Query 012323
Match_columns 466
No_of_seqs 315 out of 968
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 01:25:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012323.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012323hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2814 Transcription coactiva 100.0 4.4E-52 9.5E-57 409.8 16.2 338 12-459 2-345 (345)
2 PLN00108 unknown protein; Prov 100.0 5.7E-48 1.2E-52 375.5 22.8 224 179-461 33-256 (257)
3 PF10469 AKAP7_NLS: AKAP7 2'5' 100.0 1.3E-42 2.7E-47 332.5 21.5 207 182-459 1-209 (209)
4 COG1514 LigT 2'-5' RNA ligase 99.9 1.6E-25 3.4E-30 210.2 16.0 179 240-461 2-180 (180)
5 TIGR02258 2_5_ligase 2'-5' RNA 99.9 1.5E-24 3.3E-29 201.9 16.2 178 240-459 2-179 (179)
6 PRK15124 2'-5' RNA ligase; Pro 99.9 1.2E-24 2.7E-29 203.3 15.3 170 240-460 6-175 (176)
7 PRK13679 hypothetical protein; 99.7 1.3E-15 2.9E-20 141.3 17.4 139 288-460 30-168 (168)
8 PHA02574 57B hypothetical prot 99.6 2.1E-15 4.6E-20 137.4 7.3 109 240-399 10-118 (149)
9 PF13563 2_5_RNA_ligase2: 2'-5 99.3 1.1E-11 2.4E-16 111.3 10.1 129 289-443 21-150 (153)
10 cd02394 vigilin_like_KH K homo 99.3 9.5E-12 2.1E-16 96.6 6.1 60 108-168 2-62 (62)
11 cd02393 PNPase_KH Polynucleoti 99.2 1.8E-11 3.9E-16 95.3 6.7 59 107-168 3-61 (61)
12 PF00013 KH_1: KH domain syndr 99.2 1.2E-11 2.6E-16 95.3 3.6 60 107-167 1-60 (60)
13 PF05213 Corona_NS2A: Coronavi 99.1 1E-09 2.2E-14 103.8 12.1 166 181-456 5-176 (248)
14 cd00105 KH-I K homology RNA-bi 99.0 1.3E-09 2.8E-14 84.4 6.3 59 108-167 2-63 (64)
15 cd02396 PCBP_like_KH K homolog 98.8 8.5E-09 1.8E-13 81.0 6.5 59 108-167 2-64 (65)
16 PF02834 LigT_PEase: LigT like 98.8 3.7E-09 7.9E-14 87.1 3.6 60 287-353 28-87 (87)
17 smart00322 KH K homology RNA-b 98.8 3.3E-08 7.2E-13 76.0 8.1 66 105-171 2-68 (69)
18 PF13014 KH_3: KH domain 98.8 7.9E-09 1.7E-13 74.7 4.2 39 116-154 1-43 (43)
19 cd02395 SF1_like-KH Splicing f 98.7 3.9E-08 8.4E-13 86.8 7.3 59 115-173 15-95 (120)
20 KOG1676 K-homology type RNA bi 98.5 3.1E-07 6.7E-12 98.3 8.4 107 103-210 227-346 (600)
21 KOG0119 Splicing factor 1/bran 98.3 9E-07 2E-11 92.8 6.8 72 105-176 137-233 (554)
22 PRK13763 putative RNA-processi 98.3 1.2E-06 2.5E-11 82.7 6.5 65 106-172 3-70 (180)
23 TIGR03665 arCOG04150 arCOG0415 98.2 1.1E-06 2.3E-11 82.4 5.0 61 110-172 2-64 (172)
24 PRK13763 putative RNA-processi 98.0 8E-06 1.7E-10 77.1 5.8 54 115-173 104-157 (180)
25 TIGR03665 arCOG04150 arCOG0415 98.0 6E-06 1.3E-10 77.3 4.4 54 115-173 98-151 (172)
26 COG5176 MSL5 Splicing factor ( 98.0 1.2E-05 2.6E-10 76.3 5.6 77 97-173 139-221 (269)
27 KOG2193 IGF-II mRNA-binding pr 97.9 8.5E-06 1.8E-10 84.1 4.6 92 105-202 198-296 (584)
28 KOG2191 RNA-binding protein NO 97.9 0.00016 3.4E-09 73.0 13.0 107 103-210 36-160 (402)
29 KOG2208 Vigilin [Lipid transpo 97.8 3.1E-05 6.8E-10 87.5 7.1 104 104-211 345-449 (753)
30 TIGR02696 pppGpp_PNP guanosine 97.8 3.7E-05 8.1E-10 85.7 7.0 65 106-173 578-642 (719)
31 KOG1588 RNA-binding protein Sa 97.6 0.00014 3E-09 71.7 7.3 70 105-176 91-187 (259)
32 TIGR03591 polynuc_phos polyrib 97.6 7.5E-05 1.6E-09 83.8 6.0 65 106-173 551-615 (684)
33 KOG1676 K-homology type RNA bi 97.5 0.00013 2.8E-09 78.6 5.6 111 101-212 49-169 (600)
34 KOG2193 IGF-II mRNA-binding pr 97.4 0.00013 2.9E-09 75.5 4.5 65 111-176 285-355 (584)
35 KOG2113 Predicted RNA binding 97.3 0.0003 6.4E-09 70.6 5.1 66 103-169 23-88 (394)
36 PRK04163 exosome complex RNA-b 97.3 0.00048 1E-08 67.7 6.3 64 107-173 146-209 (235)
37 KOG2191 RNA-binding protein NO 97.2 0.00073 1.6E-08 68.3 6.6 67 106-173 132-204 (402)
38 COG1094 Predicted RNA-binding 97.2 0.00089 1.9E-08 63.5 6.6 67 104-172 6-76 (194)
39 KOG2190 PolyC-binding proteins 97.1 0.0015 3.3E-08 70.5 8.7 67 106-173 138-208 (485)
40 PLN00207 polyribonucleotide nu 97.1 0.00058 1.3E-08 78.0 5.1 65 106-173 685-750 (891)
41 KOG2192 PolyC-binding hnRNP-K 97.1 0.0014 3E-08 64.6 6.9 68 105-173 314-384 (390)
42 COG1185 Pnp Polyribonucleotide 97.0 0.0012 2.5E-08 72.8 6.2 68 106-176 552-619 (692)
43 PF02834 LigT_PEase: LigT like 96.7 0.0014 3.1E-08 53.7 3.4 76 362-451 8-87 (87)
44 PRK11824 polynucleotide phosph 96.7 0.0015 3.2E-08 73.7 4.4 64 107-173 555-618 (693)
45 TIGR03319 YmdA_YtgF conserved 96.6 0.0042 9.2E-08 67.7 6.9 69 103-173 201-270 (514)
46 PF09749 HVSL: Uncharacterised 96.6 0.02 4.4E-07 56.3 10.9 103 290-401 86-190 (239)
47 KOG0336 ATP-dependent RNA heli 96.5 0.002 4.3E-08 67.3 3.8 70 104-174 45-114 (629)
48 PRK00106 hypothetical protein; 96.5 0.0053 1.2E-07 67.0 6.9 69 103-173 222-291 (535)
49 PRK12704 phosphodiesterase; Pr 96.5 0.0053 1.1E-07 67.1 6.7 69 103-173 207-276 (520)
50 COG1094 Predicted RNA-binding 96.3 0.0064 1.4E-07 57.8 5.5 54 115-173 111-164 (194)
51 PF07823 CPDase: Cyclic phosph 95.8 0.066 1.4E-06 51.2 10.0 137 295-459 40-196 (196)
52 COG1097 RRP4 RNA-binding prote 95.4 0.031 6.8E-07 54.8 6.0 63 108-173 148-210 (239)
53 cd02134 NusA_KH NusA_K homolog 95.4 0.022 4.7E-07 44.3 3.9 37 105-141 24-60 (61)
54 KOG2814 Transcription coactiva 95.3 0.0012 2.6E-08 67.0 -4.1 152 292-457 128-282 (345)
55 PRK12705 hypothetical protein; 95.2 0.024 5.1E-07 61.7 5.0 69 103-173 195-264 (508)
56 KOG2279 Kinase anchor protein 93.9 0.045 9.7E-07 59.0 3.4 100 104-208 66-166 (608)
57 KOG2192 PolyC-binding hnRNP-K 93.8 0.18 3.9E-06 50.1 7.0 69 104-173 46-115 (390)
58 KOG2190 PolyC-binding proteins 93.2 0.13 2.9E-06 55.7 5.5 102 108-210 45-166 (485)
59 KOG1067 Predicted RNA-binding 93.0 0.085 1.8E-06 57.2 3.6 63 107-173 598-660 (760)
60 TIGR03223 Phn_opern_protn puta 92.5 1.8 3.8E-05 42.6 11.7 143 292-461 56-228 (228)
61 KOG2208 Vigilin [Lipid transpo 92.3 0.087 1.9E-06 60.1 2.8 40 104-143 707-746 (753)
62 PF14611 SLS: Mitochondrial in 89.0 2 4.4E-05 41.0 8.5 73 108-190 28-100 (210)
63 COG1855 ATPase (PilT family) [ 86.8 0.41 8.8E-06 51.3 2.3 42 105-146 485-526 (604)
64 PRK02821 hypothetical protein; 86.1 0.78 1.7E-05 37.6 3.1 32 104-135 29-60 (77)
65 COG1837 Predicted RNA-binding 85.7 0.79 1.7E-05 37.4 3.0 31 103-133 27-57 (76)
66 KOG3273 Predicted RNA-binding 85.6 0.51 1.1E-05 45.2 2.1 54 115-173 178-231 (252)
67 KOG2113 Predicted RNA binding 85.5 0.73 1.6E-05 46.9 3.2 138 6-171 42-181 (394)
68 PRK00468 hypothetical protein; 85.3 0.86 1.9E-05 37.1 3.0 30 104-133 28-57 (75)
69 COG5166 Uncharacterized conser 84.7 1.3 2.8E-05 48.0 4.8 42 102-143 445-486 (657)
70 cd02409 KH-II KH-II (K homolo 83.8 1.5 3.3E-05 33.3 3.7 34 106-139 25-58 (68)
71 PRK08406 transcription elongat 83.6 1.1 2.3E-05 40.8 3.2 38 105-142 98-135 (140)
72 PRK13764 ATPase; Provisional 82.7 0.9 2E-05 50.7 2.8 43 104-146 479-521 (602)
73 PF13083 KH_4: KH domain; PDB: 82.5 0.66 1.4E-05 37.0 1.3 34 103-136 26-59 (73)
74 PRK01064 hypothetical protein; 81.1 1.8 4E-05 35.4 3.4 31 104-134 28-58 (78)
75 PHA02977 hypothetical protein; 78.9 10 0.00022 34.8 7.6 94 295-402 71-174 (201)
76 KOG3102 Uncharacterized conser 78.2 7.8 0.00017 37.7 7.1 99 291-400 119-218 (269)
77 TIGR01952 nusA_arch NusA famil 76.5 2.2 4.7E-05 38.9 2.7 39 104-142 98-136 (141)
78 cd02414 jag_KH jag_K homology 74.2 3 6.5E-05 33.6 2.8 35 107-141 25-59 (77)
79 PRK08406 transcription elongat 73.9 3.6 7.9E-05 37.4 3.5 37 106-142 32-68 (140)
80 PF07650 KH_2: KH domain syndr 73.9 1.7 3.8E-05 34.9 1.3 36 105-140 24-59 (78)
81 PF10469 AKAP7_NLS: AKAP7 2'5' 73.7 0.7 1.5E-05 44.2 -1.3 25 239-263 1-25 (209)
82 PF13184 KH_5: NusA-like KH do 72.5 3.2 6.9E-05 33.2 2.5 25 117-141 19-44 (69)
83 KOG2874 rRNA processing protei 68.0 7.9 0.00017 39.1 4.6 48 114-166 157-204 (356)
84 cd02413 40S_S3_KH K homology R 64.1 5.2 0.00011 32.9 2.2 37 107-143 31-67 (81)
85 TIGR01953 NusA transcription t 63.3 7.4 0.00016 40.6 3.6 39 105-143 300-338 (341)
86 KOG2279 Kinase anchor protein 63.0 4.7 0.0001 44.1 2.1 67 102-169 136-205 (608)
87 PRK12328 nusA transcription el 62.6 7.7 0.00017 40.9 3.6 42 105-146 307-348 (374)
88 TIGR01952 nusA_arch NusA famil 59.1 12 0.00025 34.2 3.7 35 107-141 34-68 (141)
89 PLN00108 unknown protein; Prov 58.6 2.1 4.7E-05 42.7 -1.2 29 235-263 32-61 (257)
90 COG0195 NusA Transcription elo 56.5 11 0.00023 36.1 3.2 37 107-143 143-179 (190)
91 PRK12327 nusA transcription el 55.2 13 0.00028 39.2 3.7 40 105-144 302-341 (362)
92 PRK06418 transcription elongat 53.1 15 0.00033 34.4 3.5 33 108-141 63-95 (166)
93 PRK09202 nusA transcription el 53.1 12 0.00025 40.8 3.2 39 105-143 301-339 (470)
94 PF08302 tRNA_lig_CPD: Fungal 52.8 65 0.0014 32.2 8.2 106 291-425 113-227 (257)
95 cd02412 30S_S3_KH K homology R 50.1 14 0.00029 32.0 2.5 32 108-139 63-94 (109)
96 PF07823 CPDase: Cyclic phosph 50.1 16 0.00034 34.9 3.2 42 351-400 4-46 (196)
97 COG5255 Uncharacterized protei 45.8 26 0.00056 34.0 3.8 108 283-403 71-189 (239)
98 COG1702 PhoH Phosphate starvat 45.1 51 0.0011 34.4 6.2 55 114-173 23-79 (348)
99 PRK12329 nusA transcription el 44.4 22 0.00048 38.3 3.5 39 105-143 334-372 (449)
100 PF00352 TBP: Transcription fa 42.5 55 0.0012 26.8 4.9 35 136-173 49-84 (86)
101 TIGR00436 era GTP-binding prot 42.0 29 0.00063 34.3 3.8 29 106-134 221-250 (270)
102 PRK15494 era GTPase Era; Provi 33.7 29 0.00063 35.9 2.4 36 106-141 273-317 (339)
103 cd02410 archeal_CPSF_KH The ar 33.6 43 0.00094 30.7 3.2 34 108-141 78-111 (145)
104 COG0799 Uncharacterized homolo 33.3 2.1E+02 0.0045 25.3 7.3 61 308-383 6-66 (115)
105 cd02411 archeal_30S_S3_KH K ho 32.7 41 0.00089 27.6 2.7 31 108-138 40-70 (85)
106 PRK00089 era GTPase Era; Revie 32.4 33 0.00071 34.2 2.5 36 106-141 226-270 (292)
107 COG0195 NusA Transcription elo 31.8 44 0.00095 32.0 3.1 36 106-141 76-111 (190)
108 PF09749 HVSL: Uncharacterised 31.3 49 0.0011 32.4 3.4 69 240-321 141-210 (239)
109 COG1782 Predicted metal-depend 31.2 37 0.00081 37.3 2.7 45 89-141 90-134 (637)
110 COG0092 RpsC Ribosomal protein 30.5 40 0.00088 33.3 2.6 37 106-142 51-87 (233)
111 PRK09256 hypothetical protein; 29.7 1.1E+02 0.0024 27.8 5.1 54 121-176 23-100 (138)
112 PRK11538 ribosome-associated p 28.3 2.9E+02 0.0063 23.8 7.3 60 309-383 7-66 (105)
113 PF06299 DUF1045: Protein of u 28.1 2E+02 0.0043 26.9 6.6 79 356-442 47-151 (160)
114 KOG3429 Predicted peptidyl-tRN 27.6 87 0.0019 29.4 4.1 56 120-177 49-129 (172)
115 PF00472 RF-1: RF-1 domain; I 27.4 85 0.0018 27.3 3.9 48 121-174 22-73 (113)
116 COG1159 Era GTPase [General fu 24.6 40 0.00086 34.6 1.4 27 105-131 228-255 (298)
117 PRK10334 mechanosensitive chan 23.4 3.5E+02 0.0076 27.4 8.0 83 293-383 185-268 (286)
118 TIGR00090 iojap_ybeB iojap-lik 22.0 4.2E+02 0.0091 22.4 7.1 46 330-383 16-61 (99)
119 KOG4369 RTK signaling protein 21.4 35 0.00077 40.9 0.4 64 109-173 1343-1410(2131)
120 smart00411 BHL bacterial (prok 21.1 1E+02 0.0022 24.9 3.1 35 305-343 17-51 (90)
121 TIGR00637 ModE_repress ModE mo 20.5 2.9E+02 0.0062 23.4 5.7 62 126-191 35-98 (99)
122 cd00591 HU_IHF Integration hos 20.2 1.2E+02 0.0025 24.4 3.2 35 305-343 16-50 (87)
123 PF10105 DUF2344: Uncharacteri 20.0 1.2E+02 0.0026 28.8 3.7 31 366-398 18-48 (187)
No 1
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=100.00 E-value=4.4e-52 Score=409.81 Aligned_cols=338 Identities=36% Similarity=0.548 Sum_probs=292.7
Q ss_pred ccccccccCCceeecccccccccccccccccCCCCCceEEe-eecCCCcccccccceeeeeecccccccccCcccccccc
Q 012323 12 YGDKKQKIINPVWRPVSTQASVNEESLVKDVSEDGSQIQEM-HCSTSSNVSDAQLGVEVAEAVNEGTDLTLSSSVSLDDI 90 (466)
Q Consensus 12 ~~~~~~k~~~~~wrp~~t~a~~~~~~~~~~~~~~~~~~~e~-~~~~~~~~~~~~~~~~~~~~~~e~~~~~~s~~~~~~~~ 90 (466)
+.+++++..|.+|+|++|+.++.. .+++...|++ .|+++...+.+ +. |+.
T Consensus 2 ~~~~~~~~~n~~~~~~~~~t~~~~-------~~~~~e~~~~~~c~d~p~~~~d------------v~----------~~~ 52 (345)
T KOG2814|consen 2 YRKTRYNLVNDVSFDLNTDTTFAD-------MSEEFEAQTSAECVDMPGDTVD------------VE----------DDA 52 (345)
T ss_pred cchhhhhhhhhcccCccccccccc-------CchhhHHHhHhhcccCCCChHH------------hh----------hcc
Confidence 467889999999999999988763 3345556666 67776643222 00 000
Q ss_pred cccccCCCCCCCCCCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHH
Q 012323 91 KDETLEGEPVPSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQA 169 (466)
Q Consensus 91 ~~~~~~~~~~~s~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~~~~~v~~A~~~I~~ 169 (466)
-..+|+.++.|+++|+++|||++|.|+++||+||+|+|.+|++++ .+.|+|+|.++.+|.+|.+||..
T Consensus 53 -----------~~~~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~ 121 (345)
T KOG2814|consen 53 -----------GAKDFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAK 121 (345)
T ss_pred -----------ccccchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHH
Confidence 112789999999999999999999999999999999999999995 78899999999999999999999
Q ss_pred HHHHhhhCCCCcceEEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCCCCCchHHHhhhhcccceeeeeecc
Q 012323 170 IIAEAVESPSLDYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNI 249 (466)
Q Consensus 170 i~~~~~~~~k~~~ThFIsIPl~~hp~I~~~~~~f~~~Il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rp~~fva~~~~~ 249 (466)
++++.++ +++.|||+.+|++ ...++++|..|+.-.+-.
