Query 027823
Match_columns 218
No_of_seqs 161 out of 425
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 15:44:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027823.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027823hhsearch_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 1.4E-53 2.9E-58 376.9 14.3 155 61-217 83-241 (259)
2 cd02395 SF1_like-KH Splicing f 100.0 8.8E-42 1.9E-46 272.7 13.6 119 71-193 1-120 (120)
3 KOG0119 Splicing factor 1/bran 100.0 2.7E-40 5.9E-45 311.7 6.7 175 13-197 79-261 (554)
4 COG5176 MSL5 Splicing factor ( 100.0 3.8E-33 8.3E-38 241.6 5.2 176 14-195 90-269 (269)
5 KOG1960 Predicted RNA-binding 98.6 3.1E-08 6.7E-13 93.6 3.5 97 68-178 208-304 (531)
6 cd00105 KH-I K homology RNA-bi 98.5 5.2E-07 1.1E-11 62.3 7.1 62 72-163 2-63 (64)
7 cd02393 PNPase_KH Polynucleoti 98.5 3.5E-07 7.7E-12 64.7 5.7 59 71-164 3-61 (61)
8 PF00013 KH_1: KH domain syndr 98.4 2.6E-07 5.7E-12 64.0 2.9 59 72-163 2-60 (60)
9 smart00322 KH K homology RNA-b 98.3 3.9E-06 8.4E-11 56.9 7.9 65 71-167 4-68 (69)
10 PF13014 KH_3: KH domain 98.2 9.2E-07 2E-11 58.1 3.2 28 86-113 1-28 (43)
11 cd02396 PCBP_like_KH K homolog 98.2 6E-06 1.3E-10 58.5 6.0 35 72-112 2-36 (65)
12 cd02394 vigilin_like_KH K homo 98.1 4.7E-06 1E-10 58.0 4.5 59 73-163 3-61 (62)
13 TIGR03665 arCOG04150 arCOG0415 98.0 9.5E-06 2.1E-10 68.3 5.0 53 86-169 99-151 (172)
14 PRK13763 putative RNA-processi 97.9 2.3E-05 4.9E-10 66.5 5.8 53 86-169 105-157 (180)
15 PRK13763 putative RNA-processi 97.5 0.00019 4.1E-09 60.9 5.8 65 71-169 4-71 (180)
16 COG1094 Predicted RNA-binding 97.5 0.0002 4.4E-09 62.1 5.8 55 86-171 112-166 (194)
17 TIGR03665 arCOG04150 arCOG0415 97.5 0.00015 3.2E-09 61.1 4.3 57 85-169 7-65 (172)
18 TIGR02696 pppGpp_PNP guanosine 97.4 0.00047 1E-08 69.7 7.8 71 64-169 572-642 (719)
19 KOG2874 rRNA processing protei 97.0 0.002 4.3E-08 59.2 6.6 68 88-186 161-228 (356)
20 TIGR03591 polynuc_phos polyrib 96.9 0.0015 3.3E-08 65.7 5.5 64 70-168 551-614 (684)
21 KOG1676 K-homology type RNA bi 96.7 0.0029 6.3E-08 62.6 5.9 62 85-170 239-301 (600)
22 KOG1676 K-homology type RNA bi 96.6 0.0048 1E-07 61.1 6.7 75 67-169 136-210 (600)
23 KOG2193 IGF-II mRNA-binding pr 96.4 0.0011 2.3E-08 63.9 0.7 38 75-112 279-316 (584)
24 PRK04163 exosome complex RNA-b 96.3 0.0054 1.2E-07 54.1 4.4 56 85-169 154-209 (235)
25 PLN00207 polyribonucleotide nu 96.2 0.0043 9.3E-08 64.2 3.6 69 66-169 681-750 (891)
26 KOG1960 Predicted RNA-binding 95.8 0.0024 5.1E-08 61.1 0.1 78 88-178 307-384 (531)
27 KOG2191 RNA-binding protein NO 95.6 0.054 1.2E-06 51.0 8.1 37 70-112 39-75 (402)
28 KOG2193 IGF-II mRNA-binding pr 95.6 0.014 3.1E-07 56.3 4.2 40 75-114 198-237 (584)
29 PRK11824 polynucleotide phosph 95.5 0.013 2.8E-07 59.2 3.8 56 85-169 563-618 (693)
30 KOG2814 Transcription coactiva 94.9 0.034 7.3E-07 52.0 4.5 30 84-113 65-94 (345)
31 KOG2191 RNA-binding protein NO 94.7 0.16 3.5E-06 47.8 8.2 38 70-113 132-169 (402)
32 PRK00106 hypothetical protein; 94.5 0.099 2.1E-06 51.7 6.8 65 71-168 226-290 (535)
33 PRK12704 phosphodiesterase; Pr 94.2 0.13 2.8E-06 50.5 6.9 51 72-150 212-262 (520)
34 TIGR03319 YmdA_YtgF conserved 94.2 0.11 2.4E-06 50.9 6.4 65 71-168 205-269 (514)
35 KOG2190 PolyC-binding proteins 93.4 0.22 4.9E-06 48.6 6.8 40 69-114 137-176 (485)
36 COG1185 Pnp Polyribonucleotide 92.4 0.19 4E-06 51.0 4.8 63 71-168 553-615 (692)
37 cd02134 NusA_KH NusA_K homolog 91.6 0.4 8.6E-06 33.7 4.5 36 70-111 25-60 (61)
38 KOG0336 ATP-dependent RNA heli 87.3 0.3 6.6E-06 47.7 1.5 29 84-112 55-83 (629)
39 KOG1067 Predicted RNA-binding 85.9 0.58 1.3E-05 47.0 2.7 53 87-169 608-660 (760)
40 PF13184 KH_5: NusA-like KH do 82.2 0.64 1.4E-05 33.9 0.9 32 81-112 13-45 (69)
41 PRK12705 hypothetical protein; 81.2 2.4 5.1E-05 41.9 4.8 36 72-112 200-235 (508)
42 cd02409 KH-II KH-II (K homolo 78.8 1.9 4.2E-05 29.0 2.4 23 87-109 36-58 (68)
43 KOG2190 PolyC-binding proteins 78.6 1.6 3.4E-05 42.8 2.6 38 71-114 339-376 (485)
44 COG1094 Predicted RNA-binding 73.3 11 0.00024 33.0 6.2 28 87-114 19-46 (194)
45 PRK08406 transcription elongat 71.9 3.2 6.8E-05 34.1 2.4 29 85-113 41-69 (140)
46 cd02414 jag_KH jag_K homology 71.3 2.7 5.8E-05 30.6 1.7 23 87-109 35-57 (77)
47 COG1097 RRP4 RNA-binding prote 70.5 12 0.00026 33.8 5.9 29 84-112 154-182 (239)
48 KOG4797 Transcriptional regula 66.6 0.98 2.1E-05 36.4 -1.6 43 152-195 46-89 (123)
49 TIGR00436 era GTP-binding prot 66.1 14 0.0003 32.5 5.4 40 68-112 219-266 (270)
50 KOG2192 PolyC-binding hnRNP-K 65.1 22 0.00048 33.2 6.6 37 70-112 48-84 (390)
51 COG1702 PhoH Phosphate starvat 63.7 14 0.00031 35.0 5.2 30 85-114 24-53 (348)
52 KOG2113 Predicted RNA binding 63.5 4 8.7E-05 38.5 1.5 37 68-110 24-60 (394)
53 PRK15494 era GTPase Era; Provi 60.4 18 0.0004 33.2 5.3 40 68-112 271-318 (339)
54 PRK00089 era GTPase Era; Revie 60.0 20 0.00043 31.6 5.3 40 68-112 224-271 (292)
55 PF13083 KH_4: KH domain; PDB: 54.1 2.8 6.2E-05 29.9 -0.9 20 87-106 40-59 (73)
56 KOG2208 Vigilin [Lipid transpo 53.4 9.2 0.0002 39.5 2.3 38 69-112 708-745 (753)
57 PRK02821 hypothetical protein; 51.3 9.1 0.0002 28.6 1.4 21 86-106 41-61 (77)
58 TIGR01952 nusA_arch NusA famil 51.0 13 0.00029 30.7 2.5 29 85-113 42-70 (141)
59 PRK12329 nusA transcription el 50.2 23 0.00049 34.8 4.2 34 80-113 272-306 (449)
60 PRK00468 hypothetical protein; 49.7 9.9 0.00022 28.2 1.4 19 87-105 41-59 (75)
61 PRK12327 nusA transcription el 47.9 20 0.00043 34.0 3.4 34 80-113 240-274 (362)
62 PRK08406 transcription elongat 46.7 17 0.00037 29.8 2.5 25 87-111 110-134 (140)
63 KOG0334 RNA helicase [RNA proc 46.6 19 0.0004 38.5 3.3 77 74-168 900-976 (997)
64 PRK01064 hypothetical protein; 46.1 13 0.00028 27.8 1.6 20 87-106 41-60 (78)
65 TIGR01953 NusA transcription t 45.0 26 0.00056 32.9 3.7 34 80-113 238-272 (341)
66 COG0195 NusA Transcription elo 42.2 21 0.00046 30.9 2.5 35 80-114 80-114 (190)
67 COG1837 Predicted RNA-binding 41.8 16 0.00034 27.4 1.4 18 87-104 41-58 (76)
68 KOG2113 Predicted RNA binding 41.2 12 0.00026 35.5 0.8 31 84-114 123-153 (394)
69 PRK06418 transcription elongat 41.0 22 0.00049 30.3 2.4 27 88-114 72-98 (166)
70 PRK12328 nusA transcription el 39.0 40 0.00086 32.3 4.0 43 71-119 309-351 (374)
71 PF00126 HTH_1: Bacterial regu 38.0 27 0.00058 23.9 2.0 19 97-115 33-51 (60)
72 COG1159 Era GTPase [General fu 33.3 81 0.0018 29.4 4.9 41 67-112 226-274 (298)
73 PRK12328 nusA transcription el 33.1 31 0.00068 33.0 2.3 33 80-112 246-279 (374)
74 PRK13348 chromosome replicatio 32.5 33 0.00073 29.5 2.2 21 96-116 35-55 (294)
75 PRK05424 rplA 50S ribosomal pr 32.3 1.4E+02 0.003 26.4 6.1 9 87-95 126-134 (230)
76 PTZ00225 60S ribosomal protein 29.9 1.4E+02 0.0031 26.2 5.7 61 87-167 117-191 (214)
77 COG0484 DnaJ DnaJ-class molecu 29.1 84 0.0018 30.1 4.4 36 103-150 300-335 (371)
78 PRK09202 nusA transcription el 27.7 49 0.0011 32.4 2.7 34 79-112 239-273 (470)
79 KOG1423 Ras-like GTPase ERA [C 27.1 68 0.0015 30.7 3.3 39 74-112 326-373 (379)
80 PF14611 SLS: Mitochondrial in 26.1 1.9E+02 0.0042 24.3 5.7 83 86-197 36-133 (210)
81 KOG2192 PolyC-binding hnRNP-K 25.6 48 0.001 31.0 2.1 40 65-112 312-351 (390)
82 TIGR01169 rplA_bact ribosomal 24.4 2.3E+02 0.0049 25.0 6.0 10 86-95 124-133 (227)
83 KOG3273 Predicted RNA-binding 24.0 19 0.00041 32.2 -0.8 28 86-113 179-206 (252)
84 TIGR03298 argP transcriptional 23.9 46 0.001 28.6 1.6 20 97-116 35-54 (292)
85 TIGR01170 rplA_mito ribosomal 23.8 27 0.00059 28.8 0.1 19 78-96 100-118 (141)
86 PRK03635 chromosome replicatio 23.8 61 0.0013 28.1 2.3 21 97-117 36-56 (294)
87 KOG1852 Cell cycle-associated 23.5 67 0.0015 27.9 2.4 37 153-190 44-83 (223)
88 PRK11074 putative DNA-binding 23.3 70 0.0015 27.8 2.6 18 96-113 35-52 (300)
89 PRK15421 DNA-binding transcrip 22.1 75 0.0016 28.2 2.6 18 96-113 35-52 (317)
90 PRK03601 transcriptional regul 22.0 72 0.0016 27.5 2.4 17 97-113 35-51 (275)
91 PRK12684 transcriptional regul 21.5 78 0.0017 27.9 2.5 19 97-115 36-55 (313)
92 TIGR01953 NusA transcription t 21.3 94 0.002 29.2 3.1 37 71-113 302-338 (341)
93 PRK12683 transcriptional regul 20.5 83 0.0018 27.7 2.5 20 97-116 36-56 (309)
94 CHL00129 rpl1 ribosomal protei 20.2 36 0.00078 30.2 0.1 9 87-95 126-134 (229)
95 PRK12682 transcriptional regul 20.1 90 0.0019 27.3 2.6 20 97-116 36-56 (309)
No 1
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=100.00 E-value=1.4e-53 Score=376.95 Aligned_cols=155 Identities=55% Similarity=0.896 Sum_probs=147.5
Q ss_pred CCCCccceeeEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCce
Q 027823 61 ASPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLH 140 (218)
Q Consensus 61 ~~~~~~~vk~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLH 140 (218)
-.++.+++|.+.||+|||++||+||||||||||||+|+||||++|||||+||||||+||..||+++|++|+|+|+++|||
T Consensus 83 ~~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLH 162 (259)
T KOG1588|consen 83 DVYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLH 162 (259)
T ss_pred cCccCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcE
Confidence 47889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEecCchhhHHHHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHHHhcCc-cCCCCCCCCC---CCCCCCccccccccc
Q 027823 141 ILIEADLPANIVDIRLRQAQEIIEELLKPVDESQDYIKRQQLRELAMLNSN-FREDSPGPSG---SVSPFNSSGMKRAKT 216 (218)
Q Consensus 141 VlI~a~~~~~~~~~rl~~A~e~Ie~LL~pv~e~~d~~K~~QL~ELA~lNGt-~r~~~~~~~~---~~~p~~~~~~~~~~~ 216 (218)
|+|++++++++|+.||++|++.|++||+|.+++.| |++||+|||++||| +++.+..++| +.+||++.++||+||
T Consensus 163 VlIe~~~p~~ea~~rl~~AleeI~klL~P~~e~~d--k~~QL~ELa~lngt~~~~~~~~~~g~~~~~~~~~~~~~~r~~~ 240 (259)
T KOG1588|consen 163 VLIETEAPPAEAYARLAYALEEIKKLLVPDHEDED--KREQLRELAILNGTYLRSESRKPSGGNGRGVPGNSAGGKRGKT 240 (259)
T ss_pred EEEEEeCCHHHHHHHHHHHHHHHHHhcCCCCCCch--HHHHHHHHhhcCCccccccccccCCCCCcCCCCCCCCcccccC
Confidence 99999999999999999999999999999998888 99999999999999 6666666666 799999999999998
Q ss_pred C
Q 027823 217 G 217 (218)
Q Consensus 217 ~ 217 (218)
+
T Consensus 241 ~ 241 (259)
T KOG1588|consen 241 G 241 (259)
T ss_pred C
Confidence 6
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=8.8e-42 Score=272.69 Aligned_cols=119 Identities=57% Similarity=0.975 Sum_probs=112.1
Q ss_pred EEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchh
Q 027823 71 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 150 (218)
Q Consensus 71 ~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~ 150 (218)
++|||||+++||+|||+|+||||+|+|+|+||++|||+|.|||+||+++.+++.++++ +.++|++|||||+|+|.++.
