Query psy12968
Match_columns 402
No_of_seqs 189 out of 405
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 15:43:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12968.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12968hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1588|consensus 100.0 1.7E-59 3.7E-64 448.1 22.5 187 8-197 23-216 (259)
2 cd02395 SF1_like-KH Splicing f 100.0 4.2E-38 9.2E-43 271.6 12.9 117 72-194 1-120 (120)
3 KOG0119|consensus 100.0 2.5E-34 5.4E-39 293.4 13.0 141 39-196 113-259 (554)
4 COG5176 MSL5 Splicing factor ( 99.9 7.1E-27 1.5E-31 220.0 9.8 119 67-194 144-267 (269)
5 cd00105 KH-I K homology RNA-bi 98.3 4.2E-06 9.1E-11 62.3 7.5 38 73-116 2-39 (64)
6 cd02393 PNPase_KH Polynucleoti 98.2 7.9E-06 1.7E-10 62.9 8.0 36 72-113 3-38 (61)
7 smart00322 KH K homology RNA-b 98.2 1.3E-05 2.8E-10 58.2 8.4 40 71-116 3-42 (69)
8 PF13014 KH_3: KH domain 98.0 3.7E-06 8.1E-11 60.0 3.2 28 87-114 1-28 (43)
9 cd02396 PCBP_like_KH K homolog 97.9 4.5E-05 9.8E-10 58.7 7.1 35 73-113 2-36 (65)
10 PF00013 KH_1: KH domain syndr 97.9 1E-05 2.2E-10 60.6 3.3 37 72-114 1-37 (60)
11 cd02394 vigilin_like_KH K homo 97.8 4.3E-05 9.2E-10 57.6 5.6 37 73-115 2-38 (62)
12 KOG1960|consensus 97.2 0.00021 4.6E-09 74.1 3.1 86 69-170 208-293 (531)
13 PRK13763 putative RNA-processi 97.0 0.0014 3E-08 60.4 6.1 52 87-171 105-156 (180)
14 TIGR03665 arCOG04150 arCOG0415 97.0 0.0012 2.7E-08 60.3 5.3 52 87-171 99-150 (172)
15 KOG1676|consensus 96.8 0.0032 7E-08 67.7 7.7 100 34-171 110-209 (600)
16 PRK13763 putative RNA-processi 96.5 0.0053 1.1E-07 56.7 5.8 65 72-172 4-71 (180)
17 TIGR02696 pppGpp_PNP guanosine 96.2 0.013 2.9E-07 64.6 7.9 65 71-172 578-642 (719)
18 KOG1676|consensus 96.0 0.019 4.1E-07 62.0 7.9 28 86-113 239-266 (600)
19 KOG2193|consensus 96.0 0.0021 4.6E-08 67.3 0.6 38 76-113 279-316 (584)
20 TIGR03591 polynuc_phos polyrib 95.8 0.016 3.5E-07 63.4 6.2 63 71-170 551-613 (684)
21 TIGR03665 arCOG04150 arCOG0415 95.6 0.0046 9.9E-08 56.6 1.1 29 86-114 7-35 (172)
22 COG1094 Predicted RNA-binding 95.5 0.011 2.5E-07 56.1 3.2 29 87-115 112-140 (194)
23 PLN00207 polyribonucleotide nu 95.2 0.031 6.8E-07 63.1 5.9 64 71-171 685-749 (891)
24 KOG2190|consensus 94.3 0.2 4.3E-06 53.3 9.0 70 70-170 137-206 (485)
25 PRK12704 phosphodiesterase; Pr 94.3 0.42 9.1E-06 51.1 11.4 50 74-153 213-262 (520)
26 KOG2814|consensus 93.9 0.088 1.9E-06 53.8 5.1 61 86-168 66-128 (345)
27 PRK04163 exosome complex RNA-b 93.0 0.14 3.1E-06 49.0 4.9 54 86-170 154-207 (235)
28 KOG2874|consensus 92.9 0.062 1.3E-06 54.2 2.2 27 89-115 161-187 (356)
29 KOG2191|consensus 92.7 0.11 2.5E-06 53.3 3.9 38 70-113 38-75 (402)
30 PRK11824 polynucleotide phosph 92.1 0.13 2.9E-06 56.4 3.8 55 86-171 563-617 (693)
31 KOG2191|consensus 91.2 1.7 3.8E-05 45.0 10.2 38 71-114 132-169 (402)
32 TIGR03319 YmdA_YtgF conserved 90.8 1.6 3.4E-05 46.8 10.0 54 74-157 207-260 (514)
33 PRK00106 hypothetical protein; 90.5 2 4.3E-05 46.5 10.4 53 73-155 227-279 (535)
34 KOG2193|consensus 87.3 0.35 7.5E-06 51.4 2.1 38 71-114 199-236 (584)
