Query 012372
Match_columns 465
No_of_seqs 215 out of 439
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 01:57:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012372.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012372hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2814 Transcription coactiva 100.0 1.4E-43 3E-48 354.1 16.7 275 60-442 2-281 (345)
2 PLN00108 unknown protein; Prov 100.0 3.2E-35 6.9E-40 288.4 16.7 160 227-442 33-195 (257)
3 PF10469 AKAP7_NLS: AKAP7 2'5' 100.0 1.5E-28 3.3E-33 232.2 14.6 146 230-445 1-151 (209)
4 cd02393 PNPase_KH Polynucleoti 99.3 2.6E-12 5.7E-17 101.1 6.8 59 155-216 3-61 (61)
5 cd02394 vigilin_like_KH K homo 99.3 5.3E-12 1.2E-16 98.0 6.0 60 156-216 2-62 (62)
6 PF00013 KH_1: KH domain syndr 99.2 1.2E-11 2.5E-16 95.5 3.9 60 155-215 1-60 (60)
7 cd00105 KH-I K homology RNA-bi 99.0 7.4E-10 1.6E-14 85.3 6.1 59 156-215 2-63 (64)
8 smart00322 KH K homology RNA-b 98.9 1.4E-08 3.1E-13 76.9 8.3 66 153-219 2-68 (69)
9 cd02396 PCBP_like_KH K homolog 98.8 7.3E-09 1.6E-13 81.9 6.3 59 156-215 2-64 (65)
10 TIGR02696 pppGpp_PNP guanosine 98.8 6E-09 1.3E-13 115.6 6.5 82 153-238 577-669 (719)
11 PF13014 KH_3: KH domain 98.7 1.8E-08 4E-13 73.6 4.0 39 164-202 1-43 (43)
12 cd02395 SF1_like-KH Splicing f 98.7 4.3E-08 9.2E-13 87.4 6.7 59 163-221 15-95 (120)
13 TIGR03591 polynuc_phos polyrib 98.6 3.7E-08 8.1E-13 109.5 6.1 82 153-238 550-640 (684)
14 PRK13763 putative RNA-processi 98.6 9.3E-08 2E-12 90.3 6.8 66 153-220 2-70 (180)
15 COG1185 Pnp Polyribonucleotide 98.6 7.7E-08 1.7E-12 105.6 6.5 83 153-239 551-642 (692)
16 TIGR02258 2_5_ligase 2'-5' RNA 98.6 7.2E-07 1.6E-11 82.0 11.8 91 336-438 33-131 (179)
17 TIGR03665 arCOG04150 arCOG0415 98.5 1.4E-07 3.1E-12 88.3 4.9 61 158-220 2-64 (172)
18 PLN00207 polyribonucleotide nu 98.4 1.6E-07 3.4E-12 106.5 4.8 82 153-238 684-776 (891)
19 KOG1676 K-homology type RNA bi 98.3 9.8E-07 2.1E-11 95.6 7.5 107 151-258 227-346 (600)
20 PRK11824 polynucleotide phosph 98.2 9.3E-07 2E-11 98.6 4.0 80 155-238 555-643 (693)
21 PRK15124 2'-5' RNA ligase; Pro 98.0 9E-05 2E-09 69.1 12.2 94 336-443 36-130 (176)
22 KOG2193 IGF-II mRNA-binding pr 98.0 6.4E-06 1.4E-10 86.6 4.7 104 152-258 197-308 (584)
23 COG1514 LigT 2'-5' RNA ligase 98.0 8E-05 1.7E-09 70.6 11.7 93 336-439 32-132 (180)
24 TIGR03665 arCOG04150 arCOG0415 97.9 1.4E-05 3E-10 75.1 6.0 54 163-221 98-151 (172)
25 PRK04163 exosome complex RNA-b 97.9 1.8E-05 3.9E-10 77.7 6.6 63 156-221 147-209 (235)
26 PRK13763 putative RNA-processi 97.9 2E-05 4.4E-10 74.5 6.2 53 164-221 105-157 (180)
27 KOG0119 Splicing factor 1/bran 97.9 2E-05 4.4E-10 84.1 6.4 72 153-224 137-233 (554)
28 KOG2208 Vigilin [Lipid transpo 97.8 3.2E-05 7E-10 87.3 6.9 104 152-259 345-449 (753)
29 KOG2191 RNA-binding protein NO 97.7 0.00021 4.5E-09 73.6 10.7 107 151-258 36-160 (402)
30 PHA02574 57B hypothetical prot 97.5 0.00048 1E-08 63.9 8.7 78 336-436 37-118 (149)
31 PRK13679 hypothetical protein; 97.4 0.0011 2.3E-08 61.4 10.3 82 343-436 34-120 (168)
32 KOG1676 K-homology type RNA bi 97.4 0.00022 4.7E-09 77.8 6.5 106 152-258 137-258 (600)
33 KOG2191 RNA-binding protein NO 97.3 0.00044 9.5E-09 71.3 6.4 66 155-221 133-204 (402)
34 KOG2190 PolyC-binding proteins 97.2 0.0011 2.4E-08 71.8 8.6 67 154-221 138-208 (485)
35 KOG2193 IGF-II mRNA-binding pr 97.2 0.00039 8.5E-09 73.5 4.6 67 155-222 281-353 (584)
36 KOG2192 PolyC-binding hnRNP-K 97.0 0.0016 3.4E-08 65.8 7.1 71 151-222 312-385 (390)
37 KOG1067 Predicted RNA-binding 97.0 0.00057 1.2E-08 74.5 3.5 82 153-239 596-691 (760)
38 KOG1588 RNA-binding protein Sa 96.9 0.0022 4.8E-08 64.3 7.1 42 153-194 91-138 (259)
39 COG5176 MSL5 Splicing factor ( 96.9 0.0013 2.9E-08 64.2 5.1 75 145-219 139-219 (269)
40 KOG2113 Predicted RNA binding 96.9 0.0013 2.9E-08 67.4 5.1 65 152-217 24-88 (394)
41 PF05213 Corona_NS2A: Coronavi 96.8 0.015 3.2E-07 57.2 11.8 118 229-437 5-131 (248)
42 PF13563 2_5_RNA_ligase2: 2'-5 96.4 0.0078 1.7E-07 53.0 6.4 93 340-445 24-118 (153)
43 COG1094 Predicted RNA-binding 96.0 0.011 2.3E-07 57.3 5.4 53 164-221 112-164 (194)
44 COG1094 Predicted RNA-binding 96.0 0.015 3.3E-07 56.2 6.4 66 152-219 6-75 (194)
45 TIGR03319 YmdA_YtgF conserved 96.0 0.015 3.3E-07 63.5 7.0 68 152-221 202-270 (514)
46 PRK12704 phosphodiesterase; Pr 95.8 0.017 3.6E-07 63.2 6.6 68 152-221 208-276 (520)
47 KOG0336 ATP-dependent RNA heli 95.8 0.0062 1.4E-07 65.0 3.2 69 152-221 45-113 (629)
48 PRK00106 hypothetical protein; 95.7 0.024 5.3E-07 62.3 7.1 68 152-221 223-291 (535)
49 cd02134 NusA_KH NusA_K homolog 95.6 0.014 3.1E-07 46.0 3.7 37 153-189 24-60 (61)
50 COG1097 RRP4 RNA-binding prote 95.1 0.037 8E-07 55.2 5.6 62 157-221 149-210 (239)
51 PF02834 LigT_PEase: LigT like 95.0 0.042 9.2E-07 44.8 4.8 57 338-401 31-87 (87)
52 PRK12705 hypothetical protein; 94.2 0.058 1.3E-06 59.0 5.0 68 152-221 196-264 (508)
53 KOG2190 PolyC-binding proteins 93.6 0.1 2.2E-06 56.9 5.3 101 156-258 45-166 (485)
54 KOG2192 PolyC-binding hnRNP-K 93.1 0.29 6.2E-06 49.9 7.2 68 152-220 46-114 (390)
55 KOG2208 Vigilin [Lipid transpo 92.4 0.083 1.8E-06 60.3 2.8 42 150-191 705-746 (753)
56 KOG2279 Kinase anchor protein 91.3 0.14 3.1E-06 56.2 2.9 102 151-257 65-167 (608)
57 COG1855 ATPase (PilT family) [ 88.4 0.3 6.5E-06 53.3 2.5 41 153-193 485-525 (604)
58 PRK08406 transcription elongat 88.1 0.59 1.3E-05 43.0 3.9 37 153-189 98-134 (140)
59 PF14611 SLS: Mitochondrial in 87.3 1.9 4.2E-05 41.1 7.1 63 157-222 29-91 (210)
60 PRK13764 ATPase; Provisional 86.7 0.47 1E-05 53.1 2.8 41 152-192 479-519 (602)
61 cd02409 KH-II KH-II (K homolo 86.5 1 2.2E-05 34.3 3.8 35 153-187 24-58 (68)
62 PRK00468 hypothetical protein; 85.9 0.81 1.8E-05 38.1 3.2 30 152-181 28-57 (75)
63 PRK02821 hypothetical protein; 85.8 0.84 1.8E-05 38.2 3.3 32 152-183 29-60 (77)
64 KOG3273 Predicted RNA-binding 85.5 0.53 1.1E-05 46.3 2.2 52 164-220 179-230 (252)
65 COG1837 Predicted RNA-binding 85.4 0.9 1.9E-05 38.1 3.2 31 151-181 27-57 (76)
66 PF13083 KH_4: KH domain; PDB: 83.9 0.6 1.3E-05 37.6 1.6 34 151-184 26-59 (73)
67 PRK01064 hypothetical protein; 81.0 1.6 3.4E-05 36.7 3.0 31 151-181 27-57 (78)
68 PRK08406 transcription elongat 80.4 1.9 4E-05 39.7 3.5 36 155-190 33-68 (140)
69 TIGR01952 nusA_arch NusA famil 79.7 2.1 4.6E-05 39.6 3.7 38 152-189 98-135 (141)
70 COG5166 Uncharacterized conser 77.9 2.6 5.6E-05 46.6 4.2 70 153-222 448-525 (657)
71 PF13184 KH_5: NusA-like KH do 76.5 2.2 4.7E-05 34.8 2.5 25 165-189 19-44 (69)
72 PF07650 KH_2: KH domain syndr 75.0 1.7 3.6E-05 35.3 1.4 36 153-188 24-59 (78)
73 cd02414 jag_KH jag_K homology 73.7 3 6.4E-05 34.1 2.6 35 155-189 25-59 (77)
74 PF07823 CPDase: Cyclic phosph 73.6 6.6 0.00014 37.7 5.4 74 343-426 40-114 (196)
75 KOG2113 Predicted RNA binding 71.5 3.4 7.4E-05 43.2 3.0 70 150-219 111-181 (394)
76 TIGR01952 nusA_arch NusA famil 69.6 5.6 0.00012 36.8 3.7 35 155-189 34-68 (141)
77 TIGR01953 NusA transcription t 65.7 6.6 0.00014 41.2 3.8 38 153-190 300-337 (341)
78 PF09749 HVSL: Uncharacterised 65.4 39 0.00084 33.3 8.9 102 338-444 86-189 (239)
79 PRK06418 transcription elongat 65.0 7.2 0.00016 37.2 3.5 32 157-189 64-95 (166)
80 KOG2814 Transcription coactiva 64.7 13 0.00028 39.2 5.6 80 340-427 128-207 (345)
81 COG0195 NusA Transcription elo 64.4 7.2 0.00016 37.9 3.5 35 155-189 143-177 (190)
82 KOG2874 rRNA processing protei 62.6 14 0.0003 38.4 5.2 50 165-223 160-209 (356)
83 PRK12328 nusA transcription el 62.0 8.5 0.00019 41.0 3.8 43 152-194 306-348 (374)
84 cd02413 40S_S3_KH K homology R 60.6 5.5 0.00012 33.4 1.7 35 156-190 32-66 (81)
85 PRK12327 nusA transcription el 55.5 13 0.00028 39.5 3.8 38 153-190 302-339 (362)
86 PRK09202 nusA transcription el 54.8 11 0.00024 41.2 3.3 37 153-189 301-337 (470)
87 KOG2279 Kinase anchor protein 50.7 7.6 0.00016 43.3 1.3 70 149-219 135-207 (608)
88 PF00352 TBP: Transcription fa 47.8 42 0.00092 27.9 5.1 35 184-221 49-84 (86)
89 cd02412 30S_S3_KH K homology R 46.3 17 0.00036 31.9 2.5 33 156-188 63-95 (109)
90 COG0195 NusA Transcription elo 44.3 21 0.00045 34.7 3.1 36 154-189 76-111 (190)
91 PRK12329 nusA transcription el 43.7 24 0.00052 38.6 3.6 37 153-189 334-370 (449)
92 TIGR00436 era GTP-binding prot 32.7 44 0.00095 33.0 3.3 28 153-180 220-248 (270)
93 cd02410 archeal_CPSF_KH The ar 32.4 39 0.00084 31.8 2.7 33 157-189 79-111 (145)
94 cd02411 archeal_30S_S3_KH K ho 31.2 43 0.00093 27.9 2.5 34 152-187 38-71 (85)
95 PRK00089 era GTPase Era; Revie 29.7 47 0.001 32.9 3.0 27 153-179 225-252 (292)
96 COG1702 PhoH Phosphate starvat 29.1 1.4E+02 0.0031 31.8 6.4 55 162-221 23-79 (348)
97 COG5255 Uncharacterized protei 28.4 97 0.0021 31.1 4.8 45 340-388 177-222 (239)
98 COG0092 RpsC Ribosomal protein 27.9 48 0.001 33.4 2.6 35 155-189 52-86 (233)
99 COG1782 Predicted metal-depend 20.9 1.8E+02 0.0038 33.0 5.5 35 157-191 102-136 (637)
100 smart00411 BHL bacterial (prok 20.7 1.4E+02 0.003 24.5 3.7 32 359-391 20-51 (90)
No 1
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=100.00 E-value=1.4e-43 Score=354.07 Aligned_cols=275 Identities=31% Similarity=0.446 Sum_probs=236.5
Q ss_pred ccccccccCCceeeeccccccccccccccccCCCCCceEee-ecccCCcccccccceeeeeecccccccccCcccccccc
Q 012372 60 YGDKKQKIINPVWRPVSTQASVNEESLVKDVSEDGSQIQEM-HCSTSSNVSDAQLGVEVAEAVNEGTDLTLSSSVSLDDI 138 (465)
Q Consensus 60 ~~~kk~k~~~~~wrpvst~as~~~~~l~~~~~~~~~~v~e~-~~~~s~~~s~~~~~~~~~~~~~e~~~~~~sss~~~~~~ 138 (465)
+..++++..|.+|+|++|+..+.. .+++...|++ .|.++...+. ++ .