T Consensus 1 ~~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~-~~~~~~~eplhV~I~a~~~~- 78 (120)
T cd02395 1 TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRG-PKYAHLNEPLHVLITAETPP- 78 (120)
T ss_pred CCEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccC-cccccCCCCcEEEEEeCCcH-
Confidence 3689999999999999999999999999999999999999999999999999988886 88999999999999999852
Q ss_pred hHHHHHHHHHHHHHHhcCCCCch-hHHHHHHHHHHHHHhcCccC
Q 027823 151 IVDIRLRQAQEIIEELLKPVDES-QDYIKRQQLRELAMLNSNFR 193 (218)
Q Consensus 151 ~~~~rl~~A~e~Ie~LL~pv~e~-~d~~K~~QL~ELA~lNGt~r 193 (218)
..++++|+++|+.||.++.++ .|++|++||+|||++|||||
T Consensus 79 --~e~~~~A~~~I~~ll~~~~~~~~~~~k~~ql~~la~~nGt~~ 120 (120)
T cd02395 79 --EEALAKAVEAIEELLKPAIEGGNDELKREQLRELALLNGTYR 120 (120)
T ss_pred --HHHHHHHHHHHHHHhccCCCccchHHHHHHHHHHHHhcccCC
Confidence 357999999999999998877 99999999999999999997
No 3
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=100.00 E-value=2.7e-40 Score=311.74 Aligned_cols=175 Identities=37% Similarity=0.530 Sum_probs=144.4
Q ss_pred CCCCCCCCCCCC---CCCCCCCCCCCCCCCCCcccccCC-CCCCCCCCCCCCCCCCccceeeEEEEecCCCCCCCCCeee
Q 027823 13 LRHRSPSPMASS---NLMSNVAGTGLGGWNGLPQERLGG-PPGMTMDWQSAPASPSSYTVKRILRLEIPVDTYPNFNFVG 88 (218)
Q Consensus 13 ~~~~sp~~~~~~---~~~~n~~~~~~~~w~~~~~er~~~-~~~~~~~~~~~p~~~~~~~vk~~~ki~IPv~~yP~~NfvG 88 (218)
..-+||||.+-+ |.+.|+|.... -..|.+||+.. .+.+.+.+-+.|+.-..+..+++.||||||++||+|||||
T Consensus 79 ~e~rSPsp~p~yda~g~R~ntRe~R~--r~~Le~er~e~I~~~lk~nP~fkpP~DYk~p~~~~~Kv~IPvke~Pd~NFvG 156 (554)
T KOG0119|consen 79 RELRSPSPEPVYDAKGKRLNTREQRA--RKKLEDERHEIIEEILKLNPGFKPPADYKPPAKLHDKVYIPVKEFPDINFVG 156 (554)
T ss_pred ccccCCCcchhhhhhccchhhHHHHH--HHHHHHHHHHHHHHHHHhCcCCCCCcccCcccccccceecchhhcCCcceeE
Confidence 344899988743 78888875332 34666788863 4667788877755544444499999999999999999999
Q ss_pred eEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCC-CCCCCceEEEEecCchhhHHHHHHHHHHHHHHhc
Q 027823 89 RLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYE-HLNDPLHILIEADLPANIVDIRLRQAQEIIEELL 167 (218)
Q Consensus 89 rIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e-~~~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL 167 (218)
+||||||+|+|+||++|||||+||||||+|+++. ..++.+|. ..+|||||+|+|++++ +|++|+++||.||
T Consensus 157 LiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~---~~~d~~~~~~~~epLH~~Isadt~e-----ki~~Ai~vienli 228 (554)
T KOG0119|consen 157 LIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKG---RSDDLSYIPKENEPLHCLISADTQE-----KIKKAIAVIENLI 228 (554)
T ss_pred EEecCCccHHHHHHHHhCCeEEEecccccccccc---CCcccccccccccceeEEEecchHH-----HHHHHHHHHHHHH
Confidence 9999999999999999999999999999998762 22334443 4799999999999976 7899999999999
Q ss_pred C---CCCchhHHHHHHHHHHHHHhcCccCCCCC
Q 027823 168 K---PVDESQDYIKRQQLRELAMLNSNFREDSP 197 (218)
Q Consensus 168 ~---pv~e~~d~~K~~QL~ELA~lNGt~r~~~~ 197 (218)
. .++|+++++|+.||+|||-||||+|++.+
T Consensus 229 ~~av~~~e~~n~l~~~Qlrela~lNgt~r~~d~ 261 (554)
T KOG0119|consen 229 QSAVSVPEGQNDLKRLQLRELARLNGTLRDDDN 261 (554)
T ss_pred HhhccCccccccccHHHHHHHHHhCCCCCcccc
Confidence 8 67999999999999999999999999984
No 4
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.97 E-value=3.8e-33 Score=241.60 Aligned_cols=176 Identities=32% Similarity=0.399 Sum_probs=135.7
Q ss_pred CCCCCCCCCCC---CCCCCCCCCCCCCCCCCcccccCC-CCCCCCCCCCCCCCCCccceeeEEEEecCCCCCCCCCeeee
Q 027823 14 RHRSPSPMASS---NLMSNVAGTGLGGWNGLPQERLGG-PPGMTMDWQSAPASPSSYTVKRILRLEIPVDTYPNFNFVGR 89 (218)
Q Consensus 14 ~~~sp~~~~~~---~~~~n~~~~~~~~w~~~~~er~~~-~~~~~~~~~~~p~~~~~~~vk~~~ki~IPv~~yP~~NfvGr 89 (218)
+-|||||+|-+ |.+.|++.... -..|.+||+.+ ..++.+=+-+.+|.-.-.+.|.+.||||||++||+.||||+
T Consensus 90 e~Rspsppp~yd~~GrRlntre~ry--~kkLeder~~l~era~k~lp~fv~p~dy~rpsk~q~KiYIPV~eyPe~NFVGL 167 (269)
T COG5176 90 ELRSPSPPPRYDEIGRRLNTREARY--NKKLEDERLWLKERAQKILPRFVLPNDYIRPSKYQNKIYIPVQEYPESNFVGL 167 (269)
T ss_pred hccCCCCCcchhHHhhhhhHHHHHH--hhhhhHHHHHHHHHHHHhcCcccCCccccCcccccceEEeehhhCcccceeEE
Confidence 34899988744 88888875443 34566788764 34455656566666666778889999999999999999999
Q ss_pred EeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHHHhcCC
Q 027823 90 LLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLKP 169 (218)
Q Consensus 90 IlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL~p 169 (218)
||||||+|+|+||+.|+|||.|||+||.|.++...++. ++.....++||+||++++...++ ..+......|.+.-.
T Consensus 168 liGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p--~~~~N~e~~lhcLI~adsedki~-~~ik~~~n~I~~a~~- 243 (269)
T COG5176 168 LIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTP--ESLKNAEAVLHCLIEADSEDKIC-RLIKSQLNAIREARR- 243 (269)
T ss_pred EecCCcchHHHHHHHhCCeEEEecccccccCcccccCc--hhhhhhHHhHHHHhhcchhhhHH-HHHHHHHHHHHHHhc-
Confidence 99999999999999999999999999999776443322 12224678999999998755333 234444455555555
Q ss_pred CCchhHHHHHHHHHHHHHhcCccCCC
Q 027823 170 VDESQDYIKRQQLRELAMLNSNFRED 195 (218)
Q Consensus 170 v~e~~d~~K~~QL~ELA~lNGt~r~~ 195 (218)
++++++.+|+-||++||-+|||+|++
T Consensus 244 ~PeGqnDlkR~qlr~la~lngtlr~d 269 (269)
T COG5176 244 NPEGQNDLKRFQLRWLAHLNGTLRAD 269 (269)
T ss_pred CCcccchHHHHHHHHHHHhcceecCC
Confidence 57899999999999999999999975
No 5
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=98.59 E-value=3.1e-08 Score=93.58 Aligned_cols=97 Identities=13% Similarity=-0.050 Sum_probs=82.0
Q ss_pred eeeEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecC
Q 027823 68 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADL 147 (218)
Q Consensus 68 vk~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~ 147 (218)
+++.-|++|++| .|.||.-+..=||+..||..+|.+|+.+++||||+|+.-+.-++ ++.+|||+|+|+...
T Consensus 208 ~~Y~~k~~v~~~-~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G--------~EsnEPMYI~i~h~~ 278 (531)
T KOG1960|consen 208 RYYPNKALATDK-DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEG--------NESNEPMYIFSTHGN 278 (531)
T ss_pred ccchhheecccC-CcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCcccc--------cccCCceeEEeecCC
Confidence 455558999998 78999999999999999999999999999999999988754322 258999999999988
Q ss_pred chhhHHHHHHHHHHHHHHhcCCCCchhHHHH
Q 027823 148 PANIVDIRLRQAQEIIEELLKPVDESQDYIK 178 (218)
Q Consensus 148 ~~~~~~~rl~~A~e~Ie~LL~pv~e~~d~~K 178 (218)
.+ .+++|+.+|++|+.-+..++..+-
T Consensus 279 ~~-----g~~~A~r~~~nl~~~v~~~~sr~~ 304 (531)
T KOG1960|consen 279 GN-----GENGAPRRKWNLEEKVYINLSRGF 304 (531)
T ss_pred ch-----hhccchhHHHhHHHHHHHHhhhhh
Confidence 76 578999999999998865554443
No 6
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.50 E-value=5.2e-07 Score=62.26 Aligned_cols=62 Identities=29% Similarity=0.569 Sum_probs=46.2
Q ss_pred EEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhh
Q 027823 72 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANI 151 (218)
Q Consensus 72 ~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~~ 151 (218)
.++.||. +++|+||||+|+++++|+++|||+|.|...++ ...+-.|.|.+. .
