Query 022785
Match_columns 292
No_of_seqs 218 out of 464
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 06:07:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022785.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022785hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1588 RNA-binding protein Sa 100.0 5.6E-64 1.2E-68 461.0 23.3 217 28-291 21-241 (259)
2 KOG0119 Splicing factor 1/bran 100.0 3.3E-46 7.1E-51 365.6 13.5 205 60-276 52-270 (554)
3 cd02395 SF1_like-KH Splicing f 100.0 3.3E-41 7.2E-46 280.8 12.5 119 144-266 1-120 (120)
4 COG5176 MSL5 Splicing factor ( 100.0 8.1E-38 1.8E-42 280.6 8.8 195 66-268 69-269 (269)
5 cd00105 KH-I K homology RNA-bi 98.3 1.8E-06 4E-11 62.3 6.9 62 145-236 2-63 (64)
6 KOG1960 Predicted RNA-binding 98.3 2.9E-07 6.3E-12 90.5 3.2 96 141-250 208-303 (531)
7 cd02393 PNPase_KH Polynucleoti 98.3 1.5E-06 3.3E-11 64.1 5.6 51 158-237 11-61 (61)
8 smart00322 KH K homology RNA-b 98.3 4.2E-06 9.1E-11 59.4 7.3 65 144-240 4-68 (69)
9 PF00013 KH_1: KH domain syndr 98.2 1.9E-06 4.1E-11 62.3 3.7 59 145-236 2-60 (60)
10 PF13014 KH_3: KH domain 98.1 1.9E-06 4.1E-11 59.0 3.0 28 159-186 1-28 (43)
11 cd02394 vigilin_like_KH K homo 97.9 2.5E-05 5.4E-10 56.8 4.8 53 158-236 9-61 (62)
12 cd02396 PCBP_like_KH K homolog 97.8 7E-05 1.5E-09 55.4 6.4 36 145-186 2-37 (65)
13 TIGR03665 arCOG04150 arCOG0415 97.6 8.5E-05 1.8E-09 65.4 5.3 53 159-242 99-151 (172)
14 PRK13763 putative RNA-processi 97.5 0.00016 3.4E-09 64.2 5.5 53 159-242 105-157 (180)
15 TIGR03665 arCOG04150 arCOG0415 97.2 0.00048 1E-08 60.7 4.9 57 158-242 7-65 (172)
16 COG1094 Predicted RNA-binding 97.1 0.0012 2.5E-08 59.9 5.9 53 159-242 112-164 (194)
17 PRK13763 putative RNA-processi 97.0 0.0013 2.8E-08 58.5 5.4 57 158-242 12-71 (180)
18 TIGR02696 pppGpp_PNP guanosine 96.8 0.0024 5.2E-08 67.6 6.5 64 144-242 579-642 (719)
19 KOG1676 K-homology type RNA bi 96.4 0.0072 1.6E-07 62.4 6.7 71 146-243 231-301 (600)
20 TIGR03591 polynuc_phos polyrib 96.4 0.005 1.1E-07 64.9 5.6 63 144-241 552-614 (684)
21 KOG2193 IGF-II mRNA-binding pr 96.3 0.0014 3E-08 65.5 1.0 39 148-186 279-317 (584)
22 KOG2874 rRNA processing protei 96.0 0.02 4.3E-07 54.8 6.9 67 161-259 161-228 (356)
23 PLN00207 polyribonucleotide nu 95.6 0.011 2.3E-07 64.1 3.9 64 144-242 686-750 (891)
24 PRK04163 exosome complex RNA-b 95.6 0.017 3.8E-07 53.2 4.8 55 158-241 154-208 (235)
25 KOG1676 K-homology type RNA bi 95.6 0.03 6.5E-07 58.0 6.8 74 141-242 137-210 (600)
26 PRK11824 polynucleotide phosph 94.5 0.036 7.7E-07 58.7 4.1 56 158-242 563-618 (693)
27 KOG2191 RNA-binding protein NO 94.5 0.07 1.5E-06 52.2 5.6 37 143-185 39-75 (402)
28 KOG1960 Predicted RNA-binding 94.3 0.018 3.8E-07 57.5 1.1 77 162-251 308-384 (531)
29 KOG2814 Transcription coactiva 93.9 0.086 1.9E-06 51.4 4.9 31 158-188 66-96 (345)
30 KOG2190 PolyC-binding proteins 91.8 0.41 8.9E-06 49.0 6.7 39 143-187 138-176 (485)
31 KOG2193 IGF-II mRNA-binding pr 91.6 0.16 3.5E-06 51.2 3.3 31 157-187 207-237 (584)
32 PRK00106 hypothetical protein; 91.2 0.41 8.9E-06 49.6 5.9 63 146-241 228-290 (535)
33 KOG2191 RNA-binding protein NO 91.1 1.1 2.4E-05 44.1 8.4 38 143-186 132-169 (402)
34 TIGR03319 YmdA_YtgF conserved 90.4 0.48 1E-05 48.7 5.6 63 146-241 207-269 (514)
35 PRK12704 phosphodiesterase; Pr 90.0 0.63 1.4E-05 47.9 6.1 50 146-223 213-262 (520)
36 COG1185 Pnp Polyribonucleotide 88.6 0.65 1.4E-05 49.3 5.0 62 145-241 554-615 (692)
37 cd02134 NusA_KH NusA_K homolog 88.2 0.85 1.8E-05 33.5 4.1 35 144-184 26-60 (61)
38 KOG0336 ATP-dependent RNA heli 83.8 0.59 1.3E-05 47.5 1.7 29 157-185 55-83 (629)
39 KOG1067 Predicted RNA-binding 80.2 1.6 3.6E-05 45.7 3.4 54 159-242 607-660 (760)
40 PF13184 KH_5: NusA-like KH do 80.1 1.5 3.3E-05 33.3 2.5 30 155-184 14-44 (69)
41 cd02409 KH-II KH-II (K homolo 74.4 2.7 5.8E-05 29.7 2.3 24 159-182 35-58 (68)
42 KOG2190 PolyC-binding proteins 72.5 2.6 5.7E-05 43.2 2.5 39 143-187 338-376 (485)
43 COG1094 Predicted RNA-binding 72.1 11 0.00024 34.5 6.1 29 159-187 18-46 (194)
44 PRK12705 hypothetical protein; 68.7 4.8 0.0001 41.6 3.4 31 155-185 205-235 (508)
45 KOG2113 Predicted RNA binding 66.7 4.5 9.7E-05 39.8 2.5 37 141-183 24-60 (394)
46 PRK08406 transcription elongat 65.7 4.9 0.00011 34.5 2.4 29 158-186 41-69 (140)
47 cd02414 jag_KH jag_K homology 64.5 4.2 9.1E-05 31.0 1.6 21 160-180 35-55 (77)
48 COG1097 RRP4 RNA-binding prote 58.6 7.9 0.00017 36.4 2.6 28 158-185 155-182 (239)
49 PF13083 KH_4: KH domain; PDB: 49.0 4.6 9.9E-05 30.2 -0.5 21 159-179 39-59 (73)
50 KOG4797 Transcriptional regula 45.4 4.8 0.0001 33.8 -1.0 52 226-278 47-99 (123)
51 TIGR01952 nusA_arch NusA famil 42.5 21 0.00046 30.9 2.5 37 146-186 34-70 (141)
52 PRK12329 nusA transcription el 42.1 36 0.00078 34.9 4.4 44 142-186 262-306 (449)
53 KOG0334 RNA helicase [RNA proc 41.0 19 0.00042 40.1 2.5 77 147-241 900-976 (997)
54 PRK02821 hypothetical protein; 40.6 17 0.00036 28.5 1.4 22 158-179 40-61 (77)
55 PRK00468 hypothetical protein; 38.8 18 0.00039 28.0 1.4 19 159-177 40-58 (75)
56 KOG2113 Predicted RNA binding 38.6 15 0.00034 36.1 1.2 31 157-187 123-153 (394)
57 PRK12327 nusA transcription el 37.6 32 0.00069 34.2 3.2 40 146-186 234-274 (362)
58 PRK06418 transcription elongat 35.1 29 0.00064 30.9 2.3 38 145-187 61-98 (166)
59 KOG2192 PolyC-binding hnRNP-K 34.9 73 0.0016 31.0 5.0 38 142-185 47-84 (390)
60 COG0195 NusA Transcription elo 34.6 32 0.0007 31.2 2.5 34 155-188 82-115 (190)
61 COG1702 PhoH Phosphate starvat 33.6 78 0.0017 31.5 5.1 29 158-186 24-52 (348)
62 KOG2279 Kinase anchor protein 33.5 32 0.00069 36.2 2.5 54 126-186 278-333 (608)
63 TIGR01953 NusA transcription t 33.4 43 0.00092 33.0 3.3 40 146-186 232-272 (341)
64 COG1837 Predicted RNA-binding 33.0 26 0.00056 27.5 1.4 19 159-177 40-58 (76)
65 PRK01064 hypothetical protein; 33.0 24 0.00052 27.6 1.2 20 160-179 41-60 (78)
66 TIGR00436 era GTP-binding prot 32.5 40 0.00086 31.1 2.8 40 141-185 219-266 (270)
67 PRK00089 era GTPase Era; Revie 32.1 84 0.0018 29.0 4.9 40 141-185 224-271 (292)
68 PF00126 HTH_1: Bacterial regu 31.3 35 0.00075 24.4 1.8 19 170-188 33-51 (60)
69 KOG2208 Vigilin [Lipid transpo 29.4 23 0.0005 38.4 0.8 38 142-185 708-745 (753)
70 PRK08406 transcription elongat 28.6 27 0.00059 30.0 0.9 26 159-184 109-134 (140)
71 KOG2192 PolyC-binding hnRNP-K 28.0 65 0.0014 31.4 3.5 36 144-185 316-351 (390)
72 PRK15494 era GTPase Era; Provi 27.9 1E+02 0.0022 29.7 4.9 40 141-185 271-318 (339)
73 PRK13348 chromosome replicatio 25.7 47 0.001 30.1 2.0 22 169-190 35-56 (294)
74 PRK12328 nusA transcription el 25.6 52 0.0011 33.0 2.4 40 146-186 240-280 (374)
75 TIGR01170 rplA_mito ribosomal 23.7 17 0.00036 31.5 -1.3 20 150-169 99-118 (141)
76 PTZ00225 60S ribosomal protein 22.6 2.3E+02 0.0049 26.1 5.8 27 160-186 117-156 (214)
77 KOG3273 Predicted RNA-binding 22.5 26 0.00057 32.6 -0.2 29 158-186 178-206 (252)
78 TIGR03298 argP transcriptional 20.0 58 0.0013 29.5 1.4 21 170-190 35-55 (292)
No 1
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=100.00 E-value=5.6e-64 Score=461.00 Aligned_cols=217 Identities=53% Similarity=0.787 Sum_probs=189.3
Q ss_pred cCCcccchhHHHHHHHHHHHHhhcCCCCCchHHHHHHHHHHHHHHHHHhhcCccCCCCCCCCCCCCCCCCCcCCCCCCcc
Q 022785 28 RSASSAILDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTN 107 (292)
Q Consensus 28 r~~~~~~~~~~~YL~eLl~E~~~L~~~~~~~~h~~rLL~~EI~RV~~~l~~~~~~~~~~~~~~SP~~s~g~~~N~~~~~~ 107 (292)
+..+......++||.+|++|+++|++|+. |+||.|||++||.||...+++.. +.+|
T Consensus 21 ~~~~~~~~~~~~yl~el~~e~~~l~~~~~-~~~~~rLL~~Ei~rv~~~~~~~~--------~~~~--------------- 76 (259)
T KOG1588|consen 21 RYQPQLNEKASKYLSELLAERKSLSPFFP-FPHAERLLDEEIERVQTSGRQHG--------SKEP--------------- 76 (259)
T ss_pred ccccchhhHHHHHHHHHHhhHHhcCcccc-hHHHHHHHHHHHHHHHhhhhhcc--------CCCc---------------
Confidence 33444456678999999999999999987 99999999999999999876532 0000
Q ss_pred chhhhhHHHHhhhhhccccCccCCCCCCCCccceeeEEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEecc
Q 022785 108 GLASRFQSEISGLMQSSSAQNWLSSQGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (292)
Q Consensus 108 ~~~~~~~~Er~~li~~~~~~~~~~p~~~~~~~~vk~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGr 187 (292)
++. +. .+.++.+++|++.||+|||++||+||||||||||||||+||||++|||||+||||
T Consensus 77 --------~~~----------~~--~~~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr 136 (259)
T KOG1588|consen 77 --------EEL----------PY--ADVYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR 136 (259)
T ss_pred --------hhc----------cc--ccCccCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence 000 00 0234567899999999999999999999999999999999999999999999999
