Query 012600
Match_columns 460
No_of_seqs 257 out of 765
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 04:20:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012600.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012600hhsearch_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 5.1E-44 1.1E-48 355.4 15.1 287 60-456 2-291 (345)
2 PLN00108 unknown protein; Prov 100.0 4.3E-36 9.3E-41 293.9 16.2 174 227-457 33-206 (257)
3 PF10469 AKAP7_NLS: AKAP7 2'5' 100.0 1.3E-32 2.9E-37 262.0 15.8 151 230-451 1-153 (209)
4 COG1514 LigT 2'-5' RNA ligase 99.8 1.1E-20 2.4E-25 177.8 13.2 130 288-450 2-132 (180)
5 PRK15124 2'-5' RNA ligase; Pro 99.8 3.2E-20 7E-25 173.1 12.5 127 288-449 6-132 (176)
6 TIGR02258 2_5_ligase 2'-5' RNA 99.8 7.1E-19 1.5E-23 162.8 12.4 132 288-451 2-133 (179)
7 PHA02574 57B hypothetical prot 99.6 7.5E-16 1.6E-20 141.1 9.9 109 288-447 10-118 (149)
8 PRK13679 hypothetical protein; 99.5 2.3E-13 5.1E-18 126.0 11.5 122 288-450 2-123 (168)
9 cd02394 vigilin_like_KH K homo 99.3 4.4E-12 9.6E-17 98.6 6.1 60 156-216 2-62 (62)
10 cd02393 PNPase_KH Polynucleoti 99.2 2.4E-11 5.2E-16 95.3 6.4 59 155-216 3-61 (61)
11 PF00013 KH_1: KH domain syndr 99.2 1.3E-11 2.7E-16 95.5 4.0 60 155-215 1-60 (60)
12 PF13563 2_5_RNA_ligase2: 2'-5 99.0 6.4E-10 1.4E-14 99.1 7.6 102 337-453 21-122 (153)
13 cd00105 KH-I K homology RNA-bi 99.0 8.8E-10 1.9E-14 85.2 6.0 59 156-215 2-63 (64)
14 PF02834 LigT_PEase: LigT like 98.8 1.6E-09 3.5E-14 89.1 1.9 82 299-401 6-87 (87)
15 cd02396 PCBP_like_KH K homolog 98.8 9.6E-09 2.1E-13 81.1 6.2 59 156-215 2-64 (65)
16 smart00322 KH K homology RNA-b 98.8 2.3E-08 5.1E-13 76.4 8.0 66 153-219 2-68 (69)
17 PF13014 KH_3: KH domain 98.8 5.3E-09 1.1E-13 76.2 4.0 39 164-202 1-43 (43)
18 PF05213 Corona_NS2A: Coronavi 98.6 1.5E-07 3.3E-12 90.3 9.9 128 285-449 4-132 (248)
19 KOG1676 K-homology type RNA bi 98.6 9.9E-08 2.2E-12 102.6 8.0 106 152-258 228-346 (600)
20 cd02395 SF1_like-KH Splicing f 98.6 1.4E-07 3E-12 83.9 6.7 59 163-221 15-95 (120)
21 KOG0119 Splicing factor 1/bran 98.1 4.7E-06 1E-10 88.3 6.1 72 153-224 137-233 (554)
22 PRK13763 putative RNA-processi 98.0 9.5E-06 2.1E-10 76.8 6.9 65 154-220 3-70 (180)
23 KOG2208 Vigilin [Lipid transpo 98.0 1.3E-05 2.9E-10 90.4 7.2 105 151-259 344-449 (753)
24 TIGR03665 arCOG04150 arCOG0415 98.0 1.1E-05 2.3E-10 75.9 5.3 61 158-220 2-64 (172)
25 TIGR03665 arCOG04150 arCOG0415 97.9 1.3E-05 2.8E-10 75.3 5.6 53 164-221 99-151 (172)
26 PRK13763 putative RNA-processi 97.9 1.8E-05 3.8E-10 74.9 5.7 53 164-221 105-157 (180)
27 KOG2191 RNA-binding protein NO 97.7 0.00022 4.8E-09 72.7 10.8 107 151-258 36-160 (402)
28 KOG2193 IGF-II mRNA-binding pr 97.7 3.4E-05 7.4E-10 80.6 4.6 103 152-258 197-308 (584)
29 TIGR02696 pppGpp_PNP guanosine 97.6 8.3E-05 1.8E-09 83.2 6.9 64 154-220 578-641 (719)
30 KOG1676 K-homology type RNA bi 97.6 8.3E-05 1.8E-09 80.6 6.0 110 150-260 50-169 (600)
31 TIGR03591 polynuc_phos polyrib 97.6 0.00011 2.3E-09 82.6 6.3 64 155-221 552-615 (684)
32 COG5176 MSL5 Splicing factor ( 97.5 9.9E-05 2.2E-09 71.1 5.0 77 145-221 139-221 (269)
33 KOG2193 IGF-II mRNA-binding pr 97.5 0.00012 2.6E-09 76.7 4.7 61 160-221 286-352 (584)
34 KOG2192 PolyC-binding hnRNP-K 97.3 0.00053 1.2E-08 68.3 6.8 68 153-221 314-384 (390)
35 KOG1588 RNA-binding protein Sa 97.2 0.0008 1.7E-08 66.9 7.2 71 152-224 90-187 (259)
36 KOG2190 PolyC-binding proteins 97.1 0.0013 2.7E-08 71.3 8.3 67 154-221 138-208 (485)
37 KOG2113 Predicted RNA binding 97.1 0.00055 1.2E-08 69.5 5.2 65 152-217 24-88 (394)
38 KOG2191 RNA-binding protein NO 97.0 0.0011 2.4E-08 67.8 6.3 67 154-221 132-204 (402)
39 PLN00207 polyribonucleotide nu 97.0 0.00075 1.6E-08 77.3 5.5 64 155-221 686-750 (891)
40 PRK04163 exosome complex RNA-b 97.0 0.0016 3.4E-08 64.2 6.6 64 155-221 146-209 (235)
41 COG1185 Pnp Polyribonucleotide 96.7 0.0025 5.5E-08 70.6 6.3 68 154-224 552-619 (692)
42 PRK11824 polynucleotide phosph 96.7 0.0016 3.5E-08 73.3 4.9 64 155-221 555-618 (693)
43 KOG0336 ATP-dependent RNA heli 96.5 0.0021 4.6E-08 67.8 3.5 70 152-222 45-114 (629)
44 PF09749 HVSL: Uncharacterised 96.4 0.026 5.7E-07 55.5 10.8 103 338-449 86-190 (239)
45 TIGR03319 YmdA_YtgF conserved 95.6 0.026 5.6E-07 61.8 7.0 68 152-221 202-270 (514)
46 PRK12704 phosphodiesterase; Pr 95.6 0.025 5.4E-07 62.0 6.6 68 152-221 208-276 (520)
47 PRK00106 hypothetical protein; 95.4 0.035 7.6E-07 60.9 7.1 68 152-221 223-291 (535)
48 COG1094 Predicted RNA-binding 95.1 0.035 7.6E-07 53.4 5.3 53 164-221 112-164 (194)
49 cd02134 NusA_KH NusA_K homolog 95.0 0.028 6E-07 44.1 3.5 37 153-189 24-60 (61)
50 PF07823 CPDase: Cyclic phosph 94.8 0.051 1.1E-06 52.1 5.5 92 343-448 40-139 (196)
51 KOG2814 Transcription coactiva 94.7 0.0067 1.4E-07 62.3 -0.9 100 340-449 128-227 (345)
52 PRK12705 hypothetical protein; 93.8 0.08 1.7E-06 57.9 5.0 68 152-221 196-264 (508)
53 KOG2192 PolyC-binding hnRNP-K 93.8 0.18 3.8E-06 50.8 7.0 69 152-221 46-115 (390)
54 KOG2190 PolyC-binding proteins 93.6 0.12 2.7E-06 56.1 6.1 103 156-258 45-166 (485)
55 KOG2279 Kinase anchor protein 93.5 0.053 1.2E-06 59.0 3.1 102 151-257 65-167 (608)
56 COG1097 RRP4 RNA-binding prote 93.3 0.15 3.3E-06 50.5 5.6 63 156-221 148-210 (239)
57 KOG2208 Vigilin [Lipid transpo 92.4 0.086 1.9E-06 60.2 2.9 42 150-191 705-746 (753)
58 COG1094 Predicted RNA-binding 92.2 0.36 7.9E-06 46.5 6.4 65 153-219 7-75 (194)
59 KOG1067 Predicted RNA-binding 92.0 0.14 3E-06 56.2 3.6 63 155-221 598-660 (760)
60 PF02834 LigT_PEase: LigT like 89.6 0.21 4.6E-06 40.7 1.9 37 410-450 8-44 (87)
61 PHA02977 hypothetical protein; 87.9 2 4.2E-05 40.0 7.1 95 343-451 71-175 (201)
62 PF10469 AKAP7_NLS: AKAP7 2'5' 86.6 0.36 7.9E-06 46.1 1.7 25 287-311 1-25 (209)
63 PF14611 SLS: Mitochondrial in 86.3 2.7 5.8E-05 40.2 7.5 73 156-238 28-100 (210)
64 COG1855 ATPase (PilT family) [ 83.3 0.83 1.8E-05 49.6 2.7 41 152-192 484-524 (604)
65 cd02409 KH-II KH-II (K homolo 83.2 1.5 3.2E-05 33.3 3.5 34 154-187 25-58 (68)
66 PRK08406 transcription elongat 83.0 1.2 2.6E-05 40.8 3.3 37 153-189 98-134 (140)
67 PF13083 KH_4: KH domain; PDB: 82.2 0.76 1.6E-05 36.8 1.5 34 151-184 26-59 (73)
68 PRK13764 ATPase; Provisional 80.1 1.3 2.8E-05 49.6 2.9 40 152-191 479-518 (602)
69 KOG3273 Predicted RNA-binding 79.2 1.4 3.1E-05 42.9 2.4 53 164-221 179-231 (252)
70 COG5166 Uncharacterized conser 79.0 2.3 5E-05 46.5 4.2 69 153-221 448-524 (657)
71 PRK02821 hypothetical protein; 77.9 2.3 5E-05 35.3 3.0 33 152-184 29-61 (77)
72 PRK00468 hypothetical protein; 77.7 2.3 5.1E-05 35.0 3.0 30 152-181 28-57 (75)
73 TIGR01952 nusA_arch NusA famil 77.7 2 4.4E-05 39.5 2.9 38 152-189 98-135 (141)
74 KOG2113 Predicted RNA binding 77.5 2 4.4E-05 44.3 3.1 69 151-219 112-181 (394)
75 COG1837 Predicted RNA-binding 76.4 2.6 5.6E-05 35.0 2.9 31 151-181 27-57 (76)
76 PF07650 KH_2: KH domain syndr 76.0 1.6 3.5E-05 35.2 1.6 37 152-188 23-59 (78)
77 PRK01064 hypothetical protein; 75.5 2.6 5.7E-05 35.0 2.7 32 151-182 27-58 (78)
78 PF05213 Corona_NS2A: Coronavi 74.0 4.8 0.0001 39.7 4.5 62 230-309 6-67 (248)
79 PLN00108 unknown protein; Prov 74.0 1.9 4.1E-05 43.4 1.9 29 283-311 32-61 (257)
80 TIGR03223 Phn_opern_protn puta 71.3 16 0.00034 36.4 7.5 69 341-426 57-129 (228)
81 PRK08406 transcription elongat 71.0 4.4 9.5E-05 37.1 3.4 37 154-190 32-68 (140)
82 cd02414 jag_KH jag_K homology 68.2 4.4 9.5E-05 33.0 2.5 35 155-189 25-59 (77)
83 TIGR01953 NusA transcription t 67.2 5.7 0.00012 41.6 3.7 40 152-191 299-338 (341)
84 COG5255 Uncharacterized protei 66.9 17 0.00036 35.7 6.5 130 288-449 42-187 (239)
85 PF13184 KH_5: NusA-like KH do 66.8 5.5 0.00012 32.2 2.7 25 165-189 19-44 (69)
86 PRK12328 nusA transcription el 65.7 6.3 0.00014 41.8 3.7 44 151-194 305-348 (374)
87 KOG3102 Uncharacterized conser 64.8 22 0.00049 35.1 6.9 97 339-446 119-216 (269)
88 cd02413 40S_S3_KH K homology R 63.8 4.7 0.0001 33.5 1.9 37 156-192 32-68 (81)
89 COG0195 NusA Transcription elo 58.9 9.4 0.0002 36.8 3.2 36 155-190 143-178 (190)
90 PRK09202 nusA transcription el 56.9 9.9 0.00022 41.5 3.4 39 153-191 301-339 (470)
91 PRK12327 nusA transcription el 56.7 11 0.00025 39.7 3.7 40 153-192 302-341 (362)
92 TIGR01952 nusA_arch NusA famil 55.8 15 0.00032 33.8 3.8 36 155-190 34-69 (141)
93 PF08975 2H-phosphodiest: Doma 54.1 5.5 0.00012 35.7 0.7 47 287-347 13-59 (118)
94 PRK06418 transcription elongat 53.4 14 0.0003 35.0 3.3 34 155-189 62-95 (166)
95 PF09749 HVSL: Uncharacterised 50.0 26 0.00056 34.5 4.8 66 288-367 141-208 (239)
96 KOG2279 Kinase anchor protein 49.4 9.7 0.00021 42.1 1.8 69 150-219 136-207 (608)
97 cd02412 30S_S3_KH K homology R 46.8 16 0.00035 31.8 2.5 32 156-187 63-94 (109)
98 PRK12329 nusA transcription el 46.2 20 0.00043 39.0 3.5 39 153-191 334-372 (449)
99 KOG2874 rRNA processing protei 45.5 27 0.00059 35.8 4.1 51 165-224 160-210 (356)
100 PRK15245 type III effector pho 40.8 1.5E+02 0.0032 29.5 8.1 80 340-433 103-196 (241)
101 PRK10334 mechanosensitive chan 35.3 1.9E+02 0.0042 29.4 8.6 83 341-431 185-268 (286)
102 KOG1960 Predicted RNA-binding 34.6 54 0.0012 35.3 4.4 69 153-221 213-295 (531)
103 PF00352 TBP: Transcription fa 31.9 93 0.002 25.7 4.7 35 184-221 49-84 (86)
104 cd02411 archeal_30S_S3_KH K ho 31.8 41 0.00088 27.9 2.5 32 153-186 39-70 (85)
105 TIGR00436 era GTP-binding prot 28.6 31 0.00067 34.1 1.5 28 154-181 221-249 (270)
106 COG1702 PhoH Phosphate starvat 27.4 1.5E+02 0.0032 31.4 6.2 52 162-218 23-74 (348)
107 COG0195 NusA Transcription elo 26.6 64 0.0014 31.2 3.2 35 155-189 77-111 (190)
108 PRK11538 ribosome-associated p 26.4 3.3E+02 0.0071 23.8 7.3 60 357-431 7-66 (105)
109 smart00411 BHL bacterial (prok 25.6 75 0.0016 25.9 3.1 36 353-392 17-52 (90)
110 PRK15494 era GTPase Era; Provi 24.6 40 0.00087 34.9 1.5 26 154-179 273-299 (339)
111 COG1159 Era GTPase [General fu 24.4 42 0.00091 34.7 1.6 27 153-179 228-255 (298)
112 COG0799 Uncharacterized homolo 24.4 3.7E+02 0.008 24.1 7.3 60 357-431 7-66 (115)
113 PRK00089 era GTPase Era; Revie 23.7 43 0.00094 33.2 1.6 26 154-179 226-252 (292)
114 cd00591 HU_IHF Integration hos 23.1 92 0.002 25.1 3.2 32 360-392 20-51 (87)
115 cd02410 archeal_CPSF_KH The ar 22.9 72 0.0016 29.7 2.7 33 157-189 79-111 (145)
116 COG1847 Jag Predicted RNA-bind 22.6 40 0.00086 33.1 1.0 76 145-223 82-157 (208)
117 COG0092 RpsC Ribosomal protein 22.5 32 0.0007 34.3 0.3 35 156-190 53-87 (233)
118 PF03536 VRP3: Salmonella viru 22.4 5.4E+02 0.012 25.7 8.6 80 340-432 102-194 (240)
119 PF06299 DUF1045: Protein of u 20.7 2.6E+02 0.0056 26.4 5.9 21 406-426 49-69 (160)
120 COG1782 Predicted metal-depend 20.2 70 0.0015 35.6 2.3 35 156-190 101-135 (637)
121 TIGR00090 iojap_ybeB iojap-lik 20.1 4.6E+02 0.01 22.4 6.9 46 378-431 16-61 (99)
No 1
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=100.00 E-value=5.1e-44 Score=355.41 Aligned_cols=287 Identities=34% Similarity=0.494 Sum_probs=246.2
Q ss_pred ccccccccCCceeeeccccccccccccccccCCCCCceEee-ecccCCcccccccceeeeeecccccccccCcccccccc
Q 012600 60 YGDKKQKIINPVWRPVSTQASVNEESLVKDVSEDGSQIQEM-HCSTSSNVSDAQLGVEVAEAVNEGTDLTLSSSVSLDDI 138 (460)
Q Consensus 60 ~~~~k~k~~~~~wrpv~t~as~~~~~l~~~~~~~~~~v~e~-~~~~s~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~ 138 (460)
+..++++..|.+|+|++|+.++.. .+++...|++ .|.++...+. . ..
