Query 022661
Match_columns 294
No_of_seqs 191 out of 412
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 05:13:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022661.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022661hhsearch_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 9.6E-65 2.1E-69 467.4 22.3 213 30-293 28-241 (259)
2 cd02395 SF1_like-KH Splicing f 100.0 1E-41 2.2E-46 284.3 13.1 119 142-265 1-120 (120)
3 KOG0119 Splicing factor 1/bran 100.0 8.6E-39 1.9E-43 314.6 11.6 199 55-269 55-261 (554)
4 COG5176 MSL5 Splicing factor ( 100.0 9.2E-31 2E-35 236.7 8.1 153 101-267 114-269 (269)
5 cd02393 PNPase_KH Polynucleoti 98.4 1.1E-06 2.5E-11 65.0 7.3 58 143-236 4-61 (61)
6 cd00105 KH-I K homology RNA-bi 98.3 2.1E-06 4.5E-11 61.9 7.0 62 143-235 2-63 (64)
7 PF00013 KH_1: KH domain syndr 98.3 4.1E-07 8.8E-12 65.8 2.6 60 142-235 1-60 (60)
8 smart00322 KH K homology RNA-b 98.2 1.1E-05 2.4E-10 56.9 7.6 65 142-239 4-68 (69)
9 PF13014 KH_3: KH domain 98.1 2.1E-06 4.6E-11 59.0 3.0 28 158-185 1-28 (43)
10 cd02394 vigilin_like_KH K homo 98.0 9.3E-06 2E-10 59.1 5.0 53 157-235 9-61 (62)
11 cd02396 PCBP_like_KH K homolog 97.9 3.1E-05 6.7E-10 57.4 6.3 35 143-184 2-36 (65)
12 KOG1960 Predicted RNA-binding 97.9 6.7E-06 1.5E-10 81.5 2.2 90 139-243 208-297 (531)
13 TIGR03665 arCOG04150 arCOG0415 97.7 5.3E-05 1.1E-09 66.8 4.5 53 158-241 99-151 (172)
14 PRK13763 putative RNA-processi 97.6 0.0001 2.3E-09 65.4 5.3 53 158-241 105-157 (180)
15 COG1094 Predicted RNA-binding 97.2 0.0008 1.7E-08 61.2 6.1 55 158-243 112-166 (194)
16 PRK13763 putative RNA-processi 97.1 0.00092 2E-08 59.4 5.4 57 157-241 12-71 (180)
17 TIGR03665 arCOG04150 arCOG0415 96.8 0.0011 2.4E-08 58.5 3.7 57 157-241 7-65 (172)
18 TIGR02696 pppGpp_PNP guanosine 96.8 0.0035 7.7E-08 66.5 8.0 66 140-241 577-642 (719)
19 TIGR03591 polynuc_phos polyrib 96.3 0.0075 1.6E-07 63.6 6.2 64 141-240 551-614 (684)
20 KOG2193 IGF-II mRNA-binding pr 96.2 0.0016 3.5E-08 65.5 0.6 38 146-184 279-316 (584)
21 PLN00207 polyribonucleotide nu 95.9 0.007 1.5E-07 65.7 4.0 66 140-241 684-750 (891)
22 KOG2874 rRNA processing protei 95.8 0.018 3.9E-07 55.5 5.9 77 160-269 161-238 (356)
23 KOG1676 K-homology type RNA bi 95.8 0.017 3.7E-07 60.0 6.1 61 157-241 239-300 (600)
24 KOG1676 K-homology type RNA bi 95.7 0.025 5.5E-07 58.7 6.7 74 138-240 136-209 (600)
25 PRK04163 exosome complex RNA-b 94.7 0.035 7.6E-07 51.3 4.1 56 156-240 153-208 (235)
26 PRK11824 polynucleotide phosph 94.4 0.035 7.5E-07 58.8 3.6 57 156-241 562-618 (693)
27 KOG2814 Transcription coactiva 94.4 0.06 1.3E-06 52.7 4.9 60 157-236 66-127 (345)
28 KOG2191 RNA-binding protein NO 92.8 0.49 1.1E-05 46.8 8.2 38 141-185 132-169 (402)
29 KOG2191 RNA-binding protein NO 92.7 0.11 2.4E-06 51.2 3.6 37 141-184 39-75 (402)
30 KOG2193 IGF-II mRNA-binding pr 92.6 0.14 3.1E-06 52.0 4.3 31 156-186 207-237 (584)
31 KOG2190 PolyC-binding proteins 90.8 0.93 2E-05 46.5 8.0 40 140-186 137-176 (485)
32 COG1185 Pnp Polyribonucleotide 88.9 0.62 1.4E-05 49.6 5.1 64 141-240 552-615 (692)
33 PRK00106 hypothetical protein; 88.9 0.72 1.6E-05 47.9 5.5 57 156-240 234-290 (535)
34 KOG1960 Predicted RNA-binding 88.8 0.17 3.6E-06 51.1 0.9 72 161-245 308-379 (531)
35 TIGR03319 YmdA_YtgF conserved 87.6 0.82 1.8E-05 47.1 5.0 57 156-240 213-269 (514)
36 PRK12704 phosphodiesterase; Pr 86.9 3.4 7.4E-05 42.7 8.9 44 156-222 219-262 (520)
37 cd02134 NusA_KH NusA_K homolog 85.8 0.8 1.7E-05 33.8 2.8 36 141-183 25-60 (61)
38 KOG0336 ATP-dependent RNA heli 85.5 1.5 3.4E-05 44.9 5.5 29 156-184 55-83 (629)
39 KOG2190 PolyC-binding proteins 84.5 0.97 2.1E-05 46.4 3.6 42 138-186 335-376 (485)
40 PF13184 KH_5: NusA-like KH do 78.3 0.83 1.8E-05 35.0 0.5 31 153-184 14-45 (69)
41 KOG1067 Predicted RNA-binding 73.9 3 6.5E-05 44.1 3.2 54 158-241 607-660 (760)
42 cd02409 KH-II KH-II (K homolo 72.6 3.4 7.3E-05 29.2 2.4 23 159-181 36-58 (68)
43 COG1094 Predicted RNA-binding 67.1 16 0.00035 33.6 6.1 28 159-186 19-46 (194)
44 PRK08406 transcription elongat 62.8 5.5 0.00012 34.3 2.1 29 157-185 41-69 (140)
45 cd02414 jag_KH jag_K homology 61.5 5.4 0.00012 30.5 1.7 21 159-179 35-55 (77)
46 COG1097 RRP4 RNA-binding prote 56.3 9.2 0.0002 36.2 2.6 29 156-184 154-182 (239)
47 KOG0334 RNA helicase [RNA proc 52.8 8.6 0.00019 42.9 2.1 76 146-240 901-976 (997)
48 PRK12705 hypothetical protein; 52.2 8.5 0.00018 39.9 1.8 29 156-184 207-235 (508)
49 KOG2208 Vigilin [Lipid transpo 51.3 10 0.00022 41.0 2.4 39 139-184 707-745 (753)
50 COG1702 PhoH Phosphate starvat 47.3 34 0.00073 34.1 5.0 30 157-186 24-53 (348)
51 KOG2113 Predicted RNA binding 45.6 17 0.00036 36.2 2.6 37 139-182 24-60 (394)
52 PRK12327 nusA transcription el 44.9 21 0.00046 35.5 3.2 33 152-185 241-274 (362)
53 TIGR01953 NusA transcription t 43.4 26 0.00057 34.5 3.6 33 152-185 239-272 (341)
54 PRK02821 hypothetical protein; 39.3 17 0.00038 28.6 1.4 21 158-178 41-61 (77)
55 TIGR00436 era GTP-binding prot 38.3 32 0.00068 31.7 3.2 40 139-184 219-266 (270)
56 TIGR01952 nusA_arch NusA famil 37.7 25 0.00054 30.6 2.2 29 157-185 42-70 (141)
57 PRK00468 hypothetical protein; 37.0 20 0.00042 28.0 1.3 19 159-177 41-59 (75)
58 PF00126 HTH_1: Bacterial regu 36.8 26 0.00056 25.2 1.9 20 169-188 33-52 (60)
59 COG0195 NusA Transcription elo 36.5 26 0.00055 32.0 2.2 33 153-186 82-114 (190)
60 PF13083 KH_4: KH domain; PDB: 35.3 6.1 0.00013 29.6 -1.7 20 159-178 40-59 (73)
61 PRK01064 hypothetical protein; 33.1 33 0.00071 27.0 2.0 20 159-178 41-60 (78)
62 PRK12329 nusA transcription el 32.5 56 0.0012 33.7 4.1 33 152-185 273-306 (449)
63 PRK05424 rplA 50S ribosomal pr 32.4 1.1E+02 0.0025 28.4 5.8 31 209-239 168-199 (230)
64 PRK06418 transcription elongat 32.2 33 0.00072 30.7 2.1 27 160-186 72-98 (166)
65 PRK00089 era GTPase Era; Revie 32.1 45 0.00097 30.8 3.1 40 139-184 224-271 (292)
66 KOG2192 PolyC-binding hnRNP-K 31.1 89 0.0019 30.7 4.9 37 141-184 48-84 (390)
67 COG1837 Predicted RNA-binding 30.8 29 0.00062 27.4 1.3 18 159-176 41-58 (76)
68 KOG2113 Predicted RNA binding 30.7 27 0.00058 34.8 1.4 31 156-186 123-153 (394)
69 PRK13348 chromosome replicatio 30.7 34 0.00073 31.0 2.0 22 168-189 35-56 (294)
70 PRK12328 nusA transcription el 29.5 34 0.00074 34.4 1.9 34 151-185 246-280 (374)
71 PRK15494 era GTPase Era; Provi 28.5 55 0.0012 31.6 3.2 40 139-184 271-318 (339)
72 KOG4797 Transcriptional regula 27.4 9 0.00019 32.5 -2.1 45 224-269 46-91 (123)
73 TIGR01170 rplA_mito ribosomal 26.5 12 0.00027 32.4 -1.5 18 150-168 101-118 (141)
74 PTZ00225 60S ribosomal protein 26.1 1.6E+02 0.0034 27.2 5.6 62 159-240 117-192 (214)
75 TIGR01169 rplA_bact ribosomal 25.4 1.8E+02 0.0039 27.0 5.8 31 209-239 167-198 (227)
76 PRK09202 nusA transcription el 25.2 51 0.0011 33.9 2.4 33 151-184 240-273 (470)
77 TIGR03298 argP transcriptional 24.6 42 0.0009 30.4 1.5 23 169-191 35-57 (292)
78 PRK03635 chromosome replicatio 23.0 59 0.0013 29.6 2.1 23 169-191 36-58 (294)
79 PRK08406 transcription elongat 22.2 39 0.00084 29.1 0.7 25 159-183 110-134 (140)
80 PRK03601 transcriptional regul 22.0 66 0.0014 29.1 2.3 18 169-186 35-52 (275)
81 PRK11074 putative DNA-binding 21.9 69 0.0015 29.3 2.4 23 168-190 35-57 (300)
82 PRK12684 transcriptional regul 21.2 74 0.0016 29.5 2.4 20 169-188 36-56 (313)
83 KOG3564 GTPase-activating prot 21.0 1.3E+02 0.0027 31.8 4.2 41 30-70 49-89 (604)
84 PRK15421 DNA-binding transcrip 21.0 75 0.0016 29.7 2.5 19 168-186 35-53 (317)
85 KOG2192 PolyC-binding hnRNP-K 20.4 3E+02 0.0065 27.2 6.4 42 134-184 310-351 (390)
86 PF07582 AP_endonuc_2_N: AP en 20.4 1.2E+02 0.0027 22.4 3.0 32 212-243 17-48 (55)
87 PRK12683 transcriptional regul 20.2 77 0.0017 29.3 2.3 20 169-188 36-56 (309)
No 1
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=100.00 E-value=9.6e-65 Score=467.40 Aligned_cols=213 Identities=49% Similarity=0.741 Sum_probs=183.7
Q ss_pred chHHHHHHHHHHHHhhcCCcccchhHHHHHHHHHHHHHHhCCCCCCCCCcccCCCCCCCCCCCCCCCCCccccccchhhh
Q 022661 30 LDRERYLAELLAERQKLGPFVQVLPLCSRLLSQEIRRITGYNPSFVDHERFEHDSPFRSLGQPNGRPMDLEGLSAMQTEE 109 (294)
Q Consensus 30 ~~~~~YL~ELl~E~~~L~~~~~~f~h~~rLL~~EI~RV~~~~~~~~~~~~~~~~sp~~s~~~~n~~~~~~~~~~~l~~E~ 109 (294)
....+||.||++|+++|++|+. |+||.|||++||.||+....... ...+++
T Consensus 28 ~~~~~yl~el~~e~~~l~~~~~-~~~~~rLL~~Ei~rv~~~~~~~~----------------------------~~~~~~ 78 (259)
T KOG1588|consen 28 EKASKYLSELLAERKSLSPFFP-FPHAERLLDEEIERVQTSGRQHG----------------------------SKEPEE 78 (259)
T ss_pred hHHHHHHHHHHhhHHhcCcccc-hHHHHHHHHHHHHHHHhhhhhcc----------------------------CCCchh
Confidence 3457999999999999999998 99999999999999998622010 000111
Q ss_pred hcccccCCCCCCCCCCCCCCCCCCCCCCceeEEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEecccCC
Q 022661 110 NGHLQRMAPFQTPPSMGWQGIPGIPTTPVVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSV 189 (294)
Q Consensus 110 ~~~~~~~~~~~~~~~~~~~~~p~~~~~~~vk~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~ 189 (294)
.. ....++++.||+++||+|||++||+ ||||||||||||||+||||++|||||+||||||+
