Query 023068
Match_columns 287
No_of_seqs 203 out of 430
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 08:12:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023068.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023068hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1588 RNA-binding protein Sa 100.0 9.8E-66 2.1E-70 471.9 21.1 234 1-286 3-241 (259)
2 cd02395 SF1_like-KH Splicing f 100.0 1E-41 2.2E-46 283.3 13.1 119 136-262 1-120 (120)
3 KOG0119 Splicing factor 1/bran 100.0 6.8E-41 1.5E-45 327.8 6.8 195 58-266 59-261 (554)
4 COG5176 MSL5 Splicing factor ( 100.0 2.9E-33 6.3E-38 251.2 5.5 184 71-264 83-269 (269)
5 cd02393 PNPase_KH Polynucleoti 98.6 9.2E-08 2E-12 70.6 6.6 59 136-233 3-61 (61)
6 PF00013 KH_1: KH domain syndr 98.5 1E-07 2.2E-12 68.8 3.6 60 136-232 1-60 (60)
7 cd00105 KH-I K homology RNA-bi 98.4 1.1E-06 2.3E-11 63.3 6.8 38 137-180 2-39 (64)
8 smart00322 KH K homology RNA-b 98.3 4.6E-06 9.9E-11 59.0 7.7 65 136-236 4-68 (69)
9 KOG1960 Predicted RNA-binding 98.2 1.3E-06 2.8E-11 85.9 5.0 89 134-240 209-297 (531)
10 cd02394 vigilin_like_KH K homo 98.2 2.2E-06 4.7E-11 62.2 5.0 37 138-180 3-39 (62)
11 cd02396 PCBP_like_KH K homolog 98.2 5E-06 1.1E-10 61.5 6.9 36 137-178 2-37 (65)
12 PF13014 KH_3: KH domain 98.2 1.6E-06 3.5E-11 59.3 3.1 28 151-178 1-28 (43)
13 TIGR03665 arCOG04150 arCOG0415 97.8 2.6E-05 5.6E-10 68.5 5.2 53 151-238 99-151 (172)
14 PRK13763 putative RNA-processi 97.7 4.9E-05 1.1E-09 67.3 5.7 53 151-238 105-157 (180)
15 TIGR02696 pppGpp_PNP guanosine 97.7 8.5E-05 1.9E-09 78.1 8.2 71 129-238 572-642 (719)
16 PRK13763 putative RNA-processi 97.7 7.5E-05 1.6E-09 66.1 6.0 64 137-238 5-71 (180)
17 TIGR03665 arCOG04150 arCOG0415 97.5 0.00011 2.4E-09 64.5 4.5 58 149-238 6-65 (172)
18 TIGR03591 polynuc_phos polyrib 97.5 0.00023 5E-09 74.6 6.9 69 130-237 546-614 (684)
19 COG1094 Predicted RNA-binding 97.4 0.00034 7.5E-09 63.2 5.8 55 151-240 112-166 (194)
20 PLN00207 polyribonucleotide nu 97.1 0.00056 1.2E-08 73.6 4.7 71 129-238 679-750 (891)
21 KOG1676 K-homology type RNA bi 96.4 0.0069 1.5E-07 62.4 6.8 71 136-239 231-301 (600)
22 PRK11824 polynucleotide phosph 96.4 0.0031 6.7E-08 66.4 4.3 57 149-238 562-618 (693)
23 PRK04163 exosome complex RNA-b 96.3 0.0051 1.1E-07 56.6 4.7 57 149-238 153-209 (235)
24 KOG2193 IGF-II mRNA-binding pr 96.2 0.0018 3.9E-08 64.7 1.1 38 140-177 279-316 (584)
25 KOG1676 K-homology type RNA bi 96.2 0.011 2.3E-07 61.1 6.5 75 132-238 136-210 (600)
26 KOG2874 rRNA processing protei 95.8 0.027 5.9E-07 53.9 6.9 27 153-179 161-187 (356)
27 KOG2814 Transcription coactiva 95.2 0.026 5.6E-07 54.9 4.7 61 149-233 65-127 (345)
28 KOG2190 PolyC-binding proteins 94.5 0.082 1.8E-06 53.8 6.5 40 134-179 137-176 (485)
29 KOG2193 IGF-II mRNA-binding pr 94.2 0.042 9.2E-07 55.2 3.5 37 137-179 201-237 (584)
30 KOG2191 RNA-binding protein NO 94.1 0.054 1.2E-06 52.9 3.9 37 135-177 39-75 (402)
31 PRK12704 phosphodiesterase; Pr 92.8 0.24 5.2E-06 50.8 6.4 49 139-219 214-262 (520)
32 COG1185 Pnp Polyribonucleotide 92.8 0.15 3.2E-06 53.8 4.9 66 133-237 550-615 (692)
33 TIGR03319 YmdA_YtgF conserved 92.7 0.2 4.2E-06 51.4 5.7 63 138-237 207-269 (514)
34 KOG2191 RNA-binding protein NO 92.4 0.64 1.4E-05 45.7 8.2 38 135-178 132-169 (402)
35 PRK00106 hypothetical protein; 91.4 0.35 7.6E-06 50.0 5.6 63 138-237 228-290 (535)
36 cd02134 NusA_KH NusA_K homolog 90.0 0.56 1.2E-05 34.4 4.2 36 135-176 25-60 (61)
37 KOG2190 PolyC-binding proteins 86.7 0.58 1.2E-05 47.8 3.2 41 133-179 336-376 (485)
38 KOG1960 Predicted RNA-binding 84.7 0.45 9.8E-06 47.8 1.3 72 154-242 308-379 (531)
39 KOG0336 ATP-dependent RNA heli 83.6 0.59 1.3E-05 47.5 1.6 29 149-177 55-83 (629)
40 PF13184 KH_5: NusA-like KH do 83.2 0.72 1.6E-05 35.1 1.6 32 146-177 13-45 (69)
41 COG1097 RRP4 RNA-binding prote 78.3 5.4 0.00012 37.5 5.9 30 149-178 154-183 (239)
42 cd02409 KH-II KH-II (K homolo 75.1 2.5 5.4E-05 29.8 2.2 23 152-174 36-58 (68)
43 KOG1067 Predicted RNA-binding 74.4 4.9 0.00011 42.3 4.9 70 151-261 607-676 (760)
44 PRK08406 transcription elongat 70.9 3.6 7.7E-05 35.3 2.6 29 150-178 41-69 (140)
45 COG1094 Predicted RNA-binding 69.3 13 0.00027 34.0 5.9 37 137-179 10-46 (194)
46 PRK12705 hypothetical protein; 69.1 7.9 0.00017 40.0 5.0 35 139-178 202-236 (508)
47 KOG2113 Predicted RNA binding 62.7 5.4 0.00012 39.2 2.3 37 133-175 24-60 (394)
48 cd02414 jag_KH jag_K homology 61.7 4.9 0.00011 30.6 1.5 22 152-173 35-56 (77)
49 PF13083 KH_4: KH domain; PDB: 51.8 4.6 0.0001 30.1 -0.1 20 152-171 40-59 (73)
50 COG1702 PhoH Phosphate starvat 50.6 29 0.00062 34.4 5.1 30 150-179 24-53 (348)
51 TIGR00436 era GTP-binding prot 49.1 32 0.00069 31.6 5.0 40 133-177 219-266 (270)
52 TIGR01952 nusA_arch NusA famil 48.8 16 0.00034 31.6 2.7 29 150-178 42-70 (141)
53 PRK12327 nusA transcription el 46.7 19 0.00042 35.6 3.3 34 145-178 240-274 (362)
54 PRK02821 hypothetical protein; 45.9 12 0.00026 29.2 1.4 23 150-172 40-62 (77)
55 PRK00468 hypothetical protein; 45.0 13 0.00028 28.8 1.4 19 152-170 41-59 (75)
56 COG0195 NusA Transcription elo 43.4 21 0.00045 32.4 2.7 33 147-179 82-114 (190)
57 PRK15494 era GTPase Era; Provi 43.1 41 0.00089 32.4 4.9 40 133-177 271-318 (339)
58 TIGR01953 NusA transcription t 42.5 25 0.00054 34.5 3.3 34 145-178 238-272 (341)
59 PRK00089 era GTPase Era; Revie 42.3 45 0.00097 30.7 4.8 40 133-177 224-271 (292)
60 KOG2208 Vigilin [Lipid transpo 41.3 20 0.00042 38.8 2.6 37 136-178 710-746 (753)
61 PRK06418 transcription elongat 40.5 23 0.0005 31.5 2.5 27 153-179 72-98 (166)
62 PRK08406 transcription elongat 39.6 26 0.00057 30.0 2.6 25 152-176 110-134 (140)
63 PRK01064 hypothetical protein; 37.5 17 0.00037 28.4 1.1 20 152-171 41-60 (78)
64 PF00126 HTH_1: Bacterial regu 36.9 26 0.00057 25.0 1.9 19 162-180 33-51 (60)
65 COG1837 Predicted RNA-binding 36.7 21 0.00046 28.0 1.4 18 152-169 41-58 (76)
66 PRK12328 nusA transcription el 34.7 31 0.00067 34.5 2.6 34 145-178 246-280 (374)
67 PRK12329 nusA transcription el 34.4 55 0.0012 33.5 4.4 34 145-178 272-306 (449)
68 KOG2192 PolyC-binding hnRNP-K 33.3 46 0.00099 32.4 3.4 35 137-177 317-351 (390)
69 KOG2192 PolyC-binding hnRNP-K 31.6 88 0.0019 30.5 5.0 38 135-178 48-85 (390)
70 PRK13348 chromosome replicatio 31.6 34 0.00074 30.9 2.2 20 161-180 35-54 (294)
71 PRK12328 nusA transcription el 31.0 67 0.0014 32.2 4.2 41 137-183 310-350 (374)
72 KOG4797 Transcriptional regula 30.0 7.8 0.00017 32.6 -2.0 43 222-265 47-90 (123)
73 KOG2113 Predicted RNA binding 29.5 22 0.00047 35.2 0.5 31 149-179 123-153 (394)
74 TIGR01170 rplA_mito ribosomal 28.0 12 0.00027 32.2 -1.2 18 144-161 101-118 (141)
75 PRK09202 nusA transcription el 28.0 49 0.0011 33.9 2.8 34 144-177 239-273 (470)
76 KOG0334 RNA helicase [RNA proc 27.4 57 0.0012 36.5 3.3 79 137-237 898-976 (997)
77 KOG3273 Predicted RNA-binding 26.0 20 0.00044 33.4 -0.3 29 150-178 178-206 (252)
78 COG1855 ATPase (PilT family) [ 26.0 41 0.0009 35.1 1.9 42 137-184 488-529 (604)
79 TIGR03298 argP transcriptional 24.2 43 0.00094 30.2 1.5 19 162-180 35-53 (292)
80 PRK03635 chromosome replicatio 23.6 58 0.0013 29.6 2.2 19 162-180 36-54 (294)
81 PRK11074 putative DNA-binding 22.4 70 0.0015 29.2 2.5 22 161-182 35-56 (300)
82 PRK03601 transcriptional regul 21.7 68 0.0015 29.0 2.3 18 162-179 35-52 (275)
83 PRK15421 DNA-binding transcrip 21.2 79 0.0017 29.4 2.6 19 161-179 35-53 (317)
84 PF07650 KH_2: KH domain syndr 20.9 32 0.00068 25.7 -0.1 23 152-174 36-58 (78)
85 PRK12684 transcriptional regul 20.7 77 0.0017 29.3 2.4 19 162-180 36-55 (313)
86 PRK12683 transcriptional regul 20.7 78 0.0017 29.2 2.5 20 161-180 35-55 (309)
87 PRK09791 putative DNA-binding 20.6 84 0.0018 28.5 2.6 22 162-183 39-60 (302)
88 CHL00129 rpl1 ribosomal protei 20.6 38 0.00082 31.4 0.4 10 152-161 126-135 (229)
89 TIGR01169 rplA_bact ribosomal 20.4 23 0.0005 32.7 -1.1 10 151-160 124-133 (227)
90 PTZ00225 60S ribosomal protein 20.0 2.7E+02 0.0058 25.6 5.8 61 152-236 117-191 (214)
No 1
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=100.00 E-value=9.8e-66 Score=471.85 Aligned_cols=234 Identities=50% Similarity=0.766 Sum_probs=197.5
Q ss_pred CCCCCCCC-CCCCCCCCCCcCCCCCcchHHHHHHHHHHHHhhcCCCccchhHHHHhhhhhhhhhhccCCCCCCCCccccc
Q 023068 1 MSGLYNPN-FSPARAASPQIRSTPDINIDSQYLSELLAEHQKLGPFTQVLPICSRLLTQEIFRVSGMMPNQGFGDFDRLR 79 (287)
Q Consensus 1 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~YL~eLl~Ek~~L~~~~~~~~~~~rLl~~EI~RV~~~~~~~~~~d~d~~~ 79 (287)
+.+.|++. ++|+...+++..+. .....++||.+|++||++|++|+. |+||.|||++||.||+..+++.+ + .