T Consensus 2 ~~i~ip~------~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~------------------~~~~~~v~i~G~-~--- 53 (64)
T cd00105 2 ERVLVPS------SLVGRIIGKGGSTIKEIREETGAKIKIPDSGS------------------GSEERIVTITGT-P--- 53 (64)
T ss_pred EEEEEch------hhcceeECCCCHHHHHHHHHHCCEEEEcCCCC------------------CCCceEEEEEcC-H---
Confidence 4667775 78899999999999999999999999986432 123346778776 2
Q ss_pred HHHHHHHHHHHH
Q 027823 152 VDIRLRQAQEII 163 (218)
Q Consensus 152 ~~~rl~~A~e~I 163 (218)
..+..|..+|
T Consensus 54 --~~v~~a~~~i 63 (64)
T cd00105 54 --EAVEKAKELI 63 (64)
T ss_pred --HHHHHHHHHh
Confidence 2466777665
No 7
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.47 E-value=3.5e-07 Score=64.73 Aligned_cols=59 Identities=27% Similarity=0.501 Sum_probs=45.2
Q ss_pred EEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchh
Q 027823 71 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 150 (218)
Q Consensus 71 ~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~ 150 (218)
...+.||. .++|+|||++|+|+|.|+++|||+|.|-- + -.|.|++.+++
T Consensus 3 ~~~i~Ip~------~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----~-------------------g~v~I~G~~~~- 51 (61)
T cd02393 3 IETMKIPP------DKIRDVIGPGGKTIKKIIEETGVKIDIED-----D-------------------GTVYIAASDKE- 51 (61)
T ss_pred EEEEEeCh------hheeeeECCCchHHHHHHHHHCCEEEeCC-----C-------------------CEEEEEeCCHH-
Confidence 34455653 57799999999999999999999998752 0 14889997654
Q ss_pred hHHHHHHHHHHHHH
Q 027823 151 IVDIRLRQAQEIIE 164 (218)
Q Consensus 151 ~~~~rl~~A~e~Ie 164 (218)
.++.|+++|+
T Consensus 52 ----~v~~A~~~I~ 61 (61)
T cd02393 52 ----AAEKAKKMIE 61 (61)
T ss_pred ----HHHHHHHHhC
Confidence 5788888774
No 8
>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=98.37 E-value=2.6e-07 Score=63.96 Aligned_cols=59 Identities=29% Similarity=0.639 Sum_probs=44.9
Q ss_pred EEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhh
Q 027823 72 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANI 151 (218)
Q Consensus 72 ~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~~ 151 (218)
.++.|| ..++|+|||++|.++|+|+++|||+|.|... ++.-.|.|++ +++
T Consensus 2 ~~i~vp------~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~---------------------~~~~~v~I~G-~~~-- 51 (60)
T PF00013_consen 2 ERIEVP------SSLVGRIIGKKGSNIKEIEEETGVKIQIPDD---------------------DERDIVTISG-SPE-- 51 (60)
T ss_dssp EEEEEE------HHHHHHHHTGGGHHHHHHHHHHTSEEEEEST---------------------TEEEEEEEEE-SHH--
T ss_pred EEEEEC------HHHcCEEECCCCCcHHHhhhhcCeEEEEcCC---------------------CCcEEEEEEe-CHH--
Confidence 456665 3678999999999999999999999999643 0223788888 444
Q ss_pred HHHHHHHHHHHH
Q 027823 152 VDIRLRQAQEII 163 (218)
Q Consensus 152 ~~~rl~~A~e~I 163 (218)
.+++|+++|
T Consensus 52 ---~v~~A~~~I 60 (60)
T PF00013_consen 52 ---QVEKAKKMI 60 (60)
T ss_dssp ---HHHHHHHHH
T ss_pred ---HHHHHHhhC
Confidence 577787765
No 9
>smart00322 KH K homology RNA-binding domain.
Probab=98.33 E-value=3.9e-06 Score=56.85 Aligned_cols=65 Identities=31% Similarity=0.577 Sum_probs=48.8
Q ss_pred EEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchh
Q 027823 71 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 150 (218)
Q Consensus 71 ~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~ 150 (218)
..++.||. +++|++||++|.+++.|++.|||+|.+....+ ..-.|.|.+. +.
T Consensus 4 ~~~i~i~~------~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--------------------~~~~v~i~g~-~~- 55 (69)
T smart00322 4 TIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--------------------EERVVEITGP-PE- 55 (69)
T ss_pred EEEEEEcc------hhcceeECCCchHHHHHHHHHCCEEEECCCCC--------------------CccEEEEEcC-HH-
Confidence 45667764 67799999999999999999999999975432 2235777776 22
Q ss_pred hHHHHHHHHHHHHHHhc
Q 027823 151 IVDIRLRQAQEIIEELL 167 (218)
Q Consensus 151 ~~~~rl~~A~e~Ie~LL 167 (218)
.+..|.+.|.+.+
T Consensus 56 ----~v~~a~~~i~~~~ 68 (69)
T smart00322 56 ----NVEKAAELILEIL 68 (69)
T ss_pred ----HHHHHHHHHHHHh
Confidence 4677888777765
No 10
>PF13014 KH_3: KH domain
Probab=98.25 E-value=9.2e-07 Score=58.09 Aligned_cols=28 Identities=36% Similarity=0.789 Sum_probs=26.7
Q ss_pred eeeeEeCCCcchHHHHHHHhCCeEEEec
Q 027823 86 FVGRLLGPRGNSLKRVEATTGCRVYIRG 113 (218)
Q Consensus 86 fvGrIlGPrG~TlKrIE~eTgckI~IRG 113 (218)
|+|+|||++|.|+++|+++|||+|.|--
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 6899999999999999999999999985
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=98.15 E-value=6e-06 Score=58.53 Aligned_cols=35 Identities=29% Similarity=0.670 Sum_probs=30.5
Q ss_pred EEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEe
Q 027823 72 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 112 (218)
Q Consensus 72 ~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IR 112 (218)
.|+.||. +.+|+|||.+|.++++|+++|||+|.|-
T Consensus 2 ~r~~ip~------~~vg~iIG~~G~~i~~i~~~tga~I~i~ 36 (65)
T cd02396 2 LRLLVPS------SQAGSIIGKGGSTIKEIREETGAKIRVS 36 (65)
T ss_pred EEEEECH------HHcCeeECCCcHHHHHHHHHHCCEEEEc
Confidence 4667763 5679999999999999999999999995
No 12
>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=98.10 E-value=4.7e-06 Score=58.01 Aligned_cols=59 Identities=22% Similarity=0.451 Sum_probs=43.6
Q ss_pred EEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhH
Q 027823 73 RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIV 152 (218)
Q Consensus 73 ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~~~ 152 (218)
++.||. .++|+|||++|.++++|+++|||+|.|-... +..=.|.|++. .+
T Consensus 3 ~i~Vp~------~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--------------------~~~~~v~I~G~-~~--- 52 (62)
T cd02394 3 EVEIPK------KLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--------------------SKSDTITITGP-KE--- 52 (62)
T ss_pred EEEeCH------HHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--------------------CCCCEEEEEcC-HH---
Confidence 455654 4669999999999999999999999998543 11226788886 22
Q ss_pred HHHHHHHHHHH
Q 027823 153 DIRLRQAQEII 163 (218)
Q Consensus 153 ~~rl~~A~e~I 163 (218)
.+..|+++|
T Consensus 53 --~v~~A~~~i 61 (62)
T cd02394 53 --NVEKAKEEI 61 (62)
T ss_pred --HHHHHHHHh
Confidence 467777765
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=97.98 E-value=9.5e-06 Score=68.29 Aligned_cols=53 Identities=30% Similarity=0.506 Sum_probs=45.3
Q ss_pred eeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHHH
Q 027823 86 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEE 165 (218)
Q Consensus 86 fvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 165 (218)
.+|||||+.|.|++.||..|||+|.|-|+ .|.|.+ +++ +++.|.+.|+.
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~~-------------------------~v~i~G-~~~-----~~~~A~~~i~~ 147 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYGK-------------------------TVGIIG-DPE-----QVQIAREAIEM 147 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcCC-------------------------EEEEEC-CHH-----HHHHHHHHHHH
Confidence 68999999999999999999999998641 477888 444 68899999999
Q ss_pred hcCC
Q 027823 166 LLKP 169 (218)
Q Consensus 166 LL~p 169 (218)
|+.-
T Consensus 148 li~~ 151 (172)
T TIGR03665 148 LIEG 151 (172)
T ss_pred HHcC
Confidence 9963
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.89 E-value=2.3e-05 Score=66.52 Aligned_cols=53 Identities=30% Similarity=0.518 Sum_probs=44.1
Q ss_pred eeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHHH
Q 027823 86 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEE 165 (218)
Q Consensus 86 fvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 165 (218)
.+|||||++|.|.|.||..|||+|.|-++ .|.|.+ +++ +++.|.+.|+.
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~-------------------------~v~i~G-~~~-----~~~~A~~~I~~ 153 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGK-------------------------TVAIIG-DPE-----QVEIAREAIEM 153 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCC-------------------------EEEEEe-CHH-----HHHHHHHHHHH
Confidence 68999999999999999999999999641 266666 444 67899999999
Q ss_pred hcCC
Q 027823 166 LLKP 169 (218)
Q Consensus 166 LL~p 169 (218)
|+.-
T Consensus 154 li~g 157 (180)
T PRK13763 154 LIEG 157 (180)
T ss_pred HHcC
Confidence 9863
No 15
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.51 E-value=0.00019 Score=60.91 Aligned_cols=65 Identities=25% Similarity=0.495 Sum_probs=50.4
Q ss_pred EEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEE---ecC
Q 027823 71 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIE---ADL 147 (218)
Q Consensus 71 ~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~---a~~ 147 (218)
...+.||. +-+|.||||.|.|+|.|+++|||+|.|.-. .=.|.|. +.+
T Consensus 4 ~~~i~IP~------~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----------------------~g~V~I~~~~~~d 54 (180)
T PRK13763 4 MEYVKIPK------DRIGVLIGKKGETKKEIEERTGVKLEIDSE-----------------------TGEVIIEPTDGED 54 (180)
T ss_pred eEEEEcCH------HHhhhHhccchhHHHHHHHHHCcEEEEECC-----------------------CCeEEEEeCCCCC
Confidence 34556664 346999999999999999999999999842 0156676 455
Q ss_pred chhhHHHHHHHHHHHHHHhcCC
Q 027823 148 PANIVDIRLRQAQEIIEELLKP 169 (218)
Q Consensus 148 ~~~~~~~rl~~A~e~Ie~LL~p 169 (218)
++ .+.+|+++|+.|+..
T Consensus 55 ~~-----~i~kA~~~I~ai~~g 71 (180)
T PRK13763 55 PL-----AVLKARDIVKAIGRG 71 (180)
T ss_pred HH-----HHHHHHHHHHHHhcC
Confidence 54 689999999999884
No 16
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.50 E-value=0.0002 Score=62.10 Aligned_cols=55 Identities=25% Similarity=0.452 Sum_probs=47.0
Q ss_pred eeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHHH
Q 027823 86 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEE 165 (218)
Q Consensus 86 fvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 165 (218)
..|||||+.|.|.+.||..|||.|.|.|+ +|.|-+. ++ .++.|.+.|+.
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~-------------------------tVaiiG~-~~-----~v~iAr~AVem 160 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK-------------------------TVAIIGG-FE-----QVEIAREAVEM 160 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc-------------------------EEEEecC-hh-----hhHHHHHHHHH
Confidence 57999999999999999999999999985 6777774 33 57889999999
Q ss_pred hcCCCC
Q 027823 166 LLKPVD 171 (218)
Q Consensus 166 LL~pv~ 171 (218)
|+.-.+
T Consensus 161 li~G~~ 166 (194)
T COG1094 161 LINGAP 166 (194)
T ss_pred HHcCCC
Confidence 998644
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=97.45 E-value=0.00015 Score=61.12 Aligned_cols=57 Identities=25% Similarity=0.448 Sum_probs=45.5
Q ss_pred CeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEE--EecCchhhHHHHHHHHHHH
Q 027823 85 NFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILI--EADLPANIVDIRLRQAQEI 162 (218)
Q Consensus 85 NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI--~a~~~~~~~~~rl~~A~e~ 162 (218)
+.+|.||||+|.|+|.|+++|||+|.|--. .=.|.| .+.++. .+.+|+++
T Consensus 7 ~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----------------------~g~V~I~~~t~d~~-----~i~kA~~~ 58 (172)
T TIGR03665 7 DRIGVLIGKGGETKKEIEERTGVKLDIDSE-----------------------TGEVKIEEEDEDPL-----AVMKAREV 58 (172)
T ss_pred HHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----------------------CceEEEecCCCCHH-----HHHHHHHH
Confidence 578999999999999999999999999832 014666 344443 68999999
Q ss_pred HHHhcCC
Q 027823 163 IEELLKP 169 (218)
Q Consensus 163 Ie~LL~p 169 (218)
|+.|...
