Query 010252
Match_columns 514
No_of_seqs 302 out of 932
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 22:49:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010252.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010252hhsearch_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 1.5E-49 3.3E-54 398.1 16.0 338 60-507 2-345 (345)
2 PLN00108 unknown protein; Prov 100.0 1.1E-45 2.3E-50 365.2 22.7 224 227-509 33-256 (257)
3 PF10469 AKAP7_NLS: AKAP7 2'5' 100.0 1.6E-41 3.6E-46 329.1 21.5 207 230-507 1-209 (209)
4 COG1514 LigT 2'-5' RNA ligase 99.9 6.1E-27 1.3E-31 223.1 17.9 179 288-509 2-180 (180)
5 TIGR02258 2_5_ligase 2'-5' RNA 99.9 4.4E-25 9.6E-30 208.3 17.5 178 288-507 2-179 (179)
6 PRK15124 2'-5' RNA ligase; Pro 99.9 3.5E-25 7.7E-30 209.9 16.7 170 288-508 6-175 (176)
7 PRK13679 hypothetical protein; 99.7 1.3E-16 2.8E-21 150.2 15.7 167 288-508 2-168 (168)
8 PHA02574 57B hypothetical prot 99.7 1.8E-16 3.8E-21 146.8 9.2 109 288-447 10-118 (149)
9 PF13563 2_5_RNA_ligase2: 2'-5 99.3 1.6E-11 3.5E-16 111.7 9.6 128 337-490 21-149 (153)
10 cd02394 vigilin_like_KH K homo 99.2 1.5E-11 3.4E-16 96.9 6.1 60 156-216 2-62 (62)
11 cd02393 PNPase_KH Polynucleoti 99.2 2.2E-11 4.8E-16 96.5 6.4 59 155-216 3-61 (61)
12 PF00013 KH_1: KH domain syndr 99.2 2.3E-11 5.1E-16 95.2 4.0 60 155-215 1-60 (60)
13 PF05213 Corona_NS2A: Coronavi 99.0 4.6E-09 9.9E-14 101.2 11.2 167 285-505 4-177 (248)
14 cd00105 KH-I K homology RNA-bi 98.9 1.9E-09 4.1E-14 84.7 6.0 59 156-215 2-63 (64)
15 PF02834 LigT_PEase: LigT like 98.9 1.6E-09 3.5E-14 90.6 3.4 60 335-401 28-87 (87)
16 cd02396 PCBP_like_KH K homolog 98.8 1.2E-08 2.6E-13 81.5 6.1 59 156-215 2-64 (65)
17 cd02395 SF1_like-KH Splicing f 98.7 1.9E-08 4.1E-13 90.3 6.7 59 163-221 15-95 (120)
18 smart00322 KH K homology RNA-b 98.7 3.8E-08 8.3E-13 76.7 7.6 66 153-219 2-68 (69)
19 PF13014 KH_3: KH domain 98.7 1.4E-08 3.1E-13 74.6 4.0 39 164-202 1-43 (43)
20 KOG1676 K-homology type RNA bi 98.5 2E-07 4.2E-12 101.4 8.3 106 152-258 228-346 (600)
21 KOG0119 Splicing factor 1/bran 98.4 5.4E-07 1.2E-11 96.0 6.3 72 153-224 137-233 (554)
22 PRK13763 putative RNA-processi 98.3 9.3E-07 2E-11 84.7 6.9 65 154-220 3-70 (180)
23 TIGR03665 arCOG04150 arCOG0415 98.3 8.1E-07 1.8E-11 84.5 5.3 61 158-220 2-64 (172)
24 PRK13763 putative RNA-processi 98.0 8.8E-06 1.9E-10 78.0 5.8 54 163-221 104-157 (180)
25 COG5176 MSL5 Splicing factor ( 97.9 9.8E-06 2.1E-10 78.2 5.0 76 146-221 140-221 (269)
26 TIGR03665 arCOG04150 arCOG0415 97.9 1.4E-05 3.1E-10 76.0 5.6 54 163-221 98-151 (172)
27 KOG2191 RNA-binding protein NO 97.9 0.0002 4.2E-09 73.6 13.9 107 151-258 36-160 (402)
28 TIGR02696 pppGpp_PNP guanosine 97.8 3.1E-05 6.8E-10 87.6 7.0 65 154-221 578-642 (719)
29 KOG2208 Vigilin [Lipid transpo 97.8 4E-05 8.7E-10 87.9 7.1 104 152-259 345-449 (753)
30 KOG2193 IGF-II mRNA-binding pr 97.7 2.4E-05 5.2E-10 82.2 4.1 104 151-258 196-308 (584)
31 TIGR03591 polynuc_phos polyrib 97.7 5.2E-05 1.1E-09 86.3 6.1 65 154-221 551-615 (684)
32 KOG1588 RNA-binding protein Sa 97.6 0.00015 3.2E-09 72.7 7.3 70 153-224 91-187 (259)
33 KOG1676 K-homology type RNA bi 97.5 0.00013 2.8E-09 79.9 5.1 110 150-260 50-169 (600)
34 KOG2193 IGF-II mRNA-binding pr 97.4 0.00017 3.7E-09 76.0 4.8 61 161-222 287-353 (584)
35 COG1094 Predicted RNA-binding 97.3 0.00049 1.1E-08 66.4 6.4 67 152-220 6-76 (194)
36 PRK04163 exosome complex RNA-b 97.3 0.00047 1E-08 68.8 6.6 64 155-221 146-209 (235)
37 KOG2113 Predicted RNA binding 97.2 0.0004 8.7E-09 70.9 4.8 66 151-217 23-88 (394)
38 KOG2191 RNA-binding protein NO 97.2 0.00075 1.6E-08 69.5 6.4 66 155-221 133-204 (402)
39 PLN00207 polyribonucleotide nu 97.2 0.00047 1E-08 79.9 5.5 65 154-221 685-750 (891)
40 KOG2190 PolyC-binding proteins 97.0 0.0018 3.8E-08 71.1 8.3 67 154-221 138-208 (485)
41 COG1185 Pnp Polyribonucleotide 97.0 0.001 2.2E-08 74.4 6.3 69 153-224 551-619 (692)
42 PRK11824 polynucleotide phosph 96.8 0.00099 2.1E-08 76.2 4.5 64 155-221 555-618 (693)
43 PF09749 HVSL: Uncharacterised 96.6 0.015 3.3E-07 58.1 10.7 103 338-449 86-190 (239)
44 KOG2192 PolyC-binding hnRNP-K 96.6 0.005 1.1E-07 61.9 6.7 67 154-221 315-384 (390)
45 TIGR03319 YmdA_YtgF conserved 96.6 0.0047 1E-07 68.4 7.1 69 151-221 201-270 (514)
46 PF02834 LigT_PEase: LigT like 96.5 0.0024 5.3E-08 53.1 3.4 76 410-499 8-87 (87)
47 PRK00106 hypothetical protein; 96.4 0.0059 1.3E-07 67.7 7.0 69 151-221 222-291 (535)
48 PRK12704 phosphodiesterase; Pr 96.4 0.006 1.3E-07 67.7 6.7 68 152-221 208-276 (520)
49 KOG0336 ATP-dependent RNA heli 96.2 0.0035 7.5E-08 66.7 3.6 69 152-221 45-113 (629)
50 COG1094 Predicted RNA-binding 96.2 0.0084 1.8E-07 58.0 5.4 54 163-221 111-164 (194)
51 PF07823 CPDase: Cyclic phosph 95.7 0.084 1.8E-06 51.3 10.3 137 343-507 40-196 (196)
52 PRK12705 hypothetical protein; 95.0 0.028 6.2E-07 62.1 5.1 68 152-221 196-264 (508)
53 COG1097 RRP4 RNA-binding prote 95.0 0.042 9E-07 54.9 5.7 63 156-221 148-210 (239)
54 cd02134 NusA_KH NusA_K homolog 95.0 0.026 5.7E-07 44.6 3.4 37 153-189 24-60 (61)
55 KOG2279 Kinase anchor protein 94.6 0.025 5.5E-07 61.9 3.1 103 150-257 64-167 (608)
56 KOG2814 Transcription coactiva 94.0 0.01 2.3E-07 61.3 -1.1 151 340-504 128-281 (345)
57 KOG1067 Predicted RNA-binding 93.8 0.052 1.1E-06 59.8 3.7 63 155-221 598-660 (760)
58 KOG2192 PolyC-binding hnRNP-K 93.1 0.26 5.7E-06 49.9 7.0 70 151-221 45-115 (390)
59 KOG2190 PolyC-binding proteins 92.5 0.24 5.2E-06 54.7 6.4 102 156-258 45-166 (485)
60 KOG2208 Vigilin [Lipid transpo 90.9 0.16 3.5E-06 58.9 3.0 41 151-191 706-746 (753)
61 TIGR03223 Phn_opern_protn puta 90.9 4.4 9.5E-05 40.6 12.6 140 340-509 56-228 (228)
62 PF14611 SLS: Mitochondrial in 87.7 2.4 5.2E-05 41.2 8.2 73 156-238 28-100 (210)
63 COG1855 ATPase (PilT family) [ 85.7 0.54 1.2E-05 51.3 2.6 42 153-194 485-526 (604)
64 cd02409 KH-II KH-II (K homolo 84.8 1.1 2.5E-05 34.5 3.5 35 153-187 24-58 (68)
65 KOG2113 Predicted RNA binding 84.3 0.86 1.9E-05 47.2 3.2 69 151-219 112-181 (394)
66 KOG3273 Predicted RNA-binding 83.6 0.8 1.7E-05 44.7 2.5 54 163-221 178-231 (252)
67 PF13083 KH_4: KH domain; PDB: 83.5 0.62 1.3E-05 37.8 1.5 34 151-184 26-59 (73)
68 PRK02821 hypothetical protein; 83.1 0.96 2.1E-05 37.8 2.5 32 152-183 29-60 (77)
69 PRK08406 transcription elongat 83.0 1.2 2.5E-05 41.3 3.2 38 153-190 98-135 (140)
70 PRK00468 hypothetical protein; 81.8 1.4 3E-05 36.6 2.9 30 152-181 28-57 (75)
71 COG5166 Uncharacterized conser 81.5 1.7 3.8E-05 47.8 4.3 70 152-221 447-524 (657)
72 PRK13764 ATPase; Provisional 81.0 1.1 2.4E-05 50.8 2.8 43 152-194 479-521 (602)
73 COG1837 Predicted RNA-binding 80.9 1.6 3.4E-05 36.5 2.9 30 151-180 27-56 (76)
74 PHA02977 hypothetical protein; 80.1 6 0.00013 36.9 6.7 94 343-450 71-174 (201)
75 PF10469 AKAP7_NLS: AKAP7 2'5' 79.1 0.86 1.9E-05 44.3 1.0 25 287-311 1-25 (209)
76 PRK01064 hypothetical protein; 77.9 2.1 4.5E-05 35.9 2.8 31 152-182 28-58 (78)
77 PF07650 KH_2: KH domain syndr 75.4 1.7 3.6E-05 35.6 1.6 36 153-188 24-59 (78)
78 TIGR01952 nusA_arch NusA famil 74.8 2.7 5.8E-05 39.1 2.9 38 153-190 99-136 (141)
79 PRK08406 transcription elongat 72.9 3.7 8.1E-05 38.0 3.4 37 155-191 33-69 (140)
80 cd02414 jag_KH jag_K homology 72.8 3 6.5E-05 34.3 2.5 35 155-189 25-59 (77)
81 PF13184 KH_5: NusA-like KH do 70.0 4.3 9.4E-05 33.0 2.8 25 165-189 19-44 (69)
82 KOG2874 rRNA processing protei 69.4 8.6 0.00019 39.5 5.3 53 163-224 158-210 (356)
83 KOG3102 Uncharacterized conser 68.0 18 0.00038 36.0 6.9 101 337-448 117-218 (269)
84 COG5255 Uncharacterized protei 66.7 17 0.00037 35.9 6.5 124 298-452 52-190 (239)
85 KOG2279 Kinase anchor protein 65.6 3.4 7.4E-05 45.9 1.7 72 146-218 132-206 (608)
86 PLN00108 unknown protein; Prov 64.0 3.3 7.1E-05 42.2 1.1 29 284-312 33-62 (257)
87 cd02413 40S_S3_KH K homology R 63.2 4.8 0.0001 33.8 1.8 36 156-191 32-67 (81)
88 TIGR01953 NusA transcription t 62.4 7.8 0.00017 41.1 3.6 39 153-191 300-338 (341)
89 PF05213 Corona_NS2A: Coronavi 60.5 9.8 0.00021 37.8 3.6 61 230-309 6-67 (248)
90 PRK12328 nusA transcription el 59.8 9.5 0.00021 40.9 3.8 42 153-194 307-348 (374)
91 TIGR01952 nusA_arch NusA famil 57.5 12 0.00026 34.8 3.6 36 155-190 34-69 (141)
92 COG0195 NusA Transcription elo 56.8 11 0.00023 36.9 3.2 37 155-191 143-179 (190)
93 PRK12327 nusA transcription el 51.3 16 0.00034 39.2 3.7 40 153-192 302-341 (362)
94 PRK06418 transcription elongat 51.3 16 0.00034 35.0 3.4 33 156-189 63-95 (166)
95 PRK09202 nusA transcription el 49.9 15 0.00033 40.7 3.4 39 153-191 301-339 (470)
96 PF09749 HVSL: Uncharacterised 49.5 26 0.00056 35.0 4.8 68 288-369 141-210 (239)
97 cd02412 30S_S3_KH K homology R 47.8 15 0.00032 32.4 2.4 32 156-187 63-94 (109)
98 PRK12329 nusA transcription el 41.5 26 0.00056 38.5 3.5 39 153-191 334-372 (449)
99 PF06299 DUF1045: Protein of u 41.2 88 0.0019 29.8 6.6 109 353-489 13-150 (160)
100 COG1702 PhoH Phosphate starvat 39.8 68 0.0015 34.2 6.2 53 161-218 22-74 (348)
101 PRK10334 mechanosensitive chan 38.8 1.3E+02 0.0027 31.2 8.0 83 341-431 185-268 (286)
102 PF00352 TBP: Transcription fa 38.5 69 0.0015 26.8 5.0 35 184-221 49-84 (86)
103 PF08302 tRNA_lig_CPD: Fungal 36.9 1.6E+02 0.0034 30.1 8.2 105 340-473 114-227 (257)
104 PF07823 CPDase: Cyclic phosph 35.5 39 0.00084 32.8 3.5 41 399-447 4-45 (196)
105 COG0195 NusA Transcription elo 33.7 41 0.00089 32.8 3.2 36 154-189 76-111 (190)
106 PF07485 DUF1529: Domain of Un 31.8 1.9E+02 0.0042 26.3 7.1 55 354-425 67-121 (123)
107 PRK15494 era GTPase Era; Provi 31.7 41 0.00088 35.4 3.1 36 154-189 273-317 (339)
108 cd02410 archeal_CPSF_KH The ar 30.2 44 0.00095 31.3 2.7 33 157-189 79-111 (145)
109 COG0799 Uncharacterized homolo 29.7 2.5E+02 0.0054 25.4 7.3 61 356-431 6-66 (115)
110 cd02411 archeal_30S_S3_KH K ho 29.6 45 0.00098 27.9 2.5 32 153-186 39-70 (85)
111 TIGR00436 era GTP-binding prot 28.9 35 0.00075 34.4 2.0 28 154-181 221-249 (270)
112 PRK11538 ribosome-associated p 28.2 2.8E+02 0.006 24.4 7.3 60 357-431 7-66 (105)
113 COG0092 RpsC Ribosomal protein 27.0 33 0.00073 34.5 1.4 38 153-190 50-87 (233)
114 PF08975 2H-phosphodiest: Doma 26.6 23 0.0005 32.0 0.2 47 288-348 14-60 (118)
115 PRK00089 era GTPase Era; Revie 26.6 41 0.00089 34.0 2.0 36 154-189 226-270 (292)
116 COG1782 Predicted metal-depend 26.4 44 0.00094 37.4 2.2 35 156-190 101-135 (637)
117 PF10105 DUF2344: Uncharacteri 24.9 81 0.0018 30.5 3.6 46 397-445 2-47 (187)
118 COG1847 Jag Predicted RNA-bind 23.4 1.4E+02 0.003 29.7 4.8 74 146-222 83-156 (208)
119 TIGR00090 iojap_ybeB iojap-lik 21.1 4.3E+02 0.0093 22.8 7.0 46 378-431 16-61 (99)
120 COG1159 Era GTPase [General fu 20.3 49 0.0011 34.5 1.2 26 154-179 229-255 (298)
121 smart00411 BHL bacterial (prok 20.2 1E+02 0.0022 25.4 2.9 35 353-391 17-51 (90)
No 1
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=100.00 E-value=1.5e-49 Score=398.11 Aligned_cols=338 Identities=36% Similarity=0.560 Sum_probs=289.7
Q ss_pred cccccccccCceeeeccccccccccccccccCCCCCceEEe-eeccCCcccccccceeeeecccccccccCCcccccccc
Q 010252 60 YGDKKQKIINPVWRPVSTQASVNEESLVKDVSEDGSQIQEM-HCSTSSNVSDAQLGVEVAEAVNEGTDLTLSSSVSLDDI 138 (514)
Q Consensus 60 ~~~~~~k~~~~~wrp~~t~a~~~~~~~~~~~~~~~~~~~e~-~~~~s~~~~~~~~~~~~~~~~~~~~~~~~ss~~~~~~~ 138 (514)
+..++++..|.+|+|++|+.++.. .+++...|++ .|+++...+. ++
T Consensus 2 ~~~~~~~~~n~~~~~~~~~t~~~~-------~~~~~e~~~~~~c~d~p~~~~--------------------------dv 48 (345)
T KOG2814|consen 2 YRKTRYNLVNDVSFDLNTDTTFAD-------MSEEFEAQTSAECVDMPGDTV--------------------------DV 48 (345)
T ss_pred cchhhhhhhhhcccCccccccccc-------CchhhHHHhHhhcccCCCChH--------------------------Hh
Confidence 456789999999999999988763 3345556665 6666643322 11
Q ss_pred cccccCCCCccCCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHH
Q 010252 139 KDETLEGEPVPSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQA 217 (514)
Q Consensus 139 ~~~~~~~~~~~~~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~~ 217 (514)
+.- .-.++|+.++.|+++|+++|||++|.|+++||+||+|+|.+|++++ .+.|+|+|.++.+|.+|.+||..