T Consensus 79 ~~------------------~~~~~~~~~vk~~~Kv~vPv~~yP~-fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSm 139 (259)
T KOG1588|consen 79 LP------------------YADVYSGKPVKLTEKVLVPVKEYPK-FNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSM 139 (259)
T ss_pred cc------------------cccCccCCceeEEEEEEeccCCCCC-CccccccccCCcchHHHHHHHHCCeEEEecCCcc
Confidence 10 0024577899999999999999999 9999999999999999999999999999999999
Q ss_pred CCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHHhccCCCCcchhHHHHHHHHHHHHHcCccC-CCC
Q 022661 190 KDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILENLLKPVDESLDHYKKQQLRELAMLNGTLR-EES 268 (294)
Q Consensus 190 kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL~p~~e~~delK~~QL~ELA~lNGt~r-~~~ 268 (294)
||..||++||++|+||||++||||+|++++++++|++||++|+++|++||+|.+|+.| |++||||||++||||. +.+
T Consensus 140 rD~~KEE~lR~~p~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~P~~e~~d--k~~QL~ELa~lngt~~~~~~ 217 (259)
T KOG1588|consen 140 RDKAKEEELRGDPGYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLVPDHEDED--KREQLRELAILNGTYLRSES 217 (259)
T ss_pred cchHHHHHhhcCcchHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcCCCCCCch--HHHHHHHHhhcCCccccccc
Confidence 9999999999999999999999999999999999999999999999999999998877 9999999999999955 444
Q ss_pred CCCCCCCCCCCCCCCcccccccccC
Q 022661 269 PSMSPSMSPSMSPFNNAGMKRAKTG 293 (294)
Q Consensus 269 ~~~~~~~~~~~spf~~~~~~~~~~~ 293 (294)
..++ .-.|+++||++.|+||+|++
T Consensus 218 ~~~~-g~~~~~~~~~~~~~~r~~~~ 241 (259)
T KOG1588|consen 218 RKPS-GGNGRGVPGNSAGGKRGKTG 241 (259)
T ss_pred cccC-CCCCcCCCCCCCCcccccCC
Confidence 4411 11148999999999999985
No 2
>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=1e-41 Score=284.26 Aligned_cols=119 Identities=55% Similarity=0.907 Sum_probs=112.6
Q ss_pred EEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCch
Q 022661 142 VIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPE 221 (294)
Q Consensus 142 ~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~ 221 (294)
++|||||+++||+ |||||+||||+|+|+|+||++|||+|.|||+||+++.++++++++ +.|+|++|||||+|+|.++
T Consensus 1 ~~ki~iP~~~~P~-~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~-~~~~~~~eplhV~I~a~~~- 77 (120)
T cd02395 1 TEKVYIPVKQYPK-YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRG-PKYAHLNEPLHVLITAETP- 77 (120)
T ss_pred CCEEEcCcccCCC-CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccC-cccccCCCCcEEEEEeCCc-
Confidence 3689999999999 999999999999999999999999999999999999999999887 8999999999999999986
Q ss_pred hHHHHHHHHHHHHHHhccCCCCcc-hhHHHHHHHHHHHHHcCccC
Q 022661 222 DIINSRLDHAVAILENLLKPVDES-LDHYKKQQLRELAMLNGTLR 265 (294)
Q Consensus 222 ~~~~~rl~~A~e~Ie~LL~p~~e~-~delK~~QL~ELA~lNGt~r 265 (294)
+..++++|+++|+.||.++.++ .|++|++||+|||++|||||
T Consensus 78 --~~e~~~~A~~~I~~ll~~~~~~~~~~~k~~ql~~la~~nGt~~ 120 (120)
T cd02395 78 --PEEALAKAVEAIEELLKPAIEGGNDELKREQLRELALLNGTYR 120 (120)
T ss_pred --HHHHHHHHHHHHHHHhccCCCccchHHHHHHHHHHHHhcccCC
Confidence 3458999999999999998777 99999999999999999997
No 3
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=100.00 E-value=8.6e-39 Score=314.62 Aligned_cols=199 Identities=34% Similarity=0.518 Sum_probs=148.6
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCCCcccCCCCCCCCCC-CCCCCC---CccccccchhhhhcccccCCCCCCCCCCCCCCC
Q 022661 55 LCSRLLSQEIRRITGYNPSFVDHERFEHDSPFRSLGQ-PNGRPM---DLEGLSAMQTEENGHLQRMAPFQTPPSMGWQGI 130 (294)
Q Consensus 55 h~~rLL~~EI~RV~~~~~~~~~~~~~~~~sp~~s~~~-~n~~~~---~~~~~~~l~~E~~~~~~~~~~~~~~~~~~~~~~ 130 (294)
-+..|..|||.|.+..++ |......+.+||.++..+ .+|+.. .......|.+|+...+..+... ...| .+
T Consensus 55 y~l~~~iee~t~kLrt~d-~~~p~~~e~rSPsp~p~yda~g~R~ntRe~R~r~~Le~er~e~I~~~lk~----nP~f-kp 128 (554)
T KOG0119|consen 55 YSLNLRIEEITRKLRTGD-VGVPPPRELRSPSPEPVYDAKGKRLNTREQRARKKLEDERHEIIEEILKL----NPGF-KP 128 (554)
T ss_pred hhHHHHHHHhhhhhcccc-CCCCCCccccCCCcchhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHh----CcCC-CC
Confidence 344566688888887755 322333455777666554 444431 1222345666665543322110 1112 56
Q ss_pred CCCCCCCceeEEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCC-CCCC
Q 022661 131 PGIPTTPVVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYE-HLNE 209 (294)
Q Consensus 131 p~~~~~~~vk~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~e-hl~e 209 (294)
|++..-+. |+++|||||||+||+ |||||+||||||+|+|+||+||||||+||||||+|+++ ...++.+|. ..+|
T Consensus 129 P~DYk~p~-~~~~Kv~IPvke~Pd-~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk---~~~~d~~~~~~~~e 203 (554)
T KOG0119|consen 129 PADYKPPA-KLHDKVYIPVKEFPD-INFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGK---GRSDDLSYIPKENE 203 (554)
T ss_pred CcccCccc-ccccceecchhhcCC-cceeEEEecCCccHHHHHHHHhCCeEEEeccccccccc---cCCccccccccccc
Confidence 66666665 899999999999999 99999999999999999999999999999999999875 112334443 4589
Q ss_pred CcEEEEEecCchhHHHHHHHHHHHHHHhccC---CCCcchhHHHHHHHHHHHHHcCccCCCCC
Q 022661 210 PLHVLVEAEFPEDIINSRLDHAVAILENLLK---PVDESLDHYKKQQLRELAMLNGTLREESP 269 (294)
Q Consensus 210 pLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL~---p~~e~~delK~~QL~ELA~lNGt~r~~~~ 269 (294)
||||+|+|++.+ +|++|++.|+.||+ .++|+++++|+.||+|||-+|||+|++..
T Consensus 204 pLH~~Isadt~e-----ki~~Ai~vienli~~av~~~e~~n~l~~~Qlrela~lNgt~r~~d~ 261 (554)
T KOG0119|consen 204 PLHCLISADTQE-----KIKKAIAVIENLIQSAVSVPEGQNDLKRLQLRELARLNGTLRDDDN 261 (554)
T ss_pred ceeEEEecchHH-----HHHHHHHHHHHHHHhhccCccccccccHHHHHHHHHhCCCCCcccc
Confidence 999999999854 89999999999998 68999999999999999999999999984
No 4
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.97 E-value=9.2e-31 Score=236.66 Aligned_cols=153 Identities=31% Similarity=0.472 Sum_probs=112.2
Q ss_pred ccccchhhhhccc---ccCCCCCCCCCCCCCCCCCCCCCCceeEEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhh
Q 022661 101 GLSAMQTEENGHL---QRMAPFQTPPSMGWQGIPGIPTTPVVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMT 177 (294)
Q Consensus 101 ~~~~l~~E~~~~~---~~~~~~~~~~~~~~~~~p~~~~~~~vk~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eT 177 (294)
+-..|.+|++-+. |.+-++ +-.|.+.-.| .|.+.||||||++||+ .||||+||||||.|+|+||+.|
T Consensus 114 y~kkLeder~~l~era~k~lp~--------fv~p~dy~rp-sk~q~KiYIPV~eyPe-~NFVGLliGPRG~Tlk~le~~s 183 (269)
T COG5176 114 YNKKLEDERLWLKERAQKILPR--------FVLPNDYIRP-SKYQNKIYIPVQEYPE-SNFVGLLIGPRGSTLKQLERIS 183 (269)
T ss_pred HhhhhhHHHHHHHHHHHHhcCc--------ccCCccccCc-ccccceEEeehhhCcc-cceeEEEecCCcchHHHHHHHh
Confidence 3446777777653 222222 2233333333 5778999999999999 9999999999999999999999
Q ss_pred CCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHHhccCCCCcchhHHHHHHHHHH
Q 022661 178 ECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILENLLKPVDESLDHYKKQQLREL 257 (294)
Q Consensus 178 GckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL~p~~e~~delK~~QL~EL 257 (294)
+|||.|||+||+|.++-..++. ++.....++||+||+++..-..+ ..++-....|.+.-. .+++++++|+-||++|
T Consensus 184 ~akIaIRG~gsvKegk~ssd~p--~~~~N~e~~lhcLI~adsedki~-~~ik~~~n~I~~a~~-~PeGqnDlkR~qlr~l 259 (269)
T COG5176 184 RAKIAIRGSGSVKEGKISSDTP--ESLKNAEAVLHCLIEADSEDKIC-RLIKSQLNAIREARR-NPEGQNDLKRFQLRWL 259 (269)
T ss_pred CCeEEEecccccccCcccccCc--hhhhhhHHhHHHHhhcchhhhHH-HHHHHHHHHHHHHhc-CCcccchHHHHHHHHH
Confidence 9999999999999765332221 22234569999999997644333 234444555555555 4689999999999999
Q ss_pred HHHcCccCCC
Q 022661 258 AMLNGTLREE 267 (294)
Q Consensus 258 A~lNGt~r~~ 267 (294)
|.+|||+|++
T Consensus 260 a~lngtlr~d 269 (269)
T COG5176 260 AHLNGTLRAD 269 (269)
T ss_pred HHhcceecCC
Confidence 9999999975
No 5
>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=98.41 E-value=1.1e-06 Score=65.01 Aligned_cols=58 Identities=22% Similarity=0.397 Sum_probs=45.1
Q ss_pred EEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchh
Q 022661 143 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPED 222 (294)
Q Consensus 143 ~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~ 222 (294)
+.+.|| -.++|+|||++|.|+|+|+++|||+|.|-- + -.|.|++.+++
T Consensus 4 ~~i~Ip-------~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----~-------------------g~v~I~G~~~~- 51 (61)
T cd02393 4 ETMKIP-------PDKIRDVIGPGGKTIKKIIEETGVKIDIED-----D-------------------GTVYIAASDKE- 51 (61)
T ss_pred EEEEeC-------hhheeeeECCCchHHHHHHHHHCCEEEeCC-----C-------------------CEEEEEeCCHH-
Confidence 446665 278999999999999999999999998741 0 14999997654
Q ss_pred HHHHHHHHHHHHHH
Q 022661 223 IINSRLDHAVAILE 236 (294)
Q Consensus 223 ~~~~rl~~A~e~Ie 236 (294)
.++.|.++|+
T Consensus 52 ----~v~~A~~~I~ 61 (61)
T cd02393 52 ----AAEKAKKMIE 61 (61)
T ss_pred ----HHHHHHHHhC
Confidence 5677887764
No 6
>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=98.33 E-value=2.1e-06 Score=61.86 Aligned_cols=62 Identities=29% Similarity=0.485 Sum_probs=46.1
Q ss_pred EEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchh
Q 022661 143 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPED 222 (294)
Q Consensus 143 ~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~ 222 (294)
.+|.|| -+++|+|+||+|.++++|+++|||+|.|...++ ...+-.|.|.+. .