Q ss_pred CCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHHhcCc-cc
Q 022785 188 GSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEIVDARLMQAREILEDLLKPVDESHDFYKKQQLRELALLNGT-LR 266 (292)
Q Consensus 188 GS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL~pv~e~~d~~Kr~QL~ELA~lNGt-~r 266 (292)
||+||..||+++|++|+|+||++||||+|++++++++|++||.+|+++|++||+|++++.| |++||+|||++||| ++
T Consensus 137 gSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~P~~e~~d--k~~QL~ELa~lngt~~~ 214 (259)
T KOG1588|consen 137 GSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLVPDHEDED--KREQLRELAILNGTYLR 214 (259)
T ss_pred CcccchHHHHHhhcCcchHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcCCCCCCch--HHHHHHHHhhcCCcccc
Confidence 9999999999999999999999999999999999999999999999999999999999877 99999999999999 66
Q ss_pred CCCCCCCC---CcCCCCCcccccccccC
Q 022785 267 EEGSPMSG---SVSPFHNSLGMKRAKTR 291 (292)
Q Consensus 267 ~~~~~~~~---~~spf~~~~~~~~~~~~ 291 (292)
+.++.++| +++||+ +.|+||+||+
T Consensus 215 ~~~~~~~g~~~~~~~~~-~~~~~r~~~~ 241 (259)
T KOG1588|consen 215 SESRKPSGGNGRGVPGN-SAGGKRGKTG 241 (259)
T ss_pred ccccccCCCCCcCCCCC-CCCcccccCC
Confidence 77666666 888996 6699999986
No 2
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=100.00 E-value=3.3e-46 Score=365.58 Aligned_cols=205 Identities=32% Similarity=0.490 Sum_probs=172.5
Q ss_pred HHHHHHHHHHHHHHHHhhcCcc-CCCC-CCCCCCC---CCCCCCcCCCCCCccchhhhhHHHHhhhhhccc--cCccCCC
Q 022785 60 NAYRLLNQEIMRVTTLLGNASV-LGQS-GLEHASP---LTSGGIFSNGGADTNGLASRFQSEISGLMQSSS--AQNWLSS 132 (292)
Q Consensus 60 h~~rLL~~EI~RV~~~l~~~~~-~~~~-~~~~~SP---~~s~g~~~N~~~~~~~~~~~~~~Er~~li~~~~--~~~~~~p 132 (292)
.-.-+|+-+|++++.+|+.++| +++. ..+++|| |+..|.+.||++ .+++++|++||+++|+.++ +++|++|
T Consensus 52 ~~~y~l~~~iee~t~kLrt~d~~~p~~~e~rSPsp~p~yda~g~R~ntRe--~R~r~~Le~er~e~I~~~lk~nP~fkpP 129 (554)
T KOG0119|consen 52 KESYSLNLRIEEITRKLRTGDVGVPPPRELRSPSPEPVYDAKGKRLNTRE--QRARKKLEDERHEIIEEILKLNPGFKPP 129 (554)
T ss_pred hhhhhHHHHHHHhhhhhccccCCCCCCccccCCCcchhhhhhccchhhHH--HHHHHHHHHHHHHHHHHHHHhCcCCCCC
Confidence 3456788999999999999999 4443 4477776 577888888875 3467899999999999874 6899988
Q ss_pred CCCCCccceeeEEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCC-CCCCCC
Q 022785 133 QGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGY-EHLNEP 211 (292)
Q Consensus 133 ~~~~~~~~vk~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~-ehl~ep 211 (292)
.||. +..++++||||||++||+|||||+||||||+|+|+||+||||||+||||||+|+++. ..++..| ...+||
T Consensus 130 ~DYk--~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~---~~~d~~~~~~~~ep 204 (554)
T KOG0119|consen 130 ADYK--PPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKG---RSDDLSYIPKENEP 204 (554)
T ss_pred cccC--cccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEecccccccccc---CCcccccccccccc
Confidence 8763 334999999999999999999999999999999999999999999999999999872 1233333 236899
Q ss_pred ceEEEEecCchhHHHHHHHHHHHHHHHhcC---CCcchHHHHHHHHHHHHHHhcCcccCCCC---CCCCCc
Q 022785 212 LHILVEAELPVEIVDARLMQAREILEDLLK---PVDESHDFYKKQQLRELALLNGTLREEGS---PMSGSV 276 (292)
Q Consensus 212 LHVlI~a~~~~~~~~~rl~~A~e~Ie~LL~---pv~e~~d~~Kr~QL~ELA~lNGt~r~~~~---~~~~~~ 276 (292)
|||+|+|++++ +|++|+++|+.||. .++|+++++|+.||+|||-||||+|+++. ..+|+.
T Consensus 205 LH~~Isadt~e-----ki~~Ai~vienli~~av~~~e~~n~l~~~Qlrela~lNgt~r~~d~~~c~~cg~~ 270 (554)
T KOG0119|consen 205 LHCLISADTQE-----KIKKAIAVIENLIQSAVSVPEGQNDLKRLQLRELARLNGTLRDDDNRACRNCGST 270 (554)
T ss_pred eeEEEecchHH-----HHHHHHHHHHHHHHhhccCccccccccHHHHHHHHHhCCCCCccccccccccCCC
Confidence 99999999976 68999999999997 68999999999999999999999999984 344544
No 3
>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=100.00 E-value=3.3e-41 Score=280.78 Aligned_cols=119 Identities=57% Similarity=0.952 Sum_probs=111.8
Q ss_pred EEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchh
Q 022785 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVE 223 (292)
Q Consensus 144 ~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~ 223 (292)
++|||||+++||+|||+|+||||+|+|+|+||++|||+|.|||+||+++.+++..+++ +.|+|++|||||+|+|+++
T Consensus 1 ~~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~-~~~~~~~eplhV~I~a~~~-- 77 (120)
T cd02395 1 TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRG-PKYAHLNEPLHVLITAETP-- 77 (120)
T ss_pred CCEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccC-cccccCCCCcEEEEEeCCc--
Confidence 3699999999999999999999999999999999999999999999999999988876 8999999999999999995
Q ss_pred HHHHHHHHHHHHHHHhcCCCcch-HHHHHHHHHHHHHHhcCccc
Q 022785 224 IVDARLMQAREILEDLLKPVDES-HDFYKKQQLRELALLNGTLR 266 (292)
Q Consensus 224 ~~~~rl~~A~e~Ie~LL~pv~e~-~d~~Kr~QL~ELA~lNGt~r 266 (292)
+..++++|+++|+.||.++.++ .|++|++||+|||++|||||
T Consensus 78 -~~e~~~~A~~~I~~ll~~~~~~~~~~~k~~ql~~la~~nGt~~ 120 (120)
T cd02395 78 -PEEALAKAVEAIEELLKPAIEGGNDELKREQLRELALLNGTYR 120 (120)
T ss_pred -HHHHHHHHHHHHHHHhccCCCccchHHHHHHHHHHHHhcccCC
Confidence 2347999999999999998777 89999999999999999997
No 4
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=100.00 E-value=8.1e-38 Score=280.63 Aligned_cols=195 Identities=27% Similarity=0.357 Sum_probs=153.0
Q ss_pred HHHHHHHHHHhhcCccCCCCC-CCCCCC---CCCCCCcCCCCCCccchhhhhHHHHhhhhhccc--cCccCCCCCCCCcc
Q 022785 66 NQEIMRVTTLLGNASVLGQSG-LEHASP---LTSGGIFSNGGADTNGLASRFQSEISGLMQSSS--AQNWLSSQGSSSGL 139 (292)
Q Consensus 66 ~~EI~RV~~~l~~~~~~~~~~-~~~~SP---~~s~g~~~N~~~~~~~~~~~~~~Er~~li~~~~--~~~~~~p~~~~~~~ 139 (292)
+-.+.++..+|++.+++++.+ +|++|| ++..|.+.||++ -.|+.+|++||+.|++... -+.|..|.++- .
T Consensus 69 ~~r~~eit~Klrt~d~Vp~~re~Rspsppp~yd~~GrRlntre--~ry~kkLeder~~l~era~k~lp~fv~p~dy~--r 144 (269)
T COG5176 69 MMRPFEITEKLRTPDGVPSKRELRSPSPPPRYDEIGRRLNTRE--ARYNKKLEDERLWLKERAQKILPRFVLPNDYI--R 144 (269)
T ss_pred hccHhhhhhhhcCCCCCCchhhccCCCCCcchhHHhhhhhHHH--HHHhhhhhHHHHHHHHHHHHhcCcccCCcccc--C
Confidence 345778888999999988764 488887 466788888875 2478999999999998764 36677666653 3
Q ss_pred ceeeEEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEec
Q 022785 140 IVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAE 219 (292)
Q Consensus 140 ~vk~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~ 219 (292)
+.|++.||||||++||+.||||+||||||.|+|+||+.|+|||.|||+||+|+++....+ .++.....++||+||+++
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~--p~~~~N~e~~lhcLI~ad 222 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDT--PESLKNAEAVLHCLIEAD 222 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccC--chhhhhhHHhHHHHhhcc
Confidence 589999999999999999999999999999999999999999999999999987643222 122234679999999998
Q ss_pred CchhHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHHhcCcccCC
Q 022785 220 LPVEIVDARLMQAREILEDLLKPVDESHDFYKKQQLRELALLNGTLREE 268 (292)
Q Consensus 220 ~~~~~~~~rl~~A~e~Ie~LL~pv~e~~d~~Kr~QL~ELA~lNGt~r~~ 268 (292)
....++.. +......|.+.- .+++|++++||.||++||-+|||+|+|
T Consensus 223 sedki~~~-ik~~~n~I~~a~-~~PeGqnDlkR~qlr~la~lngtlr~d 269 (269)
T COG5176 223 SEDKICRL-IKSQLNAIREAR-RNPEGQNDLKRFQLRWLAHLNGTLRAD 269 (269)
T ss_pred hhhhHHHH-HHHHHHHHHHHh-cCCcccchHHHHHHHHHHHhcceecCC
Confidence 86544332 222333444443 356899999999999999999999975
No 5
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.34 E-value=1.8e-06 Score=62.25 Aligned_cols=62 Identities=27% Similarity=0.523 Sum_probs=46.5
Q ss_pred EEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhH
Q 022785 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEI 224 (292)
Q Consensus 145 ~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~ 224 (292)
.++.||. +++|+||||+|.++++|+++|||+|.|...++ ...+-.|.|.+. .+
T Consensus 2 ~~i~ip~------~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~------------------~~~~~~v~i~G~-~~-- 54 (64)
T cd00105 2 ERVLVPS------SLVGRIIGKGGSTIKEIREETGAKIKIPDSGS------------------GSEERIVTITGT-PE-- 54 (64)
T ss_pred EEEEEch------hhcceeECCCCHHHHHHHHHHCCEEEEcCCCC------------------CCCceEEEEEcC-HH--
Confidence 3577775 78999999999999999999999999987543 123356777775 22
Q ss_pred HHHHHHHHHHHH
Q 022785 225 VDARLMQAREIL 236 (292)
Q Consensus 225 ~~~rl~~A~e~I 236 (292)
.+..|..+|
T Consensus 55 ---~v~~a~~~i 63 (64)
T cd00105 55 ---AVEKAKELI 63 (64)
T ss_pred ---HHHHHHHHh
Confidence 466776665
No 6
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=98.33 E-value=2.9e-07 Score=90.46 Aligned_cols=96 Identities=18% Similarity=0.005 Sum_probs=81.3
Q ss_pred eeeEEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecC
Q 022785 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAEL 220 (292)
Q Consensus 141 vk~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~ 220 (292)
+++..|.+|+++ .|.||.-+..=||+..||..+|.+|+.++.||||||+.-+.-+ | ++.+||++|+|+...