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 1123789999999999999999999999999999999999999995 78899999999999999999999
Q ss_pred HHHHhhhCCCCcceEEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCccccchHHhhhcccCCceEEEEecC
Q 010252 218 IIAEAVESPSLDYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNI 297 (514)
Q Consensus 218 iv~~~~~~~k~~~tHFIsIPl~~hp~I~~~~~~f~~sIl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rpn~FVAv~i~~ 297 (514)
++++.++ +++.|||+.+|++ ...++++|..|+...+..
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 588999999997322211
Q ss_pred CcchhhHhhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCC
Q 010252 298 GDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDN 377 (514)
Q Consensus 298 ~~~~~~vk~~q~~i~~~~~~~~~~r~~~~~~~Gi~~s~fv~p~~LHLTL~fLgl~~eeev~~A~~~L~~i~~~i~e~l~~ 377 (514)
++ +-+.|++.+.|++|..+||||+|+.+++++++++|+++|+.+.+++..+...
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 1256889999999999999999999999999999999999998888888889
Q ss_pred CCeEEEecccccCCCCCCCceEEEEeeeccCChhHHHHHH-HHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccC
Q 010252 378 RPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHAC-QVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKG 456 (514)
Q Consensus 378 ~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~La-~~L~~~f~~~Gl~~e~~~~r~fkPHiTLar~k~~~~~~~ 456 (514)
.|+.+.++|+.+|++||..++||||+|++.+....|+..+ +.|..+|...|+... +.++.++|+|+||++|+++++.
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 4789999999999999876532
Q ss_pred ---CCccccccHHHHHHHhCCCccccEEecEEEEeeeccCCCCCceeEEEEEeC
Q 010252 457 ---TRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPF 507 (514)
Q Consensus 457 ---~~~~~~fda~~il~~~~~~~fG~~~V~eI~Ls~l~~~~~~g~Y~~lasi~L 507 (514)
.+....||+++++++|+++.||++.+.++|+|.+...+.+|||.+++++||
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 145668999999999999999999999999999999888999999999987
No 2
>PLN00108 unknown protein; Provisional
Probab=100.00 E-value=1.1e-45 Score=365.17 Aligned_cols=224 Identities=56% Similarity=0.968 Sum_probs=198.3
Q ss_pred CCcceEEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCccccchHHhhhcccCCceEEEEecCCcchhhHhh
Q 010252 227 SLDYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKV 306 (514)
Q Consensus 227 k~~~tHFIsIPl~~hp~I~~~~~~f~~sIl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rpn~FVAv~i~~~~~~~~vk~ 306 (514)
|.++|||||||+..+|.|..++..|++.|++..+ ..|.-|
T Consensus 33 ~~~~THFlavPL~~~p~i~~~~~~Fk~~Vl~~~~------------------------~~~~~f---------------- 72 (257)
T PLN00108 33 REVFTHFVSLPLAIYPDLKKNIEAFQNSVLGNND------------------------KDPLKF---------------- 72 (257)
T ss_pred CCCCCeEEEEEcCCCHHHHHHHHHHHHHHHhccc------------------------cccccc----------------
Confidence 5689999999996589999999999999997521 001000
Q ss_pred hhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEecc
Q 010252 307 DRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKG 386 (514)
Q Consensus 307 ~q~~i~~~~~~~~~~r~~~~~~~Gi~~s~fv~p~~LHLTL~fLgl~~eeev~~A~~~L~~i~~~i~e~l~~~pf~L~l~G 386 (514)
| +.++++||++++|++|.+|||||+||.|.+++++++|.++|+++...+.+++.++|+.|+|+|
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 013478999999999999999999999999999999999999999889999989999999999
Q ss_pred cccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHH
Q 010252 387 LDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDAR 466 (514)
Q Consensus 387 Lg~F~~dp~~pRVLyagV~~~~~~~~L~~La~~L~~~f~~~Gl~~e~~~~r~fkPHiTLar~k~~~~~~~~~~~~~fda~ 466 (514)
|++|++||++++||||+|++.+..++|+.+|+.|.+.|.++||...+ .+++++||+||||+++++.+. +++.+|||+
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 99999999999999999998777789999999999999999998642 346899999999999876532 466789999
Q ss_pred HHHHHhCCCccccEEecEEEEeeeccCCCCCceeEEEEEeCCC
Q 010252 467 DIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 509 (514)
Q Consensus 467 ~il~~~~~~~fG~~~V~eI~Ls~l~~~~~~g~Y~~lasi~L~~ 509 (514)
+||++|++++||++.|++||||+++..+.+|||+++++++|++
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=1.6e-41 Score=329.10 Aligned_cols=207 Identities=37% Similarity=0.626 Sum_probs=179.0
Q ss_pred ceEEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCccccchHHhhhcccCCceEEEEecCCcchhhHhhhhc
Q 010252 230 YSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKVDRT 309 (514)
Q Consensus 230 ~tHFIsIPl~~hp~I~~~~~~f~~sIl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rpn~FVAv~i~~~~~~~~vk~~q~ 309 (514)
||||||||++ +|.|+..+..|++.|+..
T Consensus 1 pthFl~ipl~-~~~i~~~~~~fq~~v~~~--------------------------------------------------- 28 (209)
T PF10469_consen 1 PTHFLCIPLN-SPEIQEKFKEFQNEVLSK--------------------------------------------------- 28 (209)
T ss_pred CCeEEEEECC-CHHHHHHHHHHHHHHHhh---------------------------------------------------
Confidence 5889999985 888888888888888743
Q ss_pred cccccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCC-CCeEEEecccc
Q 010252 310 SIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDN-RPLFIRLKGLD 388 (514)
Q Consensus 310 ~i~~~~~~~~~~r~~~~~~~Gi~~s~fv~p~~LHLTL~fLgl~~eeev~~A~~~L~~i~~~i~e~l~~-~pf~L~l~GLg 388 (514)
.+|+++++|++|.+|||||+||++.+++++++|.++|+++.+.+.+.+.. +|+.|+|+||+
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 34677789999999999999999999999999999999999888877654 99999999999
Q ss_pred cCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHHHH
Q 010252 389 LMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDI 468 (514)
Q Consensus 389 ~F~~dp~~pRVLyagV~~~~~~~~L~~La~~L~~~f~~~Gl~~e~~~~r~fkPHiTLar~k~~~~~~~~~~~~~fda~~i 468 (514)
+|++||+++|||||+|.++++...|+++++.|++.|.++||...++.+.+|+||+||||++++..... +...+||++++
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 99999999999999999866679999999999999999999985422334899999999998521111 11256899999
Q ss_pred HHHhCCCccccEEecEEEEeeeccCCC-CCceeEEEEEeC
Q 010252 469 FKQFGSKEWGEYLIKEAHLSQRFVYDE-SGFYHCCASIPF 507 (514)
Q Consensus 469 l~~~~~~~fG~~~V~eI~Ls~l~~~~~-~g~Y~~lasi~L 507 (514)
+++|.+++||.+.|++|+||+|+..++ +|||.++++|+|
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 999999999999999999999977665 999999999987
No 4
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=6.1e-27 Score=223.09 Aligned_cols=179 Identities=19% Similarity=0.313 Sum_probs=151.5
Q ss_pred CceEEEEecCCcchhhHhhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHh
Q 010252 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 367 (514)
Q Consensus 288 n~FVAv~i~~~~~~~~vk~~q~~i~~~~~~~~~~r~~~~~~~Gi~~s~fv~p~~LHLTL~fLgl~~eeev~~A~~~L~~i 367 (514)
-+|+||++ ++++.+++..++..+. ..+ ..+|++++|+||||.|||+++++.++.+.++|.++
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 6777899999988663 112 34799999999999999999999999999999998
Q ss_pred HHhhhhhcCCCCeEEEecccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeee
Q 010252 368 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 447 (514)
Q Consensus 368 ~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~La~~L~~~f~~~Gl~~e~~~~r~fkPHiTLar 447 (514)
.. .. ||.|+|+|+|.||+ +.+|||+|+++.+ .+.|.+|++.|...+.++|+..+ .++|.||+||+|
T Consensus 64 ~~------~~-~f~i~l~g~g~F~~-~~~~rvi~~~v~~---~~~L~~L~~~l~~~~~~~g~~~~---~r~F~PHvTl~r 129 (180)
T COG1514 64 AA------PE-PFPITLDGAGSFPN-PRRPRVIWVGVEE---TEELRALAEELERALARLGLRPE---ERPFVPHVTLAR 129 (180)
T ss_pred hc------CC-ceEEEEeeEcccCC-CCCCcEEEEcCCC---cHHHHHHHHHHHHHHHhcCCCCC---CCCcCCCEEEEe
Confidence 52 12 99999999999998 9999999999985 57899999999999999999986 689999999999
Q ss_pred ecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEeeeccCCCCCceeEEEEEeCCC
Q 010252 448 IRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 509 (514)
Q Consensus 448 ~k~~~~~~~~~~~~~fda~~il~~~~~~~fG~~~V~eI~Ls~l~~~~~~g~Y~~lasi~L~~ 509 (514)
.+. + -.+.+++..+.+..||++.|+++.|.....+..+|+|.++..++|.+
T Consensus 130 ~k~-~----------~~~~~~~~~~~~~~~~~~~vd~~~L~~S~l~~~gp~Y~~~~~~~L~~ 180 (180)
T COG1514 130 VKS-K----------DKLVEALGEFKNVEFGEMEVDRFSLYSSTLTPGGPIYETLKEFPLSG 180 (180)
T ss_pred ecc-c----------chhhhhhhhhccccccceEeeEEEEEEEeeCCCCCEEEEEEEEecCC
Confidence 865 1 12346778899999999999999995444433579999999999864
No 5
>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=99.93 E-value=4.4e-25 Score=208.26 Aligned_cols=178 Identities=19% Similarity=0.359 Sum_probs=147.8
Q ss_pred CceEEEEecCCcchhhHhhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHh
Q 010252 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 367 (514)
Q Consensus 288 n~FVAv~i~~~~~~~~vk~~q~~i~~~~~~~~~~r~~~~~~~Gi~~s~fv~p~~LHLTL~fLgl~~eeev~~A~~~L~~i 367 (514)
-+|+||.+.++ +.+.+.++|..+. + . .....|+++++|||||.|+|++++++++.+.++|.++
T Consensus 2 R~FiAl~~p~~-~~~~l~~~~~~l~---------~-----~--~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~ 64 (179)
T TIGR02258 2 RLFIAIDLPPE-IREQLSRIQRKLK---------S-----P--LDGIKWVPPENLHITLKFLGEVDEEQVEELEDALAKI 64 (179)
T ss_pred eEEEEecCCHH-HHHHHHHHHHHhh---------c-----c--CCCcEECChHHCEEEEEEccCCCHHHHHHHHHHHHHh
Confidence 37999999865 8999999998763 0 0 1233799999999999999999999999999888876
Q ss_pred HHhhhhhcCCCCeEEEecccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeee
Q 010252 368 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 447 (514)
Q Consensus 368 ~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~La~~L~~~f~~~Gl~~e~~~~r~fkPHiTLar 447 (514)
. .++|.++|.|+|+|++ +.+++|||++++. ...|.+|++.|.+.+...|+..+ .++|+|||||+|
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 3679999999999987 7889999999985 24899999999999999999865 578999999999
Q ss_pred ecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEeeeccCCCCCceeEEEEEeC
Q 010252 448 IRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPF 507 (514)
Q Consensus 448 ~k~~~~~~~~~~~~~fda~~il~~~~~~~fG~~~V~eI~Ls~l~~~~~~g~Y~~lasi~L 507 (514)
..... .++.++++.+....++.+.|++|+|.++.....++.|.++++++|
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 54221 234567788888889999999999977766555799999999987
No 6
>PRK15124 2'-5' RNA ligase; Provisional
Probab=99.93 E-value=3.5e-25 Score=209.87 Aligned_cols=170 Identities=13% Similarity=0.148 Sum_probs=135.3
Q ss_pred CceEEEEecCCcchhhHhhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHh
Q 010252 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 367 (514)
Q Consensus 288 n~FVAv~i~~~~~~~~vk~~q~~i~~~~~~~~~~r~~~~~~~Gi~~s~fv~p~~LHLTL~fLgl~~eeev~~A~~~L~~i 367 (514)
-.|+||++.+ ++.+.+.+.++.+. +.....|++|+||||||.|||++++++++.+.++|.++
T Consensus 6 RlFiAl~~p~-~~~~~l~~~~~~~~-----------------~~~~~rwv~~~nlHiTL~FlG~v~~~~~~~l~~~l~~~ 67 (176)
T PRK15124 6 RLFFAIDLPD-EIRQQIIHWRATHF-----------------PPEAGRPVAAANLHLTLAFLGEVSAEKQQALSQLAGRI 67 (176)
T ss_pred EEEEEeCCCH-HHHHHHHHHHHHhc-----------------cccCcccccccccEEEEEecCCCCHHHHHHHHHHHHhc
Confidence 4799999884 56788888886652 11124799999999999999999999999998888876
Q ss_pred HHhhhhhcCCCCeEEEecccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeee
Q 010252 368 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 447 (514)
Q Consensus 368 ~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~La~~L~~~f~~~Gl~~e~~~~r~fkPHiTLar 447 (514)
..+||.|+|.|+|+||+ |||||+++++ +...|..|++.|++.+..+|+..+ .++|+|||||+|
T Consensus 68 --------~~~pF~l~l~~~g~Fp~----prvlwlg~~~--~~~~L~~L~~~l~~~l~~~G~~~e---~r~f~PHiTLaR 130 (176)
T PRK15124 68 --------RQPGFTLTLDDAGQWPR----SRVVWLGMRQ--PPRGLLQLANMLRSQAARSGCYQS---PQPFHPHITLLR 130 (176)
T ss_pred --------ccCCeEEEECcccCcCC----CCEEEEEcCC--CCHHHHHHHHHHHHHHHHcCCCCC---CCCCCCCEeecc
Confidence 25899999999999974 5999999974 356899999999999999999875 689999999999
Q ss_pred ecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEeeeccCCCCCceeEEEEEeCC
Q 010252 448 IRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFP 508 (514)
Q Consensus 448 ~k~~~~~~~~~~~~~fda~~il~~~~~~~fG~~~V~eI~Ls~l~~~~~~g~Y~~lasi~L~ 508 (514)
.+.... . .. . ..+.+ .+.|++|+|.++..+..++.|.++++++|.