T Consensus 122 ~ids~r~--s~p~thflal~ln-e~eVqe~f~~fke~~~~~--------------------------------------- 159 (345)
T KOG2814|consen 122 LIDSDRK--SFPITHFLALPLN-EHEVQEGFLAFKELKPFI--------------------------------------- 159 (345)
T ss_pred HHHhhhh--cCchhhhhhhhcc-hHHHHHHHHHHHhhhhhH---------------------------------------
Confidence 9999887 7899999999998 688999999998422211
Q ss_pred CCCccccccccccccccccccccCCCCCCCCCCCCCccccCCCcceEEeeccccCCHHHHHHHHHHHHHhhHHhhhhcCC
Q 012323 250 GDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDN 329 (466)
Q Consensus 250 ~~~~~~vk~~~~~i~~~~~~~~~~r~~~~~~~gi~~~~~v~p~~LHLTL~fLgl~~~eei~~a~~~L~~i~~~i~~~L~~ 329 (466)
+ .+-+.|++.++|++|.+|||||+|+.+++++++++|+++|+.+.+++...+..
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 01256899999999999999999999999999999999999998888888889
Q ss_pred CCeEEEEcccccCCCCCCCceEEEEeeeccCChhHHHHHH-HHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccC
Q 012323 330 RPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHAC-QVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKG 408 (466)
Q Consensus 330 ~pf~L~l~GLg~F~~dp~~~rVLya~V~~~~~~~~L~~L~-~~L~~~f~~~Gl~~e~d~~r~fkPHiTLar~~~~~~~~~ 408 (466)
.|+.+.++|+.+|+++|..++||||+|.+.+....|+..+ +.|..+|..+|+... +.++.++|+||||++|++.++.
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 9999999999999999999999999999988888899999 999999999999985 4889999999999999876432
Q ss_pred C---CccccccHHHHHHHhCCCccccEEecEEEEEeeeccCCCCceeEEEEEeC
Q 012323 409 T---RRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPF 459 (466)
Q Consensus 409 ~---~~~~~fda~~il~~~~~~~fG~~~V~eI~Ls~~~~~~~~g~Y~~l~si~L 459 (466)
. +....||+++|++.|+++.||++.+.++|||.+...+.+|||.+++++||
T Consensus 292 ~g~~K~~~~Fdar~ilk~fg~f~fg~~~~~eih~~~~~~~d~ng~y~~~gsi~f 345 (345)
T KOG2814|consen 292 PGLVKESESFDAREILKAFGQFLFGELKLQEIHLSVRFAADQNGNYNECGSIPF 345 (345)
T ss_pred cchhhHhhhccHHHHHHHHhhHhHhhcccceeeeeeeeccccccchhhhcCCCC
Confidence 1 45678999999999999999999999999999999889999999999987
No 2
>PLN00108 unknown protein; Provisional
Probab=100.00 E-value=5.7e-48 Score=375.48 Aligned_cols=224 Identities=56% Similarity=0.966 Sum_probs=199.3
Q ss_pred CCcceEEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCCCCCchHHHhhhhcccceeeeeeccCCCcccccc
Q 012323 179 SLDYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKV 258 (466)
Q Consensus 179 k~~~ThFIsIPl~~hp~I~~~~~~f~~~Il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rp~~fva~~~~~~~~~~~vk~ 258 (466)
|.+||||||||++++|.|++++..|++.||+..+ ..|.-
T Consensus 33 ~~~~THFlavPL~~~p~i~~~~~~Fk~~Vl~~~~------------------------~~~~~----------------- 71 (257)
T PLN00108 33 REVFTHFVSLPLAIYPDLKKNIEAFQNSVLGNND------------------------KDPLK----------------- 71 (257)
T ss_pred CCCCCeEEEEEcCCCHHHHHHHHHHHHHHHhccc------------------------ccccc-----------------
Confidence 5689999999996589999999999999997521 00000
Q ss_pred ccccccccccccccCCCCCCCCCCCCCccccCCCcceEEeeccccCCHHHHHHHHHHHHHhhHHhhhhcCCCCeEEEEcc
Q 012323 259 DRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKG 338 (466)
Q Consensus 259 ~~~~i~~~~~~~~~~r~~~~~~~gi~~~~~v~p~~LHLTL~fLgl~~~eei~~a~~~L~~i~~~i~~~L~~~pf~L~l~G 338 (466)
-+. .++++||++++|++|.+|||||+||.|.+++++++|.++|++|...+.+++.++|+.|+|+|
T Consensus 72 --------------f~~-~l~~~gid~siF~~p~~LHLTLgmL~L~~~eev~kA~~~L~s~~~~i~~~l~~~pl~I~lkG 136 (257)
T PLN00108 72 --------------FQS-TLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNILKSICSNVRQALKDRPVFIRLRG 136 (257)
T ss_pred --------------ccc-cccccCCCHHHcCCCCceEEEEEEEEcCCHHHHHHHHHHHHHHHHHHHHhhCCCCeEEEEEe
Confidence 011 23478999999999999999999999999999999999999999888899999999999999
Q ss_pred cccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHH
Q 012323 339 LDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDAR 418 (466)
Q Consensus 339 Lg~F~~dp~~~rVLya~V~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fkPHiTLar~~~~~~~~~~~~~~~fda~ 418 (466)
|++|++||++++||||+|++.+..++|+.+|+.|.+.|.++||...+ .+++++||+||||++|++.+. +++.+|||+
T Consensus 137 L~~Mnddps~~~VLYA~Ve~~~~~~rLq~~ad~i~~~F~~aGL~~~d-~~~~vKLH~TlmNt~~rk~k~--~k~~sFDA~ 213 (257)
T PLN00108 137 LDCMNGSLDKTRVLYAPVEEVGHEGRLLNACHVIIDAFENAGFAGKD-AKSRLKLHATLMNASYRKDKS--KKMDTFDAR 213 (257)
T ss_pred ehhcCCCcccceEEEEeccccCchhHHHHHHHHHHHHHHHcCCcccc-cCcceeeEeEEechhhhhccc--CccccccHH
Confidence 99999999999999999998777789999999999999999999743 457999999999999976532 467899999
Q ss_pred HHHHHhCCCccccEEecEEEEEeeeccCCCCceeEEEEEeCCC
Q 012323 419 DIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 461 (466)
Q Consensus 419 ~il~~~~~~~fG~~~V~eI~Ls~~~~~~~~g~Y~~l~si~L~~ 461 (466)
+||+.|++++||.+.|++||||+++..+.+|||+|+++++|++
T Consensus 214 ~Il~~f~d~~FG~~~i~~vhls~r~s~~~dGyY~~~~sl~~~~ 256 (257)
T PLN00108 214 EIHKEFENKDWGTYLIREAHISQRYKYDPNGYFHCCASLPFPH 256 (257)
T ss_pred HHHHhccCcccceEEecEEEEEeecccCCCCCEEEEEEeecCC
Confidence 9999999999999999999999999988899999999999986
No 3
>PF10469 AKAP7_NLS: AKAP7 2'5' RNA ligase-like domain; InterPro: IPR019510 This entry represents the N-terminal nuclear localisation signal-containing domain found in the cyclic AMP-dependent protein kinase A (PKA) anchor protein, AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes []. This domain carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein []. Binding to the regulatory subunits RI and RII of PKA is mediated via the RI-RII subunit-binding domain at the C terminus.
Probab=100.00 E-value=1.3e-42 Score=332.48 Aligned_cols=207 Identities=37% Similarity=0.627 Sum_probs=182.1
Q ss_pred ceEEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCCCCCchHHHhhhhcccceeeeeeccCCCccccccccc
Q 012323 182 YSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKVDRT 261 (466)
Q Consensus 182 ~ThFIsIPl~~hp~I~~~~~~f~~~Il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rp~~fva~~~~~~~~~~~vk~~~~ 261 (466)
||||||||++ +|.|+..+..|++.|+..
T Consensus 1 pthFl~ipl~-~~~i~~~~~~fq~~v~~~--------------------------------------------------- 28 (209)
T PF10469_consen 1 PTHFLCIPLN-SPEIQEKFKEFQNEVLSK--------------------------------------------------- 28 (209)
T ss_pred CCeEEEEECC-CHHHHHHHHHHHHHHHhh---------------------------------------------------
Confidence 6999999995 899999999999999854
Q ss_pred cccccccccccCCCCCCCCCCCCCccccCCCcceEEeeccccCCHHHHHHHHHHHHHhhHHhhhhcCC-CCeEEEEcccc
Q 012323 262 SIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDN-RPLFIRLKGLD 340 (466)
Q Consensus 262 ~i~~~~~~~~~~r~~~~~~~gi~~~~~v~p~~LHLTL~fLgl~~~eei~~a~~~L~~i~~~i~~~L~~-~pf~L~l~GLg 340 (466)
++|+++++|++|.+|||||+||+|.+++++++|+++|+++.+.+.+.+.. +|+.|+|+||+
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 23678889999999999999999999999999999999999888877654 99999999999
Q ss_pred cCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHHHH
Q 012323 341 LMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDI 420 (466)
Q Consensus 341 ~F~~dp~~~rVLya~V~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fkPHiTLar~~~~~~~~~~~~~~~fda~~i 420 (466)
+|++||+++|||||+|.+.++...|+++++.|++.|.++||...++.+.+|+||+||||++++.... .+...+||++++
T Consensus 91 ~f~~d~~~~~VLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~~~~~~~~H~Tl~n~~~~~~~~-~~~~~~~d~~~~ 169 (209)
T PF10469_consen 91 YFNDDPSKARVLYAKVSEDSNSERLQELANKLRERFQEAGLLVTDDRRFSFKPHITLMNTSYRKKKK-RRQGNKFDASEL 169 (209)
T ss_pred hhCCCCCcceEEEEcccccchHHHHHHHHHHHHHHHHHcCCccccccCCCcceEEEEEecccccccc-ccccCccccHHH
Confidence 9999999999999999986667999999999999999999999642223489999999999852111 112267999999
Q ss_pred HHHhCCCccccEEecEEEEEeeeccCC-CCceeEEEEEeC
Q 012323 421 FKQFGSKEWGEYLIKEAHLSQRFVYDE-SGFYHCCASIPF 459 (466)
Q Consensus 421 l~~~~~~~fG~~~V~eI~Ls~~~~~~~-~g~Y~~l~si~L 459 (466)
++.|.+++||.+.|++|+||+|+..+. +|||+++++++|
T Consensus 170 ~~~~~~~~fG~~~v~~i~Lc~m~~~~~~dg~Y~~~~~i~l 209 (209)
T PF10469_consen 170 LEKYKDFDFGEQPVEEIQLCSMGSTKPSDGYYQCIASIPL 209 (209)
T ss_pred HHHcCCCccceEEECEEEEEeCCCCCCCCCeEEEEEEecC
Confidence 999999999999999999999977655 999999999987
No 4
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=1.6e-25 Score=210.19 Aligned_cols=179 Identities=19% Similarity=0.321 Sum_probs=150.2
Q ss_pred cceeeeeeccCCCccccccccccccccccccccCCCCCCCCCCCCCccccCCCcceEEeeccccCCHHHHHHHHHHHHHh
Q 012323 240 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 319 (466)
Q Consensus 240 ~~fva~~~~~~~~~~~vk~~~~~i~~~~~~~~~~r~~~~~~~gi~~~~~v~p~~LHLTL~fLgl~~~eei~~a~~~L~~i 319 (466)
-+|+||.+ .+++.+++...+..+. ..+ ...|++++++||||.|||+++++.++.++++|.++
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 47999987 4556666766665431 111 45699999999999999999999999999999988
Q ss_pred hHHhhhhcCCCCeEEEEcccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeee
Q 012323 320 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 399 (466)
Q Consensus 320 ~~~i~~~L~~~pf~L~l~GLg~F~~dp~~~rVLya~V~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fkPHiTLar 399 (466)
.. .. ||.|+|+|+|.|++ +.++||+|+++.+ .+.|.+|++.|...+..+||..+ .++|.||+||+|
T Consensus 64 ~~------~~-~f~i~l~g~g~F~~-~~~~rvi~~~v~~---~~~L~~L~~~l~~~~~~~g~~~~---~r~F~PHvTl~r 129 (180)
T COG1514 64 AA------PE-PFPITLDGAGSFPN-PRRPRVIWVGVEE---TEELRALAEELERALARLGLRPE---ERPFVPHVTLAR 129 (180)
T ss_pred hc------CC-ceEEEEeeEcccCC-CCCCcEEEEcCCC---cHHHHHHHHHHHHHHHhcCCCCC---CCCcCCCEEEEe
Confidence 52 12 99999999999998 8999999999985 57899999999999999999986 699999999999
Q ss_pred ecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeeccCCCCceeEEEEEeCCC
Q 012323 400 IRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 461 (466)
Q Consensus 400 ~~~~~~~~~~~~~~~fda~~il~~~~~~~fG~~~V~eI~Ls~~~~~~~~g~Y~~l~si~L~~ 461 (466)
.+. +. ...+++..+.+..||++.|+++.|.++..+..++.|.++.+|+|.+
T Consensus 130 ~k~-~~----------~~~~~~~~~~~~~~~~~~vd~~~L~~S~l~~~gp~Y~~~~~~~L~~ 180 (180)
T COG1514 130 VKS-KD----------KLVEALGEFKNVEFGEMEVDRFSLYSSTLTPGGPIYETLKEFPLSG 180 (180)
T ss_pred ecc-cc----------hhhhhhhhhccccccceEeeEEEEEEEeeCCCCCEEEEEEEEecCC
Confidence 875 11 1236778889999999999999999888877899999999999975
No 5
>TIGR02258 2_5_ligase 2'-5' RNA ligase. This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles.
Probab=99.92 E-value=1.5e-24 Score=201.93 Aligned_cols=178 Identities=19% Similarity=0.357 Sum_probs=146.5
Q ss_pred cceeeeeeccCCCccccccccccccccccccccCCCCCCCCCCCCCccccCCCcceEEeeccccCCHHHHHHHHHHHHHh
Q 012323 240 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 319 (466)
Q Consensus 240 ~~fva~~~~~~~~~~~vk~~~~~i~~~~~~~~~~r~~~~~~~gi~~~~~v~p~~LHLTL~fLgl~~~eei~~a~~~L~~i 319 (466)
.+|+||.++.+ +.+++...+..+. + ......|+++++|||||.|+|++++++++.+.++|.++
T Consensus 2 R~FiAl~~p~~-~~~~l~~~~~~l~---------~-------~~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~ 64 (179)
T TIGR02258 2 RLFIAIDLPPE-IREQLSRIQRKLK---------S-------PLDGIKWVPPENLHITLKFLGEVDEEQVEELEDALAKI 64 (179)
T ss_pred eEEEEecCCHH-HHHHHHHHHHHhh---------c-------cCCCcEECChHHCEEEEEEccCCCHHHHHHHHHHHHHh
Confidence 47999998753 7777877776541 0 01234699999999999999999999999998888776
Q ss_pred hHHhhhhcCCCCeEEEEcccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeee
Q 012323 320 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 399 (466)
Q Consensus 320 ~~~i~~~L~~~pf~L~l~GLg~F~~dp~~~rVLya~V~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fkPHiTLar 399 (466)
. .++|.++|+|+|+|++ +.+++|||+++.+ ...|.+|++.|.+.+...|+..+ .++|+|||||+|
T Consensus 65 ~--------~~~f~l~l~~~~~F~~-~~~~~vl~l~~~~---~~~L~~L~~~l~~~~~~~g~~~~---~~~f~PHiTlar 129 (179)
T TIGR02258 65 A--------EPPFTLKLEGIGVFGN-PKRPRVLWAGVEQ---SEELTQLHADLERELAKLGFSKE---ERPFTPHITLAR 129 (179)
T ss_pred c--------CCCeEEEEeeeeeCCC-CCCCeEEEEeeCC---CHHHHHHHHHHHHHHHHcCCCCC---CCCcCCCEEEEE
Confidence 3 3679999999999987 7788999999985 24899999999999999999864 689999999998
Q ss_pred ecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeeccCCCCceeEEEEEeC
Q 012323 400 IRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPF 459 (466)
Q Consensus 400 ~~~~~~~~~~~~~~~fda~~il~~~~~~~fG~~~V~eI~Ls~~~~~~~~g~Y~~l~si~L 459 (466)
..... .++.++++.+..+.++.+.|++|+|+++.....++.|.++++|+|
T Consensus 130 ~~~~~----------~~~~~~~~~~~~~~~~~~~v~~i~L~~S~~~~~g~~Y~~l~~~~l 179 (179)
T TIGR02258 130 KKSGK----------PGVPEFLQEFANEEFGSFHVDEFHLYSSTLTPGGPIYEPLARFQL 179 (179)
T ss_pred ecCCc----------HhHHHHHHHhCCCCCCceEeeEEEEEEeeccCCCCcceEEEEEcC
Confidence 65321 134467778887888999999999999988777899999999997
No 6
>PRK15124 2'-5' RNA ligase; Provisional
Probab=99.92 E-value=1.2e-24 Score=203.30 Aligned_cols=170 Identities=13% Similarity=0.146 Sum_probs=134.1
Q ss_pred cceeeeeeccCCCccccccccccccccccccccCCCCCCCCCCCCCccccCCCcceEEeeccccCCHHHHHHHHHHHHHh
Q 012323 240 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 319 (466)
Q Consensus 240 ~~fva~~~~~~~~~~~vk~~~~~i~~~~~~~~~~r~~~~~~~gi~~~~~v~p~~LHLTL~fLgl~~~eei~~a~~~L~~i 319 (466)
-.|+|+.+. +++.+.+...+..+. +.....|++|++|||||.|||.+++++++.+.++|..+
T Consensus 6 RlFiAl~~p-~~~~~~l~~~~~~~~-----------------~~~~~rwv~~~nlHiTL~FlG~v~~~~~~~l~~~l~~~ 67 (176)
T PRK15124 6 RLFFAIDLP-DEIRQQIIHWRATHF-----------------PPEAGRPVAAANLHLTLAFLGEVSAEKQQALSQLAGRI 67 (176)
T ss_pred EEEEEeCCC-HHHHHHHHHHHHHhc-----------------cccCcccccccccEEEEEecCCCCHHHHHHHHHHHHhc
Confidence 579999886 345556666554331 11234699999999999999999999999988888766
Q ss_pred hHHhhhhcCCCCeEEEEcccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeee
Q 012323 320 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 399 (466)
Q Consensus 320 ~~~i~~~L~~~pf~L~l~GLg~F~~dp~~~rVLya~V~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fkPHiTLar 399 (466)
..+||.|+|+|+|+|++ +||||+++++ +...|..|++.|.+++..+|+..+ .|+|+|||||+|
T Consensus 68 --------~~~pF~l~l~~~g~Fp~----prvlwlg~~~--~~~~L~~L~~~l~~~l~~~G~~~e---~r~f~PHiTLaR 130 (176)
T PRK15124 68 --------RQPGFTLTLDDAGQWPR----SRVVWLGMRQ--PPRGLLQLANMLRSQAARSGCYQS---PQPFHPHITLLR 130 (176)
T ss_pred --------ccCCeEEEECcccCcCC----CCEEEEEcCC--CCHHHHHHHHHHHHHHHHcCCCCC---CCCCCCCEeecc
Confidence 35899999999999974 5999999974 357899999999999999999875 699999999999
Q ss_pred ecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeeccCCCCceeEEEEEeCC
Q 012323 400 IRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFP 460 (466)
Q Consensus 400 ~~~~~~~~~~~~~~~fda~~il~~~~~~~fG~~~V~eI~Ls~~~~~~~~g~Y~~l~si~L~ 460 (466)
..... ... . . ..+.| .+.|++|+|+++..+..++.|.++++|+|.
