~~~v~ldv--~~yRerR~e~L~~LA~~~A 157 (208)
T COG1847 83 TITVSEEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK-IGGKFKRVTLDV--GDYRERRKETLIKLAERAA 157 (208)
T ss_pred EEEEeecCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh-hcCcceEEEEEh--hhHHHHHHHHHHHHHHHHH
Confidence 33444456677888888889999999999999999998877765 222233444432 1233444455555544443
No 118
>COG1159 Era GTPase [General function prediction only]
Probab=22.59 E-value=41 Score=35.00 Aligned_cols=26 Identities=27% Similarity=0.291 Sum_probs=19.8
Q ss_pred eEEEEeccccc-cccccCCCchhHHHH
Q 010498 149 HSLSVEVGASV-IRFIKGKEGSTQKKF 174 (509)
Q Consensus 149 ~~~~v~Vp~~~-~~~IIGk~G~t~k~i 174 (509)
....+.|+++- -+.||||+|+++|+|
T Consensus 229 I~a~I~Ver~sQK~IiIGk~G~~iK~I 255 (298)
T COG1159 229 IHATIYVERESQKGIIIGKNGAMIKKI 255 (298)
T ss_pred EEEEEEEecCCccceEECCCcHHHHHH
Confidence 34556677644 577899999999987
No 119
>PF10105 DUF2344: Uncharacterized protein conserved in bacteria (DUF2344); InterPro: IPR018768 This domain, found in various hypothetical bacterial proteins and Radical Sam domain proteins, has no known function.
Probab=22.02 E-value=1e+02 Score=29.83 Aligned_cols=30 Identities=27% Similarity=0.441 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHCCCccccCCCCCceeeEEe
Q 010498 409 LHACQVIIDAFNEAGLVFHRDYNKKLKLHATL 440 (509)
Q Consensus 409 ~~L~~~L~~~f~~~Gl~~e~~~~r~fkPHiTL 440 (509)
.++...++++|+.+|++.. ..+.|+||.-+
T Consensus 18 Ldl~r~~eRa~rRA~lp~a--~SqGFnP~Pki 47 (187)
T PF10105_consen 18 LDLMRVFERALRRAGLPVA--YSQGFNPHPKI 47 (187)
T ss_pred HHHHHHHHHHhhhcCCCee--ecCCCCCCcce
Confidence 3567889999999999985 47899999544
No 120
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=20.80 E-value=1e+02 Score=25.46 Aligned_cols=35 Identities=23% Similarity=0.399 Sum_probs=21.5
Q ss_pred CHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEEceeccCC
Q 010498 348 NKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMR 386 (509)
Q Consensus 348 dee~v~~a~~aL~~i~~~i~~~L~~~pf~L~l~GLg~F~ 386 (509)
+..++..+.++|.++ +.+.|... -.+.|.|+|.|.
T Consensus 17 ~~~~v~~vl~~l~~~---i~~~L~~g-~~V~i~g~G~F~ 51 (90)
T smart00411 17 SKKDAKAAVDAFLEI---ITEALKKG-EKVELRGFGTFE 51 (90)
T ss_pred CHHHHHHHHHHHHHH---HHHHHhCC-CeEEEeCcEEEE
Confidence 466666665555443 44444322 278899999994
No 121
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=20.24 E-value=3.6e+02 Score=24.69 Aligned_cols=36 Identities=17% Similarity=0.413 Sum_probs=28.4
Q ss_pred CCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcc
Q 010498 388 SKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 426 (509)
Q Consensus 388 dp~~pRVLyagV~~~~~~~~L~~L~~~L~~~f~~~Gl~~ 426 (509)
+|++.|++|+...+ .+++.+..+...+.+.++|=.+
T Consensus 93 e~eRv~~~wiSa~E---~ekf~e~~~efv~~i~~lGpnp 128 (132)
T COG1908 93 EPERVRVLWISAAE---GEKFAETINEFVERIKELGPNP 128 (132)
T ss_pred CcceEEEEEEehhh---HHHHHHHHHHHHHHHHHhCCCc
Confidence 37888999999986 4778888888888888887544
No 122
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=20.03 E-value=41 Score=40.98 Aligned_cols=64 Identities=20% Similarity=0.106 Sum_probs=50.5
Q ss_pred EEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHHHHHHHH
Q 010498 152 SVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIAE 216 (509)
Q Consensus 152 ~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~----~~~I~I~G~s~~~v~~A~~~I~~i~~~ 216 (509)
.+.||.-....+||+||.+++.+..-||+-|.|-+-.. ++.+.+.|. .+.+.-|..-|...+.+
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 46688888999999999999999999999999977322 356777775 46777777777766544
Done!