T Consensus 131 ~~~~~~-----~---~~------~-~~~~~-~~~v~~~~L~~S~l~~~g~~Y~~l~~~~L~ 175 (176)
T PRK15124 131 DASRPV-----A---IP------P-PGFNW-SFPVTEFTLYASSFARGRTRYTPLQRWPLT 175 (176)
T ss_pred CCCCcc-----c---cc------C-CCCCC-ceEcCEEEEEEEeccCCCCEEEEEEEEeCC
Confidence 542110 0 00 0 11234 588999999776655567999999999986
No 7
>PRK13679 hypothetical protein; Provisional
Probab=99.72 E-value=1.3e-16 Score=150.16 Aligned_cols=167 Identities=14% Similarity=0.138 Sum_probs=124.6
Q ss_pred CceEEEEecCCcchhhHhhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHh
Q 010252 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 367 (514)
Q Consensus 288 n~FVAv~i~~~~~~~~vk~~q~~i~~~~~~~~~~r~~~~~~~Gi~~s~fv~p~~LHLTL~fLgl~~eeev~~A~~~L~~i 367 (514)
.+||||.+.. .+.+.+..+|+.+. .+ ..|++| ||||.|+|.+++++++++.++|+++
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 4799999886 47888888886542 11 237777 9999999999999999999999887
Q ss_pred HHhhhhhcCCCCeEEEecccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeee
Q 010252 368 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 447 (514)
Q Consensus 368 ~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~La~~L~~~f~~~Gl~~e~~~~r~fkPHiTLar 447 (514)
.. ..+||.|++.|+|+|++ + ++|||+++++ ...|.+|++.|...+. + ..+ .++|.|||||+|
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 24899999999999986 2 4899999985 4689999998887543 1 222 578999999998
Q ss_pred ecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEeeeccCCCCCceeEEEEEeCC
Q 010252 448 IRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFP 508 (514)
Q Consensus 448 ~k~~~~~~~~~~~~~fda~~il~~~~~~~fG~~~V~eI~Ls~l~~~~~~g~Y~~lasi~L~ 508 (514)
..... ...++.+.++. .+..+ .+.|++|+|.... .++-|..+.++.|+
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 53321 11233344433 55666 7889999997552 35899999999885
No 8
>PHA02574 57B hypothetical protein; Provisional
Probab=99.67 E-value=1.8e-16 Score=146.79 Aligned_cols=109 Identities=12% Similarity=0.059 Sum_probs=88.1
Q ss_pred CceEEEEecCCcchhhHhhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHHHHHh
Q 010252 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 367 (514)
Q Consensus 288 n~FVAv~i~~~~~~~~vk~~q~~i~~~~~~~~~~r~~~~~~~Gi~~s~fv~p~~LHLTL~fLgl~~eeev~~A~~~L~~i 367 (514)
-.|||+++++ .+.+++..+|+.+. . .+||+++||||||.| ++++++.+..
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 4699999977 77999999998652 1 479999999999999 4555544421
Q ss_pred HHhhhhhcCCCCeEEEecccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeee
Q 010252 368 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 447 (514)
Q Consensus 368 ~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~La~~L~~~f~~~Gl~~e~~~~r~fkPHiTLar 447 (514)
..+||.+++.|+|+|++ + ++||||+|++ ...|..|++.|++.+.. .+ .++|+|||||+|
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 35899999999999974 2 3699999996 37899999999999888 22 357999999999
No 9
>PF13563 2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB: 1IUH_A.
Probab=99.27 E-value=1.6e-11 Score=111.65 Aligned_cols=128 Identities=16% Similarity=0.229 Sum_probs=77.0
Q ss_pred cCCCCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEecccccCCCCCCCceEEEEeeeccCChhHHHHH
Q 010252 337 IKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHA 416 (514)
Q Consensus 337 v~p~~LHLTL~fLgl~~eeev~~A~~~L~~i~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~L 416 (514)
.....+||||.+.+..++.. +.+.+.|..+.. ..+||.|+|.|+++|++ +.+|||+.+.. ...|.+|
T Consensus 21 ~~~~~pHITL~~~~~~~~~~-~~~~~~l~~~~~------~~~~f~l~l~~~~~F~~---~~~vi~l~~~~---~~~L~~L 87 (153)
T PF13563_consen 21 YPRWPPHITLAFPFDIDDSL-DELVEALARLAA------GFPPFELRLDGFGSFPG---KGRVIFLNVEP---SPELEAL 87 (153)
T ss_dssp --GGG-EEEEEEEEE--GGG-HHHHHHHHHHHH------HS--EEEEEEEEEEESS---SSSSEEEEEEE----HHHHHH
T ss_pred CCCCCCEeEEEecCcccccH-HHHHHHHHHHHc------cCCCeEEEEccEEEcCC---CCCEEEEEcCC---CHHHHHH
Confidence 44455899999999987743 445555555421 25899999999999975 22699999964 5899999
Q ss_pred HHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHHHHHHHh-CCCccccEEecEEEEeee
Q 010252 417 CQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQF-GSKEWGEYLIKEAHLSQR 490 (514)
Q Consensus 417 a~~L~~~f~~~Gl~~e~~~~r~fkPHiTLar~k~~~~~~~~~~~~~fda~~il~~~-~~~~fG~~~V~eI~Ls~l 490 (514)
++.|.+.|...|...+. .++|+|||||++...... +..+++.+ ....-.++.|++|.|...
T Consensus 88 ~~~l~~~~~~~~~~~~~--~~~~~PHiTia~~~~~~~-----------~~~~~~~~~~~~~~~~~~v~~l~L~~~ 149 (153)
T PF13563_consen 88 HRALREALRPFGFKQDS--YRPFRPHITIARRLSPKQ-----------AAEAIEKLQSEFPPISFTVDELALVRS 149 (153)
T ss_dssp HHHHHHHHHHHHGGGGG--GS----EEEEEEESS----------------------------EEEEE-EEEEEEE
T ss_pred HHHHHHHHHHcCCcccc--CCCcceEEEEeccCCcch-----------hHHHHHHHhCcCCCcEEEEeEEEEEEE
Confidence 99999999999887641 278999999999643321 12334444 222334789999999665
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=99.23 E-value=1.5e-11 Score=96.87 Aligned_cols=60 Identities=42% Similarity=0.612 Sum_probs=54.9
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHH
Q 010252 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQ 216 (514)
Q Consensus 156 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~ 216 (514)
..+.||..+|++|||++|+++++|+++|||+|+||..+. .+.|+|+|+ .++|..|+++|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP-KENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC-HHHHHHHHHHhC
Confidence 578999999999999999999999999999999998654 678999997 799999999873
No 11
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.22 E-value=2.2e-11 Score=96.46 Aligned_cols=59 Identities=27% Similarity=0.402 Sum_probs=54.5
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHH
Q 010252 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQ 216 (514)
Q Consensus 155 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~ 216 (514)
...+.||.+++++|||++|+++|+|+++|||+|+|+. ++.|.|+|.++++++.|++.|+
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---CCEEEEEeCCHHHHHHHHHHhC
Confidence 4679999999999999999999999999999999997 4679999988899999999873
No 12
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.16 E-value=2.3e-11 Score=95.22 Aligned_cols=60 Identities=40% Similarity=0.598 Sum_probs=54.0
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHH
Q 010252 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKI 215 (514)
Q Consensus 155 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I 215 (514)
+..+.||..++++|||++|.++++||++|||+|.||..++...|.|+| ++++|++|++.|
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 689999999876
No 13
>PF05213 Corona_NS2A: Coronavirus NS2A protein; InterPro: IPR007878 This entry is represented by Coronavirus non-structural protein 2A (32kDa); it is a family of uncharacterised viral proteins. Members have a phosphoesterase module (2H) [] and are predicted to be involved in RNA modification. The viral group of 2H phosphoesterases contains proteins from two unrelated virus types: the type C rotaviruses (VP3 protein, IPR011181 from INTERPRO) that are double stranded multipartite RNA viruses and the coronaviruses (NS2 protein, this group) that are positive strand RNA viruses. Given that these viruses have vertebrate hosts, it is likely that the 2H phosphoesterase domain was derived from the host by one of virus groups followed by rapid sequence divergence []. Subsequently, it may have been exchanged between the viral families. Although the direction of the exchange is not clear, it is possible that a double stranded replicative form of a subgenomic RNA transcript of the coronavirus NS2 was stabilised by a rotavirus and incorporated into its multiple double stranded RNA genome []. These proteins can be utilised as novel drug targets because of their predicted RNA modification role.
Probab=98.96 E-value=4.6e-09 Score=101.20 Aligned_cols=167 Identities=17% Similarity=0.253 Sum_probs=120.1
Q ss_pred ccCCceEEEEecC-CcchhhHhhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCHHHHHHHHHH
Q 010252 285 VDQEHKVAVELNI-GDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNV 363 (514)
Q Consensus 285 ~rpn~FVAv~i~~-~~~~~~vk~~q~~i~~~~~~~~~~r~~~~~~~Gi~~s~fv~p~~LHLTL~fLgl~~eeev~~A~~~ 363 (514)
.+||||+..+|.. ..+....+..|-+|. +-|+|-.+=.-| ||||+||-. +++++..+..+
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 889999999997664 456655333333 999999987 57889989888
Q ss_pred HHHhHHhhhhhcCCCCeEEEecccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeE
Q 010252 364 LKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHA 443 (514)
Q Consensus 364 L~~i~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~La~~L~~~f~~~Gl~~e~~~~r~fkPHi 443 (514)
|+++.+. +.- ....+++..--.+ + |..-+.|+ .+.+++..|...|.+.|+..++ .|.|.||+
T Consensus 65 iq~Vidd---M~~-~~~~it~tnp~ML-g-----~~yV~nV~------Gv~slh~ki~n~~~~kgit~gQ--SRmwIPHi 126 (248)
T PF05213_consen 65 IQKVIDD---MVW-FEGDITFTNPHML-G-----RCYVANVK------GVLSLHDKIVNVFRKKGITFGQ--SRMWIPHI 126 (248)
T ss_pred HHHHHHH---hhc-ccceEEecCceee-c-----cEEEEecc------cHHHHHHHHHHHHHHhCcCcCc--ccccccce
Confidence 8887442 221 1226777766666 3 55556676 3778899999999999999974 89999999
Q ss_pred EeeeecccccccCCCccccccHHHHHHHhCCCccc-cEEe-----cEEEEeeeccCCCCCceeEEEEE
Q 010252 444 TLMNIRHKKRRKGTRRVDYFDARDIFKQFGSKEWG-EYLI-----KEAHLSQRFVYDESGFYHCCASI 505 (514)
Q Consensus 444 TLar~k~~~~~~~~~~~~~fda~~il~~~~~~~fG-~~~V-----~eI~Ls~l~~~~~~g~Y~~lasi 505 (514)
||+.+....-+ + +. .+|+ +.++ .++.|-.++....+|+|..+.+.
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 99987433210 0 01 2233 3344 77778788877778999988763
No 14
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.92 E-value=1.9e-09 Score=84.69 Aligned_cols=59 Identities=41% Similarity=0.516 Sum_probs=53.0
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEccChhHHHHHHHHH
Q 010252 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKI 215 (514)
Q Consensus 156 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~---~~~I~I~G~s~~~v~~A~~~I 215 (514)
..+.||..++++|||++|+++++|+++|||+|.||..++ .+.|.|.|. .+.+..|...|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~-~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT-PEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcC-HHHHHHHHHHh
Confidence 578999999999999999999999999999999998643 567999997 78999998876
No 15
>PF02834 LigT_PEase: LigT like Phosphoesterase; InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases. These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.
Probab=98.85 E-value=1.6e-09 Score=90.59 Aligned_cols=60 Identities=20% Similarity=0.411 Sum_probs=52.7
Q ss_pred cccCCCCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEecccccCCCCCCCceEEE
Q 010252 335 IFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILY 401 (514)
Q Consensus 335 ~fv~p~~LHLTL~fLgl~~eeev~~A~~~L~~i~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRVLy 401 (514)
.|++|.++||||+|||.+++++++.+++.|.++.. ..+||.+++.|+++|++ ..++||+|
T Consensus 28 r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~------~~~~f~~~~~~~~~f~s-~~~~rvi~ 87 (87)
T PF02834_consen 28 RWVRPFNPHITLAFLGEVPPDQLPELIEALANIAS------RFPPFTLTVDGFGLFPS-RLRPRVIW 87 (87)
T ss_dssp EEGSCGGSEEEEEEEEEESHHHHHHHHHHHHHHHC------CCB-EEEEEEEEEEEEE-EETCEEEE
T ss_pred cccCCCCCeEEEEeCCCCCHHHHHHHHHHHHhhhc------cCCCeEEEEeEEEEeCC-CCCCCCcC
Confidence 69999999999999999999999999999988731 35899999999999997 45889999
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=98.78 E-value=1.2e-08 Score=81.51 Aligned_cols=59 Identities=37% Similarity=0.387 Sum_probs=52.4
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHH
Q 010252 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKI 215 (514)
Q Consensus 156 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~----~~~I~I~G~s~~~v~~A~~~I 215 (514)
..+.||...++.|||++|+++++|+++|||+|+|++... ...|+|+|. .+.+.+|...|
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~-~~~v~~A~~~I 64 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK-PSAVQKALLLI 64 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeC-HHHHHHHHHhh
Confidence 578999999999999999999999999999999987643 346899996 79999999876
No 17
>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=90.31 Aligned_cols=59 Identities=29% Similarity=0.486 Sum_probs=53.1
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCC--------------------CCcEEEEccC--hhHHHHHHHHHHHHHH
Q 010252 163 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK--------------------EDSIIIEGNS--TDSVAKASEKIQAIIA 220 (514)
Q Consensus 163 ~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~--------------------~~~I~I~G~s--~~~v~~A~~~I~~iv~ 220 (514)
.|+|.|||++|.|+|+||++|||+|.|...++ ..+|.|+|.+ .+++.+|++.|+.|+.
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 78899999999999999999999999987642 3789999998 8999999999998876
Q ss_pred H
Q 010252 221 E 221 (514)
Q Consensus 221 ~ 221 (514)
.
T Consensus 95 ~ 95 (120)
T cd02395 95 P 95 (120)
T ss_pred c
Confidence 4
No 18
>smart00322 KH K homology RNA-binding domain.