T Consensus 131 ~~~~~------~~~--~-----~--~~~~~-~~~v~~~~L~~S~l~~~g~~Y~~l~~~~L~ 175 (176)
T PRK15124 131 DASRP------VAI--P-----P--PGFNW-SFPVTEFTLYASSFARGRTRYTPLQRWPLT 175 (176)
T ss_pred CCCCc------ccc--c-----C--CCCCC-ceEcCEEEEEEEeccCCCCEEEEEEEEeCC
Confidence 64211 000 0 0 11344 588999999999887788999999999985
No 7
>PRK13679 hypothetical protein; Provisional
Probab=99.68 E-value=1.3e-15 Score=141.32 Aligned_cols=139 Identities=16% Similarity=0.193 Sum_probs=104.9
Q ss_pred ccCCCcceEEeeccccCCHHHHHHHHHHHHHhhHHhhhhcCCCCeEEEEcccccCCCCCCCceEEEEeeeccCChhHHHH
Q 012323 288 FIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLH 367 (466)
Q Consensus 288 ~v~p~~LHLTL~fLgl~~~eei~~a~~~L~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~~rVLya~V~~~~~~~~L~~ 367 (466)
|++| ||||.|+|.+++++++.+.++|+++.. ...||.+++.|+++|++ + .+|||+++.+ ...|.+
T Consensus 30 ~v~p---HITL~f~g~~~~~~~~~l~~~l~~~~~------~~~pf~l~l~~~~~F~~-~--~~vl~l~~~~---~~~L~~ 94 (168)
T PRK13679 30 LIPP---HITLKEPFEISDEQLDSIVEELRAIAS------ETKPFTLHVTKVSSFAP-T--NNVIYFKVEK---TEELEE 94 (168)
T ss_pred cCCC---ceEEecCCCCCHHHHHHHHHHHHHHHh------cCCCEEEEEeccccCCC-C--CCEEEEEccC---CHHHHH
Confidence 6666 999999999999999999998887742 24899999999999975 2 3899999985 468999
Q ss_pred HHHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeeccCC
Q 012323 368 ACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDE 447 (466)
Q Consensus 368 L~~~L~~~f~~~Gl~~e~d~~r~fkPHiTLar~~~~~~~~~~~~~~~fda~~il~~~~~~~fG~~~V~eI~Ls~~~~~~~ 447 (466)
|++.|...+. + .. +.++|.|||||+|..... ..-++.+.++. .++.+ .+.|++|+|..+. .
T Consensus 95 L~~~l~~~~~--~-~~---~~~~f~PHiTlar~~~~~--------~~~~~~~~l~~-~~~~~-~~~v~~i~L~~~~---~ 155 (168)
T PRK13679 95 LHERLHSGDF--Y-GE---AEYAFVPHITIGQGLSDD--------EHEDVLGQLKM-ADVDH-EETIDRFHLLYQL---E 155 (168)
T ss_pred HHHHHHhccc--c-cc---cCCCCCCeEEeeCCCCcH--------HHHHHHHHHhc-CCcce-eEEECeEEEEEEC---C
Confidence 9999987553 1 22 257899999999764321 11123344433 55555 6789999998552 3
Q ss_pred CCceeEEEEEeCC
Q 012323 448 SGFYHCCASIPFP 460 (466)
Q Consensus 448 ~g~Y~~l~si~L~ 460 (466)
++-|..+.++.|+
T Consensus 156 ~~~w~~~~~~~~~ 168 (168)
T PRK13679 156 NGSWTVYETFRLG 168 (168)
T ss_pred CCeEEEEEEeeCC
Confidence 7899999999885
No 8
>PHA02574 57B hypothetical protein; Provisional
Probab=99.59 E-value=2.1e-15 Score=137.37 Aligned_cols=109 Identities=11% Similarity=0.040 Sum_probs=84.6
Q ss_pred cceeeeeeccCCCccccccccccccccccccccCCCCCCCCCCCCCccccCCCcceEEeeccccCCHHHHHHHHHHHHHh
Q 012323 240 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 319 (466)
Q Consensus 240 ~~fva~~~~~~~~~~~vk~~~~~i~~~~~~~~~~r~~~~~~~gi~~~~~v~p~~LHLTL~fLgl~~~eei~~a~~~L~~i 319 (466)
--|||+.++. +..+++...|..+. ...||+++||||||.| ++++++.+..
T Consensus 10 RlF~Al~~~~-~~r~~L~~lq~~l~--------------------~~r~V~~enLHlTL~F----~~~~v~~l~~----- 59 (149)
T PHA02574 10 GTYVAAKFSE-ATLDALERLQRTLR--------------------IPNPVPRDKLHSTIVY----SRVYVPFIPA----- 59 (149)
T ss_pred eEEEEEcCCH-HHHHHHHHHHHhcc--------------------CCcccCHHHCEEEEec----CHHHhHHHhc-----
Confidence 4599998864 56677777765431 1459999999999999 3555554422
Q ss_pred hHHhhhhcCCCCeEEEEcccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeee
Q 012323 320 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 399 (466)
Q Consensus 320 ~~~i~~~L~~~pf~L~l~GLg~F~~dp~~~rVLya~V~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fkPHiTLar 399 (466)
..+||.++++|+|+|++ + ++||||++++ ...|..|++.+++++.. .+ .++|+|||||+|
T Consensus 60 --------~~~~F~l~l~glG~F~~-~-~~rvlWlg~~----~~~L~~L~~~l~~~l~~----~~---~r~F~PHITLaR 118 (149)
T PHA02574 60 --------SGSTEVASSGHLEVWET-Q-DKNALVLVLE----SEYLQCRHKYARALGAT----HD---FDDYTPHITLSY 118 (149)
T ss_pred --------cCCCeEEEeccccccCC-C-CCCEEEEEeC----CHHHHHHHHHHHHHhhc----CC---CCCcCCcEEEee
Confidence 35999999999999964 1 2599999996 47899999999999887 22 468999999998
No 9
>PF13563 2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB: 1IUH_A.
Probab=99.30 E-value=1.1e-11 Score=111.32 Aligned_cols=129 Identities=16% Similarity=0.216 Sum_probs=78.8
Q ss_pred cCCCcceEEeeccccCCHHHHHHHHHHHHHhhHHhhhhcCCCCeEEEEcccccCCCCCCCceEEEEeeeccCChhHHHHH
Q 012323 289 IKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHA 368 (466)
Q Consensus 289 v~p~~LHLTL~fLgl~~~eei~~a~~~L~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~~rVLya~V~~~~~~~~L~~L 368 (466)
.....+||||.+.+..++.. +.+.+.|..+.. ..+||.|+|.|+++|++ +.+|||+.+.. ...|.+|
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 44555999999999987744 555555555532 24889999999999974 22699999965 5899999
Q ss_pred HHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHHHHHHHh-CCCccccEEecEEEEEeee
Q 012323 369 CQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQF-GSKEWGEYLIKEAHLSQRF 443 (466)
Q Consensus 369 ~~~L~~~f~~~Gl~~e~d~~r~fkPHiTLar~~~~~~~~~~~~~~~fda~~il~~~-~~~~fG~~~V~eI~Ls~~~ 443 (466)
++.|.+.|...|...+. .++|.|||||++...... +..+++.+ ....-..+.|++|.|.+..
T Consensus 88 ~~~l~~~~~~~~~~~~~--~~~~~PHiTia~~~~~~~-----------~~~~~~~~~~~~~~~~~~v~~l~L~~~~ 150 (153)
T PF13563_consen 88 HRALREALRPFGFKQDS--YRPFRPHITIARRLSPKQ-----------AAEAIEKLQSEFPPISFTVDELALVRSD 150 (153)
T ss_dssp HHHHHHHHHHHHGGGGG--GS----EEEEEEESS----------------------------EEEEE-EEEEEEEE
T ss_pred HHHHHHHHHHcCCcccc--CCCcceEEEEeccCCcch-----------hHHHHHHHhCcCCCcEEEEeEEEEEEEC
Confidence 99999999999887752 389999999999754321 01334444 2222346899999998764
No 10
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.26 E-value=9.5e-12 Score=96.56 Aligned_cols=60 Identities=42% Similarity=0.612 Sum_probs=55.0
Q ss_pred EEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHH
Q 012323 108 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQ 168 (466)
Q Consensus 108 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~~~~~v~~A~~~I~ 168 (466)
.++.||+.+|++|||++|+++++|+++|||+|+||..+. ++.|+|+|+ .++|..|+++|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP-KENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC-HHHHHHHHHHhC
Confidence 578999999999999999999999999999999998654 678999998 789999999873
No 11
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.24 E-value=1.8e-11 Score=95.34 Aligned_cols=59 Identities=27% Similarity=0.402 Sum_probs=54.4
Q ss_pred eEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHH
Q 012323 107 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQ 168 (466)
Q Consensus 107 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~ 168 (466)
...+.||++++++|||++|+++++|+++|||+|.|+. ++.|.|+|.+++++..|++.|+
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---CCEEEEEeCCHHHHHHHHHHhC
Confidence 4579999999999999999999999999999999997 4679999987899999999873
No 12
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.19 E-value=1.2e-11 Score=95.32 Aligned_cols=60 Identities=40% Similarity=0.598 Sum_probs=54.0
Q ss_pred eEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHH
Q 012323 107 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKI 167 (466)
Q Consensus 107 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I 167 (466)
+..|.||..+|++|||++|.++++||++|||+|+||..++...|+|+| +.++|.+|++.|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G-~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISG-SPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEE-SHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEe-CHHHHHHHHhhC
Confidence 468999999999999999999999999999999999764345799999 689999999886
No 13
>PF05213 Corona_NS2A: Coronavirus NS2A protein; InterPro: IPR007878 This entry is represented by Coronavirus non-structural protein 2A (32kDa); it is a family of uncharacterised viral proteins. Members have a phosphoesterase module (2H) [] and are predicted to be involved in RNA modification. The viral group of 2H phosphoesterases contains proteins from two unrelated virus types: the type C rotaviruses (VP3 protein, IPR011181 from INTERPRO) that are double stranded multipartite RNA viruses and the coronaviruses (NS2 protein, this group) that are positive strand RNA viruses. Given that these viruses have vertebrate hosts, it is likely that the 2H phosphoesterase domain was derived from the host by one of virus groups followed by rapid sequence divergence []. Subsequently, it may have been exchanged between the viral families. Although the direction of the exchange is not clear, it is possible that a double stranded replicative form of a subgenomic RNA transcript of the coronavirus NS2 was stabilised by a rotavirus and incorporated into its multiple double stranded RNA genome []. These proteins can be utilised as novel drug targets because of their predicted RNA modification role.
Probab=99.09 E-value=1e-09 Score=103.83 Aligned_cols=166 Identities=18% Similarity=0.302 Sum_probs=118.9
Q ss_pred cceEEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCCCCCchHHHhhhhcccceeeeeeccCCCcccccccc
Q 012323 181 DYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKVDR 260 (466)
Q Consensus 181 ~~ThFIsIPl~~hp~I~~~~~~f~~~Il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rp~~fva~~~~~~~~~~~vk~~~ 260 (466)
.|||||++|+..-....++|..+|-.+++++=.| + .|
T Consensus 5 ~P~HFin~Pl~~f~~f~~~~~~LQ~~~~~eG~d~----------------k---------------------------~Q 41 (248)
T PF05213_consen 5 KPTHFINFPLVQFEGFMLNFKDLQFQLLEEGVDC----------------K---------------------------LQ 41 (248)
T ss_pred CCCceeeccchhhhhHHHHHHHHHHHHHHcCCCc----------------c---------------------------cc
Confidence 3899999999855888999999999998863111 0 00
Q ss_pred ccccccccccccCCCCCCCCCCCCCccccCCCcceEEeeccccCCHHHHHHHHHHHHHhhHHhhhhcCCCCeEEEEcccc
Q 012323 261 TSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLD 340 (466)
Q Consensus 261 ~~i~~~~~~~~~~r~~~~~~~gi~~~~~v~p~~LHLTL~fLgl~~~eei~~a~~~L~~i~~~i~~~L~~~pf~L~l~GLg 340 (466)
..=||||+||-+ +++++.....+|+++...+ .- ....+++..-.
T Consensus 42 -------------------------------kaPHlSl~mL~I-sd~~i~~V~~~iq~ViddM---~~-~~~~it~tnp~ 85 (248)
T PF05213_consen 42 -------------------------------KAPHLSLGMLDI-SDEDIPDVETAIQKVIDDM---VW-FEGDITFTNPH 85 (248)
T ss_pred -------------------------------ccCeeEEEEEEc-ChhhhhhHHHHHHHHHHHh---hc-ccceEEecCce
Confidence 112999999977 5889999988888875432 11 22277777776
Q ss_pred cCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHHHH
Q 012323 341 LMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDI 420 (466)
Q Consensus 341 ~F~~dp~~~rVLya~V~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fkPHiTLar~~~~~~~~~~~~~~~fda~~i 420 (466)
.++ |.+-+.|+. +..|+..|...|.+.|+..+ ..|.|.||+||+......-+ .
T Consensus 86 MLg------~~yV~nV~G------v~slh~ki~n~~~~kgit~g--QSRmwIPHiTia~~~~~av~-----I-------- 138 (248)
T PF05213_consen 86 MLG------RCYVANVKG------VLSLHDKIVNVFRKKGITFG--QSRMWIPHITIAQLNDAAVR-----I-------- 138 (248)
T ss_pred eec------cEEEEeccc------HHHHHHHHHHHHHHhCcCcC--cccccccceehhhhhchheE-----e--------
Confidence 663 566667763 88899999999999999997 48999999999987532110 0
Q ss_pred HHHhCCCccc-cEEe-----cEEEEEeeeccCCCCceeEEEE
Q 012323 421 FKQFGSKEWG-EYLI-----KEAHLSQRFVYDESGFYHCCAS 456 (466)
Q Consensus 421 l~~~~~~~fG-~~~V-----~eI~Ls~~~~~~~~g~Y~~l~s 456 (466)
++ .+|+ +.++ .++.|...+....+|+|..+.+
T Consensus 139 --~~--~qFny~~~~n~~~~~rle~VKlGa~K~dgfYe~i~s 176 (248)
T PF05213_consen 139 --KE--KQFNYKITINPSSPARLEFVKLGAEKKDGFYESIVS 176 (248)
T ss_pred --cc--ceeeeEeeccCCChhcCeEEEcCCcccCceeeeehh
Confidence 11 1222 2334 7788888887777899998876
No 14
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.97 E-value=1.3e-09 Score=84.39 Aligned_cols=59 Identities=41% Similarity=0.516 Sum_probs=53.0
Q ss_pred EEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEccChhHHHHHHHHH
Q 012323 108 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKI 167 (466)
Q Consensus 108 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~---~~~I~I~G~~~~~v~~A~~~I 167 (466)
..+.||..+|++|||++|+++++|+++|||+|.||..+. ...|.|.|. .+++..|...|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~-~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT-PEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcC-HHHHHHHHHHh
Confidence 578999999999999999999999999999999998643 567999997 68999998876
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=98.82 E-value=8.5e-09 Score=81.05 Aligned_cols=59 Identities=37% Similarity=0.387 Sum_probs=52.4
Q ss_pred EEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHH
Q 012323 108 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKI 167 (466)
Q Consensus 108 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~----~~~I~I~G~~~~~v~~A~~~I 167 (466)
..+.||...++.|||++|.++++|+++|||+|+|++... ...|+|+|. .+++..|...|
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~-~~~v~~A~~~I 64 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK-PSAVQKALLLI 64 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeC-HHHHHHHHHhh
Confidence 578999999999999999999999999999999987643 346899996 78999999877
No 16
>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=98.79 E-value=3.7e-09 Score=87.12 Aligned_cols=60 Identities=20% Similarity=0.411 Sum_probs=52.1
Q ss_pred cccCCCcceEEeeccccCCHHHHHHHHHHHHHhhHHhhhhcCCCCeEEEEcccccCCCCCCCceEEE
Q 012323 287 IFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILY 353 (466)
Q Consensus 287 ~~v~p~~LHLTL~fLgl~~~eei~~a~~~L~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~~rVLy 353 (466)
.|++|.++||||.|||.+++++++.+++.|..+.. ...||.+++.|+++|++ ..++||+|
T Consensus 28 r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~------~~~~f~~~~~~~~~f~s-~~~~rvi~ 87 (87)
T PF02834_consen 28 RWVRPFNPHITLAFLGEVPPDQLPELIEALANIAS------RFPPFTLTVDGFGLFPS-RLRPRVIW 87 (87)
T ss_dssp EEGSCGGSEEEEEEEEEESHHHHHHHHHHHHHHHC------CCB-EEEEEEEEEEEEE-EETCEEEE
T ss_pred cccCCCCCeEEEEeCCCCCHHHHHHHHHHHHhhhc------cCCCeEEEEeEEEEeCC-CCCCCCcC
Confidence 48999999999999999999999999998887742 35899999999999987 44889999
No 17
>smart00322 KH K homology RNA-binding domain.
Probab=98.77 E-value=3.3e-08 Score=75.99 Aligned_cols=66 Identities=39% Similarity=0.530 Sum_probs=58.1
Q ss_pred CceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHH
Q 012323 105 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAII 171 (466)
Q Consensus 105 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~~~~~v~~A~~~I~~i~ 171 (466)
.....+.||..+++++||++|.++++|+++||++|.++.... ...|.|.|+ ..++..|++.|...+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~-~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGP-PENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcC-HHHHHHHHHHHHHHh
Confidence 356789999999999999999999999999999999987653 567999998 789999999987654
No 18
>PF13014 KH_3: KH domain
Probab=98.77 E-value=7.9e-09 Score=74.66 Aligned_cols=39 Identities=38% Similarity=0.572 Sum_probs=34.3
Q ss_pred cceeecCCCchhHHHHHHHhCcEEEcCC---CCC-CCcEEEEc
Q 012323 116 VIRFIKGKEGSTQKKFEKEMGVKIILPS---SKK-EDSIIIEG 154 (466)
Q Consensus 116 ~~~~IIGk~G~t~k~iE~eT~~~I~iP~---~~~-~~~I~I~G 154 (466)
+|++|||++|+++++|+++|+|+|+||+ .+. +..|+|+|
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 56788887
No 19
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.70 E-value=3.9e-08 Score=86.85 Aligned_cols=59 Identities=29% Similarity=0.486 Sum_probs=53.1
Q ss_pred ccceeecCCCchhHHHHHHHhCcEEEcCCCCC--------------------CCcEEEEccC--hhHHHHHHHHHHHHHH
Q 012323 115 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK--------------------EDSIIIEGNS--TDSVAKASEKIQAIIA 172 (466)
Q Consensus 115 ~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~--------------------~~~I~I~G~~--~~~v~~A~~~I~~i~~ 172 (466)
.|+|.|||++|.|+|+||++|||+|.|...|+ ...|.|+|.+ .+++.+|++.|+.|+.
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 68899999999999999999999999998742 2679999988 8999999999998886
Q ss_pred H
Q 012323 173 E 173 (466)
Q Consensus 173 ~ 173 (466)
.