T Consensus 59 I~~i~~g 65 (172)
T TIGR03665 59 VKAIGRG 65 (172)
T ss_pred HHHHHcC
Confidence 9998884
No 18
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.39 E-value=0.00047 Score=69.71 Aligned_cols=71 Identities=27% Similarity=0.507 Sum_probs=56.8
Q ss_pred CccceeeEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEE
Q 027823 64 SSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILI 143 (218)
Q Consensus 64 ~~~~vk~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI 143 (218)
.++..-+...+.||.+ -+|.||||+|.|+|.|+++|||+|.|--. =+|.|
T Consensus 572 ~s~~aP~~~~~~I~~~------ki~~vIG~gGk~I~~i~~~tg~~Idi~d~------------------------G~V~I 621 (719)
T TIGR02696 572 MSPYAPRIITVKIPVD------KIGEVIGPKGKMINQIQDETGAEISIEDD------------------------GTVYI 621 (719)
T ss_pred cccCCCeeEEEEeChH------HhhheeCCCcHhHHHHHHHHCCEEEEecC------------------------cEEEE
Confidence 3334445667778755 46999999999999999999999998732 27889
Q ss_pred EecCchhhHHHHHHHHHHHHHHhcCC
Q 027823 144 EADLPANIVDIRLRQAQEIIEELLKP 169 (218)
Q Consensus 144 ~a~~~~~~~~~rl~~A~e~Ie~LL~p 169 (218)
.+.+.+ ++++|+++|+.+..+
T Consensus 622 ~a~d~~-----~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 622 GAADGP-----SAEAARAMINAIANP 642 (719)
T ss_pred EeCCHH-----HHHHHHHHHHHhhCc
Confidence 997754 789999999999995
No 19
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=96.97 E-value=0.002 Score=59.19 Aligned_cols=68 Identities=31% Similarity=0.506 Sum_probs=49.7
Q ss_pred eeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHHHhc
Q 027823 88 GRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELL 167 (218)
Q Consensus 88 GrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL 167 (218)
.|||||.|+|||.||-.|.|-|.+-|. -| ++-.+ ...|..+..+|++.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~-------------------------TV--saiGp----fkGlkevr~IV~DcM 209 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN-------------------------TV--SAIGP----FKGLKEVRKIVEDCM 209 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc-------------------------EE--EeecC----cchHHHHHHHHHHHH
Confidence 589999999999999999999999984 12 33333 236888899999988
Q ss_pred CCCCchhHHHHHHHHHHHH
Q 027823 168 KPVDESQDYIKRQQLRELA 186 (218)
Q Consensus 168 ~pv~e~~d~~K~~QL~ELA 186 (218)
..++.-++.---.--+|||
T Consensus 210 ~NiHPiY~IK~LmiKRel~ 228 (356)
T KOG2874|consen 210 KNIHPIYNIKTLMIKRELA 228 (356)
T ss_pred hccchHHHHHHHHHHHHhh
Confidence 8877655543333334554
No 20
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=96.87 E-value=0.0015 Score=65.70 Aligned_cols=64 Identities=23% Similarity=0.381 Sum_probs=50.7
Q ss_pred eEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCch
Q 027823 70 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPA 149 (218)
Q Consensus 70 ~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~ 149 (218)
+...+.||.+ .+|.||||+|.|+|.|+++|||+|.|--. =+|.|.+.+.+
T Consensus 551 ~~~~~~I~~~------kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd------------------------G~V~i~~~~~~ 600 (684)
T TIGR03591 551 RIETIKINPD------KIRDVIGPGGKVIREITEETGAKIDIEDD------------------------GTVKIAASDGE 600 (684)
T ss_pred eEEEEecCHH------HHHhhcCCCcHHHHHHHHHHCCEEEEecC------------------------eEEEEEECcHH
Confidence 3556667644 57999999999999999999999999521 16778887643
Q ss_pred hhHHHHHHHHHHHHHHhcC
Q 027823 150 NIVDIRLRQAQEIIEELLK 168 (218)
Q Consensus 150 ~~~~~rl~~A~e~Ie~LL~ 168 (218)
.+++|.+.|+.+..
T Consensus 601 -----~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 601 -----AAEAAIKMIEGITA 614 (684)
T ss_pred -----HHHHHHHHHHhhhc
Confidence 68899999998865
No 21
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=96.71 E-value=0.0029 Score=62.59 Aligned_cols=62 Identities=24% Similarity=0.491 Sum_probs=44.8
Q ss_pred CeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCce-EEEEecCchhhHHHHHHHHHHHH
Q 027823 85 NFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLH-ILIEADLPANIVDIRLRQAQEII 163 (218)
Q Consensus 85 NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLH-VlI~a~~~~~~~~~rl~~A~e~I 163 (218)
+=||.|||=.|.|+|+|+.+||+||.++= |. .| .-++. +.|.+. . .++.+|.++|
T Consensus 239 ~~VG~IIGkgGE~IKklq~etG~KIQfkp-----Dd--------~p-----~speR~~~IiG~--~----d~ie~Aa~lI 294 (600)
T KOG1676|consen 239 SKVGIIIGKGGEMIKKLQNETGAKIQFKP-----DD--------DP-----SSPERPAQIIGT--V----DQIEHAAELI 294 (600)
T ss_pred cceeeEEecCchHHHHHhhccCceeEeec-----CC--------CC-----CCccceeeeecC--H----HHHHHHHHHH
Confidence 45899999999999999999999999983 11 11 11222 223332 2 2789999999
Q ss_pred HHhcCCC
Q 027823 164 EELLKPV 170 (218)
Q Consensus 164 e~LL~pv 170 (218)
.+||.-.
T Consensus 295 ~eii~~~ 301 (600)
T KOG1676|consen 295 NEIIAEA 301 (600)
T ss_pred HHHHHHH
Confidence 9999843
No 22
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=96.61 E-value=0.0048 Score=61.11 Aligned_cols=75 Identities=25% Similarity=0.608 Sum_probs=58.2
Q ss_pred ceeeEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEec
Q 027823 67 TVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEAD 146 (218)
Q Consensus 67 ~vk~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~ 146 (218)
.++.+..|.||... +|+|||=.|.|+|.|+..||||+.+-=.|+..+. .+.||. |+++
T Consensus 136 ~~~ttqeI~IPa~k------~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~--------------~~Kplr--itGd 193 (600)
T KOG1676|consen 136 SVETTQEILIPANK------CGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG--------------ADKPLR--ITGD 193 (600)
T ss_pred ccceeeeeccCccc------eeeEeccCccHHHHHHhhcCCceEEEecCCcCCC--------------CCCcee--ecCC
Confidence 46667888888654 5999999999999999999999998876665442 344554 4554
Q ss_pred CchhhHHHHHHHHHHHHHHhcCC
Q 027823 147 LPANIVDIRLRQAQEIIEELLKP 169 (218)
Q Consensus 147 ~~~~~~~~rl~~A~e~Ie~LL~p 169 (218)
+. ++++|+++|.++|.-
T Consensus 194 -p~-----~ve~a~~lV~dil~e 210 (600)
T KOG1676|consen 194 -PD-----KVEQAKQLVADILRE 210 (600)
T ss_pred -HH-----HHHHHHHHHHHHHHh
Confidence 32 689999999999983
No 23
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.39 E-value=0.0011 Score=63.85 Aligned_cols=38 Identities=42% Similarity=0.785 Sum_probs=34.5
Q ss_pred ecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEe
Q 027823 75 EIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 112 (218)
Q Consensus 75 ~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IR 112 (218)
.||++-.-.-||+|||||--|.++|.||++||+||.|-
T Consensus 279 e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis 316 (584)
T KOG2193|consen 279 EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITIS 316 (584)
T ss_pred hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeee
Confidence 57777666789999999999999999999999999996
No 24
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.28 E-value=0.0054 Score=54.08 Aligned_cols=56 Identities=23% Similarity=0.407 Sum_probs=45.9
Q ss_pred CeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHH
Q 027823 85 NFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIE 164 (218)
Q Consensus 85 NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~~~~~rl~~A~e~Ie 164 (218)
+++++||||+|.+++.|.++|+|+|.|-=. | .|+|.+.+.+ .+..|++.|+
T Consensus 154 ~~i~~lig~~g~~i~~l~~~~~~~I~ig~N----------------G--------~VwI~~~~~~-----~~~~a~~~I~ 204 (235)
T PRK04163 154 VKVPRVIGKKGSMINMLKEETGCDIIVGQN----------------G--------RIWIKGPDEE-----DEEIAIEAIK 204 (235)
T ss_pred HHHHhhcCCCChhHhhhhhhhCcEEEEcCC----------------c--------EEEEeeCCHH-----HHHHHHHHHH
Confidence 568999999999999999999999998411 1 7999998865 4678888888
Q ss_pred HhcCC
Q 027823 165 ELLKP 169 (218)
Q Consensus 165 ~LL~p 169 (218)
.+-.-
T Consensus 205 ~~e~~ 209 (235)
T PRK04163 205 KIERE 209 (235)
T ss_pred HHHhh
Confidence 77664
No 25
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.15 E-value=0.0043 Score=64.25 Aligned_cols=69 Identities=19% Similarity=0.223 Sum_probs=54.5
Q ss_pred cceeeEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCe-EEEecccCCCCCCcccccCCCCCCCCCCCCceEEEE
Q 027823 66 YTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCR-VYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIE 144 (218)
Q Consensus 66 ~~vk~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgck-I~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~ 144 (218)
+..-++..+.||. +-+|.||||+|.|+|.|+++||++ |.|+- +-+|.|.
T Consensus 681 ~~aP~i~~~~i~~------~ki~~vIG~GGktIk~I~eetg~~~Idi~d------------------------dg~V~I~ 730 (891)
T PLN00207 681 KYAPLIHIMKVKP------EKVNMIIGSGGKKVKSIIEETGVEAIDTQD------------------------DGTVKIT 730 (891)
T ss_pred ccCCeeEEEEcCH------HHHHHHhcCCchhHHHHHHHHCCCccCcCC------------------------CeeEEEE
Confidence 3334466666764 457999999999999999999998 77763 3478898
Q ss_pred ecCchhhHHHHHHHHHHHHHHhcCC
Q 027823 145 ADLPANIVDIRLRQAQEIIEELLKP 169 (218)
Q Consensus 145 a~~~~~~~~~rl~~A~e~Ie~LL~p 169 (218)
+.+.+ ++++|+++|+.|..-
T Consensus 731 a~d~~-----~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 731 AKDLS-----SLEKSKAIISSLTMV 750 (891)
T ss_pred eCCHH-----HHHHHHHHHHHHhcC
Confidence 88754 789999999998873
No 26
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=95.83 E-value=0.0024 Score=61.13 Aligned_cols=78 Identities=26% Similarity=0.457 Sum_probs=64.3
Q ss_pred eeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHHHhc
Q 027823 88 GRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELL 167 (218)
Q Consensus 88 GrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~LL 167 (218)
--|.||.|.+.|.++.+|-+++.|.|-||.+... +.....++|.||+|.+.++. .|+.|+-++++++
T Consensus 307 ~~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i~p--------~~~~~~~~p~~~~~~~~~~~-----~~~~~~~~~~~~i 373 (531)
T KOG1960|consen 307 QAIVGPQGAYVKHIQQETRTRVQIKGQGSAFIEP--------STNRESDEPIHLCIMSHDPN-----AIQRAKVLCEDLI 373 (531)
T ss_pred cccccCCcccccccCCCCCcceeccCccceeecC--------CCCCCCCCCcccccccCChh-----hhhhhhhcccccC
Confidence 3478999999999999999999999999988542 22335899999999998765 4677999999999
Q ss_pred CCCCchhHHHH
Q 027823 168 KPVDESQDYIK 178 (218)
Q Consensus 168 ~pv~e~~d~~K 178 (218)
-+|+..+...|
T Consensus 374 ~~v~~qy~~~~ 384 (531)
T KOG1960|consen 374 ASVHQQYKAWK 384 (531)
T ss_pred CcccccCcccc
Confidence 99986655555
No 27
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=95.64 E-value=0.054 Score=50.95 Aligned_cols=37 Identities=24% Similarity=0.552 Sum_probs=33.3
Q ss_pred eEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEe
Q 027823 70 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 112 (218)
Q Consensus 70 ~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IR 112 (218)
+..||+||- +-+|-|||-+|.|+.+||++|||+|.+-
T Consensus 39 y~ikvLips------~AaGsIIGKGG~ti~~lqk~tgariklS 75 (402)
T KOG2191|consen 39 YFLKVLIPS------YAAGSIIGKGGQTIVQLQKETGARIKLS 75 (402)
T ss_pred eEEEEEeec------ccccceeccchHHHHHHHhccCcEEEec
Confidence 688999982 4579999999999999999999999986
No 28
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=95.57 E-value=0.014 Score=56.35 Aligned_cols=40 Identities=23% Similarity=0.502 Sum_probs=32.0
Q ss_pred ecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecc
Q 027823 75 EIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 114 (218)
Q Consensus 75 ~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGr 114 (218)
++|+--.-.--|+|-||||.|+|+|-|-+.|.|||-+.-+
T Consensus 198 D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrk 237 (584)
T KOG2193|consen 198 DWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRK 237 (584)
T ss_pred CcceeeeeccceeEEEecCCCccccCcchhhhheeeeeec
Confidence 3444433235799999999999999999999999999853
No 29
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.49 E-value=0.013 Score=59.17 Aligned_cols=56 Identities=21% Similarity=0.362 Sum_probs=45.8
Q ss_pred CeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHH
Q 027823 85 NFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIE 164 (218)
Q Consensus 85 NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~~~~~rl~~A~e~Ie 164 (218)
+-++.+|||+|.|+|.|+++||++|-|+- .-.|.|.+.+.+ .+++|.+.|+
T Consensus 563 ~kI~~vIG~gg~~ik~I~~~~~~~idi~d------------------------~G~v~i~~~~~~-----~~~~a~~~I~ 613 (693)
T PRK11824 563 DKIRDVIGPGGKTIREITEETGAKIDIED------------------------DGTVKIAATDGE-----AAEAAKERIE 613 (693)
T ss_pred HHHHHHhcCCchhHHHHHHHHCCccccCC------------------------CceEEEEcccHH-----HHHHHHHHHH
Confidence 45799999999999999999999988753 126777776643 6899999999
Q ss_pred HhcCC
Q 027823 165 ELLKP 169 (218)
Q Consensus 165 ~LL~p 169 (218)
.+...
