Query 023341
Match_columns 283
No_of_seqs 204 out of 427
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 03:17:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023341.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023341hhsearch_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 8.5E-66 1.8E-70 471.3 21.6 234 1-282 3-241 (259)
2 cd02395 SF1_like-KH Splicing f 100.0 2.2E-41 4.7E-46 280.7 13.1 118 137-258 2-120 (120)
3 KOG0119 Splicing factor 1/bran 100.0 6.2E-40 1.3E-44 320.4 6.9 174 79-262 82-261 (554)
4 COG5176 MSL5 Splicing factor ( 100.0 2.6E-32 5.6E-37 244.5 5.4 183 71-260 83-269 (269)
5 cd02393 PNPase_KH Polynucleoti 98.6 8.4E-08 1.8E-12 70.6 6.7 59 136-229 3-61 (61)
6 PF00013 KH_1: KH domain syndr 98.5 9.5E-08 2.1E-12 68.8 3.8 59 137-228 2-60 (60)
7 cd00105 KH-I K homology RNA-bi 98.4 9.2E-07 2E-11 63.5 6.9 62 137-228 2-63 (64)
8 KOG1960 Predicted RNA-binding 98.4 2.6E-07 5.6E-12 90.5 4.5 90 133-236 208-297 (531)
9 smart00322 KH K homology RNA-b 98.3 5.4E-06 1.2E-10 58.5 7.6 65 136-232 4-68 (69)
10 cd02394 vigilin_like_KH K homo 98.2 2.6E-06 5.7E-11 61.7 5.4 59 138-228 3-61 (62)
11 PF13014 KH_3: KH domain 98.2 1.6E-06 3.4E-11 59.2 3.1 28 151-178 1-28 (43)
12 cd02396 PCBP_like_KH K homolog 98.1 1.2E-05 2.7E-10 59.2 6.9 36 137-178 2-37 (65)
13 TIGR03665 arCOG04150 arCOG0415 97.9 2.2E-05 4.8E-10 68.8 5.2 52 151-233 99-150 (172)
14 PRK13763 putative RNA-processi 97.8 4.1E-05 8.8E-10 67.7 5.7 52 151-233 105-156 (180)
15 TIGR02696 pppGpp_PNP guanosine 97.7 8.6E-05 1.9E-09 77.9 8.2 71 129-234 572-642 (719)
16 PRK13763 putative RNA-processi 97.7 7.2E-05 1.6E-09 66.1 6.0 64 137-234 5-71 (180)
17 TIGR03665 arCOG04150 arCOG0415 97.5 0.0001 2.2E-09 64.6 4.5 58 149-234 6-65 (172)
18 TIGR03591 polynuc_phos polyrib 97.5 0.00021 4.6E-09 74.7 7.0 69 130-233 546-614 (684)
19 COG1094 Predicted RNA-binding 97.5 0.0002 4.3E-09 64.5 5.7 55 151-236 112-166 (194)
20 PLN00207 polyribonucleotide nu 97.0 0.00067 1.5E-08 72.8 4.9 71 129-234 679-750 (891)
21 KOG1676 K-homology type RNA bi 96.5 0.0058 1.3E-07 62.8 6.7 69 136-234 231-300 (600)
22 KOG2874 rRNA processing protei 96.5 0.0065 1.4E-07 57.9 6.5 55 153-238 161-215 (356)
23 PRK04163 exosome complex RNA-b 96.4 0.0072 1.6E-07 55.5 6.1 58 149-235 153-210 (235)
24 PRK11824 polynucleotide phosph 96.4 0.0035 7.5E-08 65.8 4.4 56 149-233 562-617 (693)
25 KOG2193 IGF-II mRNA-binding pr 96.1 0.002 4.4E-08 64.2 1.0 38 140-177 279-316 (584)
26 KOG1676 K-homology type RNA bi 96.0 0.013 2.9E-07 60.2 6.4 74 132-233 136-209 (600)
27 KOG2814 Transcription coactiva 95.0 0.034 7.4E-07 54.0 4.7 61 149-229 65-127 (345)
28 KOG2193 IGF-II mRNA-binding pr 94.9 0.023 5.1E-07 56.9 3.4 37 137-179 201-237 (584)
29 KOG2191 RNA-binding protein NO 94.6 0.13 2.9E-06 50.2 7.8 37 135-177 39-75 (402)
30 KOG2190 PolyC-binding proteins 94.6 0.075 1.6E-06 54.0 6.4 40 134-179 137-176 (485)
31 KOG2191 RNA-binding protein NO 93.5 0.32 7E-06 47.6 8.0 38 135-178 132-169 (402)
32 COG1185 Pnp Polyribonucleotide 93.0 0.14 2.9E-06 54.0 4.9 67 132-233 549-615 (692)
33 PRK00106 hypothetical protein; 92.1 0.26 5.6E-06 50.8 5.6 63 138-233 228-290 (535)
34 TIGR03319 YmdA_YtgF conserved 91.4 0.3 6.6E-06 49.9 5.2 62 139-233 208-269 (514)
35 PRK12704 phosphodiesterase; Pr 91.0 0.43 9.3E-06 48.9 5.8 49 139-215 214-262 (520)
36 cd02134 NusA_KH NusA_K homolog 88.3 0.46 1E-05 34.8 2.7 36 135-176 25-60 (61)
37 KOG1960 Predicted RNA-binding 88.0 0.18 3.9E-06 50.4 0.5 72 154-238 308-379 (531)
38 KOG2190 PolyC-binding proteins 87.6 0.48 1E-05 48.3 3.3 41 133-179 336-376 (485)
39 KOG0336 ATP-dependent RNA heli 85.8 0.41 8.9E-06 48.5 1.6 29 149-177 55-83 (629)
40 PF13184 KH_5: NusA-like KH do 83.0 0.72 1.6E-05 35.0 1.6 32 146-177 13-45 (69)
41 COG1097 RRP4 RNA-binding prote 80.9 4 8.6E-05 38.3 5.9 30 149-178 154-183 (239)
42 PRK12705 hypothetical protein; 79.0 3.3 7.1E-05 42.6 5.1 31 147-177 205-235 (508)
43 COG1094 Predicted RNA-binding 78.6 5.4 0.00012 36.3 5.8 65 137-235 10-78 (194)
44 KOG1067 Predicted RNA-binding 75.9 2.3 4.9E-05 44.6 3.0 54 151-234 607-660 (760)
45 cd02409 KH-II KH-II (K homolo 74.8 2.6 5.5E-05 29.7 2.2 23 152-174 36-58 (68)
46 PRK08406 transcription elongat 71.9 3.3 7.2E-05 35.4 2.6 29 150-178 41-69 (140)
47 KOG2113 Predicted RNA binding 62.4 5.5 0.00012 39.0 2.3 37 133-175 24-60 (394)
48 cd02414 jag_KH jag_K homology 61.7 4.9 0.00011 30.5 1.5 23 152-174 35-57 (77)
49 PF13083 KH_4: KH domain; PDB: 51.6 4.6 0.0001 30.1 -0.1 21 152-172 40-60 (73)
50 COG1702 PhoH Phosphate starvat 51.5 27 0.00059 34.5 5.1 30 150-179 24-53 (348)
51 TIGR01952 nusA_arch NusA famil 51.0 13 0.00029 32.0 2.5 29 150-178 42-70 (141)
52 TIGR00436 era GTP-binding prot 48.2 34 0.00074 31.3 5.0 40 133-177 219-266 (270)
53 PRK02821 hypothetical protein; 47.8 11 0.00024 29.4 1.4 23 150-172 40-62 (77)
54 PRK00468 hypothetical protein; 46.9 12 0.00025 29.0 1.4 19 152-170 41-59 (75)
55 PRK12327 nusA transcription el 46.2 20 0.00043 35.4 3.3 34 145-178 240-274 (362)
56 KOG2192 PolyC-binding hnRNP-K 43.8 44 0.00095 32.4 5.0 38 135-178 48-85 (390)
57 COG0195 NusA Transcription elo 42.6 22 0.00047 32.2 2.7 33 147-179 82-114 (190)
58 KOG2208 Vigilin [Lipid transpo 42.2 19 0.00041 38.8 2.6 37 136-178 710-746 (753)
59 TIGR01953 NusA transcription t 41.9 26 0.00056 34.3 3.3 34 145-178 238-272 (341)
60 PRK15494 era GTPase Era; Provi 41.4 46 0.00099 32.0 4.9 40 133-177 271-318 (339)
61 PRK00089 era GTPase Era; Revie 41.2 48 0.001 30.4 4.8 40 133-177 224-271 (292)
62 KOG4165 Gamma-glutamyl phospha 41.1 29 0.00062 34.6 3.4 61 150-233 190-259 (433)
63 PRK06418 transcription elongat 40.6 23 0.0005 31.4 2.5 27 153-179 72-98 (166)
64 PRK08406 transcription elongat 39.9 26 0.00056 29.9 2.6 25 152-176 110-134 (140)
65 COG1837 Predicted RNA-binding 39.5 18 0.00038 28.3 1.4 17 152-168 41-57 (76)
66 PRK12329 nusA transcription el 38.8 43 0.00093 34.2 4.4 34 145-178 272-306 (449)
67 PRK12328 nusA transcription el 38.4 42 0.00091 33.5 4.1 41 137-183 310-350 (374)
68 PRK01064 hypothetical protein; 36.3 19 0.0004 28.1 1.1 20 152-171 41-60 (78)
69 KOG2192 PolyC-binding hnRNP-K 35.2 52 0.0011 31.9 4.1 41 130-178 312-352 (390)
70 PRK12328 nusA transcription el 34.1 32 0.00069 34.3 2.6 34 145-178 246-280 (374)
71 KOG2113 Predicted RNA binding 33.9 16 0.00036 35.8 0.5 31 149-179 123-153 (394)
72 PRK05424 rplA 50S ribosomal pr 32.8 1.3E+02 0.0028 27.8 6.2 31 202-232 168-199 (230)
73 COG1855 ATPase (PilT family) [ 31.0 48 0.001 34.5 3.3 39 137-181 488-526 (604)
74 PF00126 HTH_1: Bacterial regu 30.4 40 0.00086 24.0 2.0 19 162-180 33-51 (60)
75 TIGR01170 rplA_mito ribosomal 28.4 13 0.00027 32.0 -1.1 18 144-161 101-118 (141)
76 PTZ00225 60S ribosomal protein 28.0 1.5E+02 0.0032 27.2 5.7 61 152-232 117-191 (214)
77 TIGR01169 rplA_bact ribosomal 27.6 1E+02 0.0023 28.3 4.6 11 150-160 123-133 (227)
78 PRK09202 nusA transcription el 27.5 51 0.0011 33.7 2.8 34 144-177 239-273 (470)
79 KOG0334 RNA helicase [RNA proc 26.8 56 0.0012 36.5 3.1 79 137-233 898-976 (997)
80 KOG3273 Predicted RNA-binding 26.5 19 0.00042 33.4 -0.3 29 150-178 178-206 (252)
81 KOG4797 Transcriptional regula 25.3 10 0.00022 31.8 -2.1 42 218-260 47-89 (123)
82 PRK13348 chromosome replicatio 24.9 54 0.0012 29.6 2.2 21 161-181 35-55 (294)
83 COG0484 DnaJ DnaJ-class molecu 21.5 1.3E+02 0.0029 30.0 4.4 36 168-215 300-335 (371)
84 COG0080 RplK Ribosomal protein 20.6 3.6E+02 0.0079 23.5 6.3 97 135-253 6-110 (141)
85 CHL00129 rpl1 ribosomal protei 20.6 38 0.00083 31.3 0.4 29 203-231 169-198 (229)
86 PF07650 KH_2: KH domain syndr 20.2 33 0.00072 25.6 -0.1 23 152-174 36-58 (78)
No 1
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=100.00 E-value=8.5e-66 Score=471.25 Aligned_cols=234 Identities=50% Similarity=0.773 Sum_probs=197.1
Q ss_pred CCCCCCCC-CCCCCCCCCCCCCCCCcchHHHHHHHHHHHHhhcCCCccchhHHHHHhhhhHHhhhccCCCCCCCCccccc
Q 023341 1 MSGLYNPN-FSPARAASPQIRSTPDINIDSQYLSELLAEHQKLGPFTQVLPICSRLLTQEIFRVSGMMPNQGFGDFDRLR 79 (283)
Q Consensus 1 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~YL~eLl~Ek~~L~~~~~~~~~~~rLL~~EI~RV~~~~~~~~~~d~~~~~ 79 (283)
+.+.|++. ++|+...+++..+. .....++||.+|++||++|++|+. |+||.|||++||.||+..+++.+ +
T Consensus 3 ~~~~~~~~~~s~~~~~~~~~~~~-~~~~~~~yl~el~~e~~~l~~~~~-~~~~~rLL~~Ei~rv~~~~~~~~----~--- 73 (259)
T KOG1588|consen 3 TGGGYTQEPGSPAGGGGPRYQPQ-LNEKASKYLSELLAERKSLSPFFP-FPHAERLLDEEIERVQTSGRQHG----S--- 73 (259)
T ss_pred CCCCCCCCCCCCcccCCCccccc-hhhHHHHHHHHHHhhHHhcCcccc-hHHHHHHHHHHHHHHHhhhhhcc----C---
Confidence 34566655 34444444443332 225579999999999999999998 99999999999999999765532 1
Q ss_pred CCCCCCCCccccccCcCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCcceeeEEEEecCCCCCCCCccccceeCCC
Q 023341 80 HRSPSPMASSNLMSNVAGTGLGGWNGLPQERLGGPPGMTMDWQSAPASPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPR 159 (283)
Q Consensus 80 ~~SP~p~~~~g~~~N~~~~~~~~~~~l~~Er~~~~~~~~~~~~~~p~~~~~~~vk~~~kv~IPv~~~P~~NfvGrILGPr 159 (283)
..| ++.. ....++.+++|.++||+|||++||+|||||||||||
T Consensus 74 -~~~-------------------------~~~~-----------~~~~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPr 116 (259)
T KOG1588|consen 74 -KEP-------------------------EELP-----------YADVYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPR 116 (259)
T ss_pred -CCc-------------------------hhcc-----------cccCccCCceeEEEEEEeccCCCCCCccccccccCC
Confidence 001 1110 002345678999999999999999999999999999
Q ss_pred chhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHHHccCCCCCch
Q 023341 160 GNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLKPVDESQ 239 (283)
Q Consensus 160 G~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL~p~~e~~ 239 (283)
|||+||||++|||||+|||||||||..|||+||++|+|+||++||||+|++++++++|++||++|+++|++||+|.+|+.