T Consensus 95 ~ 95 (120)
T cd02395 95 P 95 (120)
T ss_pred c
Confidence 4
No 20
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.49 E-value=3.1e-07 Score=98.29 Aligned_cols=107 Identities=26% Similarity=0.305 Sum_probs=86.3
Q ss_pred CCCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHHHHHHHHhhhCC
Q 012323 103 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIAEAVESP 178 (466)
Q Consensus 103 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~----~~~I~I~G~~~~~v~~A~~~I~~i~~~~~~~~ 178 (466)
..+.+..|.||..-+|.||||+|+|||+|..|||+||+|-..++ +....|.|. ++.|+.|.+.|..||.++.+.+
T Consensus 227 g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~-~d~ie~Aa~lI~eii~~~~~~~ 305 (600)
T KOG1676|consen 227 GGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGT-VDQIEHAAELINEIIAEAEAGA 305 (600)
T ss_pred cccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecC-HHHHHHHHHHHHHHHHHHhccC
Confidence 34558999999999999999999999999999999999944333 567899996 7999999999999999977641
Q ss_pred ---------CCcceEEEEeccccchhhhccHHHHHHHHhcc
Q 012323 179 ---------SLDYSHFVSLPLAVHPELVDKLVNFQNTILGI 210 (466)
Q Consensus 179 ---------k~~~ThFIsIPl~~hp~I~~~~~~f~~~Il~~ 210 (466)
-..-.-.+.||-.----|+|+..+-++.|-.+
T Consensus 306 ~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~q 346 (600)
T KOG1676|consen 306 GGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQ 346 (600)
T ss_pred CCCcCCCCccceeeEEEeccccccccccCCCccchhhhccc
Confidence 01114456689875566889999988887665
No 21
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.32 E-value=9e-07 Score=92.82 Aligned_cols=72 Identities=26% Similarity=0.409 Sum_probs=62.6
Q ss_pred CceEEEEecc------ccceeecCCCchhHHHHHHHhCcEEEcCCCCC-------------------CCcEEEEccChhH
Q 012323 105 RHSLSVEVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-------------------EDSIIIEGNSTDS 159 (466)
Q Consensus 105 ~~~~~v~Vp~------~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-------------------~~~I~I~G~~~~~ 159 (466)
++...|.||. .|+|+|||.+|.|+|+||+|||+||.|-.+|+ .-.|.|++.+.+.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 7778888885 68999999999999999999999999988543 1158999999999
Q ss_pred HHHHHHHHHHHHHHhhh
Q 012323 160 VAKASEKIQAIIAEAVE 176 (466)
Q Consensus 160 v~~A~~~I~~i~~~~~~ 176 (466)
|.+|...|+.|+.++.-
T Consensus 217 i~~Ai~vienli~~av~ 233 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSAVS 233 (554)
T ss_pred HHHHHHHHHHHHHhhcc
Confidence 99999999999987443
No 22
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.30 E-value=1.2e-06 Score=82.73 Aligned_cols=65 Identities=32% Similarity=0.439 Sum_probs=59.3
Q ss_pred ceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEE---ccChhHHHHHHHHHHHHHH
Q 012323 106 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIE---GNSTDSVAKASEKIQAIIA 172 (466)
Q Consensus 106 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~---G~~~~~v~~A~~~I~~i~~ 172 (466)
...++.||+..++.|||++|.+++.|+++||++|+|.. +.+.|.|. +.+++.+.+|++.|++|..
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~--~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS--ETGEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC--CCCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 46789999999999999999999999999999999985 34789998 7789999999999999987
No 23
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.25 E-value=1.1e-06 Score=82.36 Aligned_cols=61 Identities=33% Similarity=0.432 Sum_probs=54.9
Q ss_pred EEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEE--EccChhHHHHHHHHHHHHHH
Q 012323 110 VEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIII--EGNSTDSVAKASEKIQAIIA 172 (466)
Q Consensus 110 v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I--~G~~~~~v~~A~~~I~~i~~ 172 (466)
+.||++.++.|||++|+++|+|+++||++|+|-. +.+.|.| .+.++..+.+|++.|.+|..
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~--~~g~V~I~~~t~d~~~i~kA~~~I~~i~~ 64 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS--ETGEVKIEEEDEDPLAVMKAREVVKAIGR 64 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc--CCceEEEecCCCCHHHHHHHHHHHHHHHc
Confidence 6899999999999999999999999999999975 3467999 55678999999999999876
No 24
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.01 E-value=8e-06 Score=77.07 Aligned_cols=54 Identities=28% Similarity=0.409 Sum_probs=49.1
Q ss_pred ccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 115 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 115 ~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
..+|.|||++|.|++.||..|||+|+|+. +.|.|.|. .++++.|++.|+.|++.
T Consensus 104 r~~griIG~~G~~~k~ie~~t~~~i~i~~----~~v~i~G~-~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 104 RIKGRIIGEGGKTRRIIEELTGVDISVYG----KTVAIIGD-PEQVEIAREAIEMLIEG 157 (180)
T ss_pred HHhhheeCCCcHHHHHHHHHHCcEEEEcC----CEEEEEeC-HHHHHHHHHHHHHHHcC
Confidence 37999999999999999999999999985 45999995 79999999999999955
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=97.99 E-value=6e-06 Score=77.34 Aligned_cols=54 Identities=28% Similarity=0.383 Sum_probs=49.8
Q ss_pred ccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 115 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 115 ~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
...|.|||++|.|++.||..|||+|.|+. ..|.|+|. .++++.|++.|+.|++.
T Consensus 98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~----~~v~i~G~-~~~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEELTGVSISVYG----KTVGIIGD-PEQVQIAREAIEMLIEG 151 (172)
T ss_pred HHHhhhcCCCcHHHHHHHHHHCCeEEEcC----CEEEEECC-HHHHHHHHHHHHHHHcC
Confidence 46899999999999999999999999985 67999994 79999999999999965
No 26
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=97.95 E-value=1.2e-05 Score=76.28 Aligned_cols=77 Identities=17% Similarity=0.239 Sum_probs=63.1
Q ss_pred CCCCCCCCCceEEEEecc------ccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHH
Q 012323 97 GEPVPSAERHSLSVEVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAI 170 (466)
Q Consensus 97 ~~~~~s~~~~~~~v~Vp~------~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i 170 (466)
++-+.+..+|+-.+.||. .|+|+|||+.|.|+|+||+.++|+|-|..+++-....|....++....|.+-|.-+
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 455667889999999984 79999999999999999999999999999887666667766667777777777766
Q ss_pred HHH
Q 012323 171 IAE 173 (466)
Q Consensus 171 ~~~ 173 (466)
+..
T Consensus 219 I~a 221 (269)
T COG5176 219 IEA 221 (269)
T ss_pred hhc
Confidence 654
No 27
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.93 E-value=8.5e-06 Score=84.12 Aligned_cols=92 Identities=27% Similarity=0.399 Sum_probs=70.6
Q ss_pred CceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHHHHHHHH-hhhCCC
Q 012323 105 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIAE-AVESPS 179 (466)
Q Consensus 105 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~----~~~I~I~G~~~~~v~~A~~~I~~i~~~-~~~~~k 179 (466)
-|-+.+-||..||+.||||.|+|+|.|-..|.|||+|=+..+ +..|+|-|. .++..+|+.+|..|+.. +.+
T Consensus 198 D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~t-pEg~s~Ac~~ILeimqkEA~~--- 273 (584)
T KOG2193|consen 198 DWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHST-PEGTSKACKMILEIMQKEAVD--- 273 (584)
T ss_pred CcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecC-ccchHHHHHHHHHHHHHhhhc---
Confidence 466788899999999999999999999999999999977644 457999996 68999999999988754 333
Q ss_pred CcceEEEEecc--ccchhhhccHHH
Q 012323 180 LDYSHFVSLPL--AVHPELVDKLVN 202 (466)
Q Consensus 180 ~~~ThFIsIPl--~~hp~I~~~~~~ 202 (466)
-..+ -.||| --|..++|++..
T Consensus 274 ~k~~--~e~pLk~lAHN~lvGRLIG 296 (584)
T KOG2193|consen 274 DKVA--EEIPLKILAHNNLVGRLIG 296 (584)
T ss_pred cchh--hhcchhhhhhcchhhhhhh
Confidence 2233 34555 236666655543
No 28
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.91 E-value=0.00016 Score=73.04 Aligned_cols=107 Identities=23% Similarity=0.234 Sum_probs=79.2
Q ss_pred CCCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEccChhHHHHHHHHHHHHHHHhhh
Q 012323 103 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAEAVE 176 (466)
Q Consensus 103 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~------~~~I~I~G~~~~~v~~A~~~I~~i~~~~~~ 176 (466)
..+|.+.|.||.-..|-||||+|.|+.+|+.||||||++-+..+ +..|-|+|. -+.++.-.+-|..-+++.-+
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 456889995 56777666555444433211
Q ss_pred ---------CCCC---cceEEEEeccccchhhhccHHHHHHHHhcc
Q 012323 177 ---------SPSL---DYSHFVSLPLAVHPELVDKLVNFQNTILGI 210 (466)
Q Consensus 177 ---------~~k~---~~ThFIsIPl~~hp~I~~~~~~f~~~Il~~ 210 (466)
.|+. ....-|.+|-..---|+++...+++.|+++
T Consensus 115 ~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eq 160 (402)
T KOG2191|consen 115 AVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQ 160 (402)
T ss_pred hhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHh
Confidence 1000 012455577766677888888888888876
No 29
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=97.82 E-value=3.1e-05 Score=87.47 Aligned_cols=104 Identities=27% Similarity=0.414 Sum_probs=93.7
Q ss_pred CCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCCcc
Q 012323 104 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDY 182 (466)
Q Consensus 104 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~~~~~v~~A~~~I~~i~~~~~~~~k~~~ 182 (466)
..+.+.+.|.++++.+++||+|.++.+|+++++|.|.+|.+++ ...++++|. ..++.+|.+.++.+..+...+ ..
T Consensus 345 nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~-~~~~~ka~~~v~~~~~ei~n~---~~ 420 (753)
T KOG2208|consen 345 NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGV-SANDEKAVEDVEKIIAEILNS---IV 420 (753)
T ss_pred cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEecc-ccchhHHHHHHHHHHHhhhcc---cc
Confidence 4578899999999999999999999999999999999999777 678999997 579999999999999997763 35
Q ss_pred eEEEEeccccchhhhccHHHHHHHHhccc
Q 012323 183 SHFVSLPLAVHPELVDKLVNFQNTILGIT 211 (466)
Q Consensus 183 ThFIsIPl~~hp~I~~~~~~f~~~Il~~~ 211 (466)
.+.+.||-.+|.+|.|......+.|+.+.
T Consensus 421 ~~~~~iP~k~~~~iig~~g~~i~~I~~k~ 449 (753)
T KOG2208|consen 421 KEEVQIPTKSHKRIIGTKGALINYIMGKH 449 (753)
T ss_pred cceeecCccchhhhhccccccHHHHHhhc
Confidence 67777999999999999999999999883
No 30
>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=97.79 E-value=3.7e-05 Score=85.68 Aligned_cols=65 Identities=20% Similarity=0.319 Sum_probs=59.9
Q ss_pred ceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 106 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 106 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
-..++.||++.++-|||+||.++|.|.++||++|+|-. .+.|.|.|.+.+.+.+|++.|+.|+..
T Consensus 578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 46788999999999999999999999999999999974 588999999999999999999998873
No 31
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.62 E-value=0.00014 Score=71.68 Aligned_cols=70 Identities=23% Similarity=0.335 Sum_probs=53.7
Q ss_pred CceEEEEecc------ccceeecCCCchhHHHHHHHhCcEEEcCCCCC-C--------------------CcEEEEccCh
Q 012323 105 RHSLSVEVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-E--------------------DSIIIEGNST 157 (466)
Q Consensus 105 ~~~~~v~Vp~------~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~--------------------~~I~I~G~~~ 157 (466)
+-+..|.||. .|+|.|+|++|.|+|+||++|+|+|-|-.+|+ . =.|.|+-.
T Consensus 91 k~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~-- 168 (259)
T KOG1588|consen 91 KLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETE-- 168 (259)
T ss_pred eEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEe--
Confidence 4566777775 59999999999999999999999999998875 1 13666654
Q ss_pred hHHHHHHHHHHHHHHHhhh
Q 012323 158 DSVAKASEKIQAIIAEAVE 176 (466)
Q Consensus 158 ~~v~~A~~~I~~i~~~~~~ 176 (466)
.--..|..||...+++.++
T Consensus 169 ~p~~ea~~rl~~AleeI~k 187 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKK 187 (259)
T ss_pred CCHHHHHHHHHHHHHHHHH
Confidence 2456677777777777554
No 32
>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=97.61 E-value=7.5e-05 Score=83.82 Aligned_cols=65 Identities=22% Similarity=0.366 Sum_probs=58.8
Q ss_pred ceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 106 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 106 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
-..++.||++.++.|||+||.++|+|+++||++|+|-. .+.|.|.+.+.+.+.+|.+.|..+...
T Consensus 551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d---dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED---DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 35678999999999999999999999999999999964 588999999899999999999888654
No 33
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=97.50 E-value=0.00013 Score=78.65 Aligned_cols=111 Identities=14% Similarity=0.243 Sum_probs=89.9
Q ss_pred CCCCCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEccChhHHHHHHHHHHHHHHHhhhC
Q 012323 101 PSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKIQAIIAEAVES 177 (466)
Q Consensus 101 ~s~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~---~~~I~I~G~~~~~v~~A~~~I~~i~~~~~~~ 177 (466)
.+...-+...+||.+..++|||++|+-++.|.++.+|+++||+... .+.|.|+|. .++|+.|+..|..++++-+-.
T Consensus 49 ~s~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~-pe~v~~aK~li~evv~r~~~~ 127 (600)
T KOG1676|consen 49 PSDTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGS-PENVEVAKQLIGEVVSRGRPP 127 (600)
T ss_pred CcccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCC-cccHHHHHHhhhhhhhccCCC
Confidence 3446667788999999999999999999999999999999988655 578999997 589999999999999874310
Q ss_pred ---C-CCc---ceEEEEeccccchhhhccHHHHHHHHhcccc
Q 012323 178 ---P-SLD---YSHFVSLPLAVHPELVDKLVNFQNTILGITD 212 (466)
Q Consensus 178 ---~-k~~---~ThFIsIPl~~hp~I~~~~~~f~~~Il~~~~ 212 (466)
+ -+. .|.-|.||-+----|++..++-.+.+-+...
T Consensus 128 ~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg 169 (600)
T KOG1676|consen 128 GGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSG 169 (600)
T ss_pred CCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcC
Confidence 0 111 4777888888778899999999888776643
No 34
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.43 E-value=0.00013 Score=75.50 Aligned_cols=65 Identities=28% Similarity=0.450 Sum_probs=54.6
Q ss_pred EeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEccChhHHHHHHHHHHHHHHHhhh
Q 012323 111 EVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAEAVE 176 (466)
Q Consensus 111 ~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~------~~~I~I~G~~~~~v~~A~~~I~~i~~~~~~ 176 (466)
.--..|.|.||||.|+++|+||++|||+|.|.+--+ +..|++.| +-+++.+|-..|.+-++++-.
T Consensus 285 lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkG-siEac~~AE~eImkKlre~yE 355 (584)
T KOG2193|consen 285 LAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKG-SIEACVQAEAEIMKKLRECYE 355 (584)
T ss_pred hhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecc-cHHHHHHHHHHHHHHHHHHHh
Confidence 334689999999999999999999999999987644 56899999 578999999988877766443
No 35
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.30 E-value=0.0003 Score=70.57 Aligned_cols=66 Identities=24% Similarity=0.332 Sum_probs=60.8
Q ss_pred CCCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHH
Q 012323 103 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQA 169 (466)
Q Consensus 103 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~ 169 (466)
..+...+++||.++.+.|.|++|.++|.|.++|+++|.-|++++.-...++|. .+.|..||..|..
T Consensus 23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~-~edv~~aRrei~s 88 (394)
T KOG2113|consen 23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGR-HEDVRRARREIPS 88 (394)
T ss_pred CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCCcceeccC-chhHHHHhhcCcc
Confidence 37888999999999999999999999999999999999999999877788997 5899999999975
No 36
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.28 E-value=0.00048 Score=67.69 Aligned_cols=64 Identities=28% Similarity=0.374 Sum_probs=58.6
Q ss_pred eEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 107 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 107 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
-..+.||..+.+.+||++|.+++.|.++|+++|.|- .++.|.|.|.+.+.+.+|.+.|+.+-.+
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig---~NG~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG---QNGRIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc---CCcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 357899999999999999999999999999999994 4689999999999999999999888766
No 37
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.19 E-value=0.00073 Score=68.34 Aligned_cols=67 Identities=27% Similarity=0.361 Sum_probs=57.1
Q ss_pred ceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 106 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 106 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~------~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
..+.+-||..--+.||||+|+|+|.|.++.+|-|+|-.+.+ +..|++.|. .+..++|.++|..-+.+
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 45888999999999999999999999999999999954443 346788996 78999999998776665
No 38
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.17 E-value=0.00089 Score=63.50 Aligned_cols=67 Identities=30% Similarity=0.388 Sum_probs=59.1
Q ss_pred CCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEcc----ChhHHHHHHHHHHHHHH
Q 012323 104 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGN----STDSVAKASEKIQAIIA 172 (466)
Q Consensus 104 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~----~~~~v~~A~~~I~~i~~ 172 (466)
..+...+.||+...+.+||+.|.+.+.||+.++|+|.+.. .++.|.|+.. ++-.+++|++-|++|..
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~--~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgr 76 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS--KTGSVTIRTTRKTEDPLALLKARDVVKAIGR 76 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC--CCCeEEEEecCCCCChHHHHHHHHHHHHHhc
Confidence 3556789999999999999999999999999999999987 4577888775 78899999999999864
No 39
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.13 E-value=0.0015 Score=70.50 Aligned_cols=67 Identities=31% Similarity=0.404 Sum_probs=58.4
Q ss_pred ceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCC---CC-CCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 106 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS---KK-EDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 106 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~---~~-~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
..+.+-||....|-||||+|..+|+|.++||++|.+-+. .. ...|+|.|. .+.|.+|.-.|-.++.+
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 578889999999999999999999999999999998543 11 455999997 68999999999988877
No 40
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.07 E-value=0.00058 Score=77.96 Aligned_cols=65 Identities=20% Similarity=0.269 Sum_probs=59.1
Q ss_pred ceEEEEeccccceeecCCCchhHHHHHHHhCcE-EEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 106 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVK-IILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 106 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~-I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
-..++.||++.++.|||+||.|+|.|.++||++ |+|-. .+.|.|.|.+.+.+++|++.|+.|..+
T Consensus 685 ~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 685 LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 467889999999999999999999999999999 88864 588999999999999999999988764
No 41
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=97.06 E-value=0.0014 Score=64.62 Aligned_cols=68 Identities=22% Similarity=0.285 Sum_probs=56.0
Q ss_pred CceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcC--CCCC-CCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 105 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP--SSKK-EDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 105 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP--~~~~-~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
-.+..|.||+.+-+-||||+|..+++|.+|.|..|.|. ..+. ...|+|+|. .+.+..|.=-++.-|+.
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 35778999999999999999999999999999999995 4454 445789996 67888887766666553
No 42
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.97 E-value=0.0012 Score=72.82 Aligned_cols=68 Identities=29% Similarity=0.410 Sum_probs=61.9
Q ss_pred ceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhhh
Q 012323 106 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVE 176 (466)
Q Consensus 106 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~~~~ 176 (466)
...++.|+++-++-+||+||.++++|-++||++|+|- +.+.|.|.+.+.+.+.+|+++|+.|+.+..-
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 4567889999999999999999999999999999997 4678999998889999999999999987544
No 43
>PF02834 LigT_PEase: LigT like Phosphoesterase; InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases. These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.