T Consensus 2 ~~~~~~~~~n~~~~~~~~~t~~~~-------~~~~~e~~~~~~c~d~p~~~~-----d--------------------v~ 49 (345)
T KOG2814|consen 2 YRKTRYNLVNDVSFDLNTDTTFAD-------MSEEFEAQTSAECVDMPGDTV-----D--------------------VE 49 (345)
T ss_pred cchhhhhhhhhcccCccccccccc-------CchhhHHHhHhhcccCCCChH-----H--------------------hh
Confidence 456789999999999999988763 3445566666 6777754332 1 00
Q ss_pred cccccCCCCccCCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHH
Q 012600 139 KDETLEGEPVPSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQA 217 (460)
Q Consensus 139 ~~~~~~~~~~~~~~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~-~~~I~ItG~s~e~V~~A~~rI~~ 217 (460)
+.. -.++|+.++.|+++|+++|||++|.|+++||.||+|+|.+|++++ .+.|+|+|.++++|.+|.+||..
T Consensus 50 ~~~--------~~~~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~ 121 (345)
T KOG2814|consen 50 DDA--------GAKDFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAK 121 (345)
T ss_pred hcc--------ccccchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHH
Confidence 011 122899999999999999999999999999999999999999995 88999999999999999999999
Q ss_pred HHHHhhhCCCCCcceEEeeccccchhhhhhHHHHHHHHhcccccccccccCCCCCccccchHHhhhcccCCceEEEEccC
Q 012600 218 IIAEAVESPSLDYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNI 297 (460)
Q Consensus 218 iv~e~~~~~k~~~THFIsIPl~~hP~I~g~~~~F~~sIl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rpn~FVAv~i~~ 297 (460)
++++.++ +.+.|||+++|++ ...+.++|..|+...+..
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 6889999999998 688999999998432211
Q ss_pred CcchHHHHHhhccccccccccccCCCCCCCCCCCCcCCccCCCcceEEeeccccCChhHHHHHHHHHHHhHHhhhhhcCC
Q 012600 298 GDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDN 377 (460)
Q Consensus 298 ~~i~~~v~~vq~~i~~~~~~~~~~k~~~~~~~Gld~~~fv~p~~LHLTL~~L~L~~eeev~~A~~~L~~i~~~i~d~L~~ 377 (460)
+ .+.+.|++.+.|++|.++||||+|+.|++++++++|+++|+.+.+++...+..
T Consensus 160 -------e-------------------sl~~~g~~~s~F~~p~~~HLTvgm~~L~~dd~vq~a~e~les~~~e~~~~~~~ 213 (345)
T KOG2814|consen 160 -------E-------------------SLLDGGIDKSLFQGPGTFHLTVGMLKLLNDDDVQKALEILESTFQEIRIDVGE 213 (345)
T ss_pred -------H-------------------HhhccchhhccccCCceeeEEEEEEEecChHHHHHHHHHHHHHHHHHHhccCC
Confidence 0 01245778889999999999999999999999999999999999999888889
Q ss_pred CCeEEEeccccCCCCCCCCceEEEEeceecCCchHHHHHH-HHHHHHHHHCCCCcccCCCCCcceeEEeeeecccccccc
Q 012600 378 RPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHAC-QVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRQKR 456 (460)
Q Consensus 378 ~pf~l~lkGLg~F~~dp~~~rVLya~V~~~d~~~~L~~L~-~~L~~~f~~~Gl~~~~de~r~fkpHlTL~n~k~~k~~~~ 456 (460)
.|+.+.++|+.+|++||..++||||+|++.+....|+.++ +.|..+|...|+... +.++.++|+|+||++|+|+.+.
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 9999999999999999999999999999877778899999 999999999999984 6789999999999999998773
No 2
>PLN00108 unknown protein; Provisional
Probab=100.00 E-value=4.3e-36 Score=293.91 Aligned_cols=174 Identities=55% Similarity=0.858 Sum_probs=151.0
Q ss_pred CCCcceEEeeccccchhhhhhHHHHHHHHhcccccccccccCCCCCccccchHHhhhcccCCceEEEEccCCcchHHHHH
Q 012600 227 SLDYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKV 306 (460)
Q Consensus 227 k~~~THFIsIPl~~hP~I~g~~~~F~~sIl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rpn~FVAv~i~~~~i~~~v~~ 306 (460)
+.++|||||||+..+|+|.+++.+|+++|++..+. .|.-|
T Consensus 33 ~~~~THFlavPL~~~p~i~~~~~~Fk~~Vl~~~~~------------------------~~~~f---------------- 72 (257)
T PLN00108 33 REVFTHFVSLPLAIYPDLKKNIEAFQNSVLGNNDK------------------------DPLKF---------------- 72 (257)
T ss_pred CCCCCeEEEEEcCCCHHHHHHHHHHHHHHHhcccc------------------------ccccc----------------
Confidence 56799999999965899999999999999975200 01000
Q ss_pred hhccccccccccccCCCCCCCCCCCCcCCccCCCcceEEeeccccCChhHHHHHHHHHHHhHHhhhhhcCCCCeEEEecc
Q 012600 307 DRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKG 386 (460)
Q Consensus 307 vq~~i~~~~~~~~~~k~~~~~~~Gld~~~fv~p~~LHLTL~~L~L~~eeev~~A~~~L~~i~~~i~d~L~~~pf~l~lkG 386 (460)
.+.++++||++++|++|.+|||||+||.|.+++++++|.++|+++...+.++++++|+.|+|+|
T Consensus 73 ----------------~~~l~~~gid~siF~~p~~LHLTLgmL~L~~~eev~kA~~~L~s~~~~i~~~l~~~pl~I~lkG 136 (257)
T PLN00108 73 ----------------QSTLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNILKSICSNVRQALKDRPVFIRLRG 136 (257)
T ss_pred ----------------cccccccCCCHHHcCCCCceEEEEEEEEcCCHHHHHHHHHHHHHHHHHHHHhhCCCCeEEEEEe
Confidence 0123478999999999999999999999999999999999999999889999999999999999
Q ss_pred ccCCCCCCCCceEEEEeceecCCchHHHHHHHHHHHHHHHCCCCcccCCCCCcceeEEeeeeccccccccc
Q 012600 387 LDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRQKRN 457 (460)
Q Consensus 387 Lg~F~~dp~~~rVLya~V~~~d~~~~L~~L~~~L~~~f~~~Gl~~~~de~r~fkpHlTL~n~k~~k~~~~~ 457 (460)
|++||+||++++||||+|++.++.++|+++|+.|.+.|.++||... |..++++||+||||++|+++++++
T Consensus 137 L~~Mnddps~~~VLYA~Ve~~~~~~rLq~~ad~i~~~F~~aGL~~~-d~~~~vKLH~TlmNt~~rk~k~~k 206 (257)
T PLN00108 137 LDCMNGSLDKTRVLYAPVEEVGHEGRLLNACHVIIDAFENAGFAGK-DAKSRLKLHATLMNASYRKDKSKK 206 (257)
T ss_pred ehhcCCCcccceEEEEeccccCchhHHHHHHHHHHHHHHHcCCccc-ccCcceeeEeEEechhhhhcccCc
Confidence 9999999999999999999877778999999999999999999974 234699999999999999876543
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=1.3e-32 Score=261.99 Aligned_cols=151 Identities=38% Similarity=0.628 Sum_probs=133.0
Q ss_pred cceEEeeccccchhhhhhHHHHHHHHhcccccccccccCCCCCccccchHHhhhcccCCceEEEEccCCcchHHHHHhhc
Q 012600 230 YSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKVDRT 309 (460)
Q Consensus 230 ~THFIsIPl~~hP~I~g~~~~F~~sIl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rpn~FVAv~i~~~~i~~~v~~vq~ 309 (460)
||||||||++ +|.|+..+..|++.|+..
T Consensus 1 pthFl~ipl~-~~~i~~~~~~fq~~v~~~--------------------------------------------------- 28 (209)
T PF10469_consen 1 PTHFLCIPLN-SPEIQEKFKEFQNEVLSK--------------------------------------------------- 28 (209)
T ss_pred CCeEEEEECC-CHHHHHHHHHHHHHHHhh---------------------------------------------------
Confidence 5888888885 788888888888888743
Q ss_pred cccccccccccCCCCCCCCCCCCcCCccCCCcceEEeeccccCChhHHHHHHHHHHHhHHhhhhhcCC-CCeEEEecccc
Q 012600 310 SIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDN-RPLFIRLKGLD 388 (460)
Q Consensus 310 ~i~~~~~~~~~~k~~~~~~~Gld~~~fv~p~~LHLTL~~L~L~~eeev~~A~~~L~~i~~~i~d~L~~-~pf~l~lkGLg 388 (460)
..|+++++|++|++|||||+||+|.+++++++|.++|+++.+.+.+.+.. .|+.|+|+||+
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 23556668999999999999999999999999999999999888877664 99999999999
Q ss_pred CCCCCCCCceEEEEeceecCCchHHHHHHHHHHHHHHHCCCCcccCCCC-CcceeEEeeeeccc
Q 012600 389 LMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNK-KLKLHATLMNIRHK 451 (460)
Q Consensus 389 ~F~~dp~~~rVLya~V~~~d~~~~L~~L~~~L~~~f~~~Gl~~~~de~r-~fkpHlTL~n~k~~ 451 (460)
+|++||+++|||||+|.+.++...|+++++.|.+.|.++||...+ +.+ +|+||+||||++|+
T Consensus 91 ~f~~d~~~~~VLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~-~~~~~~~~H~Tl~n~~~~ 153 (209)
T PF10469_consen 91 YFNDDPSKARVLYAKVSEDSNSERLQELANKLRERFQEAGLLVTD-DRRFSFKPHITLMNTSYR 153 (209)
T ss_pred hhCCCCCcceEEEEcccccchHHHHHHHHHHHHHHHHHcCCcccc-ccCCCcceEEEEEecccc
Confidence 999999999999999997656799999999999999999999854 334 48999999999996
No 4
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=99.84 E-value=1.1e-20 Score=177.84 Aligned_cols=130 Identities=20% Similarity=0.333 Sum_probs=115.5
Q ss_pred CceEEEEccCCcchHHHHHhhccccccccccccCCCCCCCCCCCCcCCccCCCcceEEeeccccCChhHHHHHHHHHHHh
Q 012600 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 367 (460)
Q Consensus 288 n~FVAv~i~~~~i~~~v~~vq~~i~~~~~~~~~~k~~~~~~~Gld~~~fv~p~~LHLTL~~L~L~~eeev~~A~~~L~~i 367 (460)
-+|+||++ ++++.+++..++..+. ..+ ..+|++++++||||.|||.++++.++.+.++|.++
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 5688999999998762 112 23799999999999999999999999999999988
Q ss_pred HHhhhhhcCCC-CeEEEeccccCCCCCCCCceEEEEeceecCCchHHHHHHHHHHHHHHHCCCCcccCCCCCcceeEEee
Q 012600 368 SSKVMDALDNR-PLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLM 446 (460)
Q Consensus 368 ~~~i~d~L~~~-pf~l~lkGLg~F~~dp~~~rVLya~V~~~d~~~~L~~L~~~L~~~f~~~Gl~~~~de~r~fkpHlTL~ 446 (460)
. .. ||.|+|+|+|+|++ +.++||+|+++.+ .+.|.+|++.|...+.++||..+ .++|.||+||+
T Consensus 64 ~--------~~~~f~i~l~g~g~F~~-~~~~rvi~~~v~~---~~~L~~L~~~l~~~~~~~g~~~~---~r~F~PHvTl~ 128 (180)
T COG1514 64 A--------APEPFPITLDGAGSFPN-PRRPRVIWVGVEE---TEELRALAEELERALARLGLRPE---ERPFVPHVTLA 128 (180)
T ss_pred h--------cCCceEEEEeeEcccCC-CCCCcEEEEcCCC---cHHHHHHHHHHHHHHHhcCCCCC---CCCcCCCEEEE
Confidence 5 24 99999999999999 9999999999984 67899999999999999999984 68999999999
Q ss_pred eecc
Q 012600 447 NIRH 450 (460)
Q Consensus 447 n~k~ 450 (460)
|.+.
T Consensus 129 r~k~ 132 (180)
T COG1514 129 RVKS 132 (180)
T ss_pred eecc
Confidence 9996
No 5
>PRK15124 2'-5' RNA ligase; Provisional
Probab=99.83 E-value=3.2e-20 Score=173.09 Aligned_cols=127 Identities=13% Similarity=0.141 Sum_probs=108.6
Q ss_pred CceEEEEccCCcchHHHHHhhccccccccccccCCCCCCCCCCCCcCCccCCCcceEEeeccccCChhHHHHHHHHHHHh
Q 012600 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 367 (460)
Q Consensus 288 n~FVAv~i~~~~i~~~v~~vq~~i~~~~~~~~~~k~~~~~~~Gld~~~fv~p~~LHLTL~~L~L~~eeev~~A~~~L~~i 367 (460)
-+|+|+++++ ++.+.+.++++.+. ...+ ..|++|++|||||.|||..++++++.+.+++..+
T Consensus 6 RlFiAl~~p~-~~~~~l~~~~~~~~--------------~~~~---~rwv~~~nlHiTL~FlG~v~~~~~~~l~~~l~~~ 67 (176)
T PRK15124 6 RLFFAIDLPD-EIRQQIIHWRATHF--------------PPEA---GRPVAAANLHLTLAFLGEVSAEKQQALSQLAGRI 67 (176)
T ss_pred EEEEEeCCCH-HHHHHHHHHHHHhc--------------cccC---cccccccccEEEEEecCCCCHHHHHHHHHHHHhc
Confidence 5899999985 77888999887762 0111 2699999999999999999999999888888766
Q ss_pred HHhhhhhcCCCCeEEEeccccCCCCCCCCceEEEEeceecCCchHHHHHHHHHHHHHHHCCCCcccCCCCCcceeEEeee
Q 012600 368 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 447 (460)
Q Consensus 368 ~~~i~d~L~~~pf~l~lkGLg~F~~dp~~~rVLya~V~~~d~~~~L~~L~~~L~~~f~~~Gl~~~~de~r~fkpHlTL~n 447 (460)
..+||.|+|.|+|+|++ +||||+++++ +.+.|..|++.|.+.+..+|+.. +.++|+||+||+|
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--PPRGLLQLANMLRSQAARSGCYQ---SPQPFHPHITLLR 130 (176)
T ss_pred --------ccCCeEEEECcccCcCC----CCEEEEEcCC--CCHHHHHHHHHHHHHHHHcCCCC---CCCCCCCCEeecc
Confidence 25899999999999974 6999999974 46799999999999999999987 4689999999999
Q ss_pred ec
Q 012600 448 IR 449 (460)
Q Consensus 448 ~k 449 (460)
.+
T Consensus 131 ~~ 132 (176)
T PRK15124 131 DA 132 (176)
T ss_pred CC
Confidence 65
No 6
>TIGR02258 2_5_ligase 2'-5' RNA ligase. This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles.
Probab=99.79 E-value=7.1e-19 Score=162.84 Aligned_cols=132 Identities=18% Similarity=0.339 Sum_probs=111.9
Q ss_pred CceEEEEccCCcchHHHHHhhccccccccccccCCCCCCCCCCCCcCCccCCCcceEEeeccccCChhHHHHHHHHHHHh
Q 012600 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 367 (460)
Q Consensus 288 n~FVAv~i~~~~i~~~v~~vq~~i~~~~~~~~~~k~~~~~~~Gld~~~fv~p~~LHLTL~~L~L~~eeev~~A~~~L~~i 367 (460)
-+|+||.+++ ++.+.+.++|+.+. + .. ....|++++++||||.|+|..++++++.+.++|.++
T Consensus 2 R~FiAl~~p~-~~~~~l~~~~~~l~---------~----~~---~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~ 64 (179)
T TIGR02258 2 RLFIAIDLPP-EIREQLSRIQRKLK---------S----PL---DGIKWVPPENLHITLKFLGEVDEEQVEELEDALAKI 64 (179)
T ss_pred eEEEEecCCH-HHHHHHHHHHHHhh---------c----cC---CCcEECChHHCEEEEEEccCCCHHHHHHHHHHHHHh
Confidence 3799999986 58999999999872 0 01 122699999999999999999999999888888766
Q ss_pred HHhhhhhcCCCCeEEEeccccCCCCCCCCceEEEEeceecCCchHHHHHHHHHHHHHHHCCCCcccCCCCCcceeEEeee
Q 012600 368 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 447 (460)
Q Consensus 368 ~~~i~d~L~~~pf~l~lkGLg~F~~dp~~~rVLya~V~~~d~~~~L~~L~~~L~~~f~~~Gl~~~~de~r~fkpHlTL~n 447 (460)
. ..+|.++|.|+|+|++ +..++|||+++++ ...|.+|++.|.+.+...|+.. +.++|+||+||++
T Consensus 65 ~--------~~~f~l~l~~~~~F~~-~~~~~vl~l~~~~---~~~L~~L~~~l~~~~~~~g~~~---~~~~f~PHiTlar 129 (179)
T TIGR02258 65 A--------EPPFTLKLEGIGVFGN-PKRPRVLWAGVEQ---SEELTQLHADLERELAKLGFSK---EERPFTPHITLAR 129 (179)
T ss_pred c--------CCCeEEEEeeeeeCCC-CCCCeEEEEeeCC---CHHHHHHHHHHHHHHHHcCCCC---CCCCcCCCEEEEE
Confidence 2 3679999999999998 7889999999974 3589999999999999999986 3578999999999
Q ss_pred eccc
Q 012600 448 IRHK 451 (460)
Q Consensus 448 ~k~~ 451 (460)
.+..