Probab=98.74 E-value=3.8e-08 Score=76.69 Aligned_cols=66 Identities=39% Similarity=0.530 Sum_probs=58.1
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHH
Q 010252 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAII 219 (514)
Q Consensus 153 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~~iv 219 (514)
.....+.||..+++++||++|.++++|+++||++|.++.... ...|.|.|+ .+++..|.+.|...+
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 356789999999999999999999999999999999987653 567899998 799999999987654
No 19
>PF13014 KH_3: KH domain
Probab=98.71 E-value=1.4e-08 Score=74.61 Aligned_cols=39 Identities=38% Similarity=0.572 Sum_probs=34.2
Q ss_pred ccccccCCCchhHHHHHHHhCcEEEcCC---CCC-CCcEEEEc
Q 010252 164 VIRFIKGKEGSTQKKFEKEMGVKIILPS---SKK-EDSIIIEG 202 (514)
Q Consensus 164 ~~~~IIGk~G~t~k~iE~eT~~kI~iP~---~~~-~~~I~I~G 202 (514)
+|++|||++|+++++|+++|||+|+||+ ++. +..|+|+|
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 332 56788887
No 20
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.53 E-value=2e-07 Score=101.37 Aligned_cols=106 Identities=26% Similarity=0.306 Sum_probs=86.7
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHHHHHHHHhhhCC-
Q 010252 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIAEAVESP- 226 (514)
Q Consensus 152 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~----~~~I~I~G~s~~~v~~A~~~I~~iv~~~~~~~- 226 (514)
.+.+..|+||..-+|.||||+|+|||+|..|||+||+|-..++ .+.+.|.|. ++.|+.|.+.|..||.++...+
T Consensus 228 ~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~-~d~ie~Aa~lI~eii~~~~~~~~ 306 (600)
T KOG1676|consen 228 GSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGT-VDQIEHAAELINEIIAEAEAGAG 306 (600)
T ss_pred ccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecC-HHHHHHHHHHHHHHHHHHhccCC
Confidence 4458999999999999999999999999999999999944333 467899996 7999999999999999876641
Q ss_pred --------CCcceEEEEeccccchhhhccHHHHHHHHhcc
Q 010252 227 --------SLDYSHFVSLPLAVHPELVDKLVNFQNTILGI 258 (514)
Q Consensus 227 --------k~~~tHFIsIPl~~hp~I~~~~~~f~~sIl~~ 258 (514)
-..-.-++.||-.----++|+..+-+..|-.+
T Consensus 307 ~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~q 346 (600)
T KOG1676|consen 307 GGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQ 346 (600)
T ss_pred CCcCCCCccceeeEEEeccccccccccCCCccchhhhccc
Confidence 11114556689765677899999999988765
No 21
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.36 E-value=5.4e-07 Score=95.99 Aligned_cols=72 Identities=26% Similarity=0.409 Sum_probs=62.8
Q ss_pred CeEEEEeccc------cccccccCCCchhHHHHHHHhCcEEEcCCCCC-------------------CCcEEEEccChhH
Q 010252 153 RHSLSVEVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-------------------EDSIIIEGNSTDS 207 (514)
Q Consensus 153 ~~~~~v~Vp~------~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~-------------------~~~I~I~G~s~~~ 207 (514)
++...|.||. .|+|+|||.+|.|+|+||+|||+||.|-..+. .-++-|++.+.+.
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 7777888885 79999999999999999999999999987432 1268999999999
Q ss_pred HHHHHHHHHHHHHHhhh
Q 010252 208 VAKASEKIQAIIAEAVE 224 (514)
Q Consensus 208 v~~A~~~I~~iv~~~~~ 224 (514)
|.+|...|+.|+.+++-
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=9.3e-07 Score=84.72 Aligned_cols=65 Identities=32% Similarity=0.439 Sum_probs=59.3
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEE---ccChhHHHHHHHHHHHHHH
Q 010252 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIE---GNSTDSVAKASEKIQAIIA 220 (514)
Q Consensus 154 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~---G~s~~~v~~A~~~I~~iv~ 220 (514)
....+.||++.++.|||++|.+++.|+++||++|+|.. +.+.|.|. +.+++.+.+|++.|++|+.
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~--~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS--ETGEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC--CCCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 45789999999999999999999999999999999985 34789998 7789999999999999986
No 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=98.29 E-value=8.1e-07 Score=84.51 Aligned_cols=61 Identities=33% Similarity=0.432 Sum_probs=55.2
Q ss_pred EeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEE--EccChhHHHHHHHHHHHHHH
Q 010252 158 VEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIII--EGNSTDSVAKASEKIQAIIA 220 (514)
Q Consensus 158 v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I--~G~s~~~v~~A~~~I~~iv~ 220 (514)
+.||++.++.|||+||+++|+|+++||++|+|.. +.+.|.| .+.+++.+.+|++.|.+|..
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=98.00 E-value=8.8e-06 Score=78.03 Aligned_cols=54 Identities=28% Similarity=0.409 Sum_probs=49.0
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 163 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 163 ~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
..+|.|||++|+|++.||..|||+|+|+. +.|.|.|. .++++.|++.|..|++.
T Consensus 104 r~~griIG~~G~~~k~ie~~t~~~i~i~~----~~v~i~G~-~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 104 RIKGRIIGEGGKTRRIIEELTGVDISVYG----KTVAIIGD-PEQVEIAREAIEMLIEG 157 (180)
T ss_pred HHhhheeCCCcHHHHHHHHHHCcEEEEcC----CEEEEEeC-HHHHHHHHHHHHHHHcC
Confidence 36999999999999999999999999985 45999995 89999999999999954
No 25
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=97.95 E-value=9.8e-06 Score=78.22 Aligned_cols=76 Identities=17% Similarity=0.249 Sum_probs=61.3
Q ss_pred CCccCCCCeEEEEeccc------cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHH
Q 010252 146 EPVPSAERHSLSVEVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAII 219 (514)
Q Consensus 146 ~~~~~~~~~~~~v~Vp~------~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv 219 (514)
.-+.+.++|+-.++||. .|+|+|||+.|.|+|+||+.++|+|.|..++...+..|....+++...|.+-|.-++
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 34557788888888885 799999999999999999999999999998876566666666677777777776666
Q ss_pred HH
Q 010252 220 AE 221 (514)
Q Consensus 220 ~~ 221 (514)
..
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=97.92 E-value=1.4e-05 Score=75.99 Aligned_cols=54 Identities=28% Similarity=0.372 Sum_probs=49.8
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 163 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 163 ~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
...|.|||++|+|++.||..|||+|.|+. ..|.|.| +.++++.|++.|+.|++.
T Consensus 98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~----~~v~i~G-~~~~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEELTGVSISVYG----KTVGIIG-DPEQVQIAREAIEMLIEG 151 (172)
T ss_pred HHHhhhcCCCcHHHHHHHHHHCCeEEEcC----CEEEEEC-CHHHHHHHHHHHHHHHcC
Confidence 36899999999999999999999999985 6799999 489999999999999965
No 27
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.91 E-value=0.0002 Score=73.61 Aligned_cols=107 Identities=23% Similarity=0.234 Sum_probs=80.5
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEccChhHHHHHHHHHHHHHHHhhh
Q 010252 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAEAVE 224 (514)
Q Consensus 151 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~------~~~I~I~G~s~~~v~~A~~~I~~iv~~~~~ 224 (514)
..+|.+.|.||.--.|-||||||.|+.+|++||||||++.+..+ .+.|-|.|. -+.++.-.+-|..-+.|.-+
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 34699999999999999999999999999999999999988766 356889995 57777776666554444211
Q ss_pred ---------CCCC---cceEEEEeccccchhhhccHHHHHHHHhcc
Q 010252 225 ---------SPSL---DYSHFVSLPLAVHPELVDKLVNFQNTILGI 258 (514)
Q Consensus 225 ---------~~k~---~~tHFIsIPl~~hp~I~~~~~~f~~sIl~~ 258 (514)
.|+. ....-|.+|-..---|+|+...+++.|+++
T Consensus 115 ~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eq 160 (402)
T KOG2191|consen 115 AVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQ 160 (402)
T ss_pred hhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHh
Confidence 1110 112445578766677889989999888876
No 28
>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=97.81 E-value=3.1e-05 Score=87.61 Aligned_cols=65 Identities=20% Similarity=0.319 Sum_probs=60.1
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 154 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
-..++.||++.+|-|||+||.++|.|.++||++|+|-. ++.|.|.|.+.+.+++|++.|+.|+..
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 36788999999999999999999999999999999974 688999999999999999999998873
No 29
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=97.77 E-value=4e-05 Score=87.91 Aligned_cols=104 Identities=27% Similarity=0.414 Sum_probs=93.1
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCCcc
Q 010252 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDY 230 (514)
Q Consensus 152 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~~iv~~~~~~~k~~~ 230 (514)
..+.+.+.|-++++.+++||+|.++.+|+++++|.|++|.+++ ...++++|. ..++.+|.+.|+.+..+...+ ..
T Consensus 345 nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~-~~~~~ka~~~v~~~~~ei~n~---~~ 420 (753)
T KOG2208|consen 345 NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGV-SANDEKAVEDVEKIIAEILNS---IV 420 (753)
T ss_pred cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEecc-ccchhHHHHHHHHHHHhhhcc---cc
Confidence 4478899999999999999999999999999999999999766 678999997 589999999999999987663 34
Q ss_pred eEEEEeccccchhhhccHHHHHHHHhccc
Q 010252 231 SHFVSLPLAVHPELVDKLVNFQNTILGIT 259 (514)
Q Consensus 231 tHFIsIPl~~hp~I~~~~~~f~~sIl~~~ 259 (514)
.+.+.||-..|.+|.|.....++.|+.+.
T Consensus 421 ~~~~~iP~k~~~~iig~~g~~i~~I~~k~ 449 (753)
T KOG2208|consen 421 KEEVQIPTKSHKRIIGTKGALINYIMGKH 449 (753)
T ss_pred cceeecCccchhhhhccccccHHHHHhhc
Confidence 67777999999999999999999999873
No 30
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.74 E-value=2.4e-05 Score=82.25 Aligned_cols=104 Identities=25% Similarity=0.289 Sum_probs=74.8
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHHHHHHH-HhhhC
Q 010252 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIA-EAVES 225 (514)
Q Consensus 151 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~----~~~I~I~G~s~~~v~~A~~~I~~iv~-~~~~~ 225 (514)
...|-+.+-||..||+.||||.|+|+|.|-..|+|||+|-+..+ ...|+|-|. +++..+|+.+|..|+. |+.+-
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 34567888999999999999999999999999999999977544 457899986 6999999999998874 43332
Q ss_pred CCCcceEEEEeccccchhhh----ccHHHHHHHHhcc
Q 010252 226 PSLDYSHFVSLPLAVHPELV----DKLVNFQNTILGI 258 (514)
Q Consensus 226 ~k~~~tHFIsIPl~~hp~I~----~~~~~f~~sIl~~ 258 (514)
| .+.-+-+.+--|..++ |.-++-...|+++
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 3333323322354443 3444555556554
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=97.68 E-value=5.2e-05 Score=86.35 Aligned_cols=65 Identities=22% Similarity=0.366 Sum_probs=59.1
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 154 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
-...+.||++.++.|||+||.++|+|+++||++|+|-. ++.|.|.+.+.+.+.+|.+.|..+..+
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=97.60 E-value=0.00015 Score=72.66 Aligned_cols=70 Identities=23% Similarity=0.335 Sum_probs=53.3
Q ss_pred CeEEEEeccc------cccccccCCCchhHHHHHHHhCcEEEcCCCCC-C--------------------CcEEEEccCh
Q 010252 153 RHSLSVEVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-E--------------------DSIIIEGNST 205 (514)
Q Consensus 153 ~~~~~v~Vp~------~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~-~--------------------~~I~I~G~s~ 205 (514)
+-+..|.||. .|+|.|+|++|.|+|+||++|||||-|-..|+ . -+|.|+..
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 4556677775 69999999999999999999999999988765 0 14667654
Q ss_pred hHHHHHHHHHHHHHHHhhh
Q 010252 206 DSVAKASEKIQAIIAEAVE 224 (514)
Q Consensus 206 ~~v~~A~~~I~~iv~~~~~ 224 (514)
.--..|..||...+++.++
T Consensus 169 ~p~~ea~~rl~~AleeI~k 187 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKK 187 (259)
T ss_pred CCHHHHHHHHHHHHHHHHH
Confidence 3456677777777777544
No 33
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=97.45 E-value=0.00013 Score=79.89 Aligned_cols=110 Identities=12% Similarity=0.197 Sum_probs=89.7
Q ss_pred CCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEccChhHHHHHHHHHHHHHHHhhhC-
Q 010252 150 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKIQAIIAEAVES- 225 (514)
Q Consensus 150 ~~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~---~~~I~I~G~s~~~v~~A~~~I~~iv~~~~~~- 225 (514)
+.+..+...+||.+..++|||++|+-++.|.++.||+++||+... .+.|.|+|. .+.|+.|+..|..+++.-+-.
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 445667788999999999999999999999999999999988654 578999996 599999999999998864300
Q ss_pred ---CCCc---ceEEEEeccccchhhhccHHHHHHHHhcccc
Q 010252 226 ---PSLD---YSHFVSLPLAVHPELVDKLVNFQNTILGITD 260 (514)
Q Consensus 226 ---~k~~---~tHFIsIPl~~hp~I~~~~~~f~~sIl~~~~ 260 (514)
..+. .|.-|.||-+---.|+|..++-++.+.+..+
T Consensus 129 ~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg 169 (600)
T KOG1676|consen 129 GFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSG 169 (600)
T ss_pred CccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcC
Confidence 0111 4777888977678899999999998877643
No 34
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.39 E-value=0.00017 Score=76.01 Aligned_cols=61 Identities=28% Similarity=0.480 Sum_probs=52.4
Q ss_pred cccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEccChhHHHHHHHHHHHHHHHh
Q 010252 161 GASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAEA 222 (514)
Q Consensus 161 p~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~------~~~I~I~G~s~~~v~~A~~~I~~iv~~~ 222 (514)
-..|.|.||||.|.++|+||++|||+|.|.+--+ ...|++.| +-+.+.+|-..|-+-+.++
T Consensus 287 HN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkG-siEac~~AE~eImkKlre~ 353 (584)
T KOG2193|consen 287 HNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKG-SIEACVQAEAEIMKKLREC 353 (584)
T ss_pred hcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecc-cHHHHHHHHHHHHHHHHHH
Confidence 3689999999999999999999999999987644 46899999 5799999999887766653
No 35
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.30 E-value=0.00049 Score=66.39 Aligned_cols=67 Identities=30% Similarity=0.388 Sum_probs=59.5
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEcc----ChhHHHHHHHHHHHHHH
Q 010252 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGN----STDSVAKASEKIQAIIA 220 (514)
Q Consensus 152 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~----s~~~v~~A~~~I~~iv~ 220 (514)
...+..+.||+...+.+||+.|++.+.||+.|+|+|.|.. +.+.|.|+.. ++..+++|++-|++|..
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~--~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgr 76 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS--KTGSVTIRTTRKTEDPLALLKARDVVKAIGR 76 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC--CCCeEEEEecCCCCChHHHHHHHHHHHHHhc
Confidence 3556789999999999999999999999999999999987 4677888775 78999999999999864
No 36
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.30 E-value=0.00047 Score=68.82 Aligned_cols=64 Identities=28% Similarity=0.374 Sum_probs=58.6
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 155 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
-..+.||..+.+.+||++|.+++.|.++|+++|.|- .++.|.|.|++.+.+.+|.+.|+.+-.+
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 356889999999999999999999999999999994 4789999999999999999999988765
No 37
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.19 E-value=0.0004 Score=70.85 Aligned_cols=66 Identities=24% Similarity=0.332 Sum_probs=61.0
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHH
Q 010252 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQA 217 (514)
Q Consensus 151 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~ 217 (514)
..+.+.+++||.++.+.|.|++|.++|.|.++|+++|.-|++++.....++|. .+.|..||..|..