Probab=96.72 E-value=0.0014 Score=53.66 Aligned_cols=76 Identities=9% Similarity=0.118 Sum_probs=52.1
Q ss_pred hhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHHHHHHHhCCC--ccc--cEEecEE
Q 012323 362 GDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGSK--EWG--EYLIKEA 437 (466)
Q Consensus 362 ~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fkPHiTLar~~~~~~~~~~~~~~~fda~~il~~~~~~--~fG--~~~V~eI 437 (466)
.+.|.++++.+.+.+...|+... +++.|||||++...... -.+..+.+..... .+. .+.++++
T Consensus 8 ~~~L~~l~~~l~~~~~~~~~r~~----~~~~~HiTL~flg~~~~---------~~~~~l~~~l~~~~~~~~~f~~~~~~~ 74 (87)
T PF02834_consen 8 KEQLNQLQERLRQALPPLGIRWV----RPFNPHITLAFLGEVPP---------DQLPELIEALANIASRFPPFTLTVDGF 74 (87)
T ss_dssp HHHHHHHHHHHHHHCCSCTEEEG----SCGGSEEEEEEEEEESH---------HHHHHHHHHHHHHHCCCB-EEEEEEEE
T ss_pred HHHHHHHHHHHhhhccccCCccc----CCCCCeEEEEeCCCCCH---------HHHHHHHHHHHhhhccCCCeEEEEeEE
Confidence 46799999999988888899874 79999999999864321 1223444443332 222 3789999
Q ss_pred EEEeeeccCCCCce
Q 012323 438 HLSQRFVYDESGFY 451 (466)
Q Consensus 438 ~Ls~~~~~~~~g~Y 451 (466)
.++.+.. ..+..|
T Consensus 75 ~~f~s~~-~~rvi~ 87 (87)
T PF02834_consen 75 GLFPSRL-RPRVIW 87 (87)
T ss_dssp EEEEEEE-TCEEEE
T ss_pred EEeCCCC-CCCCcC
Confidence 9987765 445555
No 44
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.70 E-value=0.0015 Score=73.73 Aligned_cols=64 Identities=25% Similarity=0.413 Sum_probs=57.9
Q ss_pred eEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 107 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 107 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
...+.||++.++-+||+||.|+|.|.++||++|+|- +++.|.|.+.+.+.+.+|++.|+.+..+
T Consensus 555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~---d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE---DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC---CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 457889999999999999999999999999999984 3688999999899999999999988854
No 45
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.59 E-value=0.0042 Score=67.72 Aligned_cols=69 Identities=22% Similarity=0.335 Sum_probs=59.9
Q ss_pred CCCceEEEEecc-ccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 103 AERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 103 ~~~~~~~v~Vp~-~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
.......|.+|. ++-|.|||+.|.++|-||.-||+-|.|.. ..+.|+|+|-++-.-+-|+..++.|+.+
T Consensus 201 ~e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd--tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 201 AETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred hhheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC--CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 345566889998 78899999999999999999999999974 4567999997778889999999999987
No 46
>PF09749 HVSL: Uncharacterised conserved protein; InterPro: IPR019146 This entry is of proteins of approximately 300 residues conserved from plants to humans. It contains two conserved motifs, HxSL and FHVSL. The function is unknown.
Probab=96.56 E-value=0.02 Score=56.29 Aligned_cols=103 Identities=19% Similarity=0.354 Sum_probs=79.1
Q ss_pred CCCcceEEeeccccCCHHHHHHHHHHHHHhhHHhhhhcCCCCeEEEEcccccCCCCCCCceEEEE-eeeccCChhHHHHH
Q 012323 290 KPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYA-PVEEIGDGDRLLHA 368 (466)
Q Consensus 290 ~p~~LHLTL~fLgl~~~eei~~a~~~L~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~~rVLya-~V~~~~~~~~L~~L 368 (466)
.+.-|||+|.=-=-+...+++...+.|+.. +.. ....+|.+.|.++.+|.+ .++.|...+ .|.. +....|..|
T Consensus 86 ~~~~lHISLSr~~~lr~~~id~f~~~lr~~---l~~-~~~~~F~v~f~~~~~~~N-~e~TR~FL~l~V~~-~~~~~l~~l 159 (239)
T PF09749_consen 86 SPDPLHISLSRTFPLRTHQIDPFVDSLRQA---LRS-SNIRPFYVSFSGLDVYTN-DEKTRSFLALRVSE-GSNNELKRL 159 (239)
T ss_pred CCCCeEEEeCCCccccHHHHHHHHHHHHHH---Hhh-cCCceEEEEeCceEEEec-CCCCeEEEEEEecc-cccHHHHHH
Confidence 678899999765555668888777766654 211 245899999999999987 677776665 5654 333349999
Q ss_pred HHHHHHHHHHCCCccccCCC-CCceeeEEeeeec
Q 012323 369 CQVIIDAFNEAGLVFHRDYN-KKLKLHATLMNIR 401 (466)
Q Consensus 369 ~~~L~~~f~~~Gl~~e~d~~-r~fkPHiTLar~~ 401 (466)
.+.+.+.+.+.|+..- . ..-.+||.||-+-
T Consensus 160 ~~~i~~~l~~~~lp~~---Y~~~~~fHvSIAw~~ 190 (239)
T PF09749_consen 160 LDRINEVLKEFGLPPF---YDEDPSFHVSIAWTL 190 (239)
T ss_pred HHHHHHHHHHhCCCcc---cCCCCCCEEEEEEEC
Confidence 9999999999999874 5 7899999999875
No 47
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.54 E-value=0.002 Score=67.30 Aligned_cols=70 Identities=17% Similarity=0.233 Sum_probs=61.2
Q ss_pred CCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHh
Q 012323 104 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEA 174 (466)
Q Consensus 104 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~~ 174 (466)
+.+...+.|-..++|.+||++|+++++|+..|+|+|+|-.....--|+|-|. +..-.+|+..|...++..
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 4567889999999999999999999999999999999998666677899996 677788999998888763
No 48
>PRK00106 hypothetical protein; Provisional
Probab=96.50 E-value=0.0053 Score=67.01 Aligned_cols=69 Identities=17% Similarity=0.340 Sum_probs=59.4
Q ss_pred CCCceEEEEecc-ccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 103 AERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 103 ~~~~~~~v~Vp~-~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
.......|.+|. ++-|.|||+.|.++|.||.-|||-|.|.. ..+.|+|+|-++-.-+-|+..++.++.+
T Consensus 222 ~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 222 TEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD--TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred hhheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC--CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 345566889998 88899999999999999999999999974 4567999997778888899888888876
No 49
>PRK12704 phosphodiesterase; Provisional
Probab=96.47 E-value=0.0053 Score=67.08 Aligned_cols=69 Identities=20% Similarity=0.322 Sum_probs=58.1
Q ss_pred CCCceEEEEecc-ccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 103 AERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 103 ~~~~~~~v~Vp~-~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
.......|.+|. ++-|.|||+.|.++|.||.-||+-|.|.. ..+.|+|+|-++..-+-|+..++.++.+
T Consensus 207 ~e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd--tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 207 AETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hhhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC--CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 345566788998 78899999999999999999999999975 4568999997666666899999888876
No 50
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.33 E-value=0.0064 Score=57.76 Aligned_cols=54 Identities=28% Similarity=0.407 Sum_probs=48.7
Q ss_pred ccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 115 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 115 ~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
...|.|||++|.|++.||+=|+|.|.+-. ..|-|.|. .++|+-|++.|+.+++.
T Consensus 111 R~kgRIIG~~GkTr~~IE~lt~~~I~V~g----~tVaiiG~-~~~v~iAr~AVemli~G 164 (194)
T COG1094 111 RIKGRIIGREGKTRRAIEELTGVYISVYG----KTVAIIGG-FEQVEIAREAVEMLING 164 (194)
T ss_pred HhhceeeCCCchHHHHHHHHhCCeEEEeC----cEEEEecC-hhhhHHHHHHHHHHHcC
Confidence 45789999999999999999999999964 57999997 58999999999999986
No 51
>PF07823 CPDase: Cyclic phosphodiesterase-like protein; InterPro: IPR012386 2',3' Cyclic nucleotide phosphodiesterases (CPDases) are enzymes that catalyse at least two distinct steps in the splicing of tRNA introns in eukaryotes. The active site is characterised by two conserved histidine residues []. The enzyme has six cysteine residues, four of which are involved in forming two intra-molecular disulphide bridges. One of these bridges is involved in the catalytic activity of the enzyme as it opens when CPDase is semi-reduced []. Proteins in this entryand belong to 3.1.4.37 from EC and catalyse the reaction Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate. ; GO: 0004112 cyclic-nucleotide phosphodiesterase activity; PDB: 1JH7_A 1JH6_B 1FSI_B.
Probab=95.85 E-value=0.066 Score=51.23 Aligned_cols=137 Identities=19% Similarity=0.188 Sum_probs=66.3
Q ss_pred eEEeec-cccCCHHHHHHHHHHHHHhhHHhhhhcCCCCe-----EEEEcccccCCCCCCCceEEEEeeeccCChhHHHHH
Q 012323 295 HLTVLM-LKLWNKDRVNAATNVLKSISSKVMDALDNRPL-----FIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHA 368 (466)
Q Consensus 295 HLTL~f-Lgl~~~eei~~a~~~L~~i~~~i~~~L~~~pf-----~L~l~GLg~F~~dp~~~rVLya~V~~~~~~~~L~~L 368 (466)
|+||.- +.+...+++++ .|+.+... ..++ .++|+++.+= ...-+=+|+.+.. ...|..|
T Consensus 40 HiTL~s~i~~~~~~~~~~---~L~~~~~~------~~~~~~~~~~v~~~~v~~g---~~yfq~vyl~v~~---t~~L~~l 104 (196)
T PF07823_consen 40 HITLTSGISLDSSDDVQK---VLDSAAAA------LKPLPKNHFTVRFDKVASG---DKYFQCVYLEVEK---TPELMSL 104 (196)
T ss_dssp -EEEEEEEEE--HHHHHH---HHHHHHHH-------B-E-----EEEEEEEEEE---EETTEEEEEEE------HHHHHH
T ss_pred eEEEeCCCccCCHHHHHH---HHHHHHHh------ccCcccceeEEEeeeEeeC---CeEEEEEEEEecC---ChhHHHH
Confidence 999987 44434555544 45554332 2444 8888776531 1222678999986 4789999
Q ss_pred HHHHHHHHHHC-------CCccccCCCCCceeeEEeeeecccccccCCCccccccHHHHHHHhCCC-------ccccEEe
Q 012323 369 CQVIIDAFNEA-------GLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGSK-------EWGEYLI 434 (466)
Q Consensus 369 ~~~L~~~f~~~-------Gl~~e~d~~r~fkPHiTLar~~~~~~~~~~~~~~~fda~~il~~~~~~-------~fG~~~V 434 (466)
++.+++.|... |-- ...+|.||+.|+..--.... + -.++.+.....+. ..+.|.+
T Consensus 105 ~~~~r~~~~~~~~~~~~~~~~----~~~~y~PHlSLlY~d~~~~e----~---~~~~~~~~~i~~~l~~~~~~~~~~~~~ 173 (196)
T PF07823_consen 105 AQIARELFVEGPPDEVKAAEW----PREPYMPHLSLLYGDLPPEE----K---AEAAEIAQRIDDALGVDSGISGLGWEG 173 (196)
T ss_dssp HCHHHHCT----------T--------S----EEEEE-----HHH----H---HHHHHHHHHH-TT------GTT-EEEE
T ss_pred HHHHHHHhhhccccccccccc----cCCCCCCeEEEEEcCCCccc----H---HHHHHHHHHhcccccccccCCCCCEec
Confidence 99999988532 121 24689999999975311000 0 0122333344433 3346789
Q ss_pred cEEEEEeeeccCCCCceeEEEEEeC
Q 012323 435 KEAHLSQRFVYDESGFYHCCASIPF 459 (466)
Q Consensus 435 ~eI~Ls~~~~~~~~g~Y~~l~si~L 459 (466)
.+|.|..... +=.-..++++++|
T Consensus 174 ~~l~lv~t~g--~v~~W~~l~~~~l 196 (196)
T PF07823_consen 174 GELKLVRTDG--PVEEWEVLASVDL 196 (196)
T ss_dssp EEEEEEE--T--T-TT-EEEEEEE-
T ss_pred cEEEEEEcCC--CCCcEEEEEEEeC
Confidence 9999976532 2346778887765
No 52
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=95.38 E-value=0.031 Score=54.77 Aligned_cols=63 Identities=25% Similarity=0.360 Sum_probs=55.0
Q ss_pred EEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 108 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 108 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
.-+.||+.+++.+||++|++++.|.++|+|+|.+= .++-|.|.|+......-|...|..|-.+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG---~NG~IWV~~~~~~~e~~~~~aI~~ie~e 210 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVG---QNGRIWVDGENESLEELAIEAIRKIERE 210 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEe---cCCEEEecCCCcchHHHHHHHHHHHhhh
Confidence 46899999999999999999999999999999994 5789999998655688888888777665
No 53
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=95.36 E-value=0.022 Score=44.29 Aligned_cols=37 Identities=24% Similarity=0.269 Sum_probs=34.2
Q ss_pred CceEEEEeccccceeecCCCchhHHHHHHHhCcEEEc
Q 012323 105 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 141 (466)
Q Consensus 105 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~i 141 (466)
.....+.||....+..|||+|.+++.++..++.+|++
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3678999999999999999999999999999988875
No 54
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.32 E-value=0.0012 Score=66.98 Aligned_cols=152 Identities=15% Similarity=0.115 Sum_probs=106.0
Q ss_pred CcceEEeeccccCCHHHHHHHHHHHHHhhHHhhhhcCCCCeEEEEcccccCCCCCCCceEEEEeeeccCChhHHHHHHHH
Q 012323 292 KTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQV 371 (466)
Q Consensus 292 ~~LHLTL~fLgl~~~eei~~a~~~L~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~~rVLya~V~~~~~~~~L~~L~~~ 371 (466)
.++|+|+...-.+++.+++.-..+|++....+..++...-...-|.|.++|+- .|-.+++.. ...++..++.
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 58999999999999999999999998665544454555555667799999987 788888875 3678999999
Q ss_pred HHHHHHHCCCccccCCCCCceeeEEeeeecccc--cccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeeccC-CC
Q 012323 372 IIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKK--RRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYD-ES 448 (466)
Q Consensus 372 L~~~f~~~Gl~~e~d~~r~fkPHiTLar~~~~~--~~~~~~~~~~fda~~il~~~~~~~fG~~~V~eI~Ls~~~~~~-~~ 448 (466)
+...|.+.+.... +++-|.+|-+++....-. .+-...+..+-+. +.+.+..+|++....++.|.+.... ..
T Consensus 200 les~~~e~~~~~~--~kp~~i~lkG~~~mnddP~~~kVLYAkv~~~~~----e~~l~~~~~~~i~~~f~~~~li~k~~~~ 273 (345)
T KOG2814|consen 200 LESTFQEIRIDVG--EKPLFIDLKGLDKMNDDPSLTKVLYAKVEPDDY----EKFLQHRCGERILERFVASGLIKKESSS 273 (345)
T ss_pred HHHHHHHHHhccC--CCceeeeccchhhhcCCHhHheeeeeeccCcch----HHHHHHHHHHHHHHHHHHhcchhccccc
Confidence 9999999988886 367799999998775321 1111223333233 2333344566677777777765543 34
Q ss_pred CceeEEEEE
Q 012323 449 GFYHCCASI 457 (466)
Q Consensus 449 g~Y~~l~si 457 (466)
.+|||....
T Consensus 274 ~kLH~TvmN 282 (345)
T KOG2814|consen 274 LKLHCTVMN 282 (345)
T ss_pred cEEEEEEeh
Confidence 677776543
No 55
>PRK12705 hypothetical protein; Provisional
Probab=95.21 E-value=0.024 Score=61.67 Aligned_cols=69 Identities=19% Similarity=0.318 Sum_probs=57.7
Q ss_pred CCCceEEEEecc-ccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 103 AERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 103 ~~~~~~~v~Vp~-~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
.......|.+|. ++-|.|||+.|.++|.+|..||+-|.|+. ....|+|.+-++..-+.|+..++.++..
T Consensus 195 ~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--tp~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 195 SDLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD--TPEAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred hhheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC--CccchhhcccCccchHHHHHHHHHHHhc
Confidence 345566788887 78899999999999999999999999975 3557888887777888888888888765
No 56
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=93.94 E-value=0.045 Score=59.04 Aligned_cols=100 Identities=21% Similarity=0.320 Sum_probs=79.2
Q ss_pred CCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCCcc
Q 012323 104 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDY 182 (466)
Q Consensus 104 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~~~~~v~~A~~~I~~i~~~~~~~~k~~~ 182 (466)
.+..+++-||.+++..|+|+.|++++.|+..|+.||.+..... ...+-+.+.....+..|+..|-.++-+ . -++
T Consensus 66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~~--~---~pv 140 (608)
T KOG2279|consen 66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTE--N---TPV 140 (608)
T ss_pred hheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHhc--C---Ccc
Confidence 4567788899999999999999999999999999999976544 334545553456788888888777765 2 246
Q ss_pred eEEEEeccccchhhhccHHHHHHHHh
Q 012323 183 SHFVSLPLAVHPELVDKLVNFQNTIL 208 (466)
Q Consensus 183 ThFIsIPl~~hp~I~~~~~~f~~~Il 208 (466)
..-++.|...|+.|.++....+.++-
T Consensus 141 k~~lsvpqr~~~~i~grgget~~si~ 166 (608)
T KOG2279|consen 141 SEQLSVPQRSVGRIIGRGGETIRSIC 166 (608)
T ss_pred cccccchhhhcccccccchhhhcchh
Confidence 77788898888999999888877664
No 57
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=93.83 E-value=0.18 Score=50.11 Aligned_cols=69 Identities=19% Similarity=0.329 Sum_probs=53.3
Q ss_pred CCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 104 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 104 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~-~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
+++.+.+.+.+.--+.||||+|.++|+|..+.+..|++|.+.. +..++|+.. .+.|-.-...|.-.+++
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 4677888888999999999999999999999999999998655 566788875 45555444444444443
No 58
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=93.19 E-value=0.13 Score=55.69 Aligned_cols=102 Identities=25% Similarity=0.213 Sum_probs=76.2
Q ss_pred EEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCC--CC-CCcEEEEc---------cChhHHHHHHHHHHHHHH---
Q 012323 108 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS--KK-EDSIIIEG---------NSTDSVAKASEKIQAIIA--- 172 (466)
Q Consensus 108 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~--~~-~~~I~I~G---------~~~~~v~~A~~~I~~i~~--- 172 (466)
..+-.+....|.||||+|.++++|.++|+.+|.|-.. +. +..|+|+| . .+++.+|-++|-...+
T Consensus 45 ~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~-~~al~ka~~~iv~~~~~d~ 123 (485)
T KOG2190|consen 45 YRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPA-TDALFKAFDMIVFKLEEDD 123 (485)
T ss_pred EEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCch-HHHHHHHHHHHhhcccccc
Confidence 5777888999999999999999999888888877443 33 56788999 5 5899999998866321
Q ss_pred -Hhhh----CCCCcceEEEEeccccchhhhccHHHHHHHHhcc
Q 012323 173 -EAVE----SPSLDYSHFVSLPLAVHPELVDKLVNFQNTILGI 210 (466)
Q Consensus 173 -~~~~----~~k~~~ThFIsIPl~~hp~I~~~~~~f~~~Il~~ 210 (466)
+... ..+...+-.+-+|-..--.|+|+.+..+++|.++
T Consensus 124 ~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~ 166 (485)
T KOG2190|consen 124 EAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREE 166 (485)
T ss_pred cccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHh
Confidence 0000 0022245666688876688899999999999876
No 59
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=92.99 E-value=0.085 Score=57.24 Aligned_cols=63 Identities=25% Similarity=0.280 Sum_probs=55.4
Q ss_pred eEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 107 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 107 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
..+++|+.+-...+||++|-.+|+|+.|||+.-++. ++.+.|-.++....++|++.|.-|...