T Consensus 2 ~~i~ip-------~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~------------------~~~~~~v~i~G~-~-- 53 (64)
T cd00105 2 ERVLVP-------SSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS------------------GSEERIVTITGT-P-- 53 (64)
T ss_pred EEEEEc-------hhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC------------------CCCceEEEEEcC-H--
Confidence 457777 378999999999999999999999999986433 123446788775 1
Q ss_pred HHHHHHHHHHHHH
Q 022661 223 IINSRLDHAVAIL 235 (294)
Q Consensus 223 ~~~~rl~~A~e~I 235 (294)
..+..|..+|
T Consensus 54 ---~~v~~a~~~i 63 (64)
T cd00105 54 ---EAVEKAKELI 63 (64)
T ss_pred ---HHHHHHHHHh
Confidence 2566666655
No 7
>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=98.30 E-value=4.1e-07 Score=65.85 Aligned_cols=60 Identities=30% Similarity=0.552 Sum_probs=45.8
Q ss_pred EEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCch
Q 022661 142 VIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPE 221 (294)
Q Consensus 142 ~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~ 221 (294)
+.+|.|| -.++|+|||++|.++|+|+++|||+|.|...+ +.-.|.|++ +++
T Consensus 1 T~~i~vp-------~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~---------------------~~~~v~I~G-~~~ 51 (60)
T PF00013_consen 1 TERIEVP-------SSLVGRIIGKKGSNIKEIEEETGVKIQIPDDD---------------------ERDIVTISG-SPE 51 (60)
T ss_dssp EEEEEEE-------HHHHHHHHTGGGHHHHHHHHHHTSEEEEESTT---------------------EEEEEEEEE-SHH
T ss_pred CEEEEEC-------HHHcCEEECCCCCcHHHhhhhcCeEEEEcCCC---------------------CcEEEEEEe-CHH
Confidence 3567777 47899999999999999999999999996431 223788888 543
Q ss_pred hHHHHHHHHHHHHH
Q 022661 222 DIINSRLDHAVAIL 235 (294)
Q Consensus 222 ~~~~~rl~~A~e~I 235 (294)
.+++|+++|
T Consensus 52 -----~v~~A~~~I 60 (60)
T PF00013_consen 52 -----QVEKAKKMI 60 (60)
T ss_dssp -----HHHHHHHHH
T ss_pred -----HHHHHHhhC
Confidence 566777765
No 8
>smart00322 KH K homology RNA-binding domain.
Probab=98.16 E-value=1.1e-05 Score=56.94 Aligned_cols=65 Identities=29% Similarity=0.513 Sum_probs=48.0
Q ss_pred EEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCch
Q 022661 142 VIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPE 221 (294)
Q Consensus 142 ~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~ 221 (294)
+.+|.||. +++|+|||++|.+++.|++.|||+|.+.+.++ ..-.|.|.++ +.
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 45677763 78899999999999999999999999975433 2336777776 22
Q ss_pred hHHHHHHHHHHHHHHhcc
Q 022661 222 DIINSRLDHAVAILENLL 239 (294)
Q Consensus 222 ~~~~~rl~~A~e~Ie~LL 239 (294)
.+..|.+.|.+.+
T Consensus 56 -----~v~~a~~~i~~~~ 68 (69)
T smart00322 56 -----NVEKAAELILEIL 68 (69)
T ss_pred -----HHHHHHHHHHHHh
Confidence 4566777776654
No 9
>PF13014 KH_3: KH domain
Probab=98.12 E-value=2.1e-06 Score=58.98 Aligned_cols=28 Identities=36% Similarity=0.682 Sum_probs=26.8
Q ss_pred eeeEEeCCCCchHHHHHHhhCCeEEEec
Q 022661 158 FVGRILGPRGNSLKRVEAMTECRVFIRG 185 (294)
Q Consensus 158 FvGrILGPrG~TlK~LE~eTGckI~IRG 185 (294)
|+|+|||++|.|+|+|+++|||+|.|--
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 6899999999999999999999999986
No 10
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.02 E-value=9.3e-06 Score=59.07 Aligned_cols=53 Identities=13% Similarity=0.317 Sum_probs=40.7
Q ss_pred ceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHH
Q 022661 157 NFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAIL 235 (294)
Q Consensus 157 NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~I 235 (294)
.++|+|||++|.++++|+++|||+|.|-..+ +..=.|.|++. ++ .+..|+++|
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 5678899999999999999999999998643 12226888886 22 466777765
No 11
>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=97.92 E-value=3.1e-05 Score=57.43 Aligned_cols=35 Identities=29% Similarity=0.543 Sum_probs=31.2
Q ss_pred EEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEe
Q 022661 143 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIR 184 (294)
Q Consensus 143 ~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IR 184 (294)
.|++|| -+.+|+|||.+|.++|+|+++|||+|.|-
T Consensus 2 ~r~~ip-------~~~vg~iIG~~G~~i~~i~~~tga~I~i~ 36 (65)
T cd02396 2 LRLLVP-------SSQAGSIIGKGGSTIKEIREETGAKIRVS 36 (65)
T ss_pred EEEEEC-------HHHcCeeECCCcHHHHHHHHHHCCEEEEc
Confidence 467777 37899999999999999999999999994
No 12
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=97.85 E-value=6.7e-06 Score=81.50 Aligned_cols=90 Identities=17% Similarity=0.013 Sum_probs=76.1
Q ss_pred eeEEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEec
Q 022661 139 VKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAE 218 (294)
Q Consensus 139 vk~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~ 218 (294)
++...|++|++| -|. ||.-+..=||+-.||..+|.+|+.++.||||||++-.- .-|. ..+||++|+|+..
T Consensus 208 ~~Y~~k~~v~~~-~P~-~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP-------~~G~-EsnEPMYI~i~h~ 277 (531)
T KOG1960|consen 208 RYYPNKALATDK-DPP-LYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREP-------NEGN-ESNEPMYIFSTHG 277 (531)
T ss_pred ccchhheecccC-Ccc-hhhhhhccCccchhhhhhhhhhhhhhhhccccccccCc-------cccc-ccCCceeEEeecC
Confidence 455568999998 688 99999999999999999999999999999999988632 1233 3799999999998
Q ss_pred CchhHHHHHHHHHHHHHHhccCCCC
Q 022661 219 FPEDIINSRLDHAVAILENLLKPVD 243 (294)
Q Consensus 219 ~~~~~~~~rl~~A~e~Ie~LL~p~~ 243 (294)
..+ -+.+|+.++.+|+.-+.
T Consensus 278 ~~~-----g~~~A~r~~~nl~~~v~ 297 (531)
T KOG1960|consen 278 NGN-----GENGAPRRKWNLEEKVY 297 (531)
T ss_pred Cch-----hhccchhHHHhHHHHHH
Confidence 876 46789999999998654
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=97.65 E-value=5.3e-05 Score=66.76 Aligned_cols=53 Identities=26% Similarity=0.441 Sum_probs=44.9
Q ss_pred eeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHHh
Q 022661 158 FVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILEN 237 (294)
Q Consensus 158 FvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 237 (294)
.+|||||+.|.|+|.||..|||+|.|-|+ .|.|.+ +++ +++.|.+.|+.
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~~-------------------------~v~i~G-~~~-----~~~~A~~~i~~ 147 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYGK-------------------------TVGIIG-DPE-----QVQIAREAIEM 147 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcCC-------------------------EEEEEC-CHH-----HHHHHHHHHHH
Confidence 69999999999999999999999998641 578887 443 67889999999
Q ss_pred ccCC
Q 022661 238 LLKP 241 (294)
Q Consensus 238 LL~p 241 (294)
|+.-
T Consensus 148 li~~ 151 (172)
T TIGR03665 148 LIEG 151 (172)
T ss_pred HHcC
Confidence 9863
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.58 E-value=0.0001 Score=65.41 Aligned_cols=53 Identities=26% Similarity=0.471 Sum_probs=43.4
Q ss_pred eeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHHh
Q 022661 158 FVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILEN 237 (294)
Q Consensus 158 FvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 237 (294)
.+|||||+.|.|.|.||..|||+|.|-++ .|.|.+ ++. +++.|.+.|+.
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 69999999999999999999999998531 266666 433 67888999998
Q ss_pred ccCC
Q 022661 238 LLKP 241 (294)
Q Consensus 238 LL~p 241 (294)
|+.-
T Consensus 154 li~g 157 (180)
T PRK13763 154 LIEG 157 (180)
T ss_pred HHcC
Confidence 8863
No 15
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.18 E-value=0.0008 Score=61.18 Aligned_cols=55 Identities=24% Similarity=0.404 Sum_probs=46.6
Q ss_pred eeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHHh
Q 022661 158 FVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILEN 237 (294)
Q Consensus 158 FvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 237 (294)
..|||||+.|.|.+.||.-|||.|.|.|+ +|.|-+. +. .++.|.+.|+.
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~-------------------------tVaiiG~-~~-----~v~iAr~AVem 160 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK-------------------------TVAIIGG-FE-----QVEIAREAVEM 160 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc-------------------------EEEEecC-hh-----hhHHHHHHHHH
Confidence 57999999999999999999999999995 6777764 33 57788999999
Q ss_pred ccCCCC
Q 022661 238 LLKPVD 243 (294)
Q Consensus 238 LL~p~~ 243 (294)
|+.-.+
T Consensus 161 li~G~~ 166 (194)
T COG1094 161 LINGAP 166 (194)
T ss_pred HHcCCC
Confidence 997544
No 16
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.08 E-value=0.00092 Score=59.43 Aligned_cols=57 Identities=23% Similarity=0.357 Sum_probs=47.0
Q ss_pred ceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEE---ecCchhHHHHHHHHHHH
Q 022661 157 NFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVE---AEFPEDIINSRLDHAVA 233 (294)
Q Consensus 157 NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~---a~~~~~~~~~rl~~A~e 233 (294)
+-+|.|+||.|.|.|.|+++|||+|.|--. .=.|.|. +.++. .+.+|++
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 678999999999999999999999999742 1167776 45543 6889999
Q ss_pred HHHhccCC
Q 022661 234 ILENLLKP 241 (294)
Q Consensus 234 ~Ie~LL~p 241 (294)
+|+.++..
T Consensus 64 ~I~ai~~g 71 (180)
T PRK13763 64 IVKAIGRG 71 (180)
T ss_pred HHHHHhcC
Confidence 99999884
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=96.83 E-value=0.0011 Score=58.50 Aligned_cols=57 Identities=21% Similarity=0.301 Sum_probs=45.7
Q ss_pred ceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEE--EecCchhHHHHHHHHHHHH
Q 022661 157 NFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLV--EAEFPEDIINSRLDHAVAI 234 (294)
Q Consensus 157 NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI--~a~~~~~~~~~rl~~A~e~ 234 (294)
+.+|.||||+|.|+|+|+++|||+|.|--. .=.|.| .+.++. .+.+|+++
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 789999999999999999999999999731 014666 344443 68899999
Q ss_pred HHhccCC
Q 022661 235 LENLLKP 241 (294)
Q Consensus 235 Ie~LL~p 241 (294)
|+.+...