T Consensus 2 ~~~~~~~~~n~~~~~~~~~t~~~~-------~~~~~e~~~~~~c~d~p~~~~------------dv-------------~ 49 (345)
T KOG2814|consen 2 YRKTRYNLVNDVSFDLNTDTTFAD-------MSEEFEAQTSAECVDMPGDTV------------DV-------------E 49 (345)
T ss_pred cchhhhhhhhhcccCccccccccc-------CchhhHHHhHhhcccCCCChH------------Hh-------------h
Confidence 456789999999999999988763 3445566666 7777764433 11 0
Q ss_pred cccccCCCCccCCCCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCC-CCCcEEEEecCHHHHHHHHHHHHH
Q 012372 139 KDETLEGEPVPSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSK-KEDSIIIEGNSTDSVAKASEKIQA 217 (465)
Q Consensus 139 e~~~~~~~~~~~~~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~-~sg~I~ItG~ske~V~~A~~rI~~ 217 (465)
+.. -.++|+.+++|++.++++|||+.|.|+|+||+||+|+|-+|+++ +.+.|+|+|.++++|.+|.+||..
T Consensus 50 ~~~--------~~~~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~ 121 (345)
T KOG2814|consen 50 DDA--------GAKDFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAK 121 (345)
T ss_pred hcc--------ccccchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHH
Confidence 011 12289999999999999999999999999999999999999998 589999999999999999999999
Q ss_pred HHHHHhhCCCCcccceEeeccccchhhhhhHHHHHHHHhcCcCcccccccCCCCCCCCCchHHHHHhhhhhhhhhhhhcc
Q 012372 218 IIAEAVESPSLDYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNI 297 (465)
Q Consensus 218 Iv~e~~kk~k~~~thFVsIPl~~hP~I~~~~~~Fq~sIL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~ 297 (465)
++++.++ +.++|||+++|++ ..++.++|..|+...+-..
T Consensus 122 ~ids~r~--s~p~thflal~ln-e~eVqe~f~~fke~~~~~e-------------------------------------- 160 (345)
T KOG2814|consen 122 LIDSDRK--SFPITHFLALPLN-EHEVQEGFLAFKELKPFIE-------------------------------------- 160 (345)
T ss_pred HHHhhhh--cCchhhhhhhhcc-hHHHHHHHHHHHhhhhhHH--------------------------------------
Confidence 9999887 6999999999998 7889999999983322210
Q ss_pred CCCCcceecccccccccccccccCCCCCCCCCCCCCcCccCCCeeeEEEeeeEeCChhHHHHHHHHHHHhHHHHHhhhCC
Q 012372 298 GDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDN 377 (465)
Q Consensus 298 ~~~~~~v~~~~~~~~~v~~~~~~~~~~~~~~~GIdesiF~~p~tLHLTLgVL~L~~~eev~kA~~~L~slk~~I~~iL~~ 377 (465)
..-+.|++.++|++|+++||||||++|++++++++|+++|+++.++++..+++
T Consensus 161 ---------------------------sl~~~g~~~s~F~~p~~~HLTvgm~~L~~dd~vq~a~e~les~~~e~~~~~~~ 213 (345)
T KOG2814|consen 161 ---------------------------SLLDGGIDKSLFQGPGTFHLTVGMLKLLNDDDVQKALEILESTFQEIRIDVGE 213 (345)
T ss_pred ---------------------------HhhccchhhccccCCceeeEEEEEEEecChHHHHHHHHHHHHHHHHHHhccCC
Confidence 01256899999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEeecccCCCCCCcceEEEEeceecCCcchHHHHH-HHHHHHHHHh--ccCCCcceEEeeeeh
Q 012372 378 RPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHAC-RILIAFVSSI--FAPLCTSLIIKMKQY 442 (465)
Q Consensus 378 ~pL~I~LkGL~~MnddPs~a~VLYAk~~~~d~~~rL~~~c-q~I~d~F~e~--F~p~~~~~i~~~~~~ 442 (465)
+|+.|.++|+++|||||+.++||||+|.+.+...+|+.+| +.|..+|+.. +.--...++|||+..
T Consensus 214 kp~~i~lkG~~~mnddP~~~kVLYAkv~~~~~e~~l~~~~~~~i~~~f~~~~li~k~~~~~kLH~Tvm 281 (345)
T KOG2814|consen 214 KPLFIDLKGLDKMNDDPSLTKVLYAKVEPDDYEKFLQHRCGERILERFVASGLIKKESSSLKLHCTVM 281 (345)
T ss_pred CceeeeccchhhhcCCHhHheeeeeeccCcchHHHHHHHHHHHHHHHHHHhcchhccccccEEEEEEe
Confidence 9999999999999999999999999999888899999999 9999999985 666677899999975
No 2
>PLN00108 unknown protein; Provisional
Probab=100.00 E-value=3.2e-35 Score=288.45 Aligned_cols=160 Identities=51% Similarity=0.801 Sum_probs=140.0
Q ss_pred CCcccceEeeccccchhhhhhHHHHHHHHhcCcCcccccccCCCCCCCCCchHHHHHhhhhhhhhhhhhccCCCCcceec
Q 012372 227 SLDYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKV 306 (465)
Q Consensus 227 k~~~thFVsIPl~~hP~I~~~~~~Fq~sIL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~v~~ 306 (465)
+..||||||||+..+|+|.+++.+|++.|++..+.+
T Consensus 33 ~~~~THFlavPL~~~p~i~~~~~~Fk~~Vl~~~~~~-------------------------------------------- 68 (257)
T PLN00108 33 REVFTHFVSLPLAIYPDLKKNIEAFQNSVLGNNDKD-------------------------------------------- 68 (257)
T ss_pred CCCCCeEEEEEcCCCHHHHHHHHHHHHHHHhccccc--------------------------------------------
Confidence 578999999999658999999999999999862100
Q ss_pred ccccccccccccccCCCCCCCCCCCCCcCccCCCeeeEEEeeeEeCChhHHHHHHHHHHHhHHHHHhhhCCCCcEEEEee
Q 012372 307 DRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKG 386 (465)
Q Consensus 307 ~~~~~~~v~~~~~~~~~~~~~~~GIdesiF~~p~tLHLTLgVL~L~~~eev~kA~~~L~slk~~I~~iL~~~pL~I~LkG 386 (465)
|++. + ++.+++||++++|++|++||||||||+|++++++++|+++|++|+..|+++++++|+.|+|+|
T Consensus 69 -----~~~f------~-~~l~~~gid~siF~~p~~LHLTLgmL~L~~~eev~kA~~~L~s~~~~i~~~l~~~pl~I~lkG 136 (257)
T PLN00108 69 -----PLKF------Q-STLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNILKSICSNVRQALKDRPVFIRLRG 136 (257)
T ss_pred -----cccc------c-ccccccCCCHHHcCCCCceEEEEEEEEcCCHHHHHHHHHHHHHHHHHHHHhhCCCCeEEEEEe
Confidence 1100 0 123488999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCcceEEEEeceecCCcchHHHHHHHHHHHHHHh-ccC--CCcceEEeeeeh
Q 012372 387 LDLMRGSKDKARILYAPVEEIGDGDRLLHACRILIAFVSSI-FAP--LCTSLIIKMKQY 442 (465)
Q Consensus 387 L~~MnddPs~a~VLYAk~~~~d~~~rL~~~cq~I~d~F~e~-F~p--~~~~~i~~~~~~ 442 (465)
|++|||||++++||||+|++.++.++|++||+.|++.|+++ |.. ...+++|||++.
T Consensus 137 L~~Mnddps~~~VLYA~Ve~~~~~~rLq~~ad~i~~~F~~aGL~~~d~~~~vKLH~Tlm 195 (257)
T PLN00108 137 LDCMNGSLDKTRVLYAPVEEVGHEGRLLNACHVIIDAFENAGFAGKDAKSRLKLHATLM 195 (257)
T ss_pred ehhcCCCcccceEEEEeccccCchhHHHHHHHHHHHHHHHcCCcccccCcceeeEeEEe
Confidence 99999999999999999998888899999999999999994 653 235899999974
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=99.96 E-value=1.5e-28 Score=232.20 Aligned_cols=146 Identities=34% Similarity=0.504 Sum_probs=128.8
Q ss_pred ccceEeeccccchhhhhhHHHHHHHHhcCcCcccccccCCCCCCCCCchHHHHHhhhhhhhhhhhhccCCCCcceecccc
Q 012372 230 YSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKVDRT 309 (465)
Q Consensus 230 ~thFVsIPl~~hP~I~~~~~~Fq~sIL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~v~~~~~ 309 (465)
||||||||++ +|+|++.+.+|++.|+..
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 999999999999999853
Q ss_pred cccccccccccCCCCCCCCCCCCCcCccCCCeeeEEEeeeEeCChhHHHHHHHHHHHhHHHHHhhhCC-CCcEEEEeecc
Q 012372 310 SIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDN-RPLFIRLKGLD 388 (465)
Q Consensus 310 ~~~~v~~~~~~~~~~~~~~~GIdesiF~~p~tLHLTLgVL~L~~~eev~kA~~~L~slk~~I~~iL~~-~pL~I~LkGL~ 388 (465)
++|+++++|++|++||||||||+|.+++++++|.++|+++++.+.+.+.+ .|+.|+|+||+
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 34678889999999999999999999999999999999999999988776 99999999999
Q ss_pred cCCCCCCcceEEEEeceecCCcchHHHHHHHHHHHHHHh-ccC--CCc-ceEEeeeehhHH
Q 012372 389 LMRGSKDKARILYAPVEEIGDGDRLLHACRILIAFVSSI-FAP--LCT-SLIIKMKQYYII 445 (465)
Q Consensus 389 ~MnddPs~a~VLYAk~~~~d~~~rL~~~cq~I~d~F~e~-F~p--~~~-~~i~~~~~~~~~ 445 (465)
+|++||++++||||+|.+.++..+|+++|+.|++.|.++ +.. ..+ ..++|+++.-.+
T Consensus 91 ~f~~d~~~~~VLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~~~~~~~~H~Tl~n~~ 151 (209)
T PF10469_consen 91 YFNDDPSKARVLYAKVSEDSNSERLQELANKLRERFQEAGLLVTDDRRFSFKPHITLMNTS 151 (209)
T ss_pred hhCCCCCcceEEEEcccccchHHHHHHHHHHHHHHHHHcCCccccccCCCcceEEEEEecc
Confidence 999999999999999987667899999999999999994 443 223 268888875443
No 4
>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=99.33 E-value=2.6e-12 Score=101.07 Aligned_cols=59 Identities=27% Similarity=0.402 Sum_probs=54.8
Q ss_pred EEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHH
Q 012372 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQ 216 (465)
Q Consensus 155 ~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~ 216 (465)
+.++.||+++++.|||+||+|+|+|+++|||+|+|+. ++.|.|+|+++++++.|+++|+
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 5689999999999999999999999999999999975 5789999998999999999873
No 5
>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=99.29 E-value=5.3e-12 Score=98.05 Aligned_cols=60 Identities=42% Similarity=0.612 Sum_probs=54.9
Q ss_pred EEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCC-CCcEEEEecCHHHHHHHHHHHH
Q 012372 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQ 216 (465)
Q Consensus 156 ~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~-sg~I~ItG~ske~V~~A~~rI~ 216 (465)
..+.||+.+|+.|||++|+++++|+++|||+|+||+.++ ++.|+|+|+ .++|..|+++|+
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 688999998 789999999873
No 6
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.20 E-value=1.2e-11 Score=95.55 Aligned_cols=60 Identities=40% Similarity=0.598 Sum_probs=54.2
Q ss_pred EEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHH
Q 012372 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKI 215 (465)
Q Consensus 155 ~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI 215 (465)
+..+.||..++++|||++|+++|+|+++|||+|.||+.++...|+|+| +.++|++|+++|
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 467999999999999999999999999999999999764335899999 799999999987
No 7
>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=99.00 E-value=7.4e-10 Score=85.31 Aligned_cols=59 Identities=41% Similarity=0.516 Sum_probs=53.2
Q ss_pred EEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCC---CCcEEEEecCHHHHHHHHHHH
Q 012372 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKI 215 (465)
Q Consensus 156 ~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~---sg~I~ItG~ske~V~~A~~rI 215 (465)
..+.||..++++|||++|+++++|+++|||+|.||..++ ...|.|.|. .+++..|...|
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 478999999999999999999999999999999998642 577999997 78999998876
No 8
>smart00322 KH K homology RNA-binding domain.