T Consensus 614 ~~~~~ 618 (693)
T PRK11824 614 GITAE 618 (693)
T ss_pred Hhccc
Confidence 98863
No 30
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=94.93 E-value=0.034 Score=52.01 Aligned_cols=30 Identities=27% Similarity=0.620 Sum_probs=27.5
Q ss_pred CCeeeeEeCCCcchHHHHHHHhCCeEEEec
Q 027823 84 FNFVGRLLGPRGNSLKRVEATTGCRVYIRG 113 (218)
Q Consensus 84 ~NfvGrIlGPrG~TlKrIE~eTgckI~IRG 113 (218)
=-|+|.|+|=+|.|.|+||.+|+|+|.+==
T Consensus 65 s~~~~~lig~~g~trkkle~Etq~~i~lp~ 94 (345)
T KOG2814|consen 65 SSFIGWLIGKQGKTRKKLEEETQTNIFLPR 94 (345)
T ss_pred HHHhhhhhcccchHHHHHHHhhccceEccC
Confidence 368899999999999999999999999863
No 31
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=94.67 E-value=0.16 Score=47.83 Aligned_cols=38 Identities=21% Similarity=0.552 Sum_probs=32.6
Q ss_pred eEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEec
Q 027823 70 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 113 (218)
Q Consensus 70 ~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRG 113 (218)
++.||.+|-.. .|.|||+.|.|+|.+.+++||-|+|--
T Consensus 132 kqikivvPNst------ag~iigkggAtiK~~~Eqsga~iqisP 169 (402)
T KOG2191|consen 132 KQIKIVVPNST------AGMIIGKGGATIKAIQEQSGAWIQISP 169 (402)
T ss_pred ceeEEeccCCc------ccceecCCcchHHHHHHhhCcceEecc
Confidence 46788887544 499999999999999999999999973
No 32
>PRK00106 hypothetical protein; Provisional
Probab=94.50 E-value=0.099 Score=51.68 Aligned_cols=65 Identities=29% Similarity=0.530 Sum_probs=51.5
Q ss_pred EEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchh
Q 027823 71 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 150 (218)
Q Consensus 71 ~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~ 150 (218)
+--|.+|-|+ +-|||||--|-+++.+|+.||+-|.|= +.|=-|.||+++|.
T Consensus 226 vs~v~lp~de-----mkGriIGreGrNir~~E~~tGvdliid-----------------------dtp~~v~lS~fdpv- 276 (535)
T PRK00106 226 ITTVHLPDDN-----MKGRIIGREGRNIRTLESLTGIDVIID-----------------------DTPEVVVLSGFDPI- 276 (535)
T ss_pred eeeEEcCChH-----hhcceeCCCcchHHHHHHHhCceEEEc-----------------------CCCCeEEEeCCChH-
Confidence 3445566655 559999999999999999999999984 34557899999986
Q ss_pred hHHHHHHHHHHHHHHhcC
Q 027823 151 IVDIRLRQAQEIIEELLK 168 (218)
Q Consensus 151 ~~~~rl~~A~e~Ie~LL~ 168 (218)
|-.-|..-++.|+.
T Consensus 277 ----RReiAr~~le~Li~ 290 (535)
T PRK00106 277 ----RREIARMTLESLIK 290 (535)
T ss_pred ----HHHHHHHHHHHHHH
Confidence 55677777888776
No 33
>PRK12704 phosphodiesterase; Provisional
Probab=94.23 E-value=0.13 Score=50.51 Aligned_cols=51 Identities=24% Similarity=0.520 Sum_probs=40.7
Q ss_pred EEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchh
Q 027823 72 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 150 (218)
Q Consensus 72 ~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~ 150 (218)
--|.+|-|+ +-|||||--|-++|.+|+.||+-|.|= +.|=-|+||+.+|..
T Consensus 212 ~~v~lp~d~-----mkgriigreGrnir~~e~~tgvd~iid-----------------------dtp~~v~ls~~~~~r 262 (520)
T PRK12704 212 SVVNLPNDE-----MKGRIIGREGRNIRALETLTGVDLIID-----------------------DTPEAVILSGFDPIR 262 (520)
T ss_pred eeeecCCch-----hhcceeCCCcchHHHHHHHhCCeEEEc-----------------------CCCCeEEEecCChhh
Confidence 334566555 559999999999999999999999984 335578999988863
No 34
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.19 E-value=0.11 Score=50.88 Aligned_cols=65 Identities=25% Similarity=0.520 Sum_probs=49.3
Q ss_pred EEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchh
Q 027823 71 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 150 (218)
Q Consensus 71 ~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~ 150 (218)
+.-|.+|-|+ +-|||||--|-+++.+|+.||+-|.|= +.|=-|.||+.+|.
T Consensus 205 ~~~v~lp~d~-----~kgriigreGrnir~~e~~tgvd~iid-----------------------dtp~~v~ls~fdp~- 255 (514)
T TIGR03319 205 VSVVNLPNDE-----MKGRIIGREGRNIRALETLTGVDLIID-----------------------DTPEAVILSGFDPV- 255 (514)
T ss_pred eeeEEcCChh-----hhccccCCCcchHHHHHHHhCceEEEc-----------------------CCCCeEEecCCchH-
Confidence 3345566555 559999999999999999999999985 23446889999886
Q ss_pred hHHHHHHHHHHHHHHhcC
Q 027823 151 IVDIRLRQAQEIIEELLK 168 (218)
Q Consensus 151 ~~~~rl~~A~e~Ie~LL~ 168 (218)
|=.-|..-++.|+.
T Consensus 256 ----rreia~~~l~~li~ 269 (514)
T TIGR03319 256 ----RREIARMALEKLIQ 269 (514)
T ss_pred ----HHHHHHHHHHHHHH
Confidence 44556666677665
No 35
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=93.40 E-value=0.22 Score=48.64 Aligned_cols=40 Identities=28% Similarity=0.541 Sum_probs=35.3
Q ss_pred eeEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecc
Q 027823 69 KRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 114 (218)
Q Consensus 69 k~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGr 114 (218)
....|+.||-. -+|-|||=+|+.+|.|..+|||+|.|-+.
T Consensus 137 ~v~~RLlVp~s------q~GslIGK~G~~Ik~Ire~TgA~I~v~~~ 176 (485)
T KOG2190|consen 137 EVTCRLLVPSS------QVGSLIGKGGSLIKEIREETGAKIRVSSD 176 (485)
T ss_pred ceEEEEEechh------heeeeeccCcHHHHHHHHhcCceEEecCC
Confidence 45789999854 46999999999999999999999999974
No 36
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=92.41 E-value=0.19 Score=51.04 Aligned_cols=63 Identities=27% Similarity=0.485 Sum_probs=48.5
Q ss_pred EEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchh
Q 027823 71 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 150 (218)
Q Consensus 71 ~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~ 150 (218)
..-+-|+.+.. +-+|||+|.|++.|..+|||+|.|--.|+ |.|.+.+.+
T Consensus 553 i~t~~i~~dKI------~dvIG~gGk~I~~I~eetg~~IdieddGt------------------------v~i~~s~~~- 601 (692)
T COG1185 553 IETIKIDPDKI------RDVIGPGGKTIKAITEETGVKIDIEDDGT------------------------VKIAASDGE- 601 (692)
T ss_pred eEEEccCHHHH------hhccCCcccchhhhhhhhCcEEEecCCCc------------------------EEEEecchH-
Confidence 44455776664 56899999999999999999999985544 456665533
Q ss_pred hHHHHHHHHHHHHHHhcC
Q 027823 151 IVDIRLRQAQEIIEELLK 168 (218)
Q Consensus 151 ~~~~rl~~A~e~Ie~LL~ 168 (218)
++.+|++.|+.+..
T Consensus 602 ----~~~~ak~~I~~i~~ 615 (692)
T COG1185 602 ----SAKKAKERIEAITR 615 (692)
T ss_pred ----HHHHHHHHHHHHHh
Confidence 57889999998884
No 37
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=91.64 E-value=0.4 Score=33.74 Aligned_cols=36 Identities=22% Similarity=0.416 Sum_probs=29.9
Q ss_pred eEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEE
Q 027823 70 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYI 111 (218)
Q Consensus 70 ~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~I 111 (218)
...++.++.+ -+|+.||.+|.+++.++..+|.+|-|
T Consensus 25 ~~~~v~V~~~------~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDD------QLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcc------cceeeECCCCHHHHHHHHHHCCCeEE
Confidence 4566777654 45999999999999999999988876
No 38
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=87.27 E-value=0.3 Score=47.67 Aligned_cols=29 Identities=31% Similarity=0.628 Sum_probs=26.6
Q ss_pred CCeeeeEeCCCcchHHHHHHHhCCeEEEe
Q 027823 84 FNFVGRLLGPRGNSLKRVEATTGCRVYIR 112 (218)
Q Consensus 84 ~NfvGrIlGPrG~TlKrIE~eTgckI~IR 112 (218)
-+|||.+||=.|+.+|+||..|+++|.|-
T Consensus 55 s~mvg~vigrggskik~iq~~tnt~iqii 83 (629)
T KOG0336|consen 55 SEMVGKVIGRGGSKIKRIQNDTNTRIQII 83 (629)
T ss_pred hhhhheeeccCcchhhhhhcccceeEEEe
Confidence 48999999999999999999999988764
No 39
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=85.86 E-value=0.58 Score=47.05 Aligned_cols=53 Identities=30% Similarity=0.420 Sum_probs=42.2
Q ss_pred eeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHHHh
Q 027823 87 VGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEEL 166 (218)
Q Consensus 87 vGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~L 166 (218)
+..+|||.|-.+|+|+.|||+.-++ +.=|+-|-|.++. .+++|.++|..+
T Consensus 608 ~~~lIGp~G~~~kki~~EtGai~~v-------------------------De~t~~i~A~~~~-----am~~Ak~~I~~i 657 (760)
T KOG1067|consen 608 RATLIGPGGVLKKKIEVETGAISQV-------------------------DEGTFSIFAPTQA-----AMEEAKEFIDGI 657 (760)
T ss_pred hheeecCccceeeeEeeeccceeee-------------------------cCceEEEEecCHH-----HHHHHHHHHHHH
Confidence 4679999999999999999944332 1227888888764 689999999999
Q ss_pred cCC
Q 027823 167 LKP 169 (218)
Q Consensus 167 L~p 169 (218)
..-
T Consensus 658 ~~~ 660 (760)
T KOG1067|consen 658 IKD 660 (760)
T ss_pred hcC
Confidence 883
No 40
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=82.18 E-value=0.64 Score=33.90 Aligned_cols=32 Identities=25% Similarity=0.518 Sum_probs=24.8
Q ss_pred CCCCCeeeeEeCCCcchHHHHHHHh-CCeEEEe
Q 027823 81 YPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIR 112 (218)
Q Consensus 81 yP~~NfvGrIlGPrG~TlKrIE~eT-gckI~IR 112 (218)
.++++-+|..+|.+|..+|.|+++. |-+|.|=
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 6555544
No 41
>PRK12705 hypothetical protein; Provisional
Probab=81.20 E-value=2.4 Score=41.89 Aligned_cols=36 Identities=31% Similarity=0.596 Sum_probs=29.4
Q ss_pred EEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEe
Q 027823 72 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 112 (218)
Q Consensus 72 ~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IR 112 (218)
--|.+|-| .+-|||||--|.+++.+|..||+-|.|-
T Consensus 200 s~v~lp~d-----emkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 200 SVVPIPSD-----AMKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred eeeecCCh-----HhhccccCccchhHHHHHHhhCCceEec
Confidence 33445544 4569999999999999999999998885
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=78.84 E-value=1.9 Score=29.02 Aligned_cols=23 Identities=13% Similarity=0.368 Sum_probs=20.5
Q ss_pred eeeEeCCCcchHHHHHHHhCCeE
Q 027823 87 VGRLLGPRGNSLKRVEATTGCRV 109 (218)
Q Consensus 87 vGrIlGPrG~TlKrIE~eTgckI 109 (218)
.|++||.+|.+++.|+..++-.+
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
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=78.61 E-value=1.6 Score=42.84 Aligned_cols=38 Identities=26% Similarity=0.551 Sum_probs=33.0
Q ss_pred EEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecc
Q 027823 71 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 114 (218)
Q Consensus 71 ~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGr 114 (218)
..++.|| .+++|.|||..|+.+-.|++.|||.|.|-++
T Consensus 339 ~~~l~vp------s~~igciiGk~G~~iseir~~tgA~I~I~~~ 376 (485)
T KOG2190|consen 339 TQRLLVP------SDLIGCIIGKGGAKISEIRQRTGASISILNK 376 (485)
T ss_pred eeeeccC------ccccceeecccccchHHHHHhcCCceEEccc
Confidence 4555555 5789999999999999999999999999874
No 44
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=73.33 E-value=11 Score=32.97 Aligned_cols=28 Identities=36% Similarity=0.617 Sum_probs=26.2
Q ss_pred eeeEeCCCcchHHHHHHHhCCeEEEecc
Q 027823 87 VGRLLGPRGNSLKRVEATTGCRVYIRGK 114 (218)
Q Consensus 87 vGrIlGPrG~TlKrIE~eTgckI~IRGr 114 (218)
+|-|+|+.|.+.|.||+.++|+|.|-.+
T Consensus 19 ~~~lig~~g~v~k~ie~~~~~~~~iD~~ 46 (194)
T COG1094 19 IGVLIGKWGEVKKAIEEKTGVKLRIDSK 46 (194)
T ss_pred heeeecccccchHHHHhhcCeEEEEECC
Confidence 4899999999999999999999999875
No 45
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=71.93 E-value=3.2 Score=34.11 Aligned_cols=29 Identities=24% Similarity=0.400 Sum_probs=26.4
Q ss_pred CeeeeEeCCCcchHHHHHHHhCCeEEEec
Q 027823 85 NFVGRLLGPRGNSLKRVEATTGCRVYIRG 113 (218)
Q Consensus 85 NfvGrIlGPrG~TlKrIE~eTgckI~IRG 113 (218)
+.+|..+|++|+.+|.|++..|-+|-|=.