35 KOG2190|consensus 84.5 0.9 2E-05 48.5 3.5 41 69-115 336-376 (485)
36 cd02134 NusA_KH NusA_K homolog 84.3 1.1 2.4E-05 34.6 3.1 36 71-112 25-60 (61)
37 COG1185 Pnp Polyribonucleotide 82.9 1.8 3.8E-05 48.2 5.0 37 75-117 556-592 (692)
38 KOG0336|consensus 81.7 0.73 1.6E-05 49.2 1.5 29 85-113 55-83 (629)
39 PF13184 KH_5: NusA-like KH do 76.8 1.4 3E-05 35.3 1.4 32 83-114 14-46 (69)
40 PRK12705 hypothetical protein; 74.6 5.3 0.00011 43.1 5.4 35 74-113 201-235 (508)
41 TIGR00436 era GTP-binding prot 72.6 13 0.00028 35.6 7.0 41 68-113 218-266 (270)
42 cd02409 KH-II KH-II (K homolo 70.1 4 8.7E-05 29.9 2.4 24 87-110 35-58 (68)
43 KOG1960|consensus 69.0 7 0.00015 41.7 4.6 62 90-167 107-168 (531)
44 PRK15494 era GTPase Era; Provi 65.1 20 0.00042 36.1 6.8 41 68-113 270-318 (339)
45 KOG1924|consensus 62.2 16 0.00034 42.0 6.0 17 96-113 422-438 (1102)
46 PRK00089 era GTPase Era; Revie 60.5 31 0.00068 33.0 7.0 41 68-113 223-271 (292)
47 PRK08406 transcription elongat 60.5 6.9 0.00015 35.3 2.4 29 86-114 41-69 (140)
48 COG1097 RRP4 RNA-binding prote 57.3 8.6 0.00019 38.1 2.7 29 85-113 154-182 (239)
49 KOG1924|consensus 50.7 31 0.00068 39.8 5.9 8 129-136 440-447 (1102)
50 PF08926 DUF1908: Domain of un 50.3 5.3 0.00011 40.3 0.0 32 322-357 28-63 (282)
51 cd02414 jag_KH jag_K homology 49.8 10 0.00023 30.2 1.6 21 88-108 35-55 (77)
52 PRK12328 nusA transcription el 45.5 27 0.00059 36.6 4.2 71 36-114 209-280 (374)
53 KOG1067|consensus 44.8 16 0.00035 40.6 2.6 53 88-172 608-660 (760)
54 PRK12327 nusA transcription el 42.2 25 0.00053 36.5 3.3 33 82-114 241-274 (362)
55 COG1094 Predicted RNA-binding 41.9 20 0.00044 34.5 2.5 38 72-115 9-46 (194)
56 KOG2113|consensus 39.7 24 0.00053 36.7 2.8 39 67-111 22-60 (394)
57 TIGR01953 NusA transcription t 39.4 32 0.00069 35.4 3.6 40 74-114 232-272 (341)
58 PRK09202 nusA transcription el 38.7 45 0.00098 35.8 4.7 71 36-114 203-274 (470)
59 PF00126 HTH_1: Bacterial regu 38.1 24 0.00053 26.5 2.0 19 98-116 33-51 (60)
60 COG0195 NusA Transcription elo 36.0 27 0.00059 33.3 2.4 34 83-116 82-115 (190)
61 COG1159 Era GTPase [General fu 36.0 96 0.0021 31.8 6.3 41 67-112 225-273 (298)
62 KOG0334|consensus 35.2 31 0.00067 40.3 3.0 76 76-171 901-976 (997)
63 TIGR01952 nusA_arch NusA famil 34.8 31 0.00067 31.4 2.4 37 74-114 34-70 (141)
64 PRK13348 chromosome replicatio 33.6 30 0.00066 32.4 2.3 24 97-120 35-58 (294)
65 PRK06418 transcription elongat 33.0 34 0.00073 32.1 2.4 73 33-115 15-98 (166)
66 KOG2208|consensus 32.7 19 0.0004 40.7 0.8 38 70-113 708-745 (753)
67 COG1855 ATPase (PilT family) [ 31.6 64 0.0014 35.5 4.4 41 73-119 488-528 (604)
68 PF13083 KH_4: KH domain; PDB: 29.5 12 0.00025 29.4 -1.0 20 88-107 40-59 (73)
69 KOG2236|consensus 28.9 4E+02 0.0087 29.2 9.7 30 132-161 305-334 (483)
70 TIGR03298 argP transcriptional 27.9 35 0.00075 32.0 1.6 24 98-121 35-58 (292)
71 PRK05424 rplA 50S ribosomal pr 27.4 1.7E+02 0.0036 28.5 6.2 30 141-170 169-199 (230)
72 KOG2113|consensus 27.4 29 0.00064 36.2 1.1 31 85-115 123-153 (394)