Probab=98.85 E-value=1.4e-08 Score=76.90 Aligned_cols=66 Identities=39% Similarity=0.536 Sum_probs=58.3
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCC-CCCcEEEEecCHHHHHHHHHHHHHHH
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSK-KEDSIIIEGNSTDSVAKASEKIQAII 219 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~-~sg~I~ItG~ske~V~~A~~rI~~Iv 219 (465)
.....+.||..+++++||++|+++++|+++||++|.+|... ....|.|.|+ .+++..|...|...+
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 45778999999999999999999999999999999998765 3577899998 789999999987654
No 9
>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=98.83 E-value=7.3e-09 Score=81.87 Aligned_cols=59 Identities=37% Similarity=0.387 Sum_probs=52.8
Q ss_pred EEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCC----CCcEEEEecCHHHHHHHHHHH
Q 012372 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKI 215 (465)
Q Consensus 156 ~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~----sg~I~ItG~ske~V~~A~~rI 215 (465)
..+.||..+.+.|||++|.++++|+++|||+|.|++..+ ...|+|+|. .+++..|+.+|
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 568899999999999999999999999999999987653 356899996 78999999887
No 10
>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=98.80 E-value=6e-09 Score=115.65 Aligned_cols=82 Identities=22% Similarity=0.332 Sum_probs=73.3
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHH--H--------
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE--A-------- 222 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e--~-------- 222 (465)
--..++.||+++++.|||+||++||+|+++||++|+| +++|.|.|.|.+++.+++|+++|+.|+.. .
T Consensus 577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi---~d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~G 653 (719)
T TIGR02696 577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISI---EDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLG 653 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEE---ecCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEE
Confidence 3467899999999999999999999999999999999 66899999999999999999999999983 2
Q ss_pred -hhCCCCcccceEeecc
Q 012372 223 -VESPSLDYSHFVSLPL 238 (465)
Q Consensus 223 -~kk~k~~~thFVsIPl 238 (465)
+++ ..+|+.||.|..
T Consensus 654 kV~~-I~dfGaFVel~~ 669 (719)
T TIGR02696 654 TVVK-TTAFGAFVSLLP 669 (719)
T ss_pred EEEE-EECceEEEEecC
Confidence 333 678999999853
No 11
>PF13014 KH_3: KH domain
Probab=98.68 E-value=1.8e-08 Score=73.64 Aligned_cols=39 Identities=38% Similarity=0.572 Sum_probs=34.0
Q ss_pred eeccccCCCChhHHHHHHHhCcEEEcCC---CCC-CCcEEEEe
Q 012372 164 VIRFIKGKEGSTQKKFEKEMGVKIILPS---SKK-EDSIIIEG 202 (465)
Q Consensus 164 ~~r~IIGkgG~tiK~IEeETgtkI~IPr---~~~-sg~I~ItG 202 (465)
+|++|||++|++|++|+++|||+|+||+ .++ +..|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5899999999999999999999999999 222 56788887
No 12
>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=98.67 E-value=4.3e-08 Score=87.44 Aligned_cols=59 Identities=29% Similarity=0.486 Sum_probs=52.3
Q ss_pred ceeccccCCCChhHHHHHHHhCcEEEcCCCCC--------------------CCcEEEEecC--HHHHHHHHHHHHHHHH
Q 012372 163 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK--------------------EDSIIIEGNS--TDSVAKASEKIQAIIA 220 (465)
Q Consensus 163 ~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~--------------------sg~I~ItG~s--ke~V~~A~~rI~~Iv~ 220 (465)
.|++.|||+||+|+|+||++|||+|.|-..++ .+.|.|+|.+ .+++++|+++|+.|+.
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 57899999999999999999999999976531 2789999999 9999999999998886
Q ss_pred H
Q 012372 221 E 221 (465)
Q Consensus 221 e 221 (465)
.
T Consensus 95 ~ 95 (120)
T cd02395 95 P 95 (120)
T ss_pred c
Confidence 4
No 13
>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=98.62 E-value=3.7e-08 Score=109.49 Aligned_cols=82 Identities=22% Similarity=0.378 Sum_probs=72.1
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHHH---------h
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEA---------V 223 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e~---------~ 223 (465)
--..++.||+++++.|||+||++||+|+++||++|+| +++|.|.|.+.+++.+++|+++|..+..+. +
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i---~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V 626 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDI---EDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKV 626 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEE---ecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEE
Confidence 3467899999999999999999999999999999999 668999999999999999999999998763 2
Q ss_pred hCCCCcccceEeecc
Q 012372 224 ESPSLDYSHFVSLPL 238 (465)
Q Consensus 224 kk~k~~~thFVsIPl 238 (465)
.+ ...++.||.+..
T Consensus 627 ~~-I~~~GafVei~~ 640 (684)
T TIGR03591 627 VR-IMDFGAFVEILP 640 (684)
T ss_pred EE-EeCCEEEEEECC
Confidence 22 567899998854
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.58 E-value=9.3e-08 Score=90.28 Aligned_cols=66 Identities=32% Similarity=0.424 Sum_probs=59.9
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEE---ecCHHHHHHHHHHHHHHHH
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIE---GNSTDSVAKASEKIQAIIA 220 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~It---G~ske~V~~A~~rI~~Iv~ 220 (465)
....++.||++.++.|||+||+++|.|+++||++|+|-. +.+.|.|. +.+.+++.+|++.|+.|..
T Consensus 2 ~~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~--~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 2 MMMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS--ETGEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred CceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC--CCCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 356789999999999999999999999999999999942 24899998 8899999999999999986
No 15
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.57 E-value=7.7e-08 Score=105.64 Aligned_cols=83 Identities=30% Similarity=0.440 Sum_probs=75.4
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHHH---------h
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEA---------V 223 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e~---------~ 223 (465)
--..+++|++++++.+||+||++||+|.++||++|+| +++|.|.|.+.+.+.+.+|+++|+.|+.++ +
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idi---eddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V 627 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDI---EDDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTV 627 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEe---cCCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEE
Confidence 4467899999999999999999999999999999999 578999999999999999999999999887 3
Q ss_pred hCCCCcccceEeeccc
Q 012372 224 ESPSLDYSHFVSLPLA 239 (465)
Q Consensus 224 kk~k~~~thFVsIPl~ 239 (465)
++ ...|+.||.+...
T Consensus 628 ~r-i~~fGaFv~l~~g 642 (692)
T COG1185 628 VR-IVDFGAFVELLPG 642 (692)
T ss_pred EE-EeecceEEEecCC
Confidence 43 7789999998863
No 16
>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=98.56 E-value=7.2e-07 Score=82.01 Aligned_cols=91 Identities=23% Similarity=0.425 Sum_probs=69.7
Q ss_pred ccCCCeeeEEEeeeEeCChhHHHHHHHHHHHhHHHHHhhhCCCCcEEEEeecccCCCCCCcceEEEEeceecCCcchHHH
Q 012372 336 FIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLH 415 (465)
Q Consensus 336 F~~p~tLHLTLgVL~L~~~eev~kA~~~L~slk~~I~~iL~~~pL~I~LkGL~~MnddPs~a~VLYAk~~~~d~~~rL~~ 415 (465)
..++..+||||..+-..++++++...+.|+++. ..++.++|.|+++|++ +...+|||+++.. ...|.+
T Consensus 33 ~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~--------~~~f~l~l~~~~~F~~-~~~~~vl~l~~~~---~~~L~~ 100 (179)
T TIGR02258 33 WVPPENLHITLKFLGEVDEEQVEELEDALAKIA--------EPPFTLKLEGIGVFGN-PKRPRVLWAGVEQ---SEELTQ 100 (179)
T ss_pred ECChHHCEEEEEEccCCCHHHHHHHHHHHHHhc--------CCCeEEEEeeeeeCCC-CCCCeEEEEeeCC---CHHHHH
Confidence 456789999999988878888877777666532 2569999999999974 6778999999963 347888
Q ss_pred HHHHHHHHHHH--------hccCCCcceEEe
Q 012372 416 ACRILIAFVSS--------IFAPLCTSLIIK 438 (465)
Q Consensus 416 ~cq~I~d~F~e--------~F~p~~~~~i~~ 438 (465)
+.+.+.+.+.. .|.||+|-.-..
T Consensus 101 L~~~l~~~~~~~g~~~~~~~f~PHiTlar~~ 131 (179)
T TIGR02258 101 LHADLERELAKLGFSKEERPFTPHITLARKK 131 (179)
T ss_pred HHHHHHHHHHHcCCCCCCCCcCCCEEEEEec
Confidence 88888888863 466777765443
No 17
>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=98.48 E-value=1.4e-07 Score=88.34 Aligned_cols=61 Identities=33% Similarity=0.432 Sum_probs=54.9
Q ss_pred EEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEE--EecCHHHHHHHHHHHHHHHH
Q 012372 158 VEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIII--EGNSTDSVAKASEKIQAIIA 220 (465)
Q Consensus 158 I~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~I--tG~ske~V~~A~~rI~~Iv~ 220 (465)
+.||++.++.|||+||+++|+|+++||++|+|-. +++.|.| .+.+.+++.+|++.|..|..
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 6799999999999999999999999999999942 2488999 67789999999999999876
No 18
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.43 E-value=1.6e-07 Score=106.55 Aligned_cols=82 Identities=21% Similarity=0.306 Sum_probs=72.0
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcE-EEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHHH---------
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVK-IILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEA--------- 222 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtk-I~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e~--------- 222 (465)
--+.++.||+++++.|||+||.|||+|+++||++ |+| +++|.|.|.|.+.+.+++|+++|+.|+.+.
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi---~ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~g 760 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDT---QDDGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNC 760 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCc---CCCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEECc
Confidence 3467899999999999999999999999999999 999 678999999999999999999999997543
Q ss_pred -hhCCCCcccceEeecc
Q 012372 223 -VESPSLDYSHFVSLPL 238 (465)
Q Consensus 223 -~kk~k~~~thFVsIPl 238 (465)
+.+ ...|+.||.|..
T Consensus 761 ~V~~-I~~FGaFVeL~~ 776 (891)
T PLN00207 761 EIKS-IAPYGAFVEIAP 776 (891)
T ss_pred EEEE-EeccEEEEEeCC
Confidence 222 567899998864
No 19
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.33 E-value=9.8e-07 Score=95.56 Aligned_cols=107 Identities=27% Similarity=0.327 Sum_probs=82.7
Q ss_pred CCCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCC----CCcEEEEecCHHHHHHHHHHHHHHHHHHhhC-
Q 012372 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIAEAVES- 225 (465)
Q Consensus 151 ~~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~----sg~I~ItG~ske~V~~A~~rI~~Iv~e~~kk- 225 (465)
....+..|.||....+.||||+|+|||+|..||||||+|=+.++ +....|.|+ +++|+.|.++|.+||.+..+.
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 34458899999999999999999999999999999999954433 478899996 899999999999999987542
Q ss_pred --------CCCcccceEeeccccchhhhhhHHHHHHHHhcC
Q 012372 226 --------PSLDYSHFVSLPLAVHPELVDKLVNFQNTILGI 258 (465)
Q Consensus 226 --------~k~~~thFVsIPl~~hP~I~~~~~~Fq~sIL~~ 258 (465)
|......++.||..----++++-++-+..|-.+
T Consensus 306 ~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~q 346 (600)
T KOG1676|consen 306 GGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQ 346 (600)
T ss_pred CCCcCCCCccceeeEEEeccccccccccCCCccchhhhccc
Confidence 111113455678654455677777777776654
No 20
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.20 E-value=9.3e-07 Score=98.64 Aligned_cols=80 Identities=25% Similarity=0.420 Sum_probs=70.9
Q ss_pred EEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHHH---------hhC
Q 012372 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEA---------VES 225 (465)
Q Consensus 155 ~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e~---------~kk 225 (465)
..++.||+++++.+||+||.|||+|.++||++|+| .++|.|.|.+.+++.+++|+++|+.++.+. +.+
T Consensus 555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi---~d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~ 631 (693)
T PRK11824 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDI---EDDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVR 631 (693)
T ss_pred heeecCCHHHHHHHhcCCchhHHHHHHHHCCcccc---CCCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEE
Confidence 46889999999999999999999999999999999 678999999999999999999999999763 222
Q ss_pred CCCcccceEeecc
Q 012372 226 PSLDYSHFVSLPL 238 (465)
Q Consensus 226 ~k~~~thFVsIPl 238 (465)
...++.||.|..
T Consensus 632 -I~~fGafVei~~ 643 (693)
T PRK11824 632 -IVDFGAFVEILP 643 (693)
T ss_pred -EECCeEEEEECC
Confidence 567899998863
No 21
>PRK15124 2'-5' RNA ligase; Provisional
Probab=97.99 E-value=9e-05 Score=69.08 Aligned_cols=94 Identities=12% Similarity=0.121 Sum_probs=68.7
Q ss_pred ccCCCeeeEEEeeeEeCChhHHHHHHHHHHHhHHHHHhhhCCCCcEEEEeecccCCCCCCcceEEEEeceecCCcchHHH
Q 012372 336 FIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLH 415 (465)
Q Consensus 336 F~~p~tLHLTLgVL~L~~~eev~kA~~~L~slk~~I~~iL~~~pL~I~LkGL~~MnddPs~a~VLYAk~~~~d~~~rL~~ 415 (465)
..+|..|||||--+-=.+++.++...++|+.+ ...|+.+.|.|+++|++ .+|||+++. ++...|..
T Consensus 36 wv~~~nlHiTL~FlG~v~~~~~~~l~~~l~~~--------~~~pF~l~l~~~g~Fp~----prvlwlg~~--~~~~~L~~ 101 (176)
T PRK15124 36 PVAAANLHLTLAFLGEVSAEKQQALSQLAGRI--------RQPGFTLTLDDAGQWPR----SRVVWLGMR--QPPRGLLQ 101 (176)
T ss_pred cccccccEEEEEecCCCCHHHHHHHHHHHHhc--------ccCCeEEEECcccCcCC----CCEEEEEcC--CCCHHHHH
Confidence 35578999999988777788777666665553 34789999999999963 589999996 34568999
Q ss_pred HHHHHHHHHHHh-ccCCCcceEEeeeehh
Q 012372 416 ACRILIAFVSSI-FAPLCTSLIIKMKQYY 443 (465)
Q Consensus 416 ~cq~I~d~F~e~-F~p~~~~~i~~~~~~~ 443 (465)
+.+.|.+.+... |.+..+.-.=|||+.+
T Consensus 102 L~~~l~~~l~~~G~~~e~r~f~PHiTLaR 130 (176)
T PRK15124 102 LANMLRSQAARSGCYQSPQPFHPHITLLR 130 (176)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCCCEeecc
Confidence 999999988752 4344444444555544
No 22
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.98 E-value=6.4e-06 Score=86.59 Aligned_cols=104 Identities=21% Similarity=0.239 Sum_probs=77.3
Q ss_pred CCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCC----CCcEEEEecCHHHHHHHHHHHHHHHHHHhhCCC
Q 012372 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPS 227 (465)
Q Consensus 152 ~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~----sg~I~ItG~ske~V~~A~~rI~~Iv~e~~kk~k 227 (465)
..|-..+.||..+++-||||.|+|||.|...|.+||||-+.++ +..|+|-|. .|+..+|+.+|+.|+..-.. .