T Consensus 208 ~~Y~~k~~v~~~-~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~----G----~EsnEPMYI~i~h~~ 278 (531)
T KOG1960|consen 208 RYYPNKALATDK-DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNE----G----NESNEPMYIFSTHGN 278 (531)
T ss_pred ccchhheecccC-CcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCccc----c----cccCCceeEEeecCC
Confidence 456669999999 7899999999999999999999999999999999999876432 1 247999999999998
Q ss_pred chhHHHHHHHHHHHHHHHhcCCCcchHHHH
Q 022785 221 PVEIVDARLMQAREILEDLLKPVDESHDFY 250 (292)
Q Consensus 221 ~~~~~~~rl~~A~e~Ie~LL~pv~e~~d~~ 250 (292)
.+. +..|+.+|++|+.-|+-.+-.+
T Consensus 279 ~~g-----~~~A~r~~~nl~~~v~~~~sr~ 303 (531)
T KOG1960|consen 279 GNG-----ENGAPRRKWNLEEKVYINLSRG 303 (531)
T ss_pred chh-----hccchhHHHhHHHHHHHHhhhh
Confidence 864 7899999999998876544433
No 7
>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=98.29 E-value=1.5e-06 Score=64.14 Aligned_cols=51 Identities=20% Similarity=0.393 Sum_probs=41.4
Q ss_pred CccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHHHHH
Q 022785 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEIVDARLMQAREILE 237 (292)
Q Consensus 158 NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie 237 (292)
.++|+|||++|.|+|+||++|||+|.|-- + -.|.|++.+++ .++.|.++|+
T Consensus 11 ~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----~-------------------g~v~I~G~~~~-----~v~~A~~~I~ 61 (61)
T cd02393 11 DKIRDVIGPGGKTIKKIIEETGVKIDIED-----D-------------------GTVYIAASDKE-----AAEKAKKMIE 61 (61)
T ss_pred hheeeeECCCchHHHHHHHHHCCEEEeCC-----C-------------------CEEEEEeCCHH-----HHHHHHHHhC
Confidence 58899999999999999999999998742 0 14889997665 4788888763
No 8
>smart00322 KH K homology RNA-binding domain.
Probab=98.27 E-value=4.2e-06 Score=59.39 Aligned_cols=65 Identities=31% Similarity=0.521 Sum_probs=49.1
Q ss_pred EEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchh
Q 022785 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVE 223 (292)
Q Consensus 144 ~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~ 223 (292)
+.+|.||. +++|++||++|.++++|++.|||+|.+.+.++ ..-.|.|.++ +.
T Consensus 4 ~~~i~i~~------~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--------------------~~~~v~i~g~-~~- 55 (69)
T smart00322 4 TIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--------------------EERVVEITGP-PE- 55 (69)
T ss_pred EEEEEEcc------hhcceeECCCchHHHHHHHHHCCEEEECCCCC--------------------CccEEEEEcC-HH-
Confidence 45677765 78899999999999999999999999976433 2245777776 22
Q ss_pred HHHHHHHHHHHHHHHhc
Q 022785 224 IVDARLMQAREILEDLL 240 (292)
Q Consensus 224 ~~~~rl~~A~e~Ie~LL 240 (292)
.+..|.+.|.+.+
T Consensus 56 ----~v~~a~~~i~~~~ 68 (69)
T smart00322 56 ----NVEKAAELILEIL 68 (69)
T ss_pred ----HHHHHHHHHHHHh
Confidence 4677777777654
No 9
>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=98.17 E-value=1.9e-06 Score=62.33 Aligned_cols=59 Identities=24% Similarity=0.556 Sum_probs=45.2
Q ss_pred EEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhH
Q 022785 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEI 224 (292)
Q Consensus 145 ~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~ 224 (292)
.+|.|| -.++|+|||++|.++|+|+++|||+|.|...+ +.-.|.|++ +++
T Consensus 2 ~~i~vp------~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~---------------------~~~~v~I~G-~~~-- 51 (60)
T PF00013_consen 2 ERIEVP------SSLVGRIIGKKGSNIKEIEEETGVKIQIPDDD---------------------ERDIVTISG-SPE-- 51 (60)
T ss_dssp EEEEEE------HHHHHHHHTGGGHHHHHHHHHHTSEEEEESTT---------------------EEEEEEEEE-SHH--
T ss_pred EEEEEC------HHHcCEEECCCCCcHHHhhhhcCeEEEEcCCC---------------------CcEEEEEEe-CHH--
Confidence 456666 36899999999999999999999999996530 224778888 554
Q ss_pred HHHHHHHHHHHH
Q 022785 225 VDARLMQAREIL 236 (292)
Q Consensus 225 ~~~rl~~A~e~I 236 (292)
.+++|.++|
T Consensus 52 ---~v~~A~~~I 60 (60)
T PF00013_consen 52 ---QVEKAKKMI 60 (60)
T ss_dssp ---HHHHHHHHH
T ss_pred ---HHHHHHhhC
Confidence 467777765
No 10
>PF13014 KH_3: KH domain
Probab=98.13 E-value=1.9e-06 Score=59.04 Aligned_cols=28 Identities=32% Similarity=0.706 Sum_probs=26.9
Q ss_pred ccceeeCCCcchHHHHHhhhCceEEEec
Q 022785 159 FVGRLLGPRGNSLKRVEASTECRVLIRG 186 (292)
Q Consensus 159 fvGrIlGPrG~TlK~le~eTgckI~IRG 186 (292)
|+|+|||++|.|+|+|+++|||+|.|--
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC
Confidence 6899999999999999999999999977
No 11
>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=97.86 E-value=2.5e-05 Score=56.77 Aligned_cols=53 Identities=13% Similarity=0.327 Sum_probs=40.9
Q ss_pred CccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHHHH
Q 022785 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEIVDARLMQAREIL 236 (292)
Q Consensus 158 NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~I 236 (292)
.++|.|||++|.++++|+++|||+|.|-..+ +..=.|.|++. ++ .+..|+++|
T Consensus 9 ~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--------------------~~~~~v~I~G~-~~-----~v~~A~~~i 61 (62)
T cd02394 9 KLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--------------------SKSDTITITGP-KE-----NVEKAKEEI 61 (62)
T ss_pred HHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--------------------CCCCEEEEEcC-HH-----HHHHHHHHh
Confidence 5789999999999999999999999987643 12236788886 22 467777765
No 12
>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=97.80 E-value=7e-05 Score=55.44 Aligned_cols=36 Identities=19% Similarity=0.529 Sum_probs=30.8
Q ss_pred EEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEec
Q 022785 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRG 186 (292)
Q Consensus 145 ~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRG 186 (292)
.++.||. +.+|+|||.+|.++|+|+++|||+|.|--
T Consensus 2 ~r~~ip~------~~vg~iIG~~G~~i~~i~~~tga~I~i~~ 37 (65)
T cd02396 2 LRLLVPS------SQAGSIIGKGGSTIKEIREETGAKIRVSK 37 (65)
T ss_pred EEEEECH------HHcCeeECCCcHHHHHHHHHHCCEEEEcC
Confidence 3566663 57899999999999999999999999943
No 13
>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=97.62 E-value=8.5e-05 Score=65.42 Aligned_cols=53 Identities=25% Similarity=0.393 Sum_probs=44.6
Q ss_pred ccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHHHHHH
Q 022785 159 FVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEIVDARLMQAREILED 238 (292)
Q Consensus 159 fvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 238 (292)
.+|||||+.|.|++.||..|||+|.|-| =.|.|.+ +++ +++.|.+.|+.
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~-------------------------~~v~i~G-~~~-----~~~~A~~~i~~ 147 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYG-------------------------KTVGIIG-DPE-----QVQIAREAIEM 147 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcC-------------------------CEEEEEC-CHH-----HHHHHHHHHHH
Confidence 6899999999999999999999999854 0366777 554 58999999999
Q ss_pred hcCC
Q 022785 239 LLKP 242 (292)
Q Consensus 239 LL~p 242 (292)
|+.-
T Consensus 148 li~~ 151 (172)
T TIGR03665 148 LIEG 151 (172)
T ss_pred HHcC
Confidence 9853
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.51 E-value=0.00016 Score=64.20 Aligned_cols=53 Identities=25% Similarity=0.436 Sum_probs=43.6
Q ss_pred ccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHHHHHH
Q 022785 159 FVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEIVDARLMQAREILED 238 (292)
Q Consensus 159 fvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 238 (292)
.+|||||++|.|.|.||..|||+|.|-++ .|.|.+ +++ +++.|.+.|+.
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~-------------------------~v~i~G-~~~-----~~~~A~~~I~~ 153 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGK-------------------------TVAIIG-DPE-----QVEIAREAIEM 153 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCC-------------------------EEEEEe-CHH-----HHHHHHHHHHH
Confidence 68999999999999999999999998541 155666 554 57899999999
Q ss_pred hcCC
Q 022785 239 LLKP 242 (292)
Q Consensus 239 LL~p 242 (292)
|+.-
T Consensus 154 li~g 157 (180)
T PRK13763 154 LIEG 157 (180)
T ss_pred HHcC
Confidence 9853
No 15
>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=97.21 E-value=0.00048 Score=60.67 Aligned_cols=57 Identities=26% Similarity=0.455 Sum_probs=45.9
Q ss_pred CccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEE--EecCchhHHHHHHHHHHHH
Q 022785 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILV--EAELPVEIVDARLMQAREI 235 (292)
Q Consensus 158 NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI--~a~~~~~~~~~rl~~A~e~ 235 (292)
+.+|.||||+|.|.|.||++|||+|.|--. .=.|.| .+.|+. .+.+|.++
T Consensus 7 ~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----------------------~g~V~I~~~t~d~~-----~i~kA~~~ 58 (172)
T TIGR03665 7 DRIGVLIGKGGETKKEIEERTGVKLDIDSE-----------------------TGEVKIEEEDEDPL-----AVMKAREV 58 (172)
T ss_pred HHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----------------------CceEEEecCCCCHH-----HHHHHHHH
Confidence 689999999999999999999999999742 013556 344554 58999999
Q ss_pred HHHhcCC
Q 022785 236 LEDLLKP 242 (292)
Q Consensus 236 Ie~LL~p 242 (292)
|+.+...