73 PRK02821 hypothetical protein; 27.1 36 0.00077 28.2 1.3 22 86-107 40-61 (77)
74 PRK12329 nusA transcription el 26.9 48 0.001 35.7 2.6 41 73-114 265-306 (449)
75 TIGR01169 rplA_bact ribosomal 26.7 1E+02 0.0022 29.9 4.6 29 141-169 168-197 (227)
76 PRK00468 hypothetical protein; 25.3 41 0.00088 27.6 1.4 19 88-106 41-59 (75)
77 COG1702 PhoH Phosphate starvat 24.6 56 0.0012 34.1 2.5 30 86-115 24-53 (348)
78 PRK03635 chromosome replicatio 24.5 55 0.0012 30.9 2.3 24 97-120 35-58 (294)
79 PRK11074 putative DNA-binding 24.2 62 0.0013 30.7 2.6 19 97-115 35-53 (300)
80 PRK03601 transcriptional regul 24.1 57 0.0012 30.6 2.3 17 98-114 35-51 (275)
81 PRK01064 hypothetical protein; 23.1 59 0.0013 26.9 1.9 20 88-107 41-60 (78)
82 PRK09986 DNA-binding transcrip 23.0 66 0.0014 29.9 2.5 23 97-119 40-62 (294)
83 PRK09791 putative DNA-binding 22.5 72 0.0016 30.1 2.7 22 98-119 39-60 (302)
84 PRK15421 DNA-binding transcrip 22.5 67 0.0015 31.1 2.5 19 97-115 35-53 (317)
85 KOG2192|consensus 22.5 1.7E+02 0.0038 30.2 5.4 39 69-113 46-84 (390)
86 TIGR01170 rplA_mito ribosomal 22.2 18 0.00038 32.9 -1.4 18 80-97 101-118 (141)
87 PRK12684 transcriptional regul 22.2 68 0.0015 30.8 2.5 21 97-117 35-56 (313)
88 COG1837 Predicted RNA-binding 22.1 52 0.0011 27.4 1.4 17 88-104 41-57 (76)
89 PRK12683 transcriptional regul 21.9 70 0.0015 30.8 2.5 21 97-117 35-56 (309)
90 PRK12682 transcriptional regul 21.2 77 0.0017 30.2 2.6 20 98-117 36-56 (309)
91 PRK11242 DNA-binding transcrip 20.7 78 0.0017 29.5 2.4 19 97-115 34-52 (296)
92 PRK08406 transcription elongat 20.4 49 0.0011 29.8 1.0 26 87-112 109-134 (140)
No 1
>KOG1588|consensus
Probab=100.00 E-value=1.7e-59 Score=448.10 Aligned_cols=187 Identities=47% Similarity=0.757 Sum_probs=172.3
Q ss_pred ccCCcchHHHHHHHHHHHHhhCCCCC--hHHHHHHHHHHHHhhhhcCCC-----CCCCCccccccCCCceEEEEEEccCC
Q psy12968 8 EDGNDTKANEYVKTLLKEKMTLDSDS--HSYTLKLLDDEINKAMASNKK-----KYDSPYLDLFREKPILVKVKVLVPVK 80 (402)
Q Consensus 8 ~~~~~~~~~~YL~ELl~Ek~~L~~~~--F~ha~rLLd~EI~RV~~~~~p-----~~~~~y~D~~~ekpvkl~eKI~IPvk 80 (402)
..+.++..++||.+|++|+++|+ .. |.||.+||++||.||+..+.. .....+.|++.++++|+++||+|||+
T Consensus 23 ~~~~~~~~~~yl~el~~e~~~l~-~~~~~~~~~rLL~~Ei~rv~~~~~~~~~~~~~~~~~~~~~~~~~vk~~~Kv~vPv~ 101 (259)
T KOG1588|consen 23 QPQLNEKASKYLSELLAERKSLS-PFFPFPHAERLLDEEIERVQTSGRQHGSKEPEELPYADVYSGKPVKLTEKVLVPVK 101 (259)
T ss_pred ccchhhHHHHHHHHHHhhHHhcC-cccchHHHHHHHHHHHHHHHhhhhhccCCCchhcccccCccCCceeEEEEEEeccC
Confidence 44667889999999999999999 44 559999999999999998762 33344568899999999999999999
Q ss_pred CCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecCChhHHHHHHH
Q psy12968 81 EHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALAPPAEAHARIA 160 (402)
Q Consensus 81 eyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~~~~~A~~rLa 160 (402)
+||+||||||||||||||+||||++|||||+|||||||||..||++||+ ||+|+||++||||+|++++++++|+.||+
T Consensus 102 ~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~--~p~yeHL~epLHVlIe~~~p~~ea~~rl~ 179 (259)