T Consensus 598 ~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD----e~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 598 LETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD----EGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred eeEEeecchhhheeecCccceeeeEeeeccceeeec----CceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 578889999999999999999999999999666654 478999999999999999999887654
No 60
>TIGR03223 Phn_opern_protn putative phosphonate metabolism protein. This family of proteins is observed in the vicinity of other caharacterized genes involved in the catabolism of phosphonates via the3 C-P lyase system (GenProp0232), its function is unknown. These proteins are members of the somewhat broader pfam06299 model "Protein of unknown function (DUF1045)" which contains proteins found in a different genomic context as well.
Probab=92.54 E-value=1.8 Score=42.62 Aligned_cols=143 Identities=10% Similarity=0.094 Sum_probs=80.5
Q ss_pred CcceEEeec-cccCCHHHHHHHHHHHHHhhHHhhhhcCCCCeEE---EEcccccCCCCCCCceEEEEeeeccCChhHHHH
Q 012323 292 KTFHLTVLM-LKLWNKDRVNAATNVLKSISSKVMDALDNRPLFI---RLKGLDLMRGSKDKARILYAPVEEIGDGDRLLH 367 (466)
Q Consensus 292 ~~LHLTL~f-Lgl~~~eei~~a~~~L~~i~~~i~~~L~~~pf~L---~l~GLg~F~~dp~~~rVLya~V~~~~~~~~L~~ 367 (466)
--||.||+- +.+.+........++++.+... ..||.| .+.-||-|- .+.+.+....|+.
T Consensus 56 YGfHaTLKaPFrLa~g~~~a~L~~al~~fA~~------~~pf~i~~L~l~~Lg~Fl-----------AL~P~~~~~~L~~ 118 (228)
T TIGR03223 56 YGFHATLKAPFRLAPGVTEAELLAAVAAFAAT------RAPFALPPLRVALLGGFL-----------ALRPAAPCPALQA 118 (228)
T ss_pred cccceeecCCcccCCCCCHHHHHHHHHHHHhc------CCCccCCcceeeeeCCEE-----------EEeeCCCCHHHHH
Confidence 358999984 4554433344445555554321 355544 445554442 1222234688999
Q ss_pred HHHHHHHHHHHC---------------CCccccC----------CCCCceeeEEeeeecccccccCCCccccccHHHHHH
Q 012323 368 ACQVIIDAFNEA---------------GLVFHRD----------YNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFK 422 (466)
Q Consensus 368 L~~~L~~~f~~~---------------Gl~~e~d----------~~r~fkPHiTLar~~~~~~~~~~~~~~~fda~~il~ 422 (466)
|+..+.+.|... ||...++ --..|..||||-.---... . . .+...++
T Consensus 119 LAa~~V~~~d~fRAPls~aelaRRr~~~Ls~~Q~~~L~~WGYPYV~deFrFHmTLTg~l~~~~------~-~-~~~~~l~ 190 (228)
T TIGR03223 119 LAAACVRELDPFRAPLTEAELARRRPDQLTPRQRALLERWGYPYVLEEFRFHMTLTGRLDEEE------R-A-AVLARLE 190 (228)
T ss_pred HHHHHHHhhhhccCCCCHHHHhhcCccCCCHHHHHHHHHcCCCceecceEEEEEecCCCChHH------H-H-HHHHHHH
Confidence 999999988432 2221100 0146999999985421110 0 0 1123333
Q ss_pred -HhCCCccccEEecEEEEEeeeccCCCCceeEEEEEeCCC
Q 012323 423 -QFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 461 (466)
Q Consensus 423 -~~~~~~fG~~~V~eI~Ls~~~~~~~~g~Y~~l~si~L~~ 461 (466)
.|...--..+.|+.|.|+--. ..|.-++.+..++|.+
T Consensus 191 ~~~~~~l~~p~~id~laLf~e~--~~g~pF~~~~~~~l~~ 228 (228)
T TIGR03223 191 ARFAPLLADPLAVDGLALFVEP--EPGAPFRLIARVALAG 228 (228)
T ss_pred HHhhhccCCCeeeeeEEEEecc--CCCCCcEEEEeecCCC
Confidence 344444457899999997542 2355689999999864
No 61
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=92.32 E-value=0.087 Score=60.11 Aligned_cols=40 Identities=30% Similarity=0.595 Sum_probs=37.1
Q ss_pred CCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCC
Q 012323 104 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 143 (466)
Q Consensus 104 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 143 (466)
...+.++.||.++|+.|||++|+++|+++.+++|.|.+|.
T Consensus 707 ~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 707 NLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred cceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence 4556788899999999999999999999999999999998
No 62
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=88.96 E-value=2 Score=41.05 Aligned_cols=73 Identities=18% Similarity=0.249 Sum_probs=59.2
Q ss_pred EEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCCcceEEEE
Q 012323 108 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDYSHFVS 187 (466)
Q Consensus 108 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~~~~~~k~~~ThFIs 187 (466)
+.+.+++..+-+|...+|..++.|-...|++|.+-. +.+.|.|+|. +..+..+...|..++... .+..+.
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~--~~~~i~I~g~-k~~~~~i~~~i~~~l~~i-------~~~~i~ 97 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR--SENRIRITGT-KSTAEYIEASINEILSNI-------RTEEID 97 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEec--CCcEEEEEcc-HHHHHHHHHHHHHHHhhc-------EEEEEe
Confidence 466677999999999999999999888899999976 4568999996 678888888888888762 345555
Q ss_pred ecc
Q 012323 188 LPL 190 (466)
Q Consensus 188 IPl 190 (466)
+|.
T Consensus 98 l~~ 100 (210)
T PF14611_consen 98 LSP 100 (210)
T ss_pred cch
Confidence 553
No 63
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=86.83 E-value=0.41 Score=51.32 Aligned_cols=42 Identities=29% Similarity=0.374 Sum_probs=37.1
Q ss_pred CceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC
Q 012323 105 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 146 (466)
Q Consensus 105 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~ 146 (466)
-....+.||..+++.+|||+|.++++||+..|.+|.+-..++
T Consensus 485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 456789999999999999999999999999999999954433
No 64
>PRK02821 hypothetical protein; Provisional
Probab=86.11 E-value=0.78 Score=37.56 Aligned_cols=32 Identities=19% Similarity=0.293 Sum_probs=27.3
Q ss_pred CCceEEEEeccccceeecCCCchhHHHHHHHh
Q 012323 104 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEM 135 (466)
Q Consensus 104 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT 135 (466)
......+.+.++-.|.||||+|.+++.|..=.
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 34678999999999999999999999886543
No 65
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=85.71 E-value=0.79 Score=37.42 Aligned_cols=31 Identities=16% Similarity=0.297 Sum_probs=27.0
Q ss_pred CCCceEEEEeccccceeecCCCchhHHHHHH
Q 012323 103 AERHSLSVEVGASVIRFIKGKEGSTQKKFEK 133 (466)
Q Consensus 103 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~ 133 (466)
+......+.|-++-.|.+|||+|.|++.|..
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHH
Confidence 4566789999999999999999999998853
No 66
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=85.56 E-value=0.51 Score=45.19 Aligned_cols=54 Identities=26% Similarity=0.352 Sum_probs=46.3
Q ss_pred ccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 115 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 115 ~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
-.+|.|+||+|.|+=.||+-|.|||.+.. .-|-|-|. -+++.-|++.|-.++-.
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad----~kIHiLG~-~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLAD----SKIHILGA-FQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecC----ceEEEeec-chhhHHHHHhhHhhhcc
Confidence 46899999999999999999999999964 46888995 47999999998777654
No 67
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=85.52 E-value=0.73 Score=46.90 Aligned_cols=138 Identities=19% Similarity=0.236 Sum_probs=90.3
Q ss_pred CCCCccccccccccCCceeecccccc-cccccccccccCCCCCceEEeeecCCCcccccccceeeeeecccccccccCcc
Q 012323 6 DNQGAVYGDKKQKIINPVWRPVSTQA-SVNEESLVKDVSEDGSQIQEMHCSTSSNVSDAQLGVEVAEAVNEGTDLTLSSS 84 (466)
Q Consensus 6 ~~~~~~~~~~~~k~~~~~wrp~~t~a-~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~s~~ 84 (466)
|.+|..+|+-.+|++.++--|+--+- .+..-.+-+++-..-+++.- +-+|.+...+ |-+
T Consensus 42 g~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~~edv~~aRrei~s---------aaeH~~l~~~-----------s~s 101 (394)
T KOG2113|consen 42 GRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGRHEDVRRARREIPS---------AAEHFGLIRA-----------SRS 101 (394)
T ss_pred ccCccccchhhhhhcceeccCCCCCCCcceeccCchhHHHHhhcCcc---------ccceeeeeee-----------ccc
Confidence 66778899999999999988875543 22222222222111112211 1223333222 111
Q ss_pred cccccccccccCCCCCCCCCCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHH
Q 012323 85 VSLDDIKDETLEGEPVPSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKAS 164 (466)
Q Consensus 85 ~~~~~~~~~~~~~~~~~s~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~ 164 (466)
- --+..++. ..++....+.+|....+.+.|.+|++++++.+-|++-|.-|.+......-++|-...++.+|+
T Consensus 102 ~------Sgg~~~~s--~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~~~~Vf~Vtg~~~nC~kra~ 173 (394)
T KOG2113|consen 102 F------SGGTNGAS--ASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRCGEPVFCVTGAPKNCVKRAR 173 (394)
T ss_pred c------cCCCcccc--ccCCCceeeeccceeeeeccccccCccchheecccceEeeeccCCCceEEEecCCcchhhhcc
Confidence 1 01112332 367778899999999999999999999999999999999998777777889997666688888
Q ss_pred -HHHHHHH
Q 012323 165 -EKIQAII 171 (466)
Q Consensus 165 -~~I~~i~ 171 (466)
..|+...
T Consensus 174 s~eie~ta 181 (394)
T KOG2113|consen 174 SCEIEQTA 181 (394)
T ss_pred ccchhhhh
Confidence 6665543
No 68
>PRK00468 hypothetical protein; Provisional
Probab=85.32 E-value=0.86 Score=37.10 Aligned_cols=30 Identities=20% Similarity=0.302 Sum_probs=26.0
Q ss_pred CCceEEEEeccccceeecCCCchhHHHHHH
Q 012323 104 ERHSLSVEVGASVIRFIKGKEGSTQKKFEK 133 (466)
Q Consensus 104 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~ 133 (466)
......+.+.++-.|.||||+|.|++.|..
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRt 57 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRT 57 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHH
Confidence 346678999999999999999999998854
No 69
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=84.69 E-value=1.3 Score=47.96 Aligned_cols=42 Identities=14% Similarity=0.097 Sum_probs=36.7
Q ss_pred CCCCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCC
Q 012323 102 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 143 (466)
Q Consensus 102 s~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 143 (466)
..--...++-||...|+.|||.||..+++.....++-|++-.
T Consensus 445 ~EFpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n 486 (657)
T COG5166 445 TEFPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKN 486 (657)
T ss_pred ccCchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhh
Confidence 344567789999999999999999999999999999988754
No 70
>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=83.83 E-value=1.5 Score=33.29 Aligned_cols=34 Identities=15% Similarity=0.251 Sum_probs=27.7
Q ss_pred ceEEEEeccccceeecCCCchhHHHHHHHhCcEE
Q 012323 106 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKI 139 (466)
Q Consensus 106 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I 139 (466)
....+.+...-.+.+||++|.+++.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4455666665689999999999999999999665
No 71
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=83.57 E-value=1.1 Score=40.84 Aligned_cols=38 Identities=16% Similarity=0.110 Sum_probs=34.3
Q ss_pred CceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcC
Q 012323 105 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 142 (466)
Q Consensus 105 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP 142 (466)
+....+.|+..-++..|||+|.+++.++.-++-.|+|-
T Consensus 98 ~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 98 DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred cEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 45678899999999999999999999999999988873
No 72
>PRK13764 ATPase; Provisional
Probab=82.68 E-value=0.9 Score=50.68 Aligned_cols=43 Identities=28% Similarity=0.332 Sum_probs=38.0
Q ss_pred CCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC
Q 012323 104 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 146 (466)
Q Consensus 104 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~ 146 (466)
+..+..|.||...++.+|||+|.++++||+..|..|.|-...+
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence 5567789999999999999999999999999999999954433
No 73
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=82.53 E-value=0.66 Score=36.96 Aligned_cols=34 Identities=15% Similarity=0.251 Sum_probs=28.6
Q ss_pred CCCceEEEEeccccceeecCCCchhHHHHHHHhC
Q 012323 103 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMG 136 (466)
Q Consensus 103 ~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~ 136 (466)
.......+.|..+-.|.||||+|.|++.|+.=++
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 3456778899999999999999999999986544
No 74
>PRK01064 hypothetical protein; Provisional
Probab=81.07 E-value=1.8 Score=35.45 Aligned_cols=31 Identities=29% Similarity=0.245 Sum_probs=26.9
Q ss_pred CCceEEEEeccccceeecCCCchhHHHHHHH
Q 012323 104 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKE 134 (466)
Q Consensus 104 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~e 134 (466)
......+.|.++-.|.+|||+|.|++.|..=
T Consensus 28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 4567889999999999999999999988653
No 75
>PHA02977 hypothetical protein; Provisional
Probab=78.89 E-value=10 Score=34.77 Aligned_cols=94 Identities=18% Similarity=0.169 Sum_probs=53.9
Q ss_pred eEEeeccccCCHHHHHHHHHHHHHhhHHhhhhcCCCCeEEEEcccccCCCCC------CCceEEEEeeeccCChhHHHHH
Q 012323 295 HLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSK------DKARILYAPVEEIGDGDRLLHA 368 (466)
Q Consensus 295 HLTL~fLgl~~~eei~~a~~~L~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp------~~~rVLya~V~~~~~~~~L~~L 368 (466)
|+||+.-.-...+..+.-++....+ .-..++++-+..-|||.+. .+-+-+.++++. ++.|..|
T Consensus 71 hitlgian~dq~~~f~~fk~~~~d~--------dl~sis~~cke~icfpqs~askelga~g~avvmkle~---sddlkal 139 (201)
T PHA02977 71 HITLGIANKDQCDNFENFKELIKDI--------DLQSISFTCKEEICFPQSNASKELGAKGCAVVMKLEA---SDDLKAL 139 (201)
T ss_pred ceeeeccCccHhHHHHHHHHHhhcc--------cceeEEEEeeeeEeccccchhhhhCcCccEEEEEEEe---chHHHHH
Confidence 8998765443223333333322222 2366778888888998632 123555666665 3557777
Q ss_pred HHHHHHHHH----HCCCccccCCCCCceeeEEeeeecc
Q 012323 369 CQVIIDAFN----EAGLVFHRDYNKKLKLHATLMNIRH 402 (466)
Q Consensus 369 ~~~L~~~f~----~~Gl~~e~d~~r~fkPHiTLar~~~ 402 (466)
.+.|-.+.- -.|=... ..++.||+|+..++.
T Consensus 140 rnvl~n~vp~pkdifg~i~~---d~~w~phitigyv~~ 174 (201)
T PHA02977 140 RNVLFNAVPCPKDIFGDILS---DNPWCPHITIGYVKA 174 (201)
T ss_pred HHHhhcccCCcHHhhccccc---CCCCCCceEEEeecc
Confidence 777644321 1233332 368999999998864
No 76
>KOG3102 consensus Uncharacterized conserved protein [Function unknown]
Probab=78.24 E-value=7.8 Score=37.66 Aligned_cols=99 Identities=11% Similarity=0.249 Sum_probs=68.4
Q ss_pred CCcceEEeeccccCCHHHHHHHHHHHHHhhHHhhhhcCCCCeEEEEcccccCCCCCCCceEEEE-eeeccCChhHHHHHH
Q 012323 291 PKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYA-PVEEIGDGDRLLHAC 369 (466)
Q Consensus 291 p~~LHLTL~fLgl~~~eei~~a~~~L~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~~rVLya-~V~~~~~~~~L~~L~ 369 (466)
-.-|||.|.=-.-+.--+|...+.+|+.- +. ....|-+++.++.+|-+ .++.|..-+ .+. ..+...+.++.
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 46789988754444445666666666543 22 24778999999999987 466666444 444 35667788888
Q ss_pred HHHHHHHHHCCCccccCCCCCceeeEEeeee
Q 012323 370 QVIIDAFNEAGLVFHRDYNKKLKLHATLMNI 400 (466)
Q Consensus 370 ~~L~~~f~~~Gl~~e~d~~r~fkPHiTLar~ 400 (466)
+.+.+.+....|..- .++| .+|+.|+=.
T Consensus 191 ~~vd~Vm~~~nL~~F--Y~DP-sfHiSL~Wc 218 (269)
T KOG3102|consen 191 DAVDEVMKLHNLPEF--YKDP-SFHISLVWC 218 (269)
T ss_pred HHHHHHHHHcCchhh--hcCC-CCCceEEEE
Confidence 899999998888763 1244 999999855
No 77
>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=76.46 E-value=2.2 Score=38.94 Aligned_cols=39 Identities=15% Similarity=0.071 Sum_probs=34.9
Q ss_pred CCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcC
Q 012323 104 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 142 (466)
Q Consensus 104 ~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP 142 (466)
++....+.||.+-++..|||+|.+++...+=|+-+|+|-
T Consensus 98 ~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 98 GKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 356788999999999999999999999999999888774
No 78
>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=74.17 E-value=3 Score=33.65 Aligned_cols=35 Identities=17% Similarity=0.282 Sum_probs=28.7
Q ss_pred eEEEEeccccceeecCCCchhHHHHHHHhCcEEEc
Q 012323 107 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 141 (466)
Q Consensus 107 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~i 141 (466)
...+.|..+-.+.||||+|.|+..|+-=++.-++-
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 45677778889999999999999998877755553
No 79
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=73.87 E-value=3.6 Score=37.36 Aligned_cols=37 Identities=24% Similarity=0.364 Sum_probs=31.9
Q ss_pred ceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcC
Q 012323 106 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 142 (466)
Q Consensus 106 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP 142 (466)
-.+-+-|+....|..||++|+.++.|++..|-+|.+=
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 3456778888999999999999999999999888773
No 80
>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=73.86 E-value=1.7 Score=34.85 Aligned_cols=36 Identities=25% Similarity=0.351 Sum_probs=31.0
Q ss_pred CceEEEEeccccceeecCCCchhHHHHHHHhCcEEE
Q 012323 105 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKII 140 (466)
Q Consensus 105 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~ 140 (466)
.....+.+-...-+.+||++|+++++|..+.+-.+.