T Consensus 117 GnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~P~~e~~ 196 (259)
T KOG1588|consen 117 GNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLVPDHEDE 196 (259)
T ss_pred cchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcCCCCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999887
Q ss_pred HHHHHHHHHHHHHHcCc-cCCCCCCCCC---CCCCCCcccccccccC
Q 023341 240 DYIKRQQLRELAMLNSN-FREDSPGPSG---SVSPFNSSGMKRAKTG 282 (283)
Q Consensus 240 D~~K~~QL~ELA~lNGt-~r~~~~~~~~---~~spf~~~~~~r~~~~ 282 (283)
| |++||+|||++||| +++.+..++| +++||++.|+||+|++
T Consensus 197 d--k~~QL~ELa~lngt~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~ 241 (259)
T KOG1588|consen 197 D--KREQLRELAILNGTYLRSESRKPSGGNGRGVPGNSAGGKRGKTG 241 (259)
T ss_pred h--HHHHHHHHhhcCCccccccccccCCCCCcCCCCCCCCcccccCC
Confidence 7 99999999999999 5666655666 8999999999999885
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=2.2e-41 Score=280.73 Aligned_cols=118 Identities=58% Similarity=0.979 Sum_probs=112.3
Q ss_pred EEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhh
Q 023341 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANI 216 (283)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~ 216 (283)
+|||||+++||+|||||+||||+|+|+|+||++|||+|.|||+||+++.++++++++ +.|+|++|||||+|+|.++
T Consensus 2 ~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~-~~~~~~~eplhV~I~a~~~--- 77 (120)
T cd02395 2 EKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRG-PKYAHLNEPLHVLITAETP--- 77 (120)
T ss_pred CEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccC-cccccCCCCcEEEEEeCCc---
Confidence 689999999999999999999999999999999999999999999999999998887 8999999999999999986
Q ss_pred HHHHHHHHHHHHHHccCCCCCc-hHHHHHHHHHHHHHHcCccC
Q 023341 217 VDIRLRQAQEIIEELLKPVDES-QDYIKRQQLRELAMLNSNFR 258 (283)
Q Consensus 217 ~~~rl~~A~e~Ie~LL~p~~e~-~D~~K~~QL~ELA~lNGt~r 258 (283)
+..++++|+++|+.||.++.++ .|++|++||+|||++|||||
T Consensus 78 ~~e~~~~A~~~I~~ll~~~~~~~~~~~k~~ql~~la~~nGt~~ 120 (120)
T cd02395 78 PEEALAKAVEAIEELLKPAIEGGNDELKREQLRELALLNGTYR 120 (120)
T ss_pred HHHHHHHHHHHHHHHhccCCCccchHHHHHHHHHHHHhcccCC
Confidence 3458999999999999998877 99999999999999999997
No 3
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=100.00 E-value=6.2e-40 Score=320.36 Aligned_cols=174 Identities=36% Similarity=0.544 Sum_probs=143.1
Q ss_pred cCCCCCCC-CccccccCcCCCCCCCCCCCcccccCCCC-CCCCCCCCCCCCCCCcceeeEEEEecCCCCCCCCcccccee
Q 023341 79 RHRSPSPM-ASSNLMSNVAGTGLGGWNGLPQERLGGPP-GMTMDWQSAPASPSSYTVKRILRLEIPVDTYPNFNFVGRLL 156 (283)
Q Consensus 79 ~~~SP~p~-~~~g~~~N~~~~~~~~~~~l~~Er~~~~~-~~~~~~~~~p~~~~~~~vk~~~kv~IPv~~~P~~NfvGrIL 156 (283)
+.+||+|. +.-|.+.|+++ ++....|.+||..+++ .+.+...+.++....+..+++.|||||||+||+|||||+||
T Consensus 82 rSPsp~p~yda~g~R~ntRe--~R~r~~Le~er~e~I~~~lk~nP~fkpP~DYk~p~~~~~Kv~IPvke~Pd~NFvGLii 159 (554)
T KOG0119|consen 82 RSPSPEPVYDAKGKRLNTRE--QRARKKLEDERHEIIEEILKLNPGFKPPADYKPPAKLHDKVYIPVKEFPDINFVGLII 159 (554)
T ss_pred cCCCcchhhhhhccchhhHH--HHHHHHHHHHHHHHHHHHHHhCcCCCCCcccCcccccccceecchhhcCCcceeEEEe
Confidence 44444444 34678888885 5556788889887654 45677766665544445589999999999999999999999
Q ss_pred CCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCC-CCCCCceEEEEecCchhhHHHHHHHHHHHHHHccC--
Q 023341 157 GPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYE-HLNDPLHILIEADLPANIVDIRLRQAQEIIEELLK-- 233 (283)
Q Consensus 157 GPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~e-hl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL~-- 233 (283)
||||+|+|+||++|||||+||||||+|+++ ....+.+|. ..+|||||+|+|++.+ +|++|+++||.||.
T Consensus 160 GPRG~TqK~lE~etgAKI~IRGkgSvkEgk---~~~~d~~~~~~~~epLH~~Isadt~e-----ki~~Ai~vienli~~a 231 (554)
T KOG0119|consen 160 GPRGNTQKRLERETGAKIAIRGKGSVKEGK---GRSDDLSYIPKENEPLHCLISADTQE-----KIKKAIAVIENLIQSA 231 (554)
T ss_pred cCCccHHHHHHHHhCCeEEEeccccccccc---cCCcccccccccccceeEEEecchHH-----HHHHHHHHHHHHHHhh
Confidence 999999999999999999999999999875 122334443 4689999999999865 89999999999998
Q ss_pred -CCCCchHHHHHHHHHHHHHHcCccCCCCC
Q 023341 234 -PVDESQDYIKRQQLRELAMLNSNFREDSP 262 (283)
Q Consensus 234 -p~~e~~D~~K~~QL~ELA~lNGt~r~~~~ 262 (283)
.++|+++++|+.||+|||-+|||+|++++
T Consensus 232 v~~~e~~n~l~~~Qlrela~lNgt~r~~d~ 261 (554)
T KOG0119|consen 232 VSVPEGQNDLKRLQLRELARLNGTLRDDDN 261 (554)
T ss_pred ccCccccccccHHHHHHHHHhCCCCCcccc
Confidence 68999999999999999999999999984
No 4
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.97 E-value=2.6e-32 Score=244.47 Aligned_cols=183 Identities=32% Similarity=0.360 Sum_probs=134.7
Q ss_pred CCCCcccccCCCCCCCC---ccccccCcCCCCCCCCCCCcccccCCCC-CCCCCCCCCCCCCCCcceeeEEEEecCCCCC
Q 023341 71 GFGDFDRLRHRSPSPMA---SSNLMSNVAGTGLGGWNGLPQERLGGPP-GMTMDWQSAPASPSSYTVKRILRLEIPVDTY 146 (283)
Q Consensus 71 ~~~d~~~~~~~SP~p~~---~~g~~~N~~~~~~~~~~~l~~Er~~~~~-~~~~~~~~~p~~~~~~~vk~~~kv~IPv~~~ 146 (283)
.|+...+- .+||+|++ ..|.+.|+++ .++...|.+||+.+.+ .+.+-.-..++...-.+.+.+.||||||++|
T Consensus 83 d~Vp~~re-~Rspsppp~yd~~GrRlntre--~ry~kkLeder~~l~era~k~lp~fv~p~dy~rpsk~q~KiYIPV~ey 159 (269)
T COG5176 83 DGVPSKRE-LRSPSPPPRYDEIGRRLNTRE--ARYNKKLEDERLWLKERAQKILPRFVLPNDYIRPSKYQNKIYIPVQEY 159 (269)
T ss_pred CCCCchhh-ccCCCCCcchhHHhhhhhHHH--HHHhhhhhHHHHHHHHHHHHhcCcccCCccccCcccccceEEeehhhC
Confidence 35555542 24555543 3688888885 3445778889887654 3444444445554455778899999999999
Q ss_pred CCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHH
Q 023341 147 PNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQE 226 (283)
Q Consensus 147 P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e 226 (283)
|+.||||+||||||.|+|+||+.|+|||.|||+||+|.++-..++.. .--...++||+||+++....++. .++....