T KOG1588|consen 102 EYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRG--DPGYEHLNEPLHVLIETEAPPAEAYARLA 179 (259)
T ss_pred CCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhc--CcchHHhCCCcEEEEEEeCCHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999996 99999999999999999999999999999
Q ss_pred HHHHHHHhhcCCCccHHHHHHHHHHHHhhcCCCCCCC
Q psy12968 161 YALSELRKYIIPDVNDEIRQEQFREMGYVHHEPRPQM 197 (402)
Q Consensus 161 ~AveeIeklL~Pd~~DelKq~QLrELA~iNg~~~P~~ 197 (402)
+|+++|++||+|+.+|+.|++||||||++||++....
T Consensus 180 ~AleeI~klL~P~~e~~dk~~QL~ELa~lngt~~~~~ 216 (259)
T KOG1588|consen 180 YALEEIKKLLVPDHEDEDKREQLRELAILNGTYLRSE 216 (259)
T ss_pred HHHHHHHHhcCCCCCCchHHHHHHHHhhcCCcccccc
Confidence 9999999999999888889999999999999865533
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=4.2e-38 Score=271.59 Aligned_cols=117 Identities=48% Similarity=0.786 Sum_probs=108.3
Q ss_pred EEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecCC
Q psy12968 72 KVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALAP 151 (402)
Q Consensus 72 ~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~~ 151 (402)
++|||||+++||+|||||+||||+|+|+|+||++|||+|.|||+||++++++++++++ +.|+|++|||||+|+++++
T Consensus 1 ~~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~---~~~~~~~eplhV~I~a~~~ 77 (120)
T cd02395 1 TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRG---PKYAHLNEPLHVLITAETP 77 (120)
T ss_pred CCEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccC---cccccCCCCcEEEEEeCCc
Confidence 4799999999999999999999999999999999999999999999999999988874 8899999999999999986
Q ss_pred hhHHHHHHHHHHHHHHhhcCCC---ccHHHHHHHHHHHHhhcCCCC
Q psy12968 152 PAEAHARIAYALSELRKYIIPD---VNDEIRQEQFREMGYVHHEPR 194 (402)
Q Consensus 152 ~~~A~~rLa~AveeIeklL~Pd---~~DelKq~QLrELA~iNg~~~ 194 (402)
|...+++|++.|+.||.+. ++|++|++||+|||++||+++
T Consensus 78 ---~~e~~~~A~~~I~~ll~~~~~~~~~~~k~~ql~~la~~nGt~~ 120 (120)
T cd02395 78 ---PEEALAKAVEAIEELLKPAIEGGNDELKREQLRELALLNGTYR 120 (120)
T ss_pred ---HHHHHHHHHHHHHHHhccCCCccchHHHHHHHHHHHHhcccCC
Confidence 4577889999999999862 379999999999999999874
No 3
>KOG0119|consensus
Probab=100.00 E-value=2.5e-34 Score=293.41 Aligned_cols=141 Identities=32% Similarity=0.503 Sum_probs=113.8
Q ss_pred HHHHHHHHhhhhcCCCCCCCCccccccCCCceEEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCCCC
Q psy12968 39 KLLDDEINKAMASNKKKYDSPYLDLFREKPILVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSM 118 (402)
Q Consensus 39 rLLd~EI~RV~~~~~p~~~~~y~D~~~ekpvkl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~ 118 (402)
+++.+||.++.-.-+++. .|+ .+.+++.|||||||+||+|||||+||||||+|||+||+||||||+||||||+
T Consensus 113 ~e~I~~~lk~nP~fkpP~------DYk-~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSv 185 (554)
T KOG0119|consen 113 HEIIEEILKLNPGFKPPA------DYK-PPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSV 185 (554)
T ss_pred HHHHHHHHHhCcCCCCCc------ccC-cccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccc
Confidence 344456655554333332 233 2339999999999999999999999999999999999999999999999999