T Consensus 197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~t-pEg~s~Ac~~ILeimqkEA~--~ 273 (584)
T KOG2193|consen 197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHST-PEGTSKACKMILEIMQKEAV--D 273 (584)
T ss_pred cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecC-ccchHHHHHHHHHHHHHhhh--c
Confidence 4567788999999999999999999999999999999988765 457899996 68999999999999854333 2
Q ss_pred CcccceEeeccccchhhhhh----HHHHHHHHhcC
Q 012372 228 LDYSHFVSLPLAVHPELVDK----LVNFQNTILGI 258 (465)
Q Consensus 228 ~~~thFVsIPl~~hP~I~~~----~~~Fq~sIL~~ 258 (465)
..++.-+-+.+--|..++|. -++-+..|..+
T Consensus 274 ~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~ 308 (584)
T KOG2193|consen 274 DKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQD 308 (584)
T ss_pred cchhhhcchhhhhhcchhhhhhhhccccHHHHHhh
Confidence 34444443333336555444 34555556554
No 23
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=97.97 E-value=8e-05 Score=70.65 Aligned_cols=93 Identities=23% Similarity=0.403 Sum_probs=71.2
Q ss_pred ccCCCeeeEEEeeeEeCChhHHHHHHHHHHHhHHHHHhhhCCCCcEEEEeecccCCCCCCcceEEEEeceecCCcchHHH
Q 012372 336 FIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLH 415 (465)
Q Consensus 336 F~~p~tLHLTLgVL~L~~~eev~kA~~~L~slk~~I~~iL~~~pL~I~LkGL~~MnddPs~a~VLYAk~~~~d~~~rL~~ 415 (465)
+..+..+||||--+-=.+++.++...+.|.++. -+. |+.|+|+|++.|++ |..-+|+|+++.. .+.|.+
T Consensus 32 ~v~~en~HiTL~flGev~e~~~~~l~~~l~~i~------~~~-~f~i~l~g~g~F~~-~~~~rvi~~~v~~---~~~L~~ 100 (180)
T COG1514 32 WVEPENLHITLKFLGEVDEDKADELIEALARIA------APE-PFPITLDGAGSFPN-PRRPRVIWVGVEE---TEELRA 100 (180)
T ss_pred cccccCceEEEEccCCcCchHHHHHHHHHHHhh------cCC-ceEEEEeeEcccCC-CCCCcEEEEcCCC---cHHHHH
Confidence 456789999998876667777777776666643 112 89999999999985 8889999999973 566777
Q ss_pred HHHHHHHHHHHh--------ccCCCcceEEee
Q 012372 416 ACRILIAFVSSI--------FAPLCTSLIIKM 439 (465)
Q Consensus 416 ~cq~I~d~F~e~--------F~p~~~~~i~~~ 439 (465)
+++.|.....+. |.||+|-.-+.-
T Consensus 101 L~~~l~~~~~~~g~~~~~r~F~PHvTl~r~k~ 132 (180)
T COG1514 101 LAEELERALARLGLRPEERPFVPHVTLARVKS 132 (180)
T ss_pred HHHHHHHHHHhcCCCCCCCCcCCCEEEEeecc
Confidence 788887776653 888888777665
No 24
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=97.95 E-value=1.4e-05 Score=75.08 Aligned_cols=54 Identities=28% Similarity=0.372 Sum_probs=49.2
Q ss_pred ceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHH
Q 012372 163 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (465)
Q Consensus 163 ~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e 221 (465)
...+.|||++|.|+|.||+.|||+|.|+. ..|.|.| +.++++.|++.|+.|++.
T Consensus 98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~----~~v~i~G-~~~~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEELTGVSISVYG----KTVGIIG-DPEQVQIAREAIEMLIEG 151 (172)
T ss_pred HHHhhhcCCCcHHHHHHHHHHCCeEEEcC----CEEEEEC-CHHHHHHHHHHHHHHHcC
Confidence 36899999999999999999999999973 6799999 589999999999999954
No 25
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.93 E-value=1.8e-05 Score=77.72 Aligned_cols=63 Identities=29% Similarity=0.380 Sum_probs=59.0
Q ss_pred EEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHH
Q 012372 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (465)
Q Consensus 156 ~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e 221 (465)
..+.||+.+++.+||++|.+++.|.++|+++|.| +++|.|-|.|++.+.+.+|+++|+.+-.+
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~i---g~NG~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIV---GQNGRIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEE---cCCcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 3588999999999999999999999999999999 78899999999999999999999887765
No 26
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.90 E-value=2e-05 Score=74.54 Aligned_cols=53 Identities=28% Similarity=0.400 Sum_probs=47.8
Q ss_pred eeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHH
Q 012372 164 VIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (465)
Q Consensus 164 ~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e 221 (465)
.++.|||+||.|+|.||+.|||+|.|+ ...|.|.| +.++++.|++.|..|+..
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~----~~~v~i~G-~~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVY----GKTVAIIG-DPEQVEIAREAIEMLIEG 157 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEc----CCEEEEEe-CHHHHHHHHHHHHHHHcC
Confidence 689999999999999999999999996 24599999 589999999999999844
No 27
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.88 E-value=2e-05 Score=84.14 Aligned_cols=72 Identities=28% Similarity=0.455 Sum_probs=60.2
Q ss_pred CeEEEEEeCcc------eeccccCCCChhHHHHHHHhCcEEEcCCCCC--C---------------C--cEEEEecCHHH
Q 012372 153 RHSLSVEVGAS------VIRFIKGKEGSTQKKFEKEMGVKIILPSSKK--E---------------D--SIIIEGNSTDS 207 (465)
Q Consensus 153 k~~~sI~VP~~------~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~--s---------------g--~I~ItG~ske~ 207 (465)
++...|.||.+ |++.|||..|.|+|+||+|||+||.|=..+. + . -+-|++.+.|.
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 77777888764 7889999999999999999999999965322 0 1 36799999999
Q ss_pred HHHHHHHHHHHHHHHhh
Q 012372 208 VAKASEKIQAIIAEAVE 224 (465)
Q Consensus 208 V~~A~~rI~~Iv~e~~k 224 (465)
|++|+..|+.|+.+++-
T Consensus 217 i~~Ai~vienli~~av~ 233 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSAVS 233 (554)
T ss_pred HHHHHHHHHHHHHhhcc
Confidence 99999999999988543
No 28
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=97.81 E-value=3.2e-05 Score=87.26 Aligned_cols=104 Identities=27% Similarity=0.414 Sum_probs=92.7
Q ss_pred CCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCC-CCcEEEEecCHHHHHHHHHHHHHHHHHHhhCCCCcc
Q 012372 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDY 230 (465)
Q Consensus 152 ~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~-sg~I~ItG~ske~V~~A~~rI~~Iv~e~~kk~k~~~ 230 (465)
..+.+.+.|.+.++.+++||+|.++.+|+++++|.|++|.+++ ...++++|. ..++.+|.++++.++.+...+ ..
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 4488899999999999999999999999999999999999665 678999997 679999999999999997662 34
Q ss_pred cceEeeccccchhhhhhHHHHHHHHhcCc
Q 012372 231 SHFVSLPLAVHPELVDKLVNFQNTILGIT 259 (465)
Q Consensus 231 thFVsIPl~~hP~I~~~~~~Fq~sIL~~~ 259 (465)
.+.+.||-.+|.+|.+.....++.|+.+.
T Consensus 421 ~~~~~iP~k~~~~iig~~g~~i~~I~~k~ 449 (753)
T KOG2208|consen 421 KEEVQIPTKSHKRIIGTKGALINYIMGKH 449 (753)
T ss_pred cceeecCccchhhhhccccccHHHHHhhc
Confidence 57777999999999999999999999874
No 29
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.74 E-value=0.00021 Score=73.59 Aligned_cols=107 Identities=24% Similarity=0.243 Sum_probs=82.7
Q ss_pred CCCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCC------CCcEEEEecCHHHHHHHHHHHHHHHHHH--
Q 012372 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAEA-- 222 (465)
Q Consensus 151 ~~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~------sg~I~ItG~ske~V~~A~~rI~~Iv~e~-- 222 (465)
..+|...|.||.---+-||||||.||.+|+.|||+||++-+..+ +..+-|.|. -+.+..-.+-|..-+.|.
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 55799999999999999999999999999999999999988766 456789995 678888777777666554
Q ss_pred -hhC---------CCCcccceEeeccccchhhhhhHHHHHHHHhcC
Q 012372 223 -VES---------PSLDYSHFVSLPLAVHPELVDKLVNFQNTILGI 258 (465)
Q Consensus 223 -~kk---------~k~~~thFVsIPl~~hP~I~~~~~~Fq~sIL~~ 258 (465)
..+ |.+....-+.+|-..---|+++-..++.+|+++
T Consensus 115 ~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eq 160 (402)
T KOG2191|consen 115 AVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQ 160 (402)
T ss_pred hhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHh
Confidence 111 011122455577665677889989999999886
No 30
>PHA02574 57B hypothetical protein; Provisional
Probab=97.50 E-value=0.00048 Score=63.87 Aligned_cols=78 Identities=13% Similarity=0.096 Sum_probs=55.7
Q ss_pred ccCCCeeeEEEeeeEeCChhHHHHHHHHHHHhHHHHHhhhCCCCcEEEEeecccCCCCCCcceEEEEeceecCCcchHHH
Q 012372 336 FIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLH 415 (465)
Q Consensus 336 F~~p~tLHLTLgVL~L~~~eev~kA~~~L~slk~~I~~iL~~~pL~I~LkGL~~MnddPs~a~VLYAk~~~~d~~~rL~~ 415 (465)
..++..|||||.- .++.+.... . ...|+.++|.|+++|.. + ..+|||+++. ...|..
T Consensus 37 ~V~~enLHlTL~F----~~~~v~~l~-----------~--~~~~F~l~l~glG~F~~-~-~~rvlWlg~~----~~~L~~ 93 (149)
T PHA02574 37 PVPRDKLHSTIVY----SRVYVPFIP-----------A--SGSTEVASSGHLEVWET-Q-DKNALVLVLE----SEYLQC 93 (149)
T ss_pred ccCHHHCEEEEec----CHHHhHHHh-----------c--cCCCeEEEeccccccCC-C-CCCEEEEEeC----CHHHHH
Confidence 4567899999987 233332221 1 55899999999999952 1 2499999995 567888
Q ss_pred HHHHHHHHHHH----hccCCCcceE
Q 012372 416 ACRILIAFVSS----IFAPLCTSLI 436 (465)
Q Consensus 416 ~cq~I~d~F~e----~F~p~~~~~i 436 (465)
+.+.+.+.... .|.||.|-.-
T Consensus 94 L~~~l~~~l~~~~~r~F~PHITLaR 118 (149)
T PHA02574 94 RHKYARALGATHDFDDYTPHITLSY 118 (149)
T ss_pred HHHHHHHHhhcCCCCCcCCcEEEee
Confidence 88888888765 3888887543
No 31
>PRK13679 hypothetical protein; Provisional
Probab=97.45 E-value=0.0011 Score=61.39 Aligned_cols=82 Identities=16% Similarity=0.202 Sum_probs=57.2
Q ss_pred eEEEeeeEeCChhHHHHHHHHHHHhHHHHHhhhCCCCcEEEEeecccCCCCCCcceEEEEeceecCCcchHHHHHHHHHH
Q 012372 343 HLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACRILIA 422 (465)
Q Consensus 343 HLTLgVL~L~~~eev~kA~~~L~slk~~I~~iL~~~pL~I~LkGL~~MnddPs~a~VLYAk~~~~d~~~rL~~~cq~I~d 422 (465)
||||..+-=.+++++++..+.|+.+. -.-.|+.|+|.|+++|.. + .+|||+.+.. .+.|.++.+.+..