T Consensus 160 Pe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~--~~~N~e~~lhcLI~adsedki~~-~ik~~~n 236 (269)
T COG5176 160 PESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPE--SLKNAEAVLHCLIEADSEDKICR-LIKSQLN 236 (269)
T ss_pred cccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCch--hhhhhHHhHHHHhhcchhhhHHH-HHHHHHH
Confidence 99999999999999999999999999999999999997654333221 11235789999999987654433 3334445
Q ss_pred HHHHccCCCCCchHHHHHHHHHHHHHHcCccCCC
Q 023341 227 IIEELLKPVDESQDYIKRQQLRELAMLNSNFRED 260 (283)
Q Consensus 227 ~Ie~LL~p~~e~~D~~K~~QL~ELA~lNGt~r~~ 260 (283)
.|.+... .|++++++|+-||++||-+|||+|++
T Consensus 237 ~I~~a~~-~PeGqnDlkR~qlr~la~lngtlr~d 269 (269)
T COG5176 237 AIREARR-NPEGQNDLKRFQLRWLAHLNGTLRAD 269 (269)
T ss_pred HHHHHhc-CCcccchHHHHHHHHHHHhcceecCC
Confidence 5555544 57999999999999999999999975
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=98.65 E-value=8.4e-08 Score=70.59 Aligned_cols=59 Identities=25% Similarity=0.466 Sum_probs=46.8
Q ss_pred EEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchh
Q 023341 136 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 215 (283)
Q Consensus 136 ~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~ 215 (283)
.+.+.|| -+++|+|||++|.|+|+||++|||+|.|--. -.|.|++.+++
T Consensus 3 ~~~i~Ip------~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~------------------------g~v~I~G~~~~- 51 (61)
T cd02393 3 IETMKIP------PDKIRDVIGPGGKTIKKIIEETGVKIDIEDD------------------------GTVYIAASDKE- 51 (61)
T ss_pred EEEEEeC------hhheeeeECCCchHHHHHHHHHCCEEEeCCC------------------------CEEEEEeCCHH-
Confidence 4557777 4788999999999999999999999988521 15889887654
Q ss_pred hHHHHHHHHHHHHH
Q 023341 216 IVDIRLRQAQEIIE 229 (283)
Q Consensus 216 ~~~~rl~~A~e~Ie 229 (283)
.++.|.++|+
T Consensus 52 ----~v~~A~~~I~ 61 (61)
T cd02393 52 ----AAEKAKKMIE 61 (61)
T ss_pred ----HHHHHHHHhC
Confidence 5778888764
No 6
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=98.52 E-value=9.5e-08 Score=68.85 Aligned_cols=59 Identities=29% Similarity=0.627 Sum_probs=46.4
Q ss_pred EEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhh
Q 023341 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANI 216 (283)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~ 216 (283)
.+|.|| ..++|+|||++|.++|+|+++|||+|.|...+ +.-.|.|++ +++
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 567787 68999999999999999999999999997541 122778888 543
Q ss_pred HHHHHHHHHHHH
Q 023341 217 VDIRLRQAQEII 228 (283)
Q Consensus 217 ~~~rl~~A~e~I 228 (283)
.+++|.++|
T Consensus 52 ---~v~~A~~~I 60 (60)
T PF00013_consen 52 ---QVEKAKKMI 60 (60)
T ss_dssp ---HHHHHHHHH
T ss_pred ---HHHHHHhhC
Confidence 567777765
No 7
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.42 E-value=9.2e-07 Score=63.50 Aligned_cols=62 Identities=29% Similarity=0.560 Sum_probs=46.5
Q ss_pred EEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhh
Q 023341 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANI 216 (283)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~ 216 (283)
.++.|| -+++|+||||+|+++++|+++|||+|.|...++ ...+-.|.|.+. .
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 467788 388999999999999999999999999986532 122336777775 1
Q ss_pred HHHHHHHHHHHH
Q 023341 217 VDIRLRQAQEII 228 (283)
Q Consensus 217 ~~~rl~~A~e~I 228 (283)
..+..|..+|
T Consensus 54 --~~v~~a~~~i 63 (64)
T cd00105 54 --EAVEKAKELI 63 (64)
T ss_pred --HHHHHHHHHh
Confidence 2566776665
No 8
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=98.39 E-value=2.6e-07 Score=90.53 Aligned_cols=90 Identities=14% Similarity=-0.010 Sum_probs=75.8
Q ss_pred eeeEEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecC
Q 023341 133 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADL 212 (283)
Q Consensus 133 vk~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~ 212 (283)
++...|.+|+++ .|.||.-+..=||+..+|..+|.+|+.++.||||||++-. ...| ++.+|||+|+|+...
T Consensus 208 ~~Y~~k~~v~~~-~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iE----P~~G----~EsnEPMYI~i~h~~ 278 (531)
T KOG1960|consen 208 RYYPNKALATDK-DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRRE----PNEG----NESNEPMYIFSTHGN 278 (531)
T ss_pred ccchhheecccC-CcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccC----cccc----cccCCceeEEeecCC
Confidence 334448899988 8999999999999999999999999999999999998753 1222 258999999999988
Q ss_pred chhhHHHHHHHHHHHHHHccCCCC
Q 023341 213 PANIVDIRLRQAQEIIEELLKPVD 236 (283)
Q Consensus 213 ~~~~~~~rl~~A~e~Ie~LL~p~~ 236 (283)
++ -+.+|+.++++|+.-+.
T Consensus 279 ~~-----g~~~A~r~~~nl~~~v~ 297 (531)
T KOG1960|consen 279 GN-----GENGAPRRKWNLEEKVY 297 (531)
T ss_pred ch-----hhccchhHHHhHHHHHH
Confidence 76 57899999999998653
No 9
>smart00322 KH K homology RNA-binding domain.
Probab=98.26 E-value=5.4e-06 Score=58.50 Aligned_cols=65 Identities=31% Similarity=0.563 Sum_probs=49.0
Q ss_pred EEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchh
Q 023341 136 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 215 (283)
Q Consensus 136 ~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~ 215 (283)
..+|.||. +++|++||++|.+++.|++.|||+|.+.+.++ ..-.|.|.+. +
T Consensus 4 ~~~i~i~~------~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--------------------~~~~v~i~g~-~-- 54 (69)
T smart00322 4 TIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--------------------EERVVEITGP-P-- 54 (69)
T ss_pred EEEEEEcc------hhcceeECCCchHHHHHHHHHCCEEEECCCCC--------------------CccEEEEEcC-H--
Confidence 45677873 78899999999999999999999999986533 1226777765 2
Q ss_pred hHHHHHHHHHHHHHHcc
Q 023341 216 IVDIRLRQAQEIIEELL 232 (283)
Q Consensus 216 ~~~~rl~~A~e~Ie~LL 232 (283)
..+..|.+.|.+.+
T Consensus 55 ---~~v~~a~~~i~~~~ 68 (69)
T smart00322 55 ---ENVEKAAELILEIL 68 (69)
T ss_pred ---HHHHHHHHHHHHHh
Confidence 25667777777654
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=98.22 E-value=2.6e-06 Score=61.66 Aligned_cols=59 Identities=24% Similarity=0.434 Sum_probs=44.4
Q ss_pred EEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhH
Q 023341 138 RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIV 217 (283)
Q Consensus 138 kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~~ 217 (283)
++.|| -.++|.|||++|.++++|+++|||+|.|-..++ .+=.|.|.+. .
T Consensus 3 ~i~Vp------~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~--------------------~~~~v~I~G~-~---- 51 (62)
T cd02394 3 EVEIP------KKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGS--------------------KSDTITITGP-K---- 51 (62)
T ss_pred EEEeC------HHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCC--------------------CCCEEEEEcC-H----
Confidence 46666 267799999999999999999999999986531 1126788776 2
Q ss_pred HHHHHHHHHHH
Q 023341 218 DIRLRQAQEII 228 (283)
Q Consensus 218 ~~rl~~A~e~I 228 (283)
..+..|+++|
T Consensus 52 -~~v~~A~~~i 61 (62)
T cd02394 52 -ENVEKAKEEI 61 (62)
T ss_pred -HHHHHHHHHh
Confidence 2566777765
No 11
>PF13014 KH_3: KH domain
Probab=98.17 E-value=1.6e-06 Score=59.22 Aligned_cols=28 Identities=36% Similarity=0.789 Sum_probs=26.9
Q ss_pred cccceeCCCchhHHHHHHhhCCeEEEec
Q 023341 151 FVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (283)
Q Consensus 151 fvGrILGPrG~TlK~le~eTgckI~IRG 178 (283)
|+|+|||++|.|+|+|+++|||+|.|--
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 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=98.09 E-value=1.2e-05 Score=59.20 Aligned_cols=36 Identities=28% Similarity=0.624 Sum_probs=32.4
Q ss_pred EEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEec
Q 023341 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (283)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRG 178 (283)
.|+.|| -+.+|+|||.+|.++|+|+++|||+|.|.-
T Consensus 2 ~r~~ip------~~~vg~iIG~~G~~i~~i~~~tga~I~i~~ 37 (65)
T cd02396 2 LRLLVP------SSQAGSIIGKGGSTIKEIREETGAKIRVSK 37 (65)
T ss_pred EEEEEC------HHHcCeeECCCcHHHHHHHHHHCCEEEEcC
Confidence 467888 688999999999999999999999999953
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=97.85 E-value=2.2e-05 Score=68.81 Aligned_cols=52 Identities=31% Similarity=0.526 Sum_probs=44.9
Q ss_pred cccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHHH
Q 023341 151 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEE 230 (283)
Q Consensus 151 fvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 230 (283)
.+|||||+.|.|++.||..|||+|.|-|+ .|.|.+ +++ +++.|.+.|+.
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 68999999999999999999999999751 577877 544 67889999999
Q ss_pred ccC
Q 023341 231 LLK 233 (283)
Q Consensus 231 LL~ 233 (283)
|+.
T Consensus 148 li~ 150 (172)
T TIGR03665 148 LIE 150 (172)
T ss_pred HHc
Confidence 986
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.78 E-value=4.1e-05 Score=67.65 Aligned_cols=52 Identities=31% Similarity=0.539 Sum_probs=43.6
Q ss_pred cccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHHH
Q 023341 151 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEE 230 (283)
Q Consensus 151 fvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 230 (283)
.+|||||+.|.|.|.||..|||+|.|-++ .|.|.+ +++ ++..|.+.|+.
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 68999999999999999999999999642 366666 443 67889999999
Q ss_pred ccC
Q 023341 231 LLK 233 (283)
Q Consensus 231 LL~ 233 (283)
|+.
T Consensus 154 li~ 156 (180)
T PRK13763 154 LIE 156 (180)
T ss_pred HHc
Confidence 886
No 15
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.74 E-value=8.6e-05 Score=77.91 Aligned_cols=71 Identities=25% Similarity=0.531 Sum_probs=60.0
Q ss_pred CCcceeeEEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEE
Q 023341 129 SSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILI 208 (283)
Q Consensus 129 ~~~~vk~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI 208 (283)
-++..-++..+.|| -..||.||||+|.|+|.|+++|||+|.|--.| +|.|
T Consensus 572 ~s~~aP~~~~~~I~------~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G------------------------~V~I 621 (719)
T TIGR02696 572 MSPYAPRIITVKIP------VDKIGEVIGPKGKMINQIQDETGAEISIEDDG------------------------TVYI 621 (719)
T ss_pred cccCCCeeEEEEeC------hHHhhheeCCCcHhHHHHHHHHCCEEEEecCc------------------------EEEE
Confidence 34456677788888 46689999999999999999999999998543 8899
Q ss_pred EecCchhhHHHHHHHHHHHHHHccCC
Q 023341 209 EADLPANIVDIRLRQAQEIIEELLKP 234 (283)
Q Consensus 209 ~a~~~~~~~~~rl~~A~e~Ie~LL~p 234 (283)
.+.+.+ ++++|++.|+.+..+
T Consensus 622 ~a~d~~-----~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 622 GAADGP-----SAEAARAMINAIANP 642 (719)
T ss_pred EeCCHH-----HHHHHHHHHHHhhCc
Confidence 998754 789999999999984
No 16
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.70 E-value=7.2e-05 Score=66.10 Aligned_cols=64 Identities=25% Similarity=0.475 Sum_probs=51.8
Q ss_pred EEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEE---ecCc
Q 023341 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIE---ADLP 213 (283)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~---a~~~ 213 (283)
..+.|| -+-+|.||||.|.|+|.|+++|||+|.|.-.. =.|.|. +.++
T Consensus 5 ~~i~IP------~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~-----------------------g~V~I~~~~~~d~ 55 (180)
T PRK13763 5 EYVKIP------KDRIGVLIGKKGETKKEIEERTGVKLEIDSET-----------------------GEVIIEPTDGEDP 55 (180)
T ss_pred EEEEcC------HHHhhhHhccchhHHHHHHHHHCcEEEEECCC-----------------------CeEEEEeCCCCCH
Confidence 456777 46789999999999999999999999998530 166776 4555
Q ss_pred hhhHHHHHHHHHHHHHHccCC
Q 023341 214 ANIVDIRLRQAQEIIEELLKP 234 (283)
Q Consensus 214 ~~~~~~rl~~A~e~Ie~LL~p 234 (283)
. .+.+|+++|+.++..