T Consensus 3 ~~~~~~~~~~s~~~~~~~~~~~~-~~~~~~~yl~el~~e~~~l~~~~~-~~~~~rLL~~Ei~rv~~~~~~~~----~-~- 74 (259)
T KOG1588|consen 3 TGGGYTQEPGSPAGGGGPRYQPQ-LNEKASKYLSELLAERKSLSPFFP-FPHAERLLDEEIERVQTSGRQHG----S-K- 74 (259)
T ss_pred CCCCCCCCCCCCcccCCCccccc-hhhHHHHHHHHHHhhHHhcCcccc-hHHHHHHHHHHHHHHHhhhhhcc----C-C-
Confidence 34566655 44444444444332 225579999999999999999998 99999999999999999865542 0 0
Q ss_pred cCCCCCCCccccccCcCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCcceeeEEEEecCCCCCCCCCcccceeCCC
Q 023068 80 HRSPSPMASSNLMSNVAGTGLGGWNGLPQERLGGPPGMTMDWQSAPASPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPR 159 (287)
Q Consensus 80 ~~SP~p~~~~g~~~N~~~~~~~~~~~l~~Er~~~~~~~~~d~~~~p~~~~~~~vkk~~kv~IPv~~~P~~NfvGrIlGPr 159 (287)
.| ++.. ....++.+++|.++||+|||++||+|||||||||||
T Consensus 75 --~~-------------------------~~~~-----------~~~~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPr 116 (259)
T KOG1588|consen 75 --EP-------------------------EELP-----------YADVYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPR 116 (259)
T ss_pred --Cc-------------------------hhcc-----------cccCccCCceeEEEEEEeccCCCCCCccccccccCC
Confidence 01 1110 002345679999999999999999999999999999
Q ss_pred chhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHHHHHHccCCC
Q 023068 160 GNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLKPV 239 (287)
Q Consensus 160 G~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~~~~~~~~~rl~~A~e~Ie~LL~p~ 239 (287)
|||+||||++|||||+||||||+||..| ||++|++|+|+||++||||+|++++++++|++||++|+++|++||+|.
T Consensus 117 GnSlkrLe~eTgCki~IrGrgSmrD~~K----EE~lR~~p~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~P~ 192 (259)
T KOG1588|consen 117 GNSLKRLEEETGCKIMIRGRGSMRDKAK----EEELRGDPGYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLVPD 192 (259)
T ss_pred cchHHHHHHHHCCeEEEecCCcccchHH----HHHhhcCcchHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcCCC
Confidence 9999999999999999999999999999 999999999999999999999999999999999999999999999999
Q ss_pred CcchHHHHHHHHHHHHHHcCc-cCCCCCCCCC---CCCCCCcccccccccC
Q 023068 240 DESQDYIKRQQLRELAMLNSN-FREDSPGPSG---SVSPFNSSGMKRAKTG 286 (287)
Q Consensus 240 ~e~~D~lK~~QL~ELA~lNGt-~r~~~~~~~~---~~spf~~~~~~~~~~~ 286 (287)
+++.| |++||+|||++||| +++.+..++| +++||++.|+||+|++
T Consensus 193 ~e~~d--k~~QL~ELa~lngt~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~ 241 (259)
T KOG1588|consen 193 HEDED--KREQLRELAILNGTYLRSESRKPSGGNGRGVPGNSAGGKRGKTG 241 (259)
T ss_pred CCCch--HHHHHHHHhhcCCccccccccccCCCCCcCCCCCCCCcccccCC
Confidence 98877 99999999999999 5666655666 8999999999999985
No 2
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=100.00 E-value=1e-41 Score=283.34 Aligned_cols=119 Identities=57% Similarity=0.969 Sum_probs=111.7
Q ss_pred EEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEec
Q 023068 136 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEAD 215 (287)
Q Consensus 136 ~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~ 215 (287)
++|||||+++||+|||||+||||+|+|+|+||++|||+|.|||+||+++.++ |+.+++ +.|+|++|||||+|+|.
T Consensus 1 ~~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~----~~~~~~-~~~~~~~eplhV~I~a~ 75 (120)
T cd02395 1 TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKK----EEELRG-PKYAHLNEPLHVLITAE 75 (120)
T ss_pred CCEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccc----cccccC-cccccCCCCcEEEEEeC
Confidence 3689999999999999999999999999999999999999999999999988 777777 89999999999999999
Q ss_pred CchhHHHHHHHHHHHHHHHccCCCCcc-hHHHHHHHHHHHHHHcCccC
Q 023068 216 LPANIVDIRLRQAQEIIEELLKPVDES-QDYIKRQQLRELAMLNSNFR 262 (287)
Q Consensus 216 ~~~~~~~~rl~~A~e~Ie~LL~p~~e~-~D~lK~~QL~ELA~lNGt~r 262 (287)
++ +..++++|+++|+.||.++.++ .|++|++||+|||++|||||
T Consensus 76 ~~---~~e~~~~A~~~I~~ll~~~~~~~~~~~k~~ql~~la~~nGt~~ 120 (120)
T cd02395 76 TP---PEEALAKAVEAIEELLKPAIEGGNDELKREQLRELALLNGTYR 120 (120)
T ss_pred Cc---HHHHHHHHHHHHHHHhccCCCccchHHHHHHHHHHHHhcccCC
Confidence 85 3458999999999999998877 99999999999999999997
No 3
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=100.00 E-value=6.8e-41 Score=327.80 Aligned_cols=195 Identities=34% Similarity=0.492 Sum_probs=150.3
Q ss_pred hhhhhhhccCCCCCC-CCccc-cccCCCCCC-CccccccCcCCCCCCCCCCCcccccCCCC-CCCCCCCCCCCCCCCcce
Q 023068 58 QEIFRVSGMMPNQGF-GDFDR-LRHRSPSPM-ASSNLMSNVAGTGLGGWNGLPQERLGGPP-GMTMDWQSAPASPSSYTV 133 (287)
Q Consensus 58 ~EI~RV~~~~~~~~~-~d~d~-~~~~SP~p~-~~~g~~~N~~~~~~~~~~~l~~Er~~~~~-~~~~d~~~~p~~~~~~~v 133 (287)
-+|.++...|.-..| ++..+ .+++||+|. +.-|.+.|+++ ++....|.+||..+++ .+.+...+.++....+..
T Consensus 59 ~~iee~t~kLrt~d~~~p~~~e~rSPsp~p~yda~g~R~ntRe--~R~r~~Le~er~e~I~~~lk~nP~fkpP~DYk~p~ 136 (554)
T KOG0119|consen 59 LRIEEITRKLRTGDVGVPPPRELRSPSPEPVYDAKGKRLNTRE--QRARKKLEDERHEIIEEILKLNPGFKPPADYKPPA 136 (554)
T ss_pred HHHHHhhhhhccccCCCCCCccccCCCcchhhhhhccchhhHH--HHHHHHHHHHHHHHHHHHHHhCcCCCCCcccCccc
Confidence 344444433333334 22222 345555554 44678889885 6667888899887654 456666555444333344
Q ss_pred eeEEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCC-CCCCCceEEE
Q 023068 134 KRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYE-HLNDPLHILI 212 (287)
Q Consensus 134 kk~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~e-hl~epLHVlI 212 (287)
+++.|||||||+||+|||||+||||||+|+|+||+||||||+||||||+|+++. ...+.+|. ..+|||||+|
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~-------~~~d~~~~~~~~epLH~~I 209 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKG-------RSDDLSYIPKENEPLHCLI 209 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEecccccccccc-------CCcccccccccccceeEEE
Confidence 999999999999999999999999999999999999999999999999998762 11233342 3589999999
Q ss_pred EecCchhHHHHHHHHHHHHHHHccC---CCCcchHHHHHHHHHHHHHHcCccCCCCC
Q 023068 213 EADLPANIVDIRLRQAQEIIEELLK---PVDESQDYIKRQQLRELAMLNSNFREDSP 266 (287)
Q Consensus 213 sa~~~~~~~~~rl~~A~e~Ie~LL~---p~~e~~D~lK~~QL~ELA~lNGt~r~~~~ 266 (287)
+|++.+ +|++|+++||.||. .++|+++++|+.||+|||-+|||+|++.+
T Consensus 210 sadt~e-----ki~~Ai~vienli~~av~~~e~~n~l~~~Qlrela~lNgt~r~~d~ 261 (554)
T KOG0119|consen 210 SADTQE-----KIKKAIAVIENLIQSAVSVPEGQNDLKRLQLRELARLNGTLRDDDN 261 (554)
T ss_pred ecchHH-----HHHHHHHHHHHHHHhhccCccccccccHHHHHHHHHhCCCCCcccc
Confidence 999976 89999999999998 68999999999999999999999999984
No 4
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.98 E-value=2.9e-33 Score=251.18 Aligned_cols=184 Identities=32% Similarity=0.369 Sum_probs=134.9
Q ss_pred CCCCccc-cccCCCCCC-CccccccCcCCCCCCCCCCCcccccCCCC-CCCCCCCCCCCCCCCcceeeEEEEecCCCCCC
Q 023068 71 GFGDFDR-LRHRSPSPM-ASSNLMSNVAGTGLGGWNGLPQERLGGPP-GMTMDWQSAPASPSSYTVKRILRLEIPVDTYP 147 (287)
Q Consensus 71 ~~~d~d~-~~~~SP~p~-~~~g~~~N~~~~~~~~~~~l~~Er~~~~~-~~~~d~~~~p~~~~~~~vkk~~kv~IPv~~~P 147 (287)
.|+...+ ++.+||.|. ...|.+.|+++ .++...|.+||+.+.+ ++.+-.-..++...-...|.+.||||||++||
T Consensus 83 d~Vp~~re~Rspsppp~yd~~GrRlntre--~ry~kkLeder~~l~era~k~lp~fv~p~dy~rpsk~q~KiYIPV~eyP 160 (269)
T COG5176 83 DGVPSKRELRSPSPPPRYDEIGRRLNTRE--ARYNKKLEDERLWLKERAQKILPRFVLPNDYIRPSKYQNKIYIPVQEYP 160 (269)
T ss_pred CCCCchhhccCCCCCcchhHHhhhhhHHH--HHHhhhhhHHHHHHHHHHHHhcCcccCCccccCcccccceEEeehhhCc
Confidence 3555544 454444433 23788888885 5566888899987664 44444434444434447788999999999999
Q ss_pred CCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhHHHHHHHH
Q 023068 148 NFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQ 227 (287)
Q Consensus 148 ~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~~~~~~~~~rl~~ 227 (287)
+.||||+||||||.|+|+||+.|+|||.|||+||+|+++-.+. + .++-....++||+||+++....++. -+..