T Consensus 130 ~~~~ 133 (179)
T TIGR02258 130 KKSG 133 (179)
T ss_pred ecCC
Confidence 8754
No 7
>PHA02574 57B hypothetical protein; Provisional
Probab=99.64 E-value=7.5e-16 Score=141.10 Aligned_cols=109 Identities=12% Similarity=0.049 Sum_probs=88.4
Q ss_pred CceEEEEccCCcchHHHHHhhccccccccccccCCCCCCCCCCCCcCCccCCCcceEEeeccccCChhHHHHHHHHHHHh
Q 012600 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 367 (460)
Q Consensus 288 n~FVAv~i~~~~i~~~v~~vq~~i~~~~~~~~~~k~~~~~~~Gld~~~fv~p~~LHLTL~~L~L~~eeev~~A~~~L~~i 367 (460)
-.|||+++++ ++++++.++|+.+. . ..||+++||||||.| +++.++....
T Consensus 10 RlF~Al~~~~-~~r~~L~~lq~~l~------------------~--~r~V~~enLHlTL~F----~~~~v~~l~~----- 59 (149)
T PHA02574 10 GTYVAAKFSE-ATLDALERLQRTLR------------------I--PNPVPRDKLHSTIVY----SRVYVPFIPA----- 59 (149)
T ss_pred eEEEEEcCCH-HHHHHHHHHHHhcc------------------C--CcccCHHHCEEEEec----CHHHhHHHhc-----
Confidence 4799999987 88999999998752 0 269999999999999 3444443311
Q ss_pred HHhhhhhcCCCCeEEEeccccCCCCCCCCceEEEEeceecCCchHHHHHHHHHHHHHHHCCCCcccCCCCCcceeEEeee
Q 012600 368 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 447 (460)
Q Consensus 368 ~~~i~d~L~~~pf~l~lkGLg~F~~dp~~~rVLya~V~~~d~~~~L~~L~~~L~~~f~~~Gl~~~~de~r~fkpHlTL~n 447 (460)
..+||.+++.|+|+|++ + ++||||++++ .+.|..|++.+++.+.. . +.++|+||+||+|
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----H---DFDDYTPHITLSY 118 (149)
T ss_pred --------cCCCeEEEeccccccCC-C-CCCEEEEEeC----CHHHHHHHHHHHHHhhc----C---CCCCcCCcEEEee
Confidence 35999999999999974 2 2699999995 57899999999999988 2 2357999999999
No 8
>PRK13679 hypothetical protein; Provisional
Probab=99.48 E-value=2.3e-13 Score=126.00 Aligned_cols=122 Identities=12% Similarity=0.104 Sum_probs=96.7
Q ss_pred CceEEEEccCCcchHHHHHhhccccccccccccCCCCCCCCCCCCcCCccCCCcceEEeeccccCChhHHHHHHHHHHHh
Q 012600 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 367 (460)
Q Consensus 288 n~FVAv~i~~~~i~~~v~~vq~~i~~~~~~~~~~k~~~~~~~Gld~~~fv~p~~LHLTL~~L~L~~eeev~~A~~~L~~i 367 (460)
.|||||.++. ++.+.+..+|+.+. .+ ..+++| ||||.|++..++++++++.++|+.+
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 4899999987 58999999987651 11 136777 9999999999999999898888876
Q ss_pred HHhhhhhcCCCCeEEEeccccCCCCCCCCceEEEEeceecCCchHHHHHHHHHHHHHHHCCCCcccCCCCCcceeEEeee
Q 012600 368 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 447 (460)
Q Consensus 368 ~~~i~d~L~~~pf~l~lkGLg~F~~dp~~~rVLya~V~~~d~~~~L~~L~~~L~~~f~~~Gl~~~~de~r~fkpHlTL~n 447 (460)
.. ...||.+++.|+++|+. + .+|||+++++ .+.|.+|++.|...+. + .. +.++|.||+||+|
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-GE---AEYAFVPHITIGQ 120 (168)
T ss_pred Hh------cCCCEEEEEeccccCCC-C--CCEEEEEccC---CHHHHHHHHHHHhccc--c-cc---cCCCCCCeEEeeC
Confidence 42 24899999999999986 2 4899999984 5799999999887553 1 12 3578999999997
Q ss_pred ecc
Q 012600 448 IRH 450 (460)
Q Consensus 448 ~k~ 450 (460)
...
T Consensus 121 ~~~ 123 (168)
T PRK13679 121 GLS 123 (168)
T ss_pred CCC
Confidence 753
No 9
>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=99.30 E-value=4.4e-12 Score=98.64 Aligned_cols=60 Identities=42% Similarity=0.612 Sum_probs=55.3
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHH
Q 012600 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQ 216 (460)
Q Consensus 156 ~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~-~~~I~ItG~s~e~V~~A~~rI~ 216 (460)
..+.||+.+|++|||++|+++++|+++|||+|+||...+ .+.|+|+|+ .++|..|+++|+
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 578999999999999999999999999999999999765 678999998 799999999873
No 10
>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=99.21 E-value=2.4e-11 Score=95.30 Aligned_cols=59 Identities=27% Similarity=0.389 Sum_probs=54.2
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHH
Q 012600 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQ 216 (460)
Q Consensus 155 ~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~ 216 (460)
..++.||..++++|||++|+++++|+++|||+|+|+.. +.|.|+|+++++++.|++.|+
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~---g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDD---GTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCCC---CEEEEEeCCHHHHHHHHHHhC
Confidence 46799999999999999999999999999999999973 679999988899999999873
No 11
>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=99.20 E-value=1.3e-11 Score=95.47 Aligned_cols=60 Identities=40% Similarity=0.598 Sum_probs=54.0
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHH
Q 012600 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKI 215 (460)
Q Consensus 155 ~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI 215 (460)
+..+.||..+|++|||++|.++++||++|||+|.||..++...|.|+| +.++|++|++.|
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 467899999999999999999999999999999998764334799999 689999999876
No 12
>PF13563 2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB: 1IUH_A.
Probab=99.02 E-value=6.4e-10 Score=99.10 Aligned_cols=102 Identities=18% Similarity=0.248 Sum_probs=68.4
Q ss_pred cCCCcceEEeeccccCChhHHHHHHHHHHHhHHhhhhhcCCCCeEEEeccccCCCCCCCCceEEEEeceecCCchHHHHH
Q 012600 337 IKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHA 416 (460)
Q Consensus 337 v~p~~LHLTL~~L~L~~eeev~~A~~~L~~i~~~i~d~L~~~pf~l~lkGLg~F~~dp~~~rVLya~V~~~d~~~~L~~L 416 (460)
.....+||||.+.+..++.. +.+.+.|..+-. ..+||.|+|.|+++|++ +.+|||+.+.. .+.|.+|
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 44456999999999987754 445555554421 25899999999999975 23599999964 7899999
Q ss_pred HHHHHHHHHHCCCCcccCCCCCcceeEEeeeeccccc
Q 012600 417 CQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKR 453 (460)
Q Consensus 417 ~~~L~~~f~~~Gl~~~~de~r~fkpHlTL~n~k~~k~ 453 (460)
++.|.+.|...|.... ..++|.||+||++......
T Consensus 88 ~~~l~~~~~~~~~~~~--~~~~~~PHiTia~~~~~~~ 122 (153)
T PF13563_consen 88 HRALREALRPFGFKQD--SYRPFRPHITIARRLSPKQ 122 (153)
T ss_dssp HHHHHHHHHHHHGGGG--GGS----EEEEEEESS---
T ss_pred HHHHHHHHHHcCCccc--cCCCcceEEEEeccCCcch
Confidence 9999999999988874 2379999999999875543
No 13
>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=98.98 E-value=8.8e-10 Score=85.23 Aligned_cols=59 Identities=41% Similarity=0.516 Sum_probs=53.2
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEccChhHHHHHHHHH
Q 012600 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKI 215 (460)
Q Consensus 156 ~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~---~~~I~ItG~s~e~V~~A~~rI 215 (460)
..+.||..+|++|||++|+++++|+++|||+|.||...+ .+.|.|.|. .+++..|...|
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 578999999999999999999999999999999988653 567999997 79999998876
No 14
>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=98.81 E-value=1.6e-09 Score=89.13 Aligned_cols=82 Identities=20% Similarity=0.376 Sum_probs=64.6
Q ss_pred cchHHHHHhhccccccccccccCCCCCCCCCCCCcCCccCCCcceEEeeccccCChhHHHHHHHHHHHhHHhhhhhcCCC
Q 012600 299 DNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNR 378 (460)
Q Consensus 299 ~i~~~v~~vq~~i~~~~~~~~~~k~~~~~~~Gld~~~fv~p~~LHLTL~~L~L~~eeev~~A~~~L~~i~~~i~d~L~~~ 378 (460)
++.+.+..+|+.+. ..+...|+ .|+.|.++||||.|+|..++++++..++.|..+.. ...
T Consensus 6 ~~~~~L~~l~~~l~-----------~~~~~~~~---r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~------~~~ 65 (87)
T PF02834_consen 6 EIKEQLNQLQERLR-----------QALPPLGI---RWVRPFNPHITLAFLGEVPPDQLPELIEALANIAS------RFP 65 (87)
T ss_dssp HHHHHHHHHHHHHH-----------HHCCSCTE---EEGSCGGSEEEEEEEEEESHHHHHHHHHHHHHHHC------CCB
T ss_pred HHHHHHHHHHHHHh-----------hhccccCC---cccCCCCCeEEEEeCCCCCHHHHHHHHHHHHhhhc------cCC
Confidence 55778888888762 00123444 68999999999999999999999999888887631 358
Q ss_pred CeEEEeccccCCCCCCCCceEEE
Q 012600 379 PLFIRLKGLDLMRGSKDKARILY 401 (460)
Q Consensus 379 pf~l~lkGLg~F~~dp~~~rVLy 401 (460)
||.+++.|+++|++ ..++||+|
T Consensus 66 ~f~~~~~~~~~f~s-~~~~rvi~ 87 (87)
T PF02834_consen 66 PFTLTVDGFGLFPS-RLRPRVIW 87 (87)
T ss_dssp -EEEEEEEEEEEEE-EETCEEEE
T ss_pred CeEEEEeEEEEeCC-CCCCCCcC
Confidence 99999999999998 55889999
No 15
>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=98.80 E-value=9.6e-09 Score=81.10 Aligned_cols=59 Identities=37% Similarity=0.387 Sum_probs=52.5
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHH
Q 012600 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKI 215 (460)
Q Consensus 156 ~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~----~~~I~ItG~s~e~V~~A~~rI 215 (460)
..+.||....+.|||++|.++++|+++|||+|++++... ...|+|+|. .+++..|...|
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 578899999999999999999999999999999987643 346899997 79999999877
No 16
>smart00322 KH K homology RNA-binding domain.
Probab=98.80 E-value=2.3e-08 Score=76.42 Aligned_cols=66 Identities=39% Similarity=0.530 Sum_probs=58.5
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHH
Q 012600 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAII 219 (460)
Q Consensus 153 ~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~-~~~I~ItG~s~e~V~~A~~rI~~iv 219 (460)
.....+.||..+++++||++|.+++.|+++||++|.++.... ...|.|.|+ .+++..|...|...+
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 456789999999999999999999999999999999987763 567999998 799999999887654
No 17
>PF13014 KH_3: KH domain
Probab=98.79 E-value=5.3e-09 Score=76.17 Aligned_cols=39 Identities=38% Similarity=0.572 Sum_probs=34.4
Q ss_pred ccccccCCCchhHHHHHHHhCcEEEcCC---CCC-CCcEEEEc
Q 012600 164 VIRFIKGKEGSTQKKFEKEMGVKIILPS---SKK-EDSIIIEG 202 (460)
Q Consensus 164 ~h~~IIGk~G~t~k~LE~eT~trI~iP~---~~~-~~~I~ItG 202 (460)
+|++|||++|+++++|+++|||+|+||+ +++ .+.|+|+|
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 6899999999999999999999999999 333 56788987
No 18
>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=98.64 E-value=1.5e-07 Score=90.32 Aligned_cols=128 Identities=16% Similarity=0.189 Sum_probs=96.9
Q ss_pred ccCCceEEEEccC-CcchHHHHHhhccccccccccccCCCCCCCCCCCCcCCccCCCcceEEeeccccCChhHHHHHHHH
Q 012600 285 VDQEHKVAVELNI-GDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNV 363 (460)
Q Consensus 285 ~rpn~FVAv~i~~-~~i~~~v~~vq~~i~~~~~~~~~~k~~~~~~~Gld~~~fv~p~~LHLTL~~L~L~~eeev~~A~~~ 363 (460)
.+||||+..++.. +.+....+.+|-+|. +-|+|-.+-.- =||||+||.+. ++++..+..+
T Consensus 4 D~P~HFin~Pl~~f~~f~~~~~~LQ~~~~---------------~eG~d~k~Qka---PHlSl~mL~Is-d~~i~~V~~~ 64 (248)
T PF05213_consen 4 DKPTHFINFPLVQFEGFMLNFKDLQFQLL---------------EEGVDCKLQKA---PHLSLGMLDIS-DEDIPDVETA 64 (248)
T ss_pred CCCCceeeccchhhhhHHHHHHHHHHHHH---------------HcCCCcccccc---CeeEEEEEEcC-hhhhhhHHHH
Confidence 4899999999998 889999999998773 44565433333 39999999774 7889999988
Q ss_pred HHHhHHhhhhhcCCCCeEEEeccccCCCCCCCCceEEEEeceecCCchHHHHHHHHHHHHHHHCCCCcccCCCCCcceeE
Q 012600 364 LKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHA 443 (460)
Q Consensus 364 L~~i~~~i~d~L~~~pf~l~lkGLg~F~~dp~~~rVLya~V~~~d~~~~L~~L~~~L~~~f~~~Gl~~~~de~r~fkpHl 443 (460)
|+++.+.+ .- ....+++..-..++ |.+.+.|+ .+..+...|...|.+.|+..+ ..|.|.||+
T Consensus 65 iq~ViddM---~~-~~~~it~tnp~MLg------~~yV~nV~------Gv~slh~ki~n~~~~kgit~g--QSRmwIPHi 126 (248)
T PF05213_consen 65 IQKVIDDM---VW-FEGDITFTNPHMLG------RCYVANVK------GVLSLHDKIVNVFRKKGITFG--QSRMWIPHI 126 (248)
T ss_pred HHHHHHHh---hc-ccceEEecCceeec------cEEEEecc------cHHHHHHHHHHHHHHhCcCcC--cccccccce
Confidence 88775432 11 12267777776664 44444564 577889999999999999996 589999999
Q ss_pred Eeeeec
Q 012600 444 TLMNIR 449 (460)
Q Consensus 444 TL~n~k 449 (460)
||+..+
T Consensus 127 Tia~~~ 132 (248)
T PF05213_consen 127 TIAQLN 132 (248)
T ss_pred ehhhhh
Confidence 999875
No 19
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.59 E-value=9.9e-08 Score=102.63 Aligned_cols=106 Identities=27% Similarity=0.328 Sum_probs=86.4
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEc-CCCCC---CCcEEEEccChhHHHHHHHHHHHHHHHhhhCC-
Q 012600 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL-PSSKK---EDSIIIEGNSTDSVAKASEKIQAIIAEAVESP- 226 (460)
Q Consensus 152 ~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~i-P~~~~---~~~I~ItG~s~e~V~~A~~rI~~iv~e~~~~~- 226 (460)
.+.+..|.||+.-.+.||||+|+|||+|..|||+||+| |..+. .+...|.|+ +++|+.|.+.|..||.++...+
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 44489999999999999999999999999999999999 44441 467899996 8999999999999999876641
Q ss_pred --------CCCcceEEeeccccchhhhhhHHHHHHHHhcc
Q 012600 227 --------SLDYSHFVSLPLAVHPELVDKLVNFQNTILGI 258 (460)
Q Consensus 227 --------k~~~THFIsIPl~~hP~I~g~~~~F~~sIl~~ 258 (460)
-..-.-++.||-.----++|+.++-+..|-.+
T Consensus 307 ~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~q 346 (600)
T KOG1676|consen 307 GGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQ 346 (600)
T ss_pred CCcCCCCccceeeEEEeccccccccccCCCccchhhhccc
Confidence 11114456689765667889999988888765
No 20
>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=98.56 E-value=1.4e-07 Score=83.90 Aligned_cols=59 Identities=29% Similarity=0.486 Sum_probs=52.0
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCC--------------------CCcEEEEccC--hhHHHHHHHHHHHHHH
Q 012600 163 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK--------------------EDSIIIEGNS--TDSVAKASEKIQAIIA 220 (460)
Q Consensus 163 ~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~--------------------~~~I~ItG~s--~e~V~~A~~rI~~iv~ 220 (460)
.|.+.|||++|.|+|+||++|||+|.|-..++ ...|.|+|.+ .+++.+|++.|+.|+.