T Consensus 23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~-~edv~~aRrei~s 88 (394)
T KOG2113|consen 23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGR-HEDVRRARREIPS 88 (394)
T ss_pred CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCCcceeccC-chhHHHHhhcCcc
Confidence 36788999999999999999999999999999999999999999877788997 6899999999986
No 38
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.16 E-value=0.00075 Score=69.45 Aligned_cols=66 Identities=27% Similarity=0.363 Sum_probs=56.4
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 155 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~------~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
.+.+-||..--+.||||+|+|+|.+.++.++-|+|-.+.+ ...|++.|+ .+..++|..+|..-+.|
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 4788899999999999999999999999999999964444 346788896 78999999998876665
No 39
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.16 E-value=0.00047 Score=79.88 Aligned_cols=65 Identities=20% Similarity=0.269 Sum_probs=59.4
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcE-EEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVK-IILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 154 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~k-I~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
-...+.||++.++-|||+||.|+|.|.++||++ |+|-. .+.|.|.|.+.+.+++|++.|+.|..+
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 367889999999999999999999999999999 88854 588999999999999999999988764
No 40
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.04 E-value=0.0018 Score=71.08 Aligned_cols=67 Identities=31% Similarity=0.393 Sum_probs=58.7
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCC---C-CCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSK---K-EDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 154 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~---~-~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
.++.+-||....|-||||+|..+|+|.++||++|.+-+.. . ...|.|.|. .+.|.+|...|-.++.+
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 5788999999999999999999999999999999985431 1 345999997 69999999999998877
No 41
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.02 E-value=0.001 Score=74.38 Aligned_cols=69 Identities=29% Similarity=0.400 Sum_probs=62.6
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhhh
Q 010252 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVE 224 (514)
Q Consensus 153 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~~~~ 224 (514)
-....+.|+++-++-+||+||.++++|-++||++|+|- +.+.|.|.+.+.+.+.+|+++|+.|+.+..-
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie---ddGtv~i~~s~~~~~~~ak~~I~~i~~e~ev 619 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE---DDGTVKIAASDGESAKKAKERIEAITREVEV 619 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec---CCCcEEEEecchHHHHHHHHHHHHHHhhccc
Confidence 34678889999999999999999999999999999997 5688999999899999999999999987544
No 42
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.85 E-value=0.00099 Score=76.21 Aligned_cols=64 Identities=25% Similarity=0.413 Sum_probs=58.1
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 155 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
...+.||++.++-+||+||.|+|.|.++||++|+|- +++.|.|.+.+.+.+++|++.|+.+..+
T Consensus 555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~---d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE---DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC---CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 457889999999999999999999999999999983 3688999999999999999999988864
No 43
>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=96.63 E-value=0.015 Score=58.09 Aligned_cols=103 Identities=18% Similarity=0.319 Sum_probs=77.7
Q ss_pred CCCCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEecccccCCCCCCCceEEEE-eeeccCChhHHHHH
Q 010252 338 KPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYA-PVEEIGDGDRLLHA 416 (514)
Q Consensus 338 ~p~~LHLTL~fLgl~~eeev~~A~~~L~~i~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRVLya-gV~~~~~~~~L~~L 416 (514)
.+..|||+|.=-=-+...+++.-.+.|+.. +.. ....+|.+.|.++.+|.+ .++.|...+ .|... ....|..|
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-DEKTRSFLALRVSEG-SNNELKRL 159 (239)
T ss_pred CCCCeEEEeCCCccccHHHHHHHHHHHHHH---Hhh-cCCceEEEEeCceEEEec-CCCCeEEEEEEeccc-ccHHHHHH
Confidence 678899999765555668887777666653 211 245899999999999988 677787444 56542 22339999
Q ss_pred HHHHHHHHHHCCCccccCCC-CCceeeEEeeeec
Q 010252 417 CQVIIDAFNEAGLVFHRDYN-KKLKLHATLMNIR 449 (514)
Q Consensus 417 a~~L~~~f~~~Gl~~e~~~~-r~fkPHiTLar~k 449 (514)
.+.|.+.+.+.|++.- . ..-.+||.||-+-
T Consensus 160 ~~~i~~~l~~~~lp~~---Y~~~~~fHvSIAw~~ 190 (239)
T PF09749_consen 160 LDRINEVLKEFGLPPF---YDEDPSFHVSIAWTL 190 (239)
T ss_pred HHHHHHHHHHhCCCcc---cCCCCCCEEEEEEEC
Confidence 9999999999999873 4 6789999999864
No 44
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=96.59 E-value=0.005 Score=61.89 Aligned_cols=67 Identities=22% Similarity=0.312 Sum_probs=55.5
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC--CCC-CCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS--SKK-EDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 154 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~--~~~-~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
.+..|-||+++-|-||||||..+++|.+|.|+.|.|.. .+. ...|+|+|. .+.+..|.--++.-|+.
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 456789995 78898888777665553
No 45
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.55 E-value=0.0047 Score=68.38 Aligned_cols=69 Identities=22% Similarity=0.335 Sum_probs=60.1
Q ss_pred CCCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 151 AERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 151 ~~~~~~~v~Vp~-~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
.......|.+|. ++-|.|||+.|.++|.||.-||+-|.|.. .++.|+|+|-++-.-+-|+.-++.++.+
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 344566789998 78899999999999999999999999975 4668999997788889999999999887
No 46
>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=96.49 E-value=0.0024 Score=53.11 Aligned_cols=76 Identities=9% Similarity=0.118 Sum_probs=50.9
Q ss_pred hhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHHHHHHHhCCC--ccc--cEEecEE
Q 010252 410 GDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGSK--EWG--EYLIKEA 485 (514)
Q Consensus 410 ~~~L~~La~~L~~~f~~~Gl~~e~~~~r~fkPHiTLar~k~~~~~~~~~~~~~fda~~il~~~~~~--~fG--~~~V~eI 485 (514)
...|.++++.+.+.+...|+..+ +++.|||||+++..... ..+..+.+.+... .+. ++.++++
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 46788889999888888999884 68999999999854321 2234444444433 233 4789999
Q ss_pred EEeeeccCCCCCce
Q 010252 486 HLSQRFVYDESGFY 499 (514)
Q Consensus 486 ~Ls~l~~~~~~g~Y 499 (514)
.+..... ..+..|
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 9965432 234555
No 47
>PRK00106 hypothetical protein; Provisional
Probab=96.45 E-value=0.0059 Score=67.73 Aligned_cols=69 Identities=17% Similarity=0.340 Sum_probs=59.2
Q ss_pred CCCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 151 AERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 151 ~~~~~~~v~Vp~-~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
.......|.+|. ++-|.|||+.|.++|.+|.-||+-|.|.. .++.|+|+|-++-.-+-|+.-++.++.+
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 4668999997788888888888888876
No 48
>PRK12704 phosphodiesterase; Provisional
Probab=96.39 E-value=0.006 Score=67.67 Aligned_cols=68 Identities=19% Similarity=0.315 Sum_probs=58.0
Q ss_pred CCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 152 ERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 152 ~~~~~~v~Vp~-~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
......|.+|. ++-|.|||+.|.++|.||.-||+-|.|.. .++.|+|+|-++..-+-|+.-++.++.+
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 4678999997667777899988888876
No 49
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.24 E-value=0.0035 Score=66.66 Aligned_cols=69 Identities=17% Similarity=0.238 Sum_probs=60.3
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 152 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
+.....+.|-.+++|.+||++|+++++|+..|+|+|+|-.....--|+|-|. +..-.+|+.-|...++.
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 4556788899999999999999999999999999999998666677899996 67888899999888875
No 50
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.15 E-value=0.0084 Score=58.03 Aligned_cols=54 Identities=28% Similarity=0.407 Sum_probs=48.6
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 163 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 163 ~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
...|.|||++|.|++.||+=|||.|.+=. ..|-|.|. .++|+-|++.|..+++.
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 69999999999999976
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=95.72 E-value=0.084 Score=51.34 Aligned_cols=137 Identities=19% Similarity=0.179 Sum_probs=65.8
Q ss_pred eEEeec-cccCCHHHHHHHHHHHHHhHHhhhhhcCCCCe-----EEEecccccCCCCCCCceEEEEeeeccCChhHHHHH
Q 010252 343 HLTVLM-LKLWNKDRVNAATNVLKSISSKVMDALDNRPL-----FIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHA 416 (514)
Q Consensus 343 HLTL~f-Lgl~~eeev~~A~~~L~~i~~~i~e~l~~~pf-----~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~L 416 (514)
||||.- +...+.+++. +.|..+... .+++ .++|.++..= ...=+=+|+.++. ...|..|
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 3443455554 444444332 2444 8888876531 1122678999986 5789999
Q ss_pred HHHHHHHHHHC-------CCccccCCCCCceeeEEeeeecccccccCCCccccccHHHHHHHhCCC-------ccccEEe
Q 010252 417 CQVIIDAFNEA-------GLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGSK-------EWGEYLI 482 (514)
Q Consensus 417 a~~L~~~f~~~-------Gl~~e~~~~r~fkPHiTLar~k~~~~~~~~~~~~~fda~~il~~~~~~-------~fG~~~V 482 (514)
++.+++.|... +.- ...+|.||+.|+-.--.... .-.+..+.....+. ..+.|.+
T Consensus 105 ~~~~r~~~~~~~~~~~~~~~~----~~~~y~PHlSLlY~d~~~~e-------~~~~~~~~~~i~~~l~~~~~~~~~~~~~ 173 (196)
T PF07823_consen 105 AQIARELFVEGPPDEVKAAEW----PREPYMPHLSLLYGDLPPEE-------KAEAAEIAQRIDDALGVDSGISGLGWEG 173 (196)
T ss_dssp HCHHHHCT----------T--------S----EEEEE-----HHH-------HHHHHHHHHHH-TT------GTT-EEEE
T ss_pred HHHHHHHhhhccccccccccc----cCCCCCCeEEEEEcCCCccc-------HHHHHHHHHHhcccccccccCCCCCEec
Confidence 99999888542 121 24689999999973211000 01122333344433 3447789
Q ss_pred cEEEEeeeccCCCCCceeEEEEEeC
Q 010252 483 KEAHLSQRFVYDESGFYHCCASIPF 507 (514)
Q Consensus 483 ~eI~Ls~l~~~~~~g~Y~~lasi~L 507 (514)
.+|.|..... +=.-..++++++|
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 9999954322 2246778888765
No 52
>PRK12705 hypothetical protein; Provisional
Probab=95.03 E-value=0.028 Score=62.06 Aligned_cols=68 Identities=19% Similarity=0.318 Sum_probs=56.9
Q ss_pred CCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 152 ERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 152 ~~~~~~v~Vp~-~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
......|.+|. ++-|.|||+.|.++|.+|..||+-|.|+. .+..|+|.+-++..-+.|+..++.++.+
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--tp~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD--TPEAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC--CccchhhcccCccchHHHHHHHHHHHhc
Confidence 34556778887 78899999999999999999999999975 3556888887778888888888888765
No 53
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=95.01 E-value=0.042 Score=54.89 Aligned_cols=63 Identities=25% Similarity=0.360 Sum_probs=55.0
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 156 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
.-++||+.+++.+||++|+.++.|.++|+|+|.+= .++-|.|.|+.......|...|..|-.+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG---~NG~IWV~~~~~~~e~~~~~aI~~ie~e 210 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVG---QNGRIWVDGENESLEELAIEAIRKIERE 210 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEe---cCCEEEecCCCcchHHHHHHHHHHHhhh
Confidence 46889999999999999999999999999999994 5789999998665678888888777665
No 54
>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=94.96 E-value=0.026 Score=44.63 Aligned_cols=37 Identities=24% Similarity=0.269 Sum_probs=34.2
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010252 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (514)
Q Consensus 153 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~i 189 (514)
.....+.||....+..|||+|.+++.++..+|.+|+|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3678899999999999999999999999999988876
No 55
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=94.58 E-value=0.025 Score=61.90 Aligned_cols=103 Identities=20% Similarity=0.308 Sum_probs=81.7
Q ss_pred CCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCC
Q 010252 150 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSL 228 (514)
Q Consensus 150 ~~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~~iv~~~~~~~k~ 228 (514)
.+++..+++-||.+++..|+|++|++++.|+..|+.||.+...+. ...+-+.+.-+..+..|+..|-.++.+ . -
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--N---T 138 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHhc--C---C
Confidence 356778899999999999999999999999999999999976543 233444443457788888887777665 2 2
Q ss_pred cceEEEEeccccchhhhccHHHHHHHHhc
Q 010252 229 DYSHFVSLPLAVHPELVDKLVNFQNTILG 257 (514)
Q Consensus 229 ~~tHFIsIPl~~hp~I~~~~~~f~~sIl~ 257 (514)
++..-++.|...|+.|.+.+...+++|-.
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
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=94.01 E-value=0.01 Score=61.34 Aligned_cols=151 Identities=15% Similarity=0.120 Sum_probs=105.1
Q ss_pred CCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEecccccCCCCCCCceEEEEeeeccCChhHHHHHHHH
Q 010252 340 KTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQV 419 (514)
Q Consensus 340 ~~LHLTL~fLgl~~eeev~~A~~~L~~i~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~La~~ 419 (514)
.++|+|+...-.+++.+++.-...+++....+.+++...-...-|.|.++|+- .|-.+++-+ ...+++.++.
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 47999999999999999999999998766555555555556677899999987 788888875 4678888999
Q ss_pred HHHHHHHCCCccccCCCCCceeeEEeeeeccccc--ccCCCccccccHHHHHHHhCCCccccEEecEEEEeeeccCCC-C
Q 010252 420 IIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKR--RKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDE-S 496 (514)
Q Consensus 420 L~~~f~~~Gl~~e~~~~r~fkPHiTLar~k~~~~--~~~~~~~~~fda~~il~~~~~~~fG~~~V~eI~Ls~l~~~~~-~ 496 (514)
+...|.+.+.... +..-|.+|-+++.....-. +-.+.+..+.+.. ++.+.-+|++.+..+..|.+...+. .
T Consensus 200 les~~~e~~~~~~--~kp~~i~lkG~~~mnddP~~~kVLYAkv~~~~~e----~~l~~~~~~~i~~~f~~~~li~k~~~~ 273 (345)
T KOG2814|consen 200 LESTFQEIRIDVG--EKPLFIDLKGLDKMNDDPSLTKVLYAKVEPDDYE----KFLQHRCGERILERFVASGLIKKESSS 273 (345)
T ss_pred HHHHHHHHHhccC--CCceeeeccchhhhcCCHhHheeeeeeccCcchH----HHHHHHHHHHHHHHHHHhcchhccccc
Confidence 9999998888775 3667999999988654211 1112233333333 3333446677777777777655433 4
Q ss_pred CceeEEEE
Q 010252 497 GFYHCCAS 504 (514)
Q Consensus 497 g~Y~~las 504 (514)
.+|+|...
T Consensus 274 ~kLH~Tvm 281 (345)
T KOG2814|consen 274 LKLHCTVM 281 (345)
T ss_pred cEEEEEEe
Confidence 56666543
No 57
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=93.85 E-value=0.052 Score=59.80 Aligned_cols=63 Identities=25% Similarity=0.280 Sum_probs=56.0
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 155 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
...++|+.+-...+||++|-.+|+|+.|||+.-++. ++.+.|-.+++...++|++.|.-|...
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 678889999999999999999999999999666664 488999999999999999999888654
No 58
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=93.11 E-value=0.26 Score=49.88 Aligned_cols=70 Identities=19% Similarity=0.321 Sum_probs=53.6
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 151 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~-~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
.+++.+.+.+...--|.||||||.++|+|..+.++.|++|.+.. ...++|+.. .+.|-.-...|.-.+++
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 34677778888889999999999999999999999999998765 456778874 45555555444444444
No 59
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=92.54 E-value=0.24 Score=54.68 Aligned_cols=102 Identities=25% Similarity=0.213 Sum_probs=76.8
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCC--CC-CCcEEEEc---------cChhHHHHHHHHHHHHHH---
Q 010252 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS--KK-EDSIIIEG---------NSTDSVAKASEKIQAIIA--- 220 (514)
Q Consensus 156 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~--~~-~~~I~I~G---------~s~~~v~~A~~~I~~iv~--- 220 (514)
..+..+....|.||||+|.++++|.++|+.+|.|-.. +. ...|+|+| . .+.+.+|-++|-...+
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 6777888999999999999999999888888887443 33 56788999 5 6899999998876421
Q ss_pred -Hhhh----CCCCcceEEEEeccccchhhhccHHHHHHHHhcc
Q 010252 221 -EAVE----SPSLDYSHFVSLPLAVHPELVDKLVNFQNTILGI 258 (514)
Q Consensus 221 -~~~~----~~k~~~tHFIsIPl~~hp~I~~~~~~f~~sIl~~ 258 (514)
+... ..+...+-.+-+|-..--.|+|+.+..+++|.++
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 0000 0022235566688775688999999999999876
No 60
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=90.90 E-value=0.16 Score=58.86 Aligned_cols=41 Identities=29% Similarity=0.577 Sum_probs=38.0
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010252 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (514)
Q Consensus 151 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~ 191 (514)
....+..+.||.++|+.|||++|+++|+++.++++.|.+|.