T Consensus 34 HITL~f~g~~~~~~~~~l~~~l~~~~------~~~~pf~l~l~~~~~F~~-~--~~vl~l~~~~---~~~L~~L~~~l~~ 101 (168)
T PRK13679 34 HITLKEPFEISDEQLDSIVEELRAIA------SETKPFTLHVTKVSSFAP-T--NNVIYFKVEK---TEELEELHERLHS 101 (168)
T ss_pred ceEEecCCCCCHHHHHHHHHHHHHHH------hcCCCEEEEEeccccCCC-C--CCEEEEEccC---CHHHHHHHHHHHh
Confidence 99999754235666777666666542 123789999999999964 2 3899999963 4688888887776
Q ss_pred HHH-----HhccCCCcceE
Q 012372 423 FVS-----SIFAPLCTSLI 436 (465)
Q Consensus 423 ~F~-----e~F~p~~~~~i 436 (465)
.+. ..|.||+|-.-
T Consensus 102 ~~~~~~~~~~f~PHiTlar 120 (168)
T PRK13679 102 GDFYGEAEYAFVPHITIGQ 120 (168)
T ss_pred cccccccCCCCCCeEEeeC
Confidence 543 13667776653
No 32
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=97.44 E-value=0.00022 Score=77.85 Aligned_cols=106 Identities=21% Similarity=0.280 Sum_probs=81.3
Q ss_pred CCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCC-----CCcEEEEecCHHHHHHHHHHHHHHHHHHhh--
Q 012372 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-----EDSIIIEGNSTDSVAKASEKIQAIIAEAVE-- 224 (465)
Q Consensus 152 ~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~-----sg~I~ItG~ske~V~~A~~rI~~Iv~e~~k-- 224 (465)
.+.+..|.||..+.+.||||||+|+|+|.+.+||++.+-..++ ..++.|+|. .+.|+.|+..+..|+.|-.+
T Consensus 137 ~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGd-p~~ve~a~~lV~dil~e~~~~~ 215 (600)
T KOG1676|consen 137 VETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGD-PDKVEQAKQLVADILREEDDEV 215 (600)
T ss_pred cceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCC-HHHHHHHHHHHHHHHHhcccCC
Confidence 4568889999999999999999999999999999999876654 247899995 78999999999999985311
Q ss_pred ---------CCCCcccceEeeccccchhhhhhHHHHHHHHhcC
Q 012372 225 ---------SPSLDYSHFVSLPLAVHPELVDKLVNFQNTILGI 258 (465)
Q Consensus 225 ---------k~k~~~thFVsIPl~~hP~I~~~~~~Fq~sIL~~ 258 (465)
+.-...+--|-||...=--|+++-++.+..|-.+
T Consensus 216 ~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~e 258 (600)
T KOG1676|consen 216 PGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNE 258 (600)
T ss_pred CccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhc
Confidence 0011113456677643466788888888877654
No 33
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.30 E-value=0.00044 Score=71.27 Aligned_cols=66 Identities=27% Similarity=0.363 Sum_probs=56.8
Q ss_pred EEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCC------CCcEEEEecCHHHHHHHHHHHHHHHHH
Q 012372 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAE 221 (465)
Q Consensus 155 ~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~------sg~I~ItG~ske~V~~A~~rI~~Iv~e 221 (465)
.+.+-||..--+.||||||+|+|.+.++.|+-|+|-.+.. +..|++.|. .|...+|+.+|..-+.|
T Consensus 133 qikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge-~e~~~~A~~~IL~Ki~e 204 (402)
T KOG2191|consen 133 QIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGE-PEQNMKAVSLILQKIQE 204 (402)
T ss_pred eeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCC-HHHHHHHHHHHHHHhhc
Confidence 4778899999999999999999999999999999965443 356788886 78999999999877766
No 34
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.21 E-value=0.0011 Score=71.79 Aligned_cols=67 Identities=31% Similarity=0.393 Sum_probs=58.7
Q ss_pred eEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCC----CCCcEEEEecCHHHHHHHHHHHHHHHHH
Q 012372 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSK----KEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (465)
Q Consensus 154 ~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~----~sg~I~ItG~ske~V~~A~~rI~~Iv~e 221 (465)
..+.+-||....+.||||||..||+|.++||++|.|-+.. .+..|+|.|. .+.|.+|...|-.++-+
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 6788999999999999999999999999999999985441 1456999997 68999999999888877
No 35
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.17 E-value=0.00039 Score=73.52 Aligned_cols=67 Identities=27% Similarity=0.462 Sum_probs=55.8
Q ss_pred EEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCC------CCcEEEEecCHHHHHHHHHHHHHHHHHH
Q 012372 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAEA 222 (465)
Q Consensus 155 ~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~------sg~I~ItG~ske~V~~A~~rI~~Iv~e~ 222 (465)
-..+..-..|.+.+|||.|+++|+||++|||+|.|.+--+ +.+|++.| +-|++.+|-..|-.-+.++
T Consensus 281 pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkG-siEac~~AE~eImkKlre~ 353 (584)
T KOG2193|consen 281 PLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKG-SIEACVQAEAEIMKKLREC 353 (584)
T ss_pred chhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecc-cHHHHHHHHHHHHHHHHHH
Confidence 3345566789999999999999999999999999977544 57899999 6889999988887766554
No 36
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=97.03 E-value=0.0016 Score=65.82 Aligned_cols=71 Identities=21% Similarity=0.274 Sum_probs=58.2
Q ss_pred CCCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCC--CC-CCcEEEEecCHHHHHHHHHHHHHHHHHH
Q 012372 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS--KK-EDSIIIEGNSTDSVAKASEKIQAIIAEA 222 (465)
Q Consensus 151 ~~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~--~~-sg~I~ItG~ske~V~~A~~rI~~Iv~e~ 222 (465)
+.-.+..|.||+++-+.||||||..|++|..|.|+.|.|..+ +. +..|+|+|. ++.+..|.-.++.-|.+.
T Consensus 312 GPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGT-qdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 312 GPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT-QDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred CceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEecc-HHHHhhHHHHHHHHHHhh
Confidence 344577899999999999999999999999999999988543 33 456799995 789999988777766543
No 37
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=96.96 E-value=0.00057 Score=74.53 Aligned_cols=82 Identities=23% Similarity=0.222 Sum_probs=68.8
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHHH----------
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEA---------- 222 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e~---------- 222 (465)
-...+++|+++..+.+||++|...|+|+.|||+.-.+ +++.++|.+++....++|++.|..|+..-
T Consensus 596 P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v----De~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~l~~g~v 671 (760)
T KOG1067|consen 596 PVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV----DEGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQDLEFGGV 671 (760)
T ss_pred ceeeEEeecchhhheeecCccceeeeEeeeccceeee----cCceEEEEecCHHHHHHHHHHHHHHhcCccccceEeeeE
Confidence 3467899999999999999999999999999966555 67999999999999999999999998542
Q ss_pred ----hhCCCCcccceEeeccc
Q 012372 223 ----VESPSLDYSHFVSLPLA 239 (465)
Q Consensus 223 ----~kk~k~~~thFVsIPl~ 239 (465)
... ..+++.||.++.-
T Consensus 672 y~~tIt~-~rd~G~~V~l~p~ 691 (760)
T KOG1067|consen 672 YTATITE-IRDTGVMVELYPM 691 (760)
T ss_pred EEEEEee-ecccceEEEecCC
Confidence 111 4567889988763
No 38
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.93 E-value=0.0022 Score=64.26 Aligned_cols=42 Identities=26% Similarity=0.398 Sum_probs=36.0
Q ss_pred CeEEEEEeCcc------eeccccCCCChhHHHHHHHhCcEEEcCCCCC
Q 012372 153 RHSLSVEVGAS------VIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 194 (465)
Q Consensus 153 k~~~sI~VP~~------~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~ 194 (465)
+.+..|.||.. |++.|+|++|.|+|+||++|||+|-|=..++
T Consensus 91 k~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgS 138 (259)
T KOG1588|consen 91 KLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGS 138 (259)
T ss_pred eEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCc
Confidence 55667778876 8899999999999999999999999965554
No 39
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.89 E-value=0.0013 Score=64.24 Aligned_cols=75 Identities=17% Similarity=0.242 Sum_probs=55.8
Q ss_pred CCCccCCCCeEEEEEeCcc------eeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHH
Q 012372 145 GEPVPSAERHSLSVEVGAS------VIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAI 218 (465)
Q Consensus 145 ~~~~~~~~k~~~sI~VP~~------~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~I 218 (465)
+..+....+|+-.+.||.+ |++.|||+.|.|+|+||+.++|+|-|-..+..-.-.|.+.+.++...|.+-|.-+
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 3445577889999999864 7899999999999999999999999976655333445555555666665555555
Q ss_pred H
Q 012372 219 I 219 (465)
Q Consensus 219 v 219 (465)
+
T Consensus 219 I 219 (269)
T COG5176 219 I 219 (269)
T ss_pred h
Confidence 4
No 40
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=96.86 E-value=0.0013 Score=67.37 Aligned_cols=65 Identities=25% Similarity=0.334 Sum_probs=60.4
Q ss_pred CCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHH
Q 012372 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQA 217 (465)
Q Consensus 152 ~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~ 217 (465)
.+..++++||..+.+.|.|++|.+||.|..+|++.|.-|+++.+-...++|. .+.|+.|++.|..
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~-~edv~~aRrei~s 88 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGR-HEDVRRARREIPS 88 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCCcceeccC-chhHHHHhhcCcc
Confidence 6888999999999999999999999999999999999999998866689997 6899999999976
No 41
>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=96.84 E-value=0.015 Score=57.24 Aligned_cols=118 Identities=15% Similarity=0.274 Sum_probs=77.9
Q ss_pred cccceEeeccccchhhhhhHHHHHHHHhcCcCcccccccCCCCCCCCCchHHHHHhhhhhhhhhhhhccCCCCcceeccc
Q 012372 229 DYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKVDR 308 (465)
Q Consensus 229 ~~thFVsIPl~~hP~I~~~~~~Fq~sIL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~v~~~~ 308 (465)
.||||+++|+..-.-..+++...|-.+++++=+ +|.
T Consensus 5 ~P~HFin~Pl~~f~~f~~~~~~LQ~~~~~eG~d---------------------------------~k~----------- 40 (248)
T PF05213_consen 5 KPTHFINFPLVQFEGFMLNFKDLQFQLLEEGVD---------------------------------CKL----------- 40 (248)
T ss_pred CCCceeeccchhhhhHHHHHHHHHHHHHHcCCC---------------------------------ccc-----------
Confidence 589999999974477888999998888875310 010
Q ss_pred ccccccccccccCCCCCCCCCCCCCcCccCCCeeeEEEeeeEeCChhHHHHHHHHHHHhHHHHHhhhCCCCcEEEEeecc
Q 012372 309 TSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLD 388 (465)
Q Consensus 309 ~~~~~v~~~~~~~~~~~~~~~GIdesiF~~p~tLHLTLgVL~L~~~eev~kA~~~L~slk~~I~~iL~~~pL~I~LkGL~ 388 (465)
-..=|||||||.+ +++++.....+|+++.+.+. +.++ .|++..-+
T Consensus 41 ------------------------------QkaPHlSl~mL~I-sd~~i~~V~~~iq~ViddM~-~~~~---~it~tnp~ 85 (248)
T PF05213_consen 41 ------------------------------QKAPHLSLGMLDI-SDEDIPDVETAIQKVIDDMV-WFEG---DITFTNPH 85 (248)
T ss_pred ------------------------------cccCeeEEEEEEc-ChhhhhhHHHHHHHHHHHhh-cccc---eEEecCce
Confidence 0123999999998 68889999888888765432 1122 67777777
Q ss_pred cCCCCCCcceEEEEeceecCCcchHHHHHHHHHHHHHH---------hccCCCcceEE
Q 012372 389 LMRGSKDKARILYAPVEEIGDGDRLLHACRILIAFVSS---------IFAPLCTSLII 437 (465)
Q Consensus 389 ~MnddPs~a~VLYAk~~~~d~~~rL~~~cq~I~d~F~e---------~F~p~~~~~i~ 437 (465)
.|. +..=|.|. -++.+=..|...|.+ -|.||+|..-+
T Consensus 86 MLg------~~yV~nV~------Gv~slh~ki~n~~~~kgit~gQSRmwIPHiTia~~ 131 (248)
T PF05213_consen 86 MLG------RCYVANVK------GVLSLHDKIVNVFRKKGITFGQSRMWIPHITIAQL 131 (248)
T ss_pred eec------cEEEEecc------cHHHHHHHHHHHHHHhCcCcCcccccccceehhhh
Confidence 774 33333443 233444556666664 28888886655
No 42
>PF13563 2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB: 1IUH_A.
Probab=96.44 E-value=0.0078 Score=52.99 Aligned_cols=93 Identities=17% Similarity=0.214 Sum_probs=54.0
Q ss_pred CeeeEEEeeeEeCChhHHHHHHHHHHHhHHHHHhhhCCCCcEEEEeecccCCCCCCcceEEEEeceecCCcchHHHHHHH
Q 012372 340 KTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACRI 419 (465)
Q Consensus 340 ~tLHLTLgVL~L~~~eev~kA~~~L~slk~~I~~iL~~~pL~I~LkGL~~MnddPs~a~VLYAk~~~~d~~~rL~~~cq~ 419 (465)
..+||||...-..++.. +.+.+.|..+-. .-.|+.|+|.|+++|.+ +-.|+|+.+. +...|.++...
T Consensus 24 ~~pHITL~~~~~~~~~~-~~~~~~l~~~~~------~~~~f~l~l~~~~~F~~---~~~vi~l~~~---~~~~L~~L~~~ 90 (153)
T PF13563_consen 24 WPPHITLAFPFDIDDSL-DELVEALARLAA------GFPPFELRLDGFGSFPG---KGRVIFLNVE---PSPELEALHRA 90 (153)
T ss_dssp GG-EEEEEEEEE--GGG-HHHHHHHHHHHH------HS--EEEEEEEEEEESS---SSSSEEEEEE---E-HHHHHHHHH
T ss_pred CCCEeEEEecCcccccH-HHHHHHHHHHHc------cCCCeEEEEccEEEcCC---CCCEEEEEcC---CCHHHHHHHHH
Confidence 34999999998876643 333333333211 23789999999999964 2359999994 36788777777
Q ss_pred HHHHHHHh-ccCCC-cceEEeeeehhHH
Q 012372 420 LIAFVSSI-FAPLC-TSLIIKMKQYYII 445 (465)
Q Consensus 420 I~d~F~e~-F~p~~-~~~i~~~~~~~~~ 445 (465)
|.+.|... +.+.- ..-+-||++-|..
T Consensus 91 l~~~~~~~~~~~~~~~~~~PHiTia~~~ 118 (153)
T PF13563_consen 91 LREALRPFGFKQDSYRPFRPHITIARRL 118 (153)
T ss_dssp HHHHHHHHHGGGGGGS----EEEEEEES
T ss_pred HHHHHHHcCCccccCCCcceEEEEeccC
Confidence 77776653 22222 5666777776644
No 43
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.03 E-value=0.011 Score=57.28 Aligned_cols=53 Identities=28% Similarity=0.415 Sum_probs=46.6
Q ss_pred eeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHH
Q 012372 164 VIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (465)
Q Consensus 164 ~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e 221 (465)
..+.|||++|.|++.||+=|||.|-| -...|-|-|. -++|+.|++-|..++..