T Consensus 59 I~~i~~g 65 (172)
T TIGR03665 59 VKAIGRG 65 (172)
T ss_pred HHHHHcC
Confidence 9998874
No 16
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.06 E-value=0.0012 Score=59.87 Aligned_cols=53 Identities=23% Similarity=0.362 Sum_probs=44.2
Q ss_pred ccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHHHHHH
Q 022785 159 FVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEIVDARLMQAREILED 238 (292)
Q Consensus 159 fvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 238 (292)
..|||||+.|.|.+.||..|||.|.|.|+ +|.|-+ +++ .++.|.+.|+.
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~-------------------------tVaiiG-~~~-----~v~iAr~AVem 160 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK-------------------------TVAIIG-GFE-----QVEIAREAVEM 160 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc-------------------------EEEEec-Chh-----hhHHHHHHHHH
Confidence 56999999999999999999999999993 455556 333 47889999999
Q ss_pred hcCC
Q 022785 239 LLKP 242 (292)
Q Consensus 239 LL~p 242 (292)
|+.-
T Consensus 161 li~G 164 (194)
T COG1094 161 LING 164 (194)
T ss_pred HHcC
Confidence 9864
No 17
>PRK13763 putative RNA-processing protein; Provisional
Probab=96.97 E-value=0.0013 Score=58.46 Aligned_cols=57 Identities=25% Similarity=0.508 Sum_probs=46.8
Q ss_pred CccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEE---ecCchhHHHHHHHHHHH
Q 022785 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVE---AELPVEIVDARLMQARE 234 (292)
Q Consensus 158 NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~---a~~~~~~~~~rl~~A~e 234 (292)
+-+|.||||.|.|.|.|+++|||+|.|.-. .=.|.|. +.+++ .+++|++
T Consensus 12 ~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----------------------~g~V~I~~~~~~d~~-----~i~kA~~ 63 (180)
T PRK13763 12 DRIGVLIGKKGETKKEIEERTGVKLEIDSE-----------------------TGEVIIEPTDGEDPL-----AVLKARD 63 (180)
T ss_pred HHhhhHhccchhHHHHHHHHHCcEEEEECC-----------------------CCeEEEEeCCCCCHH-----HHHHHHH
Confidence 568999999999999999999999999763 0255666 55654 5899999
Q ss_pred HHHHhcCC
Q 022785 235 ILEDLLKP 242 (292)
Q Consensus 235 ~Ie~LL~p 242 (292)
+|+.++..
T Consensus 64 ~I~ai~~g 71 (180)
T PRK13763 64 IVKAIGRG 71 (180)
T ss_pred HHHHHhcC
Confidence 99999884
No 18
>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=96.80 E-value=0.0024 Score=67.63 Aligned_cols=64 Identities=23% Similarity=0.474 Sum_probs=52.7
Q ss_pred EEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchh
Q 022785 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVE 223 (292)
Q Consensus 144 ~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~ 223 (292)
...+.||. .-+|.||||+|.|+|.|+++|||+|-|-- +=+|.|.+.+.+
T Consensus 579 ~~~~~I~~------~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------------------------~G~V~I~a~d~~- 627 (719)
T TIGR02696 579 IITVKIPV------DKIGEVIGPKGKMINQIQDETGAEISIED------------------------DGTVYIGAADGP- 627 (719)
T ss_pred eEEEEeCh------HHhhheeCCCcHhHHHHHHHHCCEEEEec------------------------CcEEEEEeCCHH-
Confidence 44566664 46899999999999999999999998854 237888888765
Q ss_pred HHHHHHHHHHHHHHHhcCC
Q 022785 224 IVDARLMQAREILEDLLKP 242 (292)
Q Consensus 224 ~~~~rl~~A~e~Ie~LL~p 242 (292)
++++|++.|+.+..+
T Consensus 628 ----~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 628 ----SAEAARAMINAIANP 642 (719)
T ss_pred ----HHHHHHHHHHHhhCc
Confidence 689999999999984
No 19
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=96.40 E-value=0.0072 Score=62.42 Aligned_cols=71 Identities=18% Similarity=0.456 Sum_probs=48.9
Q ss_pred EEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhHH
Q 022785 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEIV 225 (292)
Q Consensus 146 Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~~ 225 (292)
.+.|+|.. +=||.|||=.|.|+|+|+.+||+||.++= |. +|. ...-+|+ |.+ ..
T Consensus 231 ~~~V~VPr----~~VG~IIGkgGE~IKklq~etG~KIQfkp-----Dd--------~p~--speR~~~--IiG--~~--- 284 (600)
T KOG1676|consen 231 TREVKVPR----SKVGIIIGKGGEMIKKLQNETGAKIQFKP-----DD--------DPS--SPERPAQ--IIG--TV--- 284 (600)
T ss_pred eeEEeccc----cceeeEEecCchHHHHHhhccCceeEeec-----CC--------CCC--Cccceee--eec--CH---
Confidence 44555544 46999999999999999999999999975 21 111 0122233 333 22
Q ss_pred HHHHHHHHHHHHHhcCCC
Q 022785 226 DARLMQAREILEDLLKPV 243 (292)
Q Consensus 226 ~~rl~~A~e~Ie~LL~pv 243 (292)
.++.+|.++|.+||.-.
T Consensus 285 -d~ie~Aa~lI~eii~~~ 301 (600)
T KOG1676|consen 285 -DQIEHAAELINEIIAEA 301 (600)
T ss_pred -HHHHHHHHHHHHHHHHH
Confidence 27899999999998643
No 20
>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=96.38 E-value=0.005 Score=64.95 Aligned_cols=63 Identities=14% Similarity=0.240 Sum_probs=49.3
Q ss_pred EEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchh
Q 022785 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVE 223 (292)
Q Consensus 144 ~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~ 223 (292)
...+.||. ..+|.||||+|.|+|.|+++|||+|.|-- +=+|.|.+.+.+
T Consensus 552 ~~~~~I~~------~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------------------------dG~V~i~~~~~~- 600 (684)
T TIGR03591 552 IETIKINP------DKIRDVIGPGGKVIREITEETGAKIDIED------------------------DGTVKIAASDGE- 600 (684)
T ss_pred EEEEecCH------HHHHhhcCCCcHHHHHHHHHHCCEEEEec------------------------CeEEEEEECcHH-
Confidence 34455553 46899999999999999999999999832 136777787754
Q ss_pred HHHHHHHHHHHHHHHhcC
Q 022785 224 IVDARLMQAREILEDLLK 241 (292)
Q Consensus 224 ~~~~rl~~A~e~Ie~LL~ 241 (292)
.+++|.+.|+.+..
T Consensus 601 ----~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 601 ----AAEAAIKMIEGITA 614 (684)
T ss_pred ----HHHHHHHHHHhhhc
Confidence 58999999998854
No 21
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.30 E-value=0.0014 Score=65.52 Aligned_cols=39 Identities=36% Similarity=0.687 Sum_probs=34.1
Q ss_pred eccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEec
Q 022785 148 DIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRG 186 (292)
Q Consensus 148 ~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRG 186 (292)
.||++-.-.-||||||||-.|.++|.||++||+||.|--
T Consensus 279 e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~ 317 (584)
T KOG2193|consen 279 EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISK 317 (584)
T ss_pred hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeee
Confidence 567775556799999999999999999999999999953
No 22
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=95.97 E-value=0.02 Score=54.84 Aligned_cols=67 Identities=37% Similarity=0.562 Sum_probs=47.8
Q ss_pred ceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHHHHHHhc
Q 022785 161 GRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEIVDARLMQAREILEDLL 240 (292)
Q Consensus 161 GrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL 240 (292)
.|||||.|+|||.||-.|.|-|.|.|.- | ++-.+ ...|..+..+|++.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~T-------------------------V--saiGp----fkGlkevr~IV~DcM 209 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGNT-------------------------V--SAIGP----FKGLKEVRKIVEDCM 209 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCcE-------------------------E--EeecC----cchHHHHHHHHHHHH
Confidence 6899999999999999999999999931 1 22222 125778888888887
Q ss_pred CCCcchHHHHH-HHHHHHHH
Q 022785 241 KPVDESHDFYK-KQQLRELA 259 (292)
Q Consensus 241 ~pv~e~~d~~K-r~QL~ELA 259 (292)
..++--++ +| -+--||||
T Consensus 210 ~NiHPiY~-IK~LmiKRel~ 228 (356)
T KOG2874|consen 210 KNIHPIYN-IKTLMIKRELA 228 (356)
T ss_pred hccchHHH-HHHHHHHHHhh
Confidence 77666555 44 23335665
No 23
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=95.60 E-value=0.011 Score=64.12 Aligned_cols=64 Identities=14% Similarity=0.187 Sum_probs=51.4
Q ss_pred EEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCce-EEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCch
Q 022785 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECR-VLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPV 222 (292)
Q Consensus 144 ~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgck-I~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~ 222 (292)
...+.||. +-+|.||||+|.|+|.|+++||++ |-|+ |+-+|.|.+.+.+
T Consensus 686 i~~~~i~~------~ki~~vIG~GGktIk~I~eetg~~~Idi~------------------------ddg~V~I~a~d~~ 735 (891)
T PLN00207 686 IHIMKVKP------EKVNMIIGSGGKKVKSIIEETGVEAIDTQ------------------------DDGTVKITAKDLS 735 (891)
T ss_pred eEEEEcCH------HHHHHHhcCCchhHHHHHHHHCCCccCcC------------------------CCeeEEEEeCCHH
Confidence 34555553 579999999999999999999998 6554 3468888898865
Q ss_pred hHHHHHHHHHHHHHHHhcCC
Q 022785 223 EIVDARLMQAREILEDLLKP 242 (292)
Q Consensus 223 ~~~~~rl~~A~e~Ie~LL~p 242 (292)
++++|++.|+.+..-
T Consensus 736 -----~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 736 -----SLEKSKAIISSLTMV 750 (891)
T ss_pred -----HHHHHHHHHHHHhcC
Confidence 689999999999764
No 24
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.59 E-value=0.017 Score=53.23 Aligned_cols=55 Identities=20% Similarity=0.344 Sum_probs=45.8
Q ss_pred CccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHHHHH
Q 022785 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEIVDARLMQAREILE 237 (292)
Q Consensus 158 NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie 237 (292)
+.+++||||+|.+++.|.++|+|+|.| | .| =.|+|.+.+.+ .+..|++.|+
T Consensus 154 ~~i~~lig~~g~~i~~l~~~~~~~I~i-g---------------------~N--G~VwI~~~~~~-----~~~~a~~~I~ 204 (235)
T PRK04163 154 VKVPRVIGKKGSMINMLKEETGCDIIV-G---------------------QN--GRIWIKGPDEE-----DEEIAIEAIK 204 (235)
T ss_pred HHHHhhcCCCChhHhhhhhhhCcEEEE-c---------------------CC--cEEEEeeCCHH-----HHHHHHHHHH
Confidence 679999999999999999999999988 2 11 27999998875 4788888888
Q ss_pred HhcC
Q 022785 238 DLLK 241 (292)
Q Consensus 238 ~LL~ 241 (292)
.+-.