T Consensus 161 e~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd----~--p~~~~N~e~~lhcLI~adsedki~~-~ik~ 233 (269)
T COG5176 161 ESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSD----T--PESLKNAEAVLHCLIEADSEDKICR-LIKS 233 (269)
T ss_pred ccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCccccc----C--chhhhhhHHhHHHHhhcchhhhHHH-HHHH
Confidence 9999999999999999999999999999999999998764221 1 0111235789999999987654443 2333
Q ss_pred HHHHHHHccCCCCcchHHHHHHHHHHHHHHcCccCCC
Q 023068 228 AQEIIEELLKPVDESQDYIKRQQLRELAMLNSNFRED 264 (287)
Q Consensus 228 A~e~Ie~LL~p~~e~~D~lK~~QL~ELA~lNGt~r~~ 264 (287)
....|.+... .++|++++|+-||++||-+|||+|++
T Consensus 234 ~~n~I~~a~~-~PeGqnDlkR~qlr~la~lngtlr~d 269 (269)
T COG5176 234 QLNAIREARR-NPEGQNDLKRFQLRWLAHLNGTLRAD 269 (269)
T ss_pred HHHHHHHHhc-CCcccchHHHHHHHHHHHhcceecCC
Confidence 4445555544 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=98.64 E-value=9.2e-08 Score=70.56 Aligned_cols=59 Identities=25% Similarity=0.466 Sum_probs=46.9
Q ss_pred EEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEec
Q 023068 136 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEAD 215 (287)
Q Consensus 136 ~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~ 215 (287)
.+.+.|| -.++|+|||++|.|+|+||++|||+|.|--. -.|.|++.
T Consensus 3 ~~~i~Ip------~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~----------------------------g~v~I~G~ 48 (61)
T cd02393 3 IETMKIP------PDKIRDVIGPGGKTIKKIIEETGVKIDIEDD----------------------------GTVYIAAS 48 (61)
T ss_pred EEEEEeC------hhheeeeECCCchHHHHHHHHHCCEEEeCCC----------------------------CEEEEEeC
Confidence 4567777 4788999999999999999999999987421 15899997
Q ss_pred CchhHHHHHHHHHHHHHH
Q 023068 216 LPANIVDIRLRQAQEIIE 233 (287)
Q Consensus 216 ~~~~~~~~rl~~A~e~Ie 233 (287)
+.+ .++.|.++|+
T Consensus 49 ~~~-----~v~~A~~~I~ 61 (61)
T cd02393 49 DKE-----AAEKAKKMIE 61 (61)
T ss_pred CHH-----HHHHHHHHhC
Confidence 664 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=98.50 E-value=1e-07 Score=68.83 Aligned_cols=60 Identities=28% Similarity=0.613 Sum_probs=47.2
Q ss_pred EEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEec
Q 023068 136 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEAD 215 (287)
Q Consensus 136 ~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~ 215 (287)
+.+|.|| ..++|+|||++|.++|+|+++|||+|.|...+ +.-.|.|++
T Consensus 1 T~~i~vp------~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~-------------------------~~~~v~I~G- 48 (60)
T PF00013_consen 1 TERIEVP------SSLVGRIIGKKGSNIKEIEEETGVKIQIPDDD-------------------------ERDIVTISG- 48 (60)
T ss_dssp EEEEEEE------HHHHHHHHTGGGHHHHHHHHHHTSEEEEESTT-------------------------EEEEEEEEE-
T ss_pred CEEEEEC------HHHcCEEECCCCCcHHHhhhhcCeEEEEcCCC-------------------------CcEEEEEEe-
Confidence 3567788 68899999999999999999999999997541 112788988
Q ss_pred CchhHHHHHHHHHHHHH
Q 023068 216 LPANIVDIRLRQAQEII 232 (287)
Q Consensus 216 ~~~~~~~~rl~~A~e~I 232 (287)
+++ .+++|.++|
T Consensus 49 ~~~-----~v~~A~~~I 60 (60)
T PF00013_consen 49 SPE-----QVEKAKKMI 60 (60)
T ss_dssp SHH-----HHHHHHHHH
T ss_pred CHH-----HHHHHHhhC
Confidence 554 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=98.40 E-value=1.1e-06 Score=63.27 Aligned_cols=38 Identities=32% Similarity=0.693 Sum_probs=33.7
Q ss_pred EEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccC
Q 023068 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKG 180 (287)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkG 180 (287)
.++.|| -+++|+||||+|+++++|+++|||+|.|...+
T Consensus 2 ~~i~ip------~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~ 39 (64)
T cd00105 2 ERVLVP------SSLVGRIIGKGGSTIKEIREETGAKIKIPDSG 39 (64)
T ss_pred EEEEEc------hhhcceeECCCCHHHHHHHHHHCCEEEEcCCC
Confidence 467788 38899999999999999999999999998753
No 8
>smart00322 KH K homology RNA-binding domain.
Probab=98.28 E-value=4.6e-06 Score=58.98 Aligned_cols=65 Identities=31% Similarity=0.577 Sum_probs=49.3
Q ss_pred EEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEec
Q 023068 136 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEAD 215 (287)
Q Consensus 136 ~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~ 215 (287)
..+|.||. +++|++||++|.+++.|++.|||+|.+.+.++ ..-.|.|.+.
T Consensus 4 ~~~i~i~~------~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~------------------------~~~~v~i~g~ 53 (69)
T smart00322 4 TIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS------------------------EERVVEITGP 53 (69)
T ss_pred EEEEEEcc------hhcceeECCCchHHHHHHHHHCCEEEECCCCC------------------------CccEEEEEcC
Confidence 45677873 78899999999999999999999999976432 1136788776
Q ss_pred CchhHHHHHHHHHHHHHHHcc
Q 023068 216 LPANIVDIRLRQAQEIIEELL 236 (287)
Q Consensus 216 ~~~~~~~~rl~~A~e~Ie~LL 236 (287)
.. .+..|.+.|.+.+
T Consensus 54 -~~-----~v~~a~~~i~~~~ 68 (69)
T smart00322 54 -PE-----NVEKAAELILEIL 68 (69)
T ss_pred -HH-----HHHHHHHHHHHHh
Confidence 22 4667777777654
No 9
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=98.22 E-value=1.3e-06 Score=85.94 Aligned_cols=89 Identities=15% Similarity=-0.002 Sum_probs=74.8
Q ss_pred eeEEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEE
Q 023068 134 KRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIE 213 (287)
Q Consensus 134 kk~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIs 213 (287)
+...|.+|++| .|.||.-+..=||+..+|..+|.+|+.+++||||||++-. -..| ++.+||++|+|+
T Consensus 209 ~Y~~k~~v~~~-~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iE--------P~~G----~EsnEPMYI~i~ 275 (531)
T KOG1960|consen 209 YYPNKALATDK-DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRRE--------PNEG----NESNEPMYIFST 275 (531)
T ss_pred cchhheecccC-CcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccC--------cccc----cccCCceeEEee
Confidence 33347899998 7999999999999999999999999999999999998742 1122 247999999999
Q ss_pred ecCchhHHHHHHHHHHHHHHHccCCCC
Q 023068 214 ADLPANIVDIRLRQAQEIIEELLKPVD 240 (287)
Q Consensus 214 a~~~~~~~~~rl~~A~e~Ie~LL~p~~ 240 (287)
..+.+ -+.+|+.++++|+.-+.
T Consensus 276 h~~~~-----g~~~A~r~~~nl~~~v~ 297 (531)
T KOG1960|consen 276 HGNGN-----GENGAPRRKWNLEEKVY 297 (531)
T ss_pred cCCch-----hhccchhHHHhHHHHHH
Confidence 98876 57899999999998654
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=2.2e-06 Score=62.24 Aligned_cols=37 Identities=22% Similarity=0.573 Sum_probs=31.8
Q ss_pred EEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccC
Q 023068 138 RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKG 180 (287)
Q Consensus 138 kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkG 180 (287)
++.||. .++|.|||++|.++++|+++|||+|.|-..+
T Consensus 3 ~i~Vp~------~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~ 39 (62)
T cd02394 3 EVEIPK------KLHRFIIGKKGSNIRKIMEETGVKIRFPDPG 39 (62)
T ss_pred EEEeCH------HHhhhccCCCCCcHHHHHHHhCCEEEcCCCC
Confidence 466763 6779999999999999999999999998653
No 11
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=98.21 E-value=5e-06 Score=61.46 Aligned_cols=36 Identities=28% Similarity=0.624 Sum_probs=32.3
Q ss_pred EEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEec
Q 023068 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (287)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRG 178 (287)
.|+.|| -+.+|+|||.+|.++|+|+++|||+|.|--
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 578999999999999999999999999953
No 12
>PF13014 KH_3: KH domain
Probab=98.16 E-value=1.6e-06 Score=59.30 Aligned_cols=28 Identities=36% Similarity=0.789 Sum_probs=26.9
Q ss_pred cccceeCCCchhHHHHHHhhCCeEEEec
Q 023068 151 FVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (287)
Q Consensus 151 fvGrIlGPrG~TlK~lE~eTgckI~IRG 178 (287)
|+|+|||++|.|+|+|+++|||+|.|--
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 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=97.83 E-value=2.6e-05 Score=68.53 Aligned_cols=53 Identities=30% Similarity=0.506 Sum_probs=45.5
Q ss_pred cccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHH
Q 023068 151 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQE 230 (287)
Q Consensus 151 fvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~~~~~~~~~rl~~A~e 230 (287)
.+|||||+.|.|.+.||..|||+|.|-| + .|.|.+ +++ .++.|.+
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~--------~---------------------~v~i~G-~~~-----~~~~A~~ 143 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYG--------K---------------------TVGIIG-DPE-----QVQIARE 143 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcC--------C---------------------EEEEEC-CHH-----HHHHHHH
Confidence 5899999999999999999999999965 1 577888 554 6788999
Q ss_pred HHHHccCC
Q 023068 231 IIEELLKP 238 (287)
Q Consensus 231 ~Ie~LL~p 238 (287)
.|+.|+.-
T Consensus 144 ~i~~li~~ 151 (172)
T TIGR03665 144 AIEMLIEG 151 (172)
T ss_pred HHHHHHcC
Confidence 99999863
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.75 E-value=4.9e-05 Score=67.26 Aligned_cols=53 Identities=30% Similarity=0.518 Sum_probs=44.1
Q ss_pred cccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHH
Q 023068 151 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQE 230 (287)
Q Consensus 151 fvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~~~~~~~~~rl~~A~e 230 (287)
.+|||||++|.|.|.||..|||+|.|-++ .|.|.+ +++ .++.|.+
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~-----------------------------~v~i~G-~~~-----~~~~A~~ 149 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGK-----------------------------TVAIIG-DPE-----QVEIARE 149 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCC-----------------------------EEEEEe-CHH-----HHHHHHH
Confidence 68999999999999999999999999641 366766 454 6788999
Q ss_pred HHHHccCC
Q 023068 231 IIEELLKP 238 (287)
Q Consensus 231 ~Ie~LL~p 238 (287)
.|+.|+.-
T Consensus 150 ~I~~li~g 157 (180)
T PRK13763 150 AIEMLIEG 157 (180)
T ss_pred HHHHHHcC
Confidence 99999863
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=8.5e-05 Score=78.11 Aligned_cols=71 Identities=25% Similarity=0.531 Sum_probs=59.8
Q ss_pred CCcceeeEEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCc
Q 023068 129 SSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPL 208 (287)
Q Consensus 129 ~~~~vkk~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epL 208 (287)
-++..-++..+.|| -..||.||||+|.|+|.|+++|||+|.|--.|
T Consensus 572 ~s~~aP~~~~~~I~------~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G---------------------------- 617 (719)
T TIGR02696 572 MSPYAPRIITVKIP------VDKIGEVIGPKGKMINQIQDETGAEISIEDDG---------------------------- 617 (719)
T ss_pred cccCCCeeEEEEeC------hHHhhheeCCCcHhHHHHHHHHCCEEEEecCc----------------------------
Confidence 34455677788898 46789999999999999999999999997532
Q ss_pred eEEEEecCchhHHHHHHHHHHHHHHHccCC
Q 023068 209 HILIEADLPANIVDIRLRQAQEIIEELLKP 238 (287)
Q Consensus 209 HVlIsa~~~~~~~~~rl~~A~e~Ie~LL~p 238 (287)
+|.|.+.+.+ ++++|++.|+.+..+
T Consensus 618 ~V~I~a~d~~-----~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 618 TVYIGAADGP-----SAEAARAMINAIANP 642 (719)
T ss_pred EEEEEeCCHH-----HHHHHHHHHHHhhCc
Confidence 7999998765 789999999999985
No 16
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.69 E-value=7.5e-05 Score=66.11 Aligned_cols=64 Identities=25% Similarity=0.475 Sum_probs=52.0
Q ss_pred EEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEE---
Q 023068 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIE--- 213 (287)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIs--- 213 (287)
..+.|| -+-+|.||||.|.|+|.|+++|||+|.|.-.. =.|.|.