T Consensus 706 ~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 706 KNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred ccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence 44567889999999999999999999999999999999998
No 61
>TIGR03223 Phn_opern_protn putative phosphonate metabolism protein. This family of proteins is observed in the vicinity of other caharacterized genes involved in the catabolism of phosphonates via the3 C-P lyase system (GenProp0232), its function is unknown. These proteins are members of the somewhat broader pfam06299 model "Protein of unknown function (DUF1045)" which contains proteins found in a different genomic context as well.
Probab=90.86 E-value=4.4 Score=40.60 Aligned_cols=140 Identities=11% Similarity=0.114 Sum_probs=77.7
Q ss_pred CCceEEeec-cccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEE---EecccccCCCCCCCceEEEEeeeccCChhHHHH
Q 010252 340 KTFHLTVLM-LKLWNKDRVNAATNVLKSISSKVMDALDNRPLFI---RLKGLDLMRGSKDKARILYAPVEEIGDGDRLLH 415 (514)
Q Consensus 340 ~~LHLTL~f-Lgl~~eeev~~A~~~L~~i~~~i~e~l~~~pf~L---~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~ 415 (514)
--||.||+- +.+.+........++++.+.. ...||.| .+.-||-|-- +..+ .....|..
T Consensus 56 YGfHaTLKaPFrLa~g~~~a~L~~al~~fA~------~~~pf~i~~L~l~~Lg~FlA--------L~P~---~~~~~L~~ 118 (228)
T TIGR03223 56 YGFHATLKAPFRLAPGVTEAELLAAVAAFAA------TRAPFALPPLRVALLGGFLA--------LRPA---APCPALQA 118 (228)
T ss_pred cccceeecCCcccCCCCCHHHHHHHHHHHHh------cCCCccCCcceeeeeCCEEE--------EeeC---CCCHHHHH
Confidence 447999974 344333333334444444432 1356554 4455544421 2222 34578999
Q ss_pred HHHHHHHHHHHC----------------------------CCccccCCCCCceeeEEeeeecccccccCCCccccccHHH
Q 010252 416 ACQVIIDAFNEA----------------------------GLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARD 467 (514)
Q Consensus 416 La~~L~~~f~~~----------------------------Gl~~e~~~~r~fkPHiTLar~k~~~~~~~~~~~~~fda~~ 467 (514)
|+..+.+.|... |++.- -..|..||||-.--... .. -.+..
T Consensus 119 LAa~~V~~~d~fRAPls~aelaRRr~~~Ls~~Q~~~L~~WGYPYV---~deFrFHmTLTg~l~~~------~~--~~~~~ 187 (228)
T TIGR03223 119 LAAACVRELDPFRAPLTEAELARRRPDQLTPRQRALLERWGYPYV---LEEFRFHMTLTGRLDEE------ER--AAVLA 187 (228)
T ss_pred HHHHHHHhhhhccCCCCHHHHhhcCccCCCHHHHHHHHHcCCCce---ecceEEEEEecCCCChH------HH--HHHHH
Confidence 999999888432 22221 25799999998621110 00 11123
Q ss_pred HHHH-hCCCccccEEecEEEEeeeccCCCCCceeEEEEEeCCC
Q 010252 468 IFKQ-FGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 509 (514)
Q Consensus 468 il~~-~~~~~fG~~~V~eI~Ls~l~~~~~~g~Y~~lasi~L~~ 509 (514)
.++. |...--..+.|+.|.|+.-.. .+.-++.+..++|.+
T Consensus 188 ~l~~~~~~~l~~p~~id~laLf~e~~--~g~pF~~~~~~~l~~ 228 (228)
T TIGR03223 188 RLEARFAPLLADPLAVDGLALFVEPE--PGAPFRLIARVALAG 228 (228)
T ss_pred HHHHHhhhccCCCeeeeeEEEEeccC--CCCCcEEEEeecCCC
Confidence 3333 334444578899999965422 235699999999864
No 62
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=87.67 E-value=2.4 Score=41.21 Aligned_cols=73 Identities=18% Similarity=0.249 Sum_probs=59.0
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCCcceEEEE
Q 010252 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDYSHFVS 235 (514)
Q Consensus 156 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~~~~~~k~~~tHFIs 235 (514)
..+.+++..+-+|...+|..++.|-...|++|.+-. +.+.|.|+|. +..++.+...|..++... .+..|.
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~--~~~~i~I~g~-k~~~~~i~~~i~~~l~~i-------~~~~i~ 97 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR--SENRIRITGT-KSTAEYIEASINEILSNI-------RTEEID 97 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEec--CCcEEEEEcc-HHHHHHHHHHHHHHHhhc-------EEEEEe
Confidence 356666899999999999999999888899999976 4568999996 788888888888888762 355666
Q ss_pred ecc
Q 010252 236 LPL 238 (514)
Q Consensus 236 IPl 238 (514)
+|.
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=85.67 E-value=0.54 Score=51.29 Aligned_cols=42 Identities=29% Similarity=0.374 Sum_probs=37.2
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC
Q 010252 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 194 (514)
Q Consensus 153 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~ 194 (514)
.....|.||...++.+|||+|.++++||...|.+|.+-..++
T Consensus 485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 456789999999999999999999999999999999954433
No 64
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=84.82 E-value=1.1 Score=34.54 Aligned_cols=35 Identities=17% Similarity=0.288 Sum_probs=28.4
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEE
Q 010252 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKI 187 (514)
Q Consensus 153 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI 187 (514)
.....+.+...-.+.+||++|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 34556666666689999999999999999999665
No 65
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=84.27 E-value=0.86 Score=47.22 Aligned_cols=69 Identities=20% Similarity=0.290 Sum_probs=59.1
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHH-HHHHHHH
Q 010252 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKAS-EKIQAII 219 (514)
Q Consensus 151 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~-~~I~~iv 219 (514)
..+....+.+|...++.+.|.+|++++++++-|++-|.-|.+......-++|-.+-++++|+ ..|+..+
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 55677788999999999999999999999999999999998777777889997666788888 6776553
No 66
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=83.65 E-value=0.8 Score=44.74 Aligned_cols=54 Identities=26% Similarity=0.352 Sum_probs=45.9
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 010252 163 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (514)
Q Consensus 163 ~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~ 221 (514)
-.+|.|+||+|.|+=.||+-|.|||.+-. ..|-|-|. -+++.-|++-|-.++-.
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad----~kIHiLG~-~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLAD----SKIHILGA-FQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecC----ceEEEeec-chhhHHHHHhhHhhhcc
Confidence 45899999999999999999999999964 56888885 57899999988777654
No 67
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=83.48 E-value=0.62 Score=37.82 Aligned_cols=34 Identities=15% Similarity=0.251 Sum_probs=28.7
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhC
Q 010252 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMG 184 (514)
Q Consensus 151 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~ 184 (514)
.......+.|..+-.|.||||+|.|++.|+.=++
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 4456778889999999999999999999986544
No 68
>PRK02821 hypothetical protein; Provisional
Probab=83.13 E-value=0.96 Score=37.76 Aligned_cols=32 Identities=19% Similarity=0.293 Sum_probs=27.2
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHh
Q 010252 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEM 183 (514)
Q Consensus 152 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT 183 (514)
......+.+.++-.|.||||+|.+++.|..=.
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 34678899999999999999999999886543
No 69
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=82.98 E-value=1.2 Score=41.29 Aligned_cols=38 Identities=16% Similarity=0.110 Sum_probs=34.3
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 010252 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (514)
Q Consensus 153 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP 190 (514)
+....+.|+..-++..|||+|.+++.++.=++-.|+|-
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 45677899999999999999999999999999998873
No 70
>PRK00468 hypothetical protein; Provisional
Probab=81.80 E-value=1.4 Score=36.59 Aligned_cols=30 Identities=20% Similarity=0.302 Sum_probs=25.9
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHH
Q 010252 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEK 181 (514)
Q Consensus 152 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~ 181 (514)
......+.+.++-.|.||||+|.|++.|..
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRt 57 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRT 57 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHH
Confidence 346778999999999999999999998854
No 71
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=81.47 E-value=1.7 Score=47.79 Aligned_cols=70 Identities=16% Similarity=0.178 Sum_probs=51.6
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEcc--ChhHHHHHHHHHHHHHHH
Q 010252 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGN--STDSVAKASEKIQAIIAE 221 (514)
Q Consensus 152 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~------~~~I~I~G~--s~~~v~~A~~~I~~iv~~ 221 (514)
--...++-||...|+.|||.||..+++....-++-|++-..-+ .+.|.|+.+ +++++..|+.-...+|.+
T Consensus 447 Fpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~ 524 (657)
T COG5166 447 FPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ 524 (657)
T ss_pred CchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhh
Confidence 3456788999999999999999999999999999988754322 345777764 445555666555555554
No 72
>PRK13764 ATPase; Provisional
Probab=81.02 E-value=1.1 Score=50.77 Aligned_cols=43 Identities=28% Similarity=0.332 Sum_probs=38.1
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC
Q 010252 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 194 (514)
Q Consensus 152 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~ 194 (514)
+.....|+||...++.+|||+|.++++||...|..|+|-...+
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence 5667789999999999999999999999999999999954433
No 73
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=80.89 E-value=1.6 Score=36.45 Aligned_cols=30 Identities=17% Similarity=0.306 Sum_probs=26.3
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHH
Q 010252 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFE 180 (514)
Q Consensus 151 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE 180 (514)
.+.....+.+-++-.|.+|||+|.|++.|.
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIR 56 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIR 56 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHH
Confidence 445678899999999999999999999885
No 74
>PHA02977 hypothetical protein; Provisional
Probab=80.13 E-value=6 Score=36.95 Aligned_cols=94 Identities=18% Similarity=0.169 Sum_probs=54.3
Q ss_pred eEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEecccccCCCCCC------CceEEEEeeeccCChhHHHHH
Q 010252 343 HLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKD------KARILYAPVEEIGDGDRLLHA 416 (514)
Q Consensus 343 HLTL~fLgl~~eeev~~A~~~L~~i~~~i~e~l~~~pf~L~l~GLg~F~~dp~------~pRVLyagV~~~~~~~~L~~L 416 (514)
|+||+.-.-...+..+.-++....+ .-..++++-+..-+||.+.. +-+-+.++++. ++.|..|
T Consensus 71 hitlgian~dq~~~f~~fk~~~~d~--------dl~sis~~cke~icfpqs~askelga~g~avvmkle~---sddlkal 139 (201)
T PHA02977 71 HITLGIANKDQCDNFENFKELIKDI--------DLQSISFTCKEEICFPQSNASKELGAKGCAVVMKLEA---SDDLKAL 139 (201)
T ss_pred ceeeeccCccHhHHHHHHHHHhhcc--------cceeEEEEeeeeEeccccchhhhhCcCccEEEEEEEe---chHHHHH
Confidence 9999765443333333333333332 23667788888889986321 33556667765 3556666
Q ss_pred HHHHHHHHH----HCCCccccCCCCCceeeEEeeeecc
Q 010252 417 CQVIIDAFN----EAGLVFHRDYNKKLKLHATLMNIRH 450 (514)
Q Consensus 417 a~~L~~~f~----~~Gl~~e~~~~r~fkPHiTLar~k~ 450 (514)
.+.|-.+.- -+|=... ..++.||+|+.-++.
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 666544321 1232222 358999999998864
No 75
>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=79.09 E-value=0.86 Score=44.26 Aligned_cols=25 Identities=20% Similarity=0.272 Sum_probs=23.1
Q ss_pred CCceEEEEecCCcchhhHhhhhccc
Q 010252 287 QEHKVAVELNIGDNSERVKVDRTSI 311 (514)
Q Consensus 287 pn~FVAv~i~~~~~~~~vk~~q~~i 311 (514)
|||||||+|+.+++.++++.+|+.|
T Consensus 1 pthFl~ipl~~~~i~~~~~~fq~~v 25 (209)
T PF10469_consen 1 PTHFLCIPLNSPEIQEKFKEFQNEV 25 (209)
T ss_pred CCeEEEEECCCHHHHHHHHHHHHHH
Confidence 8999999999999999999999754
No 76
>PRK01064 hypothetical protein; Provisional
Probab=77.86 E-value=2.1 Score=35.88 Aligned_cols=31 Identities=29% Similarity=0.245 Sum_probs=26.9
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHH
Q 010252 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKE 182 (514)
Q Consensus 152 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~e 182 (514)
......+.|.++-.|.+|||+|.|++.|..=
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 4567888999999999999999999998653
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=75.39 E-value=1.7 Score=35.58 Aligned_cols=36 Identities=25% Similarity=0.351 Sum_probs=30.8
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEE
Q 010252 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKII 188 (514)
Q Consensus 153 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~ 188 (514)
.....+.|-...-+.+||++|+++++|..+.+-.+.
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=74.81 E-value=2.7 Score=39.05 Aligned_cols=38 Identities=16% Similarity=0.080 Sum_probs=34.5
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 010252 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (514)
Q Consensus 153 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP 190 (514)
+....+.||.+-++..|||+|.+.+...+=|+-+|+|-
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 46778999999999999999999999999999888774
No 79
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=72.85 E-value=3.7 Score=37.98 Aligned_cols=37 Identities=24% Similarity=0.362 Sum_probs=31.9
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010252 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (514)
Q Consensus 155 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~ 191 (514)
.+-+-|+....|..||++|+.++.|++..|-+|++=.
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 4466678889999999999999999999998888743
No 80
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=72.80 E-value=3 Score=34.30 Aligned_cols=35 Identities=17% Similarity=0.282 Sum_probs=28.7
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010252 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (514)
Q Consensus 155 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~i 189 (514)
...+.|..+-.+.||||+|.|+..|+-=++.-++-
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 45677778889999999999999999887755554
No 81
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=70.02 E-value=4.3 Score=33.05 Aligned_cols=25 Identities=36% Similarity=0.478 Sum_probs=21.6
Q ss_pred cccccCCCchhHHHHHHHh-CcEEEc
Q 010252 165 IRFIKGKEGSTQKKFEKEM-GVKIIL 189 (514)
Q Consensus 165 ~~~IIGk~G~t~k~iE~eT-~~kI~i 189 (514)
.|..||++|..++.|+++. |-+|+|
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 82
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=69.37 E-value=8.6 Score=39.55 Aligned_cols=53 Identities=17% Similarity=0.279 Sum_probs=40.6
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhhh
Q 010252 163 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVE 224 (514)
Q Consensus 163 ~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~~~~ 224 (514)
...-.|||++|+|++.||--|+|-|-+-. +.|.+.|+ -.++..+ +.||.+..+
T Consensus 158 KRRqRLiGpng~TLKAlelLT~CYilVqG----~TVsaiGp-fkGlkev----r~IV~DcM~ 210 (356)
T KOG2874|consen 158 KRRQRLIGPNGSTLKALELLTNCYILVQG----NTVSAIGP-FKGLKEV----RKIVEDCMK 210 (356)
T ss_pred HHHHHhcCCCchhHHHHHHHhhcEEEeeC----cEEEeecC-cchHHHH----HHHHHHHHh
Confidence 45667999999999999999999999854 67888886 3455544 456666444
No 83
>KOG3102 consensus Uncharacterized conserved protein [Function unknown]
Probab=67.96 E-value=18 Score=35.98 Aligned_cols=101 Identities=11% Similarity=0.216 Sum_probs=69.5
Q ss_pred cCCCCceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEecccccCCCCCCCceEE-EEeeeccCChhHHHH
Q 010252 337 IKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARIL-YAPVEEIGDGDRLLH 415 (514)
Q Consensus 337 v~p~~LHLTL~fLgl~~eeev~~A~~~L~~i~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRVL-yagV~~~~~~~~L~~ 415 (514)
+--.-|||.|.=-.-+.--+|.....+|++-.. ....|-+++.++..|-+ ..+.|-. -+.+.. .+...+.+
T Consensus 117 ~~~~~fHlSLsr~VvLr~HqI~~fi~~L~~~l~------s~~rf~~t~n~~~iytN-~e~TRtFi~leitt-~~~~~~~~ 188 (269)
T KOG3102|consen 117 ALGREFHLSLSRNVVLRVHQINSFISMLRQKLQ------SQKRFLITFNKWEIYTN-DEHTRTFISLEITT-SGLSEISK 188 (269)
T ss_pred hccceEEEeeccceEEEeehhhHHHHHHHHHHh------hhhhheEeecceEEEec-cccceeEEEEEech-hhHHHHHH
Confidence 335778999875444445667766666665321 25789999999999987 4566663 345543 45667777
Q ss_pred HHHHHHHHHHHCCCccccCCCCCceeeEEeeee
Q 010252 416 ACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNI 448 (514)
Q Consensus 416 La~~L~~~f~~~Gl~~e~~~~r~fkPHiTLar~ 448 (514)
+.+.+.+.+....|..= ..+| .+|+.|+=.