T Consensus 56 ~-----~i~kA~~~I~ai~~g 71 (180)
T PRK13763 56 L-----AVLKARDIVKAIGRG 71 (180)
T ss_pred H-----HHHHHHHHHHHHhcC
Confidence 3 789999999999884
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=97.53 E-value=0.0001 Score=64.62 Aligned_cols=58 Identities=24% Similarity=0.422 Sum_probs=46.7
Q ss_pred CccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEE--EecCchhhHHHHHHHHHH
Q 023341 149 FNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILI--EADLPANIVDIRLRQAQE 226 (283)
Q Consensus 149 ~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI--~a~~~~~~~~~rl~~A~e 226 (283)
-+.+|.||||+|.|+|.||++|||+|.|--. .=.|.| .+.++. .+.+|.+
T Consensus 6 ~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----------------------~g~V~I~~~t~d~~-----~i~kA~~ 57 (172)
T TIGR03665 6 KDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----------------------TGEVKIEEEDEDPL-----AVMKARE 57 (172)
T ss_pred HHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----------------------CceEEEecCCCCHH-----HHHHHHH
Confidence 4789999999999999999999999999842 014666 344543 6899999
Q ss_pred HHHHccCC
Q 023341 227 IIEELLKP 234 (283)
Q Consensus 227 ~Ie~LL~p 234 (283)
+|+.+...
T Consensus 58 ~I~~i~~g 65 (172)
T TIGR03665 58 VVKAIGRG 65 (172)
T ss_pred HHHHHHcC
Confidence 99998884
No 18
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.49 E-value=0.00021 Score=74.71 Aligned_cols=69 Identities=23% Similarity=0.369 Sum_probs=56.2
Q ss_pred CcceeeEEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEE
Q 023341 130 SYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIE 209 (283)
Q Consensus 130 ~~~vk~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~ 209 (283)
++..-++..+.|| -..||.||||+|.|+|.|+++|||+|.|--.| +|.|.
T Consensus 546 ~~~~p~~~~~~I~------~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG------------------------~V~i~ 595 (684)
T TIGR03591 546 SPYAPRIETIKIN------PDKIRDVIGPGGKVIREITEETGAKIDIEDDG------------------------TVKIA 595 (684)
T ss_pred cccCCeEEEEecC------HHHHHhhcCCCcHHHHHHHHHHCCEEEEecCe------------------------EEEEE
Confidence 3455567778888 46789999999999999999999999996433 78888
Q ss_pred ecCchhhHHHHHHHHHHHHHHccC
Q 023341 210 ADLPANIVDIRLRQAQEIIEELLK 233 (283)
Q Consensus 210 a~~~~~~~~~rl~~A~e~Ie~LL~ 233 (283)
+.+.+ .+++|.+.|+.+..
T Consensus 596 ~~~~~-----~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 596 ASDGE-----AAEAAIKMIEGITA 614 (684)
T ss_pred ECcHH-----HHHHHHHHHHhhhc
Confidence 87743 78999999998865
No 19
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.48 E-value=0.0002 Score=64.51 Aligned_cols=55 Identities=25% Similarity=0.452 Sum_probs=46.6
Q ss_pred cccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHHH
Q 023341 151 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEE 230 (283)
Q Consensus 151 fvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 230 (283)
..|||||+.|.|.+.||..|||.|.|.|+ +|.|-+. ++ .++.|.+.|+.
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 46999999999999999999999999995 6777663 33 57889999999
Q ss_pred ccCCCC
Q 023341 231 LLKPVD 236 (283)
Q Consensus 231 LL~p~~ 236 (283)
|+.-.+
T Consensus 161 li~G~~ 166 (194)
T COG1094 161 LINGAP 166 (194)
T ss_pred HHcCCC
Confidence 998654
No 20
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.04 E-value=0.00067 Score=72.82 Aligned_cols=71 Identities=20% Similarity=0.214 Sum_probs=58.7
Q ss_pred CCcceeeEEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCe-EEEeccCCCCCCCcccccCCCCCCCCCCCCceEE
Q 023341 129 SSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCR-VYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHIL 207 (283)
Q Consensus 129 ~~~~vk~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgck-I~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVl 207 (283)
-++..-++..+.|| -+.||.||||+|.|+|.|+++||++ |.|+-. -+|.
T Consensus 679 ~s~~aP~i~~~~i~------~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd------------------------g~V~ 728 (891)
T PLN00207 679 LSKYAPLIHIMKVK------PEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD------------------------GTVK 728 (891)
T ss_pred hcccCCeeEEEEcC------HHHHHHHhcCCchhHHHHHHHHCCCccCcCCC------------------------eeEE
Confidence 34455667778888 5779999999999999999999999 888753 3788
Q ss_pred EEecCchhhHHHHHHHHHHHHHHccCC
Q 023341 208 IEADLPANIVDIRLRQAQEIIEELLKP 234 (283)
Q Consensus 208 I~a~~~~~~~~~rl~~A~e~Ie~LL~p 234 (283)
|.+.+.+ ++++|++.|+.|..-
T Consensus 729 I~a~d~~-----~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 729 ITAKDLS-----SLEKSKAIISSLTMV 750 (891)
T ss_pred EEeCCHH-----HHHHHHHHHHHHhcC
Confidence 9888754 899999999998863
No 21
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=96.50 E-value=0.0058 Score=62.82 Aligned_cols=69 Identities=25% Similarity=0.481 Sum_probs=48.9
Q ss_pred EEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCce-EEEEecCch
Q 023341 136 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLH-ILIEADLPA 214 (283)
Q Consensus 136 ~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLH-VlI~a~~~~ 214 (283)
...|.|| =+-||.|||=.|.|+|.|+.+||+||.++= |.. | .-++. +.|. ...
T Consensus 231 ~~~V~VP------r~~VG~IIGkgGE~IKklq~etG~KIQfkp-----Dd~--------p-----~speR~~~Ii--G~~ 284 (600)
T KOG1676|consen 231 TREVKVP------RSKVGIIIGKGGEMIKKLQNETGAKIQFKP-----DDD--------P-----SSPERPAQII--GTV 284 (600)
T ss_pred eeEEecc------ccceeeEEecCchHHHHHhhccCceeEeec-----CCC--------C-----CCccceeeee--cCH
Confidence 3456666 367999999999999999999999999983 211 1 11222 2233 332
Q ss_pred hhHHHHHHHHHHHHHHccCC
Q 023341 215 NIVDIRLRQAQEIIEELLKP 234 (283)
Q Consensus 215 ~~~~~rl~~A~e~Ie~LL~p 234 (283)
.++.+|.++|.+|+.-
T Consensus 285 ----d~ie~Aa~lI~eii~~ 300 (600)
T KOG1676|consen 285 ----DQIEHAAELINEIIAE 300 (600)
T ss_pred ----HHHHHHHHHHHHHHHH
Confidence 3788999999999874
No 22
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=96.49 E-value=0.0065 Score=57.92 Aligned_cols=55 Identities=31% Similarity=0.593 Sum_probs=41.7
Q ss_pred cceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHHHcc
Q 023341 153 GRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELL 232 (283)
Q Consensus 153 GrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL 232 (283)
.|||||.|+|+|.||-.|.|-|.|.|. - |++-.+ ...|..+..+|++.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~-------------------------T--VsaiGp----fkGlkevr~IV~DcM 209 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN-------------------------T--VSAIGP----FKGLKEVRKIVEDCM 209 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc-------------------------E--EEeecC----cchHHHHHHHHHHHH
Confidence 489999999999999999999999995 1 334443 235777777777777
Q ss_pred CCCCCc
Q 023341 233 KPVDES 238 (283)
Q Consensus 233 ~p~~e~ 238 (283)
..++.-
T Consensus 210 ~NiHPi 215 (356)
T KOG2874|consen 210 KNIHPI 215 (356)
T ss_pred hccchH
Confidence 665543
No 23
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.39 E-value=0.0072 Score=55.52 Aligned_cols=58 Identities=22% Similarity=0.371 Sum_probs=47.7
Q ss_pred CccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHH
Q 023341 149 FNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEII 228 (283)
Q Consensus 149 ~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~I 228 (283)
-++++++|||+|.+++.|.++|+|+|.|-=.| .|+|.+.+.+ .+.+|++.|
T Consensus 153 ~~~i~~lig~~g~~i~~l~~~~~~~I~ig~NG------------------------~VwI~~~~~~-----~~~~a~~~I 203 (235)
T PRK04163 153 PVKVPRVIGKKGSMINMLKEETGCDIIVGQNG------------------------RIWIKGPDEE-----DEEIAIEAI 203 (235)
T ss_pred HHHHHhhcCCCChhHhhhhhhhCcEEEEcCCc------------------------EEEEeeCCHH-----HHHHHHHHH
Confidence 57899999999999999999999999994211 8999998865 567888888
Q ss_pred HHccCCC
Q 023341 229 EELLKPV 235 (283)
Q Consensus 229 e~LL~p~ 235 (283)
+.+-.-.
T Consensus 204 ~~~e~~~ 210 (235)
T PRK04163 204 KKIEREA 210 (235)
T ss_pred HHHHhhh
Confidence 8876643
No 24
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.38 E-value=0.0035 Score=65.85 Aligned_cols=56 Identities=23% Similarity=0.415 Sum_probs=47.4
Q ss_pred CccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHH
Q 023341 149 FNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEII 228 (283)
Q Consensus 149 ~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~I 228 (283)
.+.+|.+|||+|.|+|.|+++||++|.|+-.| .|.|.+.+.+ .+++|.+.|
T Consensus 562 ~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~G------------------------~v~i~~~~~~-----~~~~a~~~I 612 (693)
T PRK11824 562 PDKIRDVIGPGGKTIREITEETGAKIDIEDDG------------------------TVKIAATDGE-----AAEAAKERI 612 (693)
T ss_pred HHHHHHHhcCCchhHHHHHHHHCCccccCCCc------------------------eEEEEcccHH-----HHHHHHHHH
Confidence 46789999999999999999999999886433 6778877754 789999999
Q ss_pred HHccC
Q 023341 229 EELLK 233 (283)
Q Consensus 229 e~LL~ 233 (283)
+.+..
T Consensus 613 ~~~~~ 617 (693)
T PRK11824 613 EGITA 617 (693)
T ss_pred HHhcc
Confidence 99875
No 25
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.11 E-value=0.002 Score=64.20 Aligned_cols=38 Identities=42% Similarity=0.785 Sum_probs=34.0
Q ss_pred ecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEe
Q 023341 140 EIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 177 (283)
Q Consensus 140 ~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IR 177 (283)
.||++-.-.-||+|||||-.|.++|.||++||+||.|-
T Consensus 279 e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis 316 (584)
T KOG2193|consen 279 EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITIS 316 (584)
T ss_pred hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeee
Confidence 56777656679999999999999999999999999996
No 26
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=96.03 E-value=0.013 Score=60.23 Aligned_cols=74 Identities=27% Similarity=0.600 Sum_probs=57.0
Q ss_pred ceeeEEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEec
Q 023341 132 TVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEAD 211 (283)
Q Consensus 132 ~vk~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~ 211 (283)
.++.+..|.|| =|=+|+|||-.|.|+|+|++.||||+.+-=.|+.-+. .+.||. |+++
T Consensus 136 ~~~ttqeI~IP------a~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~--------------~~Kplr--itGd 193 (600)
T KOG1676|consen 136 SVETTQEILIP------ANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG--------------ADKPLR--ITGD 193 (600)
T ss_pred ccceeeeeccC------ccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC--------------CCCcee--ecCC
Confidence 45667778888 4678999999999999999999999988766664432 233444 5553
Q ss_pred CchhhHHHHHHHHHHHHHHccC
Q 023341 212 LPANIVDIRLRQAQEIIEELLK 233 (283)
Q Consensus 212 ~~~~~~~~rl~~A~e~Ie~LL~ 233 (283)
+. ++..|.++|-++|.
T Consensus 194 -p~-----~ve~a~~lV~dil~ 209 (600)
T KOG1676|consen 194 -PD-----KVEQAKQLVADILR 209 (600)
T ss_pred -HH-----HHHHHHHHHHHHHH
Confidence 32 78999999999998
No 27
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=94.96 E-value=0.034 Score=53.95 Aligned_cols=61 Identities=20% Similarity=0.301 Sum_probs=45.0
Q ss_pred CccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhh--HHHHHHHHHH
Q 023341 149 FNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANI--VDIRLRQAQE 226 (283)
Q Consensus 149 ~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~--~~~rl~~A~e 226 (283)
--|+|.|+|-+|.|.|.||+||+|+|.+=-.+..++ ||-|++-.-.++ |..||+.++.