Q ss_pred CCChhhHhhhccCCCCCC-CCCCCcEEEEEecCChhHHHHHHHHHHHHHHhhcC-----CCccHHHHHHHHHHHHhhcCC
Q psy12968 119 RDRSKEEELRKEGDPKNA-HLVEDLHVQVSALAPPAEAHARIAYALSELRKYII-----PDVNDEIRQEQFREMGYVHHE 192 (402)
Q Consensus 119 kd~kkEe~LR~sgdP~~e-hlnEpLHVlIsA~~~~~~A~~rLa~AveeIeklL~-----Pd~~DelKq~QLrELA~iNg~ 192 (402)
|+++. + +.|.++. ..+|+|||+|++++ +.+|++|++.|+.||. |++++++|+.||+|||.+||+
T Consensus 186 kEgk~----~-~~d~~~~~~~~epLH~~Isadt-----~eki~~Ai~vienli~~av~~~e~~n~l~~~Qlrela~lNgt 255 (554)
T KOG0119|consen 186 KEGKG----R-SDDLSYIPKENEPLHCLISADT-----QEKIKKAIAVIENLIQSAVSVPEGQNDLKRLQLRELARLNGT 255 (554)
T ss_pred ccccc----C-CcccccccccccceeEEEecch-----HHHHHHHHHHHHHHHHhhccCccccccccHHHHHHHHHhCCC
Confidence 99872 2 1234442 36899999999998 6899999999999884 688999999999999999987
Q ss_pred CCCC
Q psy12968 193 PRPQ 196 (402)
Q Consensus 193 ~~P~ 196 (402)
.+..
T Consensus 256 ~r~~ 259 (554)
T KOG0119|consen 256 LRDD 259 (554)
T ss_pred CCcc
Confidence 7653
No 4
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.94 E-value=7.1e-27 Score=219.95 Aligned_cols=119 Identities=24% Similarity=0.426 Sum_probs=96.4
Q ss_pred CCceEEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEE
Q psy12968 67 KPILVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQV 146 (402)
Q Consensus 67 kpvkl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlI 146 (402)
.+.+.+.||||||++||+.||||+||||||.|+|+||+.|+|||.|||+||.|.++...++- +.--...++||+||
T Consensus 144 rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p----~~~~N~e~~lhcLI 219 (269)
T COG5176 144 RPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTP----ESLKNAEAVLHCLI 219 (269)
T ss_pred CcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCc----hhhhhhHHhHHHHh
Confidence 57899999999999999999999999999999999999999999999999999887543321 11122568999999
Q ss_pred EecCChhHHHHHHHHHHHHH-----HhhcCCCccHHHHHHHHHHHHhhcCCCC
Q psy12968 147 SALAPPAEAHARIAYALSEL-----RKYIIPDVNDEIRQEQFREMGYVHHEPR 194 (402)
Q Consensus 147 sA~~~~~~A~~rLa~AveeI-----eklL~Pd~~DelKq~QLrELA~iNg~~~ 194 (402)
+++.. .++.+++..+ +..-.|++++++|+-||++||.+||+.+
T Consensus 220 ~adse-----dki~~~ik~~~n~I~~a~~~PeGqnDlkR~qlr~la~lngtlr 267 (269)
T COG5176 220 EADSE-----DKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGTLR 267 (269)
T ss_pred hcchh-----hhHHHHHHHHHHHHHHHhcCCcccchHHHHHHHHHHHhcceec
Confidence 99864 3344443332 3334799999999999999999999764
No 5
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.26 E-value=4.2e-06 Score=62.26 Aligned_cols=38 Identities=37% Similarity=0.742 Sum_probs=33.9
Q ss_pred EEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCC
Q psy12968 73 VKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKG 116 (402)
Q Consensus 73 eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKG 116 (402)
.+|.||. +++|+|+||+|.++++|+++|||+|.|...+
T Consensus 2 ~~i~ip~------~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~ 39 (64)
T cd00105 2 ERVLVPS------SLVGRIIGKGGSTIKEIREETGAKIKIPDSG 39 (64)