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 46799999999999999999999999987642 2569999998 9999999999998886
Q ss_pred H
Q 012600 221 E 221 (460)
Q Consensus 221 e 221 (460)
.
T Consensus 95 ~ 95 (120)
T cd02395 95 P 95 (120)
T ss_pred c
Confidence 4
No 21
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.08 E-value=4.7e-06 Score=88.29 Aligned_cols=72 Identities=26% Similarity=0.409 Sum_probs=61.5
Q ss_pred CeEEEEeccc------cccccccCCCchhHHHHHHHhCcEEEcCCCCC-------------------CCcEEEEccChhH
Q 012600 153 RHSLSVEVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-------------------EDSIIIEGNSTDS 207 (460)
Q Consensus 153 ~~~~~v~Vp~------~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~-------------------~~~I~ItG~s~e~ 207 (460)
++...|.||. .|+++|||..|.|+|+||+|||+||.|-..++ .=.|.|++.+.|.
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 7777888886 47899999999999999999999999976321 0148999999999
Q ss_pred HHHHHHHHHHHHHHhhh
Q 012600 208 VAKASEKIQAIIAEAVE 224 (460)
Q Consensus 208 V~~A~~rI~~iv~e~~~ 224 (460)
|.+|.+.|+.|+.+++-
T Consensus 217 i~~Ai~vienli~~av~ 233 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSAVS 233 (554)
T ss_pred HHHHHHHHHHHHHhhcc
Confidence 99999999999998554
No 22
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.04 E-value=9.5e-06 Score=76.76 Aligned_cols=65 Identities=32% Similarity=0.434 Sum_probs=58.1
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEE---ccChhHHHHHHHHHHHHHH
Q 012600 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIE---GNSTDSVAKASEKIQAIIA 220 (460)
Q Consensus 154 ~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~It---G~s~e~V~~A~~rI~~iv~ 220 (460)
...++.||+...+.|||++|.+++.|+++||++|+|-.. .+.|.|. +.+.+.+.+|++.|+.|..
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 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE--TGEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC--CCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 457899999999999999999999999999999999643 3678897 6678999999999998876
No 23
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=97.96 E-value=1.3e-05 Score=90.42 Aligned_cols=105 Identities=27% Similarity=0.410 Sum_probs=94.2
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCCC
Q 012600 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLD 229 (460)
Q Consensus 151 ~~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~-~~~I~ItG~s~e~V~~A~~rI~~iv~e~~~~~k~~ 229 (460)
...+.+.+.|.++++.+++||+|.++.+|+++++|.|++|.+++ ...++++|. ..++.+|.+.++.++.+...+ .
T Consensus 344 ~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~-~~~~~ka~~~v~~~~~ei~n~---~ 419 (753)
T KOG2208|consen 344 ENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGV-SANDEKAVEDVEKIIAEILNS---I 419 (753)
T ss_pred ccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEecc-ccchhHHHHHHHHHHHhhhcc---c
Confidence 35588999999999999999999999999999999999999776 678999997 699999999999999997763 2
Q ss_pred cceEEeeccccchhhhhhHHHHHHHHhccc
Q 012600 230 YSHFVSLPLAVHPELVDKLVNFQNTILGIT 259 (460)
Q Consensus 230 ~THFIsIPl~~hP~I~g~~~~F~~sIl~~~ 259 (460)
..+.+.||-.+|.+|.|......+.|+.+.
T Consensus 420 ~~~~~~iP~k~~~~iig~~g~~i~~I~~k~ 449 (753)
T KOG2208|consen 420 VKEEVQIPTKSHKRIIGTKGALINYIMGKH 449 (753)
T ss_pred ccceeecCccchhhhhccccccHHHHHhhc
Confidence 467677999999999999999999999873
No 24
>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=97.95 E-value=1.1e-05 Score=75.87 Aligned_cols=61 Identities=33% Similarity=0.427 Sum_probs=53.3
Q ss_pred EeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEE--EccChhHHHHHHHHHHHHHH
Q 012600 158 VEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIII--EGNSTDSVAKASEKIQAIIA 220 (460)
Q Consensus 158 v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~I--tG~s~e~V~~A~~rI~~iv~ 220 (460)
+.||+...+.|||+||+++|+|+++||++|+|-.. .+.|.| .+.+.+.+.+|++.|..|..
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 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE--TGEVKIEEEDEDPLAVMKAREVVKAIGR 64 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC--CceEEEecCCCCHHHHHHHHHHHHHHHc
Confidence 67999999999999999999999999999999542 356888 45568999999999998765
No 25
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=97.94 E-value=1.3e-05 Score=75.32 Aligned_cols=53 Identities=28% Similarity=0.391 Sum_probs=49.2
Q ss_pred ccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 164 VIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 164 ~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
..+.|||++|.|++.||..|||+|.|+. ..|.|+|. .++++.|++.|+.|++.
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~----~~v~i~G~-~~~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYG----KTVGIIGD-PEQVQIAREAIEMLIEG 151 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcC----CEEEEECC-HHHHHHHHHHHHHHHcC
Confidence 6899999999999999999999999985 57999995 79999999999999965
No 26
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.89 E-value=1.8e-05 Score=74.92 Aligned_cols=53 Identities=28% Similarity=0.418 Sum_probs=48.3
Q ss_pred ccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 164 VIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 164 ~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
.++.|||++|.|++.||..|||+|+|+. +.|.|.|. .++++.|++.|..|++.
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~----~~v~i~G~-~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYG----KTVAIIGD-PEQVEIAREAIEMLIEG 157 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcC----CEEEEEeC-HHHHHHHHHHHHHHHcC
Confidence 6999999999999999999999999974 45999996 79999999999999954
No 27
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.73 E-value=0.00022 Score=72.73 Aligned_cols=107 Identities=23% Similarity=0.239 Sum_probs=79.9
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEccChhHHHHHHHHHHHHHHHh--
Q 012600 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAEA-- 222 (460)
Q Consensus 151 ~~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~------~~~I~ItG~s~e~V~~A~~rI~~iv~e~-- 222 (460)
..+|.+.|.||...-+-||||||.|+.+|+.||||||++.+..+ ++.|-|+|. -+.|....+-|..-+.+.
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 34699999999999999999999999999999999999988765 356889996 577766555444333221
Q ss_pred --hh-----CCCC---CcceEEeeccccchhhhhhHHHHHHHHhcc
Q 012600 223 --VE-----SPSL---DYSHFVSLPLAVHPELVDKLVNFQNTILGI 258 (460)
Q Consensus 223 --~~-----~~k~---~~THFIsIPl~~hP~I~g~~~~F~~sIl~~ 258 (460)
.+ .|+. ....-|.+|-..---|+++...++.+|.++
T Consensus 115 ~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eq 160 (402)
T KOG2191|consen 115 AVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQ 160 (402)
T ss_pred hhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHh
Confidence 11 1111 112456688776678899999999999976
No 28
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.70 E-value=3.4e-05 Score=80.59 Aligned_cols=103 Identities=25% Similarity=0.295 Sum_probs=75.1
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHHHHHHH-HhhhCC
Q 012600 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIA-EAVESP 226 (460)
Q Consensus 152 ~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~----~~~I~ItG~s~e~V~~A~~rI~~iv~-e~~~~~ 226 (460)
..|-..+.||..||+.||||.|+|+|.|-..|.|||+|-+-.+ +..|+|-|. .|+..+|+.+|..|+. |+.+.
T Consensus 197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~t-pEg~s~Ac~~ILeimqkEA~~~- 274 (584)
T KOG2193|consen 197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHST-PEGTSKACKMILEIMQKEAVDD- 274 (584)
T ss_pred cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecC-ccchHHHHHHHHHHHHHhhhcc-
Confidence 4577888999999999999999999999999999999977544 457999997 5999999999998864 44432
Q ss_pred CCCcceEEeeccccchhhhh----hHHHHHHHHhcc
Q 012600 227 SLDYSHFVSLPLAVHPELVD----KLVNFQNTILGI 258 (460)
Q Consensus 227 k~~~THFIsIPl~~hP~I~g----~~~~F~~sIl~~ 258 (460)
+ .+.-+-+.+--|..++| .-+.-+..|.++
T Consensus 275 k--~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~ 308 (584)
T KOG2193|consen 275 K--VAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQD 308 (584)
T ss_pred c--hhhhcchhhhhhcchhhhhhhhccccHHHHHhh
Confidence 3 33333233222554444 344555556655
No 29
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.65 E-value=8.3e-05 Score=83.23 Aligned_cols=64 Identities=20% Similarity=0.327 Sum_probs=59.0
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHH
Q 012600 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIA 220 (460)
Q Consensus 154 ~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~ 220 (460)
-..++.||+...+-|||+||.++|+|.++||++|+|-. ++.|.|.|..++.+++|++.|+.|+.
T Consensus 578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---~G~V~I~a~d~~~~~~A~~~I~~i~~ 641 (719)
T TIGR02696 578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---DGTVYIGAADGPSAEAARAMINAIAN 641 (719)
T ss_pred eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---CcEEEEEeCCHHHHHHHHHHHHHhhC
Confidence 35788899999999999999999999999999999954 57899999999999999999998886
No 30
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=97.60 E-value=8.3e-05 Score=80.62 Aligned_cols=110 Identities=13% Similarity=0.222 Sum_probs=89.8
Q ss_pred CCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEccChhHHHHHHHHHHHHHHHhhhC-
Q 012600 150 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKIQAIIAEAVES- 225 (460)
Q Consensus 150 ~~~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~---~~~I~ItG~s~e~V~~A~~rI~~iv~e~~~~- 225 (460)
+++--+....||.+..++||||+|+-+..|.++.||+++||+... .+.|.|+|. .+.|+.|++.|..+++.-+-.
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 345566788999999999999999999999999999999988765 578999997 599999999999999874310
Q ss_pred --C-CCC---cceEEeeccccchhhhhhHHHHHHHHhcccc
Q 012600 226 --P-SLD---YSHFVSLPLAVHPELVDKLVNFQNTILGITD 260 (460)
Q Consensus 226 --~-k~~---~THFIsIPl~~hP~I~g~~~~F~~sIl~~~~ 260 (460)
+ ... .|.-|.||-+----|+|..++-++.+.+..+
T Consensus 129 ~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg 169 (600)
T KOG1676|consen 129 GFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSG 169 (600)
T ss_pred CccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcC
Confidence 0 111 4777888887778899999999998877644
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=97.56 E-value=0.00011 Score=82.62 Aligned_cols=64 Identities=22% Similarity=0.369 Sum_probs=57.8
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 155 ~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
..++.||+...+-|||+||.++|+|+++||++|+|-. ++.|.|.+..++.+++|.+.|..+...
T Consensus 552 ~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d---dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 552 IETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED---DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred EEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 5678999999999999999999999999999999943 577999999999999999999988653
No 32
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=97.54 E-value=9.9e-05 Score=71.06 Aligned_cols=77 Identities=17% Similarity=0.239 Sum_probs=60.2
Q ss_pred CCCccCCCCeEEEEeccc------cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHH
Q 012600 145 GEPVPSAERHSLSVEVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAI 218 (460)
Q Consensus 145 ~~~~~~~~~~~~~v~Vp~------~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~i 218 (460)
+..+.+.++|+-.+.||. .|.|+|||+.|.|+|+||+.++|+|.|-..++...+.|...+.++...|.+-|.-+
T Consensus 139 p~dy~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcL 218 (269)
T COG5176 139 PNDYIRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCL 218 (269)
T ss_pred CccccCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHH
Confidence 344567788888898885 57899999999999999999999999988877556666665556666666666665
Q ss_pred HHH
Q 012600 219 IAE 221 (460)
Q Consensus 219 v~e 221 (460)
+..
T Consensus 219 I~a 221 (269)
T COG5176 219 IEA 221 (269)
T ss_pred hhc
Confidence 543
No 33
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.47 E-value=0.00012 Score=76.66 Aligned_cols=61 Identities=28% Similarity=0.478 Sum_probs=52.0
Q ss_pred ccccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 160 VGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 160 Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~------~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
--..|.|.+|||.|+++|+||++|||+|.|.+--+ .+.|++.| +-|.|.+|...|-.-+.+
T Consensus 286 AHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkG-siEac~~AE~eImkKlre 352 (584)
T KOG2193|consen 286 AHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKG-SIEACVQAEAEIMKKLRE 352 (584)
T ss_pred hhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecc-cHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999999999999987544 46799999 589999999988766554
No 34
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=97.30 E-value=0.00053 Score=68.33 Aligned_cols=68 Identities=24% Similarity=0.325 Sum_probs=57.3
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEc--CCCCC-CCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL--PSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 153 ~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~i--P~~~~-~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
-.+..|-||+.+-+-||||||..+++|.+|.|..|.| |..++ +..|+|+|. ++.|..|.--++.-|..
T Consensus 314 itTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGT-qdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 314 ITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT-QDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred eeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEecc-HHHHhhHHHHHHHHHHh
Confidence 3467788999999999999999999999999999999 55555 556899996 79999998877766653
No 35
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.23 E-value=0.0008 Score=66.94 Aligned_cols=71 Identities=24% Similarity=0.359 Sum_probs=51.9
Q ss_pred CCeEEEEecccc------ccccccCCCchhHHHHHHHhCcEEEcCCCCC-CC--------------------cEEEEccC
Q 012600 152 ERHSLSVEVGAS------VIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-ED--------------------SIIIEGNS 204 (460)
Q Consensus 152 ~~~~~~v~Vp~~------~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~-~~--------------------~I~ItG~s 204 (460)
-+.+..|.||.. |.|.|+|++|.|+|+||+||||||-|-..++ .| .|.|+-.
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~- 168 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETE- 168 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEe-
Confidence 355667777765 8999999999999999999999999977654 11 2445432
Q ss_pred hhHHHHHHHHHHHHHHHhhh
Q 012600 205 TDSVAKASEKIQAIIAEAVE 224 (460)
Q Consensus 205 ~e~V~~A~~rI~~iv~e~~~ 224 (460)
.--..|..||...+++..+
T Consensus 169 -~p~~ea~~rl~~AleeI~k 187 (259)
T KOG1588|consen 169 -APPAEAYARLAYALEEIKK 187 (259)
T ss_pred -CCHHHHHHHHHHHHHHHHH
Confidence 3456677777777777554
No 36
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.14 E-value=0.0013 Score=71.28 Aligned_cols=67 Identities=31% Similarity=0.404 Sum_probs=58.3
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCC---CC-CCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS---KK-EDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 154 ~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~---~~-~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
....+.||....+-||||+|..+|+|.++||++|++-+. .. ...|.|.|. .+.|.+|...|-.++-+
T Consensus 138 v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~-~~av~~al~~Is~~L~~ 208 (485)
T KOG2190|consen 138 VTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGE-PDAVKKALVQISSRLLE 208 (485)
T ss_pred eEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCc-hHHHHHHHHHHHHHHHh
Confidence 578899999999999999999999999999999998443 22 455999998 59999999999888766
No 37
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.14 E-value=0.00055 Score=69.48 Aligned_cols=65 Identities=25% Similarity=0.334 Sum_probs=60.7
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHH
Q 012600 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQA 217 (460)
Q Consensus 152 ~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~ 217 (460)
.+..++++||.+|.+.|.|++|.++|.|.++|++.|.-|+.++...+.+||. .+.|+.|+.+|..