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 78888888888888652 1234 899999864
No 84
>COG5255 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.72 E-value=17 Score=35.86 Aligned_cols=124 Identities=21% Similarity=0.233 Sum_probs=64.9
Q ss_pred CcchhhHhhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeeccccCCH--------------HHHHHHHHH
Q 010252 298 GDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNK--------------DRVNAATNV 363 (514)
Q Consensus 298 ~~~~~~vk~~q~~i~~~~~~~~~~r~~~~~~~Gi~~s~fv~p~~LHLTL~fLgl~~e--------------eev~~A~~~ 363 (514)
.+.-+.|..++..+.. .|. ++.-.|+|+..+|+|+.= |+.++ .-++++-+.
T Consensus 52 s~t~~vvl~i~~r~~~---mpf-----------adklt~tP~sSlHMTvfq-g~~e~~R~~~~WpqdlPLDtpi~~~~~~ 116 (239)
T COG5255 52 SDTEEVVLIIRSRYLE---MPF-----------ADKLTFTPVSSLHMTVFQ-GLIEERRELPYWPQDLPLDTPIDAITDY 116 (239)
T ss_pred CchHHHHHHHHHHhhc---cch-----------hhhhccCCcchhhHHHHH-HHhhhcccCCCCCccCCCCCcHHHHHHH
Confidence 3345567777766531 122 344469999999999842 32221 124444433
Q ss_pred HHHhHHhhhhhcCCCCeEEEecccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHH-HCCCccccCCCCCceee
Q 010252 364 LKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFN-EAGLVFHRDYNKKLKLH 442 (514)
Q Consensus 364 L~~i~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~La~~L~~~f~-~~Gl~~e~~~~r~fkPH 442 (514)
+.+-- ++-+.+. .+|.+.+.+++- . .++-.++.+ .=++....+++.|. .+|+...+ .+.|..|
T Consensus 117 ~~erL-k~F~l~~-~~~~mrvte~rp--~-----~i~v~padd-----ad~~~l~~~Rd~ls~~~g~r~P~--HDaY~FH 180 (239)
T COG5255 117 YAERL-KIFPLLD-EEFNMRVTEMRP--Q-----GILVEPADD-----ADAKILEEWRDYLSEKFGYRHPD--HDAYQFH 180 (239)
T ss_pred HHHHH-hcccCCc-hhhcchhhcccc--c-----ceEeccCCH-----HHHHHHHHHHHHHhhhhcccCCC--CcceEEE
Confidence 33210 0111111 244444444331 1 234444443 22233455666665 57997763 6789999
Q ss_pred EEeeeecccc
Q 010252 443 ATLMNIRHKK 452 (514)
Q Consensus 443 iTLar~k~~~ 452 (514)
|||+-+..+.
T Consensus 181 ITlgYl~~wl 190 (239)
T COG5255 181 ITLGYLRIWL 190 (239)
T ss_pred EEeeeEeeec
Confidence 9999986553
No 85
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=65.56 E-value=3.4 Score=45.88 Aligned_cols=72 Identities=24% Similarity=0.240 Sum_probs=55.1
Q ss_pred CCccCCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEccChhHHHHHHHHHHHH
Q 010252 146 EPVPSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKIQAI 218 (514)
Q Consensus 146 ~~~~~~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~---~~~I~I~G~s~~~v~~A~~~I~~i 218 (514)
.+...++-.+....+|...++.|+|++|.+++.|+.-.+.+|.+...|. ...+.|.|. +.-++.|+..|..=
T Consensus 132 ~~~~~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~q-qk~~~~a~~~~~~~ 206 (608)
T KOG2279|consen 132 QILTENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQ-QKEVAAAKHLILEK 206 (608)
T ss_pred HHHhcCCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccc-cchHHHHHhhhhcc
Confidence 3444566778889999999999999999999999999999999988665 334556554 45555666666443
No 86
>PLN00108 unknown protein; Provisional
Probab=64.00 E-value=3.3 Score=42.19 Aligned_cols=29 Identities=17% Similarity=0.141 Sum_probs=26.6
Q ss_pred cccCCceEEEEec-CCcchhhHhhhhcccc
Q 010252 284 QVDQEHKVAVELN-IGDNSERVKVDRTSIP 312 (514)
Q Consensus 284 ~~rpn~FVAv~i~-~~~~~~~vk~~q~~i~ 312 (514)
+..+||||||+|. .+++.++++++|+.|.
T Consensus 33 ~~~~THFlavPL~~~p~i~~~~~~Fk~~Vl 62 (257)
T PLN00108 33 REVFTHFVSLPLAIYPDLKKNIEAFQNSVL 62 (257)
T ss_pred CCCCCeEEEEEcCCCHHHHHHHHHHHHHHH
Confidence 6789999999996 8999999999999874
No 87
>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=63.19 E-value=4.8 Score=33.80 Aligned_cols=36 Identities=11% Similarity=0.262 Sum_probs=29.7
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010252 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (514)
Q Consensus 156 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~ 191 (514)
+.|.|-...=|.+||++|+++++|.++..-.+.++.
T Consensus 32 i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~ 67 (81)
T cd02413 32 TEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE 67 (81)
T ss_pred EEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence 556666666799999999999999999888887754
No 88
>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=62.36 E-value=7.8 Score=41.10 Aligned_cols=39 Identities=26% Similarity=0.296 Sum_probs=36.2
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010252 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (514)
Q Consensus 153 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~ 191 (514)
.....+.||.+..+.-|||+|.+.|.--.=||.+|+|-+
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 357899999999999999999999999999999999854
No 89
>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=60.47 E-value=9.8 Score=37.79 Aligned_cols=61 Identities=16% Similarity=0.200 Sum_probs=41.3
Q ss_pred ceEEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCccccchHHhhhcccCC-ceEEEEecCCcchhhHhhhh
Q 010252 230 YSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQE-HKVAVELNIGDNSERVKVDR 308 (514)
Q Consensus 230 ~tHFIsIPl~~hp~I~~~~~~f~~sIl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rpn-~FVAv~i~~~~~~~~vk~~q 308 (514)
|||||++|+..-....++|..+|-.|++++=.| +-| .+|- .+..+.|+++++..-+..+|
T Consensus 6 P~HFin~Pl~~f~~f~~~~~~LQ~~~~~eG~d~------------------k~Q-kaPHlSl~mL~Isd~~i~~V~~~iq 66 (248)
T PF05213_consen 6 PTHFINFPLVQFEGFMLNFKDLQFQLLEEGVDC------------------KLQ-KAPHLSLGMLDISDEDIPDVETAIQ 66 (248)
T ss_pred CCceeeccchhhhhHHHHHHHHHHHHHHcCCCc------------------ccc-ccCeeEEEEEEcChhhhhhHHHHHH
Confidence 799999999855889999999999999874222 112 3343 45556777776655444444
Q ss_pred c
Q 010252 309 T 309 (514)
Q Consensus 309 ~ 309 (514)
+
T Consensus 67 ~ 67 (248)
T PF05213_consen 67 K 67 (248)
T ss_pred H
Confidence 3
No 90
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=59.84 E-value=9.5 Score=40.91 Aligned_cols=42 Identities=17% Similarity=0.056 Sum_probs=37.9
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC
Q 010252 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 194 (514)
Q Consensus 153 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~ 194 (514)
.....+.||.+.++.-|||+|.+.|.--+=||.+|+|-+-++
T Consensus 307 ~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 307 EKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred CcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 457899999999999999999999999999999999966544
No 91
>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=57.48 E-value=12 Score=34.77 Aligned_cols=36 Identities=25% Similarity=0.287 Sum_probs=32.3
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 010252 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (514)
Q Consensus 155 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP 190 (514)
.+-+-|.+...|..||++|..++.|++..|-+|+|=
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 667888889999999999999999999999888873
No 92
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=56.78 E-value=11 Score=36.86 Aligned_cols=37 Identities=19% Similarity=0.190 Sum_probs=34.7
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010252 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (514)
Q Consensus 155 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~ 191 (514)
...+.||.+-.+..|||+|.+.+...+=||-+|+|-.
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 7789999999999999999999999999999999854
No 93
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=51.30 E-value=16 Score=39.17 Aligned_cols=40 Identities=25% Similarity=0.269 Sum_probs=36.6
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCC
Q 010252 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS 192 (514)
Q Consensus 153 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~ 192 (514)
.....+.||.+..+.-|||+|.+.+.--.=||.+|+|=+.
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 3578999999999999999999999999999999999653
No 94
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=51.26 E-value=16 Score=34.96 Aligned_cols=33 Identities=24% Similarity=0.397 Sum_probs=27.1
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010252 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (514)
Q Consensus 156 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~i 189 (514)
+-+-|.+-. |.-|||+|.++++|++..|-+|.+
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 95
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=49.90 E-value=15 Score=40.66 Aligned_cols=39 Identities=28% Similarity=0.307 Sum_probs=35.9
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010252 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (514)
Q Consensus 153 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~ 191 (514)
.....+.||...++.-|||+|.+.|...+=||.+|+|=+
T Consensus 301 ~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 358899999999999999999999999999999999854
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=49.52 E-value=26 Score=34.99 Aligned_cols=68 Identities=16% Similarity=0.254 Sum_probs=44.0
Q ss_pred CceEEEEecCCcchhhHhhhhccccccccccccCCCCCCCCCCCCccccc-CCCCceEEeeccccCCHHHHHHH-HHHHH
Q 010252 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFI-KPKTFHLTVLMLKLWNKDRVNAA-TNVLK 365 (514)
Q Consensus 288 n~FVAv~i~~~~~~~~vk~~q~~i~~~~~~~~~~r~~~~~~~Gi~~s~fv-~p~~LHLTL~fLgl~~eeev~~A-~~~L~ 365 (514)
-.|+|++|..+.... ++.+.+.+- .++..+|++. +- ....+|+.|+..-....+++.+. .+.+.
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 489999999876432 555544441 1234677776 66 99999999998755455555544 45555
Q ss_pred HhHH
Q 010252 366 SISS 369 (514)
Q Consensus 366 ~i~~ 369 (514)
....
T Consensus 207 ~~~~ 210 (239)
T PF09749_consen 207 EPLD 210 (239)
T ss_pred HHHh
Confidence 5433
No 97
>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=47.81 E-value=15 Score=32.42 Aligned_cols=32 Identities=25% Similarity=0.377 Sum_probs=25.8
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEE
Q 010252 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKI 187 (514)
Q Consensus 156 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI 187 (514)
+.|.|-..+-|+|||++|+++++|.+.....+
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 98
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=41.48 E-value=26 Score=38.51 Aligned_cols=39 Identities=23% Similarity=0.244 Sum_probs=35.8
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 010252 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (514)
Q Consensus 153 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~ 191 (514)
.....+.||.+..+.-|||+|.+.|---.=||.+|+|-+
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
>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=41.18 E-value=88 Score=29.80 Aligned_cols=109 Identities=13% Similarity=0.085 Sum_probs=58.8
Q ss_pred CHHHHHHHHHHHHHhHHhhhhhcCCCCeE---EEecccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCC
Q 010252 353 NKDRVNAATNVLKSISSKVMDALDNRPLF---IRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGL 429 (514)
Q Consensus 353 ~eeev~~A~~~L~~i~~~i~e~l~~~pf~---L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~La~~L~~~f~~~Gl 429 (514)
+++++.++...+..- ..||. |.+.-+|-| +.+.+.+....|+.|+..+...|...--
T Consensus 13 ~~~~L~~a~~~~a~~---------~~pf~l~~L~v~~lg~F-----------lALvp~~~~~~L~~LAa~cV~~~d~fRA 72 (160)
T PF06299_consen 13 SEADLLAALAAFAAR---------FAPFELPGLEVARLGGF-----------LALVPAGPCPALQALAAACVRAFDPFRA 72 (160)
T ss_pred CHHHHHHHHHHHhcc---------CCCccCCceeEeeECCE-----------EEEeeCCCCHHHHHHHHHHHHhhhhccC
Confidence 455665555555432 34443 455666654 2233333457899999998888765311
Q ss_pred cccc---------------C----------CCCCceeeEEeeeecccccccCCCccccccHHHHH-HHhCCCccccEEec
Q 010252 430 VFHR---------------D----------YNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIF-KQFGSKEWGEYLIK 483 (514)
Q Consensus 430 ~~e~---------------~----------~~r~fkPHiTLar~k~~~~~~~~~~~~~fda~~il-~~~~~~~fG~~~V~ 483 (514)
+..+ . --..|..||||-.--.... + -.+...+ ..|...--..+.|+
T Consensus 73 Pls~aelaRR~~~~Ls~~Q~~~L~rWGYPYV~deFRFHmTLTg~l~~~~------~--~~~~~~l~~~f~~~l~~p~~id 144 (160)
T PF06299_consen 73 PLSEAELARRRPAGLSPRQRANLERWGYPYVMDEFRFHMTLTGRLDPAE------R--ARVEAALEAHFAPLLPEPLRID 144 (160)
T ss_pred CCChHHHhhcCcccCCHHHHHHHHHhCCCceeCcCEeeEEeCCCCCHHH------H--HHHHHHHHHHHHhhcCCCeeec
Confidence 1110 0 0257999999986211100 0 0112223 23444444688999
Q ss_pred EEEEee
Q 010252 484 EAHLSQ 489 (514)
Q Consensus 484 eI~Ls~ 489 (514)
.|.|+.
T Consensus 145 ~laLf~ 150 (160)
T PF06299_consen 145 SLALFG 150 (160)
T ss_pred ceEEEe
Confidence 999964
No 100
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=39.82 E-value=68 Score=34.17 Aligned_cols=53 Identities=17% Similarity=0.258 Sum_probs=44.7
Q ss_pred cccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHH
Q 010252 161 GASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAI 218 (514)
Q Consensus 161 p~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~i 218 (514)
+....--|.|+.|.+++.||+.+|+.|.-+. ..+.|+|. +..|..|...++.+
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG----~~~~i~g~-~~~v~~A~~~l~~l 74 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVARG----EAVRIIGA-RPLVDVATRVLLTL 74 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeCC----ceEEEEec-hHHHHHHHHHHhHH
Confidence 3566677899999999999999999998765 67899996 45999999999944
No 101
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=38.80 E-value=1.3e+02 Score=31.16 Aligned_cols=83 Identities=14% Similarity=0.195 Sum_probs=48.8
Q ss_pred CceEEeeccccCCHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEecccccCCCCCCCceE-EEEeeeccCChhHHHHHHHH
Q 010252 341 TFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARI-LYAPVEEIGDGDRLLHACQV 419 (514)
Q Consensus 341 ~LHLTL~fLgl~~eeev~~A~~~L~~i~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRV-LyagV~~~~~~~~L~~La~~ 419 (514)
..++++++=.. .++++|.+.|.++.......+..++..+.+.+++-..= .-.| .|+... +-...-.++...
T Consensus 185 r~~~~v~V~y~---~d~~~~~~il~~~~~~~~~vl~~p~p~v~~~~~~dssi---~~~v~~wv~~~--~~~~~~~~~~~~ 256 (286)
T PRK10334 185 RNEFIIGVAYD---SDIDQVKQILTNIIQSEDRILKDREMTVRLNELGASSI---NFVVRVWSNSG--DLQNVYWDVLER 256 (286)
T ss_pred EEEEEEEecCC---CCHHHHHHHHHHHHHhCCceecCCCCEEEEEeeeCceE---EEEEEEEEecc--hhHHHHHHHHHH
Confidence 45677665444 44666677777765444445555566677766543321 1122 454432 222234567788
Q ss_pred HHHHHHHCCCcc
Q 010252 420 IIDAFNEAGLVF 431 (514)
Q Consensus 420 L~~~f~~~Gl~~ 431 (514)
|.++|.++|+..