T Consensus 205 ~~e~ 208 (235)
T PRK04163 205 KIER 208 (235)
T ss_pred HHHh
Confidence 8764
No 25
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=95.56 E-value=0.03 Score=57.99 Aligned_cols=74 Identities=26% Similarity=0.566 Sum_probs=57.6
Q ss_pred eeeEEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecC
Q 022785 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAEL 220 (292)
Q Consensus 141 vk~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~ 220 (292)
++.+.+|.||- |=+|+|||=.|-|+|+|++.||||+.+-=-|+..+. ..-||. |+++
T Consensus 137 ~~ttqeI~IPa------~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~--------------~~Kplr--itGd- 193 (600)
T KOG1676|consen 137 VETTQEILIPA------NKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG--------------ADKPLR--ITGD- 193 (600)
T ss_pred cceeeeeccCc------cceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC--------------CCCcee--ecCC-
Confidence 66777888885 457999999999999999999999998877765442 234454 4553
Q ss_pred chhHHHHHHHHHHHHHHHhcCC
Q 022785 221 PVEIVDARLMQAREILEDLLKP 242 (292)
Q Consensus 221 ~~~~~~~rl~~A~e~Ie~LL~p 242 (292)
+. ++++|.++|.++|.-
T Consensus 194 p~-----~ve~a~~lV~dil~e 210 (600)
T KOG1676|consen 194 PD-----KVEQAKQLVADILRE 210 (600)
T ss_pred HH-----HHHHHHHHHHHHHHh
Confidence 32 689999999999973
No 26
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=94.53 E-value=0.036 Score=58.68 Aligned_cols=56 Identities=16% Similarity=0.287 Sum_probs=45.8
Q ss_pred CccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHHHHH
Q 022785 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEIVDARLMQAREILE 237 (292)
Q Consensus 158 NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie 237 (292)
.-+|.+|||+|.|+|.|+++||++|-|+- +-+|.|.+.+.+ .+++|.+.|+
T Consensus 563 ~kI~~vIG~gg~~ik~I~~~~~~~idi~d------------------------~G~v~i~~~~~~-----~~~~a~~~I~ 613 (693)
T PRK11824 563 DKIRDVIGPGGKTIREITEETGAKIDIED------------------------DGTVKIAATDGE-----AAEAAKERIE 613 (693)
T ss_pred HHHHHHhcCCchhHHHHHHHHCCccccCC------------------------CceEEEEcccHH-----HHHHHHHHHH
Confidence 56899999999999999999999887632 246777777754 5899999999
Q ss_pred HhcCC
Q 022785 238 DLLKP 242 (292)
Q Consensus 238 ~LL~p 242 (292)
.+...
T Consensus 614 ~~~~~ 618 (693)
T PRK11824 614 GITAE 618 (693)
T ss_pred Hhccc
Confidence 98753
No 27
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=94.46 E-value=0.07 Score=52.22 Aligned_cols=37 Identities=22% Similarity=0.452 Sum_probs=33.2
Q ss_pred eEEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEe
Q 022785 143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (292)
Q Consensus 143 ~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IR 185 (292)
+..||+||- +-+|-|||-+|.|+.+||++|||+|.+-
T Consensus 39 y~ikvLips------~AaGsIIGKGG~ti~~lqk~tgariklS 75 (402)
T KOG2191|consen 39 YFLKVLIPS------YAAGSIIGKGGQTIVQLQKETGARIKLS 75 (402)
T ss_pred eEEEEEeec------ccccceeccchHHHHHHHhccCcEEEec
Confidence 577899983 5689999999999999999999999886
No 28
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=94.31 E-value=0.018 Score=57.55 Aligned_cols=77 Identities=27% Similarity=0.498 Sum_probs=64.2
Q ss_pred eeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHHHHHHhcC
Q 022785 162 RLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEIVDARLMQAREILEDLLK 241 (292)
Q Consensus 162 rIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL~ 241 (292)
.|.||.|.+.|.++.+|-.++.|.|-||.+-... + ....++|.||+|.+.++. .|+.|+-+++.++-
T Consensus 308 ~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i~p~-------~-~~~~~~p~~~~~~~~~~~-----~~~~~~~~~~~~i~ 374 (531)
T KOG1960|consen 308 AIVGPQGAYVKHIQQETRTRVQIKGQGSAFIEPS-------T-NRESDEPIHLCIMSHDPN-----AIQRAKVLCEDLIA 374 (531)
T ss_pred ccccCCcccccccCCCCCcceeccCccceeecCC-------C-CCCCCCCcccccccCChh-----hhhhhhhcccccCC
Confidence 4789999999999999999999999999985432 2 224689999999998875 46778999999999
Q ss_pred CCcchHHHHH
Q 022785 242 PVDESHDFYK 251 (292)
Q Consensus 242 pv~e~~d~~K 251 (292)
||+..+...|
T Consensus 375 ~v~~qy~~~~ 384 (531)
T KOG1960|consen 375 SVHQQYKAWK 384 (531)
T ss_pred cccccCcccc
Confidence 9987766555
No 29
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=93.89 E-value=0.086 Score=51.44 Aligned_cols=31 Identities=26% Similarity=0.624 Sum_probs=27.9
Q ss_pred CccceeeCCCcchHHHHHhhhCceEEEeccC
Q 022785 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRG 188 (292)
Q Consensus 158 NfvGrIlGPrG~TlK~le~eTgckI~IRGrG 188 (292)
-|+|.|+|-+|.|.|+||+||+|+|.+=-.+
T Consensus 66 ~~~~~lig~~g~trkkle~Etq~~i~lp~p~ 96 (345)
T KOG2814|consen 66 SFIGWLIGKQGKTRKKLEEETQTNIFLPRPN 96 (345)
T ss_pred HHhhhhhcccchHHHHHHHhhccceEccCCC
Confidence 5899999999999999999999999985543
No 30
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=91.85 E-value=0.41 Score=48.97 Aligned_cols=39 Identities=26% Similarity=0.478 Sum_probs=35.3
Q ss_pred eEEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEecc
Q 022785 143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (292)
Q Consensus 143 ~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGr 187 (292)
.+.++.||- +-+|-|||=+|..+|.|.++|||+|.|-+.
T Consensus 138 v~~RLlVp~------sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~ 176 (485)
T KOG2190|consen 138 VTCRLLVPS------SQVGSLIGKGGSLIKEIREETGAKIRVSSD 176 (485)
T ss_pred eEEEEEech------hheeeeeccCcHHHHHHHHhcCceEEecCC
Confidence 568999984 568999999999999999999999999985
No 31
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=91.55 E-value=0.16 Score=51.22 Aligned_cols=31 Identities=23% Similarity=0.596 Sum_probs=28.4
Q ss_pred CCccceeeCCCcchHHHHHhhhCceEEEecc
Q 022785 157 FNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (292)
Q Consensus 157 ~NfvGrIlGPrG~TlK~le~eTgckI~IRGr 187 (292)
--|+|-||||.|.|+|-|-+.|.|||-+--+
T Consensus 207 tqyvgaIIGkeG~TIknItkqTqsriD~hrk 237 (584)
T KOG2193|consen 207 TQYVGAIIGKEGATIKNITKQTQSRIDVHRK 237 (584)
T ss_pred cceeEEEecCCCccccCcchhhhheeeeeec
Confidence 4699999999999999999999999998753
No 32
>PRK00106 hypothetical protein; Provisional
Probab=91.20 E-value=0.41 Score=49.57 Aligned_cols=63 Identities=32% Similarity=0.554 Sum_probs=50.1
Q ss_pred EEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhHH
Q 022785 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEIV 225 (292)
Q Consensus 146 Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~~ 225 (292)
-|.+|-+ .+-|||||--|.+++.+|..||+-|.|= +.|=-|.|++.||.
T Consensus 228 ~v~lp~d-----emkGriIGreGrNir~~E~~tGvdliid-----------------------dtp~~v~lS~fdpv--- 276 (535)
T PRK00106 228 TVHLPDD-----NMKGRIIGREGRNIRTLESLTGIDVIID-----------------------DTPEVVVLSGFDPI--- 276 (535)
T ss_pred eEEcCCh-----HhhcceeCCCcchHHHHHHHhCceEEEc-----------------------CCCCeEEEeCCChH---
Confidence 3555544 4789999999999999999999999882 34557889999986
Q ss_pred HHHHHHHHHHHHHhcC
Q 022785 226 DARLMQAREILEDLLK 241 (292)
Q Consensus 226 ~~rl~~A~e~Ie~LL~ 241 (292)
|-+-|..-+++|+.
T Consensus 277 --RReiAr~~le~Li~ 290 (535)
T PRK00106 277 --RREIARMTLESLIK 290 (535)
T ss_pred --HHHHHHHHHHHHHH
Confidence 55777777888875
No 33
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=91.06 E-value=1.1 Score=44.08 Aligned_cols=38 Identities=18% Similarity=0.468 Sum_probs=32.5
Q ss_pred eEEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEec
Q 022785 143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRG 186 (292)
Q Consensus 143 ~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRG 186 (292)
++.||.+|-. -.|.|||+.|.|+|.+.+++||-|.|--
T Consensus 132 kqikivvPNs------tag~iigkggAtiK~~~Eqsga~iqisP 169 (402)
T KOG2191|consen 132 KQIKIVVPNS------TAGMIIGKGGATIKAIQEQSGAWIQISP 169 (402)
T ss_pred ceeEEeccCC------cccceecCCcchHHHHHHhhCcceEecc
Confidence 4567888743 3699999999999999999999999974
No 34
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=90.39 E-value=0.48 Score=48.71 Aligned_cols=63 Identities=29% Similarity=0.538 Sum_probs=47.8
Q ss_pred EEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhHH
Q 022785 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEIV 225 (292)
Q Consensus 146 Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~~ 225 (292)
-|.+|-+ .+-|||||-.|-++|.+|+.||+-|.|= +.|=-|.|++.||.
T Consensus 207 ~v~lp~d-----~~kgriigreGrnir~~e~~tgvd~iid-----------------------dtp~~v~ls~fdp~--- 255 (514)
T TIGR03319 207 VVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIID-----------------------DTPEAVILSGFDPV--- 255 (514)
T ss_pred eEEcCCh-----hhhccccCCCcchHHHHHHHhCceEEEc-----------------------CCCCeEEecCCchH---
Confidence 3555544 4789999999999999999999999882 23446888999985
Q ss_pred HHHHHHHHHHHHHhcC
Q 022785 226 DARLMQAREILEDLLK 241 (292)
Q Consensus 226 ~~rl~~A~e~Ie~LL~ 241 (292)
|=+-|..-+++|+.
T Consensus 256 --rreia~~~l~~li~ 269 (514)
T TIGR03319 256 --RREIARMALEKLIQ 269 (514)
T ss_pred --HHHHHHHHHHHHHH
Confidence 44566666666664
No 35
>PRK12704 phosphodiesterase; Provisional
Probab=90.05 E-value=0.63 Score=47.90 Aligned_cols=50 Identities=22% Similarity=0.549 Sum_probs=40.1
Q ss_pred EEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchh
Q 022785 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVE 223 (292)
Q Consensus 146 Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~ 223 (292)
-|.+|-+ .+-|||||--|-++|.+|+.||+-|.|= +.|=-|+||+.+|..