T Consensus 41 ~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 41 GDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 36799999999999999999999998875
No 46
>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=71.34 E-value=2.7 Score=30.63 Aligned_cols=23 Identities=26% Similarity=0.538 Sum_probs=19.8
Q ss_pred eeeEeCCCcchHHHHHHHhCCeE
Q 027823 87 VGRLLGPRGNSLKRVEATTGCRV 109 (218)
Q Consensus 87 vGrIlGPrG~TlKrIE~eTgckI 109 (218)
.|+|||-+|.|++.||--+..-+
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~~~ 57 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANLVL 57 (77)
T ss_pred CCeEECCCCccHHHHHHHHHHHH
Confidence 49999999999999999887433
No 47
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=70.51 E-value=12 Score=33.78 Aligned_cols=29 Identities=28% Similarity=0.591 Sum_probs=26.3
Q ss_pred CCeeeeEeCCCcchHHHHHHHhCCeEEEe
Q 027823 84 FNFVGRLLGPRGNSLKRVEATTGCRVYIR 112 (218)
Q Consensus 84 ~NfvGrIlGPrG~TlKrIE~eTgckI~IR 112 (218)
..+|-|+||.+|+-++.|.+.|+|.|.|=
T Consensus 154 p~kVpRvig~~~sm~~~l~~~~~~~I~VG 182 (239)
T COG1097 154 PSKVPRVIGKKGSMLNMLKEKTGCEIIVG 182 (239)
T ss_pred hhhcceEecCCCcHHHHhhhhcCeEEEEe
Confidence 35677899999999999999999999985
No 48
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=66.63 E-value=0.98 Score=36.39 Aligned_cols=43 Identities=30% Similarity=0.528 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHH-hcCCCCchhHHHHHHHHHHHHHhcCccCCC
Q 027823 152 VDIRLRQAQEIIEE-LLKPVDESQDYIKRQQLRELAMLNSNFRED 195 (218)
Q Consensus 152 ~~~rl~~A~e~Ie~-LL~pv~e~~d~~K~~QL~ELA~lNGt~r~~ 195 (218)
+|.+|.+|+.+|+. |+-.|.|+-+.+| .|.+||...|..++.+
T Consensus 46 IDNKIeQAMDLVKtHLmfAVREEVe~Lk-~qI~eL~er~~~Le~E 89 (123)
T KOG4797|consen 46 IDNKIEQAMDLVKTHLMFAVREEVEVLK-EQIRELEERNSALERE 89 (123)
T ss_pred echHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence 35689999999997 5556677767676 8999998888777555
No 49
>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=66.05 E-value=14 Score=32.49 Aligned_cols=40 Identities=15% Similarity=0.353 Sum_probs=31.7
Q ss_pred eeeEEEEecCCCCCCCCCeeeeEeCCCcchHHHH--------HHHhCCeEEEe
Q 027823 68 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRV--------EATTGCRVYIR 112 (218)
Q Consensus 68 vk~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrI--------E~eTgckI~IR 112 (218)
++....|++.-+.+- |-|||.+|.++|+| |+..||+|.+.
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 455677788777665 88999999999987 66778988874
No 50
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=65.13 E-value=22 Score=33.17 Aligned_cols=37 Identities=19% Similarity=0.373 Sum_probs=30.1
Q ss_pred eEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEe
Q 027823 70 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 112 (218)
Q Consensus 70 ~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IR 112 (218)
...+|.+--++ .|.|||-.|.++|+|..+.++.|++-
T Consensus 48 ~e~ril~~sk~------agavigkgg~nik~lr~d~na~v~vp 84 (390)
T KOG2192|consen 48 VELRILLQSKN------AGAVIGKGGKNIKALRTDYNASVSVP 84 (390)
T ss_pred eeEEEEEeccc------ccceeccccccHHHHhhhccceeecc
Confidence 45566665443 49999999999999999999999876
No 51
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=63.72 E-value=14 Score=35.01 Aligned_cols=30 Identities=30% Similarity=0.503 Sum_probs=27.3
Q ss_pred CeeeeEeCCCcchHHHHHHHhCCeEEEecc
Q 027823 85 NFVGRLLGPRGNSLKRVEATTGCRVYIRGK 114 (218)
Q Consensus 85 NfvGrIlGPrG~TlKrIE~eTgckI~IRGr 114 (218)
|-+--|+||.|..++.||+.+|+.|.-||.
T Consensus 24 ~~~~~l~G~~~~~l~l~e~~~gv~i~~rG~ 53 (348)
T COG1702 24 NELVALFGPTDTNLSLLEIALGVSIVARGE 53 (348)
T ss_pred hhhhhhcCCCCccHHHHHHHhCcEEEeCCc
Confidence 566779999999999999999999999985
No 52
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=63.50 E-value=4 Score=38.54 Aligned_cols=37 Identities=22% Similarity=0.354 Sum_probs=29.4
Q ss_pred eeeEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEE
Q 027823 68 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVY 110 (218)
Q Consensus 68 vk~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~ 110 (218)
....+.+.+| +-||+.|.|++|.++|.|+++|.+.|.
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 3444444454 458999999999999999999999875
No 53
>PRK15494 era GTPase Era; Provisional
Probab=60.39 E-value=18 Score=33.22 Aligned_cols=40 Identities=25% Similarity=0.356 Sum_probs=32.4
Q ss_pred eeeEEEEecCCCCCCCCCeeeeEeCCCcchHHHH--------HHHhCCeEEEe
Q 027823 68 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRV--------EATTGCRVYIR 112 (218)
Q Consensus 68 vk~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrI--------E~eTgckI~IR 112 (218)
++....||+.-+.+- +-|||-+|..+|+| |+..||||.+.
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 455677888777665 88999999999987 77889998886
No 54
>PRK00089 era GTPase Era; Reviewed
Probab=60.00 E-value=20 Score=31.55 Aligned_cols=40 Identities=25% Similarity=0.456 Sum_probs=31.6
Q ss_pred eeeEEEEecCCCCCCCCCeeeeEeCCCcchHHHH--------HHHhCCeEEEe
Q 027823 68 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRV--------EATTGCRVYIR 112 (218)
Q Consensus 68 vk~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrI--------E~eTgckI~IR 112 (218)
++....|++.-+.+ .+-|||-+|.++|+| |+..||+|.+.
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 45567777776665 489999999999987 67789988876
No 55
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=54.10 E-value=2.8 Score=29.94 Aligned_cols=20 Identities=30% Similarity=0.639 Sum_probs=18.1
Q ss_pred eeeEeCCCcchHHHHHHHhC
Q 027823 87 VGRLLGPRGNSLKRVEATTG 106 (218)
Q Consensus 87 vGrIlGPrG~TlKrIE~eTg 106 (218)
.|+|||-+|.|++.||--++
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 56
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=53.39 E-value=9.2 Score=39.50 Aligned_cols=38 Identities=24% Similarity=0.454 Sum_probs=30.4
Q ss_pred eeEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEe
Q 027823 69 KRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 112 (218)
Q Consensus 69 k~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IR 112 (218)
.....++||.+-| +-|+||+|.++++++++++|-+.+-
T Consensus 708 ~~~~~~~~p~~~~------~~~ig~~g~~~r~~~~~~~~~~~~~ 745 (753)
T KOG2208|consen 708 LVTKEIEIPRSLH------RYLIGPKGSNLRQLEKEFNVNIVVP 745 (753)
T ss_pred ceeeEEeccHHHh------hhccCCCCccHHHHHHHhccceecC
Confidence 3455666776554 6799999999999999999988765
No 57
>PRK02821 hypothetical protein; Provisional
Probab=51.25 E-value=9.1 Score=28.63 Aligned_cols=21 Identities=14% Similarity=0.412 Sum_probs=17.8
Q ss_pred eeeeEeCCCcchHHHHHHHhC
Q 027823 86 FVGRLLGPRGNSLKRVEATTG 106 (218)
Q Consensus 86 fvGrIlGPrG~TlKrIE~eTg 106 (218)
=+|||||=+|.|++.|-.--.
T Consensus 41 D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 41 DLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred hCcceeCCCCchHHHHHHHHH
Confidence 469999999999999976544
No 58
>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=51.03 E-value=13 Score=30.71 Aligned_cols=29 Identities=24% Similarity=0.414 Sum_probs=26.3
Q ss_pred CeeeeEeCCCcchHHHHHHHhCCeEEEec
Q 027823 85 NFVGRLLGPRGNSLKRVEATTGCRVYIRG 113 (218)
Q Consensus 85 NfvGrIlGPrG~TlKrIE~eTgckI~IRG 113 (218)
+-+|..+|++|..+|.|++..|=||-|-.
T Consensus 42 g~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 42 GEMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred CCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 46799999999999999999999998876
No 59
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=50.16 E-value=23 Score=34.76 Aligned_cols=34 Identities=21% Similarity=0.346 Sum_probs=29.9
Q ss_pred CCCCCCeeeeEeCCCcchHHHHHHHh-CCeEEEec
Q 027823 80 TYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 113 (218)
Q Consensus 80 ~yP~~NfvGrIlGPrG~TlKrIE~eT-gckI~IRG 113 (218)
..|+++-||..+|++|+.++.|.++. |=||-|--
T Consensus 272 ~d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~ 306 (449)
T PRK12329 272 LERDVDPVGACIGARGSRIQAVVNELRGEKIDVIR 306 (449)
T ss_pred CCCCCChhhccCCCCcchHHHHHHHhCCCeEEEEE
Confidence 45889999999999999999999998 77887753
No 60
>PRK00468 hypothetical protein; Provisional
Probab=49.73 E-value=9.9 Score=28.20 Aligned_cols=19 Identities=21% Similarity=0.590 Sum_probs=16.4
Q ss_pred eeeEeCCCcchHHHHHHHh
Q 027823 87 VGRLLGPRGNSLKRVEATT 105 (218)
Q Consensus 87 vGrIlGPrG~TlKrIE~eT 105 (218)
+|||||=+|.|++.|..--
T Consensus 41 ~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CcceecCCChhHHHHHHHH
Confidence 5999999999999987643
No 61
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=47.93 E-value=20 Score=34.02 Aligned_cols=34 Identities=24% Similarity=0.510 Sum_probs=29.9
Q ss_pred CCCCCCeeeeEeCCCcchHHHHHHHh-CCeEEEec
Q 027823 80 TYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 113 (218)
Q Consensus 80 ~yP~~NfvGrIlGPrG~TlKrIE~eT-gckI~IRG 113 (218)
..|+++-+|..+|++|+.++.|.++. |=+|-|--
T Consensus 240 ~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv~ 274 (362)
T PRK12327 240 NNPNVDAKGACVGPKGQRVQNIVSELKGEKIDIID 274 (362)
T ss_pred CCCCCCchheeECCCChhHHHHHHHhCCCeEEEEE
Confidence 45899999999999999999999988 87887753
No 62
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=46.68 E-value=17 Score=29.77 Aligned_cols=25 Identities=20% Similarity=0.352 Sum_probs=21.8
Q ss_pred eeeEeCCCcchHHHHHHHhCCeEEE
Q 027823 87 VGRLLGPRGNSLKRVEATTGCRVYI 111 (218)
Q Consensus 87 vGrIlGPrG~TlKrIE~eTgckI~I 111 (218)
.|+.||.+|.|++.++..+|-.+-|
T Consensus 110 ~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 110 KGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred cchhhCCCCHHHHHHHHHhCCccCC
Confidence 4999999999999999999876644
No 63
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=46.65 E-value=19 Score=38.54 Aligned_cols=77 Identities=27% Similarity=0.406 Sum_probs=55.9
Q ss_pred EecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHH
Q 027823 74 LEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVD 153 (218)
Q Consensus 74 i~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~~~~ 153 (218)
...+++++|. |..+++.+=. +|.+|...|+|.|.+||+=- ...+ .| ...++.||.+|++.+.