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V----~g~tVaiiG~-~~~v~iAr~AVemli~G 164 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISV----YGKTVAIIGG-FEQVEIAREAVEMLING 164 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEE----eCcEEEEecC-hhhhHHHHHHHHHHHcC
Confidence 35789999999999999999999999 2357889996 68999999999998875
No 44
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.01 E-value=0.015 Score=56.24 Aligned_cols=66 Identities=30% Similarity=0.397 Sum_probs=57.3
Q ss_pred CCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEec----CHHHHHHHHHHHHHHH
Q 012372 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGN----STDSVAKASEKIQAII 219 (465)
Q Consensus 152 ~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~----ske~V~~A~~rI~~Iv 219 (465)
...+..+.||++-++.+||+.|.+.+.||+.|++++.|-. .++.|.|+.. +.-.+.+|++-|++|-
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~--~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIg 75 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS--KTGSVTIRTTRKTEDPLALLKARDVVKAIG 75 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC--CCCeEEEEecCCCCChHHHHHHHHHHHHHh
Confidence 3556679999999999999999999999999999999942 2578888876 7788999999999886
No 45
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.98 E-value=0.015 Score=63.46 Aligned_cols=68 Identities=21% Similarity=0.328 Sum_probs=54.3
Q ss_pred CCeEEEEEeCc-ceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHH
Q 012372 152 ERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (465)
Q Consensus 152 ~k~~~sI~VP~-~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e 221 (465)
......|++|. ++-|.|||+.|.+||.+|.-||+.|.|. +..+.|+|+|-+.---+-|+.-++.++.+
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid--dtp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID--DTPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc--CCCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 34556788998 6778999999999999999999999993 22467889987766667777777777754
No 46
>PRK12704 phosphodiesterase; Provisional
Probab=95.83 E-value=0.017 Score=63.21 Aligned_cols=68 Identities=19% Similarity=0.315 Sum_probs=53.3
Q ss_pred CCeEEEEEeCc-ceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHH
Q 012372 152 ERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (465)
Q Consensus 152 ~k~~~sI~VP~-~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e 221 (465)
.....+|++|. ++-+.|||+.|.+||.+|.-||+.|.|. +..+.|+|+|-+.-.-+-|+.-++.++..
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid--dtp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID--DTPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc--CCCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 34456788888 6778999999999999999999999993 22467899997655545777777777654
No 47
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=95.83 E-value=0.0062 Score=64.97 Aligned_cols=69 Identities=17% Similarity=0.238 Sum_probs=59.1
Q ss_pred CCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHH
Q 012372 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (465)
Q Consensus 152 ~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e 221 (465)
+.+...+.|-..+.+.+||+||++|+.|+..|+|+|+|-..+..-.|+|.|. ++--.+|+.-|...++.
T Consensus 45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~-~~m~~kaka~id~~~~k 113 (629)
T KOG0336|consen 45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGI-NHMRKKAKASIDRGQDK 113 (629)
T ss_pred CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCceeEEEEech-HHHHHHHHhhHhhhhhh
Confidence 4566788899999999999999999999999999999987777788999996 56677788888777754
No 48
>PRK00106 hypothetical protein; Provisional
Probab=95.68 E-value=0.024 Score=62.25 Aligned_cols=68 Identities=18% Similarity=0.342 Sum_probs=52.8
Q ss_pred CCeEEEEEeCc-ceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHH
Q 012372 152 ERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (465)
Q Consensus 152 ~k~~~sI~VP~-~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e 221 (465)
......|.+|. ++-+.|||+.|.+||.+|.-||+.|.|. +..+.|+|+|-+.---+-|+.-++.++.+
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid--dtp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID--DTPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc--CCCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 34556788998 6788999999999999999999999993 22467889987665666666666666643
No 49
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=95.60 E-value=0.014 Score=45.98 Aligned_cols=37 Identities=24% Similarity=0.269 Sum_probs=34.4
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEc
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~I 189 (465)
.....+.||++..+..|||+|.+++.+++.+|-+|+|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3677899999999999999999999999999999986
No 50
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=95.10 E-value=0.037 Score=55.16 Aligned_cols=62 Identities=26% Similarity=0.377 Sum_probs=54.1
Q ss_pred EEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHH
Q 012372 157 SVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (465)
Q Consensus 157 sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e 221 (465)
.+.||+.+++.+||++|+.++.|.++|+|+|-+ +..|-|=|.|+.......|...|..|-.+
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~V---G~NG~IWV~~~~~~~e~~~~~aI~~ie~e 210 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIV---GQNGRIWVDGENESLEELAIEAIRKIERE 210 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEE---ecCCEEEecCCCcchHHHHHHHHHHHhhh
Confidence 578999999999999999999999999999999 88899999998765677777777666544
No 51
>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=94.98 E-value=0.042 Score=44.83 Aligned_cols=57 Identities=19% Similarity=0.377 Sum_probs=42.2
Q ss_pred CCCeeeEEEeeeEeCChhHHHHHHHHHHHhHHHHHhhhCCCCcEEEEeecccCCCCCCcceEEE
Q 012372 338 KPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILY 401 (465)
Q Consensus 338 ~p~tLHLTLgVL~L~~~eev~kA~~~L~slk~~I~~iL~~~pL~I~LkGL~~MnddPs~a~VLY 401 (465)
+|..+||||+=+.=.+++++...++.|..+. -...|+.+++.|+++|.+.. ..+|+|
T Consensus 31 ~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~------~~~~~f~~~~~~~~~f~s~~-~~rvi~ 87 (87)
T PF02834_consen 31 RPFNPHITLAFLGEVPPDQLPELIEALANIA------SRFPPFTLTVDGFGLFPSRL-RPRVIW 87 (87)
T ss_dssp SCGGSEEEEEEEEEESHHHHHHHHHHHHHHH------CCCB-EEEEEEEEEEEEEEE-TCEEEE
T ss_pred CCCCCeEEEEeCCCCCHHHHHHHHHHHHhhh------ccCCCeEEEEeEEEEeCCCC-CCCCcC
Confidence 6789999999988666777776666655532 13478999999999997433 678888
No 52
>PRK12705 hypothetical protein; Provisional
Probab=94.21 E-value=0.058 Score=59.01 Aligned_cols=68 Identities=19% Similarity=0.318 Sum_probs=53.8
Q ss_pred CCeEEEEEeCc-ceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHH
Q 012372 152 ERHSLSVEVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 221 (465)
Q Consensus 152 ~k~~~sI~VP~-~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e 221 (465)
......|++|. ++-+.|||+.|.+||.+|..||+.|.|. +....|+|.+-+...-+.|+..++.++..
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid--dtp~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID--DTPEAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEec--CCccchhhcccCccchHHHHHHHHHHHhc
Confidence 34455678887 6778999999999999999999999995 22456788887777777788877777754
No 53
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=93.58 E-value=0.1 Score=56.90 Aligned_cols=101 Identities=26% Similarity=0.222 Sum_probs=73.8
Q ss_pred EEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCC--CC-CCcEEEEe--------cCHHHHHHHHHHHHHHHH---H
Q 012372 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS--KK-EDSIIIEG--------NSTDSVAKASEKIQAIIA---E 221 (465)
Q Consensus 156 ~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~--~~-sg~I~ItG--------~ske~V~~A~~rI~~Iv~---e 221 (465)
..+-.+....+.||||+|.++++|..+|+++|.|=.. ++ +..|+|+| +..+.+.+|.++|-...+ +
T Consensus 45 ~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~ 124 (485)
T KOG2190|consen 45 YRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDE 124 (485)
T ss_pred EEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccccccc
Confidence 5777889999999999999999999888888777443 22 56789999 246899999999866422 1
Q ss_pred -H------hhCCCCcccceEeeccccchhhhhhHHHHHHHHhcC
Q 012372 222 -A------VESPSLDYSHFVSLPLAVHPELVDKLVNFQNTILGI 258 (465)
Q Consensus 222 -~------~kk~k~~~thFVsIPl~~hP~I~~~~~~Fq~sIL~~ 258 (465)
. .. ....+--+-+|-..=-.|+|+-+..++.|.++
T Consensus 125 ~~~d~~~~~~--~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~ 166 (485)
T KOG2190|consen 125 AAEDNGEDAS--GPEVTCRLLVPSSQVGSLIGKGGSLIKEIREE 166 (485)
T ss_pred ccccCCcccc--CCceEEEEEechhheeeeeccCcHHHHHHHHh
Confidence 1 11 12234455567654477899999999999876
No 54
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=93.06 E-value=0.29 Score=49.94 Aligned_cols=68 Identities=18% Similarity=0.316 Sum_probs=51.7
Q ss_pred CCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCC-CCcEEEEecCHHHHHHHHHHHHHHHH
Q 012372 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIA 220 (465)
Q Consensus 152 ~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~-sg~I~ItG~ske~V~~A~~rI~~Iv~ 220 (465)
.++...+.+...--+.||||||++||+|..++++.|.+|.... +...+|++. .+.|-.-...|.--++
T Consensus 46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad-~~ti~~ilk~iip~le 114 (390)
T KOG2192|consen 46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISAD-IETIGEILKKIIPTLE 114 (390)
T ss_pred cceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCCCceeEEEecc-HHHHHHHHHHHhhhhh
Confidence 4677888888999999999999999999999999999996644 455688874 4555544444433333
No 55
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=92.43 E-value=0.083 Score=60.32 Aligned_cols=42 Identities=29% Similarity=0.572 Sum_probs=38.3
Q ss_pred CCCCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCC
Q 012372 150 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (465)
Q Consensus 150 ~~~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr 191 (465)
.....+..+.+|.++|+.|||++|.++|.++.++++.|.+|.
T Consensus 705 ~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 705 AKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred cccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence 345567788999999999999999999999999999999997
No 56
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=91.30 E-value=0.14 Score=56.16 Aligned_cols=102 Identities=21% Similarity=0.310 Sum_probs=74.6
Q ss_pred CCCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCC-CCcEEEEecCHHHHHHHHHHHHHHHHHHhhCCCCc
Q 012372 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLD 229 (465)
Q Consensus 151 ~~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~-sg~I~ItG~ske~V~~A~~rI~~Iv~e~~kk~k~~ 229 (465)
.++..+++.||.++.+.|+|++|.+++.|+..|+.||++-.... ...+-+.+.....+..|+..|-.++-+ ...
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~~-----~~p 139 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTE-----NTP 139 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHhc-----CCc
Confidence 46778889999999999999999999999999999999943322 123333332345677777777666654 123
Q ss_pred ccceEeeccccchhhhhhHHHHHHHHhc
Q 012372 230 YSHFVSLPLAVHPELVDKLVNFQNTILG 257 (465)
Q Consensus 230 ~thFVsIPl~~hP~I~~~~~~Fq~sIL~ 257 (465)
+-.-.+.|...|+.|.+..+..++++-.
T Consensus 140 vk~~lsvpqr~~~~i~grgget~~si~~ 167 (608)
T KOG2279|consen 140 VSEQLSVPQRSVGRIIGRGGETIRSICK 167 (608)
T ss_pred ccccccchhhhcccccccchhhhcchhc
Confidence 4455667877788888888888877654
No 57
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=88.43 E-value=0.3 Score=53.27 Aligned_cols=41 Identities=29% Similarity=0.373 Sum_probs=36.4
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCC
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSK 193 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~ 193 (465)
.-...+.||...++.+|||||.++++||...|.+|++-..+
T Consensus 485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 45578999999999999999999999999999999995443
No 58
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=88.14 E-value=0.59 Score=42.97 Aligned_cols=37 Identities=16% Similarity=0.119 Sum_probs=34.3
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEc
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~I 189 (465)
+....+.|+++-++..|||+|.+++.++.=+|-.|+|
T Consensus 98 ~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 98 DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred cEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 4567789999999999999999999999999999998
No 59
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=87.30 E-value=1.9 Score=41.10 Aligned_cols=63 Identities=19% Similarity=0.268 Sum_probs=53.5
Q ss_pred EEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHHH
Q 012372 157 SVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEA 222 (465)
Q Consensus 157 sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e~ 222 (465)
.+..++..+-+|.+.+|..++.|-...|++|++-+. .+.|.|+|+ +..++.+...|..+....
T Consensus 29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~--~~~i~I~g~-k~~~~~i~~~i~~~l~~i 91 (210)
T PF14611_consen 29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS--ENRIRITGT-KSTAEYIEASINEILSNI 91 (210)
T ss_pred EEEecchheeeeecCCchHHHHHHHhcCceEEEecC--CcEEEEEcc-HHHHHHHHHHHHHHHhhc
Confidence 566679999999999999999998888999999643 469999995 788888888888888763
No 60
>PRK13764 ATPase; Provisional
Probab=86.70 E-value=0.47 Score=53.15 Aligned_cols=41 Identities=29% Similarity=0.334 Sum_probs=36.3
Q ss_pred CCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCC
Q 012372 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS 192 (465)
Q Consensus 152 ~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~ 192 (465)
..-...|.||...++.+|||||.++++||+..|..|+|-..
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 44456889999999999999999999999999999999443
No 61
>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=86.54 E-value=1 Score=34.30 Aligned_cols=35 Identities=17% Similarity=0.288 Sum_probs=28.2
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEE
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKI 187 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI 187 (465)
.....+.+...-.+.+||++|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35556666665679999999999999999999554
No 62
>PRK00468 hypothetical protein; Provisional
Probab=85.88 E-value=0.81 Score=38.08 Aligned_cols=30 Identities=20% Similarity=0.302 Sum_probs=26.4
Q ss_pred CCeEEEEEeCcceeccccCCCChhHHHHHH
Q 012372 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEK 181 (465)
Q Consensus 152 ~k~~~sI~VP~~~~r~IIGkgG~tiK~IEe 181 (465)
......+.+.++=.+.||||+|.|++.|..