T Consensus 5 ~~i~IP------~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~---------------------------g~V~I~~~~ 51 (180)
T PRK13763 5 EYVKIP------KDRIGVLIGKKGETKKEIEERTGVKLEIDSET---------------------------GEVIIEPTD 51 (180)
T ss_pred EEEEcC------HHHhhhHhccchhHHHHHHHHHCcEEEEECCC---------------------------CeEEEEeCC
Confidence 456777 46789999999999999999999999998530 157776
Q ss_pred ecCchhHHHHHHHHHHHHHHHccCC
Q 023068 214 ADLPANIVDIRLRQAQEIIEELLKP 238 (287)
Q Consensus 214 a~~~~~~~~~rl~~A~e~Ie~LL~p 238 (287)
+.++. .+.+|+++|+.++..
T Consensus 52 ~~d~~-----~i~kA~~~I~ai~~g 71 (180)
T PRK13763 52 GEDPL-----AVLKARDIVKAIGRG 71 (180)
T ss_pred CCCHH-----HHHHHHHHHHHHhcC
Confidence 55554 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=97.52 E-value=0.00011 Score=64.54 Aligned_cols=58 Identities=24% Similarity=0.421 Sum_probs=47.0
Q ss_pred CCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEE--EecCchhHHHHHHH
Q 023068 149 FNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILI--EADLPANIVDIRLR 226 (287)
Q Consensus 149 ~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlI--sa~~~~~~~~~rl~ 226 (287)
-+.+|.||||+|.|+|+||++|||+|.|--. . =.|.| .+.++. .+.
T Consensus 6 ~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~------~---------------------g~V~I~~~t~d~~-----~i~ 53 (172)
T TIGR03665 6 KDRIGVLIGKGGETKKEIEERTGVKLDIDSE------T---------------------GEVKIEEEDEDPL-----AVM 53 (172)
T ss_pred HHHhhhHhCCchhHHHHHHHHhCcEEEEEcC------C---------------------ceEEEecCCCCHH-----HHH
Confidence 4789999999999999999999999999842 0 14667 344544 689
Q ss_pred HHHHHHHHccCC
Q 023068 227 QAQEIIEELLKP 238 (287)
Q Consensus 227 ~A~e~Ie~LL~p 238 (287)
+|.++|+.+...
T Consensus 54 kA~~~I~~i~~g 65 (172)
T TIGR03665 54 KAREVVKAIGRG 65 (172)
T ss_pred HHHHHHHHHHcC
Confidence 999999998884
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=97.47 E-value=0.00023 Score=74.62 Aligned_cols=69 Identities=23% Similarity=0.369 Sum_probs=56.0
Q ss_pred CcceeeEEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCce
Q 023068 130 SYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLH 209 (287)
Q Consensus 130 ~~~vkk~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLH 209 (287)
.+..-+++.+.|| -..||.||||+|.|+|.|+++|||+|.|--.| +
T Consensus 546 ~~~~p~~~~~~I~------~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG----------------------------~ 591 (684)
T TIGR03591 546 SPYAPRIETIKIN------PDKIRDVIGPGGKVIREITEETGAKIDIEDDG----------------------------T 591 (684)
T ss_pred cccCCeEEEEecC------HHHHHhhcCCCcHHHHHHHHHHCCEEEEecCe----------------------------E
Confidence 3445566778888 46789999999999999999999999996432 7
Q ss_pred EEEEecCchhHHHHHHHHHHHHHHHccC
Q 023068 210 ILIEADLPANIVDIRLRQAQEIIEELLK 237 (287)
Q Consensus 210 VlIsa~~~~~~~~~rl~~A~e~Ie~LL~ 237 (287)
|.|.+.+.+ .+++|.+.|+.+..
T Consensus 592 V~i~~~~~~-----~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 592 VKIAASDGE-----AAEAAIKMIEGITA 614 (684)
T ss_pred EEEEECcHH-----HHHHHHHHHHhhhc
Confidence 888887754 78899999998865
No 19
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.36 E-value=0.00034 Score=63.15 Aligned_cols=55 Identities=25% Similarity=0.452 Sum_probs=46.6
Q ss_pred cccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHH
Q 023068 151 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQE 230 (287)
Q Consensus 151 fvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~~~~~~~~~rl~~A~e 230 (287)
..|||||+.|.|.+.||.-|||.|.|.|+ +|-|-+. ++ .++.|.+
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~-----------------------------tVaiiG~-~~-----~v~iAr~ 156 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK-----------------------------TVAIIGG-FE-----QVEIARE 156 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc-----------------------------EEEEecC-hh-----hhHHHHH
Confidence 35999999999999999999999999994 6777774 44 5778999
Q ss_pred HHHHccCCCC
Q 023068 231 IIEELLKPVD 240 (287)
Q Consensus 231 ~Ie~LL~p~~ 240 (287)
.|+.|+.-.+
T Consensus 157 AVemli~G~~ 166 (194)
T COG1094 157 AVEMLINGAP 166 (194)
T ss_pred HHHHHHcCCC
Confidence 9999998654
No 20
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.07 E-value=0.00056 Score=73.56 Aligned_cols=71 Identities=20% Similarity=0.214 Sum_probs=58.7
Q ss_pred CCcceeeEEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCe-EEEeccCCCCCCCCCCCcccccCCCCCCCCCCCC
Q 023068 129 SSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCR-VYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDP 207 (287)
Q Consensus 129 ~~~~vkk~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgck-I~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~ep 207 (287)
-++..-++..+.|| -+.||.||||+|.|+|.|+++||++ |.|+-.
T Consensus 679 ~s~~aP~i~~~~i~------~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd---------------------------- 724 (891)
T PLN00207 679 LSKYAPLIHIMKVK------PEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD---------------------------- 724 (891)
T ss_pred hcccCCeeEEEEcC------HHHHHHHhcCCchhHHHHHHHHCCCccCcCCC----------------------------
Confidence 34455667788888 4779999999999999999999999 877643
Q ss_pred ceEEEEecCchhHHHHHHHHHHHHHHHccCC
Q 023068 208 LHILIEADLPANIVDIRLRQAQEIIEELLKP 238 (287)
Q Consensus 208 LHVlIsa~~~~~~~~~rl~~A~e~Ie~LL~p 238 (287)
-+|.|.+.+.+ ++++|+++|+.+..-
T Consensus 725 g~V~I~a~d~~-----~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 725 GTVKITAKDLS-----SLEKSKAIISSLTMV 750 (891)
T ss_pred eeEEEEeCCHH-----HHHHHHHHHHHHhcC
Confidence 37889988865 899999999999874
No 21
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=96.43 E-value=0.0069 Score=62.44 Aligned_cols=71 Identities=24% Similarity=0.471 Sum_probs=49.6
Q ss_pred EEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEec
Q 023068 136 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEAD 215 (287)
Q Consensus 136 ~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~ 215 (287)
...|.|| =+-||.|||-.|.|+|+|+.+||+||.++= |..- .++ .- -+.|.+
T Consensus 231 ~~~V~VP------r~~VG~IIGkgGE~IKklq~etG~KIQfkp-----Dd~p-~sp-------------eR--~~~IiG- 282 (600)
T KOG1676|consen 231 TREVKVP------RSKVGIIIGKGGEMIKKLQNETGAKIQFKP-----DDDP-SSP-------------ER--PAQIIG- 282 (600)
T ss_pred eeEEecc------ccceeeEEecCchHHHHHhhccCceeEeec-----CCCC-CCc-------------cc--eeeeec-
Confidence 3456666 367999999999999999999999999984 2110 001 11 233444
Q ss_pred CchhHHHHHHHHHHHHHHHccCCC
Q 023068 216 LPANIVDIRLRQAQEIIEELLKPV 239 (287)
Q Consensus 216 ~~~~~~~~rl~~A~e~Ie~LL~p~ 239 (287)
.. .++.+|.++|.+||.-.
T Consensus 283 -~~----d~ie~Aa~lI~eii~~~ 301 (600)
T KOG1676|consen 283 -TV----DQIEHAAELINEIIAEA 301 (600)
T ss_pred -CH----HHHHHHHHHHHHHHHHH
Confidence 22 27899999999998743
No 22
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.41 E-value=0.0031 Score=66.37 Aligned_cols=57 Identities=23% Similarity=0.405 Sum_probs=47.7
Q ss_pred CCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhHHHHHHHHH
Q 023068 149 FNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQA 228 (287)
Q Consensus 149 ~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~~~~~~~~~rl~~A 228 (287)
...+|.+|||+|.|+|.|+++||++|-|+-.| .|.|.+.+.+ .+++|
T Consensus 562 ~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~G----------------------------~v~i~~~~~~-----~~~~a 608 (693)
T PRK11824 562 PDKIRDVIGPGGKTIREITEETGAKIDIEDDG----------------------------TVKIAATDGE-----AAEAA 608 (693)
T ss_pred HHHHHHHhcCCchhHHHHHHHHCCccccCCCc----------------------------eEEEEcccHH-----HHHHH
Confidence 46689999999999999999999998885432 6788887754 78999
Q ss_pred HHHHHHccCC
Q 023068 229 QEIIEELLKP 238 (287)
Q Consensus 229 ~e~Ie~LL~p 238 (287)
.+.|+.+...
T Consensus 609 ~~~I~~~~~~ 618 (693)
T PRK11824 609 KERIEGITAE 618 (693)
T ss_pred HHHHHHhccc
Confidence 9999998853
No 23
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.32 E-value=0.0051 Score=56.61 Aligned_cols=57 Identities=23% Similarity=0.377 Sum_probs=47.2
Q ss_pred CCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhHHHHHHHHH
Q 023068 149 FNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQA 228 (287)
Q Consensus 149 ~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~~~~~~~~~rl~~A 228 (287)
-++++++|||+|.+++.|.++|+|+|.|-=.| .|+|.+.+.+ .+..|
T Consensus 153 ~~~i~~lig~~g~~i~~l~~~~~~~I~ig~NG----------------------------~VwI~~~~~~-----~~~~a 199 (235)
T PRK04163 153 PVKVPRVIGKKGSMINMLKEETGCDIIVGQNG----------------------------RIWIKGPDEE-----DEEIA 199 (235)
T ss_pred HHHHHhhcCCCChhHhhhhhhhCcEEEEcCCc----------------------------EEEEeeCCHH-----HHHHH
Confidence 57899999999999999999999999983211 7999998865 56788
Q ss_pred HHHHHHccCC
Q 023068 229 QEIIEELLKP 238 (287)
Q Consensus 229 ~e~Ie~LL~p 238 (287)
++.|+.+-.-
T Consensus 200 ~~~I~~~e~~ 209 (235)
T PRK04163 200 IEAIKKIERE 209 (235)
T ss_pred HHHHHHHHhh
Confidence 8888887654
No 24
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.19 E-value=0.0018 Score=64.71 Aligned_cols=38 Identities=42% Similarity=0.785 Sum_probs=34.0
Q ss_pred ecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEe
Q 023068 140 EIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 177 (287)
Q Consensus 140 ~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IR 177 (287)
.||++-.-.-||+|||||-.|.++|.||++||+||.|-
T Consensus 279 e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis 316 (584)
T KOG2193|consen 279 EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITIS 316 (584)
T ss_pred hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeee
Confidence 56777666679999999999999999999999999996
No 25
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=96.16 E-value=0.011 Score=61.07 Aligned_cols=75 Identities=27% Similarity=0.590 Sum_probs=57.5
Q ss_pred ceeeEEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEE
Q 023068 132 TVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHIL 211 (287)
Q Consensus 132 ~vkk~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVl 211 (287)
.++.+..|.|| =|-+|+|||-.|.|+|+|++.||||+.+-=.|+..+. .+-||.