T Consensus 257 I~~~f~~~gI~i 268 (286)
T PRK10334 257 IKREFDAAGISF 268 (286)
T ss_pred HHHHHHHCCCcC
Confidence 999999999987
No 102
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=38.52 E-value=69 Score=26.76 Aligned_cols=35 Identities=31% Similarity=0.474 Sum_probs=27.4
Q ss_pred CcEEEcCCCCCCCcEEEEcc-ChhHHHHHHHHHHHHHHH
Q 010252 184 GVKIILPSSKKEDSIIIEGN-STDSVAKASEKIQAIIAE 221 (514)
Q Consensus 184 ~~kI~iP~~~~~~~I~I~G~-s~~~v~~A~~~I~~iv~~ 221 (514)
++.+.|=+ +|-|+|+|. +.+.+.+|.++|..++.+
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 56665544 478999994 889999999999888875
No 103
>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=36.88 E-value=1.6e+02 Score=30.08 Aligned_cols=105 Identities=14% Similarity=0.078 Sum_probs=54.2
Q ss_pred CCceEEeeccccCCHHHHHHHHHHHHHh-HHhhhhhc--------CCCCeEEEecccccCCCCCCCceEEEEeeeccCCh
Q 010252 340 KTFHLTVLMLKLWNKDRVNAATNVLKSI-SSKVMDAL--------DNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDG 410 (514)
Q Consensus 340 ~~LHLTL~fLgl~~eeev~~A~~~L~~i-~~~i~e~l--------~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~ 410 (514)
..||+||.-.....+..-++..+.+... ........ ....+.++|..|- |.+ ||+-+.|+-.+..
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 5689999998877653311222222221 11111110 0135788888886 877 8988887642210
Q ss_pred hHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHHHHHHHhC
Q 010252 411 DRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFG 473 (514)
Q Consensus 411 ~~L~~La~~L~~~f~~~Gl~~e~~~~r~fkPHiTLar~k~~~~~~~~~~~~~fda~~il~~~~ 473 (514)
..-.. ..++..- .=.|||||+-... ...++....+++++.
T Consensus 188 ~~~~~----------~~~~~c~-----N~~~HITVGT~~~--------~VkP~eSN~Ll~~~~ 227 (257)
T PF08302_consen 188 DEEDE----------VPEWECT-----NKIPHITVGTRDP--------GVKPKESNDLLERWL 227 (257)
T ss_pred ccccc----------cCCcccC-----CCCCEEEEEcCCC--------CCCcchHHHHHHHHH
Confidence 00000 2344332 2489999997532 222344455666554
No 104
>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=35.49 E-value=39 Score=32.81 Aligned_cols=41 Identities=17% Similarity=0.112 Sum_probs=17.8
Q ss_pred EEEEeeec-cCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeee
Q 010252 399 ILYAPVEE-IGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 447 (514)
Q Consensus 399 VLyagV~~-~~~~~~L~~La~~L~~~f~~~Gl~~e~~~~r~fkPHiTLar 447 (514)
-||+-+.. ++....|+.|-..|...|... .-.|-|||||.-
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 37776654 223455655555555443311 136999999996
No 105
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=33.68 E-value=41 Score=32.85 Aligned_cols=36 Identities=31% Similarity=0.305 Sum_probs=29.6
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010252 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (514)
Q Consensus 154 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~i 189 (514)
......+-..-.|..||++|...+.|.++.|-+|+|
T Consensus 76 av~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdV 111 (190)
T COG0195 76 AVVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDV 111 (190)
T ss_pred ceEEeecCcCchhhhccCCChHHHHHHHHhCCceEE
Confidence 345555566778999999999999999999977776
No 106
>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=31.85 E-value=1.9e+02 Score=26.26 Aligned_cols=55 Identities=16% Similarity=0.276 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHhHHhhhhhcCCCCeEEEecccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHH
Q 010252 354 KDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFN 425 (514)
Q Consensus 354 eeev~~A~~~L~~i~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~La~~L~~~f~ 425 (514)
++|++.+..+|.+ ..+.++-=-=..+.+ +||++|+-+...++ -..||+.++++|.
T Consensus 67 ~~EV~pvi~aL~~-----------~GI~vtAlHNH~l~e---~Prl~ymH~~~~gd---p~~lA~~vr~Ald 121 (123)
T PF07485_consen 67 EDEVNPVISALRK-----------NGIEVTALHNHWLFE---QPRLFYMHIWGVGD---PAKLARKVRAALD 121 (123)
T ss_pred HHHHHHHHHHHHH-----------CCceEEEEecccccC---CCCEEEEEEEecCC---HHHHHHHHHHHHh
Confidence 7899988888876 233333322233433 67999999986544 3455888888764
No 107
>PRK15494 era GTPase Era; Provisional
Probab=31.70 E-value=41 Score=35.37 Aligned_cols=36 Identities=28% Similarity=0.362 Sum_probs=25.7
Q ss_pred eEEEEeccccc-cccccCCCchhHHH--------HHHHhCcEEEc
Q 010252 154 HSLSVEVGASV-IRFIKGKEGSTQKK--------FEKEMGVKIIL 189 (514)
Q Consensus 154 ~~~~v~Vp~~~-~~~IIGk~G~t~k~--------iE~eT~~kI~i 189 (514)
....|.|+++- -+.|||++|.++|+ ||+-+|+++.+
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 45677788754 46789999999987 45556666554
No 108
>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=30.20 E-value=44 Score=31.32 Aligned_cols=33 Identities=27% Similarity=0.339 Sum_probs=28.5
Q ss_pred EEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 010252 157 SVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (514)
Q Consensus 157 ~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~i 189 (514)
.|.|-.+.=|.+||++|.++++|-.+||-+-.+
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~v 111 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKV 111 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEE
Confidence 456667778999999999999999999988666
No 109
>COG0799 Uncharacterized homolog of plant Iojap protein [Function unknown]
Probab=29.67 E-value=2.5e+02 Score=25.36 Aligned_cols=61 Identities=11% Similarity=0.153 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHhHHhhhhhcCCCCeEEEecccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcc
Q 010252 356 RVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 431 (514)
Q Consensus 356 ev~~A~~~L~~i~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~La~~L~~~f~~~Gl~~ 431 (514)
.+..+.++|...+ ......|.++|...+-+ ..+.+.- .+...+..+++.|.+.+.++|+.+
T Consensus 6 l~~~i~~alddkK-------AeDIv~lDv~~~s~~tD-----yfVIatg---~s~rhv~Aiad~i~~~~k~~g~~~ 66 (115)
T COG0799 6 LLEVIVEALDDKK-------AEDIVVLDVSGKSSLTD-----YFVIATG---NSSRHVKAIADNVKEELKEAGEVP 66 (115)
T ss_pred HHHHHHHHHHhcc-------CCCeEEEEccCCccccc-----EEEEEEe---CchHHHHHHHHHHHHHHHHcCCCc
Confidence 3444555555443 34677899999999988 3443332 345789999999999999999876
No 110
>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=29.61 E-value=45 Score=27.89 Aligned_cols=32 Identities=9% Similarity=0.254 Sum_probs=23.5
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcE
Q 010252 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVK 186 (514)
Q Consensus 153 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~k 186 (514)
+..+.+++ .+-|.+||++|.++++|.+...-.
T Consensus 39 ~i~V~I~t--~~pg~iIGk~G~~I~~l~~~l~k~ 70 (85)
T cd02411 39 GTQITIYA--ERPGMVIGRGGKNIRELTEILETK 70 (85)
T ss_pred cEEEEEEE--CCCCceECCCchhHHHHHHHHHHH
Confidence 44445554 677999999999999987765443
No 111
>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=28.90 E-value=35 Score=34.36 Aligned_cols=28 Identities=25% Similarity=0.245 Sum_probs=20.7
Q ss_pred eEEEEecccccc-ccccCCCchhHHHHHH
Q 010252 154 HSLSVEVGASVI-RFIKGKEGSTQKKFEK 181 (514)
Q Consensus 154 ~~~~v~Vp~~~~-~~IIGk~G~t~k~iE~ 181 (514)
....|.|.++-| +.|||++|+++|+|-.
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~ 249 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGI 249 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHH
Confidence 456677776554 6789999999998643
No 112
>PRK11538 ribosome-associated protein; Provisional
Probab=28.25 E-value=2.8e+02 Score=24.41 Aligned_cols=60 Identities=7% Similarity=0.185 Sum_probs=39.9
Q ss_pred HHHHHHHHHHhHHhhhhhcCCCCeEEEecccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcc
Q 010252 357 VNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 431 (514)
Q Consensus 357 v~~A~~~L~~i~~~i~e~l~~~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~La~~L~~~f~~~Gl~~ 431 (514)
+..+.++|.+.+ ...-..|.++++..|-+ -.+-+.. .+...++.+++.|.+.+.+.|+.+
T Consensus 7 ~~~i~~~l~dkK-------a~DI~vlDv~~~~~~~D-----y~VIatg---~S~rh~~aia~~v~~~~k~~~~~~ 66 (105)
T PRK11538 7 QDFVIDKIDDLK-------GQDIIALDVQGKSSITD-----CMIICTG---TSSRHVMSIADHVVQESRAAGLLP 66 (105)
T ss_pred HHHHHHHHHHcC-------CCCeEEEECCCCCcccC-----EEEEEEe---CCHHHHHHHHHHHHHHHHHcCCCC
Confidence 444555555543 23456788899988876 3333332 346789999999999998887754
No 113
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=26.96 E-value=33 Score=34.48 Aligned_cols=38 Identities=24% Similarity=0.253 Sum_probs=28.6
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 010252 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (514)
Q Consensus 153 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP 190 (514)
...+.|-|-...=|.+||++|+.+++|.++....+..+
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~ 87 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKE 87 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCC
Confidence 33445556677789999999999999888777665553
No 114
>PF08975 2H-phosphodiest: Domain of unknown function (DUF1868); InterPro: IPR015069 This family consist of hypothetical bacterial proteins. ; PDB: 2FSQ_A.
Probab=26.58 E-value=23 Score=32.02 Aligned_cols=47 Identities=15% Similarity=0.172 Sum_probs=27.3
Q ss_pred CceEEEEecCCcchhhHhhhhccccccccccccCCCCCCCCCCCCcccccCCCCceEEeec
Q 010252 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLM 348 (514)
Q Consensus 288 n~FVAv~i~~~~~~~~vk~~q~~i~~~~~~~~~~r~~~~~~~Gi~~s~fv~p~~LHLTL~f 348 (514)
|.||+==-...+....+..+|+.+. +.+ ..+.=.|.||..+|+|+.=
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 5566643333455678888888874 111 2234469999999999864
No 115
>PRK00089 era GTPase Era; Reviewed
Probab=26.56 E-value=41 Score=34.01 Aligned_cols=36 Identities=33% Similarity=0.417 Sum_probs=24.7
Q ss_pred eEEEEeccccc-cccccCCCchhHHH--------HHHHhCcEEEc
Q 010252 154 HSLSVEVGASV-IRFIKGKEGSTQKK--------FEKEMGVKIIL 189 (514)
Q Consensus 154 ~~~~v~Vp~~~-~~~IIGk~G~t~k~--------iE~eT~~kI~i 189 (514)
....|.|.++- -+.|||++|+++|+ ||+-+|++|.+
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 34556666544 46789999999987 45556666654
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=26.42 E-value=44 Score=37.43 Aligned_cols=35 Identities=26% Similarity=0.240 Sum_probs=29.7
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 010252 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (514)
Q Consensus 156 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP 190 (514)
-+|-|-..-=|.+|||+|++.++|-++||-+-.|=
T Consensus 101 GEViIea~KPGlvigk~g~~~reI~~~tgW~p~iv 135 (637)
T COG1782 101 GEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIV 135 (637)
T ss_pred ceEEEEecCCceEEecCchHHHHHHHHhCCcceee
Confidence 45667777789999999999999999999876653
No 117
>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=24.90 E-value=81 Score=30.52 Aligned_cols=46 Identities=22% Similarity=0.275 Sum_probs=30.3
Q ss_pred ceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEe
Q 010252 397 ARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATL 445 (514)
Q Consensus 397 pRVLyagV~~~~~~~~L~~La~~L~~~f~~~Gl~~e~~~~r~fkPHiTL 445 (514)
.||-|.+....-=... .++.+.+.++|..+||+.. ..+.|+||.-|
T Consensus 2 ~ri~f~K~g~~~fiSH-Ldl~r~~eRa~rRA~lp~a--~SqGFnP~Pki 47 (187)
T PF10105_consen 2 YRIRFSKKGRARFISH-LDLMRVFERALRRAGLPVA--YSQGFNPHPKI 47 (187)
T ss_pred EEEEEEecCceEEech-HHHHHHHHHHhhhcCCCee--ecCCCCCCcce
Confidence 3566665442100112 3567889999999999986 47789999543
No 118
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=23.35 E-value=1.4e+02 Score=29.72 Aligned_cols=74 Identities=15% Similarity=0.133 Sum_probs=47.5
Q ss_pred CCccCCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHh
Q 010252 146 EPVPSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEA 222 (514)
Q Consensus 146 ~~~~~~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~kI~iP~~~~~~~I~I~G~s~~~v~~A~~~I~~iv~~~ 222 (514)
++..+...-.+.+.|-.+-.+.|||+.|.|+..||-=++.-++- ..+....|++.-. .=.++=.+.+..+...+
T Consensus 83 ~i~v~~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~-~~g~~~~v~ldv~--~yRerR~e~L~~LA~~~ 156 (208)
T COG1847 83 TITVSEEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK-IGGKFKRVTLDVG--DYRERRKETLIKLAERA 156 (208)
T ss_pred EEEEeecCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh-hcCcceEEEEEhh--hHHHHHHHHHHHHHHHH
Confidence 33344456677888888889999999999999999998877765 2222334444321 23444445555554443
No 119
>TIGR00090 iojap_ybeB iojap-like ribosome-associated protein. This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown.
Probab=21.11 E-value=4.3e+02 Score=22.79 Aligned_cols=46 Identities=13% Similarity=0.203 Sum_probs=33.2
Q ss_pred CCeEEEecccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcc
Q 010252 378 RPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 431 (514)
Q Consensus 378 ~pf~L~l~GLg~F~~dp~~pRVLyagV~~~~~~~~L~~La~~L~~~f~~~Gl~~ 431 (514)
...-+.+++...+-+ |.-+-...+...++.+++.|.+.+.+.|+.+
T Consensus 16 dI~vldv~~~~~~~d--------y~VI~Tg~S~rh~~aia~~v~~~~k~~~~~~ 61 (99)
T TIGR00090 16 DIVVLDVRGKSSIAD--------YFVIASGTSSRHVKAIADNVEEELKEAGLKP 61 (99)
T ss_pred CEEEEECCCCCcccC--------EEEEEEeCCHHHHHHHHHHHHHHHHHcCCCc
Confidence 446678888887776 3333332346789999999999999888754
No 120
>COG1159 Era GTPase [General function prediction only]
Probab=20.27 E-value=49 Score=34.50 Aligned_cols=26 Identities=27% Similarity=0.285 Sum_probs=20.0
Q ss_pred eEEEEecccc-ccccccCCCchhHHHH
Q 010252 154 HSLSVEVGAS-VIRFIKGKEGSTQKKF 179 (514)
Q Consensus 154 ~~~~v~Vp~~-~~~~IIGk~G~t~k~i 179 (514)
....+.|+++ .-+.||||+|+++|+|
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 3455777764 4577899999999987
No 121
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=20.24 E-value=1e+02 Score=25.44 Aligned_cols=35 Identities=23% Similarity=0.399 Sum_probs=21.5
Q ss_pred CHHHHHHHHHHHHHhHHhhhhhcCCCCeEEEecccccCC
Q 010252 353 NKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMR 391 (514)
Q Consensus 353 ~eeev~~A~~~L~~i~~~i~e~l~~~pf~L~l~GLg~F~ 391 (514)
+..++..+.+.|.++ +.+.|... -.+.|.|+|.|.
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 456666666555443 44444322 278899999994
Done!