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRt 57 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRT 57 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHH
Confidence 446778999999999999999999999874
No 63
>PRK02821 hypothetical protein; Provisional
Probab=85.82 E-value=0.84 Score=38.24 Aligned_cols=32 Identities=19% Similarity=0.293 Sum_probs=27.6
Q ss_pred CCeEEEEEeCcceeccccCCCChhHHHHHHHh
Q 012372 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEM 183 (465)
Q Consensus 152 ~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeET 183 (465)
......+.+.++=.+.||||+|.+++.|..=-
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 44678899999999999999999999997543
No 64
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=85.53 E-value=0.53 Score=46.33 Aligned_cols=52 Identities=27% Similarity=0.386 Sum_probs=44.4
Q ss_pred eeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHH
Q 012372 164 VIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIA 220 (465)
Q Consensus 164 ~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~ 220 (465)
-++.|+||||+|.=.||+-|.|+|.+- ...|-|-|. -+++.-|++-|-.++-
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVla----d~kIHiLG~-~~niriAR~avcsLIl 230 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIENVTRTRIVLA----DSKIHILGA-FQNIRIARDAVCSLIL 230 (252)
T ss_pred HHHHhhcCCCcceeeeeccceeEEEec----CceEEEeec-chhhHHHHHhhHhhhc
Confidence 478999999999999999999999994 457889995 5789999888876664
No 65
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=85.39 E-value=0.9 Score=38.13 Aligned_cols=31 Identities=16% Similarity=0.297 Sum_probs=27.6
Q ss_pred CCCeEEEEEeCcceeccccCCCChhHHHHHH
Q 012372 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEK 181 (465)
Q Consensus 151 ~~k~~~sI~VP~~~~r~IIGkgG~tiK~IEe 181 (465)
++.....+.+.++-.+.+|||+|.|++.|..
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHH
Confidence 5567788999999999999999999999973
No 66
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=83.94 E-value=0.6 Score=37.58 Aligned_cols=34 Identities=15% Similarity=0.251 Sum_probs=28.1
Q ss_pred CCCeEEEEEeCcceeccccCCCChhHHHHHHHhC
Q 012372 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMG 184 (465)
Q Consensus 151 ~~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETg 184 (465)
.......+.+..+-.+.+|||+|.|++.|+.=++
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 3455678888999999999999999999985443
No 67
>PRK01064 hypothetical protein; Provisional
Probab=81.01 E-value=1.6 Score=36.69 Aligned_cols=31 Identities=29% Similarity=0.281 Sum_probs=27.3
Q ss_pred CCCeEEEEEeCcceeccccCCCChhHHHHHH
Q 012372 151 AERHSLSVEVGASVIRFIKGKEGSTQKKFEK 181 (465)
Q Consensus 151 ~~k~~~sI~VP~~~~r~IIGkgG~tiK~IEe 181 (465)
++.....+.|.++-.+.+|||+|.|++.|..
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~ 57 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRT 57 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHH
Confidence 4557788999999999999999999999875
No 68
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=80.36 E-value=1.9 Score=39.73 Aligned_cols=36 Identities=25% Similarity=0.370 Sum_probs=32.0
Q ss_pred EEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcC
Q 012372 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (465)
Q Consensus 155 ~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IP 190 (465)
...+-|++...+..||++|+.++.|++..|-+|+|=
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv 68 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV 68 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence 446677888999999999999999999999999983
No 69
>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=79.69 E-value=2.1 Score=39.58 Aligned_cols=38 Identities=16% Similarity=0.079 Sum_probs=35.0
Q ss_pred CCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEc
Q 012372 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (465)
Q Consensus 152 ~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~I 189 (465)
++....+.||++-++..|||+|.++|...+=||-+|+|
T Consensus 98 ~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 98 GKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred CCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 35678899999999999999999999999999999988
No 70
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=77.90 E-value=2.6 Score=46.61 Aligned_cols=70 Identities=16% Similarity=0.195 Sum_probs=54.9
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCC------CCcEEEEec--CHHHHHHHHHHHHHHHHHH
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGN--STDSVAKASEKIQAIIAEA 222 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~------sg~I~ItG~--ske~V~~A~~rI~~Iv~e~ 222 (465)
-...++-||...|+.|||.||..+++....-++-|.+--.-+ .+.|.|..| ++.++..|+.-...+|.+.
T Consensus 448 pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~ 525 (657)
T COG5166 448 PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQQ 525 (657)
T ss_pred chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhhh
Confidence 445688999999999999999999999988888877632111 356888886 6677888888888888764
No 71
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=76.54 E-value=2.2 Score=34.84 Aligned_cols=25 Identities=36% Similarity=0.478 Sum_probs=21.9
Q ss_pred eccccCCCChhHHHHHHHh-CcEEEc
Q 012372 165 IRFIKGKEGSTQKKFEKEM-GVKIIL 189 (465)
Q Consensus 165 ~r~IIGkgG~tiK~IEeET-gtkI~I 189 (465)
++..||++|..+|.|+++. |-+|+|
T Consensus 19 vG~~iG~~G~rik~i~~~L~gekIdv 44 (69)
T PF13184_consen 19 VGACIGKKGSRIKAISEELNGEKIDV 44 (69)
T ss_dssp HHHHH-CCCCCHHHHHHHTTT-EEEE
T ss_pred ceecCccccHHHHHHHHHhCCCeEEE
Confidence 7899999999999999999 999987
No 72
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=75.04 E-value=1.7 Score=35.27 Aligned_cols=36 Identities=25% Similarity=0.351 Sum_probs=30.8
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEE
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKII 188 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~ 188 (465)
.....+.+-...-+.+||++|+++++|.++.+-.+.
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 356678888899999999999999999988887764
No 73
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=73.69 E-value=3 Score=34.14 Aligned_cols=35 Identities=17% Similarity=0.282 Sum_probs=27.9
Q ss_pred EEEEEeCcceeccccCCCChhHHHHHHHhCcEEEc
Q 012372 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (465)
Q Consensus 155 ~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~I 189 (465)
...+.|..+-.+.+|||.|.|+..|+-=++.-++-
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 35677788889999999999999999766654443
No 74
>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=73.58 E-value=6.6 Score=37.73 Aligned_cols=74 Identities=20% Similarity=0.274 Sum_probs=38.9
Q ss_pred eEEEee-eEeCChhHHHHHHHHHHHhHHHHHhhhCCCCcEEEEeecccCCCCCCcceEEEEeceecCCcchHHHHHHHHH
Q 012372 343 HLTVLM-LKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACRILI 421 (465)
Q Consensus 343 HLTLgV-L~L~~~eev~kA~~~L~slk~~I~~iL~~~pL~I~LkGL~~MnddPs~a~VLYAk~~~~d~~~rL~~~cq~I~ 421 (465)
|+||.. +.+.+.+++ .++|.++-..... +..+...|++.++.+= + .--+-+|+.+. .+..|..+++.++
T Consensus 40 HiTL~s~i~~~~~~~~---~~~L~~~~~~~~~-~~~~~~~v~~~~v~~g-~--~yfq~vyl~v~---~t~~L~~l~~~~r 109 (196)
T PF07823_consen 40 HITLTSGISLDSSDDV---QKVLDSAAAALKP-LPKNHFTVRFDKVASG-D--KYFQCVYLEVE---KTPELMSLAQIAR 109 (196)
T ss_dssp -EEEEEEEEE--HHHH---HHHHHHHHHH-B--E-----EEEEEEEEEE-E--ETTEEEEEEE------HHHHHHHCHHH
T ss_pred eEEEeCCCccCCHHHH---HHHHHHHHHhccC-cccceeEEEeeeEeeC-C--eEEEEEEEEec---CChhHHHHHHHHH
Confidence 999988 566545554 4445554333222 1111248899888741 1 11256898885 3667988888888
Q ss_pred HHHHH
Q 012372 422 AFVSS 426 (465)
Q Consensus 422 d~F~e 426 (465)
+.|..
T Consensus 110 ~~~~~ 114 (196)
T PF07823_consen 110 ELFVE 114 (196)
T ss_dssp HCT--
T ss_pred HHhhh
Confidence 88853
No 75
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=71.55 E-value=3.4 Score=43.19 Aligned_cols=70 Identities=20% Similarity=0.292 Sum_probs=59.1
Q ss_pred CCCCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHH-HHHHHHH
Q 012372 150 SAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKAS-EKIQAII 219 (465)
Q Consensus 150 ~~~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~-~rI~~Iv 219 (465)
...+....+.+|-...+.+.|.+|++++.+++-|++-|.-|-+......-++|-.+.++++|+ ..|+..+
T Consensus 111 ~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~~~~Vf~Vtg~~~nC~kra~s~eie~ta 181 (394)
T KOG2113|consen 111 ASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRCGEPVFCVTGAPKNCVKRARSCEIEQTA 181 (394)
T ss_pred ccCCCceeeeccceeeeeccccccCccchheecccceEeeeccCCCceEEEecCCcchhhhccccchhhhh
Confidence 456777788899999999999999999999999999999998766667789998888899998 6665443
No 76
>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=69.62 E-value=5.6 Score=36.85 Aligned_cols=35 Identities=26% Similarity=0.320 Sum_probs=33.1
Q ss_pred EEEEEeCcceeccccCCCChhHHHHHHHhCcEEEc
Q 012372 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (465)
Q Consensus 155 ~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~I 189 (465)
...+-|.+...+..||++|..++.|++..|-+|+|
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 77889999999999999999999999999999988
No 77
>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=65.67 E-value=6.6 Score=41.23 Aligned_cols=38 Identities=26% Similarity=0.290 Sum_probs=35.5
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcC
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IP 190 (465)
.....+.||++-.+.-|||+|.++|--..=||.+|+|=
T Consensus 300 ~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~ 337 (341)
T TIGR01953 300 KHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVK 337 (341)
T ss_pred CcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEE
Confidence 35789999999999999999999999999999999993
No 78
>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=65.40 E-value=39 Score=33.29 Aligned_cols=102 Identities=14% Similarity=0.248 Sum_probs=63.8
Q ss_pred CCCeeeEEEeeeEeCChhHHHHHHHHHHHhHHHHHhhhCCCCcEEEEeecccCCCCCCcceEEEEeceecCCcchHHHHH
Q 012372 338 KPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHAC 417 (465)
Q Consensus 338 ~p~tLHLTLgVL~L~~~eev~kA~~~L~slk~~I~~iL~~~pL~I~LkGL~~MnddPs~a~VLYAk~~~~d~~~rL~~~c 417 (465)
.+.-||++|.=---..-.+++.-++.|+. .+.. -.-+++.|.+.|+..+- +..+++.-.+=....+....|.++.
T Consensus 86 ~~~~lHISLSr~~~lr~~~id~f~~~lr~---~l~~-~~~~~F~v~f~~~~~~~-N~e~TR~FL~l~V~~~~~~~l~~l~ 160 (239)
T PF09749_consen 86 SPDPLHISLSRTFPLRTHQIDPFVDSLRQ---ALRS-SNIRPFYVSFSGLDVYT-NDEKTRSFLALRVSEGSNNELKRLL 160 (239)
T ss_pred CCCCeEEEeCCCccccHHHHHHHHHHHHH---HHhh-cCCceEEEEeCceEEEe-cCCCCeEEEEEEecccccHHHHHHH
Confidence 56789999985544455666655554443 2211 23489999999999885 3555664443322222333399999
Q ss_pred HHHHHHHHHhccCCCc--ceEEeeeehhH
Q 012372 418 RILIAFVSSIFAPLCT--SLIIKMKQYYI 444 (465)
Q Consensus 418 q~I~d~F~e~F~p~~~--~~i~~~~~~~~ 444 (465)
+.|.+.+.+...|..- .-..||-+-|.
T Consensus 161 ~~i~~~l~~~~lp~~Y~~~~~fHvSIAw~ 189 (239)
T PF09749_consen 161 DRINEVLKEFGLPPFYDEDPSFHVSIAWT 189 (239)
T ss_pred HHHHHHHHHhCCCcccCCCCCCEEEEEEE
Confidence 9998888876555443 56667766554
No 79
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=64.99 E-value=7.2 Score=37.21 Aligned_cols=32 Identities=25% Similarity=0.391 Sum_probs=27.4
Q ss_pred EEEeCcceeccccCCCChhHHHHHHHhCcEEEc
Q 012372 157 SVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (465)
Q Consensus 157 sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~I 189 (465)
.+-|.+-. +.-|||+|.++|+|++..|-+|.+
T Consensus 64 IfvV~~gd-g~aIGk~G~~ik~l~~~lgk~Vev 95 (166)
T PRK06418 64 ILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRV 95 (166)
T ss_pred EEEEeCCC-cccccccchHHHHHHHHhCCcEEE
Confidence 44555555 999999999999999999999887
No 80
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=64.74 E-value=13 Score=39.19 Aligned_cols=80 Identities=18% Similarity=0.143 Sum_probs=65.1
Q ss_pred CeeeEEEeeeEeCChhHHHHHHHHHHHhHHHHHhhhCCCCcEEEEeecccCCCCCCcceEEEEeceecCCcchHHHHHHH
Q 012372 340 KTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACRI 419 (465)
Q Consensus 340 ~tLHLTLgVL~L~~~eev~kA~~~L~slk~~I~~iL~~~pL~I~LkGL~~MnddPs~a~VLYAk~~~~d~~~rL~~~cq~ 419 (465)
.++|+|+-++-+.++.+++.-...|+++++.+..+++++-..--++|-..++- .|-.+++.+ ...+|+.|+.
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 58999999999999999999999999888877777776666667788888874 888888863 4567888888
Q ss_pred HHHHHHHh
Q 012372 420 LIAFVSSI 427 (465)
Q Consensus 420 I~d~F~e~ 427 (465)
+-..|.|.