T Consensus 900 ~~~~inD~Pq-~~r~~vt~~~--~L~~i~e~~~~~it~rg~f~--~~gk------~p--~~gErklyl~ve~~~e----- 961 (997)
T KOG0334|consen 900 AELEINDFPQ-NARWRVTYKE--ALLRISEPTAAGITTRGKFN--PPGK------EP--KPGERKLYLLVEGPDE----- 961 (997)
T ss_pred eeccccccch-hcceeeechh--hhhhccCccccceeeccccC--CCCC------CC--CCcchhhhhhhhcchh-----
Confidence 3466788996 6888888764 49999999999999999621 1111 12 2357889999997653
Q ss_pred HHHHHHHHHHHHhcC
Q 027823 154 IRLRQAQEIIEELLK 168 (218)
Q Consensus 154 ~rl~~A~e~Ie~LL~ 168 (218)
.-+.+|++.++.+|.
T Consensus 962 ~~vqra~~e~~r~l~ 976 (997)
T KOG0334|consen 962 LSVQRAIEELERLLE 976 (997)
T ss_pred HHHHHHHHHHHHHHH
Confidence 257889999888665
No 64
>PRK01064 hypothetical protein; Provisional
Probab=46.11 E-value=13 Score=27.83 Aligned_cols=20 Identities=20% Similarity=0.607 Sum_probs=17.6
Q ss_pred eeeEeCCCcchHHHHHHHhC
Q 027823 87 VGRLLGPRGNSLKRVEATTG 106 (218)
Q Consensus 87 vGrIlGPrG~TlKrIE~eTg 106 (218)
+|++||=+|.|++.|..-..
T Consensus 41 ~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred ceEEECCCCccHHHHHHHHH
Confidence 59999999999999988654
No 65
>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=44.97 E-value=26 Score=32.93 Aligned_cols=34 Identities=24% Similarity=0.461 Sum_probs=29.5
Q ss_pred CCCCCCeeeeEeCCCcchHHHHHHHh-CCeEEEec
Q 027823 80 TYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 113 (218)
Q Consensus 80 ~yP~~NfvGrIlGPrG~TlKrIE~eT-gckI~IRG 113 (218)
..|+++-+|..+|++|+.++.|.++. |=+|-|--
T Consensus 238 ~~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~ 272 (341)
T TIGR01953 238 NDENIDPVGACVGPKGSRIQAISKELNGEKIDIIE 272 (341)
T ss_pred CCCCCCcceeeECCCCchHHHHHHHhCCCeEEEEE
Confidence 46899999999999999999999998 76776653
No 66
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=42.17 E-value=21 Score=30.94 Aligned_cols=35 Identities=23% Similarity=0.349 Sum_probs=29.7
Q ss_pred CCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecc
Q 027823 80 TYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 114 (218)
Q Consensus 80 ~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGr 114 (218)
..++.+=+|..+|++|..+|.|.++.|=+|-|---
T Consensus 80 ~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~ 114 (190)
T COG0195 80 NVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW 114 (190)
T ss_pred eecCcCchhhhccCCChHHHHHHHHhCCceEEEEe
Confidence 34567788999999999999999999988887653
No 67
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=41.83 E-value=16 Score=27.45 Aligned_cols=18 Identities=17% Similarity=0.702 Sum_probs=15.9
Q ss_pred eeeEeCCCcchHHHHHHH
Q 027823 87 VGRLLGPRGNSLKRVEAT 104 (218)
Q Consensus 87 vGrIlGPrG~TlKrIE~e 104 (218)
+|++||=+|.|++.|-.-
T Consensus 41 ~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 41 MGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred ccceecCCChhHHHHHHH
Confidence 599999999999999653
No 68
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=41.16 E-value=12 Score=35.47 Aligned_cols=31 Identities=26% Similarity=0.549 Sum_probs=27.8
Q ss_pred CCeeeeEeCCCcchHHHHHHHhCCeEEEecc
Q 027823 84 FNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 114 (218)
Q Consensus 84 ~NfvGrIlGPrG~TlKrIE~eTgckI~IRGr 114 (218)
+-+||++.||.|+|+|+||+.+..-|.--++
T Consensus 123 ~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 123 LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred ceeeeeccccccCccchheecccceEeeecc
Confidence 6799999999999999999999998876654
No 69
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=41.02 E-value=22 Score=30.26 Aligned_cols=27 Identities=22% Similarity=0.260 Sum_probs=25.3
Q ss_pred eeEeCCCcchHHHHHHHhCCeEEEecc
Q 027823 88 GRLLGPRGNSLKRVEATTGCRVYIRGK 114 (218)
Q Consensus 88 GrIlGPrG~TlKrIE~eTgckI~IRGr 114 (218)
|.-||++|.++|+|++..|=+|.|-.-
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEEEc
Confidence 999999999999999999999999873
No 70
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=39.05 E-value=40 Score=32.30 Aligned_cols=43 Identities=16% Similarity=0.274 Sum_probs=35.5
Q ss_pred EEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEecccCCCC
Q 027823 71 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKD 119 (218)
Q Consensus 71 ~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd 119 (218)
...++||-+++ ++-||=+|.+++.--+.||++|-|+.-+|.-.
T Consensus 309 ~~~V~V~~~ql------slAIGk~GqNvrLA~~LtGwkIDI~s~~~~~~ 351 (374)
T PRK12328 309 KAIVTLLSDQK------SKAIGKNGINIRLASMLTGYEIELNEIGSKEN 351 (374)
T ss_pred EEEEEEChHHh------hhhhcCCChhHHHHHHHhCCEEEEEECCCCcc
Confidence 45666765554 78999999999999999999999999887443
No 71
>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=37.97 E-value=27 Score=23.86 Aligned_cols=19 Identities=21% Similarity=0.433 Sum_probs=15.4
Q ss_pred hHHHHHHHhCCeEEEeccc
Q 027823 97 SLKRVEATTGCRVYIRGKG 115 (218)
Q Consensus 97 TlKrIE~eTgckI~IRGrG 115 (218)
.+++||++.|+++++|..+
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 5799999999999999543
No 72
>COG1159 Era GTPase [General function prediction only]
Probab=33.31 E-value=81 Score=29.39 Aligned_cols=41 Identities=24% Similarity=0.561 Sum_probs=31.4
Q ss_pred ceeeEEEEecCCCCCCCCCeeeeEeCCCcchHHHH--------HHHhCCeEEEe
Q 027823 67 TVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRV--------EATTGCRVYIR 112 (218)
Q Consensus 67 ~vk~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrI--------E~eTgckI~IR 112 (218)
.++....|+|+-+..- |-|||-+|..+|+| |...+|+|++-
T Consensus 226 ~~~I~a~I~Ver~sQK-----~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L~ 274 (298)
T COG1159 226 LLKIHATIYVERESQK-----GIIIGKNGAMIKKIGTAARKDIEKLLGCKVYLE 274 (298)
T ss_pred eEEEEEEEEEecCCcc-----ceEECCCcHHHHHHHHHHHHHHHHHhCCceEEE
Confidence 4555667888877665 88999999999987 66667777764
No 73
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=33.11 E-value=31 Score=32.99 Aligned_cols=33 Identities=21% Similarity=0.372 Sum_probs=29.0
Q ss_pred CCCCCCeeeeEeCCCcchHHHHHHHh-CCeEEEe
Q 027823 80 TYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIR 112 (218)
Q Consensus 80 ~yP~~NfvGrIlGPrG~TlKrIE~eT-gckI~IR 112 (218)
..|+++-+|..+|++|+.++.|.++. |=+|-|-
T Consensus 246 ~d~~iDPvGacIG~~G~rI~~I~~eL~gEkIDvI 279 (374)
T PRK12328 246 NNPNIDPIGATVGVKGVRINAVSKELNGENIDCI 279 (374)
T ss_pred CCCCCChHHhhcCCCcchHHHHHHHhCCCeEEEE
Confidence 66899999999999999999999988 7677665
No 74
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=32.53 E-value=33 Score=29.53 Aligned_cols=21 Identities=24% Similarity=0.512 Sum_probs=18.3
Q ss_pred chHHHHHHHhCCeEEEecccC
Q 027823 96 NSLKRVEATTGCRVYIRGKGS 116 (218)
Q Consensus 96 ~TlKrIE~eTgckI~IRGrGS 116 (218)
..+|+||++.|+++++|++|.
T Consensus 35 ~~i~~LE~~lg~~Lf~R~r~i 55 (294)
T PRK13348 35 QRIKALEESLGQPLLVRGRPC 55 (294)
T ss_pred HHHHHHHHHhCceeeecCCCC
Confidence 358999999999999999754
No 75
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=32.29 E-value=1.4e+02 Score=26.43 Aligned_cols=9 Identities=78% Similarity=1.678 Sum_probs=8.3
Q ss_pred eeeEeCCCc
Q 027823 87 VGRLLGPRG 95 (218)
Q Consensus 87 vGrIlGPrG 95 (218)
+|+||||||
T Consensus 126 Lg~iLGPrG 134 (230)
T PRK05424 126 LGRILGPRG 134 (230)
T ss_pred hcccccccc
Confidence 699999997
No 76
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=29.90 E-value=1.4e+02 Score=26.16 Aligned_cols=61 Identities=21% Similarity=0.126 Sum_probs=33.9
Q ss_pred eeeEeCCC-------------cchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCch-hhH
Q 027823 87 VGRLLGPR-------------GNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPA-NIV 152 (218)
Q Consensus 87 vGrIlGPr-------------G~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~-~~~ 152 (218)
+||+|||+ ...+...-.++.++|.+|=+ ..--+|+.|-..+-. +.+
T Consensus 117 lgk~LGp~~~p~gK~P~~~~~~~dl~~~i~~~k~~v~~r~~--------------------k~~~~~~~VGk~~m~~e~i 176 (214)
T PTZ00225 117 VPRLVGPHMHRMGKFPTVCSPSESLPDKVVELRSTVKFQLK--------------------KVLCLGTCVGHVEMTEEQL 176 (214)
T ss_pred hhhhcCCCCCcCCCCCcccCCccCHHHHHHHHhheeEEEec--------------------CccEEEeEEccCCCCHHHH
Confidence 49999998 33355555566666666621 112357777655432 223
Q ss_pred HHHHHHHHHHHHHhc
Q 027823 153 DIRLRQAQEIIEELL 167 (218)
Q Consensus 153 ~~rl~~A~e~Ie~LL 167 (218)
.+-+..+.+.|...|
T Consensus 177 ~eNi~a~l~~l~~~~ 191 (214)
T PTZ00225 177 RQNVVMAINFLVSLL 191 (214)
T ss_pred HHHHHHHHHHHHHhC
Confidence 334555555555554
No 77
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=29.12 E-value=84 Score=30.12 Aligned_cols=36 Identities=28% Similarity=0.326 Sum_probs=26.0
Q ss_pred HHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchh
Q 027823 103 ATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 150 (218)
Q Consensus 103 ~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~ 150 (218)
.++|+.+.|||+|--+... +-..+|+|.|..+.|.+
T Consensus 300 tq~G~~~rl~gkG~p~~~~------------~~~GDl~v~v~v~~P~~ 335 (371)
T COG0484 300 TQTGEVFRLRGKGMPKLRS------------GGRGDLYVRVKVETPKN 335 (371)
T ss_pred CccCcEEEEcCCCccccCC------------CCcCCEEEEEEEEcCCC
Confidence 3568899999988644211 12478999999998875
No 78
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=27.67 E-value=49 Score=32.42 Aligned_cols=34 Identities=24% Similarity=0.441 Sum_probs=29.7
Q ss_pred CCCCCCCeeeeEeCCCcchHHHHHHHh-CCeEEEe
Q 027823 79 DTYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIR 112 (218)
Q Consensus 79 ~~yP~~NfvGrIlGPrG~TlKrIE~eT-gckI~IR 112 (218)
...|+++-||..+|++|+.++.|..+. |=+|-|-
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 466889999999999999999999888 7777665
No 79
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=27.06 E-value=68 Score=30.66 Aligned_cols=39 Identities=23% Similarity=0.399 Sum_probs=27.8
Q ss_pred EecCCC-CCCCCCeeeeEeCCCcchHHHHH--------HHhCCeEEEe
Q 027823 74 LEIPVD-TYPNFNFVGRLLGPRGNSLKRVE--------ATTGCRVYIR 112 (218)
Q Consensus 74 i~IPv~-~yP~~NfvGrIlGPrG~TlKrIE--------~eTgckI~IR 112 (218)
++|-++ ..|+-...-.|||++|.-+++|- ...+|+|.+|
T Consensus 326 l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~dL~~if~r~V~l~ 373 (379)
T KOG1423|consen 326 LFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRANEDLEDIFQRKVFLR 373 (379)
T ss_pred EEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHHHHHHHHhhceeeEE
Confidence 344444 45566677899999999999984 4557777776
No 80
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=26.07 E-value=1.9e+02 Score=24.35 Aligned_cols=83 Identities=19% Similarity=0.259 Sum_probs=52.3
Q ss_pred eeeeEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCceEEEEecCchhhHHHHHHHHHHHHHH
Q 027823 86 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEE 165 (218)
Q Consensus 86 fvGrIlGPrG~TlKrIE~eTgckI~IRGrGS~kd~~~e~~l~g~p~~e~~~epLHVlI~a~~~~~~~~~rl~~A~e~Ie~ 165 (218)
.+-+|+.++|..++.|-+..||+|.+.-. .-.+.|+|.-. .++.+.+.|.+
T Consensus 36 ~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----------------------~~~i~I~g~k~------~~~~i~~~i~~ 86 (210)
T PF14611_consen 36 EFFLLLTGNGRILENLAARNGAKIEVSRS-----------------------ENRIRITGTKS------TAEYIEASINE 86 (210)
T ss_pred heeeeecCCchHHHHHHHhcCceEEEecC-----------------------CcEEEEEccHH------HHHHHHHHHHH
Confidence 34689999999999997778999998731 11577887432 23445555555
Q ss_pred hcCCC-------Cc--------hhHHHHHHHHHHHHHhcCccCCCCC
Q 027823 166 LLKPV-------DE--------SQDYIKRQQLRELAMLNSNFREDSP 197 (218)
Q Consensus 166 LL~pv-------~e--------~~d~~K~~QL~ELA~lNGt~r~~~~ 197 (218)
+|.-+ +. ....+...=|.+++.+-++|-+...