T Consensus 59 I~~i~~g 65 (172)
T TIGR03665 59 VKAIGRG 65 (172)
T ss_pred HHHHHcC
Confidence 9998884
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=96.82 E-value=0.0035 Score=66.50 Aligned_cols=66 Identities=23% Similarity=0.483 Sum_probs=54.3
Q ss_pred eEEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecC
Q 022661 140 KRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEF 219 (294)
Q Consensus 140 k~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~ 219 (294)
-+...+.||. .-+|.||||+|.|+|.|+++|||+|.|-- +=+|.|.+.+
T Consensus 577 P~~~~~~I~~-------~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------------------------~G~V~I~a~d 625 (719)
T TIGR02696 577 PRIITVKIPV-------DKIGEVIGPKGKMINQIQDETGAEISIED------------------------DGTVYIGAAD 625 (719)
T ss_pred CeeEEEEeCh-------HHhhheeCCCcHhHHHHHHHHCCEEEEec------------------------CcEEEEEeCC
Confidence 3445677874 46899999999999999999999998853 2379999987
Q ss_pred chhHHHHHHHHHHHHHHhccCC
Q 022661 220 PEDIINSRLDHAVAILENLLKP 241 (294)
Q Consensus 220 ~~~~~~~rl~~A~e~Ie~LL~p 241 (294)
.+ ++++|++.|+.+..+
T Consensus 626 ~~-----~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 626 GP-----SAEAARAMINAIANP 642 (719)
T ss_pred HH-----HHHHHHHHHHHhhCc
Confidence 54 789999999999984
No 19
>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=96.27 E-value=0.0075 Score=63.63 Aligned_cols=64 Identities=17% Similarity=0.337 Sum_probs=50.4
Q ss_pred EEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCc
Q 022661 141 RVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFP 220 (294)
Q Consensus 141 ~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~ 220 (294)
+...+.||. ..+|.||||+|.|+|.|+++|||+|.|-- +=+|.|.+.+.
T Consensus 551 ~~~~~~I~~-------~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------------------------dG~V~i~~~~~ 599 (684)
T TIGR03591 551 RIETIKINP-------DKIRDVIGPGGKVIREITEETGAKIDIED------------------------DGTVKIAASDG 599 (684)
T ss_pred eEEEEecCH-------HHHHhhcCCCcHHHHHHHHHHCCEEEEec------------------------CeEEEEEECcH
Confidence 345566763 56889999999999999999999999942 22788888774
Q ss_pred hhHHHHHHHHHHHHHHhccC
Q 022661 221 EDIINSRLDHAVAILENLLK 240 (294)
Q Consensus 221 ~~~~~~rl~~A~e~Ie~LL~ 240 (294)
+ .+++|.+.|+.+..
T Consensus 600 ~-----~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 600 E-----AAEAAIKMIEGITA 614 (684)
T ss_pred H-----HHHHHHHHHHhhhc
Confidence 3 67889999988865
No 20
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.17 E-value=0.0016 Score=65.47 Aligned_cols=38 Identities=32% Similarity=0.652 Sum_probs=34.1
Q ss_pred ecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEe
Q 022661 146 DVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIR 184 (294)
Q Consensus 146 ~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IR 184 (294)
.||++---. -||||||||--|.++|.||++||+||.|-
T Consensus 279 e~pLk~lAH-N~lvGRLIGKeGrnlKkIeq~TgTkITis 316 (584)
T KOG2193|consen 279 EIPLKILAH-NNLVGRLIGKEGRNLKKIEQDTGTKITIS 316 (584)
T ss_pred hcchhhhhh-cchhhhhhhhccccHHHHHhhcCCceeee
Confidence 577776666 79999999999999999999999999995
No 21
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=95.90 E-value=0.007 Score=65.65 Aligned_cols=66 Identities=20% Similarity=0.192 Sum_probs=53.4
Q ss_pred eEEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCe-EEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEec
Q 022661 140 KRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECR-VFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAE 218 (294)
Q Consensus 140 k~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGck-I~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~ 218 (294)
-+...+.|| -+-||.||||+|.|+|.|+++||++ |-|+ |+-+|.|.+.
T Consensus 684 P~i~~~~i~-------~~ki~~vIG~GGktIk~I~eetg~~~Idi~------------------------ddg~V~I~a~ 732 (891)
T PLN00207 684 PLIHIMKVK-------PEKVNMIIGSGGKKVKSIIEETGVEAIDTQ------------------------DDGTVKITAK 732 (891)
T ss_pred CeeEEEEcC-------HHHHHHHhcCCchhHHHHHHHHCCCccCcC------------------------CCeeEEEEeC
Confidence 344567776 3578999999999999999999998 7665 3468999988
Q ss_pred CchhHHHHHHHHHHHHHHhccCC
Q 022661 219 FPEDIINSRLDHAVAILENLLKP 241 (294)
Q Consensus 219 ~~~~~~~~rl~~A~e~Ie~LL~p 241 (294)
+.+ +++.|+++|+.+..-
T Consensus 733 d~~-----~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 733 DLS-----SLEKSKAIISSLTMV 750 (891)
T ss_pred CHH-----HHHHHHHHHHHHhcC
Confidence 854 789999999998763
No 22
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=95.83 E-value=0.018 Score=55.54 Aligned_cols=77 Identities=30% Similarity=0.463 Sum_probs=53.0
Q ss_pred eEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHHhcc
Q 022661 160 GRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILENLL 239 (294)
Q Consensus 160 GrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL 239 (294)
.|||||.|+|||.||--|.|-|.|-|. -|-+. ++ +..|..+..+|++.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~-------------------------TVsai--Gp----fkGlkevr~IV~DcM 209 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN-------------------------TVSAI--GP----FKGLKEVRKIVEDCM 209 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc-------------------------EEEee--cC----cchHHHHHHHHHHHH
Confidence 589999999999999999999999995 22222 22 236778888888888
Q ss_pred CCCCcchhHHH-HHHHHHHHHHcCccCCCCC
Q 022661 240 KPVDESLDHYK-KQQLRELAMLNGTLREESP 269 (294)
Q Consensus 240 ~p~~e~~delK-~~QL~ELA~lNGt~r~~~~ 269 (294)
..++.-.+ +| -+--||||- +-++++++|
T Consensus 210 ~NiHPiY~-IK~LmiKRel~k-d~~l~ne~W 238 (356)
T KOG2874|consen 210 KNIHPIYN-IKTLMIKRELAK-DPELANEDW 238 (356)
T ss_pred hccchHHH-HHHHHHHHHhhc-ChhhccccH
Confidence 76664443 33 222345543 456666666
No 23
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=95.81 E-value=0.017 Score=59.99 Aligned_cols=61 Identities=21% Similarity=0.463 Sum_probs=44.6
Q ss_pred ceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcE-EEEEecCchhHHHHHHHHHHHHH
Q 022661 157 NFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLH-VLVEAEFPEDIINSRLDHAVAIL 235 (294)
Q Consensus 157 NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLH-VlI~a~~~~~~~~~rl~~A~e~I 235 (294)
+=||.|||=.|.|+|+|+.+||+||.++= |. +| .-++. +.|. ...+ ++.+|.++|
T Consensus 239 ~~VG~IIGkgGE~IKklq~etG~KIQfkp-----Dd--------~p-----~speR~~~Ii--G~~d----~ie~Aa~lI 294 (600)
T KOG1676|consen 239 SKVGIIIGKGGEMIKKLQNETGAKIQFKP-----DD--------DP-----SSPERPAQII--GTVD----QIEHAAELI 294 (600)
T ss_pred cceeeEEecCchHHHHHhhccCceeEeec-----CC--------CC-----CCccceeeee--cCHH----HHHHHHHHH
Confidence 77999999999999999999999999983 21 11 11222 2333 3332 778999999
Q ss_pred HhccCC
Q 022661 236 ENLLKP 241 (294)
Q Consensus 236 e~LL~p 241 (294)
.+||.-
T Consensus 295 ~eii~~ 300 (600)
T KOG1676|consen 295 NEIIAE 300 (600)
T ss_pred HHHHHH
Confidence 999874
No 24
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=95.65 E-value=0.025 Score=58.72 Aligned_cols=74 Identities=20% Similarity=0.535 Sum_probs=56.6
Q ss_pred ceeEEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEe
Q 022661 138 VVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEA 217 (294)
Q Consensus 138 ~vk~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a 217 (294)
.++.+.+|.||- |=+|+|||=.|-|+|+|++.||||+.+-=-|+.-+. .+-||. |++
T Consensus 136 ~~~ttqeI~IPa-------~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~--------------~~Kplr--itG 192 (600)
T KOG1676|consen 136 SVETTQEILIPA-------NKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG--------------ADKPLR--ITG 192 (600)
T ss_pred ccceeeeeccCc-------cceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC--------------CCCcee--ecC
Confidence 356677788882 678999999999999999999999988766664432 234444 455
Q ss_pred cCchhHHHHHHHHHHHHHHhccC
Q 022661 218 EFPEDIINSRLDHAVAILENLLK 240 (294)
Q Consensus 218 ~~~~~~~~~rl~~A~e~Ie~LL~ 240 (294)
+ + .++.+|.++|.++|.
T Consensus 193 d-p-----~~ve~a~~lV~dil~ 209 (600)
T KOG1676|consen 193 D-P-----DKVEQAKQLVADILR 209 (600)
T ss_pred C-H-----HHHHHHHHHHHHHHH
Confidence 3 3 278999999999998
No 25
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.75 E-value=0.035 Score=51.28 Aligned_cols=56 Identities=18% Similarity=0.382 Sum_probs=45.6
Q ss_pred CceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHH
Q 022661 156 FNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAIL 235 (294)
Q Consensus 156 ~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~I 235 (294)
-+.+++||||+|.+++.|.++|+|+|.| |. | =.|+|.+.+.+ .+..|++.|
T Consensus 153 ~~~i~~lig~~g~~i~~l~~~~~~~I~i-g~---------------------N--G~VwI~~~~~~-----~~~~a~~~I 203 (235)
T PRK04163 153 PVKVPRVIGKKGSMINMLKEETGCDIIV-GQ---------------------N--GRIWIKGPDEE-----DEEIAIEAI 203 (235)
T ss_pred HHHHHhhcCCCChhHhhhhhhhCcEEEE-cC---------------------C--cEEEEeeCCHH-----HHHHHHHHH
Confidence 4789999999999999999999999988 21 1 17999998865 466788888
Q ss_pred HhccC
Q 022661 236 ENLLK 240 (294)
Q Consensus 236 e~LL~ 240 (294)
+.+-.
T Consensus 204 ~~~e~ 208 (235)
T PRK04163 204 KKIER 208 (235)
T ss_pred HHHHh
Confidence 77665
No 26
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=94.40 E-value=0.035 Score=58.79 Aligned_cols=57 Identities=18% Similarity=0.276 Sum_probs=46.3
Q ss_pred CceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHH
Q 022661 156 FNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAIL 235 (294)
Q Consensus 156 ~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~I 235 (294)
..-+|.+|||+|.|+|.|+++||++|-|+ |+-+|.|.+.+.+ .+++|.+.|
T Consensus 562 ~~kI~~vIG~gg~~ik~I~~~~~~~idi~------------------------d~G~v~i~~~~~~-----~~~~a~~~I 612 (693)
T PRK11824 562 PDKIRDVIGPGGKTIREITEETGAKIDIE------------------------DDGTVKIAATDGE-----AAEAAKERI 612 (693)
T ss_pred HHHHHHHhcCCchhHHHHHHHHCCccccC------------------------CCceEEEEcccHH-----HHHHHHHHH
Confidence 35589999999999999999999988774 2346888887743 788999999
Q ss_pred HhccCC
Q 022661 236 ENLLKP 241 (294)
Q Consensus 236 e~LL~p 241 (294)
+.+...
T Consensus 613 ~~~~~~ 618 (693)
T PRK11824 613 EGITAE 618 (693)
T ss_pred HHhccc
Confidence 988763
No 27
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=94.37 E-value=0.06 Score=52.73 Aligned_cols=60 Identities=17% Similarity=0.315 Sum_probs=45.0
Q ss_pred ceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchhH--HHHHHHHHHHH
Q 022661 157 NFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDI--INSRLDHAVAI 234 (294)
Q Consensus 157 NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~~--~~~rl~~A~e~ 234 (294)
-|+|.|+|-+|.|.|.||+||+|+|.+=-.+..+ =|+-|++-.-.++ |..||+.++.-
T Consensus 66 ~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~--------------------~~i~i~~~~~~~V~~a~~Ri~~~ids 125 (345)
T KOG2814|consen 66 SFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNK--------------------EEIKIIGISRNCVIQALERIAKLIDS 125 (345)
T ss_pred HHhhhhhcccchHHHHHHHhhccceEccCCCCCc--------------------ceEEEeehhHHHHHHHHHHHHHHHHh
Confidence 6899999999999999999999999986443322 1788887654443 45577777666
Q ss_pred HH
Q 022661 235 LE 236 (294)
Q Consensus 235 Ie 236 (294)
..