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~-~edv~~aRrei~s 88 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGR-HEDVRRARREIPS 88 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCCcceeccC-chhHHHHhhcCcc
Confidence 6788999999999999999999999999999999999999998877789998 6999999999976
No 38
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.04 E-value=0.0011 Score=67.78 Aligned_cols=67 Identities=27% Similarity=0.361 Sum_probs=56.6
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 154 ~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~------~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
.++.+-||..--+.||||+|+|+|.+.++.++-|+|-.+.+ +..|++.|. .+...+|..+|..-+.+
T Consensus 132 kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge-~e~~~~A~~~IL~Ki~e 204 (402)
T KOG2191|consen 132 KQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGE-PEQNMKAVSLILQKIQE 204 (402)
T ss_pred ceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCC-HHHHHHHHHHHHHHhhc
Confidence 45788999999999999999999999999999999954443 245789997 68999999998766655
No 39
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.03 E-value=0.00075 Score=77.30 Aligned_cols=64 Identities=20% Similarity=0.283 Sum_probs=58.1
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcE-EEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVK-IILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 155 ~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~tr-I~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
...+.||++..+-|||+||.|+|.|.+|||++ |+|-. ++.|.|.|+..+.+++|++.|..|..+
T Consensus 686 i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 686 IHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred eEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 56788999999999999999999999999999 88743 577999999999999999999988754
No 40
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.97 E-value=0.0016 Score=64.18 Aligned_cols=64 Identities=28% Similarity=0.376 Sum_probs=57.8
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 155 ~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
-..+.||..+.+.+||++|.+++.|.++|+++|.| +..+-|-|.|++.+.+..|.+.|+.+-.+
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~i---g~NG~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIV---GQNGRIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEE---cCCcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 35688999999999999999999999999999999 34578999999999999999999888765
No 41
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.72 E-value=0.0025 Score=70.64 Aligned_cols=68 Identities=29% Similarity=0.410 Sum_probs=61.2
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhhh
Q 012600 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVE 224 (460)
Q Consensus 154 ~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e~~~ 224 (460)
...++.|++.-++-+||+||.++++|-++||++|+|- +++.|.|.+...+.+.+|+++|+.|+.+..-
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie---ddGtv~i~~s~~~~~~~ak~~I~~i~~e~ev 619 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE---DDGTVKIAASDGESAKKAKERIEAITREVEV 619 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec---CCCcEEEEecchHHHHHHHHHHHHHHhhccc
Confidence 3567889999999999999999999999999999996 4578999999899999999999999977543
No 42
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.71 E-value=0.0016 Score=73.33 Aligned_cols=64 Identities=25% Similarity=0.421 Sum_probs=57.4
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 155 ~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
...+.||++..+-+||+||.|+|+|.++||++|+| .+++.|.|.+..++.+++|++.|+.+..+
T Consensus 555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi---~d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDI---EDDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred heeecCCHHHHHHHhcCCchhHHHHHHHHCCcccc---CCCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 35778999999999999999999999999999998 33678999999999999999999988754
No 43
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.47 E-value=0.0021 Score=67.81 Aligned_cols=70 Identities=17% Similarity=0.233 Sum_probs=61.9
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHh
Q 012600 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEA 222 (460)
Q Consensus 152 ~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e~ 222 (460)
..+...+.|-.++.|.+||+||+++++|+..|+|+|+|-.....-.|+|-|. ++--.+|+.-|+..++..
T Consensus 45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~-~~m~~kaka~id~~~~k~ 114 (629)
T KOG0336|consen 45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGI-NHMRKKAKASIDRGQDKD 114 (629)
T ss_pred CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCceeEEEEech-HHHHHHHHhhHhhhhhhh
Confidence 4566788899999999999999999999999999999988777777999996 788889999999888753
No 44
>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=96.44 E-value=0.026 Score=55.50 Aligned_cols=103 Identities=19% Similarity=0.372 Sum_probs=74.3
Q ss_pred CCCcceEEeeccccCChhHHHHHHHHHHHhHHhhhhhcCCCCeEEEeccccCCCCCCCCceEEEE-eceecCCchHHHHH
Q 012600 338 KPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYA-PVEEIGDGDRLLHA 416 (460)
Q Consensus 338 ~p~~LHLTL~~L~L~~eeev~~A~~~L~~i~~~i~d~L~~~pf~l~lkGLg~F~~dp~~~rVLya-~V~~~d~~~~L~~L 416 (460)
.+.-|||+|.=---+...+++.-.+.|+. .+.. -...+|.+.|.++.+|.| .++.|...+ .|.. +....|..|
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 SPDPLHISLSRTFPLRTHQIDPFVDSLRQ---ALRS-SNIRPFYVSFSGLDVYTN-DEKTRSFLALRVSE-GSNNELKRL 159 (239)
T ss_pred CCCCeEEEeCCCccccHHHHHHHHHHHHH---HHhh-cCCceEEEEeCceEEEec-CCCCeEEEEEEecc-cccHHHHHH
Confidence 57889999964333334555555555443 2211 245999999999999999 777786554 4554 223349999
Q ss_pred HHHHHHHHHHCCCCcccCCC-CCcceeEEeeeec
Q 012600 417 CQVIIDAFNEAGLVFHRDYN-KKLKLHATLMNIR 449 (460)
Q Consensus 417 ~~~L~~~f~~~Gl~~~~de~-r~fkpHlTL~n~k 449 (460)
.+.|.+.+.+.|+.. -+ ..-.+|+.||-+-
T Consensus 160 ~~~i~~~l~~~~lp~---~Y~~~~~fHvSIAw~~ 190 (239)
T PF09749_consen 160 LDRINEVLKEFGLPP---FYDEDPSFHVSIAWTL 190 (239)
T ss_pred HHHHHHHHHHhCCCc---ccCCCCCCEEEEEEEC
Confidence 999999999999987 35 6789999999875
No 45
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.62 E-value=0.026 Score=61.77 Aligned_cols=68 Identities=21% Similarity=0.335 Sum_probs=52.9
Q ss_pred CCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 152 ERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 152 ~~~~~~v~Vp~-~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
......|++|. ++-|.|||+.|.|+|-||.-||+-|.|-.. .+.|+|+|-..=.-+-|+.-++.|+.+
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt--p~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT--PEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC--CCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 44556788998 788999999999999999999999999322 346888885445556677777777765
No 46
>PRK12704 phosphodiesterase; Provisional
Probab=95.56 E-value=0.025 Score=61.97 Aligned_cols=68 Identities=19% Similarity=0.322 Sum_probs=53.4
Q ss_pred CCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 152 ERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 152 ~~~~~~v~Vp~-~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
......|++|. ++-|.|||+.|.|+|-||.-||+-|.|-.. .+.|+|+|-..-.-+-|+.-++.++.+
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt--p~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT--PEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC--CCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 34456788998 788999999999999999999999999422 356889995434445788888777765
No 47
>PRK00106 hypothetical protein; Provisional
Probab=95.40 E-value=0.035 Score=60.93 Aligned_cols=68 Identities=18% Similarity=0.348 Sum_probs=51.1
Q ss_pred CCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 152 ERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 152 ~~~~~~v~Vp~-~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
......|.+|. ++-|.|||+.|.|+|-||.-||+-|.|-.. .+.|+|+|-..-.-+-|+.-++.|+.+
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt--p~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT--PEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC--CCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 44566788998 788999999999999999999999999322 345888885444555566656666554
No 48
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=95.13 E-value=0.035 Score=53.36 Aligned_cols=53 Identities=28% Similarity=0.416 Sum_probs=47.2
Q ss_pred ccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 164 VIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 164 ~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
.-+.|||++|.|++-||+-|||.|.+=. ..|-|.|. -++|+-|++-|..+++.
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g----~tVaiiG~-~~~v~iAr~AVemli~G 164 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYG----KTVAIIGG-FEQVEIAREAVEMLING 164 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeC----cEEEEecC-hhhhHHHHHHHHHHHcC
Confidence 4688999999999999999999999842 47889997 59999999999999875
No 49
>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=0.028 Score=44.06 Aligned_cols=37 Identities=24% Similarity=0.269 Sum_probs=34.2
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 012600 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (460)
Q Consensus 153 ~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~i 189 (460)
+....+.||..-.+..|||+|.+++.++..+|.+|++
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 4678999999999999999999999999999988875
No 50
>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=94.76 E-value=0.051 Score=52.07 Aligned_cols=92 Identities=18% Similarity=0.224 Sum_probs=43.6
Q ss_pred eEEeec-cccCChhHHHHHHHHHHHhHHhhhhhcCCCCeEEEeccccCCCCCCCCceEEEEeceecCCchHHHHHHHHHH
Q 012600 343 HLTVLM-LKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVII 421 (460)
Q Consensus 343 HLTL~~-L~L~~eeev~~A~~~L~~i~~~i~d~L~~~pf~l~lkGLg~F~~dp~~~rVLya~V~~~d~~~~L~~L~~~L~ 421 (460)
||||.- +.+.+.++ +.++|.++...+..+ +...+.++|.++.. ++ ..-+=+|+.++. .+.|..|++.++
T Consensus 40 HiTL~s~i~~~~~~~---~~~~L~~~~~~~~~~-~~~~~~v~~~~v~~-g~--~yfq~vyl~v~~---t~~L~~l~~~~r 109 (196)
T PF07823_consen 40 HITLTSGISLDSSDD---VQKVLDSAAAALKPL-PKNHFTVRFDKVAS-GD--KYFQCVYLEVEK---TPELMSLAQIAR 109 (196)
T ss_dssp -EEEEEEEEE--HHH---HHHHHHHHHHH-B-E------EEEEEEEEE-EE--ETTEEEEEEE------HHHHHHHCHHH
T ss_pred eEEEeCCCccCCHHH---HHHHHHHHHHhccCc-ccceeEEEeeeEee-CC--eEEEEEEEEecC---ChhHHHHHHHHH
Confidence 999975 22323344 445555543222111 11113888876643 11 233559999985 688999999999
Q ss_pred HHHHHC-------CCCcccCCCCCcceeEEeeee
Q 012600 422 DAFNEA-------GLVFHRDYNKKLKLHATLMNI 448 (460)
Q Consensus 422 ~~f~~~-------Gl~~~~de~r~fkpHlTL~n~ 448 (460)
+.|... |-. ...+|.||+.|+--
T Consensus 110 ~~~~~~~~~~~~~~~~----~~~~y~PHlSLlY~ 139 (196)
T PF07823_consen 110 ELFVEGPPDEVKAAEW----PREPYMPHLSLLYG 139 (196)
T ss_dssp HCT----------T--------S----EEEEE--
T ss_pred HHhhhccccccccccc----cCCCCCCeEEEEEc
Confidence 988543 222 23589999999853
No 51
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=94.68 E-value=0.0067 Score=62.25 Aligned_cols=100 Identities=14% Similarity=0.106 Sum_probs=82.7
Q ss_pred CcceEEeeccccCChhHHHHHHHHHHHhHHhhhhhcCCCCeEEEeccccCCCCCCCCceEEEEeceecCCchHHHHHHHH
Q 012600 340 KTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQV 419 (460)
Q Consensus 340 ~~LHLTL~~L~L~~eeev~~A~~~L~~i~~~i~d~L~~~pf~l~lkGLg~F~~dp~~~rVLya~V~~~d~~~~L~~L~~~ 419 (460)
.++|+|+.+.-+.++.+++.-...+++....+..++...-...-|+|.++|.. .|-.+++.+ ...+++.++.
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 37999998888899999999999999776665565655556667799999998 888999875 5789999999
Q ss_pred HHHHHHHCCCCcccCCCCCcceeEEeeeec
Q 012600 420 IIDAFNEAGLVFHRDYNKKLKLHATLMNIR 449 (460)
Q Consensus 420 L~~~f~~~Gl~~~~de~r~fkpHlTL~n~k 449 (460)
+...|.+.+...+ +..-|.+|-+++.+.
T Consensus 200 les~~~e~~~~~~--~kp~~i~lkG~~~mn 227 (345)
T KOG2814|consen 200 LESTFQEIRIDVG--EKPLFIDLKGLDKMN 227 (345)
T ss_pred HHHHHHHHHhccC--CCceeeeccchhhhc
Confidence 9999999888875 567799999998776
No 52
>PRK12705 hypothetical protein; Provisional
Probab=93.79 E-value=0.08 Score=57.86 Aligned_cols=68 Identities=19% Similarity=0.325 Sum_probs=50.2
Q ss_pred CCeEEEEeccc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 152 ERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 152 ~~~~~~v~Vp~-~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
......|.+|. ++-|.|||+.|.|+|.+|..||+-|.|... ...|+|.+-....-+.|+..+..++.+
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt--p~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT--PEAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC--ccchhhcccCccchHHHHHHHHHHHhc
Confidence 34455778887 678999999999999999999999999543 234666665445556666666666543
No 53
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=93.79 E-value=0.18 Score=50.84 Aligned_cols=69 Identities=19% Similarity=0.329 Sum_probs=54.1
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 152 ~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~-~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
.++...+.+...--+-||||||.++|.|..|.+..|++|.+.. ...++|+.. .+.|-.-...|.-.+++
T Consensus 46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad-~~ti~~ilk~iip~lee 115 (390)
T KOG2192|consen 46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISAD-IETIGEILKKIIPTLEE 115 (390)
T ss_pred cceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCCCceeEEEecc-HHHHHHHHHHHhhhhhh
Confidence 4577778888888999999999999999999999999998766 677889885 55555544444444444
No 54
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=93.65 E-value=0.12 Score=56.14 Aligned_cols=103 Identities=24% Similarity=0.212 Sum_probs=77.0
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCC--CC-CCcEEEEc--------cChhHHHHHHHHHHHHHH----
Q 012600 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS--KK-EDSIIIEG--------NSTDSVAKASEKIQAIIA---- 220 (460)
Q Consensus 156 ~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~--~~-~~~I~ItG--------~s~e~V~~A~~rI~~iv~---- 220 (460)
..+..+-...+.||||+|.++++|..+|+.+|.|-.. +. ...|+|+| ++.+.+.+|.++|-...+
T Consensus 45 ~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~ 124 (485)
T KOG2190|consen 45 YRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDE 124 (485)
T ss_pred EEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccccccc
Confidence 6778888999999999999999999888888777443 33 56789999 237999999999876421
Q ss_pred HhhhC----CCCCcceEEeeccccchhhhhhHHHHHHHHhcc
Q 012600 221 EAVES----PSLDYSHFVSLPLAVHPELVDKLVNFQNTILGI 258 (460)
Q Consensus 221 e~~~~----~k~~~THFIsIPl~~hP~I~g~~~~F~~sIl~~ 258 (460)
+.... .+...+-.+-+|-..--.|+|+.+..+++|.++
T Consensus 125 ~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~ 166 (485)
T KOG2190|consen 125 AAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREE 166 (485)
T ss_pred ccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHh
Confidence 11110 021235666688775688999999999999976
No 55
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=93.54 E-value=0.053 Score=58.98 Aligned_cols=102 Identities=21% Similarity=0.310 Sum_probs=80.1
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCCC
Q 012600 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLD 229 (460)
Q Consensus 151 ~~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~-~~~I~ItG~s~e~V~~A~~rI~~iv~e~~~~~k~~ 229 (460)
..+..+++.||.++.+.|+|++|++++.|+..|+.||.+-.... ...+-+.+.....+..|+..|-.++.+ . -+
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~~--~---~p 139 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTE--N---TP 139 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHhc--C---Cc
Confidence 45778889999999999999999999999999999999955443 334444443356788888888777665 2 23
Q ss_pred cceEEeeccccchhhhhhHHHHHHHHhc
Q 012600 230 YSHFVSLPLAVHPELVDKLVNFQNTILG 257 (460)
Q Consensus 230 ~THFIsIPl~~hP~I~g~~~~F~~sIl~ 257 (460)
+..-++.|...|+.|.+..+..+++|-.
T Consensus 140 vk~~lsvpqr~~~~i~grgget~~si~~ 167 (608)
T KOG2279|consen 140 VSEQLSVPQRSVGRIIGRGGETIRSICK 167 (608)
T ss_pred ccccccchhhhcccccccchhhhcchhc
Confidence 5666788888899999999998888764
No 56
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=93.30 E-value=0.15 Score=50.53 Aligned_cols=63 Identities=25% Similarity=0.362 Sum_probs=53.1
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 156 ~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
.-|.||+..++.+||++|++++-|.++|+|+|.+ +..+-|-|.|+......-|..-|..+-.+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~V---G~NG~IWV~~~~~~~e~~~~~aI~~ie~e 210 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIV---GQNGRIWVDGENESLEELAIEAIRKIERE 210 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEE---ecCCEEEecCCCcchHHHHHHHHHHHhhh
Confidence 4689999999999999999999999999999998 44577999998655677777777766554
No 57
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=92.44 E-value=0.086 Score=60.24 Aligned_cols=42 Identities=29% Similarity=0.572 Sum_probs=38.3
Q ss_pred CCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 012600 150 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (460)
Q Consensus 150 ~~~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~ 191 (460)
.....+.++.||.++|+.|||++|+++|+++.++++.|.+|.
T Consensus 705 ~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 705 AKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred cccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence 345567788999999999999999999999999999999998
No 58
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=92.19 E-value=0.36 Score=46.51 Aligned_cols=65 Identities=28% Similarity=0.369 Sum_probs=53.2
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEcc----ChhHHHHHHHHHHHHH
Q 012600 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGN----STDSVAKASEKIQAII 219 (460)
Q Consensus 153 ~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~----s~e~V~~A~~rI~~iv 219 (460)
..+..+.||+.=.+.+||+.|.+.+.||+.++|+|.+-.. ++.|.|+.. ..-.+.+|++-|++|-
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~--~~~V~i~~~~~t~Dp~~~~ka~d~VkAIg 75 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK--TGSVTIRTTRKTEDPLALLKARDVVKAIG 75 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC--CCeEEEEecCCCCChHHHHHHHHHHHHHh
Confidence 5567799999999999999999999999999999999544 345666654 4567889998887663
No 59
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=92.02 E-value=0.14 Score=56.22 Aligned_cols=63 Identities=25% Similarity=0.287 Sum_probs=54.1
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 155 ~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
..++.|+.+-...+||++|-..|+|+.|||+.-++ +.+.+.|-.++....++|++-|.-|+..