T Consensus 87 ~l~~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~ 133 (210)
T PF14611_consen 87 ILSNIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNP 133 (210)
T ss_pred HHhhcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECC
Confidence 55322 11 1112345567788888888865543
No 81
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=25.62 E-value=48 Score=30.99 Aligned_cols=40 Identities=23% Similarity=0.490 Sum_probs=31.7
Q ss_pred ccceeeEEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEe
Q 027823 65 SYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 112 (218)
Q Consensus 65 ~~~vk~~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IR 112 (218)
+|+. +..|-||-| +-|-|||-.|.-+|+|-.|+|+.|.|-
T Consensus 312 GPit--TaQvtip~d------lggsiigkggqri~~ir~esGA~Ikid 351 (390)
T KOG2192|consen 312 GPIT--TAQVTIPKD------LGGSIIGKGGQRIKQIRHESGASIKID 351 (390)
T ss_pred Ccee--eeeEecccc------cCcceecccchhhhhhhhccCceEEec
Confidence 3444 345567744 559999999999999999999999885
No 82
>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=24.37 E-value=2.3e+02 Score=25.04 Aligned_cols=10 Identities=70% Similarity=1.401 Sum_probs=8.4
Q ss_pred eeeeEeCCCc
Q 027823 86 FVGRLLGPRG 95 (218)
Q Consensus 86 fvGrIlGPrG 95 (218)
.+|+||||||
T Consensus 124 ~Lg~iLGPrG 133 (227)
T TIGR01169 124 KLGRILGPRG 133 (227)
T ss_pred Hhcccccccc
Confidence 3499999996
No 83
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=24.03 E-value=19 Score=32.22 Aligned_cols=28 Identities=25% Similarity=0.453 Sum_probs=26.2
Q ss_pred eeeeEeCCCcchHHHHHHHhCCeEEEec
Q 027823 86 FVGRLLGPRGNSLKRVEATTGCRVYIRG 113 (218)
Q Consensus 86 fvGrIlGPrG~TlKrIE~eTgckI~IRG 113 (218)
-||||.|-.|.|--.||..|.++|.+-+
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVlad 206 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIENVTRTRIVLAD 206 (252)
T ss_pred HHHHhhcCCCcceeeeeccceeEEEecC
Confidence 4899999999999999999999999875
No 84
>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=23.87 E-value=46 Score=28.62 Aligned_cols=20 Identities=20% Similarity=0.350 Sum_probs=17.6
Q ss_pred hHHHHHHHhCCeEEEecccC
Q 027823 97 SLKRVEATTGCRVYIRGKGS 116 (218)
Q Consensus 97 TlKrIE~eTgckI~IRGrGS 116 (218)
.+|+||++.|++++.|++|-
T Consensus 35 ~I~~LE~~lg~~Lf~R~r~~ 54 (292)
T TIGR03298 35 RIKALEERLGQPLLVRTQPC 54 (292)
T ss_pred HHHHHHHHhCchheecCCCC
Confidence 47999999999999998654
No 85
>TIGR01170 rplA_mito ribosomal protein L1, mitochondrial. This model represents the mitochondrial homolog of bacterial ribosomal protein L1. Unlike chloroplast L1, this form was not sufficiently similar to bacterial forms to include in a single bacterial/organellar L1.
Probab=23.85 E-value=27 Score=28.76 Aligned_cols=19 Identities=42% Similarity=0.751 Sum_probs=14.7
Q ss_pred CCCCCCCCeeeeEeCCCcc
Q 027823 78 VDTYPNFNFVGRLLGPRGN 96 (218)
Q Consensus 78 v~~yP~~NfvGrIlGPrG~ 96 (218)
.+-.|....+|+||||||.
T Consensus 100 ~~~m~~l~~Lg~iLGprGl 118 (141)
T TIGR01170 100 PDIVPELAQLRRLLGPKGL 118 (141)
T ss_pred HHHHHHHHHhhcccccCcC
Confidence 3455667789999999985
No 86
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=23.82 E-value=61 Score=28.11 Aligned_cols=21 Identities=19% Similarity=0.298 Sum_probs=18.3
Q ss_pred hHHHHHHHhCCeEEEecccCC
Q 027823 97 SLKRVEATTGCRVYIRGKGSI 117 (218)
Q Consensus 97 TlKrIE~eTgckI~IRGrGS~ 117 (218)
.+|+||++.|++++.|++|-.
T Consensus 36 ~I~~LE~~lg~~LF~R~~~~~ 56 (294)
T PRK03635 36 RIKALEERVGQVLLVRTQPCR 56 (294)
T ss_pred HHHHHHHHhCceeeecCCCCc
Confidence 589999999999999987543
No 87
>KOG1852 consensus Cell cycle-associated protein [Cell cycle control, cell division, chromosome partitioning]
Probab=23.46 E-value=67 Score=27.89 Aligned_cols=37 Identities=27% Similarity=0.475 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHhcCCCCchhHH--HHHHHHHHHH-HhcC
Q 027823 153 DIRLRQAQEIIEELLKPVDESQDY--IKRQQLRELA-MLNS 190 (218)
Q Consensus 153 ~~rl~~A~e~Ie~LL~pv~e~~d~--~K~~QL~ELA-~lNG 190 (218)
..-|.+-..-|+.+|.| ++++|+ .|-+.|+++. .|||
T Consensus 44 qq~ikadpsnv~~iltp-pe~qdegvwkyehlrqfc~elng 83 (223)
T KOG1852|consen 44 QQNIKADPSNVDKILTP-PEGQDEGVWKYEHLRQFCLELNG 83 (223)
T ss_pred HHHhccCchhHHHhcCC-CcccccchhhHHHHHHHHHHhhh
Confidence 34455556678889997 566776 7888898876 5777
No 88
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=23.28 E-value=70 Score=27.81 Aligned_cols=18 Identities=11% Similarity=0.265 Sum_probs=16.1
Q ss_pred chHHHHHHHhCCeEEEec
Q 027823 96 NSLKRVEATTGCRVYIRG 113 (218)
Q Consensus 96 ~TlKrIE~eTgckI~IRG 113 (218)
..+|+||++.|+.+++|.
T Consensus 35 ~~I~~LE~~lg~~LF~R~ 52 (300)
T PRK11074 35 YTVRQLEEWLAVPLFERR 52 (300)
T ss_pred HHHHHHHHHhCCeeEEeC
Confidence 358999999999999994
No 89
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=22.08 E-value=75 Score=28.24 Aligned_cols=18 Identities=22% Similarity=0.575 Sum_probs=16.1
Q ss_pred chHHHHHHHhCCeEEEec
Q 027823 96 NSLKRVEATTGCRVYIRG 113 (218)
Q Consensus 96 ~TlKrIE~eTgckI~IRG 113 (218)
..+|+||++.|+++++|.
T Consensus 35 ~~Ik~LE~~lg~~LF~R~ 52 (317)
T PRK15421 35 HQFSDLEQRLGFRLFVRK 52 (317)
T ss_pred HHHHHHHHHhCCEEEEec
Confidence 358999999999999995
No 90
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=21.95 E-value=72 Score=27.49 Aligned_cols=17 Identities=18% Similarity=0.532 Sum_probs=15.6
Q ss_pred hHHHHHHHhCCeEEEec
Q 027823 97 SLKRVEATTGCRVYIRG 113 (218)
Q Consensus 97 TlKrIE~eTgckI~IRG 113 (218)
.+|+||++.|++++.|.
T Consensus 35 ~I~~LE~~lG~~LF~R~ 51 (275)
T PRK03601 35 RIRQLENQLGVNLFTRH 51 (275)
T ss_pred HHHHHHHHhCCceEEEC
Confidence 58999999999999994
No 91
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=21.51 E-value=78 Score=27.91 Aligned_cols=19 Identities=21% Similarity=0.457 Sum_probs=16.7
Q ss_pred hHHHHHHHhCCeEEEec-cc
Q 027823 97 SLKRVEATTGCRVYIRG-KG 115 (218)
Q Consensus 97 TlKrIE~eTgckI~IRG-rG 115 (218)
.+|+||++.||++.+|. +|
T Consensus 36 ~ik~LE~~lg~~Lf~R~~r~ 55 (313)
T PRK12684 36 AIIELEDELGVEIFTRHGKR 55 (313)
T ss_pred HHHHHHHHhCCeeEEEcCCc
Confidence 58999999999999994 55
No 92
>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=21.32 E-value=94 Score=29.22 Aligned_cols=37 Identities=16% Similarity=0.336 Sum_probs=31.1
Q ss_pred EEEEecCCCCCCCCCeeeeEeCCCcchHHHHHHHhCCeEEEec
Q 027823 71 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 113 (218)
Q Consensus 71 ~~ki~IPv~~yP~~NfvGrIlGPrG~TlKrIE~eTgckI~IRG 113 (218)
...+.+|-++. ++-||=+|.+++.--..||++|-|+-
T Consensus 302 ~~~v~V~~~~~------~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 302 SAEVVVPDDQL------SLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred EEEEEEChHHc------chhhcCCChhHHHHHHHhCCEEEEEe
Confidence 45666766654 78999999999999999999999984
No 93
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=20.46 E-value=83 Score=27.73 Aligned_cols=20 Identities=35% Similarity=0.670 Sum_probs=17.2
Q ss_pred hHHHHHHHhCCeEEEe-cccC
Q 027823 97 SLKRVEATTGCRVYIR-GKGS 116 (218)
Q Consensus 97 TlKrIE~eTgckI~IR-GrGS 116 (218)
.+|+||++.|+++++| |+|-
T Consensus 36 ~I~~LE~~lg~~Lf~R~~r~~ 56 (309)
T PRK12683 36 QIKDLEDELGVEIFIRRGKRL 56 (309)
T ss_pred HHHHHHHHhCCeeEeeCCCCc
Confidence 5899999999999999 4553
No 94
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=20.18 E-value=36 Score=30.21 Aligned_cols=9 Identities=78% Similarity=1.641 Sum_probs=7.8
Q ss_pred eeeEeCCCc
Q 027823 87 VGRLLGPRG 95 (218)
Q Consensus 87 vGrIlGPrG 95 (218)
+|+||||||
T Consensus 126 LgriLGprG 134 (229)
T CHL00129 126 LGRVLGPRG 134 (229)
T ss_pred hcCcccccC
Confidence 499999995
No 95
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=20.09 E-value=90 Score=27.26 Aligned_cols=20 Identities=25% Similarity=0.463 Sum_probs=17.0
Q ss_pred hHHHHHHHhCCeEEEec-ccC
Q 027823 97 SLKRVEATTGCRVYIRG-KGS 116 (218)
Q Consensus 97 TlKrIE~eTgckI~IRG-rGS 116 (218)
.+|+||++.||++++|. +|-
T Consensus 36 ~I~~LE~~lg~~LF~R~~~~~ 56 (309)
T PRK12682 36 AIIELEEELGIEIFIRHGKRL 56 (309)
T ss_pred HHHHHHHHhCCeeEEECCCCc
Confidence 58999999999999995 553
Done!