T Consensus 65 s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~--------------------~i~i~~~~~~~V~~a~~Ri~~~id 124 (345)
T KOG2814|consen 65 SSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKE--------------------EIKIIGISRNCVIQALERIAKLID 124 (345)
T ss_pred HHHhhhhhcccchHHHHHHHhhccceEccCCCCCcc--------------------eEEEeehhHHHHHHHHHHHHHHHH
Confidence 468899999999999999999999999864432221 788888665543 3446666666
Q ss_pred HHH
Q 023341 227 IIE 229 (283)
Q Consensus 227 ~Ie 229 (283)
-..
T Consensus 125 s~r 127 (345)
T KOG2814|consen 125 SDR 127 (345)
T ss_pred hhh
Confidence 555
No 28
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=94.86 E-value=0.023 Score=56.87 Aligned_cols=37 Identities=32% Similarity=0.674 Sum_probs=32.3
Q ss_pred EEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEecc
Q 023341 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 179 (283)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGk 179 (283)
.|++|| --|+|.||||.|.|+|.|-+.|.|||-+--+
T Consensus 201 lR~lVp------tqyvgaIIGkeG~TIknItkqTqsriD~hrk 237 (584)
T KOG2193|consen 201 LRLLVP------TQYVGAIIGKEGATIKNITKQTQSRIDVHRK 237 (584)
T ss_pred eeeeec------cceeEEEecCCCccccCcchhhhheeeeeec
Confidence 356666 5799999999999999999999999999854
No 29
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=94.63 E-value=0.13 Score=50.19 Aligned_cols=37 Identities=24% Similarity=0.536 Sum_probs=33.5
Q ss_pred eEEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEe
Q 023341 135 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 177 (283)
Q Consensus 135 ~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IR 177 (283)
...||+|| -+-.|-|||-.|.|+.+||++|||+|.+-
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 45689999 56789999999999999999999999986
No 30
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=94.59 E-value=0.075 Score=54.03 Aligned_cols=40 Identities=28% Similarity=0.529 Sum_probs=36.5
Q ss_pred eeEEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEecc
Q 023341 134 KRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 179 (283)
Q Consensus 134 k~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGk 179 (283)
....|+.|| -+-+|-|||=+|+.+|.|.++|||+|.|.+.
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 456899999 6789999999999999999999999999985
No 31
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=93.52 E-value=0.32 Score=47.57 Aligned_cols=38 Identities=18% Similarity=0.511 Sum_probs=32.4
Q ss_pred eEEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEec
Q 023341 135 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (283)
Q Consensus 135 ~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRG 178 (283)
++.||.+|-. -.|.|||+.|.|+|.+.+++||-|.|--
T Consensus 132 kqikivvPNs------tag~iigkggAtiK~~~Eqsga~iqisP 169 (402)
T KOG2191|consen 132 KQIKIVVPNS------TAGMIIGKGGATIKAIQEQSGAWIQISP 169 (402)
T ss_pred ceeEEeccCC------cccceecCCcchHHHHHHhhCcceEecc
Confidence 4567888833 3599999999999999999999999973
No 32
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=92.96 E-value=0.14 Score=54.00 Aligned_cols=67 Identities=27% Similarity=0.486 Sum_probs=51.5
Q ss_pred ceeeEEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEec
Q 023341 132 TVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEAD 211 (283)
Q Consensus 132 ~vk~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~ 211 (283)
...+++.+-|+.+. ++-+|||+|.|+|.|.++|||+|.|--.|+ |.|.+.
T Consensus 549 ~aPri~t~~i~~dK------I~dvIG~gGk~I~~I~eetg~~IdieddGt------------------------v~i~~s 598 (692)
T COG1185 549 YAPRIETIKIDPDK------IRDVIGPGGKTIKAITEETGVKIDIEDDGT------------------------VKIAAS 598 (692)
T ss_pred cCCceEEEccCHHH------HhhccCCcccchhhhhhhhCcEEEecCCCc------------------------EEEEec
Confidence 33445556666555 577999999999999999999999987664 456666
Q ss_pred CchhhHHHHHHHHHHHHHHccC
Q 023341 212 LPANIVDIRLRQAQEIIEELLK 233 (283)
Q Consensus 212 ~~~~~~~~rl~~A~e~Ie~LL~ 233 (283)
+.+ ++.+|.+.|+.++.
T Consensus 599 ~~~-----~~~~ak~~I~~i~~ 615 (692)
T COG1185 599 DGE-----SAKKAKERIEAITR 615 (692)
T ss_pred chH-----HHHHHHHHHHHHHh
Confidence 643 67889999999874
No 33
>PRK00106 hypothetical protein; Provisional
Probab=92.10 E-value=0.26 Score=50.78 Aligned_cols=63 Identities=30% Similarity=0.539 Sum_probs=48.9
Q ss_pred EEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhH
Q 023341 138 RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIV 217 (283)
Q Consensus 138 kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~~ 217 (283)
-|.+|-+ .+-|||||--|-+++.+|..||+.|.|=- .|=-|.|+++||.
T Consensus 228 ~v~lp~d-----emkGriIGreGrNir~~E~~tGvdliidd-----------------------tp~~v~lS~fdpv--- 276 (535)
T PRK00106 228 TVHLPDD-----NMKGRIIGREGRNIRTLESLTGIDVIIDD-----------------------TPEVVVLSGFDPI--- 276 (535)
T ss_pred eEEcCCh-----HhhcceeCCCcchHHHHHHHhCceEEEcC-----------------------CCCeEEEeCCChH---
Confidence 3556644 45699999999999999999999999852 2337899999996
Q ss_pred HHHHHHHHHHHHHccC
Q 023341 218 DIRLRQAQEIIEELLK 233 (283)
Q Consensus 218 ~~rl~~A~e~Ie~LL~ 233 (283)
|-.-|..-+++|+.
T Consensus 277 --RReiAr~~le~Li~ 290 (535)
T PRK00106 277 --RREIARMTLESLIK 290 (535)
T ss_pred --HHHHHHHHHHHHHH
Confidence 44556667777765
No 34
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=91.43 E-value=0.3 Score=49.89 Aligned_cols=62 Identities=26% Similarity=0.544 Sum_probs=46.4
Q ss_pred EecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHH
Q 023341 139 LEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVD 218 (283)
Q Consensus 139 v~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~~~ 218 (283)
|.+|-+ .+-|||||--|-++|.+|..||+-|.|=- .|=-|.|+++||.
T Consensus 208 v~lp~d-----~~kgriigreGrnir~~e~~tgvd~iidd-----------------------tp~~v~ls~fdp~---- 255 (514)
T TIGR03319 208 VNLPND-----EMKGRIIGREGRNIRALETLTGVDLIIDD-----------------------TPEAVILSGFDPV---- 255 (514)
T ss_pred EEcCCh-----hhhccccCCCcchHHHHHHHhCceEEEcC-----------------------CCCeEEecCCchH----
Confidence 556644 45699999999999999999999999952 2337889999986
Q ss_pred HHHHHHHHHHHHccC
Q 023341 219 IRLRQAQEIIEELLK 233 (283)
Q Consensus 219 ~rl~~A~e~Ie~LL~ 233 (283)
|=.-|..-+++|+.
T Consensus 256 -rreia~~~l~~li~ 269 (514)
T TIGR03319 256 -RREIARMALEKLIQ 269 (514)
T ss_pred -HHHHHHHHHHHHHH
Confidence 33445555566654
No 35
>PRK12704 phosphodiesterase; Provisional
Probab=91.00 E-value=0.43 Score=48.90 Aligned_cols=49 Identities=24% Similarity=0.562 Sum_probs=39.8
Q ss_pred EecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchh
Q 023341 139 LEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 215 (283)
Q Consensus 139 v~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~ 215 (283)
|.+|-+ .+-|||||--|-++|.+|..||+.|.|=- .|=-|+||+.+|..
T Consensus 214 v~lp~d-----~mkgriigreGrnir~~e~~tgvd~iidd-----------------------tp~~v~ls~~~~~r 262 (520)
T PRK12704 214 VNLPND-----EMKGRIIGREGRNIRALETLTGVDLIIDD-----------------------TPEAVILSGFDPIR 262 (520)
T ss_pred eecCCc-----hhhcceeCCCcchHHHHHHHhCCeEEEcC-----------------------CCCeEEEecCChhh
Confidence 456644 45699999999999999999999999952 23378999999874
No 36
>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=88.32 E-value=0.46 Score=34.77 Aligned_cols=36 Identities=19% Similarity=0.393 Sum_probs=30.1
Q ss_pred eEEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEE
Q 023341 135 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYI 176 (283)
Q Consensus 135 ~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~I 176 (283)
...++.||. .-+|+.||.+|.+++.++..+|.+|.|
T Consensus 25 ~~~~v~V~~------~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPD------DQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECc------ccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 345677775 446999999999999999999998876
No 37
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=88.02 E-value=0.18 Score=50.43 Aligned_cols=72 Identities=26% Similarity=0.505 Sum_probs=58.8
Q ss_pred ceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHHHccC
Q 023341 154 RLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLK 233 (283)
Q Consensus 154 rILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL~ 233 (283)
.|.||.|.+.|.++.+|-+++.|.|-||..-. . +.....++|.||.|.+.++. .|+.|+-+++.++-
T Consensus 308 ~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i~-------p-~~~~~~~~p~~~~~~~~~~~-----~~~~~~~~~~~~i~ 374 (531)
T KOG1960|consen 308 AIVGPQGAYVKHIQQETRTRVQIKGQGSAFIE-------P-STNRESDEPIHLCIMSHDPN-----AIQRAKVLCEDLIA 374 (531)
T ss_pred ccccCCcccccccCCCCCcceeccCccceeec-------C-CCCCCCCCCcccccccCChh-----hhhhhhhcccccCC
Confidence 47899999999999999999999999997732 1 22335799999999988765 56778888999999
Q ss_pred CCCCc
Q 023341 234 PVDES 238 (283)
Q Consensus 234 p~~e~ 238 (283)
||+..