T Consensus 126 ~r 127 (345)
T KOG2814|consen 126 DR 127 (345)
T ss_pred hh
Confidence 65
No 28
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=92.82 E-value=0.49 Score=46.82 Aligned_cols=38 Identities=24% Similarity=0.452 Sum_probs=32.5
Q ss_pred EEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEec
Q 022661 141 RVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRG 185 (294)
Q Consensus 141 ~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRG 185 (294)
++.||.+|- --.|.|||+.|.|+|.+.+++||-|.|--
T Consensus 132 kqikivvPN-------stag~iigkggAtiK~~~Eqsga~iqisP 169 (402)
T KOG2191|consen 132 KQIKIVVPN-------STAGMIIGKGGATIKAIQEQSGAWIQISP 169 (402)
T ss_pred ceeEEeccC-------CcccceecCCcchHHHHHHhhCcceEecc
Confidence 456788883 44689999999999999999999999974
No 29
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=92.72 E-value=0.11 Score=51.18 Aligned_cols=37 Identities=19% Similarity=0.415 Sum_probs=33.4
Q ss_pred EEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEe
Q 022661 141 RVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIR 184 (294)
Q Consensus 141 ~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IR 184 (294)
+..||+|| -+-+|-|||-.|.|+.+||++|||+|.+-
T Consensus 39 y~ikvLip-------s~AaGsIIGKGG~ti~~lqk~tgariklS 75 (402)
T KOG2191|consen 39 YFLKVLIP-------SYAAGSIIGKGGQTIVQLQKETGARIKLS 75 (402)
T ss_pred eEEEEEee-------cccccceeccchHHHHHHHhccCcEEEec
Confidence 56789998 36789999999999999999999999886
No 30
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=92.60 E-value=0.14 Score=51.96 Aligned_cols=31 Identities=26% Similarity=0.591 Sum_probs=28.6
Q ss_pred CceeeEEeCCCCchHHHHHHhhCCeEEEecc
Q 022661 156 FNFVGRILGPRGNSLKRVEAMTECRVFIRGR 186 (294)
Q Consensus 156 ~NFvGrILGPrG~TlK~LE~eTGckI~IRGr 186 (294)
--|+|-||||.|.|+|-|-+.|.|||-+--+
T Consensus 207 tqyvgaIIGkeG~TIknItkqTqsriD~hrk 237 (584)
T KOG2193|consen 207 TQYVGAIIGKEGATIKNITKQTQSRIDVHRK 237 (584)
T ss_pred cceeEEEecCCCccccCcchhhhheeeeeec
Confidence 4899999999999999999999999998753
No 31
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=90.77 E-value=0.93 Score=46.54 Aligned_cols=40 Identities=25% Similarity=0.424 Sum_probs=36.4
Q ss_pred eEEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEecc
Q 022661 140 KRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGR 186 (294)
Q Consensus 140 k~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGr 186 (294)
..+.|++|| -+-+|-|||=+|..+|.|.++|||+|.|.+.
T Consensus 137 ~v~~RLlVp-------~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~ 176 (485)
T KOG2190|consen 137 EVTCRLLVP-------SSQVGSLIGKGGSLIKEIREETGAKIRVSSD 176 (485)
T ss_pred ceEEEEEec-------hhheeeeeccCcHHHHHHHHhcCceEEecCC
Confidence 456889999 4779999999999999999999999999985
No 32
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=88.86 E-value=0.62 Score=49.58 Aligned_cols=64 Identities=23% Similarity=0.417 Sum_probs=48.5
Q ss_pred EEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCc
Q 022661 141 RVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFP 220 (294)
Q Consensus 141 ~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~ 220 (294)
+.+-+-|+++...+ +|||.|.|.|.|.++|||+|.|--.|+ |.|.+.+.
T Consensus 552 ri~t~~i~~dKI~d-------vIG~gGk~I~~I~eetg~~IdieddGt------------------------v~i~~s~~ 600 (692)
T COG1185 552 RIETIKIDPDKIRD-------VIGPGGKTIKAITEETGVKIDIEDDGT------------------------VKIAASDG 600 (692)
T ss_pred ceEEEccCHHHHhh-------ccCCcccchhhhhhhhCcEEEecCCCc------------------------EEEEecch
Confidence 34456688777665 899999999999999999999975555 45555553
Q ss_pred hhHHHHHHHHHHHHHHhccC
Q 022661 221 EDIINSRLDHAVAILENLLK 240 (294)
Q Consensus 221 ~~~~~~rl~~A~e~Ie~LL~ 240 (294)
+ +..+|++.|+.+..
T Consensus 601 ~-----~~~~ak~~I~~i~~ 615 (692)
T COG1185 601 E-----SAKKAKERIEAITR 615 (692)
T ss_pred H-----HHHHHHHHHHHHHh
Confidence 2 56778888888774
No 33
>PRK00106 hypothetical protein; Provisional
Probab=88.85 E-value=0.72 Score=47.92 Aligned_cols=57 Identities=33% Similarity=0.492 Sum_probs=46.7
Q ss_pred CceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHH
Q 022661 156 FNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAIL 235 (294)
Q Consensus 156 ~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~I 235 (294)
=.+-|||||--|-++|.+|.-||+-|.|= |.|=-|.|++.||. |-.-|..-+
T Consensus 234 demkGriIGreGrNir~~E~~tGvdliid-----------------------dtp~~v~lS~fdpv-----RReiAr~~l 285 (535)
T PRK00106 234 DNMKGRIIGREGRNIRTLESLTGIDVIID-----------------------DTPEVVVLSGFDPI-----RREIARMTL 285 (535)
T ss_pred hHhhcceeCCCcchHHHHHHHhCceEEEc-----------------------CCCCeEEEeCCChH-----HHHHHHHHH
Confidence 46779999999999999999999999983 34557999999986 445677777
Q ss_pred HhccC
Q 022661 236 ENLLK 240 (294)
Q Consensus 236 e~LL~ 240 (294)
++|+.
T Consensus 286 e~Li~ 290 (535)
T PRK00106 286 ESLIK 290 (535)
T ss_pred HHHHH
Confidence 77776
No 34
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=88.82 E-value=0.17 Score=51.10 Aligned_cols=72 Identities=28% Similarity=0.500 Sum_probs=58.9
Q ss_pred EEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHHhccC
Q 022661 161 RILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILENLLK 240 (294)
Q Consensus 161 rILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL~ 240 (294)
-|.||.|.+.|.++.+|-+++.|.|-||..-. ..+.. ..++|.||.|.+.++. .|+.|+-++++++-
T Consensus 308 ~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i~-------p~~~~-~~~~p~~~~~~~~~~~-----~~~~~~~~~~~~i~ 374 (531)
T KOG1960|consen 308 AIVGPQGAYVKHIQQETRTRVQIKGQGSAFIE-------PSTNR-ESDEPIHLCIMSHDPN-----AIQRAKVLCEDLIA 374 (531)
T ss_pred ccccCCcccccccCCCCCcceeccCccceeec-------CCCCC-CCCCCcccccccCChh-----hhhhhhhcccccCC
Confidence 36799999999999999999999999998742 22333 3789999999998765 46778889999999
Q ss_pred CCCcc
Q 022661 241 PVDES 245 (294)
Q Consensus 241 p~~e~ 245 (294)
|++..
T Consensus 375 ~v~~q 379 (531)
T KOG1960|consen 375 SVHQQ 379 (531)
T ss_pred ccccc
Confidence 88743
No 35
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=87.63 E-value=0.82 Score=47.07 Aligned_cols=57 Identities=28% Similarity=0.472 Sum_probs=44.4
Q ss_pred CceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHH
Q 022661 156 FNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAIL 235 (294)
Q Consensus 156 ~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~I 235 (294)
=.+-|||||--|-++|.+|..||+-|.|= |.|=-|.|++.||. |=.-|..-+
T Consensus 213 d~~kgriigreGrnir~~e~~tgvd~iid-----------------------dtp~~v~ls~fdp~-----rreia~~~l 264 (514)
T TIGR03319 213 DEMKGRIIGREGRNIRALETLTGVDLIID-----------------------DTPEAVILSGFDPV-----RREIARMAL 264 (514)
T ss_pred hhhhccccCCCcchHHHHHHHhCceEEEc-----------------------CCCCeEEecCCchH-----HHHHHHHHH
Confidence 46779999999999999999999999983 23447889999986 334455566
Q ss_pred HhccC
Q 022661 236 ENLLK 240 (294)
Q Consensus 236 e~LL~ 240 (294)
++|+.
T Consensus 265 ~~li~ 269 (514)
T TIGR03319 265 EKLIQ 269 (514)
T ss_pred HHHHH
Confidence 66664
No 36
>PRK12704 phosphodiesterase; Provisional
Probab=86.86 E-value=3.4 Score=42.70 Aligned_cols=44 Identities=25% Similarity=0.462 Sum_probs=37.7
Q ss_pred CceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchh
Q 022661 156 FNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPED 222 (294)
Q Consensus 156 ~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~ 222 (294)
=.+-|||||--|-++|.+|+-||+-|.|= |.|=-|+|++.+|..
T Consensus 219 d~mkgriigreGrnir~~e~~tgvd~iid-----------------------dtp~~v~ls~~~~~r 262 (520)
T PRK12704 219 DEMKGRIIGREGRNIRALETLTGVDLIID-----------------------DTPEAVILSGFDPIR 262 (520)
T ss_pred chhhcceeCCCcchHHHHHHHhCCeEEEc-----------------------CCCCeEEEecCChhh
Confidence 45779999999999999999999999983 345579999999875
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=85.85 E-value=0.8 Score=33.79 Aligned_cols=36 Identities=22% Similarity=0.374 Sum_probs=29.6
Q ss_pred EEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEE
Q 022661 141 RVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFI 183 (294)
Q Consensus 141 ~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~I 183 (294)
...+|+||.+ -+|+.||.+|.+++.++..+|.+|.|
T Consensus 25 ~~~~v~V~~~-------~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDD-------QLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcc-------cceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3456777753 47899999999999999999998876
No 38
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=85.52 E-value=1.5 Score=44.91 Aligned_cols=29 Identities=31% Similarity=0.604 Sum_probs=27.5
Q ss_pred CceeeEEeCCCCchHHHHHHhhCCeEEEe
Q 022661 156 FNFVGRILGPRGNSLKRVEAMTECRVFIR 184 (294)
Q Consensus 156 ~NFvGrILGPrG~TlK~LE~eTGckI~IR 184 (294)
-||||.+||=.|+.+|+||..|+++|.|-
T Consensus 55 s~mvg~vigrggskik~iq~~tnt~iqii 83 (629)
T KOG0336|consen 55 SEMVGKVIGRGGSKIKRIQNDTNTRIQII 83 (629)
T ss_pred hhhhheeeccCcchhhhhhcccceeEEEe
Confidence 49999999999999999999999999985
No 39
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=84.49 E-value=0.97 Score=46.42 Aligned_cols=42 Identities=24% Similarity=0.395 Sum_probs=36.4
Q ss_pred ceeEEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEecc
Q 022661 138 VVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGR 186 (294)
Q Consensus 138 ~vk~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGr 186 (294)
....+.++.|| .+++|.|||..|+.+-.|++.|||.|.|.++
T Consensus 335 ~~~v~~~l~vp-------s~~igciiGk~G~~iseir~~tgA~I~I~~~ 376 (485)
T KOG2190|consen 335 TQTVTQRLLVP-------SDLIGCIIGKGGAKISEIRQRTGASISILNK 376 (485)
T ss_pred cceeeeeeccC-------ccccceeecccccchHHHHHhcCCceEEccc
Confidence 34455678887 5999999999999999999999999999875
No 40
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=78.30 E-value=0.83 Score=34.98 Aligned_cols=31 Identities=23% Similarity=0.452 Sum_probs=24.2
Q ss_pred CCCCceeeEEeCCCCchHHHHHHhh-CCeEEEe
Q 022661 153 PNQFNFVGRILGPRGNSLKRVEAMT-ECRVFIR 184 (294)
Q Consensus 153 P~~~NFvGrILGPrG~TlK~LE~eT-GckI~IR 184 (294)
|+ ++-+|..+|.+|..+|.|+++. |-||.|=
T Consensus 14 ~~-~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 14 PN-IDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp TT-S-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred CC-cCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 77 9999999999999999999999 5555443
No 41
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=73.87 E-value=3 Score=44.13 Aligned_cols=54 Identities=17% Similarity=0.244 Sum_probs=42.7
Q ss_pred eeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHHh
Q 022661 158 FVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILEN 237 (294)
Q Consensus 158 FvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 237 (294)
=+..+|||.|..+|+|+.|||+.-+| ++=|+-|-|.++. .|.+|.+.|..