T Consensus 136 ~~~ttqeI~IP------a~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~------------------~~Kplr-- 189 (600)
T KOG1676|consen 136 SVETTQEILIP------ANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG------------------ADKPLR-- 189 (600)
T ss_pred ccceeeeeccC------ccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC------------------CCCcee--
Confidence 45566778898 4778999999999999999999999988766655432 123344
Q ss_pred EEecCchhHHHHHHHHHHHHHHHccCC
Q 023068 212 IEADLPANIVDIRLRQAQEIIEELLKP 238 (287)
Q Consensus 212 Isa~~~~~~~~~rl~~A~e~Ie~LL~p 238 (287)
|+++ +. ++++|.++|.++|.-
T Consensus 190 itGd-p~-----~ve~a~~lV~dil~e 210 (600)
T KOG1676|consen 190 ITGD-PD-----KVEQAKQLVADILRE 210 (600)
T ss_pred ecCC-HH-----HHHHHHHHHHHHHHh
Confidence 5554 33 789999999999983
No 26
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=95.77 E-value=0.027 Score=53.93 Aligned_cols=27 Identities=41% Similarity=0.879 Sum_probs=25.8
Q ss_pred cceeCCCchhHHHHHHhhCCeEEEecc
Q 023068 153 GRLLGPRGNSLKRVEATTGCRVYIRGK 179 (287)
Q Consensus 153 GrIlGPrG~TlK~lE~eTgckI~IRGk 179 (287)
-|||||.|+|+|.||--|.|-|.|.|.
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~ 187 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN 187 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc
Confidence 689999999999999999999999994
No 27
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.21 E-value=0.026 Score=54.87 Aligned_cols=61 Identities=20% Similarity=0.301 Sum_probs=44.4
Q ss_pred CCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhH--HHHHHH
Q 023068 149 FNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEADLPANI--VDIRLR 226 (287)
Q Consensus 149 ~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~~~~~~--~~~rl~ 226 (287)
--|+|.|+|-+|.|.|.||+||+|+|.+=-.+..++ |+-|++-.-..+ |..||+
T Consensus 65 s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~------------------------~i~i~~~~~~~V~~a~~Ri~ 120 (345)
T KOG2814|consen 65 SSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKE------------------------EIKIIGISRNCVIQALERIA 120 (345)
T ss_pred HHHhhhhhcccchHHHHHHHhhccceEccCCCCCcc------------------------eEEEeehhHHHHHHHHHHHH
Confidence 368899999999999999999999999865432221 788888655433 444666
Q ss_pred HHHHHHH
Q 023068 227 QAQEIIE 233 (287)
Q Consensus 227 ~A~e~Ie 233 (287)
.++.-..
T Consensus 121 ~~ids~r 127 (345)
T KOG2814|consen 121 KLIDSDR 127 (345)
T ss_pred HHHHhhh
Confidence 6655555
No 28
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=94.54 E-value=0.082 Score=53.85 Aligned_cols=40 Identities=28% Similarity=0.529 Sum_probs=36.6
Q ss_pred eeEEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEecc
Q 023068 134 KRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 179 (287)
Q Consensus 134 kk~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGk 179 (287)
....|+.|| -+-+|-|||=+|+.+|.|.++|||+|.|-+.
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 29
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=94.19 E-value=0.042 Score=55.22 Aligned_cols=37 Identities=32% Similarity=0.674 Sum_probs=32.4
Q ss_pred EEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEecc
Q 023068 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 179 (287)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGk 179 (287)
.|++|| --|+|.||||.|.|+|-|-+.|.|||-+.-+
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 5799999999999999999999999999864
No 30
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=94.07 E-value=0.054 Score=52.94 Aligned_cols=37 Identities=24% Similarity=0.536 Sum_probs=33.4
Q ss_pred eEEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEe
Q 023068 135 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 177 (287)
Q Consensus 135 k~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IR 177 (287)
...||+|| -+-.|-|||-.|.|+.+||++|||+|.+-
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 56789999999999999999999999886
No 31
>PRK12704 phosphodiesterase; Provisional
Probab=92.82 E-value=0.24 Score=50.80 Aligned_cols=49 Identities=24% Similarity=0.555 Sum_probs=39.7
Q ss_pred EecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEecCch
Q 023068 139 LEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEADLPA 218 (287)
Q Consensus 139 v~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~~~~ 218 (287)
|.+|-++ +-|||||--|-++|.+|+.||+.|.|=- .|=-|+||+.+|.
T Consensus 214 v~lp~d~-----mkgriigreGrnir~~e~~tgvd~iidd---------------------------tp~~v~ls~~~~~ 261 (520)
T PRK12704 214 VNLPNDE-----MKGRIIGREGRNIRALETLTGVDLIIDD---------------------------TPEAVILSGFDPI 261 (520)
T ss_pred eecCCch-----hhcceeCCCcchHHHHHHHhCCeEEEcC---------------------------CCCeEEEecCChh
Confidence 5566554 5599999999999999999999999842 2237899999887
Q ss_pred h
Q 023068 219 N 219 (287)
Q Consensus 219 ~ 219 (287)
.
T Consensus 262 r 262 (520)
T PRK12704 262 R 262 (520)
T ss_pred h
Confidence 4
No 32
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=92.77 E-value=0.15 Score=53.84 Aligned_cols=66 Identities=27% Similarity=0.503 Sum_probs=50.9
Q ss_pred eeeEEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEE
Q 023068 133 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILI 212 (287)
Q Consensus 133 vkk~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlI 212 (287)
..+++.+-|+.+. ++-+|||+|.|+|.|.++|||+|.|--.|+ |.|
T Consensus 550 aPri~t~~i~~dK------I~dvIG~gGk~I~~I~eetg~~IdieddGt----------------------------v~i 595 (692)
T COG1185 550 APRIETIKIDPDK------IRDVIGPGGKTIKAITEETGVKIDIEDDGT----------------------------VKI 595 (692)
T ss_pred CCceEEEccCHHH------HhhccCCcccchhhhhhhhCcEEEecCCCc----------------------------EEE
Confidence 3345556666554 577999999999999999999999986654 556
Q ss_pred EecCchhHHHHHHHHHHHHHHHccC
Q 023068 213 EADLPANIVDIRLRQAQEIIEELLK 237 (287)
Q Consensus 213 sa~~~~~~~~~rl~~A~e~Ie~LL~ 237 (287)
.+.+.+ ++.+|.+.|+.+..
T Consensus 596 ~~s~~~-----~~~~ak~~I~~i~~ 615 (692)
T COG1185 596 AASDGE-----SAKKAKERIEAITR 615 (692)
T ss_pred EecchH-----HHHHHHHHHHHHHh
Confidence 666543 67889999998874
No 33
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=92.75 E-value=0.2 Score=51.38 Aligned_cols=63 Identities=25% Similarity=0.520 Sum_probs=47.3
Q ss_pred EEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEecCc
Q 023068 138 RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEADLP 217 (287)
Q Consensus 138 kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~~~ 217 (287)
-|.+|-++ +-|||||--|-++|.+|+.||+.|.|=- .|=-|.||+.||
T Consensus 207 ~v~lp~d~-----~kgriigreGrnir~~e~~tgvd~iidd---------------------------tp~~v~ls~fdp 254 (514)
T TIGR03319 207 VVNLPNDE-----MKGRIIGREGRNIRALETLTGVDLIIDD---------------------------TPEAVILSGFDP 254 (514)
T ss_pred eEEcCChh-----hhccccCCCcchHHHHHHHhCceEEEcC---------------------------CCCeEEecCCch
Confidence 35666554 5599999999999999999999999853 122688999998
Q ss_pred hhHHHHHHHHHHHHHHHccC
Q 023068 218 ANIVDIRLRQAQEIIEELLK 237 (287)
Q Consensus 218 ~~~~~~rl~~A~e~Ie~LL~ 237 (287)
. |=.-|..-+++|+.
T Consensus 255 ~-----rreia~~~l~~li~ 269 (514)
T TIGR03319 255 V-----RREIARMALEKLIQ 269 (514)
T ss_pred H-----HHHHHHHHHHHHHH
Confidence 6 34455566666654
No 34
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=92.36 E-value=0.64 Score=45.72 Aligned_cols=38 Identities=18% Similarity=0.511 Sum_probs=32.5
Q ss_pred eEEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEec
Q 023068 135 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (287)
Q Consensus 135 k~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRG 178 (287)
++.||.+|-. -.|.|||+.|.|+|.+.+++||-|.|--
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 3599999999999999999999999974
No 35
>PRK00106 hypothetical protein; Provisional
Probab=91.38 E-value=0.35 Score=49.95 Aligned_cols=63 Identities=30% Similarity=0.539 Sum_probs=49.5
Q ss_pred EEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEecCc
Q 023068 138 RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEADLP 217 (287)
Q Consensus 138 kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~~~ 217 (287)
-|.+|-+ .+-|||||--|-+++.+|..||+.|.|=- .|=-|.||+.||
T Consensus 228 ~v~lp~d-----emkGriIGreGrNir~~E~~tGvdliidd---------------------------tp~~v~lS~fdp 275 (535)
T PRK00106 228 TVHLPDD-----NMKGRIIGREGRNIRTLESLTGIDVIIDD---------------------------TPEVVVLSGFDP 275 (535)
T ss_pred eEEcCCh-----HhhcceeCCCcchHHHHHHHhCceEEEcC---------------------------CCCeEEEeCCCh
Confidence 3566655 45599999999999999999999999842 223689999998
Q ss_pred hhHHHHHHHHHHHHHHHccC
Q 023068 218 ANIVDIRLRQAQEIIEELLK 237 (287)
Q Consensus 218 ~~~~~~rl~~A~e~Ie~LL~ 237 (287)
. |-.-|..-+++|+.
T Consensus 276 v-----RReiAr~~le~Li~ 290 (535)
T PRK00106 276 I-----RREIARMTLESLIK 290 (535)
T ss_pred H-----HHHHHHHHHHHHHH
Confidence 7 55667777777776
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=89.98 E-value=0.56 Score=34.44 Aligned_cols=36 Identities=19% Similarity=0.393 Sum_probs=30.2
Q ss_pred eEEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEE
Q 023068 135 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYI 176 (287)
Q Consensus 135 k~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~I 176 (287)
...++.||. .-+|+.||.+|.+++.++..+|.+|.|
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
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=86.67 E-value=0.58 Score=47.83 Aligned_cols=41 Identities=24% Similarity=0.483 Sum_probs=36.5
Q ss_pred eeeEEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEecc
Q 023068 133 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 179 (287)
Q Consensus 133 vkk~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGk 179 (287)
...+.++.|| .+++|.|||..|+.+-.|++.|||.|.|-++
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 3455678888 7999999999999999999999999999875
No 38
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=84.68 E-value=0.45 Score=47.79 Aligned_cols=72 Identities=26% Similarity=0.520 Sum_probs=58.2
Q ss_pred ceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHHHHH
Q 023068 154 RLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIE 233 (287)
Q Consensus 154 rIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~~~~~~~~~rl~~A~e~Ie 233 (287)
.|.||.|-+.|.++.+|-.++.|.|-||..-.- .++ ...++|.||.|.+.++. .|+.|.-+++
T Consensus 308 ~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i~p-----------~~~-~~~~~p~~~~~~~~~~~-----~~~~~~~~~~ 370 (531)
T KOG1960|consen 308 AIVGPQGAYVKHIQQETRTRVQIKGQGSAFIEP-----------STN-RESDEPIHLCIMSHDPN-----AIQRAKVLCE 370 (531)
T ss_pred ccccCCcccccccCCCCCcceeccCccceeecC-----------CCC-CCCCCCcccccccCChh-----hhhhhhhccc
Confidence 478999999999999999999999999987311 122 23689999999987765 5677888999
Q ss_pred HccCCCCcc
Q 023068 234 ELLKPVDES 242 (287)
Q Consensus 234 ~LL~p~~e~ 242 (287)
.++.||+-.