T Consensus 375 ~v~~q 379 (531)
T KOG1960|consen 375 SVHQQ 379 (531)
T ss_pred ccccc
Confidence 88743
No 38
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=87.59 E-value=0.48 Score=48.28 Aligned_cols=41 Identities=24% Similarity=0.483 Sum_probs=36.5
Q ss_pred eeeEEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEecc
Q 023341 133 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 179 (283)
Q Consensus 133 vk~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGk 179 (283)
.....++.|| .+++|.|||..|+.+-.|++.|||.|.|.++
T Consensus 336 ~~v~~~l~vp------s~~igciiGk~G~~iseir~~tgA~I~I~~~ 376 (485)
T KOG2190|consen 336 QTVTQRLLVP------SDLIGCIIGKGGAKISEIRQRTGASISILNK 376 (485)
T ss_pred ceeeeeeccC------ccccceeecccccchHHHHHhcCCceEEccc
Confidence 3445678888 7999999999999999999999999999975
No 39
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=85.78 E-value=0.41 Score=48.49 Aligned_cols=29 Identities=31% Similarity=0.628 Sum_probs=26.6
Q ss_pred CccccceeCCCchhHHHHHHhhCCeEEEe
Q 023341 149 FNFVGRLLGPRGNSLKRVEATTGCRVYIR 177 (283)
Q Consensus 149 ~NfvGrILGPrG~TlK~le~eTgckI~IR 177 (283)
-||||.+||=.|+.+|+||..|+++|.|-
T Consensus 55 s~mvg~vigrggskik~iq~~tnt~iqii 83 (629)
T KOG0336|consen 55 SEMVGKVIGRGGSKIKRIQNDTNTRIQII 83 (629)
T ss_pred hhhhheeeccCcchhhhhhcccceeEEEe
Confidence 48999999999999999999999988763
No 40
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=82.99 E-value=0.72 Score=34.97 Aligned_cols=32 Identities=25% Similarity=0.518 Sum_probs=24.9
Q ss_pred CCCCccccceeCCCchhHHHHHHhh-CCeEEEe
Q 023341 146 YPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIR 177 (283)
Q Consensus 146 ~P~~NfvGrILGPrG~TlK~le~eT-gckI~IR 177 (283)
.|+++-+|..+|++|..+|.|+++. |-||.|=
T Consensus 13 ~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 13 DPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp STTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred CCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 3789999999999999999999999 6555554
No 41
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=80.89 E-value=4 Score=38.26 Aligned_cols=30 Identities=27% Similarity=0.561 Sum_probs=27.4
Q ss_pred CccccceeCCCchhHHHHHHhhCCeEEEec
Q 023341 149 FNFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (283)
Q Consensus 149 ~NfvGrILGPrG~TlK~le~eTgckI~IRG 178 (283)
.++|-|+||.+|+-++.|.+.|+|+|.|==
T Consensus 154 p~kVpRvig~~~sm~~~l~~~~~~~I~VG~ 183 (239)
T COG1097 154 PSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ 183 (239)
T ss_pred hhhcceEecCCCcHHHHhhhhcCeEEEEec
Confidence 578889999999999999999999999853
No 42
>PRK12705 hypothetical protein; Provisional
Probab=79.04 E-value=3.3 Score=42.63 Aligned_cols=31 Identities=29% Similarity=0.600 Sum_probs=27.3
Q ss_pred CCCccccceeCCCchhHHHHHHhhCCeEEEe
Q 023341 147 PNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 177 (283)
Q Consensus 147 P~~NfvGrILGPrG~TlK~le~eTgckI~IR 177 (283)
|+=.+-|||||--|.+++.+|..||+-|.|-
T Consensus 205 p~demkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 205 PSDAMKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred CChHhhccccCccchhHHHHHHhhCCceEec
Confidence 3445669999999999999999999999885
No 43
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=78.58 E-value=5.4 Score=36.31 Aligned_cols=65 Identities=26% Similarity=0.465 Sum_probs=46.3
Q ss_pred EEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEec----C
Q 023341 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEAD----L 212 (283)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~----~ 212 (283)
+.|.||-+. +|-++|+.|.+.|.||+.|||+|.|-.+.. -|-|... |
T Consensus 10 ~~v~iPk~R------~~~lig~~g~v~k~ie~~~~~~~~iD~~~~-----------------------~V~i~~~~~t~D 60 (194)
T COG1094 10 EAVKIPKDR------IGVLIGKWGEVKKAIEEKTGVKLRIDSKTG-----------------------SVTIRTTRKTED 60 (194)
T ss_pred eeeecCchh------heeeecccccchHHHHhhcCeEEEEECCCC-----------------------eEEEEecCCCCC
Confidence 445566332 589999999999999999999999987621 2333333 3
Q ss_pred chhhHHHHHHHHHHHHHHccCCC
Q 023341 213 PANIVDIRLRQAQEIIEELLKPV 235 (283)
Q Consensus 213 ~~~~~~~rl~~A~e~Ie~LL~p~ 235 (283)
|- .+.+|.++|+.+=.-.
T Consensus 61 p~-----~~~ka~d~VkAIgrGF 78 (194)
T COG1094 61 PL-----ALLKARDVVKAIGRGF 78 (194)
T ss_pred hH-----HHHHHHHHHHHHhcCC
Confidence 32 5778888888776544
No 44
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=75.90 E-value=2.3 Score=44.59 Aligned_cols=54 Identities=28% Similarity=0.361 Sum_probs=42.5
Q ss_pred cccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHHH
Q 023341 151 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEE 230 (283)
Q Consensus 151 fvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 230 (283)
-+..+|||.|-.+|.|+.|||+.-+|- +=|+-|-|.++. .+.+|.+.|..
T Consensus 607 k~~~lIGp~G~~~kki~~EtGai~~vD-------------------------e~t~~i~A~~~~-----am~~Ak~~I~~ 656 (760)
T KOG1067|consen 607 KRATLIGPGGVLKKKIEVETGAISQVD-------------------------EGTFSIFAPTQA-----AMEEAKEFIDG 656 (760)
T ss_pred hhheeecCccceeeeEeeeccceeeec-------------------------CceEEEEecCHH-----HHHHHHHHHHH
Confidence 356799999999999999999443332 128888888764 78999999999
Q ss_pred ccCC
Q 023341 231 LLKP 234 (283)
Q Consensus 231 LL~p 234 (283)
+..-
T Consensus 657 i~~~ 660 (760)
T KOG1067|consen 657 IIKD 660 (760)
T ss_pred HhcC
Confidence 9873
No 45
>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=74.82 E-value=2.6 Score=29.67 Aligned_cols=23 Identities=13% Similarity=0.368 Sum_probs=20.7
Q ss_pred ccceeCCCchhHHHHHHhhCCeE
Q 023341 152 VGRLLGPRGNSLKRVEATTGCRV 174 (283)
Q Consensus 152 vGrILGPrG~TlK~le~eTgckI 174 (283)
.|++||.+|.+++.|+..++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 49999999999999999998554
No 46
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=71.87 E-value=3.3 Score=35.40 Aligned_cols=29 Identities=24% Similarity=0.400 Sum_probs=26.8
Q ss_pred ccccceeCCCchhHHHHHHhhCCeEEEec
Q 023341 150 NFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (283)
Q Consensus 150 NfvGrILGPrG~TlK~le~eTgckI~IRG 178 (283)
+.+|..+|++|..+|.|++..|-||.|=.
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 47
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=62.44 E-value=5.5 Score=39.03 Aligned_cols=37 Identities=22% Similarity=0.354 Sum_probs=30.2
Q ss_pred eeeEEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEE
Q 023341 133 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVY 175 (283)
Q Consensus 133 vk~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~ 175 (283)
....+.+.+| +-||+.|.|++|.++|.|+++|.+.|.
T Consensus 24 ~nvt~sv~vp------s~~v~~ivg~qg~kikalr~KTqtyi~ 60 (394)
T KOG2113|consen 24 QNVTESVEVP------SEHVAEIVGRQGCKIKALRAKTQTYIK 60 (394)
T ss_pred CccceeeecC------cccceeecccCccccchhhhhhcceec
Confidence 3344455566 678999999999999999999999885
No 48
>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=61.75 E-value=4.9 Score=30.49 Aligned_cols=23 Identities=26% Similarity=0.538 Sum_probs=20.0
Q ss_pred ccceeCCCchhHHHHHHhhCCeE
Q 023341 152 VGRLLGPRGNSLKRVEATTGCRV 174 (283)
Q Consensus 152 vGrILGPrG~TlK~le~eTgckI 174 (283)
.|+|||-+|.|++.||--+..-+
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~~~ 57 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANLVL 57 (77)
T ss_pred CCeEECCCCccHHHHHHHHHHHH
Confidence 49999999999999999987443
No 49
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=51.60 E-value=4.6 Score=30.06 Aligned_cols=21 Identities=29% Similarity=0.616 Sum_probs=18.6
Q ss_pred ccceeCCCchhHHHHHHhhCC
Q 023341 152 VGRLLGPRGNSLKRVEATTGC 172 (283)
Q Consensus 152 vGrILGPrG~TlK~le~eTgc 172 (283)
.|+|||-+|.|++.||--++.
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHHH
T ss_pred cceEECCCCeeHHHHHHHHHH
Confidence 599999999999999987653
No 50
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=51.52 E-value=27 Score=34.46 Aligned_cols=30 Identities=30% Similarity=0.503 Sum_probs=27.6
Q ss_pred ccccceeCCCchhHHHHHHhhCCeEEEecc
Q 023341 150 NFVGRLLGPRGNSLKRVEATTGCRVYIRGK 179 (283)
Q Consensus 150 NfvGrILGPrG~TlK~le~eTgckI~IRGk 179 (283)
|-+-.|+||.|..++.||+.+|+.|.-||.
T Consensus 24 ~~~~~l~G~~~~~l~l~e~~~gv~i~~rG~ 53 (348)
T COG1702 24 NELVALFGPTDTNLSLLEIALGVSIVARGE 53 (348)
T ss_pred hhhhhhcCCCCccHHHHHHHhCcEEEeCCc
Confidence 667789999999999999999999999985
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=50.95 E-value=13 Score=31.98 Aligned_cols=29 Identities=24% Similarity=0.414 Sum_probs=26.7
Q ss_pred ccccceeCCCchhHHHHHHhhCCeEEEec
Q 023341 150 NFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (283)
Q Consensus 150 NfvGrILGPrG~TlK~le~eTgckI~IRG 178 (283)
+-+|..+|++|..+|.|++..|=||.|=.
T Consensus 42 g~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 42 GEMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred CCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 57899999999999999999999998876
No 52
>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=48.22 E-value=34 Score=31.34 Aligned_cols=40 Identities=15% Similarity=0.353 Sum_probs=30.7
Q ss_pred eeeEEEEecCCCCCCCCccccceeCCCchhHHHH--------HHhhCCeEEEe
Q 023341 133 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRV--------EATTGCRVYIR 177 (283)
Q Consensus 133 vk~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~l--------e~eTgckI~IR 177 (283)
+.....|+|.-+.+- |-|||.+|.++|+| |+..||+|.+.
T Consensus 219 ~~i~~~i~v~~~s~k-----~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l~ 266 (270)
T TIGR00436 219 LKIHALISVERESQK-----KIIIGKNGSMIKAIGIAARKDILELFDCDVFLE 266 (270)
T ss_pred EEEEEEEEECcCCce-----eEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 344556777766554 89999999999986 77789988764
No 53
>PRK02821 hypothetical protein; Provisional
Probab=47.78 E-value=11 Score=29.37 Aligned_cols=23 Identities=13% Similarity=0.416 Sum_probs=18.6
Q ss_pred ccccceeCCCchhHHHHHHhhCC
Q 023341 150 NFVGRLLGPRGNSLKRVEATTGC 172 (283)
Q Consensus 150 NfvGrILGPrG~TlK~le~eTgc 172 (283)
.=+|||||=+|.|++.|-.--.+
T Consensus 40 ~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 40 DDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred hhCcceeCCCCchHHHHHHHHHH
Confidence 44799999999999998765543
No 54
>PRK00468 hypothetical protein; Provisional
Probab=46.86 E-value=12 Score=28.97 Aligned_cols=19 Identities=21% Similarity=0.590 Sum_probs=16.3
Q ss_pred ccceeCCCchhHHHHHHhh
Q 023341 152 VGRLLGPRGNSLKRVEATT 170 (283)
Q Consensus 152 vGrILGPrG~TlK~le~eT 170 (283)
+|||||=+|.|++.|-.--
T Consensus 41 ~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CcceecCCChhHHHHHHHH
Confidence 5999999999999986543
No 55
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=46.24 E-value=20 Score=35.44 Aligned_cols=34 Identities=24% Similarity=0.510 Sum_probs=30.1
Q ss_pred CCCCCccccceeCCCchhHHHHHHhh-CCeEEEec
Q 023341 145 TYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 178 (283)
Q Consensus 145 ~~P~~NfvGrILGPrG~TlK~le~eT-gckI~IRG 178 (283)
.-|+++-+|..+|++|..++.|.++. |=+|-|=-
T Consensus 240 ~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv~ 274 (362)
T PRK12327 240 NNPNVDAKGACVGPKGQRVQNIVSELKGEKIDIID 274 (362)
T ss_pred CCCCCCchheeECCCChhHHHHHHHhCCCeEEEEE
Confidence 45899999999999999999999998 88887754
No 56
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=43.84 E-value=44 Score=32.40 Aligned_cols=38 Identities=18% Similarity=0.364 Sum_probs=30.4
Q ss_pred eEEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEec
Q 023341 135 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (283)
Q Consensus 135 ~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRG 178 (283)
...+|++--+. .|.|+|-.|.++|+|-.+.++.|+|-.