T Consensus 213 ~v~lp~d-----~mkgriigreGrnir~~e~~tgvd~iid-----------------------dtp~~v~ls~~~~~r 262 (520)
T PRK12704 213 VVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIID-----------------------DTPEAVILSGFDPIR 262 (520)
T ss_pred eeecCCc-----hhhcceeCCCcchHHHHHHHhCCeEEEc-----------------------CCCCeEEEecCChhh
Confidence 3555544 4789999999999999999999999882 245578899988864
No 36
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=88.61 E-value=0.65 Score=49.26 Aligned_cols=62 Identities=21% Similarity=0.407 Sum_probs=46.7
Q ss_pred EEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhH
Q 022785 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEI 224 (292)
Q Consensus 145 ~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~ 224 (292)
+.+-|+.+. ++-+|||+|.|.|.|.++|||+|.|--.|++ .|.+.+.+
T Consensus 554 ~t~~i~~dK------I~dvIG~gGk~I~~I~eetg~~IdieddGtv------------------------~i~~s~~~-- 601 (692)
T COG1185 554 ETIKIDPDK------IRDVIGPGGKTIKAITEETGVKIDIEDDGTV------------------------KIAASDGE-- 601 (692)
T ss_pred EEEccCHHH------HhhccCCcccchhhhhhhhCcEEEecCCCcE------------------------EEEecchH--
Confidence 345556655 4568999999999999999999999766654 44554433
Q ss_pred HHHHHHHHHHHHHHhcC
Q 022785 225 VDARLMQAREILEDLLK 241 (292)
Q Consensus 225 ~~~rl~~A~e~Ie~LL~ 241 (292)
++.+|++.|+.+..
T Consensus 602 ---~~~~ak~~I~~i~~ 615 (692)
T COG1185 602 ---SAKKAKERIEAITR 615 (692)
T ss_pred ---HHHHHHHHHHHHHh
Confidence 57888999988873
No 37
>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=88.25 E-value=0.85 Score=33.52 Aligned_cols=35 Identities=20% Similarity=0.320 Sum_probs=29.2
Q ss_pred EEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEE
Q 022785 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLI 184 (292)
Q Consensus 144 ~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~I 184 (292)
..+|.||. .-+|+.||.+|.+++.++..+|.+|-|
T Consensus 26 ~~~v~V~~------~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 26 RARVVVPD------DQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred EEEEEECc------ccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 44566665 457899999999999999999998876
No 38
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=83.82 E-value=0.59 Score=47.54 Aligned_cols=29 Identities=31% Similarity=0.641 Sum_probs=26.7
Q ss_pred CCccceeeCCCcchHHHHHhhhCceEEEe
Q 022785 157 FNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (292)
Q Consensus 157 ~NfvGrIlGPrG~TlK~le~eTgckI~IR 185 (292)
-||||.+||-.|+.+|+||..|+++|.|-
T Consensus 55 s~mvg~vigrggskik~iq~~tnt~iqii 83 (629)
T KOG0336|consen 55 SEMVGKVIGRGGSKIKRIQNDTNTRIQII 83 (629)
T ss_pred hhhhheeeccCcchhhhhhcccceeEEEe
Confidence 48999999999999999999999998764
No 39
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=80.18 E-value=1.6 Score=45.72 Aligned_cols=54 Identities=20% Similarity=0.309 Sum_probs=42.8
Q ss_pred ccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHHHHHH
Q 022785 159 FVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEIVDARLMQAREILED 238 (292)
Q Consensus 159 fvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 238 (292)
=+..+|||.|..+|+|+.|||+.-+| |+=|+-|-|.++. .++.|.++|..
T Consensus 607 k~~~lIGp~G~~~kki~~EtGai~~v-------------------------De~t~~i~A~~~~-----am~~Ak~~I~~ 656 (760)
T KOG1067|consen 607 KRATLIGPGGVLKKKIEVETGAISQV-------------------------DEGTFSIFAPTQA-----AMEEAKEFIDG 656 (760)
T ss_pred hhheeecCccceeeeEeeeccceeee-------------------------cCceEEEEecCHH-----HHHHHHHHHHH
Confidence 35678999999999999999943221 3348888898875 58999999999
Q ss_pred hcCC
Q 022785 239 LLKP 242 (292)
Q Consensus 239 LL~p 242 (292)
+..-
T Consensus 657 i~~~ 660 (760)
T KOG1067|consen 657 IIKD 660 (760)
T ss_pred HhcC
Confidence 9875
No 40
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=80.11 E-value=1.5 Score=33.32 Aligned_cols=30 Identities=23% Similarity=0.514 Sum_probs=23.7
Q ss_pred CCCCccceeeCCCcchHHHHHhhh-CceEEE
Q 022785 155 PNFNFVGRLLGPRGNSLKRVEAST-ECRVLI 184 (292)
Q Consensus 155 P~~NfvGrIlGPrG~TlK~le~eT-gckI~I 184 (292)
|+++-+|..+|++|...|.|+++. |-||.|
T Consensus 14 ~~~d~vG~~iG~~G~rik~i~~~L~gekIdv 44 (69)
T PF13184_consen 14 PNIDPVGACIGKKGSRIKAISEELNGEKIDV 44 (69)
T ss_dssp TTS-HHHHHH-CCCCCHHHHHHHTTT-EEEE
T ss_pred CCcCcceecCccccHHHHHHHHHhCCCeEEE
Confidence 789999999999999999999998 544444
No 41
>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=74.38 E-value=2.7 Score=29.72 Aligned_cols=24 Identities=13% Similarity=0.343 Sum_probs=21.0
Q ss_pred ccceeeCCCcchHHHHHhhhCceE
Q 022785 159 FVGRLLGPRGNSLKRVEASTECRV 182 (292)
Q Consensus 159 fvGrIlGPrG~TlK~le~eTgckI 182 (292)
-.|++||.+|.+++.|+..++-.+
T Consensus 35 ~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 35 QPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CCceEECCCCccHHHHHHHHHHHc
Confidence 369999999999999999998554
No 42
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=72.52 E-value=2.6 Score=43.24 Aligned_cols=39 Identities=21% Similarity=0.445 Sum_probs=33.9
Q ss_pred eEEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEecc
Q 022785 143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (292)
Q Consensus 143 ~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGr 187 (292)
.+.++.|| .+++|.|||..|+.+-.|++.|||.|.|-++
T Consensus 338 v~~~l~vp------s~~igciiGk~G~~iseir~~tgA~I~I~~~ 376 (485)
T KOG2190|consen 338 VTQRLLVP------SDLIGCIIGKGGAKISEIRQRTGASISILNK 376 (485)
T ss_pred eeeeeccC------ccccceeecccccchHHHHHhcCCceEEccc
Confidence 45566665 4799999999999999999999999999884
No 43
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=72.08 E-value=11 Score=34.47 Aligned_cols=29 Identities=28% Similarity=0.464 Sum_probs=27.0
Q ss_pred ccceeeCCCcchHHHHHhhhCceEEEecc
Q 022785 159 FVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (292)
Q Consensus 159 fvGrIlGPrG~TlK~le~eTgckI~IRGr 187 (292)
=+|-|+|+.|.+.|.||+.|||+|.|-.+
T Consensus 18 R~~~lig~~g~v~k~ie~~~~~~~~iD~~ 46 (194)
T COG1094 18 RIGVLIGKWGEVKKAIEEKTGVKLRIDSK 46 (194)
T ss_pred hheeeecccccchHHHHhhcCeEEEEECC
Confidence 37899999999999999999999999886
No 44
>PRK12705 hypothetical protein; Provisional
Probab=68.70 E-value=4.8 Score=41.59 Aligned_cols=31 Identities=26% Similarity=0.550 Sum_probs=27.2
Q ss_pred CCCCccceeeCCCcchHHHHHhhhCceEEEe
Q 022785 155 PNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (292)
Q Consensus 155 P~~NfvGrIlGPrG~TlK~le~eTgckI~IR 185 (292)
|+=.+-|||||--|.+.+.+|..||+-|.|-
T Consensus 205 p~demkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 205 PSDAMKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred CChHhhccccCccchhHHHHHHhhCCceEec
Confidence 3445889999999999999999999988873
No 45
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=66.66 E-value=4.5 Score=39.77 Aligned_cols=37 Identities=24% Similarity=0.408 Sum_probs=30.3
Q ss_pred eeeEEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEE
Q 022785 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVL 183 (292)
Q Consensus 141 vk~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~ 183 (292)
..+++.+-|| |+ ||+.|.|++|.+.|.|+++|.+.|.
T Consensus 24 ~nvt~sv~vp---s~---~v~~ivg~qg~kikalr~KTqtyi~ 60 (394)
T KOG2113|consen 24 QNVTESVEVP---SE---HVAEIVGRQGCKIKALRAKTQTYIK 60 (394)
T ss_pred CccceeeecC---cc---cceeecccCccccchhhhhhcceec
Confidence 4445556555 44 9999999999999999999999886
No 46
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=65.69 E-value=4.9 Score=34.49 Aligned_cols=29 Identities=21% Similarity=0.314 Sum_probs=27.0
Q ss_pred CccceeeCCCcchHHHHHhhhCceEEEec
Q 022785 158 NFVGRLLGPRGNSLKRVEASTECRVLIRG 186 (292)
Q Consensus 158 NfvGrIlGPrG~TlK~le~eTgckI~IRG 186 (292)
+.+|..+|++|...|.|++..|-||-|=.
T Consensus 41 ~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 41 GDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 47899999999999999999999999877
No 47
>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=64.54 E-value=4.2 Score=30.98 Aligned_cols=21 Identities=29% Similarity=0.588 Sum_probs=19.0
Q ss_pred cceeeCCCcchHHHHHhhhCc
Q 022785 160 VGRLLGPRGNSLKRVEASTEC 180 (292)
Q Consensus 160 vGrIlGPrG~TlK~le~eTgc 180 (292)
.|+|||-+|.|++.||--+..
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~ 55 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANL 55 (77)
T ss_pred CCeEECCCCccHHHHHHHHHH
Confidence 599999999999999998773
No 48
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=58.63 E-value=7.9 Score=36.44 Aligned_cols=28 Identities=25% Similarity=0.611 Sum_probs=26.0
Q ss_pred CccceeeCCCcchHHHHHhhhCceEEEe
Q 022785 158 NFVGRLLGPRGNSLKRVEASTECRVLIR 185 (292)
Q Consensus 158 NfvGrIlGPrG~TlK~le~eTgckI~IR 185 (292)
++|-|+||.+|+-++-|.+.|+|.|.|=
T Consensus 155 ~kVpRvig~~~sm~~~l~~~~~~~I~VG 182 (239)
T COG1097 155 SKVPRVIGKKGSMLNMLKEKTGCEIIVG 182 (239)
T ss_pred hhcceEecCCCcHHHHhhhhcCeEEEEe
Confidence 6788999999999999999999999984
No 49
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=49.04 E-value=4.6 Score=30.24 Aligned_cols=21 Identities=29% Similarity=0.532 Sum_probs=18.7
Q ss_pred ccceeeCCCcchHHHHHhhhC
Q 022785 159 FVGRLLGPRGNSLKRVEASTE 179 (292)
Q Consensus 159 fvGrIlGPrG~TlK~le~eTg 179 (292)
-.|+|||-+|.|++.||--++
T Consensus 39 d~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 39 DAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp CCHHHCTTHHHHHHHHHHHHH
T ss_pred ccceEECCCCeeHHHHHHHHH
Confidence 379999999999999998765
No 50
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=45.36 E-value=4.8 Score=33.83 Aligned_cols=52 Identities=33% Similarity=0.445 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHhcC-CCcchHHHHHHHHHHHHHHhcCcccCCCCCCCCCcCC
Q 022785 226 DARLMQAREILEDLLK-PVDESHDFYKKQQLRELALLNGTLREEGSPMSGSVSP 278 (292)
Q Consensus 226 ~~rl~~A~e~Ie~LL~-pv~e~~d~~Kr~QL~ELA~lNGt~r~~~~~~~~~~sp 278 (292)
|-||.+|+.+|+.-|. -|.|+-+-+ |.|.+||...|..++.++.-+..-+||
T Consensus 47 DNKIeQAMDLVKtHLmfAVREEVe~L-k~qI~eL~er~~~Le~EN~lLk~~~sp 99 (123)
T KOG4797|consen 47 DNKIEQAMDLVKTHLMFAVREEVEVL-KEQIRELEERNSALERENSLLKTLASP 99 (123)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHhhCCH
Confidence 3489999999998764 566665555 599999999998888776543333333
No 51
>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=42.52 E-value=21 Score=30.87 Aligned_cols=37 Identities=24% Similarity=0.342 Sum_probs=31.1
Q ss_pred EEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEec
Q 022785 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRG 186 (292)
Q Consensus 146 Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRG 186 (292)
|+.+=|++ +-+|..+|++|...|.|++..|=||-|=.