T Consensus 598 ~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v----De~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 598 LETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV----DEGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred eeEEeecchhhheeecCccceeeeEeeeccceeee----cCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 56778999999999999999999999999955443 3477999999999999999999887654
No 60
>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=89.62 E-value=0.21 Score=40.72 Aligned_cols=37 Identities=16% Similarity=0.238 Sum_probs=31.7
Q ss_pred chHHHHHHHHHHHHHHHCCCCcccCCCCCcceeEEeeeecc
Q 012600 410 GDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRH 450 (460)
Q Consensus 410 ~~~L~~L~~~L~~~f~~~Gl~~~~de~r~fkpHlTL~n~k~ 450 (460)
.+.|.++++.+.+.+...|+... +++.||+||+++.-
T Consensus 8 ~~~L~~l~~~l~~~~~~~~~r~~----~~~~~HiTL~flg~ 44 (87)
T PF02834_consen 8 KEQLNQLQERLRQALPPLGIRWV----RPFNPHITLAFLGE 44 (87)
T ss_dssp HHHHHHHHHHHHHHCCSCTEEEG----SCGGSEEEEEEEEE
T ss_pred HHHHHHHHHHHhhhccccCCccc----CCCCCeEEEEeCCC
Confidence 46788999999988889999873 68999999999874
No 61
>PHA02977 hypothetical protein; Provisional
Probab=87.93 E-value=2 Score=39.96 Aligned_cols=95 Identities=19% Similarity=0.191 Sum_probs=55.8
Q ss_pred eEEeeccccCChhHHHHHHHHHHHhHHhhhhhcCCCCeEEEeccccCCCCC------CCCceEEEEeceecCCchHHHHH
Q 012600 343 HLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGS------KDKARILYAPVEEIGDGDRLLHA 416 (460)
Q Consensus 343 HLTL~~L~L~~eeev~~A~~~L~~i~~~i~d~L~~~pf~l~lkGLg~F~~d------p~~~rVLya~V~~~d~~~~L~~L 416 (460)
|+||+ ..+.++-..-. ..+..+.++ .-..+.++-+..-+||.. -.+.+-+.++++- ++.|..|
T Consensus 71 hitlg---ian~dq~~~f~----~fk~~~~d~-dl~sis~~cke~icfpqs~askelga~g~avvmkle~---sddlkal 139 (201)
T PHA02977 71 HITLG---IANKDQCDNFE----NFKELIKDI-DLQSISFTCKEEICFPQSNASKELGAKGCAVVMKLEA---SDDLKAL 139 (201)
T ss_pred ceeee---ccCccHhHHHH----HHHHHhhcc-cceeEEEEeeeeEeccccchhhhhCcCccEEEEEEEe---chHHHHH
Confidence 99995 45555433322 222222222 236677888888899874 2234566777764 4677777
Q ss_pred HHHHHHHHH----HCCCCcccCCCCCcceeEEeeeeccc
Q 012600 417 CQVIIDAFN----EAGLVFHRDYNKKLKLHATLMNIRHK 451 (460)
Q Consensus 417 ~~~L~~~f~----~~Gl~~~~de~r~fkpHlTL~n~k~~ 451 (460)
.+.|-.+.- -.|=... ..++.||+|+.-++--
T Consensus 140 rnvl~n~vp~pkdifg~i~~---d~~w~phitigyv~~d 175 (201)
T PHA02977 140 RNVLFNAVPCPKDIFGDILS---DNPWCPHITIGYVKAD 175 (201)
T ss_pred HHHhhcccCCcHHhhccccc---CCCCCCceEEEeeccc
Confidence 776654321 1122221 2489999999988854
No 62
>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=86.65 E-value=0.36 Score=46.10 Aligned_cols=25 Identities=20% Similarity=0.272 Sum_probs=23.3
Q ss_pred CCceEEEEccCCcchHHHHHhhccc
Q 012600 287 QEHKVAVELNIGDNSERVKVDRTSI 311 (460)
Q Consensus 287 pn~FVAv~i~~~~i~~~v~~vq~~i 311 (460)
|||||||+|+.+++.++++.+|+.|
T Consensus 1 pthFl~ipl~~~~i~~~~~~fq~~v 25 (209)
T PF10469_consen 1 PTHFLCIPLNSPEIQEKFKEFQNEV 25 (209)
T ss_pred CCeEEEEECCCHHHHHHHHHHHHHH
Confidence 8999999999999999999999865
No 63
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=86.30 E-value=2.7 Score=40.22 Aligned_cols=73 Identities=19% Similarity=0.259 Sum_probs=58.7
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCCCcceEEe
Q 012600 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDYSHFVS 235 (460)
Q Consensus 156 ~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e~~~~~k~~~THFIs 235 (460)
..+.+++..+-+|...+|..++.|-...|++|.+-.. .+.|.|+|+ +..++.+...|..+.... .+..|.
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 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS--ENRIRITGT-KSTAEYIEASINEILSNI-------RTEEID 97 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC--CcEEEEEcc-HHHHHHHHHHHHHHHhhc-------EEEEEe
Confidence 4566678999999999999999997788999999655 347999996 889999999998888762 255555
Q ss_pred ecc
Q 012600 236 LPL 238 (460)
Q Consensus 236 IPl 238 (460)
+|.
T Consensus 98 l~~ 100 (210)
T PF14611_consen 98 LSP 100 (210)
T ss_pred cch
Confidence 664
No 64
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=83.34 E-value=0.83 Score=49.56 Aligned_cols=41 Identities=29% Similarity=0.357 Sum_probs=36.6
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCC
Q 012600 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS 192 (460)
Q Consensus 152 ~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~ 192 (460)
+.....|.||....+.+|||+|.++++||...|.+|.+-..
T Consensus 484 gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 484 GDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred cCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 34567899999999999999999999999999999999443
No 65
>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=83.18 E-value=1.5 Score=33.34 Aligned_cols=34 Identities=15% Similarity=0.251 Sum_probs=27.6
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEE
Q 012600 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKI 187 (460)
Q Consensus 154 ~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI 187 (460)
....+.+...-.+.+||++|.+++.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4555666665679999999999999999999665
No 66
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=82.96 E-value=1.2 Score=40.77 Aligned_cols=37 Identities=16% Similarity=0.119 Sum_probs=33.7
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 012600 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (460)
Q Consensus 153 ~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~i 189 (460)
+....+.|++.-++..|||+|.|++.++.-+|-.|+|
T Consensus 98 ~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 98 DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred cEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 4567788999999999999999999999999988877
No 67
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=82.18 E-value=0.76 Score=36.84 Aligned_cols=34 Identities=15% Similarity=0.251 Sum_probs=28.8
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhC
Q 012600 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMG 184 (460)
Q Consensus 151 ~~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~ 184 (460)
.......+.|..+--+.||||+|.|++.|+.=++
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 4456778889999999999999999999986554
No 68
>PRK13764 ATPase; Provisional
Probab=80.07 E-value=1.3 Score=49.57 Aligned_cols=40 Identities=30% Similarity=0.360 Sum_probs=36.3
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 012600 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (460)
Q Consensus 152 ~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~ 191 (460)
......|.||....+.+|||||.++++||...|.+|++-.
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 4556789999999999999999999999999999999943
No 69
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=79.17 E-value=1.4 Score=42.85 Aligned_cols=53 Identities=26% Similarity=0.360 Sum_probs=45.2
Q ss_pred ccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012600 164 VIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (460)
Q Consensus 164 ~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e 221 (460)
..|.|+||+|.|.=-||+-|.|||.+.. ..|-|-|. -+++.-|++-|-.++--
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVlad----~kIHiLG~-~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIENVTRTRIVLAD----SKIHILGA-FQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHhhcCCCcceeeeeccceeEEEecC----ceEEEeec-chhhHHHHHhhHhhhcc
Confidence 4789999999999999999999999964 36889996 68999999888776643
No 70
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=78.95 E-value=2.3 Score=46.52 Aligned_cols=69 Identities=16% Similarity=0.199 Sum_probs=53.8
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEcc--ChhHHHHHHHHHHHHHHH
Q 012600 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGN--STDSVAKASEKIQAIIAE 221 (460)
Q Consensus 153 ~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~------~~~I~ItG~--s~e~V~~A~~rI~~iv~e 221 (460)
-...++-||...|+.|||.||..+++.....++-|++-..-+ .+.|.|..+ .++++..|+.-...+|.+
T Consensus 448 pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~ 524 (657)
T COG5166 448 PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ 524 (657)
T ss_pred chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhh
Confidence 456789999999999999999999999999999888754322 356888886 456677777776666664
No 71
>PRK02821 hypothetical protein; Provisional
Probab=77.86 E-value=2.3 Score=35.26 Aligned_cols=33 Identities=18% Similarity=0.289 Sum_probs=27.6
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhC
Q 012600 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMG 184 (460)
Q Consensus 152 ~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~ 184 (460)
......+.+.++=.|.||||+|.+++.|..=..
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 346788899999999999999999998875443
No 72
>PRK00468 hypothetical protein; Provisional
Probab=77.75 E-value=2.3 Score=34.99 Aligned_cols=30 Identities=20% Similarity=0.302 Sum_probs=25.9
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHH
Q 012600 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEK 181 (460)
Q Consensus 152 ~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~ 181 (460)
......+.+.++=.|.||||+|.|++.|..
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRt 57 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRT 57 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHH
Confidence 346678899999999999999999998864
No 73
>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=77.73 E-value=2 Score=39.45 Aligned_cols=38 Identities=16% Similarity=0.079 Sum_probs=34.3
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 012600 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (460)
Q Consensus 152 ~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~i 189 (460)
++....+.||+.-++..|||+|.|++....-||-+|+|
T Consensus 98 ~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 98 GKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred CCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 35678899999999999999999999999999988876
No 74
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=77.52 E-value=2 Score=44.30 Aligned_cols=69 Identities=20% Similarity=0.290 Sum_probs=59.0
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHH-HHHHHHH
Q 012600 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKAS-EKIQAII 219 (460)
Q Consensus 151 ~~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~-~rI~~iv 219 (460)
..+....+.+|-...+.+.|.+|++++.+++-|++-|.-|.+......-++|-++.++++|+ ..|+...
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 45666678889999999999999999999999999999998877777889998888899998 7776553
No 75
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=76.39 E-value=2.6 Score=34.96 Aligned_cols=31 Identities=16% Similarity=0.297 Sum_probs=26.6
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHH
Q 012600 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEK 181 (460)
Q Consensus 151 ~~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~ 181 (460)
.......+.+-++=.|.+|||+|.|++.|.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHH
Confidence 4556778899999999999999999998853
No 76
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=76.03 E-value=1.6 Score=35.21 Aligned_cols=37 Identities=24% Similarity=0.341 Sum_probs=31.2
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEE
Q 012600 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKII 188 (460)
Q Consensus 152 ~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~ 188 (460)
+.....+.+-...-+.+||++|+++++|..+.+-.+.
T Consensus 23 ~~~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 23 TPDQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SSSEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred cCCeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 3466778888999999999999999999988876664
No 77
>PRK01064 hypothetical protein; Provisional
Probab=75.48 E-value=2.6 Score=35.00 Aligned_cols=32 Identities=28% Similarity=0.243 Sum_probs=27.3
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHH
Q 012600 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKE 182 (460)
Q Consensus 151 ~~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~e 182 (460)
+......+.|.++=.|.+|||+|.|++.|+.=
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 34567788899999999999999999998764
No 78
>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=74.02 E-value=4.8 Score=39.67 Aligned_cols=62 Identities=16% Similarity=0.203 Sum_probs=42.3
Q ss_pred cceEEeeccccchhhhhhHHHHHHHHhcccccccccccCCCCCccccchHHhhhcccCCceEEEEccCCcchHHHHHhhc
Q 012600 230 YSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKVDRT 309 (460)
Q Consensus 230 ~THFIsIPl~~hP~I~g~~~~F~~sIl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rpn~FVAv~i~~~~i~~~v~~vq~ 309 (460)
|||||++|+..-.-..++|-.+|-.+++++=.| |.|...-=.+.-++|.++++..-+..+|+
T Consensus 6 P~HFin~Pl~~f~~f~~~~~~LQ~~~~~eG~d~------------------k~QkaPHlSl~mL~Isd~~i~~V~~~iq~ 67 (248)
T PF05213_consen 6 PTHFINFPLVQFEGFMLNFKDLQFQLLEEGVDC------------------KLQKAPHLSLGMLDISDEDIPDVETAIQK 67 (248)
T ss_pred CCceeeccchhhhhHHHHHHHHHHHHHHcCCCc------------------cccccCeeEEEEEEcChhhhhhHHHHHHH
Confidence 899999999865888999999999999764222 23332223455677887776555444444
No 79
>PLN00108 unknown protein; Provisional
Probab=73.96 E-value=1.9 Score=43.41 Aligned_cols=29 Identities=17% Similarity=0.181 Sum_probs=26.7
Q ss_pred hcccCCceEEEEcc-CCcchHHHHHhhccc
Q 012600 283 QQVDQEHKVAVELN-IGDNSERVKVDRTSI 311 (460)
Q Consensus 283 ~~~rpn~FVAv~i~-~~~i~~~v~~vq~~i 311 (460)
++..|||||||+|. .+++.++++++|+.+
T Consensus 32 ~~~~~THFlavPL~~~p~i~~~~~~Fk~~V 61 (257)
T PLN00108 32 HREVFTHFVSLPLAIYPDLKKNIEAFQNSV 61 (257)
T ss_pred cCCCCCeEEEEEcCCCHHHHHHHHHHHHHH
Confidence 36789999999996 899999999999987
No 80
>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=71.32 E-value=16 Score=36.35 Aligned_cols=69 Identities=12% Similarity=0.123 Sum_probs=38.2
Q ss_pred cceEEeec-cccCChhHHHHHHHHHHHhHHhhhhhcCCCCeEE---EeccccCCCCCCCCceEEEEeceecCCchHHHHH
Q 012600 341 TFHLTVLM-LKLWNKDRVNAATNVLKSISSKVMDALDNRPLFI---RLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHA 416 (460)
Q Consensus 341 ~LHLTL~~-L~L~~eeev~~A~~~L~~i~~~i~d~L~~~pf~l---~lkGLg~F~~dp~~~rVLya~V~~~d~~~~L~~L 416 (460)
=||.||+- +.|......+...+++..+... ..||.| .+.-||-|-- +. +.+....|+.|
T Consensus 57 GfHaTLKaPFrLa~g~~~a~L~~al~~fA~~------~~pf~i~~L~l~~Lg~FlA--------L~---P~~~~~~L~~L 119 (228)
T TIGR03223 57 GFHATLKAPFRLAPGVTEAELLAAVAAFAAT------RAPFALPPLRVALLGGFLA--------LR---PAAPCPALQAL 119 (228)
T ss_pred ccceeecCCcccCCCCCHHHHHHHHHHHHhc------CCCccCCcceeeeeCCEEE--------Ee---eCCCCHHHHHH
Confidence 47999974 4554433334444444444221 355544 3344444421 22 22457899999
Q ss_pred HHHHHHHHHH
Q 012600 417 CQVIIDAFNE 426 (460)
Q Consensus 417 ~~~L~~~f~~ 426 (460)
+..+.+.|..
T Consensus 120 Aa~~V~~~d~ 129 (228)
T TIGR03223 120 AAACVRELDP 129 (228)
T ss_pred HHHHHHhhhh
Confidence 9999998843
No 81
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=70.96 E-value=4.4 Score=37.09 Aligned_cols=37 Identities=24% Similarity=0.364 Sum_probs=32.2
Q ss_pred eEEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 012600 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (460)
Q Consensus 154 ~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP 190 (460)
-..-+-|+....|..||++|++++.|++..|-+|.+=
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv 68 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV 68 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence 3456777888999999999999999999999888873
No 82
>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=68.21 E-value=4.4 Score=32.95 Aligned_cols=35 Identities=17% Similarity=0.282 Sum_probs=28.2
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 012600 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (460)
Q Consensus 155 ~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~i 189 (460)
...+.|..+--+.+|||.|.|+..||-=++.-++-
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 45677777888999999999999999887755443
No 83
>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=67.18 E-value=5.7 Score=41.57 Aligned_cols=40 Identities=25% Similarity=0.311 Sum_probs=36.6
Q ss_pred CCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 012600 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (460)
Q Consensus 152 ~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~ 191 (460)
......+.||..-.+.-|||+|.|.+.--.-||.+|+|=+
T Consensus 299 ~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 299 DKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred CCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 3468899999999999999999999999999999999854
No 84
>COG5255 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.94 E-value=17 Score=35.74 Aligned_cols=130 Identities=20% Similarity=0.236 Sum_probs=69.6
Q ss_pred CceEEEEccCCcchHHHHHhhccccccccccccCCCCCCCCCCCCcCCccCCCcceEEeeccccCCh-------------
Q 012600 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNK------------- 354 (460)
Q Consensus 288 n~FVAv~i~~~~i~~~v~~vq~~i~~~~~~~~~~k~~~~~~~Gld~~~fv~p~~LHLTL~~L~L~~e------------- 354 (460)
|.-||-=++-.+.-+.|-.++.+++. +|.+ +.-.|.|+..+|+|+. =|+..+
T Consensus 42 NTVVchl~~gs~t~~vvl~i~~r~~~---mpfa-----------dklt~tP~sSlHMTvf-qg~~e~~R~~~~WpqdlPL 106 (239)
T COG5255 42 NTVVCHLVTGSDTEEVVLIIRSRYLE---MPFA-----------DKLTFTPVSSLHMTVF-QGLIEERRELPYWPQDLPL 106 (239)
T ss_pred CeEEEeccCCCchHHHHHHHHHHhhc---cchh-----------hhhccCCcchhhHHHH-HHHhhhcccCCCCCccCCC
Confidence 44555555555666778888887642 2222 2237999999999983 233221
Q ss_pred -hHHHHHHHHHHH-hHHhhhhhcCCCCeEEEeccccCCCCCCCCceEEEEeceecCCchHHHHHHHHHHHHHH-HCCCCc
Q 012600 355 -DRVNAATNVLKS-ISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFN-EAGLVF 431 (460)
Q Consensus 355 -eev~~A~~~L~~-i~~~i~d~L~~~pf~l~lkGLg~F~~dp~~~rVLya~V~~~d~~~~L~~L~~~L~~~f~-~~Gl~~ 431 (460)
.-++.+.+.+.+ ++ +-+.+ ..+|.+++-+++-- .++-.++.+ .=+++-..+++.|. .+|+..