T Consensus 48 ~e~ril~~sk~------agavigkgg~nik~lr~d~na~v~vpd 85 (390)
T KOG2192|consen 48 VELRILLQSKN------AGAVIGKGGKNIKALRTDYNASVSVPD 85 (390)
T ss_pred eeEEEEEeccc------ccceeccccccHHHHhhhccceeeccC
Confidence 34456665443 499999999999999999999998863
No 57
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=42.65 E-value=22 Score=32.16 Aligned_cols=33 Identities=24% Similarity=0.376 Sum_probs=29.1
Q ss_pred CCCccccceeCCCchhHHHHHHhhCCeEEEecc
Q 023341 147 PNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 179 (283)
Q Consensus 147 P~~NfvGrILGPrG~TlK~le~eTgckI~IRGk 179 (283)
++.+=+|..+|++|..+|.|.++.|=+|-|=.-
T Consensus 82 ~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~ 114 (190)
T COG0195 82 VKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW 114 (190)
T ss_pred cCcCchhhhccCCChHHHHHHHHhCCceEEEEe
Confidence 457779999999999999999999988887754
No 58
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=42.18 E-value=19 Score=38.83 Aligned_cols=37 Identities=24% Similarity=0.542 Sum_probs=29.8
Q ss_pred EEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEec
Q 023341 136 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (283)
Q Consensus 136 ~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRG 178 (283)
...+.||. -|-+-|+||+|.++++++.+++|-|.+--
T Consensus 710 ~~~~~~p~------~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 710 TKEIEIPR------SLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred eeEEeccH------HHhhhccCCCCccHHHHHHHhccceecCC
Confidence 34567774 45578999999999999999999887753
No 59
>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=41.87 E-value=26 Score=34.31 Aligned_cols=34 Identities=24% Similarity=0.461 Sum_probs=29.8
Q ss_pred CCCCCccccceeCCCchhHHHHHHhh-CCeEEEec
Q 023341 145 TYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 178 (283)
Q Consensus 145 ~~P~~NfvGrILGPrG~TlK~le~eT-gckI~IRG 178 (283)
..|+++-+|..+|++|+.++.|.++. |=+|-|=-
T Consensus 238 ~~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~ 272 (341)
T TIGR01953 238 NDENIDPVGACVGPKGSRIQAISKELNGEKIDIIE 272 (341)
T ss_pred CCCCCCcceeeECCCCchHHHHHHHhCCCeEEEEE
Confidence 45899999999999999999999998 77777654
No 60
>PRK15494 era GTPase Era; Provisional
Probab=41.42 E-value=46 Score=31.97 Aligned_cols=40 Identities=25% Similarity=0.356 Sum_probs=32.0
Q ss_pred eeeEEEEecCCCCCCCCccccceeCCCchhHHHH--------HHhhCCeEEEe
Q 023341 133 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRV--------EATTGCRVYIR 177 (283)
Q Consensus 133 vk~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~l--------e~eTgckI~IR 177 (283)
++....|+|.-+.+- |-|||-+|..+|+| |+..||||.+.
T Consensus 271 ~~i~~~i~v~~~sqk-----~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 271 VKINQVIVVSRESYK-----TIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred EEEEEEEEECCCCce-----eEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 445567888866655 89999999999986 78889998876
No 61
>PRK00089 era GTPase Era; Reviewed
Probab=41.16 E-value=48 Score=30.43 Aligned_cols=40 Identities=25% Similarity=0.456 Sum_probs=30.9
Q ss_pred eeeEEEEecCCCCCCCCccccceeCCCchhHHHH--------HHhhCCeEEEe
Q 023341 133 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRV--------EATTGCRVYIR 177 (283)
Q Consensus 133 vk~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~l--------e~eTgckI~IR 177 (283)
++....|+|.-+.+ .+-|||-+|.++|+| |+..||+|.+.
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 44455677776655 489999999999986 77889988876
No 62
>KOG4165 consensus Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism]
Probab=41.13 E-value=29 Score=34.60 Aligned_cols=61 Identities=23% Similarity=0.434 Sum_probs=42.1
Q ss_pred ccccceeCCCchh--HHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHH-------
Q 023341 150 NFVGRLLGPRGNS--LKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIR------- 220 (283)
Q Consensus 150 NfvGrILGPrG~T--lK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~~~~r------- 220 (283)
++|-+|| |||++ +++|+..|. |-+.| |.+.--||+|--+.....|..-
T Consensus 190 ~~IDLvI-PRGSs~LVr~Ik~~tk--IPVLG--------------------HA~GichvYvd~dad~~kA~riv~DaK~d 246 (433)
T KOG4165|consen 190 DYIDLVI-PRGSSDLVRSIKDTTK--IPVLG--------------------HAEGICHVYVDKDADLDKAKRIVRDAKCD 246 (433)
T ss_pred hheeEEe-cCCcHHHHHHHhhccc--Ccccc--------------------cccceeEEEeccccCHHHHHHHHhcccCC
Confidence 5677777 99998 678887775 88888 4556669999665444333211
Q ss_pred HHHHHHHHHHccC
Q 023341 221 LRQAQEIIEELLK 233 (283)
Q Consensus 221 l~~A~e~Ie~LL~ 233 (283)
.-+||.-+|.||.
T Consensus 247 YPAaCNAmETLLI 259 (433)
T KOG4165|consen 247 YPAACNAMETLLI 259 (433)
T ss_pred CchhhhhHHHHhc
Confidence 1257788888887
No 63
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=40.58 E-value=23 Score=31.42 Aligned_cols=27 Identities=22% Similarity=0.260 Sum_probs=25.5
Q ss_pred cceeCCCchhHHHHHHhhCCeEEEecc
Q 023341 153 GRLLGPRGNSLKRVEATTGCRVYIRGK 179 (283)
Q Consensus 153 GrILGPrG~TlK~le~eTgckI~IRGk 179 (283)
|.-||++|.++|+|++..|=+|.|=.-
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEEEc
Confidence 999999999999999999999998874
No 64
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=39.89 E-value=26 Score=29.94 Aligned_cols=25 Identities=20% Similarity=0.352 Sum_probs=22.3
Q ss_pred ccceeCCCchhHHHHHHhhCCeEEE
Q 023341 152 VGRLLGPRGNSLKRVEATTGCRVYI 176 (283)
Q Consensus 152 vGrILGPrG~TlK~le~eTgckI~I 176 (283)
.|+.||.+|.|++.++.-+|-.+-|
T Consensus 110 ~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 110 KGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred cchhhCCCCHHHHHHHHHhCCccCC
Confidence 5999999999999999999877654
No 65
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=39.55 E-value=18 Score=28.29 Aligned_cols=17 Identities=18% Similarity=0.769 Sum_probs=15.2
Q ss_pred ccceeCCCchhHHHHHH
Q 023341 152 VGRLLGPRGNSLKRVEA 168 (283)
Q Consensus 152 vGrILGPrG~TlK~le~ 168 (283)
+|++||=+|.|++.|-.
T Consensus 41 ~GkvIGk~GRti~AIRT 57 (76)
T COG1837 41 MGKVIGKQGRTIQAIRT 57 (76)
T ss_pred ccceecCCChhHHHHHH
Confidence 59999999999999854
No 66
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=38.75 E-value=43 Score=34.20 Aligned_cols=34 Identities=21% Similarity=0.346 Sum_probs=29.9
Q ss_pred CCCCCccccceeCCCchhHHHHHHhh-CCeEEEec
Q 023341 145 TYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 178 (283)
Q Consensus 145 ~~P~~NfvGrILGPrG~TlK~le~eT-gckI~IRG 178 (283)
.-|+++-||..+|++|+.++.|.++. |=||-|=-
T Consensus 272 ~d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~ 306 (449)
T PRK12329 272 LERDVDPVGACIGARGSRIQAVVNELRGEKIDVIR 306 (449)
T ss_pred CCCCCChhhccCCCCcchHHHHHHHhCCCeEEEEE
Confidence 44899999999999999999999998 88887754
No 67
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=38.37 E-value=42 Score=33.49 Aligned_cols=41 Identities=17% Similarity=0.286 Sum_probs=34.3
Q ss_pred EEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCC
Q 023341 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIK 183 (283)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~k 183 (283)
..|+||-+++ ++.||=+|.+++---+.||++|-|+.-+|.-
T Consensus 310 ~~V~V~~~ql------slAIGk~GqNvrLA~~LtGwkIDI~s~~~~~ 350 (374)
T PRK12328 310 AIVTLLSDQK------SKAIGKNGINIRLASMLTGYEIELNEIGSKE 350 (374)
T ss_pred EEEEEChHHh------hhhhcCCChhHHHHHHHhCCEEEEEECCCCc
Confidence 4566664443 7999999999999999999999999988743
No 68
>PRK01064 hypothetical protein; Provisional
Probab=36.29 E-value=19 Score=28.12 Aligned_cols=20 Identities=20% Similarity=0.607 Sum_probs=17.7
Q ss_pred ccceeCCCchhHHHHHHhhC
Q 023341 152 VGRLLGPRGNSLKRVEATTG 171 (283)
Q Consensus 152 vGrILGPrG~TlK~le~eTg 171 (283)
+|++||=+|.|++.|..-..
T Consensus 41 ~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred ceEEECCCCccHHHHHHHHH
Confidence 59999999999999988654
No 69
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=35.20 E-value=52 Score=31.93 Aligned_cols=41 Identities=20% Similarity=0.457 Sum_probs=32.8
Q ss_pred CcceeeEEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEec
Q 023341 130 SYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (283)
Q Consensus 130 ~~~vk~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRG 178 (283)
++++. ..|-||- .+-|-|||-.|.-+|+|-.|+|+.|.|--
T Consensus 312 GPitT--aQvtip~------dlggsiigkggqri~~ir~esGA~Ikide 352 (390)
T KOG2192|consen 312 GPITT--AQVTIPK------DLGGSIIGKGGQRIKQIRHESGASIKIDE 352 (390)
T ss_pred Cceee--eeEeccc------ccCcceecccchhhhhhhhccCceEEecC
Confidence 34444 3477883 46699999999999999999999999863
No 70
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=34.08 E-value=32 Score=34.31 Aligned_cols=34 Identities=21% Similarity=0.353 Sum_probs=29.6
Q ss_pred CCCCCccccceeCCCchhHHHHHHhh-CCeEEEec
Q 023341 145 TYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 178 (283)
Q Consensus 145 ~~P~~NfvGrILGPrG~TlK~le~eT-gckI~IRG 178 (283)
..|+++-+|..+|++|+.++.|.++. |=+|-|=-
T Consensus 246 ~d~~iDPvGacIG~~G~rI~~I~~eL~gEkIDvI~ 280 (374)
T PRK12328 246 NNPNIDPIGATVGVKGVRINAVSKELNGENIDCIE 280 (374)
T ss_pred CCCCCChHHhhcCCCcchHHHHHHHhCCCeEEEEE
Confidence 55899999999999999999999998 77776653
No 71
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=33.86 E-value=16 Score=35.84 Aligned_cols=31 Identities=26% Similarity=0.549 Sum_probs=27.9
Q ss_pred CccccceeCCCchhHHHHHHhhCCeEEEecc
Q 023341 149 FNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 179 (283)
Q Consensus 149 ~NfvGrILGPrG~TlK~le~eTgckI~IRGk 179 (283)
+-+||.+.||.|+|+|++|+.|..-|.--++
T Consensus 123 ~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 123 LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred ceeeeeccccccCccchheecccceEeeecc
Confidence 7889999999999999999999998876654
No 72
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=32.81 E-value=1.3e+02 Score=27.82 Aligned_cols=31 Identities=13% Similarity=0.045 Sum_probs=17.5
Q ss_pred CCceEEEEecCch-hhHHHHHHHHHHHHHHcc
Q 023341 202 DPLHILIEADLPA-NIVDIRLRQAQEIIEELL 232 (283)
Q Consensus 202 epLHVlI~a~~~~-~~~~~rl~~A~e~Ie~LL 232 (283)
.-+|+-|--.+.. +...+-+...++.|.+.+
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 3468887665543 334445555566666544
No 73
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=31.01 E-value=48 Score=34.53 Aligned_cols=39 Identities=15% Similarity=0.488 Sum_probs=32.7
Q ss_pred EEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCC
Q 023341 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGS 181 (283)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS 181 (283)
..|+||- -+++++||-+|..+++||...|-+|.|+-.+.