T Consensus 34 riifvV~~----g~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 34 RVVFVVKE----GEMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred EEEEEEcC----CCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 45555555 47999999999999999999999998877
No 52
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=42.12 E-value=36 Score=34.90 Aligned_cols=44 Identities=14% Similarity=0.238 Sum_probs=34.6
Q ss_pred eeEEEEeccCCCCCCCCccceeeCCCcchHHHHHhhh-CceEEEec
Q 022785 142 KRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEAST-ECRVLIRG 186 (292)
Q Consensus 142 k~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eT-gckI~IRG 186 (292)
-...||-|=- .-|+++-||..+|++|..++.|.++. |=||-|=-
T Consensus 262 G~RtKVAV~S-~d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~ 306 (449)
T PRK12329 262 GPRTKIAVDT-LERDVDPVGACIGARGSRIQAVVNELRGEKIDVIR 306 (449)
T ss_pred cceeEEEEEc-CCCCCChhhccCCCCcchHHHHHHHhCCCeEEEEE
Confidence 3344565543 34899999999999999999999998 88887654
No 53
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=41.00 E-value=19 Score=40.09 Aligned_cols=77 Identities=25% Similarity=0.352 Sum_probs=56.3
Q ss_pred EeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEeccCCCCCcchhhhccCCCCCCCCCCCceEEEEecCchhHHH
Q 022785 147 VDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAREEMMRGKPGYEHLNEPLHILVEAELPVEIVD 226 (292)
Q Consensus 147 i~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrGS~kd~~~e~~l~g~p~~ehl~epLHVlI~a~~~~~~~~ 226 (292)
.-.+++++|- |..+++.+=- +|.+|...|+|.|.+||+=--.. + .| ...+..||.+|++.+.-
T Consensus 900 ~~~~inD~Pq-~~r~~vt~~~--~L~~i~e~~~~~it~rg~f~~~g--k------~p--~~gErklyl~ve~~~e~---- 962 (997)
T KOG0334|consen 900 AELEINDFPQ-NARWRVTYKE--ALLRISEPTAAGITTRGKFNPPG--K------EP--KPGERKLYLLVEGPDEL---- 962 (997)
T ss_pred eeccccccch-hcceeeechh--hhhhccCccccceeeccccCCCC--C------CC--CCcchhhhhhhhcchhH----
Confidence 3457789994 6888888764 39999999999999999632111 1 11 22567899999987643
Q ss_pred HHHHHHHHHHHHhcC
Q 022785 227 ARLMQAREILEDLLK 241 (292)
Q Consensus 227 ~rl~~A~e~Ie~LL~ 241 (292)
-+++|++.++.+|.
T Consensus 963 -~vqra~~e~~r~l~ 976 (997)
T KOG0334|consen 963 -SVQRAIEELERLLE 976 (997)
T ss_pred -HHHHHHHHHHHHHH
Confidence 47889999888664
No 54
>PRK02821 hypothetical protein; Provisional
Probab=40.56 E-value=17 Score=28.49 Aligned_cols=22 Identities=14% Similarity=0.404 Sum_probs=18.4
Q ss_pred CccceeeCCCcchHHHHHhhhC
Q 022785 158 NFVGRLLGPRGNSLKRVEASTE 179 (292)
Q Consensus 158 NfvGrIlGPrG~TlK~le~eTg 179 (292)
.=+|||||=+|.|++.|-.--.
T Consensus 40 ~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 40 DDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred hhCcceeCCCCchHHHHHHHHH
Confidence 4689999999999999876543
No 55
>PRK00468 hypothetical protein; Provisional
Probab=38.82 E-value=18 Score=28.02 Aligned_cols=19 Identities=21% Similarity=0.494 Sum_probs=16.5
Q ss_pred ccceeeCCCcchHHHHHhh
Q 022785 159 FVGRLLGPRGNSLKRVEAS 177 (292)
Q Consensus 159 fvGrIlGPrG~TlK~le~e 177 (292)
=+|||||=+|.|++.|-.-
T Consensus 40 D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 40 DMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred hCcceecCCChhHHHHHHH
Confidence 4699999999999998664
No 56
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=38.61 E-value=15 Score=36.15 Aligned_cols=31 Identities=29% Similarity=0.580 Sum_probs=27.8
Q ss_pred CCccceeeCCCcchHHHHHhhhCceEEEecc
Q 022785 157 FNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (292)
Q Consensus 157 ~NfvGrIlGPrG~TlK~le~eTgckI~IRGr 187 (292)
+-+||++.||.|+|+|++|+.|..-|.--++
T Consensus 123 ~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 123 LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred ceeeeeccccccCccchheecccceEeeecc
Confidence 6799999999999999999999998876654
No 57
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=37.62 E-value=32 Score=34.17 Aligned_cols=40 Identities=18% Similarity=0.423 Sum_probs=32.4
Q ss_pred EEeccCCCCCCCCccceeeCCCcchHHHHHhhh-CceEEEec
Q 022785 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEAST-ECRVLIRG 186 (292)
Q Consensus 146 Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eT-gckI~IRG 186 (292)
||-|=- ..|+++-+|..+|++|..++.|.++. |=||-|=-
T Consensus 234 KVAV~s-~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv~ 274 (362)
T PRK12327 234 KIAVRS-NNPNVDAKGACVGPKGQRVQNIVSELKGEKIDIID 274 (362)
T ss_pred EEEEEc-CCCCCCchheeECCCChhHHHHHHHhCCCeEEEEE
Confidence 444432 34899999999999999999999998 88887654
No 58
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=35.12 E-value=29 Score=30.89 Aligned_cols=38 Identities=16% Similarity=0.061 Sum_probs=31.0
Q ss_pred EEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEecc
Q 022785 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (292)
Q Consensus 145 ~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRGr 187 (292)
.+|.+=|++ +. |.-||++|.++|+|++..|=+|.|=.-
T Consensus 61 drvIfvV~~----gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 61 DLVILLVTS----GP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred CEEEEEEeC----CC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 355555544 34 999999999999999999999999883
No 59
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=34.90 E-value=73 Score=31.04 Aligned_cols=38 Identities=16% Similarity=0.407 Sum_probs=30.8
Q ss_pred eeEEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEe
Q 022785 142 KRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (292)
Q Consensus 142 k~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IR 185 (292)
++..+|++.-+. .|.|+|-.|.++|+|..+.++.|.|-
T Consensus 47 r~e~ril~~sk~------agavigkgg~nik~lr~d~na~v~vp 84 (390)
T KOG2192|consen 47 RVELRILLQSKN------AGAVIGKGGKNIKALRTDYNASVSVP 84 (390)
T ss_pred ceeEEEEEeccc------ccceeccccccHHHHhhhccceeecc
Confidence 345566666554 58999999999999999999999774
No 60
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=34.62 E-value=32 Score=31.19 Aligned_cols=34 Identities=21% Similarity=0.306 Sum_probs=29.6
Q ss_pred CCCCccceeeCCCcchHHHHHhhhCceEEEeccC
Q 022785 155 PNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRG 188 (292)
Q Consensus 155 P~~NfvGrIlGPrG~TlK~le~eTgckI~IRGrG 188 (292)
++.+=+|..+|++|..+|.|.++.|=||-|=--.
T Consensus 82 ~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s 115 (190)
T COG0195 82 VKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS 115 (190)
T ss_pred cCcCchhhhccCCChHHHHHHHHhCCceEEEEeC
Confidence 4677899999999999999999999888876643
No 61
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=33.60 E-value=78 Score=31.49 Aligned_cols=29 Identities=28% Similarity=0.461 Sum_probs=27.1
Q ss_pred CccceeeCCCcchHHHHHhhhCceEEEec
Q 022785 158 NFVGRLLGPRGNSLKRVEASTECRVLIRG 186 (292)
Q Consensus 158 NfvGrIlGPrG~TlK~le~eTgckI~IRG 186 (292)
|-+--|+||.|..++.||+..|+.|.-||
T Consensus 24 ~~~~~l~G~~~~~l~l~e~~~gv~i~~rG 52 (348)
T COG1702 24 NELVALFGPTDTNLSLLEIALGVSIVARG 52 (348)
T ss_pred hhhhhhcCCCCccHHHHHHHhCcEEEeCC
Confidence 56778999999999999999999999999
No 62
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=33.53 E-value=32 Score=36.20 Aligned_cols=54 Identities=17% Similarity=0.275 Sum_probs=39.3
Q ss_pred cCccCCCCCCCCccceeeEEEEeccCC--CCCCCCccceeeCCCcchHHHHHhhhCceEEEec
Q 022785 126 AQNWLSSQGSSSGLIVKRTIRVDIPVE--KYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRG 186 (292)
Q Consensus 126 ~~~~~~p~~~~~~~~vk~~~Ki~IPv~--~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IRG 186 (292)
.+.|.+|.+.... ++...++- +.|+ -.+|+|||-.|-|++-+-..++.++.|+=
T Consensus 278 ~~s~~~~~d~s~~------k~~~l~i~e~e~p~-~lsg~lig~~gey~s~yssasn~~~hi~t 333 (608)
T KOG2279|consen 278 EGSWEKPSDDSFQ------KSEALAIPEMEMPE-ILSGDLIGHAGEYLSVYSSASNHPNHIWT 333 (608)
T ss_pred ccccCCccccccc------cccccccceeecCc-ccccchhhhhhhhhhhhhhccCccceEEe
Confidence 3578888876442 23333333 3333 36899999999999999999999999875
No 63
>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=33.39 E-value=43 Score=32.96 Aligned_cols=40 Identities=18% Similarity=0.385 Sum_probs=32.2
Q ss_pred EEeccCCCCCCCCccceeeCCCcchHHHHHhhh-CceEEEec
Q 022785 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEAST-ECRVLIRG 186 (292)
Q Consensus 146 Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eT-gckI~IRG 186 (292)
||-|=- ..|+++-+|..+|++|..++.|.++. |=+|-|=-
T Consensus 232 KvAV~s-~~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~ 272 (341)
T TIGR01953 232 KIAVES-NDENIDPVGACVGPKGSRIQAISKELNGEKIDIIE 272 (341)
T ss_pred EEEEEc-CCCCCCcceeeECCCCchHHHHHHHhCCCeEEEEE
Confidence 454433 35899999999999999999999998 77776654
No 64
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=32.99 E-value=26 Score=27.50 Aligned_cols=19 Identities=16% Similarity=0.572 Sum_probs=16.4
Q ss_pred ccceeeCCCcchHHHHHhh
Q 022785 159 FVGRLLGPRGNSLKRVEAS 177 (292)
Q Consensus 159 fvGrIlGPrG~TlK~le~e 177 (292)
=+|++||=+|.|++.|-.-
T Consensus 40 D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 40 DMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred cccceecCCChhHHHHHHH
Confidence 4799999999999998653
No 65
>PRK01064 hypothetical protein; Provisional
Probab=32.96 E-value=24 Score=27.64 Aligned_cols=20 Identities=20% Similarity=0.617 Sum_probs=17.8
Q ss_pred cceeeCCCcchHHHHHhhhC
Q 022785 160 VGRLLGPRGNSLKRVEASTE 179 (292)
Q Consensus 160 vGrIlGPrG~TlK~le~eTg 179 (292)
+|++||=+|.|++.|..-..