T Consensus 107 Dtpi~~~~~~~~erLk--~F~l~-~~~~~mrvte~rp~-------~i~v~padd-----ad~~~l~~~Rd~ls~~~g~r~ 171 (239)
T COG5255 107 DTPIDAITDYYAERLK--IFPLL-DEEFNMRVTEMRPQ-------GILVEPADD-----ADAKILEEWRDYLSEKFGYRH 171 (239)
T ss_pred CCcHHHHHHHHHHHHh--cccCC-chhhcchhhccccc-------ceEeccCCH-----HHHHHHHHHHHHHhhhhcccC
Confidence 123333333221 10 00111 13455544444321 234444432 23344455666664 668987
Q ss_pred ccCCCCCcceeEEeeeec
Q 012600 432 HRDYNKKLKLHATLMNIR 449 (460)
Q Consensus 432 ~~de~r~fkpHlTL~n~k 449 (460)
. +.+.|..|+||+-..
T Consensus 172 P--~HDaY~FHITlgYl~ 187 (239)
T COG5255 172 P--DHDAYQFHITLGYLR 187 (239)
T ss_pred C--CCcceEEEEEeeeEe
Confidence 5 457899999998765
No 85
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=66.76 E-value=5.5 Score=32.17 Aligned_cols=25 Identities=36% Similarity=0.478 Sum_probs=21.5
Q ss_pred cccccCCCchhHHHHHHHh-CcEEEc
Q 012600 165 IRFIKGKEGSTQKKFEKEM-GVKIIL 189 (460)
Q Consensus 165 h~~IIGk~G~t~k~LE~eT-~trI~i 189 (460)
.+..||++|..++.|+++. |-+|++
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 7899999999999999999 888876
No 86
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=65.70 E-value=6.3 Score=41.78 Aligned_cols=44 Identities=18% Similarity=0.080 Sum_probs=38.9
Q ss_pred CCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC
Q 012600 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 194 (460)
Q Consensus 151 ~~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~ 194 (460)
.......+.||..-++.-|||+|.|.+.--.-||.+|+|-+.++
T Consensus 305 ~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 305 EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 34468899999999999999999999999999999999966544
No 87
>KOG3102 consensus Uncharacterized conserved protein [Function unknown]
Probab=64.84 E-value=22 Score=35.12 Aligned_cols=97 Identities=11% Similarity=0.251 Sum_probs=64.0
Q ss_pred CCcceEEeeccccCChhHHHHHHHHHHHhHHhhhhhcCCCCeEEEeccccCCCCCCCCceEEE-EeceecCCchHHHHHH
Q 012600 339 PKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILY-APVEEIGDGDRLLHAC 417 (460)
Q Consensus 339 p~~LHLTL~~L~L~~eeev~~A~~~L~~i~~~i~d~L~~~pf~l~lkGLg~F~~dp~~~rVLy-a~V~~~d~~~~L~~L~ 417 (460)
-.-|||.|.=---+---++.....+|++- +. ....|-+++.++.+|-| .++.|..- +.+. ..+...+.++.
T Consensus 119 ~~~fHlSLsr~VvLr~HqI~~fi~~L~~~---l~---s~~rf~~t~n~~~iytN-~e~TRtFi~leit-t~~~~~~~~~i 190 (269)
T KOG3102|consen 119 GREFHLSLSRNVVLRVHQINSFISMLRQK---LQ---SQKRFLITFNKWEIYTN-DEHTRTFISLEIT-TSGLSEISKQI 190 (269)
T ss_pred cceEEEeeccceEEEeehhhHHHHHHHHH---Hh---hhhhheEeecceEEEec-cccceeEEEEEec-hhhHHHHHHHH
Confidence 47799998532222234555555555542 11 24778899999999998 55656544 3454 34566777788
Q ss_pred HHHHHHHHHCCCCcccCCCCCcceeEEee
Q 012600 418 QVIIDAFNEAGLVFHRDYNKKLKLHATLM 446 (460)
Q Consensus 418 ~~L~~~f~~~Gl~~~~de~r~fkpHlTL~ 446 (460)
+.+.+.+....|.. -++.-.+|+.|+
T Consensus 191 ~~vd~Vm~~~nL~~---FY~DPsfHiSL~ 216 (269)
T KOG3102|consen 191 DAVDEVMKLHNLPE---FYKDPSFHISLV 216 (269)
T ss_pred HHHHHHHHHcCchh---hhcCCCCCceEE
Confidence 88899999888875 243348899886
No 88
>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=63.82 E-value=4.7 Score=33.53 Aligned_cols=37 Identities=11% Similarity=0.258 Sum_probs=29.4
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcCCC
Q 012600 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS 192 (460)
Q Consensus 156 ~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~ 192 (460)
+.|.|-...=+.+||++|.++++|.++-...+.++.+
T Consensus 32 i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~~ 68 (81)
T cd02413 32 TEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPEG 68 (81)
T ss_pred EEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCCC
Confidence 4555555556999999999999999998888877543
No 89
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=58.90 E-value=9.4 Score=36.84 Aligned_cols=36 Identities=19% Similarity=0.182 Sum_probs=34.1
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 012600 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (460)
Q Consensus 155 ~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP 190 (460)
...+.||..-.+..|||+|.+.+...+-||-+|+|-
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~ 178 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE 178 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence 788999999999999999999999999999999884
No 90
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=56.85 E-value=9.9 Score=41.50 Aligned_cols=39 Identities=28% Similarity=0.307 Sum_probs=36.0
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 012600 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (460)
Q Consensus 153 ~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~ 191 (460)
.....|.||..-++.-|||+|.|+|....-||.+|+|=+
T Consensus 301 ~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 468899999999999999999999999999999998843
No 91
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=56.69 E-value=11 Score=39.70 Aligned_cols=40 Identities=25% Similarity=0.269 Sum_probs=36.6
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCC
Q 012600 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS 192 (460)
Q Consensus 153 ~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~ 192 (460)
.....+.||...++.-|||+|.|++.--.-||.+|+|=+.
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 4678999999999999999999999999999999998544
No 92
>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=55.83 E-value=15 Score=33.84 Aligned_cols=36 Identities=25% Similarity=0.287 Sum_probs=32.5
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 012600 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (460)
Q Consensus 155 ~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP 190 (460)
.+-+-|.+.-.|..||++|.+++.|++..|-+|.+=
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 778888999999999999999999999999888873
No 93
>PF08975 2H-phosphodiest: Domain of unknown function (DUF1868); InterPro: IPR015069 This family consist of hypothetical bacterial proteins. ; PDB: 2FSQ_A.
Probab=54.07 E-value=5.5 Score=35.67 Aligned_cols=47 Identities=15% Similarity=0.214 Sum_probs=30.2
Q ss_pred CCceEEEEccCCcchHHHHHhhccccccccccccCCCCCCCCCCCCcCCccCCCcceEEee
Q 012600 287 QEHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVL 347 (460)
Q Consensus 287 pn~FVAv~i~~~~i~~~v~~vq~~i~~~~~~~~~~k~~~~~~~Gld~~~fv~p~~LHLTL~ 347 (460)
-|.|||-=-...+....+..+|+.|. +.|.. +.-.|.||..+|+|+.
T Consensus 13 GNTvIchl~~~s~~~~al~~i~~~l~---------~~~~~-----~k~a~lP~sS~HMTVf 59 (118)
T PF08975_consen 13 GNTVICHLPQDSPFYAALLAIQQRLR---------ESPFA-----DKLAFLPPSSYHMTVF 59 (118)
T ss_dssp EEEEEEEB-TTSHHHHHHHHHHHHHH---------TSGGG-----GGEEE--GGG-EEEEE
T ss_pred CCeEEeecCCCChHHHHHHHHHHHHH---------hCccc-----cceEecCcchhhhhhh
Confidence 37788875566677889999999884 11122 2236999999999994
No 94
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=53.43 E-value=14 Score=34.99 Aligned_cols=34 Identities=24% Similarity=0.365 Sum_probs=27.8
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 012600 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (460)
Q Consensus 155 ~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~i 189 (460)
.+.+-|.+-- +.-|||+|.++++|++..|-+|.+
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~Vev 95 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRV 95 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEE
Confidence 3445555555 999999999999999999988876
No 95
>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=50.02 E-value=26 Score=34.47 Aligned_cols=66 Identities=17% Similarity=0.269 Sum_probs=41.2
Q ss_pred CceEEEEccCCcchHHHHHhhccccccccccccCCCCCCCCCCCCcCCcc-CCCcceEEeeccccCChhHHHHH-HHHHH
Q 012600 288 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFI-KPKTFHLTVLMLKLWNKDRVNAA-TNVLK 365 (460)
Q Consensus 288 n~FVAv~i~~~~i~~~v~~vq~~i~~~~~~~~~~k~~~~~~~Gld~~~fv-~p~~LHLTL~~L~L~~eeev~~A-~~~L~ 365 (460)
-.|+|++|..+.... +..+.+.+ +.++..+|++. |- ....+|+.|+-.--...+++.+. .+.+.
T Consensus 141 R~FL~l~V~~~~~~~-l~~l~~~i-----------~~~l~~~~lp~--~Y~~~~~fHvSIAw~~~~~~~~l~~~~~~~~~ 206 (239)
T PF09749_consen 141 RSFLALRVSEGSNNE-LKRLLDRI-----------NEVLKEFGLPP--FYDEDPSFHVSIAWTLGDPSEELKESSLKILQ 206 (239)
T ss_pred eEEEEEEecccccHH-HHHHHHHH-----------HHHHHHhCCCc--ccCCCCCCEEEEEEECCCchHHHHHHHHHHHH
Confidence 489999999866432 55554443 11234677766 66 99999999987543334444433 34455
Q ss_pred Hh
Q 012600 366 SI 367 (460)
Q Consensus 366 ~i 367 (460)
..
T Consensus 207 ~~ 208 (239)
T PF09749_consen 207 EP 208 (239)
T ss_pred HH
Confidence 44
No 96
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=49.38 E-value=9.7 Score=42.11 Aligned_cols=69 Identities=25% Similarity=0.261 Sum_probs=53.3
Q ss_pred CCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEccChhHHHHHHHHHHHHH
Q 012600 150 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKIQAII 219 (460)
Q Consensus 150 ~~~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~---~~~I~ItG~s~e~V~~A~~rI~~iv 219 (460)
.++-++....+|...++.|+|++|.+++.|+.-.+.+|.+-..+. ...+.|.|. +.-++.|+..|..=+
T Consensus 136 ~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~q-qk~~~~a~~~~~~~~ 207 (608)
T KOG2279|consen 136 ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQ-QKEVAAAKHLILEKV 207 (608)
T ss_pred cCCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccc-cchHHHHHhhhhccc
Confidence 455667788999999999999999999999999999999876654 345666664 455667776665433
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=46.79 E-value=16 Score=31.82 Aligned_cols=32 Identities=25% Similarity=0.377 Sum_probs=25.3
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEE
Q 012600 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKI 187 (460)
Q Consensus 156 ~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI 187 (460)
+.|.|-.+.=+.|||++|+++++|+++....+
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 45555555679999999999999998877654
No 98
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=46.20 E-value=20 Score=38.95 Aligned_cols=39 Identities=23% Similarity=0.244 Sum_probs=35.7
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCC
Q 012600 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (460)
Q Consensus 153 ~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~ 191 (460)
.....|.||..-++.-|||+|.|++.--.-||.+|+|-+
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 456789999999999999999999999999999999854
No 99
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=45.52 E-value=27 Score=35.83 Aligned_cols=51 Identities=18% Similarity=0.314 Sum_probs=39.0
Q ss_pred cccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhhh
Q 012600 165 IRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVE 224 (460)
Q Consensus 165 h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e~~~ 224 (460)
.-.+||.+|+|++.||--|+|-|-+- .+.|.+.|+ -.++.. +..||.+..+
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilVq----G~TVsaiGp-fkGlke----vr~IV~DcM~ 210 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILVQ----GNTVSAIGP-FKGLKE----VRKIVEDCMK 210 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEee----CcEEEeecC-cchHHH----HHHHHHHHHh
Confidence 45799999999999999999999874 356788887 456554 4556766554
No 100
>PRK15245 type III effector phosphothreonine lyase; Provisional
Probab=40.78 E-value=1.5e+02 Score=29.45 Aligned_cols=80 Identities=18% Similarity=0.357 Sum_probs=49.0
Q ss_pred CcceEEeeccccCChhHHHHHHHHHHHhHHhhhhhcCCCCe-EEEeccccCCCCCCCCceE-------EEEeceecCC--
Q 012600 340 KTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPL-FIRLKGLDLMRGSKDKARI-------LYAPVEEIGD-- 409 (460)
Q Consensus 340 ~~LHLTL~~L~L~~eeev~~A~~~L~~i~~~i~d~L~~~pf-~l~lkGLg~F~~dp~~~rV-------Lya~V~~~d~-- 409 (460)
.++||.+ ..++|..|.++|..+--. +..|+ .-.+.. |..-+...|| ||+++..++.
T Consensus 103 DK~HiSV------~~~qv~qAF~als~lLfS-----eDSPiDKWKVTD---M~rv~qqsRV~~GAQfTLYvKpd~edsqY 168 (241)
T PRK15245 103 DKFHISV------ARDQVPQAFQALSGLLFS-----EDSPVDKWKVTD---MERVSQQSRVGLGAQFTLYVKPDQENSQY 168 (241)
T ss_pred ceEEEEe------cHHHHHHHHHHhhhhhcC-----CCCCcceeeecc---ccccCccchhcccceEEEEecCccccccC
Confidence 6899998 468899999998876210 12232 111112 2111222343 8999987542
Q ss_pred ----chHHHHHHHHHHHHHHHCCCCccc
Q 012600 410 ----GDRLLHACQVIIDAFNEAGLVFHR 433 (460)
Q Consensus 410 ----~~~L~~L~~~L~~~f~~~Gl~~~~ 433 (460)
......+-+.|+..|.++|+.+.+
T Consensus 169 sa~~l~k~r~Fie~lE~~L~~~gi~pG~ 196 (241)
T PRK15245 169 SASFLHKTRQFIECLESRLSENGVISGQ 196 (241)
T ss_pred CHHHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence 224456777889999999998753
No 101
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=35.26 E-value=1.9e+02 Score=29.37 Aligned_cols=83 Identities=14% Similarity=0.207 Sum_probs=50.5
Q ss_pred cceEEeeccccCChhHHHHHHHHHHHhHHhhhhhcCCCCeEEEeccccCCCCCCCCceE-EEEeceecCCchHHHHHHHH
Q 012600 341 TFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARI-LYAPVEEIGDGDRLLHACQV 419 (460)
Q Consensus 341 ~LHLTL~~L~L~~eeev~~A~~~L~~i~~~i~d~L~~~pf~l~lkGLg~F~~dp~~~rV-Lya~V~~~d~~~~L~~L~~~ 419 (460)
+.+++++ ..-+.++++|.++|.++-.....++..++..+.+.+++-..= ...| .|+... +-...-.++...
T Consensus 185 r~~~~v~---V~y~~d~~~~~~il~~~~~~~~~vl~~p~p~v~~~~~~dssi---~~~v~~wv~~~--~~~~~~~~~~~~ 256 (286)
T PRK10334 185 RNEFIIG---VAYDSDIDQVKQILTNIIQSEDRILKDREMTVRLNELGASSI---NFVVRVWSNSG--DLQNVYWDVLER 256 (286)
T ss_pred EEEEEEE---ecCCCCHHHHHHHHHHHHHhCCceecCCCCEEEEEeeeCceE---EEEEEEEEecc--hhHHHHHHHHHH
Confidence 5677774 444566788888887765444445665666676665433221 1111 355432 222234577889
Q ss_pred HHHHHHHCCCCc
Q 012600 420 IIDAFNEAGLVF 431 (460)
Q Consensus 420 L~~~f~~~Gl~~ 431 (460)
+.+.|.++|+..