T Consensus 371 ~~i~~v~~q 379 (531)
T KOG1960|consen 371 DLIASVHQQ 379 (531)
T ss_pred ccCCccccc
Confidence 999998743
No 39
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=83.59 E-value=0.59 Score=47.51 Aligned_cols=29 Identities=31% Similarity=0.628 Sum_probs=26.5
Q ss_pred CCcccceeCCCchhHHHHHHhhCCeEEEe
Q 023068 149 FNFVGRLLGPRGNSLKRVEATTGCRVYIR 177 (287)
Q Consensus 149 ~NfvGrIlGPrG~TlK~lE~eTgckI~IR 177 (287)
-||||.+||=.|+.+|+||..|+++|.|-
T Consensus 55 s~mvg~vigrggskik~iq~~tnt~iqii 83 (629)
T KOG0336|consen 55 SEMVGKVIGRGGSKIKRIQNDTNTRIQII 83 (629)
T ss_pred hhhhheeeccCcchhhhhhcccceeEEEe
Confidence 58999999999999999999999988763
No 40
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=83.19 E-value=0.72 Score=35.07 Aligned_cols=32 Identities=25% Similarity=0.518 Sum_probs=24.8
Q ss_pred CCCCCcccceeCCCchhHHHHHHhh-CCeEEEe
Q 023068 146 YPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIR 177 (287)
Q Consensus 146 ~P~~NfvGrIlGPrG~TlK~lE~eT-gckI~IR 177 (287)
.|+++-+|..+|++|..+|.|+++. |-||.|=
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 5555543
No 41
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=78.30 E-value=5.4 Score=37.50 Aligned_cols=30 Identities=27% Similarity=0.561 Sum_probs=27.3
Q ss_pred CCcccceeCCCchhHHHHHHhhCCeEEEec
Q 023068 149 FNFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (287)
Q Consensus 149 ~NfvGrIlGPrG~TlK~lE~eTgckI~IRG 178 (287)
.++|-|+||++|+-++.|.+.|+|+|.|==
T Consensus 154 p~kVpRvig~~~sm~~~l~~~~~~~I~VG~ 183 (239)
T COG1097 154 PSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ 183 (239)
T ss_pred hhhcceEecCCCcHHHHhhhhcCeEEEEec
Confidence 578889999999999999999999999843
No 42
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=75.09 E-value=2.5 Score=29.79 Aligned_cols=23 Identities=13% Similarity=0.368 Sum_probs=20.6
Q ss_pred ccceeCCCchhHHHHHHhhCCeE
Q 023068 152 VGRLLGPRGNSLKRVEATTGCRV 174 (287)
Q Consensus 152 vGrIlGPrG~TlK~lE~eTgckI 174 (287)
.|++||.+|.+++.|+..++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 49999999999999999998554
No 43
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=74.38 E-value=4.9 Score=42.31 Aligned_cols=70 Identities=26% Similarity=0.308 Sum_probs=49.5
Q ss_pred cccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhHHHHHHHHHHH
Q 023068 151 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQE 230 (287)
Q Consensus 151 fvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~~~~~~~~~rl~~A~e 230 (287)
-+..+|||.|..+|+||.|||+.-+| | +=|+-|-|.++. .+.+|.+
T Consensus 607 k~~~lIGp~G~~~kki~~EtGai~~v-------D----------------------e~t~~i~A~~~~-----am~~Ak~ 652 (760)
T KOG1067|consen 607 KRATLIGPGGVLKKKIEVETGAISQV-------D----------------------EGTFSIFAPTQA-----AMEEAKE 652 (760)
T ss_pred hhheeecCccceeeeEeeeccceeee-------c----------------------CceEEEEecCHH-----HHHHHHH
Confidence 35679999999999999999943332 1 128888888865 7899999
Q ss_pred HHHHccCCCCcchHHHHHHHHHHHHHHcCcc
Q 023068 231 IIEELLKPVDESQDYIKRQQLRELAMLNSNF 261 (287)
Q Consensus 231 ~Ie~LL~p~~e~~D~lK~~QL~ELA~lNGt~ 261 (287)
.|..+..-..+ +||.-=+++++|.
T Consensus 653 ~I~~i~~~~~~-------~~l~~g~vy~~tI 676 (760)
T KOG1067|consen 653 FIDGIIKDDQV-------QDLEFGGVYTATI 676 (760)
T ss_pred HHHHHhcCccc-------cceEeeeEEEEEE
Confidence 99999874221 2333335666664
No 44
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=70.91 E-value=3.6 Score=35.30 Aligned_cols=29 Identities=24% Similarity=0.400 Sum_probs=26.9
Q ss_pred CcccceeCCCchhHHHHHHhhCCeEEEec
Q 023068 150 NFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (287)
Q Consensus 150 NfvGrIlGPrG~TlK~lE~eTgckI~IRG 178 (287)
+.+|..+|++|..+|.|++..|-||-|=.
T Consensus 41 ~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 41 GDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 57899999999999999999999998876
No 45
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=69.30 E-value=13 Score=34.04 Aligned_cols=37 Identities=35% Similarity=0.566 Sum_probs=30.9
Q ss_pred EEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEecc
Q 023068 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 179 (287)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGk 179 (287)
+.|.||-+ =+|-++|+.|.+.|.||+.|||+|.|-.+
T Consensus 10 ~~v~iPk~------R~~~lig~~g~v~k~ie~~~~~~~~iD~~ 46 (194)
T COG1094 10 EAVKIPKD------RIGVLIGKWGEVKKAIEEKTGVKLRIDSK 46 (194)
T ss_pred eeeecCch------hheeeecccccchHHHHhhcCeEEEEECC
Confidence 44566633 35899999999999999999999999876
No 46
>PRK12705 hypothetical protein; Provisional
Probab=69.07 E-value=7.9 Score=39.98 Aligned_cols=35 Identities=31% Similarity=0.653 Sum_probs=29.4
Q ss_pred EecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEec
Q 023068 139 LEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (287)
Q Consensus 139 v~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRG 178 (287)
|.+|-+ .+-|||||--|.+++.+|..||+-|.|--
T Consensus 202 v~lp~d-----emkGriIGreGrNir~~E~~tGvdliidd 236 (508)
T PRK12705 202 VPIPSD-----AMKGRIIGREGRNIRAFEGLTGVDLIIDD 236 (508)
T ss_pred eecCCh-----HhhccccCccchhHHHHHHhhCCceEecC
Confidence 556644 55699999999999999999999998853
No 47
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=62.72 E-value=5.4 Score=39.19 Aligned_cols=37 Identities=22% Similarity=0.354 Sum_probs=30.2
Q ss_pred eeeEEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEE
Q 023068 133 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVY 175 (287)
Q Consensus 133 vkk~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~ 175 (287)
...++.+.+| +-||+.|.|++|.++|.|+++|.+.|.
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 3344555565 679999999999999999999999875
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=61.72 E-value=4.9 Score=30.56 Aligned_cols=22 Identities=27% Similarity=0.536 Sum_probs=19.5
Q ss_pred ccceeCCCchhHHHHHHhhCCe
Q 023068 152 VGRLLGPRGNSLKRVEATTGCR 173 (287)
Q Consensus 152 vGrIlGPrG~TlK~lE~eTgck 173 (287)
.|+|||-+|.|++.||--+..-
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~~ 56 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANLV 56 (77)
T ss_pred CCeEECCCCccHHHHHHHHHHH
Confidence 4999999999999999988743
No 49
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=51.84 E-value=4.6 Score=30.14 Aligned_cols=20 Identities=30% Similarity=0.639 Sum_probs=18.2
Q ss_pred ccceeCCCchhHHHHHHhhC
Q 023068 152 VGRLLGPRGNSLKRVEATTG 171 (287)
Q Consensus 152 vGrIlGPrG~TlK~lE~eTg 171 (287)
.|+|||-+|.|++.||.-++
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHH
T ss_pred cceEECCCCeeHHHHHHHHH
Confidence 59999999999999998765
No 50
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=50.57 E-value=29 Score=34.41 Aligned_cols=30 Identities=30% Similarity=0.503 Sum_probs=27.7
Q ss_pred CcccceeCCCchhHHHHHHhhCCeEEEecc
Q 023068 150 NFVGRLLGPRGNSLKRVEATTGCRVYIRGK 179 (287)
Q Consensus 150 NfvGrIlGPrG~TlK~lE~eTgckI~IRGk 179 (287)
|-+-.++||.|..++.||+.+|+.|.-||.
T Consensus 24 ~~~~~l~G~~~~~l~l~e~~~gv~i~~rG~ 53 (348)
T COG1702 24 NELVALFGPTDTNLSLLEIALGVSIVARGE 53 (348)
T ss_pred hhhhhhcCCCCccHHHHHHHhCcEEEeCCc
Confidence 667789999999999999999999999994
No 51
>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=49.14 E-value=32 Score=31.59 Aligned_cols=40 Identities=15% Similarity=0.353 Sum_probs=30.5
Q ss_pred eeeEEEEecCCCCCCCCCcccceeCCCchhHHHH--------HHhhCCeEEEe
Q 023068 133 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRV--------EATTGCRVYIR 177 (287)
Q Consensus 133 vkk~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~l--------E~eTgckI~IR 177 (287)
+.....|++.-+.+- |-|||.+|.++|+| |+..||||.+.
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 66679988764
No 52
>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=48.81 E-value=16 Score=31.60 Aligned_cols=29 Identities=24% Similarity=0.414 Sum_probs=26.7
Q ss_pred CcccceeCCCchhHHHHHHhhCCeEEEec
Q 023068 150 NFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (287)
Q Consensus 150 NfvGrIlGPrG~TlK~lE~eTgckI~IRG 178 (287)
+-+|..+|++|..+|.|++..|=||-|=.
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 53
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=46.67 E-value=19 Score=35.59 Aligned_cols=34 Identities=24% Similarity=0.510 Sum_probs=30.2
Q ss_pred CCCCCCcccceeCCCchhHHHHHHhh-CCeEEEec
Q 023068 145 TYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 178 (287)
Q Consensus 145 ~~P~~NfvGrIlGPrG~TlK~lE~eT-gckI~IRG 178 (287)
.-|+++-+|..+|++|..++.+.++. |=||-|=-
T Consensus 240 ~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv~ 274 (362)
T PRK12327 240 NNPNVDAKGACVGPKGQRVQNIVSELKGEKIDIID 274 (362)
T ss_pred CCCCCCchheeECCCChhHHHHHHHhCCCeEEEEE
Confidence 34899999999999999999999998 88887754
No 54
>PRK02821 hypothetical protein; Provisional
Probab=45.90 E-value=12 Score=29.19 Aligned_cols=23 Identities=13% Similarity=0.416 Sum_probs=18.6
Q ss_pred CcccceeCCCchhHHHHHHhhCC
Q 023068 150 NFVGRLLGPRGNSLKRVEATTGC 172 (287)
Q Consensus 150 NfvGrIlGPrG~TlK~lE~eTgc 172 (287)
.=+|||||=+|.|++.|-.--.+
T Consensus 40 ~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 40 DDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred hhCcceeCCCCchHHHHHHHHHH
Confidence 44799999999999998765543
No 55
>PRK00468 hypothetical protein; Provisional
Probab=44.99 E-value=13 Score=28.79 Aligned_cols=19 Identities=21% Similarity=0.590 Sum_probs=16.4
Q ss_pred ccceeCCCchhHHHHHHhh
Q 023068 152 VGRLLGPRGNSLKRVEATT 170 (287)
Q Consensus 152 vGrIlGPrG~TlK~lE~eT 170 (287)
+|||||=+|.|++.|-.-.