T Consensus 41 ~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred ceEEECCCCccHHHHHHHHH
Confidence 69999999999999988644
No 66
>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=32.52 E-value=40 Score=31.07 Aligned_cols=40 Identities=18% Similarity=0.353 Sum_probs=29.8
Q ss_pred eeeEEEEeccCCCCCCCCccceeeCCCcchHHHH--------HhhhCceEEEe
Q 022785 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRV--------EASTECRVLIR 185 (292)
Q Consensus 141 vk~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~l--------e~eTgckI~IR 185 (292)
+.....|+|.-+.+ -|-|||.+|.++|+| |+..||||.+.
T Consensus 219 ~~i~~~i~v~~~s~-----k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l~ 266 (270)
T TIGR00436 219 LKIHALISVERESQ-----KKIIIGKNGSMIKAIGIAARKDILELFDCDVFLE 266 (270)
T ss_pred EEEEEEEEECcCCc-----eeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 45666777776654 478999999999986 55678888763
No 67
>PRK00089 era GTPase Era; Reviewed
Probab=32.05 E-value=84 Score=28.99 Aligned_cols=40 Identities=20% Similarity=0.360 Sum_probs=30.0
Q ss_pred eeeEEEEeccCCCCCCCCccceeeCCCcchHHHH--------HhhhCceEEEe
Q 022785 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRV--------EASTECRVLIR 185 (292)
Q Consensus 141 vk~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~l--------e~eTgckI~IR 185 (292)
++....|+|.-+.+ .+-|||-+|.++|+| |+..||+|.+.
T Consensus 224 ~~i~~~i~v~~~~~-----k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 224 VRIEATIYVERDSQ-----KGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEEEccCCc-----eeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 55666777776654 578999999999986 55678877764
No 68
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=31.32 E-value=35 Score=24.40 Aligned_cols=19 Identities=16% Similarity=0.256 Sum_probs=15.7
Q ss_pred hHHHHHhhhCceEEEeccC
Q 022785 170 SLKRVEASTECRVLIRGRG 188 (292)
Q Consensus 170 TlK~le~eTgckI~IRGrG 188 (292)
.+++||++.|+++.+|..+
T Consensus 33 ~i~~LE~~lg~~Lf~r~~~ 51 (60)
T PF00126_consen 33 QIKQLEEELGVPLFERSGR 51 (60)
T ss_dssp HHHHHHHHHTS-SEEECSS
T ss_pred HHHHHHHHhCCeEEEECCC
Confidence 5899999999999999654
No 69
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=29.43 E-value=23 Score=38.40 Aligned_cols=38 Identities=24% Similarity=0.537 Sum_probs=29.8
Q ss_pred eeEEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEe
Q 022785 142 KRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (292)
Q Consensus 142 k~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IR 185 (292)
..+..++||.+ |-+-|+||+|.++++++++++|-|.+-
T Consensus 708 ~~~~~~~~p~~------~~~~~ig~~g~~~r~~~~~~~~~~~~~ 745 (753)
T KOG2208|consen 708 LVTKEIEIPRS------LHRYLIGPKGSNLRQLEKEFNVNIVVP 745 (753)
T ss_pred ceeeEEeccHH------HhhhccCCCCccHHHHHHHhccceecC
Confidence 34456666655 446799999999999999999988764
No 70
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=28.58 E-value=27 Score=29.96 Aligned_cols=26 Identities=19% Similarity=0.285 Sum_probs=22.4
Q ss_pred ccceeeCCCcchHHHHHhhhCceEEE
Q 022785 159 FVGRLLGPRGNSLKRVEASTECRVLI 184 (292)
Q Consensus 159 fvGrIlGPrG~TlK~le~eTgckI~I 184 (292)
-.|+.||.+|.|++.++.-+|-++-|
T Consensus 109 d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 109 DKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred ccchhhCCCCHHHHHHHHHhCCccCC
Confidence 47999999999999999999876644
No 71
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=28.03 E-value=65 Score=31.36 Aligned_cols=36 Identities=25% Similarity=0.539 Sum_probs=30.4
Q ss_pred EEEEeccCCCCCCCCccceeeCCCcchHHHHHhhhCceEEEe
Q 022785 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (292)
Q Consensus 144 ~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eTgckI~IR 185 (292)
+..|-||-+ +-|-|||-.|.-+|+|-.|+|+.|.|-
T Consensus 316 TaQvtip~d------lggsiigkggqri~~ir~esGA~Ikid 351 (390)
T KOG2192|consen 316 TAQVTIPKD------LGGSIIGKGGQRIKQIRHESGASIKID 351 (390)
T ss_pred eeeEecccc------cCcceecccchhhhhhhhccCceEEec
Confidence 456777743 679999999999999999999999874
No 72
>PRK15494 era GTPase Era; Provisional
Probab=27.87 E-value=1e+02 Score=29.71 Aligned_cols=40 Identities=25% Similarity=0.298 Sum_probs=30.5
Q ss_pred eeeEEEEeccCCCCCCCCccceeeCCCcchHHHH--------HhhhCceEEEe
Q 022785 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRV--------EASTECRVLIR 185 (292)
Q Consensus 141 vk~~~Ki~IPv~~yP~~NfvGrIlGPrG~TlK~l--------e~eTgckI~IR 185 (292)
+++...|||.-+.+ -|-|||-+|..+|+| |+..||||.+.
T Consensus 271 ~~i~~~i~v~~~sq-----k~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 271 VKINQVIVVSRESY-----KTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred EEEEEEEEECCCCc-----eeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 55667788776654 477999999999986 66678887764
No 73
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=25.67 E-value=47 Score=30.10 Aligned_cols=22 Identities=32% Similarity=0.442 Sum_probs=18.9
Q ss_pred chHHHHHhhhCceEEEeccCCC
Q 022785 169 NSLKRVEASTECRVLIRGRGSI 190 (292)
Q Consensus 169 ~TlK~le~eTgckI~IRGrGS~ 190 (292)
..+|+||++.|+++.+|++|..
T Consensus 35 ~~i~~LE~~lg~~Lf~R~r~i~ 56 (294)
T PRK13348 35 QRIKALEESLGQPLLVRGRPCR 56 (294)
T ss_pred HHHHHHHHHhCceeeecCCCCc
Confidence 3689999999999999997643
No 74
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=25.56 E-value=52 Score=32.99 Aligned_cols=40 Identities=18% Similarity=0.276 Sum_probs=31.7
Q ss_pred EEeccCCCCCCCCccceeeCCCcchHHHHHhhh-CceEEEec
Q 022785 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEAST-ECRVLIRG 186 (292)
Q Consensus 146 Ki~IPv~~yP~~NfvGrIlGPrG~TlK~le~eT-gckI~IRG 186 (292)
||-|= ...|+++-+|..+|++|..++.|.++. |=||-|=-
T Consensus 240 KVAV~-S~d~~iDPvGacIG~~G~rI~~I~~eL~gEkIDvI~ 280 (374)
T PRK12328 240 KVALF-SNNPNIDPIGATVGVKGVRINAVSKELNGENIDCIE 280 (374)
T ss_pred EEEEE-cCCCCCChHHhhcCCCcchHHHHHHHhCCCeEEEEE
Confidence 44433 355899999999999999999999998 77776644
No 75
>TIGR01170 rplA_mito ribosomal protein L1, mitochondrial. This model represents the mitochondrial homolog of bacterial ribosomal protein L1. Unlike chloroplast L1, this form was not sufficiently similar to bacterial forms to include in a single bacterial/organellar L1.
Probab=23.71 E-value=17 Score=31.46 Aligned_cols=20 Identities=35% Similarity=0.637 Sum_probs=15.7
Q ss_pred cCCCCCCCCccceeeCCCcc
Q 022785 150 PVEKYPNFNFVGRLLGPRGN 169 (292)
Q Consensus 150 Pv~~yP~~NfvGrIlGPrG~ 169 (292)
-.+-.|....+|+||||||.
T Consensus 99 ~~~~m~~l~~Lg~iLGprGl 118 (141)
T TIGR01170 99 HPDIVPELAQLRRLLGPKGL 118 (141)
T ss_pred CHHHHHHHHHhhcccccCcC
Confidence 33456677899999999986
No 76
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=22.57 E-value=2.3e+02 Score=26.08 Aligned_cols=27 Identities=30% Similarity=0.357 Sum_probs=17.1
Q ss_pred cceeeCCC-------------cchHHHHHhhhCceEEEec
Q 022785 160 VGRLLGPR-------------GNSLKRVEASTECRVLIRG 186 (292)
Q Consensus 160 vGrIlGPr-------------G~TlK~le~eTgckI~IRG 186 (292)
+||+|||+ +..+...-+++.++|.+|=
T Consensus 117 lgk~LGp~~~p~gK~P~~~~~~~dl~~~i~~~k~~v~~r~ 156 (214)
T PTZ00225 117 VPRLVGPHMHRMGKFPTVCSPSESLPDKVVELRSTVKFQL 156 (214)
T ss_pred hhhhcCCCCCcCCCCCcccCCccCHHHHHHHHhheeEEEe
Confidence 69999998 3335555555655555553
No 77
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=22.52 E-value=26 Score=32.63 Aligned_cols=29 Identities=24% Similarity=0.479 Sum_probs=26.8
Q ss_pred CccceeeCCCcchHHHHHhhhCceEEEec
Q 022785 158 NFVGRLLGPRGNSLKRVEASTECRVLIRG 186 (292)
Q Consensus 158 NfvGrIlGPrG~TlK~le~eTgckI~IRG 186 (292)
--||||.|-.|.|--.||..|.++|.|-+
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad 206 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLAD 206 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecC
Confidence 35899999999999999999999999876
No 78
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=20.00 E-value=58 Score=29.48 Aligned_cols=21 Identities=19% Similarity=0.241 Sum_probs=18.3
Q ss_pred hHHHHHhhhCceEEEeccCCC
Q 022785 170 SLKRVEASTECRVLIRGRGSI 190 (292)
Q Consensus 170 TlK~le~eTgckI~IRGrGS~ 190 (292)
.+|+||++.|+++..|+||-.
T Consensus 35 ~I~~LE~~lg~~Lf~R~r~~~ 55 (292)
T TIGR03298 35 RIKALEERLGQPLLVRTQPCR 55 (292)
T ss_pred HHHHHHHHhCchheecCCCCc
Confidence 489999999999999997643
Done!