T Consensus 257 I~~~f~~~gI~i 268 (286)
T PRK10334 257 IKREFDAAGISF 268 (286)
T ss_pred HHHHHHHCCCcC
Confidence 999999999987
No 102
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=34.58 E-value=54 Score=35.33 Aligned_cols=69 Identities=9% Similarity=0.097 Sum_probs=51.9
Q ss_pred CeEEEEecccccccccc-CCCchhHHHHHHHhCcEEEc---------CCCCC-CCc---EEEEccChhHHHHHHHHHHHH
Q 012600 153 RHSLSVEVGASVIRFIK-GKEGSTQKKFEKEMGVKIIL---------PSSKK-EDS---IIIEGNSTDSVAKASEKIQAI 218 (460)
Q Consensus 153 ~~~~~v~Vp~~~h~~II-Gk~G~t~k~LE~eT~trI~i---------P~~~~-~~~---I~ItG~s~e~V~~A~~rI~~i 218 (460)
|+-+.+++|+...+-.- |++-.++.-+|-|++.+.-+ |..++ +.+ |.|++.+.+++..|+.++..+
T Consensus 213 k~~v~~~~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl 292 (531)
T KOG1960|consen 213 KALATDKDPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNGNGENGAPRRKWNL 292 (531)
T ss_pred heecccCCcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCcccccccCCceeEEeecCCchhhccchhHHHhH
Confidence 77788888887765444 56667999999999998555 33333 222 889998899999999999877
Q ss_pred HHH
Q 012600 219 IAE 221 (460)
Q Consensus 219 v~e 221 (460)
...
T Consensus 293 ~~~ 295 (531)
T KOG1960|consen 293 EEK 295 (531)
T ss_pred HHH
Confidence 644
No 103
>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=31.90 E-value=93 Score=25.67 Aligned_cols=35 Identities=31% Similarity=0.474 Sum_probs=26.6
Q ss_pred CcEEEcCCCCCCCcEEEEcc-ChhHHHHHHHHHHHHHHH
Q 012600 184 GVKIILPSSKKEDSIIIEGN-STDSVAKASEKIQAIIAE 221 (460)
Q Consensus 184 ~trI~iP~~~~~~~I~ItG~-s~e~V~~A~~rI~~iv~e 221 (460)
++.+.|=+ ++.|+|+|. +.+.+..|.++|..++.+
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 45555544 366999995 888999999988888765
No 104
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=31.77 E-value=41 Score=27.87 Aligned_cols=32 Identities=9% Similarity=0.254 Sum_probs=23.6
Q ss_pred CeEEEEeccccccccccCCCchhHHHHHHHhCcE
Q 012600 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVK 186 (460)
Q Consensus 153 ~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~tr 186 (460)
+..+.+.+ ..-+.+||++|.++++|...-.-.
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 44455555 667999999999999988776543
No 105
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=28.56 E-value=31 Score=34.14 Aligned_cols=28 Identities=25% Similarity=0.245 Sum_probs=21.5
Q ss_pred eEEEEecccccc-ccccCCCchhHHHHHH
Q 012600 154 HSLSVEVGASVI-RFIKGKEGSTQKKFEK 181 (460)
Q Consensus 154 ~~~~v~Vp~~~h-~~IIGk~G~t~k~LE~ 181 (460)
....|.|.++=| +.|||++|+++|+|..
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 566777887665 6778999999988743
No 106
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=27.36 E-value=1.5e+02 Score=31.42 Aligned_cols=52 Identities=17% Similarity=0.262 Sum_probs=42.8
Q ss_pred ccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHH
Q 012600 162 ASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAI 218 (460)
Q Consensus 162 ~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~i 218 (460)
....--+.|..|.+++.||+.+|+.|.-+. ..+.|+|. +..|+.|...++.+
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG----~~~~i~g~-~~~v~~A~~~l~~l 74 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVARG----EAVRIIGA-RPLVDVATRVLLTL 74 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEeCC----ceEEEEec-hHHHHHHHHHHhHH
Confidence 444556889999999999999999988654 46889996 56999999999944
No 107
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=26.58 E-value=64 Score=31.18 Aligned_cols=35 Identities=31% Similarity=0.321 Sum_probs=28.8
Q ss_pred EEEEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 012600 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (460)
Q Consensus 155 ~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~i 189 (460)
..+..+-..-.|-.||++|.+++.|.++.|-+|+|
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdV 111 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDV 111 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEE
Confidence 45555555668999999999999999999977775
No 108
>PRK11538 ribosome-associated protein; Provisional
Probab=26.41 E-value=3.3e+02 Score=23.75 Aligned_cols=60 Identities=7% Similarity=0.185 Sum_probs=41.1
Q ss_pred HHHHHHHHHHhHHhhhhhcCCCCeEEEeccccCCCCCCCCceEEEEeceecCCchHHHHHHHHHHHHHHHCCCCc
Q 012600 357 VNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 431 (460)
Q Consensus 357 v~~A~~~L~~i~~~i~d~L~~~pf~l~lkGLg~F~~dp~~~rVLya~V~~~d~~~~L~~L~~~L~~~f~~~Gl~~ 431 (460)
+..++++|...+ ...-..+.++|+..|-+ -.+-+.. .+...++.+++.|.+.+.+.|+.+
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 344555555543 23556788899988887 3333333 246789999999999999988764
No 109
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=25.55 E-value=75 Score=25.93 Aligned_cols=36 Identities=19% Similarity=0.324 Sum_probs=20.7
Q ss_pred ChhHHHHHHHHHHHhHHhhhhhcCCCCeEEEeccccCCCC
Q 012600 353 NKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRG 392 (460)
Q Consensus 353 ~eeev~~A~~~L~~i~~~i~d~L~~~pf~l~lkGLg~F~~ 392 (460)
+..++..+ |+.+...+.+.|.... .+.|.|+|.|.-
T Consensus 17 ~~~~v~~v---l~~l~~~i~~~L~~g~-~V~i~g~G~F~~ 52 (90)
T smart00411 17 SKKDAKAA---VDAFLEIITEALKKGE-KVELRGFGTFEV 52 (90)
T ss_pred CHHHHHHH---HHHHHHHHHHHHhCCC-eEEEeCcEEEEE
Confidence 34444444 4444444555554322 688899999953
No 110
>PRK15494 era GTPase Era; Provisional
Probab=24.58 E-value=40 Score=34.88 Aligned_cols=26 Identities=27% Similarity=0.319 Sum_probs=20.9
Q ss_pred eEEEEecccccc-ccccCCCchhHHHH
Q 012600 154 HSLSVEVGASVI-RFIKGKEGSTQKKF 179 (460)
Q Consensus 154 ~~~~v~Vp~~~h-~~IIGk~G~t~k~L 179 (460)
....|.|+++=| +.|||++|.++|+|
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i 299 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEI 299 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHH
Confidence 457778887765 57899999999987
No 111
>COG1159 Era GTPase [General function prediction only]
Probab=24.41 E-value=42 Score=34.67 Aligned_cols=27 Identities=26% Similarity=0.316 Sum_probs=21.3
Q ss_pred CeEEEEecccccc-ccccCCCchhHHHH
Q 012600 153 RHSLSVEVGASVI-RFIKGKEGSTQKKF 179 (460)
Q Consensus 153 ~~~~~v~Vp~~~h-~~IIGk~G~t~k~L 179 (460)
.....+.|+++=+ +.||||+|+++|+|
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~I 255 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKI 255 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHH
Confidence 4456677887654 67899999999988
No 112
>COG0799 Uncharacterized homolog of plant Iojap protein [Function unknown]
Probab=24.36 E-value=3.7e+02 Score=24.10 Aligned_cols=60 Identities=12% Similarity=0.171 Sum_probs=43.5
Q ss_pred HHHHHHHHHHhHHhhhhhcCCCCeEEEeccccCCCCCCCCceEEEEeceecCCchHHHHHHHHHHHHHHHCCCCc
Q 012600 357 VNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 431 (460)
Q Consensus 357 v~~A~~~L~~i~~~i~d~L~~~pf~l~lkGLg~F~~dp~~~rVLya~V~~~d~~~~L~~L~~~L~~~f~~~Gl~~ 431 (460)
+..+.++|...+ ......|.++|+..+.+ ..+.+.-. +...+..+++.|.+.+.++|+.+
T Consensus 7 ~~~i~~alddkK-------AeDIv~lDv~~~s~~tD-----yfVIatg~---s~rhv~Aiad~i~~~~k~~g~~~ 66 (115)
T COG0799 7 LEVIVEALDDKK-------AEDIVVLDVSGKSSLTD-----YFVIATGN---SSRHVKAIADNVKEELKEAGEVP 66 (115)
T ss_pred HHHHHHHHHhcc-------CCCeEEEEccCCccccc-----EEEEEEeC---chHHHHHHHHHHHHHHHHcCCCc
Confidence 344455554443 35777899999999998 44444332 46789999999999999999876
No 113
>PRK00089 era GTPase Era; Reviewed
Probab=23.73 E-value=43 Score=33.24 Aligned_cols=26 Identities=27% Similarity=0.285 Sum_probs=19.9
Q ss_pred eEEEEecccccc-ccccCCCchhHHHH
Q 012600 154 HSLSVEVGASVI-RFIKGKEGSTQKKF 179 (460)
Q Consensus 154 ~~~~v~Vp~~~h-~~IIGk~G~t~k~L 179 (460)
....|.|.++=| +.|||++|+++|+|
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i 252 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKI 252 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHH
Confidence 456667776655 67789999999887
No 114
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=23.12 E-value=92 Score=25.15 Aligned_cols=32 Identities=16% Similarity=0.223 Sum_probs=18.8
Q ss_pred HHHHHHHhHHhhhhhcCCCCeEEEeccccCCCC
Q 012600 360 ATNVLKSISSKVMDALDNRPLFIRLKGLDLMRG 392 (460)
Q Consensus 360 A~~~L~~i~~~i~d~L~~~pf~l~lkGLg~F~~ 392 (460)
|..+|..+...+.+.|... -.+.|.|+|.|.-
T Consensus 20 v~~vl~~~~~~i~~~L~~g-~~V~l~~~G~F~~ 51 (87)
T cd00591 20 AEAAVDAFLDVITEALAKG-EKVELPGFGTFEV 51 (87)
T ss_pred HHHHHHHHHHHHHHHHhCC-CeEEEeCCEEEEE
Confidence 4444444444455555422 2788899999953
No 115
>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=22.92 E-value=72 Score=29.67 Aligned_cols=33 Identities=27% Similarity=0.339 Sum_probs=27.2
Q ss_pred EEeccccccccccCCCchhHHHHHHHhCcEEEc
Q 012600 157 SVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (460)
Q Consensus 157 ~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~i 189 (460)
.|.|-.+-=+.+||++|.++++|-.+||-+-.+
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~v 111 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKV 111 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEE
Confidence 444555667899999999999999999988655
No 116
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=22.57 E-value=40 Score=33.11 Aligned_cols=76 Identities=14% Similarity=0.109 Sum_probs=48.3
Q ss_pred CCCccCCCCeEEEEeccccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhh
Q 012600 145 GEPVPSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAV 223 (460)
Q Consensus 145 ~~~~~~~~~~~~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP~~~~~~~I~ItG~s~e~V~~A~~rI~~iv~e~~ 223 (460)
-.+.++...-.+.+.|..+--+.|||+.|.++..||--++.-+.- ..+..-.|++-- .+=.++=++.+..+.+.+.
T Consensus 82 ~~i~v~~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~-~~g~~~~v~ldv--~~yRerR~e~L~~LA~~~A 157 (208)
T COG1847 82 VTITVSEEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK-IGGKFKRVTLDV--GDYRERRKETLIKLAERAA 157 (208)
T ss_pred eEEEEeecCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh-hcCcceEEEEEh--hhHHHHHHHHHHHHHHHHH
Confidence 344444566677888888889999999999999999998876654 222222333322 2334444555555554443
No 117
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=22.48 E-value=32 Score=34.31 Aligned_cols=35 Identities=26% Similarity=0.273 Sum_probs=26.6
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 012600 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (460)
Q Consensus 156 ~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP 190 (460)
+.|-|-..-=+.+||++|+++++|.++....+..+
T Consensus 53 ~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~ 87 (233)
T COG0092 53 TRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKE 87 (233)
T ss_pred eEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCC
Confidence 34444455568999999999999988877666664
No 118
>PF03536 VRP3: Salmonella virulence-associated 28kDa protein; InterPro: IPR003519 Salmonella typhimurium contains a 90kb plasmid that is associated with virulence. This plasmid encodes at least 6 genes needed by the bacterium for invading host macrophages during infection. These include the 70kDa mkaA protein [], a recognised virulence factor. Deletion studies into the virulence plasmid have shown that an open reading frame encoding a 28kDa protein was needed for successful invasion of the host. This protein, designated mkfA [], VRP4 [] or VirA [] by different groups, is utilised by the microbe upon entry into macrophages, although the exact mechanism is unclear.; PDB: 2Z8P_A 2Z8O_B 2Z8M_B 2Z8N_A 2P1W_A 2Q8Y_A 3I0U_B 3BO6_B.
Probab=22.42 E-value=5.4e+02 Score=25.67 Aligned_cols=80 Identities=15% Similarity=0.223 Sum_probs=43.8
Q ss_pred CcceEEeeccccCChhHHHHHHHHHHHhHHhhhhhcCCCCeEEEeccccCCCCCCCCce-------EEEEeceecCC---
Q 012600 340 KTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKAR-------ILYAPVEEIGD--- 409 (460)
Q Consensus 340 ~~LHLTL~~L~L~~eeev~~A~~~L~~i~~~i~d~L~~~pf~l~lkGLg~F~~dp~~~r-------VLya~V~~~d~--- 409 (460)
.++||.+ .+++|..|.++|..+--. +--+-....++ .+..- ....| .||++++..+.
T Consensus 102 DK~HiSv------~~~~v~~aF~ai~~lL~s--~DSPvDKWKvT--Dm~rv---~~~sRV~~GAQfTLY~kpd~eds~Ys 168 (240)
T PF03536_consen 102 DKFHISV------APEQVPQAFQAISGLLFS--EDSPVDKWKVT--DMSRV---DQQSRVTQGAQFTLYVKPDREDSQYS 168 (240)
T ss_dssp EEEEE-B-------GGGHHHHHHHHHHHHT---TT-S-SEEEEE---TTTC---CTTSCCCSS-SEEEEEE-SSTTS---
T ss_pred ceeEEEe------cHHHhHHHHHHHHHHhhc--CCCcchhhhcc--hhhhc---chhhheeccceEEEEecCccccccCC
Confidence 6899988 478899999998877311 10011222232 22111 11223 48999987543
Q ss_pred ---chHHHHHHHHHHHHHHHCCCCcc
Q 012600 410 ---GDRLLHACQVIIDAFNEAGLVFH 432 (460)
Q Consensus 410 ---~~~L~~L~~~L~~~f~~~Gl~~~ 432 (460)
......+-..|+..|.++|+.+.
T Consensus 169 ~~~l~k~r~fi~~iE~~L~~agi~pg 194 (240)
T PF03536_consen 169 AEYLHKTRQFIESIESELSEAGIQPG 194 (240)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTT--B-
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCC
Confidence 22455677788999999999874
No 119
>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=20.66 E-value=2.6e+02 Score=26.43 Aligned_cols=21 Identities=19% Similarity=0.238 Sum_probs=16.4
Q ss_pred ecCCchHHHHHHHHHHHHHHH
Q 012600 406 EIGDGDRLLHACQVIIDAFNE 426 (460)
Q Consensus 406 ~~d~~~~L~~L~~~L~~~f~~ 426 (460)
+.+....|+.|+..+...|-.
T Consensus 49 p~~~~~~L~~LAa~cV~~~d~ 69 (160)
T PF06299_consen 49 PAGPCPALQALAAACVRAFDP 69 (160)
T ss_pred eCCCCHHHHHHHHHHHHhhhh
Confidence 334568999999999888864
No 120
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=20.20 E-value=70 Score=35.62 Aligned_cols=35 Identities=26% Similarity=0.240 Sum_probs=29.1
Q ss_pred EEEeccccccccccCCCchhHHHHHHHhCcEEEcC
Q 012600 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (460)
Q Consensus 156 ~~v~Vp~~~h~~IIGk~G~t~k~LE~eT~trI~iP 190 (460)
.+|-|-.+-=|.+|||+|++++.|-++||-+-.|-
T Consensus 101 GEViIea~KPGlvigk~g~~~reI~~~tgW~p~iv 135 (637)
T COG1782 101 GEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIV 135 (637)
T ss_pred ceEEEEecCCceEEecCchHHHHHHHHhCCcceee
Confidence 35666677779999999999999999999886653
No 121
>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=20.08 E-value=4.6e+02 Score=22.36 Aligned_cols=46 Identities=13% Similarity=0.184 Sum_probs=34.2
Q ss_pred CCeEEEeccccCCCCCCCCceEEEEeceecCCchHHHHHHHHHHHHHHHCCCCc
Q 012600 378 RPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 431 (460)
Q Consensus 378 ~pf~l~lkGLg~F~~dp~~~rVLya~V~~~d~~~~L~~L~~~L~~~f~~~Gl~~ 431 (460)
....+.++++..+.+ -++-+.. .+...++.+++.|.+.+.+.|+.+
T Consensus 16 dI~vldv~~~~~~~d-----y~VI~Tg---~S~rh~~aia~~v~~~~k~~~~~~ 61 (99)
T TIGR00090 16 DIVVLDVRGKSSIAD-----YFVIASG---TSSRHVKAIADNVEEELKEAGLKP 61 (99)
T ss_pred CEEEEECCCCCcccC-----EEEEEEe---CCHHHHHHHHHHHHHHHHHcCCCc
Confidence 556678888888877 3333333 246789999999999999998865
Done!