T Consensus 24 ~~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 24 PDQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SSEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CCeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 466788888999999999999999999988876664
No 81
>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=73.69 E-value=0.7 Score=44.19 Aligned_cols=25 Identities=20% Similarity=0.272 Sum_probs=22.7
Q ss_pred ccceeeeeeccCCCccccccccccc
Q 012323 239 QEHKVAVELNIGDNSERVKVDRTSI 263 (466)
Q Consensus 239 p~~fva~~~~~~~~~~~vk~~~~~i 263 (466)
|||||||+|+.+++.+.++.+|+.|
T Consensus 1 pthFl~ipl~~~~i~~~~~~fq~~v 25 (209)
T PF10469_consen 1 PTHFLCIPLNSPEIQEKFKEFQNEV 25 (209)
T ss_pred CCeEEEEECCCHHHHHHHHHHHHHH
Confidence 8999999999999999999998654
No 82
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=72.54 E-value=3.2 Score=33.17 Aligned_cols=25 Identities=36% Similarity=0.478 Sum_probs=21.3
Q ss_pred ceeecCCCchhHHHHHHHh-CcEEEc
Q 012323 117 IRFIKGKEGSTQKKFEKEM-GVKIIL 141 (466)
Q Consensus 117 ~~~IIGk~G~t~k~iE~eT-~~~I~i 141 (466)
.|..||++|..++.|+++. |-+|++
T Consensus 19 vG~~iG~~G~rik~i~~~L~gekIdv 44 (69)
T PF13184_consen 19 VGACIGKKGSRIKAISEELNGEKIDV 44 (69)
T ss_dssp HHHHH-CCCCCHHHHHHHTTT-EEEE
T ss_pred ceecCccccHHHHHHHHHhCCCeEEE
Confidence 7999999999999999999 877776
No 83
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=68.03 E-value=7.9 Score=39.07 Aligned_cols=48 Identities=17% Similarity=0.198 Sum_probs=37.8
Q ss_pred cccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHH
Q 012323 114 ASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEK 166 (466)
Q Consensus 114 ~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~ 166 (466)
....-.|||++|+|++.||--|+|-|-+-. +.|.+.|+= .++..+++.
T Consensus 157 vKRRqRLiGpng~TLKAlelLT~CYilVqG----~TVsaiGpf-kGlkevr~I 204 (356)
T KOG2874|consen 157 VKRRQRLIGPNGSTLKALELLTNCYILVQG----NTVSAIGPF-KGLKEVRKI 204 (356)
T ss_pred HHHHHHhcCCCchhHHHHHHHhhcEEEeeC----cEEEeecCc-chHHHHHHH
Confidence 345667999999999999999999999864 578888863 466665543
No 84
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=64.08 E-value=5.2 Score=32.90 Aligned_cols=37 Identities=11% Similarity=0.253 Sum_probs=30.5
Q ss_pred eEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCC
Q 012323 107 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 143 (466)
Q Consensus 107 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 143 (466)
...|.|-...=|.|||++|..+++|.++..-.+.++.
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~ 67 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE 67 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence 3566666777799999999999999998888877754
No 85
>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=63.26 E-value=7.4 Score=40.57 Aligned_cols=39 Identities=26% Similarity=0.296 Sum_probs=36.2
Q ss_pred CceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCC
Q 012323 105 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 143 (466)
Q Consensus 105 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 143 (466)
.....+.||..-.+.-|||+|.+.|.--.=||.+|+|-+
T Consensus 300 ~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 300 KHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred CcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 367899999999999999999999999999999999854
No 86
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=62.95 E-value=4.7 Score=44.07 Aligned_cols=67 Identities=25% Similarity=0.263 Sum_probs=51.5
Q ss_pred CCCCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEccChhHHHHHHHHHHH
Q 012323 102 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKIQA 169 (466)
Q Consensus 102 s~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~---~~~I~I~G~~~~~v~~A~~~I~~ 169 (466)
-+.-++....+|...++.|+|++|.+++.|+.-.+.+|.+...|. ...+.|.|. +.-+..|+..|..
T Consensus 136 ~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~q-qk~~~~a~~~~~~ 205 (608)
T KOG2279|consen 136 ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQ-QKEVAAAKHLILE 205 (608)
T ss_pred cCCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccc-cchHHHHHhhhhc
Confidence 345667788999999999999999999999999999999987665 334555554 4455566665543
No 87
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=62.63 E-value=7.7 Score=40.88 Aligned_cols=42 Identities=17% Similarity=0.056 Sum_probs=38.1
Q ss_pred CceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC
Q 012323 105 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 146 (466)
Q Consensus 105 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~ 146 (466)
.....+.||....+.-|||+|.+.|.--+=||.+|+|-+-++
T Consensus 307 ~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 307 EKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred CcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 468899999999999999999999999999999999966544
No 88
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=59.09 E-value=12 Score=34.23 Aligned_cols=35 Identities=26% Similarity=0.320 Sum_probs=31.9
Q ss_pred eEEEEeccccceeecCCCchhHHHHHHHhCcEEEc
Q 012323 107 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 141 (466)
Q Consensus 107 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~i 141 (466)
.+-+-|.+...|..||++|..++.|++..|-+|.+
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdV 68 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIEL 68 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEE
Confidence 77888999999999999999999999888877776
No 89
>PLN00108 unknown protein; Provisional
Probab=58.59 E-value=2.1 Score=42.72 Aligned_cols=29 Identities=17% Similarity=0.181 Sum_probs=26.3
Q ss_pred hhhcccceeeeeec-cCCCccccccccccc
Q 012323 235 QQVDQEHKVAVELN-IGDNSERVKVDRTSI 263 (466)
Q Consensus 235 ~~~rp~~fva~~~~-~~~~~~~vk~~~~~i 263 (466)
++..|||||||.|+ .+++.+++++.++.|
T Consensus 32 ~~~~~THFlavPL~~~p~i~~~~~~Fk~~V 61 (257)
T PLN00108 32 HREVFTHFVSLPLAIYPDLKKNIEAFQNSV 61 (257)
T ss_pred cCCCCCeEEEEEcCCCHHHHHHHHHHHHHH
Confidence 36789999999996 899999999999876
No 90
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=56.50 E-value=11 Score=36.15 Aligned_cols=37 Identities=19% Similarity=0.190 Sum_probs=34.7
Q ss_pred eEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCC
Q 012323 107 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 143 (466)
Q Consensus 107 ~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 143 (466)
...+.||..-.+..|||+|.+.+...+=||-+|+|-.
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 7889999999999999999999999999999999854
No 91
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=55.18 E-value=13 Score=39.15 Aligned_cols=40 Identities=25% Similarity=0.269 Sum_probs=36.7
Q ss_pred CceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCCC
Q 012323 105 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS 144 (466)
Q Consensus 105 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~ 144 (466)
.....+.||....+.-|||+|.+.+.--.=||.+|+|=+.
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 4678999999999999999999999999999999999653
No 92
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=53.14 E-value=15 Score=34.43 Aligned_cols=33 Identities=24% Similarity=0.397 Sum_probs=27.2
Q ss_pred EEEEeccccceeecCCCchhHHHHHHHhCcEEEc
Q 012323 108 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 141 (466)
Q Consensus 108 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~i 141 (466)
+-+-|.+-. |.-|||+|.++++|++..|-+|.+
T Consensus 63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~Vev 95 (166)
T PRK06418 63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRV 95 (166)
T ss_pred EEEEEeCCC-cccccccchHHHHHHHHhCCcEEE
Confidence 445555556 999999999999999999987765
No 93
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=53.13 E-value=12 Score=40.78 Aligned_cols=39 Identities=28% Similarity=0.307 Sum_probs=36.0
Q ss_pred CceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCC
Q 012323 105 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 143 (466)
Q Consensus 105 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 143 (466)
.....+-||...++.-|||+|.+.|...+=||.+|+|=+
T Consensus 301 ~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 458899999999999999999999999999999998854
No 94
>PF08302 tRNA_lig_CPD: Fungal tRNA ligase phosphodiesterase domain; InterPro: IPR015965 This entry represents a phosphodiesterase domain found in fungal tRNA ligases []. Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation
Probab=52.81 E-value=65 Score=32.20 Aligned_cols=106 Identities=14% Similarity=0.071 Sum_probs=55.0
Q ss_pred CCcceEEeeccccCCHHHHHHHHHHHHHhh-HHhhhhc--------CCCCeEEEEcccccCCCCCCCceEEEEeeeccCC
Q 012323 291 PKTFHLTVLMLKLWNKDRVNAATNVLKSIS-SKVMDAL--------DNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGD 361 (466)
Q Consensus 291 p~~LHLTL~fLgl~~~eei~~a~~~L~~i~-~~i~~~L--------~~~pf~L~l~GLg~F~~dp~~~rVLya~V~~~~~ 361 (466)
-..||+||.-........-+...+.+..+. ....... ....+.++|..|- |.+ ||+-+.|+-.+.
T Consensus 113 Q~~FHVTL~H~as~k~~~~k~lW~~y~~~~~~~~~~~~~~~~~~~~~~~~~~v~L~rlv-wd~-----rimai~V~~~~~ 186 (257)
T PF08302_consen 113 QPEFHVTLIHRASSKEQPAKELWKRYTKLYKSALKKNPKQEPTQTPTLGSCDVRLERLV-WDD-----RIMAIVVRIVPP 186 (257)
T ss_pred CCCCeEEEEecccCCcCcchHHHHHHHHHHHhhcccccccccccccccceEEEEEEEEE-ECC-----cEEEEEEEccCc
Confidence 356899999987765533112222222211 1111110 0135788998887 877 999988874321
Q ss_pred hhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeeeecccccccCCCccccccHHHHHHHhC
Q 012323 362 GDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFG 425 (466)
Q Consensus 362 ~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fkPHiTLar~~~~~~~~~~~~~~~fda~~il~~~~ 425 (466)
...-.. ..++.. -.=.|||||+-... ...|+....+++.+.
T Consensus 187 ~~~~~~----------~~~~~c-----~N~~~HITVGT~~~--------~VkP~eSN~Ll~~~~ 227 (257)
T PF08302_consen 187 EDEEDE----------VPEWEC-----TNKIPHITVGTRDP--------GVKPKESNDLLERWL 227 (257)
T ss_pred cccccc----------cCCccc-----CCCCCEEEEEcCCC--------CCCcchHHHHHHHHH
Confidence 100000 234432 23489999997632 222344455666544
No 95
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=50.11 E-value=14 Score=32.02 Aligned_cols=32 Identities=25% Similarity=0.377 Sum_probs=26.3
Q ss_pred EEEEeccccceeecCCCchhHHHHHHHhCcEE
Q 012323 108 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKI 139 (466)
Q Consensus 108 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I 139 (466)
+.|.|-..+-|.|||++|+++++|.+.....+
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 56666677789999999999999988877654
No 96
>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=50.06 E-value=16 Score=34.91 Aligned_cols=42 Identities=17% Similarity=0.074 Sum_probs=20.6
Q ss_pred EEEEeeec-cCChhHHHHHHHHHHHHHHHCCCccccCCCCCceeeEEeeee
Q 012323 351 ILYAPVEE-IGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNI 400 (466)
Q Consensus 351 VLya~V~~-~~~~~~L~~L~~~L~~~f~~~Gl~~e~d~~r~fkPHiTLar~ 400 (466)
-||+-+.. .+....|+.|-..|...|-.. .-.|-|||||+-.
T Consensus 4 SlWl~P~~~~~~~~~L~~lI~~L~~~~~~~--------~p~F~PHiTL~s~ 46 (196)
T PF07823_consen 4 SLWLVPPPGSPLYERLKTLISSLASLFPGS--------PPPFEPHITLTSG 46 (196)
T ss_dssp EEEEEE-T--TTHHHHHHHHHHHHHHST-----------------EEEEEE
T ss_pred EEEEcCCCCccHHHHHHHHHHHHHHHCCCC--------CCCcCCeEEEeCC
Confidence 47886654 234566777766666654311 2479999999964
No 97
>COG5255 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.81 E-value=26 Score=34.02 Aligned_cols=108 Identities=18% Similarity=0.217 Sum_probs=0.0
Q ss_pred CCCccccCCCcceEEeeccccCCHHH----------HHHHHHHHHHhhHHhhhhcCCCCeEEEEcccccCCCCCCCceEE
Q 012323 283 IDKSIFIKPKTFHLTVLMLKLWNKDR----------VNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARIL 352 (466)
Q Consensus 283 i~~~~~v~p~~LHLTL~fLgl~~~ee----------i~~a~~~L~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~~rVL 352 (466)
.++-.|+|+..+|+|+ |=|+.++.+ ++.-.+++...-.+-.+++..-+=.+.++-.+.=+. .++
T Consensus 71 adklt~tP~sSlHMTv-fqg~~e~~R~~~~WpqdlPLDtpi~~~~~~~~erLk~F~l~~~~~~mrvte~rp~-----~i~ 144 (239)
T COG5255 71 ADKLTFTPVSSLHMTV-FQGLIEERRELPYWPQDLPLDTPIDAITDYYAERLKIFPLLDEEFNMRVTEMRPQ-----GIL 144 (239)
T ss_pred hhhhccCCcchhhHHH-HHHHhhhcccCCCCCccCCCCCcHHHHHHHHHHHHhcccCCchhhcchhhccccc-----ceE
Q ss_pred EEeeeccCChhHHHHHHHHHHHHHHH-CCCccccCCCCCceeeEEeeeeccc
Q 012323 353 YAPVEEIGDGDRLLHACQVIIDAFNE-AGLVFHRDYNKKLKLHATLMNIRHK 403 (466)
Q Consensus 353 ya~V~~~~~~~~L~~L~~~L~~~f~~-~Gl~~e~d~~r~fkPHiTLar~~~~ 403 (466)
-.++. +.=++....+++.|.+ +|+...+ .+.|..||||+..+.+
T Consensus 145 v~pad-----dad~~~l~~~Rd~ls~~~g~r~P~--HDaY~FHITlgYl~~w 189 (239)
T COG5255 145 VEPAD-----DADAKILEEWRDYLSEKFGYRHPD--HDAYQFHITLGYLRIW 189 (239)
T ss_pred eccCC-----HHHHHHHHHHHHHHhhhhcccCCC--CcceEEEEEeeeEeee
No 98
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=45.14 E-value=51 Score=34.43 Aligned_cols=55 Identities=20% Similarity=0.297 Sum_probs=45.1
Q ss_pred cccceeecCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEccChhHHHHHHHHHH--HHHHH
Q 012323 114 ASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQ--AIIAE 173 (466)
Q Consensus 114 ~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~~~~~v~~A~~~I~--~i~~~ 173 (466)
....--+.|+.|..++.||+.+|+.|.-+. ..+.|+|. +..|..|...++ .+...
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG----~~~~i~g~-~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVARG----EAVRIIGA-RPLVDVATRVLLTLELLAE 79 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEeCC----ceEEEEec-hHHHHHHHHHHhHHHHHHH
Confidence 455667899999999999999999998765 57899996 359999999998 44444
No 99
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=44.44 E-value=22 Score=38.34 Aligned_cols=39 Identities=23% Similarity=0.244 Sum_probs=35.9
Q ss_pred CceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcCC
Q 012323 105 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 143 (466)
Q Consensus 105 ~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~ 143 (466)
.....+.||....+.-|||+|.+.|---.=||.+|+|-+
T Consensus 334 ~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 334 GRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred CcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 356789999999999999999999999999999999965
No 100
>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=42.51 E-value=55 Score=26.82 Aligned_cols=35 Identities=31% Similarity=0.474 Sum_probs=27.4
Q ss_pred CcEEEcCCCCCCCcEEEEcc-ChhHHHHHHHHHHHHHHH
Q 012323 136 GVKIILPSSKKEDSIIIEGN-STDSVAKASEKIQAIIAE 173 (466)
Q Consensus 136 ~~~I~iP~~~~~~~I~I~G~-~~~~v~~A~~~I~~i~~~ 173 (466)
++.+.|=+ +|-|+|+|. +.+.+..|.++|..++.+
T Consensus 49 ~~t~~IF~---sGki~itGaks~~~~~~a~~~i~~~L~~ 84 (86)
T PF00352_consen 49 KATVLIFS---SGKIVITGAKSEEEAKKAIEKILPILQK 84 (86)
T ss_dssp TEEEEEET---TSEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred cEEEEEEc---CCEEEEEecCCHHHHHHHHHHHHHHHHH
Confidence 56666654 477999994 888889998888888875
No 101
>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=41.95 E-value=29 Score=34.34 Aligned_cols=29 Identities=24% Similarity=0.236 Sum_probs=21.2
Q ss_pred ceEEEEeccccc-eeecCCCchhHHHHHHH
Q 012323 106 HSLSVEVGASVI-RFIKGKEGSTQKKFEKE 134 (466)
Q Consensus 106 ~~~~v~Vp~~~~-~~IIGk~G~t~k~iE~e 134 (466)
....|.|.++-| +.|||++|+++|+|-.+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 456677776555 67889999999985433
No 102
>PRK15494 era GTPase Era; Provisional
Probab=33.72 E-value=29 Score=35.89 Aligned_cols=36 Identities=28% Similarity=0.375 Sum_probs=26.0
Q ss_pred ceEEEEeccccc-eeecCCCchhHHH--------HHHHhCcEEEc
Q 012323 106 HSLSVEVGASVI-RFIKGKEGSTQKK--------FEKEMGVKIIL 141 (466)
Q Consensus 106 ~~~~v~Vp~~~~-~~IIGk~G~t~k~--------iE~eT~~~I~i 141 (466)
....|.|.++-| +.|||++|.++|+ ||+-+|+++.+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 446777887555 6789999999987 45556666654
No 103
>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=33.56 E-value=43 Score=30.72 Aligned_cols=34 Identities=26% Similarity=0.286 Sum_probs=29.2
Q ss_pred EEEEeccccceeecCCCchhHHHHHHHhCcEEEc
Q 012323 108 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 141 (466)
Q Consensus 108 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~i 141 (466)
-.|.|-.+.=|++||++|.++++|-.+||-+-.+
T Consensus 78 GEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~v 111 (145)
T cd02410 78 GEVIIEAEKPGLVIGKGGSTLREITRETGWAPKV 111 (145)
T ss_pred cEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEE
Confidence 3566667778999999999999999999988666
No 104
>COG0799 Uncharacterized homolog of plant Iojap protein [Function unknown]
Probab=33.25 E-value=2.1e+02 Score=25.30 Aligned_cols=61 Identities=11% Similarity=0.153 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHhhHHhhhhcCCCCeEEEEcccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcc
Q 012323 308 RVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 383 (466)
Q Consensus 308 ei~~a~~~L~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~~rVLya~V~~~~~~~~L~~L~~~L~~~f~~~Gl~~ 383 (466)
.+..+.++|...+ ......|.++|..++-+ ..+.+.- .+...+..+++.|.+.+.++|+.+
T Consensus 6 l~~~i~~alddkK-------AeDIv~lDv~~~s~~tD-----yfVIatg---~s~rhv~Aiad~i~~~~k~~g~~~ 66 (115)
T COG0799 6 LLEVIVEALDDKK-------AEDIVVLDVSGKSSLTD-----YFVIATG---NSSRHVKAIADNVKEELKEAGEVP 66 (115)
T ss_pred HHHHHHHHHHhcc-------CCCeEEEEccCCccccc-----EEEEEEe---CchHHHHHHHHHHHHHHHHcCCCc
Confidence 3444555555443 34667899999999988 4444433 236789999999999999999877
No 105
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=32.72 E-value=41 Score=27.58 Aligned_cols=31 Identities=13% Similarity=0.259 Sum_probs=22.6
Q ss_pred EEEEeccccceeecCCCchhHHHHHHHhCcE
Q 012323 108 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVK 138 (466)
Q Consensus 108 ~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~ 138 (466)
..+.|-..+-|.+||++|.++++|.+.-.-.