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 45679999999999999999944332 2338888888854 68999999999
Q ss_pred ccCC
Q 022661 238 LLKP 241 (294)
Q Consensus 238 LL~p 241 (294)
+..-
T Consensus 657 i~~~ 660 (760)
T KOG1067|consen 657 IIKD 660 (760)
T ss_pred HhcC
Confidence 8874
No 42
>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=72.65 E-value=3.4 Score=29.20 Aligned_cols=23 Identities=13% Similarity=0.485 Sum_probs=20.5
Q ss_pred eeEEeCCCCchHHHHHHhhCCeE
Q 022661 159 VGRILGPRGNSLKRVEAMTECRV 181 (294)
Q Consensus 159 vGrILGPrG~TlK~LE~eTGckI 181 (294)
.|+++|.+|.+++.|+..++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 58999999999999999998554
No 43
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=67.12 E-value=16 Score=33.63 Aligned_cols=28 Identities=25% Similarity=0.475 Sum_probs=26.3
Q ss_pred eeEEeCCCCchHHHHHHhhCCeEEEecc
Q 022661 159 VGRILGPRGNSLKRVEAMTECRVFIRGR 186 (294)
Q Consensus 159 vGrILGPrG~TlK~LE~eTGckI~IRGr 186 (294)
+|-|+|+.|.+.|.||+.+||+|.|=.+
T Consensus 19 ~~~lig~~g~v~k~ie~~~~~~~~iD~~ 46 (194)
T COG1094 19 IGVLIGKWGEVKKAIEEKTGVKLRIDSK 46 (194)
T ss_pred heeeecccccchHHHHhhcCeEEEEECC
Confidence 6899999999999999999999999876
No 44
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=62.78 E-value=5.5 Score=34.35 Aligned_cols=29 Identities=21% Similarity=0.289 Sum_probs=26.9
Q ss_pred ceeeEEeCCCCchHHHHHHhhCCeEEEec
Q 022661 157 NFVGRILGPRGNSLKRVEAMTECRVFIRG 185 (294)
Q Consensus 157 NFvGrILGPrG~TlK~LE~eTGckI~IRG 185 (294)
+.+|..+|++|...|.|++..|-||-|=.
T Consensus 41 ~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 41 GDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 57899999999999999999999998876
No 45
>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=61.54 E-value=5.4 Score=30.50 Aligned_cols=21 Identities=24% Similarity=0.646 Sum_probs=19.0
Q ss_pred eeEEeCCCCchHHHHHHhhCC
Q 022661 159 VGRILGPRGNSLKRVEAMTEC 179 (294)
Q Consensus 159 vGrILGPrG~TlK~LE~eTGc 179 (294)
.|+|||-+|.|++.||--+..
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~ 55 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANL 55 (77)
T ss_pred CCeEECCCCccHHHHHHHHHH
Confidence 599999999999999988774
No 46
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=56.26 E-value=9.2 Score=36.19 Aligned_cols=29 Identities=24% Similarity=0.524 Sum_probs=26.6
Q ss_pred CceeeEEeCCCCchHHHHHHhhCCeEEEe
Q 022661 156 FNFVGRILGPRGNSLKRVEAMTECRVFIR 184 (294)
Q Consensus 156 ~NFvGrILGPrG~TlK~LE~eTGckI~IR 184 (294)
.++|-|+||.+|+-++-|.+.|+|+|.|=
T Consensus 154 p~kVpRvig~~~sm~~~l~~~~~~~I~VG 182 (239)
T COG1097 154 PSKVPRVIGKKGSMLNMLKEKTGCEIIVG 182 (239)
T ss_pred hhhcceEecCCCcHHHHhhhhcCeEEEEe
Confidence 47788999999999999999999999984
No 47
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=52.78 E-value=8.6 Score=42.86 Aligned_cols=76 Identities=24% Similarity=0.328 Sum_probs=57.2
Q ss_pred ecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHH
Q 022661 146 DVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIIN 225 (294)
Q Consensus 146 ~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~~~~~~~ 225 (294)
-.+++.||- |..+++.+=-- |.+|...|+|.|++||+=--... .| ....+-||.+|++.+.
T Consensus 901 ~~~inD~Pq--~~r~~vt~~~~--L~~i~e~~~~~it~rg~f~~~gk--------~p--~~gErklyl~ve~~~e----- 961 (997)
T KOG0334|consen 901 ELEINDFPQ--NARWRVTYKEA--LLRISEPTAAGITTRGKFNPPGK--------EP--KPGERKLYLLVEGPDE----- 961 (997)
T ss_pred eccccccch--hcceeeechhh--hhhccCccccceeeccccCCCCC--------CC--CCcchhhhhhhhcchh-----
Confidence 467789997 89999988654 99999999999999997321111 12 2356889999997663
Q ss_pred HHHHHHHHHHHhccC
Q 022661 226 SRLDHAVAILENLLK 240 (294)
Q Consensus 226 ~rl~~A~e~Ie~LL~ 240 (294)
.-+++|++.++.+|.
T Consensus 962 ~~vqra~~e~~r~l~ 976 (997)
T KOG0334|consen 962 LSVQRAIEELERLLE 976 (997)
T ss_pred HHHHHHHHHHHHHHH
Confidence 357889999988665
No 48
>PRK12705 hypothetical protein; Provisional
Probab=52.19 E-value=8.5 Score=39.95 Aligned_cols=29 Identities=28% Similarity=0.540 Sum_probs=26.5
Q ss_pred CceeeEEeCCCCchHHHHHHhhCCeEEEe
Q 022661 156 FNFVGRILGPRGNSLKRVEAMTECRVFIR 184 (294)
Q Consensus 156 ~NFvGrILGPrG~TlK~LE~eTGckI~IR 184 (294)
=.+-|||||--|.++|.+|..||+-|.|=
T Consensus 207 demkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 207 DAMKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred hHhhccccCccchhHHHHHHhhCCceEec
Confidence 56789999999999999999999988874
No 49
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=51.31 E-value=10 Score=41.02 Aligned_cols=39 Identities=15% Similarity=0.396 Sum_probs=30.6
Q ss_pred eeEEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEe
Q 022661 139 VKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIR 184 (294)
Q Consensus 139 vk~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IR 184 (294)
+..+..++||.+-|- -|+||+|.++++++.+++|-+.+-
T Consensus 707 ~~~~~~~~~p~~~~~-------~~ig~~g~~~r~~~~~~~~~~~~~ 745 (753)
T KOG2208|consen 707 NLVTKEIEIPRSLHR-------YLIGPKGSNLRQLEKEFNVNIVVP 745 (753)
T ss_pred cceeeEEeccHHHhh-------hccCCCCccHHHHHHHhccceecC
Confidence 334456777765544 599999999999999999988764
No 50
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=47.28 E-value=34 Score=34.14 Aligned_cols=30 Identities=23% Similarity=0.398 Sum_probs=27.6
Q ss_pred ceeeEEeCCCCchHHHHHHhhCCeEEEecc
Q 022661 157 NFVGRILGPRGNSLKRVEAMTECRVFIRGR 186 (294)
Q Consensus 157 NFvGrILGPrG~TlK~LE~eTGckI~IRGr 186 (294)
|-+--|+||.|..++.||+.+|+.|.-||.
T Consensus 24 ~~~~~l~G~~~~~l~l~e~~~gv~i~~rG~ 53 (348)
T COG1702 24 NELVALFGPTDTNLSLLEIALGVSIVARGE 53 (348)
T ss_pred hhhhhhcCCCCccHHHHHHHhCcEEEeCCc
Confidence 667779999999999999999999999985
No 51
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=45.58 E-value=17 Score=36.15 Aligned_cols=37 Identities=24% Similarity=0.373 Sum_probs=30.5
Q ss_pred eeEEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEE
Q 022661 139 VKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVF 182 (294)
Q Consensus 139 vk~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~ 182 (294)
..+++.|-+| | -||+.|.|++|-+.|.|+++|.+.|.
T Consensus 24 ~nvt~sv~vp---s----~~v~~ivg~qg~kikalr~KTqtyi~ 60 (394)
T KOG2113|consen 24 QNVTESVEVP---S----EHVAEIVGRQGCKIKALRAKTQTYIK 60 (394)
T ss_pred CccceeeecC---c----ccceeecccCccccchhhhhhcceec
Confidence 4555666666 3 47999999999999999999999875
No 52
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=44.87 E-value=21 Score=35.50 Aligned_cols=33 Identities=21% Similarity=0.413 Sum_probs=29.6
Q ss_pred CCCCCceeeEEeCCCCchHHHHHHhh-CCeEEEec
Q 022661 152 YPNQFNFVGRILGPRGNSLKRVEAMT-ECRVFIRG 185 (294)
Q Consensus 152 yP~~~NFvGrILGPrG~TlK~LE~eT-GckI~IRG 185 (294)
-|+ ++-||..+|++|..++.+.++. |=||-|=-
T Consensus 241 ~~~-iDpvGa~iG~~G~rI~~i~~el~gekIdiv~ 274 (362)
T PRK12327 241 NPN-VDAKGACVGPKGQRVQNIVSELKGEKIDIID 274 (362)
T ss_pred CCC-CCchheeECCCChhHHHHHHHhCCCeEEEEE
Confidence 488 9999999999999999999999 88887754
No 53
>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=43.35 E-value=26 Score=34.50 Aligned_cols=33 Identities=21% Similarity=0.363 Sum_probs=29.3
Q ss_pred CCCCCceeeEEeCCCCchHHHHHHhh-CCeEEEec
Q 022661 152 YPNQFNFVGRILGPRGNSLKRVEAMT-ECRVFIRG 185 (294)
Q Consensus 152 yP~~~NFvGrILGPrG~TlK~LE~eT-GckI~IRG 185 (294)
-|+ ++-||..+|++|..++.|.++. |=+|-|=-
T Consensus 239 ~~~-iDpvga~vG~~G~ri~~i~~el~ge~Idiv~ 272 (341)
T TIGR01953 239 DEN-IDPVGACVGPKGSRIQAISKELNGEKIDIIE 272 (341)
T ss_pred CCC-CCcceeeECCCCchHHHHHHHhCCCeEEEEE
Confidence 478 9999999999999999999999 77777654
No 54
>PRK02821 hypothetical protein; Provisional
Probab=39.30 E-value=17 Score=28.55 Aligned_cols=21 Identities=14% Similarity=0.450 Sum_probs=17.7
Q ss_pred eeeEEeCCCCchHHHHHHhhC
Q 022661 158 FVGRILGPRGNSLKRVEAMTE 178 (294)
Q Consensus 158 FvGrILGPrG~TlK~LE~eTG 178 (294)
=+|||||=+|.|++.|-.-..
T Consensus 41 D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 41 DLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred hCcceeCCCCchHHHHHHHHH
Confidence 489999999999999876544
No 55
>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=38.31 E-value=32 Score=31.73 Aligned_cols=40 Identities=23% Similarity=0.424 Sum_probs=28.8
Q ss_pred eeEEEEEecCCCCCCCCCceeeEEeCCCCchHHHH--------HHhhCCeEEEe
Q 022661 139 VKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRV--------EAMTECRVFIR 184 (294)
Q Consensus 139 vk~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~L--------E~eTGckI~IR 184 (294)
+.....|+|.-+.+ -|-|||.+|.++|+| |+-.||+|.+.
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 44455566665443 468999999999986 66778888764
No 56
>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=37.73 E-value=25 Score=30.56 Aligned_cols=29 Identities=21% Similarity=0.367 Sum_probs=26.7
Q ss_pred ceeeEEeCCCCchHHHHHHhhCCeEEEec
Q 022661 157 NFVGRILGPRGNSLKRVEAMTECRVFIRG 185 (294)
Q Consensus 157 NFvGrILGPrG~TlK~LE~eTGckI~IRG 185 (294)
+-+|..+|++|...|.|++..|=||-|=.