T Consensus 488 avv~vpe------~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 488 AVVKVPE------KYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred EEEEeCH------HHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 3456662 46789999999999999999999999998764
No 74
>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=30.38 E-value=40 Score=23.98 Aligned_cols=19 Identities=21% Similarity=0.433 Sum_probs=15.6
Q ss_pred hHHHHHHhhCCeEEEeccC
Q 023341 162 SLKRVEATTGCRVYIRGKG 180 (283)
Q Consensus 162 TlK~le~eTgckI~IRGkG 180 (283)
.+++||++.|+++.+|..+
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 5799999999999999654
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=28.44 E-value=13 Score=32.04 Aligned_cols=18 Identities=44% Similarity=0.826 Sum_probs=14.3
Q ss_pred CCCCCCccccceeCCCch
Q 023341 144 DTYPNFNFVGRLLGPRGN 161 (283)
Q Consensus 144 ~~~P~~NfvGrILGPrG~ 161 (283)
+-.|....+|+||||||.
T Consensus 101 ~~m~~l~~Lg~iLGprGl 118 (141)
T TIGR01170 101 DIVPELAQLRRLLGPKGL 118 (141)
T ss_pred HHHHHHHHhhcccccCcC
Confidence 345567789999999985
No 76
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=28.03 E-value=1.5e+02 Score=27.17 Aligned_cols=61 Identities=21% Similarity=0.140 Sum_probs=35.1
Q ss_pred ccceeCCC-------------chhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCch-hhH
Q 023341 152 VGRLLGPR-------------GNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPA-NIV 217 (283)
Q Consensus 152 vGrILGPr-------------G~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~-~~~ 217 (283)
+||+|||+ +..+...-+++.++|.+|=+ + .--+|+.|--.+.. +.+
T Consensus 117 lgk~LGp~~~p~gK~P~~~~~~~dl~~~i~~~k~~v~~r~~----k----------------~~~~~~~VGk~~m~~e~i 176 (214)
T PTZ00225 117 VPRLVGPHMHRMGKFPTVCSPSESLPDKVVELRSTVKFQLK----K----------------VLCLGTCVGHVEMTEEQL 176 (214)
T ss_pred hhhhcCCCCCcCCCCCcccCCccCHHHHHHHHhheeEEEec----C----------------ccEEEeEEccCCCCHHHH
Confidence 59999998 33355555566656666632 0 12358887666544 233
Q ss_pred HHHHHHHHHHHHHcc
Q 023341 218 DIRLRQAQEIIEELL 232 (283)
Q Consensus 218 ~~rl~~A~e~Ie~LL 232 (283)
.+-+..+++.|...|
T Consensus 177 ~eNi~a~l~~l~~~~ 191 (214)
T PTZ00225 177 RQNVVMAINFLVSLL 191 (214)
T ss_pred HHHHHHHHHHHHHhC
Confidence 345555666666655
No 77
>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=27.60 E-value=1e+02 Score=28.34 Aligned_cols=11 Identities=64% Similarity=1.286 Sum_probs=8.9
Q ss_pred ccccceeCCCc
Q 023341 150 NFVGRLLGPRG 160 (283)
Q Consensus 150 NfvGrILGPrG 160 (283)
..+|+||||||
T Consensus 123 ~~Lg~iLGPrG 133 (227)
T TIGR01169 123 GKLGRILGPRG 133 (227)
T ss_pred HHhcccccccc
Confidence 34599999997
No 78
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=27.47 E-value=51 Score=33.69 Aligned_cols=34 Identities=24% Similarity=0.441 Sum_probs=29.8
Q ss_pred CCCCCCccccceeCCCchhHHHHHHhh-CCeEEEe
Q 023341 144 DTYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIR 177 (283)
Q Consensus 144 ~~~P~~NfvGrILGPrG~TlK~le~eT-gckI~IR 177 (283)
..-|++.-||..+|++|+.++.|.++. |=||-|=
T Consensus 239 s~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv 273 (470)
T PRK09202 239 SNDPRIDPVGACVGMRGSRIQAISNELGGEKIDII 273 (470)
T ss_pred cCCCCCChhHccCCCCCchHHHHHHHhCCCeEEEE
Confidence 466899999999999999999999998 7777664
No 79
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=26.80 E-value=56 Score=36.50 Aligned_cols=79 Identities=27% Similarity=0.398 Sum_probs=57.1
Q ss_pred EEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhh
Q 023341 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANI 216 (283)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~~ 216 (283)
.....+++.+|- |.-+++.+=. ++.+|.+.|+|.|.+||+=- ...+ .| .....-||.+|++.+.
T Consensus 898 y~~~~~inD~Pq-~~r~~vt~~~--~L~~i~e~~~~~it~rg~f~--~~gk------~p--~~gErklyl~ve~~~e--- 961 (997)
T KOG0334|consen 898 YEAELEINDFPQ-NARWRVTYKE--ALLRISEPTAAGITTRGKFN--PPGK------EP--KPGERKLYLLVEGPDE--- 961 (997)
T ss_pred eeeeccccccch-hcceeeechh--hhhhccCccccceeeccccC--CCCC------CC--CCcchhhhhhhhcchh---
Confidence 344577788994 7888888754 39999999999999999731 1111 11 2356789999997653
Q ss_pred HHHHHHHHHHHHHHccC
Q 023341 217 VDIRLRQAQEIIEELLK 233 (283)
Q Consensus 217 ~~~rl~~A~e~Ie~LL~ 233 (283)
.-+++|++.++.+|.
T Consensus 962 --~~vqra~~e~~r~l~ 976 (997)
T KOG0334|consen 962 --LSVQRAIEELERLLE 976 (997)
T ss_pred --HHHHHHHHHHHHHHH
Confidence 357889999988665
No 80
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=26.54 E-value=19 Score=33.38 Aligned_cols=29 Identities=24% Similarity=0.441 Sum_probs=26.8
Q ss_pred ccccceeCCCchhHHHHHHhhCCeEEEec
Q 023341 150 NFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (283)
Q Consensus 150 NfvGrILGPrG~TlK~le~eTgckI~IRG 178 (283)
--||||.|-.|.|--.||..|.++|.+-+
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad 206 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLAD 206 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecC
Confidence 35899999999999999999999999976
No 81
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=25.32 E-value=10 Score=31.83 Aligned_cols=42 Identities=29% Similarity=0.512 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHH-ccCCCCCchHHHHHHHHHHHHHHcCccCCC
Q 023341 218 DIRLRQAQEIIEE-LLKPVDESQDYIKRQQLRELAMLNSNFRED 260 (283)
Q Consensus 218 ~~rl~~A~e~Ie~-LL~p~~e~~D~~K~~QL~ELA~lNGt~r~~ 260 (283)
|.||.+|+.+|+. |+..+.|.-+.+ +.|.+||..-|..++.+
T Consensus 47 DNKIeQAMDLVKtHLmfAVREEVe~L-k~qI~eL~er~~~Le~E 89 (123)
T KOG4797|consen 47 DNKIEQAMDLVKTHLMFAVREEVEVL-KEQIRELEERNSALERE 89 (123)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHH
Confidence 4589999999998 444566655555 57899998888777544
No 82
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=24.86 E-value=54 Score=29.56 Aligned_cols=21 Identities=24% Similarity=0.512 Sum_probs=18.4
Q ss_pred hhHHHHHHhhCCeEEEeccCC
Q 023341 161 NSLKRVEATTGCRVYIRGKGS 181 (283)
Q Consensus 161 ~TlK~le~eTgckI~IRGkGS 181 (283)
..+|+||++.|+++.+|++|.
T Consensus 35 ~~i~~LE~~lg~~Lf~R~r~i 55 (294)
T PRK13348 35 QRIKALEESLGQPLLVRGRPC 55 (294)
T ss_pred HHHHHHHHHhCceeeecCCCC
Confidence 458999999999999999753
No 83
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=21.48 E-value=1.3e+02 Score=29.96 Aligned_cols=36 Identities=31% Similarity=0.377 Sum_probs=26.1
Q ss_pred HhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchh
Q 023341 168 ATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 215 (283)
Q Consensus 168 ~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~~ 215 (283)
..+|+.+.|||+|--+- ++ +-..+|+|.|.++.|.+
T Consensus 300 tq~G~~~rl~gkG~p~~-------~~-----~~~GDl~v~v~v~~P~~ 335 (371)
T COG0484 300 TQTGEVFRLRGKGMPKL-------RS-----GGRGDLYVRVKVETPKN 335 (371)
T ss_pred CccCcEEEEcCCCcccc-------CC-----CCcCCEEEEEEEEcCCC
Confidence 45689999999985332 21 23378999999999875
No 84
>COG0080 RplK Ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=20.61 E-value=3.6e+02 Score=23.51 Aligned_cols=97 Identities=16% Similarity=0.175 Sum_probs=52.3
Q ss_pred eEEEEecCCCCCCCCccccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCcccccCCCCCCCCCCCCceEEEEecCch
Q 023341 135 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPA 214 (283)
Q Consensus 135 ~~~kv~IPv~~~P~~NfvGrILGPrG~TlK~le~eTgckI~IRGkGS~kd~~kee~lrg~p~~ehl~epLHVlI~a~~~~ 214 (283)
.+.|+.||-=+-.-=-=+|--|||+|-++...-++.+.+-.= . -..+++|.|++....
T Consensus 6 ~~ikl~v~aGkA~p~PpvGPALG~~Gvni~~f~k~fN~~T~~-~---------------------~G~~vPV~Itv~~dr 63 (141)
T COG0080 6 KIIKLQVPAGKANPSPPVGPALGQLGVNIMEFCKEFNAATKD-E---------------------KGLPVPVVITVYEDR 63 (141)
T ss_pred eEEEEEecccccCCCCCCCccccccCCCHHHHHHHHHHHhhc-c---------------------CCCeeeEEEEEEcCC
Confidence 344555554432222346889999999999888877754211 1 235677777776211
Q ss_pred h-hHHHHHHHHHHHHHHccCCCCCch-------HHHHHHHHHHHHHH
Q 023341 215 N-IVDIRLRQAQEIIEELLKPVDESQ-------DYIKRQQLRELAML 253 (283)
Q Consensus 215 ~-~~~~rl~~A~e~Ie~LL~p~~e~~-------D~~K~~QL~ELA~l 253 (283)
. ....+.-=|-.+|.+.+.-..-+. -.+-..|++|.|.+
T Consensus 64 sftf~~ktPPas~LlkKa~g~~~Gs~~p~k~~vG~lt~~qv~eIA~~ 110 (141)
T COG0080 64 SFTFIVKTPPASALLKKAAGIEKGSGKPNKNKVGKLTLAQVREIAKT 110 (141)
T ss_pred cEEEEECCCCHHHHHHHHhCCCCCCCCCCcceeeeeeHHHHHHHHHH
Confidence 0 000011124456666655322222 23447888888854
No 85
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=20.57 E-value=38 Score=31.33 Aligned_cols=29 Identities=21% Similarity=0.115 Sum_probs=15.2
Q ss_pred CceEEEEecCch-hhHHHHHHHHHHHHHHc
Q 023341 203 PLHILIEADLPA-NIVDIRLRQAQEIIEEL 231 (283)
Q Consensus 203 pLHVlI~a~~~~-~~~~~rl~~A~e~Ie~L 231 (283)
-+|+-|--.+.. +...+-+...++.|.+.
T Consensus 169 ~i~~~VG~~~m~~~~l~eNi~a~l~~i~~~ 198 (229)
T CHL00129 169 IVHVLFGKSNFTEEDLLENLQAIYESIEQN 198 (229)
T ss_pred EEEEEEeCCCCCHHHHHHHHHHHHHHHHHh
Confidence 468888665544 23334444444444443
No 86
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=20.16 E-value=33 Score=25.57 Aligned_cols=23 Identities=17% Similarity=0.484 Sum_probs=19.1
Q ss_pred ccceeCCCchhHHHHHHhhCCeE
Q 023341 152 VGRLLGPRGNSLKRVEATTGCRV 174 (283)
Q Consensus 152 vGrILGPrG~TlK~le~eTgckI 174 (283)
.|.+||-+|.+++.|....+-++
T Consensus 36 ~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 36 PGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp HHHHHTGGGHHHHHHHHHHHHHH
T ss_pred ccHhHHhhhHHHHHHHHHHHHHH
Confidence 39999999999999977766444
Done!