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l~k~ 70 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEILETK 70 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHHHHH
Confidence 3444444777999999999999887765433
No 106
>PRK00089 era GTPase Era; Reviewed
Probab=32.40 E-value=33 Score=34.17 Aligned_cols=36 Identities=33% Similarity=0.417 Sum_probs=24.8
Q ss_pred ceEEEEecccc-ceeecCCCchhHHH--------HHHHhCcEEEc
Q 012323 106 HSLSVEVGASV-IRFIKGKEGSTQKK--------FEKEMGVKIIL 141 (466)
Q Consensus 106 ~~~~v~Vp~~~-~~~IIGk~G~t~k~--------iE~eT~~~I~i 141 (466)
....|.|.++- -+.|||++|+++|+ ||+-++++|.+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 44556666544 46789999999987 45556666655
No 107
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=31.84 E-value=44 Score=32.03 Aligned_cols=36 Identities=31% Similarity=0.305 Sum_probs=29.3
Q ss_pred ceEEEEeccccceeecCCCchhHHHHHHHhCcEEEc
Q 012323 106 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 141 (466)
Q Consensus 106 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~i 141 (466)
......+-..-.|..||++|..++.|.++.|-+|+|
T Consensus 76 av~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdV 111 (190)
T COG0195 76 AVVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDV 111 (190)
T ss_pred ceEEeecCcCchhhhccCCChHHHHHHHHhCCceEE
Confidence 345555666778999999999999999999966665
No 108
>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=31.34 E-value=49 Score=32.45 Aligned_cols=69 Identities=14% Similarity=0.185 Sum_probs=42.5
Q ss_pred cceeeeeeccCCCccccccccccccccccccccCCCCCCCCCCCCCccccCCCcceEEeeccccCCHHHHHHH-HHHHHH
Q 012323 240 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAA-TNVLKS 318 (466)
Q Consensus 240 ~~fva~~~~~~~~~~~vk~~~~~i~~~~~~~~~~r~~~~~~~gi~~~~~v~p~~LHLTL~fLgl~~~eei~~a-~~~L~~ 318 (466)
..|++++|..+.... ++...+.|- .++..+|+++-+ .....+|+.|+..-....+++... .+.+..
T Consensus 141 R~FL~l~V~~~~~~~-l~~l~~~i~-----------~~l~~~~lp~~Y-~~~~~fHvSIAw~~~~~~~~l~~~~~~~~~~ 207 (239)
T PF09749_consen 141 RSFLALRVSEGSNNE-LKRLLDRIN-----------EVLKEFGLPPFY-DEDPSFHVSIAWTLGDPSEELKESSLKILQE 207 (239)
T ss_pred eEEEEEEecccccHH-HHHHHHHHH-----------HHHHHhCCCccc-CCCCCCEEEEEEECCCchHHHHHHHHHHHHH
Confidence 589999999876543 555554441 123455554433 488899999998754445555544 355555
Q ss_pred hhH
Q 012323 319 ISS 321 (466)
Q Consensus 319 i~~ 321 (466)
+..
T Consensus 208 ~~~ 210 (239)
T PF09749_consen 208 PLD 210 (239)
T ss_pred HHh
Confidence 433
No 109
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=31.19 E-value=37 Score=37.29 Aligned_cols=45 Identities=24% Similarity=0.299 Sum_probs=35.2
Q ss_pred cccccccCCCCCCCCCCceEEEEeccccceeecCCCchhHHHHHHHhCcEEEc
Q 012323 89 DIKDETLEGEPVPSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 141 (466)
Q Consensus 89 ~~~~~~~~~~~~~s~~~~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~i 141 (466)
.++|..|+++ +-+|-|-.+-=|.+|||+|++.++|-++||-+-.|
T Consensus 90 ~i~~i~Fd~~--------tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~i 134 (637)
T COG1782 90 GITDIYFDDD--------TGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKI 134 (637)
T ss_pred CceeEEecCC--------CceEEEEecCCceEEecCchHHHHHHHHhCCccee
Confidence 5556666444 34666777778999999999999999999987665
No 110
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=30.54 E-value=40 Score=33.28 Aligned_cols=37 Identities=24% Similarity=0.267 Sum_probs=28.2
Q ss_pred ceEEEEeccccceeecCCCchhHHHHHHHhCcEEEcC
Q 012323 106 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 142 (466)
Q Consensus 106 ~~~~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP 142 (466)
..+.|.|=...=|.+||++|+.+++|.++....+..+
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~ 87 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKE 87 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCC
Confidence 3456666677789999999999999887776655553
No 111
>PRK09256 hypothetical protein; Provisional
Probab=29.70 E-value=1.1e+02 Score=27.81 Aligned_cols=54 Identities=24% Similarity=0.399 Sum_probs=37.1
Q ss_pred cCCCchhHHHHHHHhCcEEEcCCC--------------------CCCCcEEEEc----cChhHHHHHHHHHHHHHHHhhh
Q 012323 121 KGKEGSTQKKFEKEMGVKIILPSS--------------------KKEDSIIIEG----NSTDSVAKASEKIQAIIAEAVE 176 (466)
Q Consensus 121 IGk~G~t~k~iE~eT~~~I~iP~~--------------------~~~~~I~I~G----~~~~~v~~A~~~I~~i~~~~~~ 176 (466)
=|+||...++. +|.++|.++-. ..++.++|+. ....+.+.|.+++..++.++..
T Consensus 23 SGPGGQ~VNKt--~SkV~l~~~~~~~~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~~RSQ~~Nr~~al~kL~~~i~~~~~ 100 (138)
T PRK09256 23 SGPGGQNVNKV--STAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQERNREDALERLVALIREALK 100 (138)
T ss_pred CCCCccccccc--ceeeEEEechhhccCCHHHHHHHHHHhcCcccCCCcEEEEECCcCCHHHHHHHHHHHHHHHHHHHhh
Confidence 48888888776 45555553211 1246688877 2456899999999999988665
No 112
>PRK11538 ribosome-associated protein; Provisional
Probab=28.25 E-value=2.9e+02 Score=23.78 Aligned_cols=60 Identities=7% Similarity=0.185 Sum_probs=39.6
Q ss_pred HHHHHHHHHHhhHHhhhhcCCCCeEEEEcccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcc
Q 012323 309 VNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 383 (466)
Q Consensus 309 i~~a~~~L~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~~rVLya~V~~~~~~~~L~~L~~~L~~~f~~~Gl~~ 383 (466)
+..++++|.+.+ ...-..|.++++..|-+ -.+-+.. .+...++.+++.|.+.+.+.|+.+
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 444555555443 23445678889888876 3333333 346789999999999998887754
No 113
>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=28.11 E-value=2e+02 Score=26.89 Aligned_cols=79 Identities=13% Similarity=0.085 Sum_probs=45.1
Q ss_pred eeccCChhHHHHHHHHHHHHHHHCCCcccc---------------C----------CCCCceeeEEeeeecccccccCCC
Q 012323 356 VEEIGDGDRLLHACQVIIDAFNEAGLVFHR---------------D----------YNKKLKLHATLMNIRHKKRRKGTR 410 (466)
Q Consensus 356 V~~~~~~~~L~~L~~~L~~~f~~~Gl~~e~---------------d----------~~r~fkPHiTLar~~~~~~~~~~~ 410 (466)
+.+.+....|+.|+..+...|-..-=...+ + -=..|..||||-.---...
T Consensus 47 Lvp~~~~~~L~~LAa~cV~~~d~fRAPls~aelaRR~~~~Ls~~Q~~~L~rWGYPYV~deFRFHmTLTg~l~~~~----- 121 (160)
T PF06299_consen 47 LVPAGPCPALQALAAACVRAFDPFRAPLSEAELARRRPAGLSPRQRANLERWGYPYVMDEFRFHMTLTGRLDPAE----- 121 (160)
T ss_pred EeeCCCCHHHHHHHHHHHHhhhhccCCCChHHHhhcCcccCCHHHHHHHHHhCCCceeCcCEeeEEeCCCCCHHH-----
Confidence 334345689999999999888653111110 0 0157999999985431110
Q ss_pred ccccccHHHHH-HHhCCCccccEEecEEEEEee
Q 012323 411 RVDYFDARDIF-KQFGSKEWGEYLIKEAHLSQR 442 (466)
Q Consensus 411 ~~~~fda~~il-~~~~~~~fG~~~V~eI~Ls~~ 442 (466)
.. .+...+ ..|...-...+.|+.|.|+.-
T Consensus 122 -~~--~~~~~l~~~f~~~l~~p~~id~laLf~e 151 (160)
T PF06299_consen 122 -RA--RVEAALEAHFAPLLPEPLRIDSLALFGE 151 (160)
T ss_pred -HH--HHHHHHHHHHHhhcCCCeeecceEEEec
Confidence 00 011222 234555456789999999754
No 114
>KOG3429 consensus Predicted peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=27.57 E-value=87 Score=29.38 Aligned_cols=56 Identities=21% Similarity=0.366 Sum_probs=41.8
Q ss_pred ecCCCchhHHHHHHHhCcEEEcCCCCC---------------------CCcEEEEcc----ChhHHHHHHHHHHHHHHHh
Q 012323 120 IKGKEGSTQKKFEKEMGVKIILPSSKK---------------------EDSIIIEGN----STDSVAKASEKIQAIIAEA 174 (466)
Q Consensus 120 IIGk~G~t~k~iE~eT~~~I~iP~~~~---------------------~~~I~I~G~----~~~~v~~A~~~I~~i~~~~ 174 (466)
==|+||.+.+++ -|.|.+.|+-... .+.++|... ..-+++.|.+.|..++..+
T Consensus 49 SSGPGGQNVNKv--NTKv~vrf~vs~a~Wipe~~R~~~~~~~~~rink~gelvI~Sd~TRsq~~NiaDcleKlr~~I~~~ 126 (172)
T KOG3429|consen 49 SSGPGGQNVNKV--NTKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRSQHKNIADCLEKLRDIIRAA 126 (172)
T ss_pred cCCCCCcccccc--cceEEEEEecchhhhccHHHHHHHHHHHHHhhccCccEEEecchhHHhhccHHHHHHHHHHHHHHH
Confidence 349999999887 6777777775422 256888772 3458999999999999987
Q ss_pred hhC
Q 012323 175 VES 177 (466)
Q Consensus 175 ~~~ 177 (466)
.+-
T Consensus 127 ~~~ 129 (172)
T KOG3429|consen 127 EQT 129 (172)
T ss_pred hcC
Confidence 663
No 115
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....
Probab=27.42 E-value=85 Score=27.30 Aligned_cols=48 Identities=21% Similarity=0.295 Sum_probs=35.6
Q ss_pred cCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEcc----ChhHHHHHHHHHHHHHHHh
Q 012323 121 KGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGN----STDSVAKASEKIQAIIAEA 174 (466)
Q Consensus 121 IGk~G~t~k~iE~eT~~~I~iP~~~~~~~I~I~G~----~~~~v~~A~~~I~~i~~~~ 174 (466)
=|+||...++- +|.++|.+.. ..|+|+.. ...+.+.|.+++...+.++
T Consensus 22 sGpGGQ~VNk~--~s~V~l~h~p----tgi~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~ 73 (113)
T PF00472_consen 22 SGPGGQNVNKT--NSKVRLRHIP----TGIVVKCQESRSQHQNREDALEKLREKLDEA 73 (113)
T ss_dssp SSSSSCHHHSS--SEEEEEEETT----TTEEEEEESSSSHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCccccc--CCEEEEEEec----ccEEEEEcccCCHHHHHHHHHHHHHHHHHHH
Confidence 38999999775 5667777753 23777762 4578899999999888874
No 116
>COG1159 Era GTPase [General function prediction only]
Probab=24.55 E-value=40 Score=34.55 Aligned_cols=27 Identities=26% Similarity=0.308 Sum_probs=20.3
Q ss_pred CceEEEEeccc-cceeecCCCchhHHHH
Q 012323 105 RHSLSVEVGAS-VIRFIKGKEGSTQKKF 131 (466)
Q Consensus 105 ~~~~~v~Vp~~-~~~~IIGk~G~t~k~i 131 (466)
.....+.|+++ .-+.||||+|+++|+|
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 34556777764 4567899999999887
No 117
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=23.37 E-value=3.5e+02 Score=27.36 Aligned_cols=83 Identities=14% Similarity=0.195 Sum_probs=47.9
Q ss_pred cceEEeeccccCCHHHHHHHHHHHHHhhHHhhhhcCCCCeEEEEcccccCCCCCCCceE-EEEeeeccCChhHHHHHHHH
Q 012323 293 TFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARI-LYAPVEEIGDGDRLLHACQV 371 (466)
Q Consensus 293 ~LHLTL~fLgl~~~eei~~a~~~L~~i~~~i~~~L~~~pf~L~l~GLg~F~~dp~~~rV-Lya~V~~~~~~~~L~~L~~~ 371 (466)
+.++++.+=.. .+++++.+.|.++.......+..++..+.+.+++-..= ...| .|+... +-...-.++...
T Consensus 185 r~~~~v~V~y~---~d~~~~~~il~~~~~~~~~vl~~p~p~v~~~~~~dssi---~~~v~~wv~~~--~~~~~~~~~~~~ 256 (286)
T PRK10334 185 RNEFIIGVAYD---SDIDQVKQILTNIIQSEDRILKDREMTVRLNELGASSI---NFVVRVWSNSG--DLQNVYWDVLER 256 (286)
T ss_pred EEEEEEEecCC---CCHHHHHHHHHHHHHhCCceecCCCCEEEEEeeeCceE---EEEEEEEEecc--hhHHHHHHHHHH
Confidence 45666665444 44666667777765444445555666676665433321 1111 344322 222334577888
Q ss_pred HHHHHHHCCCcc
Q 012323 372 IIDAFNEAGLVF 383 (466)
Q Consensus 372 L~~~f~~~Gl~~ 383 (466)
+.++|.++|+..
T Consensus 257 I~~~f~~~gI~i 268 (286)
T PRK10334 257 IKREFDAAGISF 268 (286)
T ss_pred HHHHHHHCCCcC
Confidence 999999999987
No 118
>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=22.02 E-value=4.2e+02 Score=22.37 Aligned_cols=46 Identities=13% Similarity=0.184 Sum_probs=33.2
Q ss_pred CCeEEEEcccccCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcc
Q 012323 330 RPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 383 (466)
Q Consensus 330 ~pf~L~l~GLg~F~~dp~~~rVLya~V~~~~~~~~L~~L~~~L~~~f~~~Gl~~ 383 (466)
.-.-+.+++...|-+ -.+-+.. .+...++.+++.|.+.+.+.|+.+
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 445677788887776 3333333 346789999999999999888754
No 119
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=21.44 E-value=35 Score=40.89 Aligned_cols=64 Identities=20% Similarity=0.106 Sum_probs=51.1
Q ss_pred EEEeccccceeecCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEccChhHHHHHHHHHHHHHHH
Q 012323 109 SVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIAE 173 (466)
Q Consensus 109 ~v~Vp~~~~~~IIGk~G~t~k~iE~eT~~~I~iP~~~~----~~~I~I~G~~~~~v~~A~~~I~~i~~~ 173 (466)
.+.+|.-....+||++|.+++.+..-||+-|.|-+-.. +..+.+.|. .+.+.-|.--|..++.+
T Consensus 1343 k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~-p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1343 KGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGR-PPSQRVATSPIGLPIID 1410 (2131)
T ss_pred ccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCC-Chhhhhhhccccceeec
Confidence 45678888999999999999999999999999987322 346778886 46788888777776654
No 120
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=21.10 E-value=1e+02 Score=24.94 Aligned_cols=35 Identities=23% Similarity=0.421 Sum_probs=21.9
Q ss_pred CHHHHHHHHHHHHHhhHHhhhhcCCCCeEEEEcccccCC
Q 012323 305 NKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMR 343 (466)
Q Consensus 305 ~~eei~~a~~~L~~i~~~i~~~L~~~pf~L~l~GLg~F~ 343 (466)
+..++..+.++|.++ +.+.|.... .+.|.|+|.|.
T Consensus 17 ~~~~v~~vl~~l~~~---i~~~L~~g~-~V~i~g~G~F~ 51 (90)
T smart00411 17 SKKDAKAAVDAFLEI---ITEALKKGE-KVELRGFGTFE 51 (90)
T ss_pred CHHHHHHHHHHHHHH---HHHHHhCCC-eEEEeCcEEEE
Confidence 466666655555443 444443332 78899999995
No 121
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=20.54 E-value=2.9e+02 Score=23.38 Aligned_cols=62 Identities=11% Similarity=0.191 Sum_probs=42.3
Q ss_pred hhHHHHHHHhCcEEEcCCCC--CCCcEEEEccChhHHHHHHHHHHHHHHHhhhCCCCcceEEEEeccc
Q 012323 126 STQKKFEKEMGVKIILPSSK--KEDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDYSHFVSLPLA 191 (466)
Q Consensus 126 ~t~k~iE~eT~~~I~iP~~~--~~~~I~I~G~~~~~v~~A~~~I~~i~~~~~~~~k~~~ThFIsIPl~ 191 (466)
..+++||++.|+.+-...++ ..+.+++|.. -+.+....+.|+..++++.. ...-+-|+ .|++
T Consensus 35 ~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~-G~~l~~~~~~~~~~~~~~~~--~~~~~~~~-~~~~ 98 (99)
T TIGR00637 35 DYIRAMNNLSGEPLVERATGGKGGGGAVLTEY-GQRLIQLYDLLERILEKAFS--VLEDEVVV-KPLK 98 (99)
T ss_pred HHHHHHHHHhCCCeEEecCCCCCCCCeeECHH-HHHHHHHHHHHHHHHHHHHH--Hhhceeee-ccCC
Confidence 35789999999998776543 2346777764 35677778888888877666 34445555 6653
No 122
>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=20.18 E-value=1.2e+02 Score=24.41 Aligned_cols=35 Identities=20% Similarity=0.356 Sum_probs=21.1
Q ss_pred CHHHHHHHHHHHHHhhHHhhhhcCCCCeEEEEcccccCC
Q 012323 305 NKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMR 343 (466)
Q Consensus 305 ~~eei~~a~~~L~~i~~~i~~~L~~~pf~L~l~GLg~F~ 343 (466)
+..++..+.+.|..+ +.+.|... -.+.|.|+|.|.
T Consensus 16 ~~~~v~~vl~~~~~~---i~~~L~~g-~~V~l~~~G~F~ 50 (87)
T cd00591 16 SKKDAEAAVDAFLDV---ITEALAKG-EKVELPGFGTFE 50 (87)
T ss_pred CHHHHHHHHHHHHHH---HHHHHhCC-CeEEEeCCEEEE
Confidence 455555555544443 44444332 288999999995
No 123
>PF10105 DUF2344: Uncharacterized protein conserved in bacteria (DUF2344); InterPro: IPR018768 This domain, found in various hypothetical bacterial proteins and Radical Sam domain proteins, has no known function.
Probab=20.00 E-value=1.2e+02 Score=28.79 Aligned_cols=31 Identities=26% Similarity=0.412 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHCCCccccCCCCCceeeEEee
Q 012323 366 LHACQVIIDAFNEAGLVFHRDYNKKLKLHATLM 398 (466)
Q Consensus 366 ~~L~~~L~~~f~~~Gl~~e~d~~r~fkPHiTLa 398 (466)
.++...+.++|..+||+.. ..+.|.||.-+.
T Consensus 18 Ldl~r~~eRa~rRA~lp~a--~SqGFnP~Pkis 48 (187)
T PF10105_consen 18 LDLMRVFERALRRAGLPVA--YSQGFNPHPKIS 48 (187)
T ss_pred HHHHHHHHHHhhhcCCCee--ecCCCCCCccee
Confidence 4678889999999999996 578999995443
Done!