T Consensus 41 ~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CcceecCCChhHHHHHHHH
Confidence 5999999999999986553
No 56
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=43.44 E-value=21 Score=32.37 Aligned_cols=33 Identities=24% Similarity=0.376 Sum_probs=29.2
Q ss_pred CCCCcccceeCCCchhHHHHHHhhCCeEEEecc
Q 023068 147 PNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 179 (287)
Q Consensus 147 P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGk 179 (287)
++.+=+|..+|++|..+|.|.++.|=||-|=--
T Consensus 82 ~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~ 114 (190)
T COG0195 82 VKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW 114 (190)
T ss_pred cCcCchhhhccCCChHHHHHHHHhCCceEEEEe
Confidence 457789999999999999999999988887764
No 57
>PRK15494 era GTPase Era; Provisional
Probab=43.08 E-value=41 Score=32.36 Aligned_cols=40 Identities=25% Similarity=0.356 Sum_probs=31.7
Q ss_pred eeeEEEEecCCCCCCCCCcccceeCCCchhHHHH--------HHhhCCeEEEe
Q 023068 133 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRV--------EATTGCRVYIR 177 (287)
Q Consensus 133 vkk~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~l--------E~eTgckI~IR 177 (287)
++....|||.-+.+- |-|||-+|..+|+| |+..||||.+.
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 445567888877655 89999999999986 77789988876
No 58
>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=42.50 E-value=25 Score=34.48 Aligned_cols=34 Identities=24% Similarity=0.461 Sum_probs=30.1
Q ss_pred CCCCCCcccceeCCCchhHHHHHHhh-CCeEEEec
Q 023068 145 TYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 178 (287)
Q Consensus 145 ~~P~~NfvGrIlGPrG~TlK~lE~eT-gckI~IRG 178 (287)
.-|+++-+|..+|++|+.++.+.++. |=+|-|=-
T Consensus 238 ~~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~ 272 (341)
T TIGR01953 238 NDENIDPVGACVGPKGSRIQAISKELNGEKIDIIE 272 (341)
T ss_pred CCCCCCcceeeECCCCchHHHHHHHhCCCeEEEEE
Confidence 35899999999999999999999998 77887754
No 59
>PRK00089 era GTPase Era; Reviewed
Probab=42.26 E-value=45 Score=30.71 Aligned_cols=40 Identities=25% Similarity=0.456 Sum_probs=30.6
Q ss_pred eeeEEEEecCCCCCCCCCcccceeCCCchhHHHH--------HHhhCCeEEEe
Q 023068 133 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRV--------EATTGCRVYIR 177 (287)
Q Consensus 133 vkk~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~l--------E~eTgckI~IR 177 (287)
++....|+|.-+.+ .+-|||-+|.++|+| |+..||+|.+.
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 67789988875
No 60
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=41.31 E-value=20 Score=38.82 Aligned_cols=37 Identities=24% Similarity=0.538 Sum_probs=29.6
Q ss_pred EEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEec
Q 023068 136 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (287)
Q Consensus 136 ~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRG 178 (287)
...+.||.+ |-+-|+||+|.++++++.+++|-|.+--
T Consensus 710 ~~~~~~p~~------~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 710 TKEIEIPRS------LHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred eeEEeccHH------HhhhccCCCCccHHHHHHHhccceecCC
Confidence 345677744 4578999999999999999999887643
No 61
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=40.47 E-value=23 Score=31.53 Aligned_cols=27 Identities=22% Similarity=0.260 Sum_probs=25.6
Q ss_pred cceeCCCchhHHHHHHhhCCeEEEecc
Q 023068 153 GRLLGPRGNSLKRVEATTGCRVYIRGK 179 (287)
Q Consensus 153 GrIlGPrG~TlK~lE~eTgckI~IRGk 179 (287)
|.-||++|.++|+|++..|=+|.|=.-
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEEEc
Confidence 999999999999999999999999874
No 62
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=39.60 E-value=26 Score=30.00 Aligned_cols=25 Identities=20% Similarity=0.352 Sum_probs=22.2
Q ss_pred ccceeCCCchhHHHHHHhhCCeEEE
Q 023068 152 VGRLLGPRGNSLKRVEATTGCRVYI 176 (287)
Q Consensus 152 vGrIlGPrG~TlK~lE~eTgckI~I 176 (287)
.|+.||.+|.|++.++.-+|-.+-|
T Consensus 110 ~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 110 KGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred cchhhCCCCHHHHHHHHHhCCccCC
Confidence 5999999999999999999877644
No 63
>PRK01064 hypothetical protein; Provisional
Probab=37.50 E-value=17 Score=28.39 Aligned_cols=20 Identities=20% Similarity=0.607 Sum_probs=17.7
Q ss_pred ccceeCCCchhHHHHHHhhC
Q 023068 152 VGRLLGPRGNSLKRVEATTG 171 (287)
Q Consensus 152 vGrIlGPrG~TlK~lE~eTg 171 (287)
+|++||-+|.|++.|..-..
T Consensus 41 ~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred ceEEECCCCccHHHHHHHHH
Confidence 59999999999999988654
No 64
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=36.91 E-value=26 Score=25.00 Aligned_cols=19 Identities=21% Similarity=0.433 Sum_probs=15.7
Q ss_pred hHHHHHHhhCCeEEEeccC
Q 023068 162 SLKRVEATTGCRVYIRGKG 180 (287)
Q Consensus 162 TlK~lE~eTgckI~IRGkG 180 (287)
.+++||++.|+++.+|..+
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 4799999999999999654
No 65
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=36.67 E-value=21 Score=27.96 Aligned_cols=18 Identities=17% Similarity=0.702 Sum_probs=15.7
Q ss_pred ccceeCCCchhHHHHHHh
Q 023068 152 VGRLLGPRGNSLKRVEAT 169 (287)
Q Consensus 152 vGrIlGPrG~TlK~lE~e 169 (287)
+|++||=+|.|++.|-.-
T Consensus 41 ~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 41 MGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred ccceecCCChhHHHHHHH
Confidence 599999999999998543
No 66
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=34.65 E-value=31 Score=34.46 Aligned_cols=34 Identities=21% Similarity=0.353 Sum_probs=29.8
Q ss_pred CCCCCCcccceeCCCchhHHHHHHhh-CCeEEEec
Q 023068 145 TYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 178 (287)
Q Consensus 145 ~~P~~NfvGrIlGPrG~TlK~lE~eT-gckI~IRG 178 (287)
..|+++-||..+|++|..++.|.++. |=||-|=-
T Consensus 246 ~d~~iDPvGacIG~~G~rI~~I~~eL~gEkIDvI~ 280 (374)
T PRK12328 246 NNPNIDPIGATVGVKGVRINAVSKELNGENIDCIE 280 (374)
T ss_pred CCCCCChHHhhcCCCcchHHHHHHHhCCCeEEEEE
Confidence 55899999999999999999999998 77777654
No 67
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=34.42 E-value=55 Score=33.52 Aligned_cols=34 Identities=21% Similarity=0.346 Sum_probs=30.0
Q ss_pred CCCCCCcccceeCCCchhHHHHHHhh-CCeEEEec
Q 023068 145 TYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 178 (287)
Q Consensus 145 ~~P~~NfvGrIlGPrG~TlK~lE~eT-gckI~IRG 178 (287)
.-|+++-||..+|++|+.++.|.++. |=||-|=-
T Consensus 272 ~d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~ 306 (449)
T PRK12329 272 LERDVDPVGACIGARGSRIQAVVNELRGEKIDVIR 306 (449)
T ss_pred CCCCCChhhccCCCCcchHHHHHHHhCCCeEEEEE
Confidence 34899999999999999999999998 88887754
No 68
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=33.29 E-value=46 Score=32.37 Aligned_cols=35 Identities=23% Similarity=0.573 Sum_probs=30.1
Q ss_pred EEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEe
Q 023068 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 177 (287)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IR 177 (287)
..|-||- .+-|-|||-.|.-+|||-.|+|+.|.|-
T Consensus 317 aQvtip~------dlggsiigkggqri~~ir~esGA~Ikid 351 (390)
T KOG2192|consen 317 AQVTIPK------DLGGSIIGKGGQRIKQIRHESGASIKID 351 (390)
T ss_pred eeEeccc------ccCcceecccchhhhhhhhccCceEEec
Confidence 3477883 4569999999999999999999999885
No 69
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=31.63 E-value=88 Score=30.50 Aligned_cols=38 Identities=18% Similarity=0.364 Sum_probs=30.1
Q ss_pred eEEEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEec
Q 023068 135 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (287)
Q Consensus 135 k~~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRG 178 (287)
...+|++--|. .|.|+|-.|.++|+|-.+.++.|.|--
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 34455555443 499999999999999999999998763
No 70
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=31.60 E-value=34 Score=30.90 Aligned_cols=20 Identities=25% Similarity=0.536 Sum_probs=17.9
Q ss_pred hhHHHHHHhhCCeEEEeccC
Q 023068 161 NSLKRVEATTGCRVYIRGKG 180 (287)
Q Consensus 161 ~TlK~lE~eTgckI~IRGkG 180 (287)
..+|+||++.|+++.+|++|
T Consensus 35 ~~i~~LE~~lg~~Lf~R~r~ 54 (294)
T PRK13348 35 QRIKALEESLGQPLLVRGRP 54 (294)
T ss_pred HHHHHHHHHhCceeeecCCC
Confidence 35899999999999999975
No 71
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=31.02 E-value=67 Score=32.17 Aligned_cols=41 Identities=17% Similarity=0.286 Sum_probs=34.3
Q ss_pred EEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCC
Q 023068 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIK 183 (287)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~k 183 (287)
..|+||-+++ ++.||-+|.+++.--+-||++|-|+.-+|--
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 7999999999999999999999999988754
No 72
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=30.02 E-value=7.8 Score=32.60 Aligned_cols=43 Identities=28% Similarity=0.480 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHccC-CCCcchHHHHHHHHHHHHHHcCccCCCC
Q 023068 222 DIRLRQAQEIIEELLK-PVDESQDYIKRQQLRELAMLNSNFREDS 265 (287)
Q Consensus 222 ~~rl~~A~e~Ie~LL~-p~~e~~D~lK~~QL~ELA~lNGt~r~~~ 265 (287)
|.||.+|+.+|+.-|. .+.|.-+ .-+.|.+||..-|..++.+-
T Consensus 47 DNKIeQAMDLVKtHLmfAVREEVe-~Lk~qI~eL~er~~~Le~EN 90 (123)
T KOG4797|consen 47 DNKIEQAMDLVKTHLMFAVREEVE-VLKEQIRELEERNSALEREN 90 (123)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
Confidence 4489999999998554 4554444 44689999988887775543
No 73
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=29.50 E-value=22 Score=35.16 Aligned_cols=31 Identities=26% Similarity=0.549 Sum_probs=27.9
Q ss_pred CCcccceeCCCchhHHHHHHhhCCeEEEecc
Q 023068 149 FNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 179 (287)
Q Consensus 149 ~NfvGrIlGPrG~TlK~lE~eTgckI~IRGk 179 (287)
+-+||++.||.|+|+|++|+.|..-|.--++
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 74
>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=27.98 E-value=12 Score=32.18 Aligned_cols=18 Identities=44% Similarity=0.826 Sum_probs=14.1
Q ss_pred CCCCCCCcccceeCCCch
Q 023068 144 DTYPNFNFVGRLLGPRGN 161 (287)
Q Consensus 144 ~~~P~~NfvGrIlGPrG~ 161 (287)
+-.|....+|+||||||.