T Consensus 42 g~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 42 GEMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred CCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 56899999999999999999999998877
No 57
>PRK00468 hypothetical protein; Provisional
Probab=37.02 E-value=20 Score=28.02 Aligned_cols=19 Identities=21% Similarity=0.641 Sum_probs=16.3
Q ss_pred eeEEeCCCCchHHHHHHhh
Q 022661 159 VGRILGPRGNSLKRVEAMT 177 (294)
Q Consensus 159 vGrILGPrG~TlK~LE~eT 177 (294)
+|||||=+|.|++.|-.-.
T Consensus 41 ~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CcceecCCChhHHHHHHHH
Confidence 6999999999999886543
No 58
>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=36.82 E-value=26 Score=25.19 Aligned_cols=20 Identities=20% Similarity=0.297 Sum_probs=16.0
Q ss_pred hHHHHHHhhCCeEEEecccC
Q 022661 169 SLKRVEAMTECRVFIRGRGS 188 (294)
Q Consensus 169 TlK~LE~eTGckI~IRGrGS 188 (294)
.+++||++.|+++.+|..+.
T Consensus 33 ~i~~LE~~lg~~Lf~r~~~~ 52 (60)
T PF00126_consen 33 QIKQLEEELGVPLFERSGRG 52 (60)
T ss_dssp HHHHHHHHHTS-SEEECSSS
T ss_pred HHHHHHHHhCCeEEEECCCC
Confidence 57999999999999996543
No 59
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=36.55 E-value=26 Score=31.98 Aligned_cols=33 Identities=21% Similarity=0.289 Sum_probs=29.2
Q ss_pred CCCCceeeEEeCCCCchHHHHHHhhCCeEEEecc
Q 022661 153 PNQFNFVGRILGPRGNSLKRVEAMTECRVFIRGR 186 (294)
Q Consensus 153 P~~~NFvGrILGPrG~TlK~LE~eTGckI~IRGr 186 (294)
++ .+-+|..+|++|..+|.|.++.|=+|-|=--
T Consensus 82 ~~-~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~ 114 (190)
T COG0195 82 VK-IDPVGACIGKRGSRVKAVSEELGEKIDVVEW 114 (190)
T ss_pred cC-cCchhhhccCCChHHHHHHHHhCCceEEEEe
Confidence 35 7889999999999999999999988887654
No 60
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=35.29 E-value=6.1 Score=29.63 Aligned_cols=20 Identities=25% Similarity=0.695 Sum_probs=18.2
Q ss_pred eeEEeCCCCchHHHHHHhhC
Q 022661 159 VGRILGPRGNSLKRVEAMTE 178 (294)
Q Consensus 159 vGrILGPrG~TlK~LE~eTG 178 (294)
.|+|||-+|.|++.||--++
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHH
T ss_pred cceEECCCCeeHHHHHHHHH
Confidence 79999999999999997665
No 61
>PRK01064 hypothetical protein; Provisional
Probab=33.05 E-value=33 Score=27.02 Aligned_cols=20 Identities=25% Similarity=0.718 Sum_probs=17.7
Q ss_pred eeEEeCCCCchHHHHHHhhC
Q 022661 159 VGRILGPRGNSLKRVEAMTE 178 (294)
Q Consensus 159 vGrILGPrG~TlK~LE~eTG 178 (294)
+|++||=+|.|++.|..-..
T Consensus 41 ~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred ceEEECCCCccHHHHHHHHH
Confidence 69999999999999987654
No 62
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=32.54 E-value=56 Score=33.70 Aligned_cols=33 Identities=18% Similarity=0.263 Sum_probs=29.3
Q ss_pred CCCCCceeeEEeCCCCchHHHHHHhh-CCeEEEec
Q 022661 152 YPNQFNFVGRILGPRGNSLKRVEAMT-ECRVFIRG 185 (294)
Q Consensus 152 yP~~~NFvGrILGPrG~TlK~LE~eT-GckI~IRG 185 (294)
-|+ ++-||..+|++|+.++.|.++. |=||-|=-
T Consensus 273 d~~-VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~ 306 (449)
T PRK12329 273 ERD-VDPVGACIGARGSRIQAVVNELRGEKIDVIR 306 (449)
T ss_pred CCC-CChhhccCCCCcchHHHHHHHhCCCeEEEEE
Confidence 477 9999999999999999999999 88887654
No 63
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=32.43 E-value=1.1e+02 Score=28.35 Aligned_cols=31 Identities=6% Similarity=0.114 Sum_probs=18.9
Q ss_pred CCcEEEEEecC-chhHHHHHHHHHHHHHHhcc
Q 022661 209 EPLHVLVEAEF-PEDIINSRLDHAVAILENLL 239 (294)
Q Consensus 209 epLHVlI~a~~-~~~~~~~rl~~A~e~Ie~LL 239 (294)
.-+|+-|=-.+ +.+.+.+-+...++.|.+.+
T Consensus 168 g~i~~~IG~~~m~~e~i~eNi~a~l~~i~~~~ 199 (230)
T PRK05424 168 GIIHAPIGKVSFDAEKLKENLKALIDAIKKAK 199 (230)
T ss_pred CEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhC
Confidence 45677775554 34445556666666666655
No 64
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=32.21 E-value=33 Score=30.74 Aligned_cols=27 Identities=15% Similarity=0.123 Sum_probs=25.5
Q ss_pred eEEeCCCCchHHHHHHhhCCeEEEecc
Q 022661 160 GRILGPRGNSLKRVEAMTECRVFIRGR 186 (294)
Q Consensus 160 GrILGPrG~TlK~LE~eTGckI~IRGr 186 (294)
|.-||++|.++|+|++..|=+|.|=.-
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEEEc
Confidence 999999999999999999999999874
No 65
>PRK00089 era GTPase Era; Reviewed
Probab=32.09 E-value=45 Score=30.77 Aligned_cols=40 Identities=30% Similarity=0.454 Sum_probs=29.3
Q ss_pred eeEEEEEecCCCCCCCCCceeeEEeCCCCchHHHH--------HHhhCCeEEEe
Q 022661 139 VKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRV--------EAMTECRVFIR 184 (294)
Q Consensus 139 vk~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~L--------E~eTGckI~IR 184 (294)
++....|+|.-+.+ .+-|||-+|.++|+| |+-.||+|.+.
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 44555566665443 578999999999876 67778888775
No 66
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=31.10 E-value=89 Score=30.73 Aligned_cols=37 Identities=16% Similarity=0.334 Sum_probs=29.5
Q ss_pred EEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEe
Q 022661 141 RVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIR 184 (294)
Q Consensus 141 ~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IR 184 (294)
...+|++--+. .|-|+|-.|.++|+|..+.++.|.|-
T Consensus 48 ~e~ril~~sk~-------agavigkgg~nik~lr~d~na~v~vp 84 (390)
T KOG2192|consen 48 VELRILLQSKN-------AGAVIGKGGKNIKALRTDYNASVSVP 84 (390)
T ss_pred eeEEEEEeccc-------ccceeccccccHHHHhhhccceeecc
Confidence 44556655333 58899999999999999999999875
No 67
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=30.84 E-value=29 Score=27.45 Aligned_cols=18 Identities=17% Similarity=0.802 Sum_probs=15.8
Q ss_pred eeEEeCCCCchHHHHHHh
Q 022661 159 VGRILGPRGNSLKRVEAM 176 (294)
Q Consensus 159 vGrILGPrG~TlK~LE~e 176 (294)
+|++||=+|.|++.|-.-
T Consensus 41 ~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 41 MGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred ccceecCCChhHHHHHHH
Confidence 799999999999998543
No 68
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=30.73 E-value=27 Score=34.77 Aligned_cols=31 Identities=29% Similarity=0.629 Sum_probs=27.6
Q ss_pred CceeeEEeCCCCchHHHHHHhhCCeEEEecc
Q 022661 156 FNFVGRILGPRGNSLKRVEAMTECRVFIRGR 186 (294)
Q Consensus 156 ~NFvGrILGPrG~TlK~LE~eTGckI~IRGr 186 (294)
+-+||++.||.|+|+|++|+.+..-|.--++
T Consensus 123 ~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 123 LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred ceeeeeccccccCccchheecccceEeeecc
Confidence 5789999999999999999999998876654
No 69
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=30.67 E-value=34 Score=30.97 Aligned_cols=22 Identities=23% Similarity=0.363 Sum_probs=18.9
Q ss_pred chHHHHHHhhCCeEEEecccCC
Q 022661 168 NSLKRVEAMTECRVFIRGRGSV 189 (294)
Q Consensus 168 ~TlK~LE~eTGckI~IRGrGS~ 189 (294)
..+|+||++.|+++.+|++|..
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 70
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=29.50 E-value=34 Score=34.39 Aligned_cols=34 Identities=18% Similarity=0.256 Sum_probs=29.4
Q ss_pred CCCCCCceeeEEeCCCCchHHHHHHhh-CCeEEEec
Q 022661 151 KYPNQFNFVGRILGPRGNSLKRVEAMT-ECRVFIRG 185 (294)
Q Consensus 151 ~yP~~~NFvGrILGPrG~TlK~LE~eT-GckI~IRG 185 (294)
.-|+ ++-||..+|++|..++.|.++. |=+|-|=-
T Consensus 246 ~d~~-iDPvGacIG~~G~rI~~I~~eL~gEkIDvI~ 280 (374)
T PRK12328 246 NNPN-IDPIGATVGVKGVRINAVSKELNGENIDCIE 280 (374)
T ss_pred CCCC-CChHHhhcCCCcchHHHHHHHhCCCeEEEEE
Confidence 4578 9999999999999999999999 77776653
No 71
>PRK15494 era GTPase Era; Provisional
Probab=28.48 E-value=55 Score=31.60 Aligned_cols=40 Identities=28% Similarity=0.330 Sum_probs=30.1
Q ss_pred eeEEEEEecCCCCCCCCCceeeEEeCCCCchHHHH--------HHhhCCeEEEe
Q 022661 139 VKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRV--------EAMTECRVFIR 184 (294)
Q Consensus 139 vk~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~L--------E~eTGckI~IR 184 (294)
++....|||.-+.+ -|-|||-+|..+|+| |+-.||||.+.
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 44556677765443 468999999999976 77788888876
No 72
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=27.40 E-value=9 Score=32.54 Aligned_cols=45 Identities=29% Similarity=0.519 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHhccC-CCCcchhHHHHHHHHHHHHHcCccCCCCC
Q 022661 224 INSRLDHAVAILENLLK-PVDESLDHYKKQQLRELAMLNGTLREESP 269 (294)
Q Consensus 224 ~~~rl~~A~e~Ie~LL~-p~~e~~delK~~QL~ELA~lNGt~r~~~~ 269 (294)
+|.||.+|+.+|+.-|. -+.|..+-| |.|.+||..-|..++.++.
T Consensus 46 IDNKIeQAMDLVKtHLmfAVREEVe~L-k~qI~eL~er~~~Le~EN~ 91 (123)
T KOG4797|consen 46 IDNKIEQAMDLVKTHLMFAVREEVEVL-KEQIRELEERNSALERENS 91 (123)
T ss_pred echHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH
Confidence 45589999999998554 455555444 5899999999888876654
No 73
>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=26.54 E-value=12 Score=32.37 Aligned_cols=18 Identities=39% Similarity=0.776 Sum_probs=14.8
Q ss_pred CCCCCCCceeeEEeCCCCc
Q 022661 150 DKYPNQFNFVGRILGPRGN 168 (294)
Q Consensus 150 ~~yP~~~NFvGrILGPrG~ 168 (294)
+-.|. +..+|+||||||.
T Consensus 101 ~~m~~-l~~Lg~iLGprGl 118 (141)
T TIGR01170 101 DIVPE-LAQLRRLLGPKGL 118 (141)
T ss_pred HHHHH-HHHhhcccccCcC
Confidence 34566 8899999999985
No 74
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=26.10 E-value=1.6e+02 Score=27.18 Aligned_cols=62 Identities=24% Similarity=0.216 Sum_probs=35.9
Q ss_pred eeEEeCCC-------------CchHHHHHHhhCCeEEEecccCCCCchhhhhccCCCCCCCCCCCcEEEEEecC-chhHH
Q 022661 159 VGRILGPR-------------GNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEF-PEDII 224 (294)
Q Consensus 159 vGrILGPr-------------G~TlK~LE~eTGckI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI~a~~-~~~~~ 224 (294)
+||+|||+ +..+...-+++.++|.+|=+ -.--+|+.|=-.+ ..+.+
T Consensus 117 lgk~LGp~~~p~gK~P~~~~~~~dl~~~i~~~k~~v~~r~~--------------------k~~~~~~~VGk~~m~~e~i 176 (214)
T PTZ00225 117 VPRLVGPHMHRMGKFPTVCSPSESLPDKVVELRSTVKFQLK--------------------KVLCLGTCVGHVEMTEEQL 176 (214)
T ss_pred hhhhcCCCCCcCCCCCcccCCccCHHHHHHHHhheeEEEec--------------------CccEEEeEEccCCCCHHHH
Confidence 59999999 23345555555555555521 0124577775554 23344
Q ss_pred HHHHHHHHHHHHhccC
Q 022661 225 NSRLDHAVAILENLLK 240 (294)
Q Consensus 225 ~~rl~~A~e~Ie~LL~ 240 (294)
.+-+..+++.|...|.