T Consensus 200 les~~~e~ 207 (345)
T KOG2814|consen 200 LESTFQEI 207 (345)
T ss_pred HHHHHHHH
Confidence 88777763
No 81
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=64.41 E-value=7.2 Score=37.88 Aligned_cols=35 Identities=20% Similarity=0.191 Sum_probs=34.0
Q ss_pred EEEEEeCcceeccccCCCChhHHHHHHHhCcEEEc
Q 012372 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (465)
Q Consensus 155 ~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~I 189 (465)
...+.||++-.+..|||+|.+++-..+=||.+|+|
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I 177 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDI 177 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEE
Confidence 78899999999999999999999999999999999
No 82
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=62.56 E-value=14 Score=38.35 Aligned_cols=50 Identities=18% Similarity=0.288 Sum_probs=38.2
Q ss_pred eccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHHHh
Q 012372 165 IRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAV 223 (465)
Q Consensus 165 ~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~~Iv~e~~ 223 (465)
...+||++|+|+|.||--|+|-|-+ ..++|.+.|+= .++..++ .|+.+..
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilV----qG~TVsaiGpf-kGlkevr----~IV~DcM 209 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILV----QGNTVSAIGPF-KGLKEVR----KIVEDCM 209 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEe----eCcEEEeecCc-chHHHHH----HHHHHHH
Confidence 4569999999999999999999998 34688888973 4665554 4555533
No 83
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=61.96 E-value=8.5 Score=41.05 Aligned_cols=43 Identities=19% Similarity=0.082 Sum_probs=38.2
Q ss_pred CCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCC
Q 012372 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 194 (465)
Q Consensus 152 ~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~ 194 (465)
......+.||++-++.-|||+|.++|--..=||.+|||=+.++
T Consensus 306 ~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 306 EEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred CCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 3457789999999999999999999999999999999966554
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=60.60 E-value=5.5 Score=33.40 Aligned_cols=35 Identities=11% Similarity=0.267 Sum_probs=28.9
Q ss_pred EEEEeCcceeccccCCCChhHHHHHHHhCcEEEcC
Q 012372 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (465)
Q Consensus 156 ~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IP 190 (465)
+.|.|-...=+.+||++|+++++|.++-...+.++
T Consensus 32 i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 32 TEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred EEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 45555566669999999999999999988888875
No 85
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=55.55 E-value=13 Score=39.47 Aligned_cols=38 Identities=24% Similarity=0.262 Sum_probs=35.4
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcC
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 190 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IP 190 (465)
.....+.||++-++.-|||+|.++|--..=||.+|+|=
T Consensus 302 ~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~ 339 (362)
T PRK12327 302 EKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIK 339 (362)
T ss_pred CcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEE
Confidence 45788999999999999999999999999999999993
No 86
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=54.80 E-value=11 Score=41.22 Aligned_cols=37 Identities=30% Similarity=0.331 Sum_probs=35.1
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEc
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~I 189 (465)
.....+-||+..++.-|||+|.++|-...=||.+|+|
T Consensus 301 ~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi 337 (470)
T PRK09202 301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDI 337 (470)
T ss_pred CCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEE
Confidence 4578899999999999999999999999999999999
No 87
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=50.70 E-value=7.6 Score=43.26 Aligned_cols=70 Identities=24% Similarity=0.257 Sum_probs=54.0
Q ss_pred cCCCCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEcCCCCC---CCcEEEEecCHHHHHHHHHHHHHHH
Q 012372 149 PSAERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKIQAII 219 (465)
Q Consensus 149 ~~~~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~---sg~I~ItG~ske~V~~A~~rI~~Iv 219 (465)
..+.-+.....+|...+..|+|+||.|++.|+.-.+++|.+-..+. ...+.|.|. +.-+..|+..|..=+
T Consensus 135 ~~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~q-qk~~~~a~~~~~~~~ 207 (608)
T KOG2279|consen 135 TENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQ-QKEVAAAKHLILEKV 207 (608)
T ss_pred hcCCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccc-cchHHHHHhhhhccc
Confidence 3556777888999999999999999999999999999999965544 234555554 556667777776555
No 88
>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=47.75 E-value=42 Score=27.91 Aligned_cols=35 Identities=29% Similarity=0.454 Sum_probs=27.8
Q ss_pred CcEEEcCCCCCCCcEEEEec-CHHHHHHHHHHHHHHHHH
Q 012372 184 GVKIILPSSKKEDSIIIEGN-STDSVAKASEKIQAIIAE 221 (465)
Q Consensus 184 gtkI~IPr~~~sg~I~ItG~-ske~V~~A~~rI~~Iv~e 221 (465)
++.+-|= .+|.|+|+|. +.+.+..|.++|..++.+
T Consensus 49 ~~t~~IF---~sGki~itGaks~~~~~~a~~~i~~~L~~ 84 (86)
T PF00352_consen 49 KATVLIF---SSGKIVITGAKSEEEAKKAIEKILPILQK 84 (86)
T ss_dssp TEEEEEE---TTSEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred cEEEEEE---cCCEEEEEecCCHHHHHHHHHHHHHHHHH
Confidence 4555552 3689999996 899999999999888875
No 89
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=46.27 E-value=17 Score=31.88 Aligned_cols=33 Identities=24% Similarity=0.321 Sum_probs=25.2
Q ss_pred EEEEeCcceeccccCCCChhHHHHHHHhCcEEE
Q 012372 156 LSVEVGASVIRFIKGKEGSTQKKFEKEMGVKII 188 (465)
Q Consensus 156 ~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~ 188 (465)
+.|.|-...=+.|||++|+++++|+++....+.
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~~~ 95 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQKLLG 95 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHHHhC
Confidence 345555555799999999999999988776543
No 90
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=44.30 E-value=21 Score=34.71 Aligned_cols=36 Identities=31% Similarity=0.305 Sum_probs=31.3
Q ss_pred eEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEc
Q 012372 154 HSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (465)
Q Consensus 154 ~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~I 189 (465)
...+..+-..-.+..||++|..+|.|.++.|-+|+|
T Consensus 76 av~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdV 111 (190)
T COG0195 76 AVVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDV 111 (190)
T ss_pred ceEEeecCcCchhhhccCCChHHHHHHHHhCCceEE
Confidence 356666777788999999999999999999988887
No 91
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=43.66 E-value=24 Score=38.62 Aligned_cols=37 Identities=24% Similarity=0.258 Sum_probs=34.7
Q ss_pred CeEEEEEeCcceeccccCCCChhHHHHHHHhCcEEEc
Q 012372 153 RHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (465)
Q Consensus 153 k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~I 189 (465)
.....+-||++-+..-|||+|.++|---.=||.+|+|
T Consensus 334 ~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI 370 (449)
T PRK12329 334 GRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDI 370 (449)
T ss_pred CcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecc
Confidence 3567899999999999999999999999999999999
No 92
>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=32.66 E-value=44 Score=33.05 Aligned_cols=28 Identities=25% Similarity=0.302 Sum_probs=21.8
Q ss_pred CeEEEEEeCccee-ccccCCCChhHHHHH
Q 012372 153 RHSLSVEVGASVI-RFIKGKEGSTQKKFE 180 (465)
Q Consensus 153 k~~~sI~VP~~~~-r~IIGkgG~tiK~IE 180 (465)
.+...|.|.++-+ +.|||++|+++|+|-
T Consensus 220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~ 248 (270)
T TIGR00436 220 KIHALISVERESQKKIIIGKNGSMIKAIG 248 (270)
T ss_pred EEEEEEEECcCCceeEEEcCCcHHHHHHH
Confidence 3667788887766 467899999999874
No 93
>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=32.37 E-value=39 Score=31.78 Aligned_cols=33 Identities=27% Similarity=0.339 Sum_probs=27.7
Q ss_pred EEEeCcceeccccCCCChhHHHHHHHhCcEEEc
Q 012372 157 SVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (465)
Q Consensus 157 sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~I 189 (465)
.|.|-.+.=+.+||++|.++++|-.+||-+-.|
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~v 111 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKV 111 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEE
Confidence 345556677899999999999999999988666
No 94
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=31.16 E-value=43 Score=27.94 Aligned_cols=34 Identities=9% Similarity=0.221 Sum_probs=24.8
Q ss_pred CCeEEEEEeCcceeccccCCCChhHHHHHHHhCcEE
Q 012372 152 ERHSLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKI 187 (465)
Q Consensus 152 ~k~~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI 187 (465)
.+..+.+++ ..-+.+||++|.++++|.+.-.-.+
T Consensus 38 ~~i~V~I~t--~~pg~iIGk~G~~I~~l~~~l~k~~ 71 (85)
T cd02411 38 LGTQITIYA--ERPGMVIGRGGKNIRELTEILETKF 71 (85)
T ss_pred CcEEEEEEE--CCCCceECCCchhHHHHHHHHHHHh
Confidence 345555555 5668999999999999987765443
No 95
>PRK00089 era GTPase Era; Reviewed
Probab=29.69 E-value=47 Score=32.90 Aligned_cols=27 Identities=30% Similarity=0.332 Sum_probs=20.8
Q ss_pred CeEEEEEeCccee-ccccCCCChhHHHH
Q 012372 153 RHSLSVEVGASVI-RFIKGKEGSTQKKF 179 (465)
Q Consensus 153 k~~~sI~VP~~~~-r~IIGkgG~tiK~I 179 (465)
.+...|.|.++-+ +.|||+||++||+|
T Consensus 225 ~i~~~i~v~~~~~k~i~ig~~g~~i~~i 252 (292)
T PRK00089 225 RIEATIYVERDSQKGIIIGKGGAMLKKI 252 (292)
T ss_pred EEEEEEEEccCCceeEEEeCCcHHHHHH
Confidence 3566777777666 56789999999887
No 96
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=29.05 E-value=1.4e+02 Score=31.83 Aligned_cols=55 Identities=20% Similarity=0.290 Sum_probs=45.0
Q ss_pred cceeccccCCCChhHHHHHHHhCcEEEcCCCCCCCcEEEEecCHHHHHHHHHHHH--HHHHH
Q 012372 162 ASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQ--AIIAE 221 (465)
Q Consensus 162 ~~~~r~IIGkgG~tiK~IEeETgtkI~IPr~~~sg~I~ItG~ske~V~~A~~rI~--~Iv~e 221 (465)
....--+.|+.|..++.||+.+|+.|.-+ ...+.|+|. ++.++.|...++ .+...
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~r----G~~~~i~g~-~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVAR----GEAVRIIGA-RPLVDVATRVLLTLELLAE 79 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEeC----CceEEEEec-hHHHHHHHHHHhHHHHHHH
Confidence 55666789999999999999999999874 346889996 459999999999 55544
No 97
>COG5255 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.44 E-value=97 Score=31.05 Aligned_cols=45 Identities=22% Similarity=0.417 Sum_probs=31.0
Q ss_pred CeeeEEEeeeEeC-ChhHHHHHHHHHHHhHHHHHhhhCCCCcEEEEeecc
Q 012372 340 KTFHLTVLMLKLW-NKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLD 388 (465)
Q Consensus 340 ~tLHLTLgVL~L~-~~eev~kA~~~L~slk~~I~~iL~~~pL~I~LkGL~ 388 (465)
-.+|+|||-+.-+ ++++...=..+|.++.+. |..+-..|+++-.+
T Consensus 177 Y~FHITlgYl~~wltpee~a~~q~~l~e~~e~----la~~~PvIe~~ap~ 222 (239)
T COG5255 177 YQFHITLGYLRIWLTPEEEAEWQAVLDELLEI----LAEKAPVIEVNAPD 222 (239)
T ss_pred eEEEEEeeeEeeecChhhhHHHHHHHHHHHHH----HHhhCCeEEecCcc
Confidence 5799999999876 777777777777776543 33344467666554
No 98
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=27.95 E-value=48 Score=33.44 Aligned_cols=35 Identities=26% Similarity=0.282 Sum_probs=26.4
Q ss_pred EEEEEeCcceeccccCCCChhHHHHHHHhCcEEEc
Q 012372 155 SLSVEVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 189 (465)
Q Consensus 155 ~~sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~I 189 (465)
.+.|.|-...=+.+||++|+.+++|.++....+..
T Consensus 52 ~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~ 86 (233)
T COG0092 52 GTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGK 86 (233)
T ss_pred ceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCC
Confidence 34455556667899999999999998776655555
No 99
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=20.89 E-value=1.8e+02 Score=32.97 Aligned_cols=35 Identities=26% Similarity=0.280 Sum_probs=29.2
Q ss_pred EEEeCcceeccccCCCChhHHHHHHHhCcEEEcCC
Q 012372 157 SVEVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 191 (465)
Q Consensus 157 sI~VP~~~~r~IIGkgG~tiK~IEeETgtkI~IPr 191 (465)
.|-|-.++=+.+|||+|+|.++|-++||-+-.|=|
T Consensus 102 EViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 102 EVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred eEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 45566777889999999999999999998866643
No 100
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=20.68 E-value=1.4e+02 Score=24.46 Aligned_cols=32 Identities=16% Similarity=0.315 Sum_probs=20.9
Q ss_pred HHHHHHHHhHHHHHhhhCCCCcEEEEeecccCC
Q 012372 359 AATNVLKSISSKVMDALDNRPLFIRLKGLDLMR 391 (465)
Q Consensus 359 kA~~~L~slk~~I~~iL~~~pL~I~LkGL~~Mn 391 (465)
.+..+|+.+.+.+.+.|..+. .|.|.|++.|.
T Consensus 20 ~v~~vl~~l~~~i~~~L~~g~-~V~i~g~G~F~ 51 (90)
T smart00411 20 DAKAAVDAFLEIITEALKKGE-KVELRGFGTFE 51 (90)
T ss_pred HHHHHHHHHHHHHHHHHhCCC-eEEEeCcEEEE
Confidence 344555555555666565444 79999999985
Done!