T Consensus 101 ~~m~~l~~Lg~iLGprGl 118 (141)
T TIGR01170 101 DIVPELAQLRRLLGPKGL 118 (141)
T ss_pred HHHHHHHHhhcccccCcC
Confidence 344566789999999985
No 75
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=27.97 E-value=49 Score=33.88 Aligned_cols=34 Identities=24% Similarity=0.441 Sum_probs=29.6
Q ss_pred CCCCCCCcccceeCCCchhHHHHHHhh-CCeEEEe
Q 023068 144 DTYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIR 177 (287)
Q Consensus 144 ~~~P~~NfvGrIlGPrG~TlK~lE~eT-gckI~IR 177 (287)
..-|++.-||..+|++|+.++.|.++. |=||-|=
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 456899999999999999999999998 7777664
No 76
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=27.43 E-value=57 Score=36.53 Aligned_cols=79 Identities=27% Similarity=0.378 Sum_probs=56.8
Q ss_pred EEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEecC
Q 023068 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEADL 216 (287)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~~ 216 (287)
...-.+++.+|- |.-+++.+=-- +.+|...|+|.|.+||+== ...+ .| ...+..||.+|++.+
T Consensus 898 y~~~~~inD~Pq-~~r~~vt~~~~--L~~i~e~~~~~it~rg~f~--~~gk----------~p--~~gErklyl~ve~~~ 960 (997)
T KOG0334|consen 898 YEAELEINDFPQ-NARWRVTYKEA--LLRISEPTAAGITTRGKFN--PPGK----------EP--KPGERKLYLLVEGPD 960 (997)
T ss_pred eeeeccccccch-hcceeeechhh--hhhccCccccceeeccccC--CCCC----------CC--CCcchhhhhhhhcch
Confidence 344577789995 77788887643 9999999999999999731 1111 11 225678999999765
Q ss_pred chhHHHHHHHHHHHHHHHccC
Q 023068 217 PANIVDIRLRQAQEIIEELLK 237 (287)
Q Consensus 217 ~~~~~~~rl~~A~e~Ie~LL~ 237 (287)
.- -+++|++.++.+|.
T Consensus 961 e~-----~vqra~~e~~r~l~ 976 (997)
T KOG0334|consen 961 EL-----SVQRAIEELERLLE 976 (997)
T ss_pred hH-----HHHHHHHHHHHHHH
Confidence 43 57889999888665
No 77
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=26.00 E-value=20 Score=33.35 Aligned_cols=29 Identities=24% Similarity=0.441 Sum_probs=26.7
Q ss_pred CcccceeCCCchhHHHHHHhhCCeEEEec
Q 023068 150 NFVGRLLGPRGNSLKRVEATTGCRVYIRG 178 (287)
Q Consensus 150 NfvGrIlGPrG~TlK~lE~eTgckI~IRG 178 (287)
--||||.|-.|.|--.||..|.++|.+-+
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad 206 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLAD 206 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecC
Confidence 35899999999999999999999999976
No 78
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=25.98 E-value=41 Score=35.06 Aligned_cols=42 Identities=14% Similarity=0.463 Sum_probs=34.4
Q ss_pred EEEecCCCCCCCCCcccceeCCCchhHHHHHHhhCCeEEEeccCCCCC
Q 023068 137 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKD 184 (287)
Q Consensus 137 ~kv~IPv~~~P~~NfvGrIlGPrG~TlK~lE~eTgckI~IRGkGS~kd 184 (287)
..|+||- -+++++||-+|..+++||...|-+|.|+-.+.-..
T Consensus 488 avv~vpe------~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~~~~ 529 (604)
T COG1855 488 AVVKVPE------KYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEEE 529 (604)
T ss_pred EEEEeCH------HHhhHHhhcccchHHHHHHHhCCceEEEEcccccc
Confidence 3466663 46789999999999999999999999998765444
No 79
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=24.16 E-value=43 Score=30.20 Aligned_cols=19 Identities=21% Similarity=0.366 Sum_probs=17.1
Q ss_pred hHHHHHHhhCCeEEEeccC
Q 023068 162 SLKRVEATTGCRVYIRGKG 180 (287)
Q Consensus 162 TlK~lE~eTgckI~IRGkG 180 (287)
.+|+||++.|+++..|++|
T Consensus 35 ~I~~LE~~lg~~Lf~R~r~ 53 (292)
T TIGR03298 35 RIKALEERLGQPLLVRTQP 53 (292)
T ss_pred HHHHHHHHhCchheecCCC
Confidence 4899999999999999865
No 80
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=23.57 E-value=58 Score=29.58 Aligned_cols=19 Identities=21% Similarity=0.370 Sum_probs=17.4
Q ss_pred hHHHHHHhhCCeEEEeccC
Q 023068 162 SLKRVEATTGCRVYIRGKG 180 (287)
Q Consensus 162 TlK~lE~eTgckI~IRGkG 180 (287)
.+|+||++.||++..|++|
T Consensus 36 ~I~~LE~~lg~~LF~R~~~ 54 (294)
T PRK03635 36 RIKALEERVGQVLLVRTQP 54 (294)
T ss_pred HHHHHHHHhCceeeecCCC
Confidence 5899999999999999875
No 81
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=22.37 E-value=70 Score=29.15 Aligned_cols=22 Identities=9% Similarity=0.265 Sum_probs=17.8
Q ss_pred hhHHHHHHhhCCeEEEeccCCC
Q 023068 161 NSLKRVEATTGCRVYIRGKGSI 182 (287)
Q Consensus 161 ~TlK~lE~eTgckI~IRGkGS~ 182 (287)
..+|+||++.|+++++|....+
T Consensus 35 ~~I~~LE~~lg~~LF~R~~r~~ 56 (300)
T PRK11074 35 YTVRQLEEWLAVPLFERRHRDV 56 (300)
T ss_pred HHHHHHHHHhCCeeEEeCCCCc
Confidence 3589999999999999954333
No 82
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=21.75 E-value=68 Score=28.98 Aligned_cols=18 Identities=17% Similarity=0.553 Sum_probs=16.1
Q ss_pred hHHHHHHhhCCeEEEecc
Q 023068 162 SLKRVEATTGCRVYIRGK 179 (287)
Q Consensus 162 TlK~lE~eTgckI~IRGk 179 (287)
.+|+||++.|+++..|..
T Consensus 35 ~I~~LE~~lG~~LF~R~~ 52 (275)
T PRK03601 35 RIRQLENQLGVNLFTRHR 52 (275)
T ss_pred HHHHHHHHhCCceEEECC
Confidence 489999999999999954
No 83
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=21.20 E-value=79 Score=29.45 Aligned_cols=19 Identities=21% Similarity=0.546 Sum_probs=16.7
Q ss_pred hhHHHHHHhhCCeEEEecc
Q 023068 161 NSLKRVEATTGCRVYIRGK 179 (287)
Q Consensus 161 ~TlK~lE~eTgckI~IRGk 179 (287)
..+|+||++.|+++.+|..
T Consensus 35 ~~Ik~LE~~lg~~LF~R~~ 53 (317)
T PRK15421 35 HQFSDLEQRLGFRLFVRKS 53 (317)
T ss_pred HHHHHHHHHhCCEEEEecC
Confidence 3589999999999999964
No 84
>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=20.89 E-value=32 Score=25.75 Aligned_cols=23 Identities=17% Similarity=0.484 Sum_probs=18.9
Q ss_pred ccceeCCCchhHHHHHHhhCCeE
Q 023068 152 VGRLLGPRGNSLKRVEATTGCRV 174 (287)
Q Consensus 152 vGrIlGPrG~TlK~lE~eTgckI 174 (287)
.|.+||-+|.++|.|....+-++
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 39999999999999977765443
No 85
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=20.72 E-value=77 Score=29.27 Aligned_cols=19 Identities=21% Similarity=0.457 Sum_probs=16.6
Q ss_pred hHHHHHHhhCCeEEEec-cC
Q 023068 162 SLKRVEATTGCRVYIRG-KG 180 (287)
Q Consensus 162 TlK~lE~eTgckI~IRG-kG 180 (287)
.+|+||++.||++.+|. +|
T Consensus 36 ~ik~LE~~lg~~Lf~R~~r~ 55 (313)
T PRK12684 36 AIIELEDELGVEIFTRHGKR 55 (313)
T ss_pred HHHHHHHHhCCeeEEEcCCc
Confidence 48999999999999994 54
No 86
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=20.71 E-value=78 Score=29.24 Aligned_cols=20 Identities=35% Similarity=0.718 Sum_probs=17.1
Q ss_pred hhHHHHHHhhCCeEEEe-ccC
Q 023068 161 NSLKRVEATTGCRVYIR-GKG 180 (287)
Q Consensus 161 ~TlK~lE~eTgckI~IR-GkG 180 (287)
..+|+||++.|+++++| |+|
T Consensus 35 ~~I~~LE~~lg~~Lf~R~~r~ 55 (309)
T PRK12683 35 KQIKDLEDELGVEIFIRRGKR 55 (309)
T ss_pred HHHHHHHHHhCCeeEeeCCCC
Confidence 35899999999999999 455
No 87
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=20.64 E-value=84 Score=28.55 Aligned_cols=22 Identities=14% Similarity=0.404 Sum_probs=18.9
Q ss_pred hHHHHHHhhCCeEEEeccCCCC
Q 023068 162 SLKRVEATTGCRVYIRGKGSIK 183 (287)
Q Consensus 162 TlK~lE~eTgckI~IRGkGS~k 183 (287)
.+|+||++.||++..|.++.+.
T Consensus 39 ~i~~LE~~lG~~LF~R~~r~~~ 60 (302)
T PRK09791 39 SIQELEEGLAAQLFFRRSKGVT 60 (302)
T ss_pred HHHHHHHHhCCeEEEEcCCCce
Confidence 4899999999999999876554
No 88
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=20.55 E-value=38 Score=31.43 Aligned_cols=10 Identities=70% Similarity=1.378 Sum_probs=8.3
Q ss_pred ccceeCCCch
Q 023068 152 VGRLLGPRGN 161 (287)
Q Consensus 152 vGrIlGPrG~ 161 (287)
+|+||||||.
T Consensus 126 LgriLGprGl 135 (229)
T CHL00129 126 LGRVLGPRGL 135 (229)
T ss_pred hcCcccccCC
Confidence 4999999963
No 89
>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=20.36 E-value=23 Score=32.69 Aligned_cols=10 Identities=70% Similarity=1.401 Sum_probs=8.6
Q ss_pred cccceeCCCc
Q 023068 151 FVGRLLGPRG 160 (287)
Q Consensus 151 fvGrIlGPrG 160 (287)
.+|+||||||
T Consensus 124 ~Lg~iLGPrG 133 (227)
T TIGR01169 124 KLGRILGPRG 133 (227)
T ss_pred Hhcccccccc
Confidence 3599999997
No 90
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=20.04 E-value=2.7e+02 Score=25.56 Aligned_cols=61 Identities=21% Similarity=0.140 Sum_probs=33.9
Q ss_pred ccceeCCC-------------chhHHHHHHhhCCeEEEeccCCCCCCCCCCCcccccCCCCCCCCCCCCceEEEEecCch
Q 023068 152 VGRLLGPR-------------GNSLKRVEATTGCRVYIRGKGSIKDPDKVSTPEDKLRGRPGYEHLNDPLHILIEADLPA 218 (287)
Q Consensus 152 vGrIlGPr-------------G~TlK~lE~eTgckI~IRGkGS~kd~~k~~~~Ee~lrg~p~~ehl~epLHVlIsa~~~~ 218 (287)
+||+|||+ +..+...-+++.+++.+|=+ + .--+|+.|=-.+..
T Consensus 117 lgk~LGp~~~p~gK~P~~~~~~~dl~~~i~~~k~~v~~r~~----k--------------------~~~~~~~VGk~~m~ 172 (214)
T PTZ00225 117 VPRLVGPHMHRMGKFPTVCSPSESLPDKVVELRSTVKFQLK----K--------------------VLCLGTCVGHVEMT 172 (214)
T ss_pred hhhhcCCCCCcCCCCCcccCCccCHHHHHHHHhheeEEEec----C--------------------ccEEEeEEccCCCC
Confidence 59999998 33355555566656666532 0 11258877555433
Q ss_pred -hHHHHHHHHHHHHHHHcc
Q 023068 219 -NIVDIRLRQAQEIIEELL 236 (287)
Q Consensus 219 -~~~~~rl~~A~e~Ie~LL 236 (287)
+.+.+-+..+++.|...|
T Consensus 173 ~e~i~eNi~a~l~~l~~~~ 191 (214)
T PTZ00225 173 EEQLRQNVVMAINFLVSLL 191 (214)
T ss_pred HHHHHHHHHHHHHHHHHhC
Confidence 233334555556565555
Done!