T Consensus 177 ~eNi~a~l~~l~~~~p 192 (214)
T PTZ00225 177 RQNVVMAINFLVSLLK 192 (214)
T ss_pred HHHHHHHHHHHHHhCC
Confidence 4566667777766653
No 75
>TIGR01169 rplA_bact ribosomal protein L1, bacterial/chloroplast. This model describes bacterial (and chloroplast) ribosomal protein L1. The apparent mitochondrial L1 is sufficiently diverged to be the subject of a separate model.
Probab=25.45 E-value=1.8e+02 Score=27.00 Aligned_cols=31 Identities=6% Similarity=0.146 Sum_probs=17.2
Q ss_pred CCcEEEEEecC-chhHHHHHHHHHHHHHHhcc
Q 022661 209 EPLHVLVEAEF-PEDIINSRLDHAVAILENLL 239 (294)
Q Consensus 209 epLHVlI~a~~-~~~~~~~rl~~A~e~Ie~LL 239 (294)
.-+|+-|=-.+ +.+.+.+-+...++.|...+
T Consensus 167 g~i~~~VG~~~m~~e~i~eNi~a~l~~i~~~~ 198 (227)
T TIGR01169 167 GNIHASIGKVSFDSEKLKENLEALLDAIKKAK 198 (227)
T ss_pred CEEEEEEecCCCCHHHHHHHHHHHHHHHHHhC
Confidence 45677775544 33344455666666565543
No 76
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=25.25 E-value=51 Score=33.93 Aligned_cols=33 Identities=21% Similarity=0.346 Sum_probs=29.0
Q ss_pred CCCCCCceeeEEeCCCCchHHHHHHhh-CCeEEEe
Q 022661 151 KYPNQFNFVGRILGPRGNSLKRVEAMT-ECRVFIR 184 (294)
Q Consensus 151 ~yP~~~NFvGrILGPrG~TlK~LE~eT-GckI~IR 184 (294)
.-|+ +.-||..+|++|+.++.|.++. |=||-|=
T Consensus 240 ~d~~-iDpvga~vG~~G~ri~~i~~el~ge~Idiv 273 (470)
T PRK09202 240 NDPR-IDPVGACVGMRGSRIQAISNELGGEKIDII 273 (470)
T ss_pred CCCC-CChhHccCCCCCchHHHHHHHhCCCeEEEE
Confidence 4577 9999999999999999999999 7777664
No 77
>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=24.63 E-value=42 Score=30.36 Aligned_cols=23 Identities=13% Similarity=0.170 Sum_probs=19.0
Q ss_pred hHHHHHHhhCCeEEEecccCCCC
Q 022661 169 SLKRVEAMTECRVFIRGRGSVKD 191 (294)
Q Consensus 169 TlK~LE~eTGckI~IRGrGS~kd 191 (294)
.+|+||++.|+++..|+||-.-.
T Consensus 35 ~I~~LE~~lg~~Lf~R~r~~~lT 57 (292)
T TIGR03298 35 RIKALEERLGQPLLVRTQPCRAT 57 (292)
T ss_pred HHHHHHHHhCchheecCCCCcCC
Confidence 47999999999999999765433
No 78
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=22.98 E-value=59 Score=29.63 Aligned_cols=23 Identities=13% Similarity=0.170 Sum_probs=19.4
Q ss_pred hHHHHHHhhCCeEEEecccCCCC
Q 022661 169 SLKRVEAMTECRVFIRGRGSVKD 191 (294)
Q Consensus 169 TlK~LE~eTGckI~IRGrGS~kd 191 (294)
.+|+||++.||++..|++|-.-.
T Consensus 36 ~I~~LE~~lg~~LF~R~~~~~lT 58 (294)
T PRK03635 36 RIKALEERVGQVLLVRTQPCRPT 58 (294)
T ss_pred HHHHHHHHhCceeeecCCCCccC
Confidence 58999999999999999865433
No 79
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=22.17 E-value=39 Score=29.13 Aligned_cols=25 Identities=20% Similarity=0.420 Sum_probs=22.0
Q ss_pred eeEEeCCCCchHHHHHHhhCCeEEE
Q 022661 159 VGRILGPRGNSLKRVEAMTECRVFI 183 (294)
Q Consensus 159 vGrILGPrG~TlK~LE~eTGckI~I 183 (294)
.|+.||.+|.|++.++.-+|-.+-|
T Consensus 110 ~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 110 KGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred cchhhCCCCHHHHHHHHHhCCccCC
Confidence 6899999999999999999876644
No 80
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=22.04 E-value=66 Score=29.12 Aligned_cols=18 Identities=22% Similarity=0.469 Sum_probs=16.0
Q ss_pred hHHHHHHhhCCeEEEecc
Q 022661 169 SLKRVEAMTECRVFIRGR 186 (294)
Q Consensus 169 TlK~LE~eTGckI~IRGr 186 (294)
.+|+||++.|+++..|..
T Consensus 35 ~I~~LE~~lG~~LF~R~~ 52 (275)
T PRK03601 35 RIRQLENQLGVNLFTRHR 52 (275)
T ss_pred HHHHHHHHhCCceEEECC
Confidence 579999999999999953
No 81
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=21.93 E-value=69 Score=29.25 Aligned_cols=23 Identities=17% Similarity=0.332 Sum_probs=18.0
Q ss_pred chHHHHHHhhCCeEEEecccCCC
Q 022661 168 NSLKRVEAMTECRVFIRGRGSVK 190 (294)
Q Consensus 168 ~TlK~LE~eTGckI~IRGrGS~k 190 (294)
..+|+||++.|+.+.+|...-+.
T Consensus 35 ~~I~~LE~~lg~~LF~R~~r~~~ 57 (300)
T PRK11074 35 YTVRQLEEWLAVPLFERRHRDVE 57 (300)
T ss_pred HHHHHHHHHhCCeeEEeCCCCce
Confidence 35899999999999999543333
No 82
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=21.18 E-value=74 Score=29.48 Aligned_cols=20 Identities=20% Similarity=0.401 Sum_probs=17.2
Q ss_pred hHHHHHHhhCCeEEEe-cccC
Q 022661 169 SLKRVEAMTECRVFIR-GRGS 188 (294)
Q Consensus 169 TlK~LE~eTGckI~IR-GrGS 188 (294)
.+|+||++.||++.+| |||-
T Consensus 36 ~ik~LE~~lg~~Lf~R~~r~~ 56 (313)
T PRK12684 36 AIIELEDELGVEIFTRHGKRL 56 (313)
T ss_pred HHHHHHHHhCCeeEEEcCCcc
Confidence 5899999999999999 4553
No 83
>KOG3564 consensus GTPase-activating protein [General function prediction only]
Probab=21.00 E-value=1.3e+02 Score=31.82 Aligned_cols=41 Identities=17% Similarity=0.132 Sum_probs=35.2
Q ss_pred chHHHHHHHHHHHHhhcCCcccchhHHHHHHHHHHHHHHhC
Q 022661 30 LDRERYLAELLAERQKLGPFVQVLPLCSRLLSQEIRRITGY 70 (294)
Q Consensus 30 ~~~~~YL~ELl~E~~~L~~~~~~f~h~~rLL~~EI~RV~~~ 70 (294)
.|-++|=++|.+-+.+++.|--.+.||.+-|+.||.|=+.+
T Consensus 49 ae~~~~~~~L~Ka~tk~~~ldvklkha~~~vda~ik~rr~a 89 (604)
T KOG3564|consen 49 AELGKYKDLLAKAETKRSALDVKLKHARNQVDAEIKRRRRA 89 (604)
T ss_pred HHHHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHHHHH
Confidence 34579999999999999998778999999999999876443
No 84
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=21.00 E-value=75 Score=29.67 Aligned_cols=19 Identities=21% Similarity=0.419 Sum_probs=16.5
Q ss_pred chHHHHHHhhCCeEEEecc
Q 022661 168 NSLKRVEAMTECRVFIRGR 186 (294)
Q Consensus 168 ~TlK~LE~eTGckI~IRGr 186 (294)
..+|+||++.|+++.+|..
T Consensus 35 ~~Ik~LE~~lg~~LF~R~~ 53 (317)
T PRK15421 35 HQFSDLEQRLGFRLFVRKS 53 (317)
T ss_pred HHHHHHHHHhCCEEEEecC
Confidence 3589999999999999953
No 85
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=20.44 E-value=3e+02 Score=27.17 Aligned_cols=42 Identities=19% Similarity=0.451 Sum_probs=33.0
Q ss_pred CCCCceeEEEEEecCCCCCCCCCceeeEEeCCCCchHHHHHHhhCCeEEEe
Q 022661 134 PTTPVVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECRVFIR 184 (294)
Q Consensus 134 ~~~~~vk~~~KI~IPv~~yP~~~NFvGrILGPrG~TlK~LE~eTGckI~IR 184 (294)
-.+|+.. ..|-||- .+-|-|||-.|.-+|||-.|+|+-|.|-
T Consensus 310 lGGPitT--aQvtip~-------dlggsiigkggqri~~ir~esGA~Ikid 351 (390)
T KOG2192|consen 310 LGGPITT--AQVTIPK-------DLGGSIIGKGGQRIKQIRHESGASIKID 351 (390)
T ss_pred CCCceee--eeEeccc-------ccCcceecccchhhhhhhhccCceEEec
Confidence 3456554 4466773 4668999999999999999999999884
No 86
>PF07582 AP_endonuc_2_N: AP endonuclease family 2 C terminus; InterPro: IPR011418 DNA damaging agents such as the anti-tumour drugs bleomycin and neocarzinostatin or those that generate oxygen radicals produce a variety of lesions in DNA. Amongst these is base-loss which forms apurinic/apyrimidinic (AP) sites or strand breaks with atypical 3' termini. DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3' terminus of DNA strand breaks. AP endonucleases can be classified into two families based on sequence similarity []. This entry represents a highly-conserved sequence found at the C terminus of several apurinic/apyrimidinic (AP) endonucleases in a range of Gram-positive and Gram-negative bacteria. ; PDB: 3LMZ_A 2ZDS_D.
Probab=20.37 E-value=1.2e+02 Score=22.36 Aligned_cols=32 Identities=22% Similarity=0.049 Sum_probs=18.3
Q ss_pred EEEEEecCchhHHHHHHHHHHHHHHhccCCCC
Q 022661 212 HVLVEAEFPEDIINSRLDHAVAILENLLKPVD 243 (294)
Q Consensus 212 HVlI~a~~~~~~~~~rl~~A~e~Ie~LL~p~~ 243 (294)
-|-|+.++..-....-+++|++.++++|..++
T Consensus 17 ~~siE~ED~~~~~~~G~~~a~~~lr~~l~~~~ 48 (55)
T PF07582_consen 17 WLSIEHEDALMDPEEGAREAAAFLRKLLIREP 48 (55)
T ss_dssp EEEE---STTTSHHHHHHHHHHHHHTT-----
T ss_pred eEEEEeecCCCCHHHHHHHHHHHHHHhcCCCC
Confidence 35666666544456789999999999998654
No 87
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=20.24 E-value=77 Score=29.35 Aligned_cols=20 Identities=30% Similarity=0.539 Sum_probs=17.5
Q ss_pred hHHHHHHhhCCeEEEe-cccC
Q 022661 169 SLKRVEAMTECRVFIR-GRGS 188 (294)
Q Consensus 169 TlK~LE~eTGckI~IR-GrGS 188 (294)
.+|+||++.|+++.+| |||-
T Consensus 36 ~I~~LE~~lg~~Lf~R~~r~~ 56 (309)
T PRK12683 36 QIKDLEDELGVEIFIRRGKRL 56 (309)
T ss_pred HHHHHHHHhCCeeEeeCCCCc
Confidence 5899999999999999 5654
Done!