T ss_pred EEEEEch------hhcceeECCCCHHHHHHHHHHCCEEEEcCCC
Confidence 4678886 8999999999999999999999999998643
No 6
>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=98.20 E-value=7.9e-06 Score=62.92 Aligned_cols=36 Identities=25% Similarity=0.513 Sum_probs=31.4
Q ss_pred EEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEe
Q psy12968 72 KVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSIL 113 (402)
Q Consensus 72 ~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IR 113 (402)
.+.|.||. +++|+|||++|.|+|+||++|||+|.|-
T Consensus 3 ~~~i~Ip~------~~ig~iIGkgG~~ik~I~~~tg~~I~i~ 38 (61)
T cd02393 3 IETMKIPP------DKIRDVIGPGGKTIKKIIEETGVKIDIE 38 (61)
T ss_pred EEEEEeCh------hheeeeECCCchHHHHHHHHHCCEEEeC
Confidence 34577775 6899999999999999999999999874
No 7
>smart00322 KH K homology RNA-binding domain.
Probab=98.18 E-value=1.3e-05 Score=58.24 Aligned_cols=40 Identities=35% Similarity=0.712 Sum_probs=34.7
Q ss_pred EEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCC
Q psy12968 71 VKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKG 116 (402)
Q Consensus 71 l~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKG 116 (402)
...+|.||. +++|+|||++|.+++.|++.|||+|.+.+.+
T Consensus 3 ~~~~i~i~~------~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~ 42 (69)
T smart00322 3 VTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPEDG 42 (69)
T ss_pred eEEEEEEcc------hhcceeECCCchHHHHHHHHHCCEEEECCCC
Confidence 456778876 8899999999999999999999999997543
No 8
>PF13014 KH_3: KH domain
Probab=98.05 E-value=3.7e-06 Score=60.05 Aligned_cols=28 Identities=36% Similarity=0.740 Sum_probs=26.9
Q ss_pred eeeEEeCCCchhHHHHHHhhCceEEEec
Q psy12968 87 FVGKLLGPKGNSLRRLQEETMTKMSILG 114 (402)
Q Consensus 87 FVGrILGPRGnTlKrLE~ETGcKI~IRG 114 (402)
|+|+|||++|.|+++|+++|||+|.|--
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 7899999999999999999999999986
No 9
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=97.91 E-value=4.5e-05 Score=58.70 Aligned_cols=35 Identities=29% Similarity=0.652 Sum_probs=32.0
Q ss_pred EEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEe
Q psy12968 73 VKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSIL 113 (402)
Q Consensus 73 eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IR 113 (402)
.+++||. +.+|+|||.+|.++++|+++|||+|.|.
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 4688886 7899999999999999999999999994
No 10
>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=97.90 E-value=1e-05 Score=60.58 Aligned_cols=37 Identities=32% Similarity=0.670 Sum_probs=32.6
Q ss_pred EEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEec
Q psy12968 72 KVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILG 114 (402)
Q Consensus 72 ~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRG 114 (402)
+.+|.||. +++|+|||++|.++|+||++|||+|.|..
T Consensus 1 T~~i~vp~------~~~~~iIG~~G~~i~~I~~~t~~~I~i~~ 37 (60)
T PF00013_consen 1 TERIEVPS------SLVGRIIGKKGSNIKEIEEETGVKIQIPD 37 (60)
T ss_dssp EEEEEEEH------HHHHHHHTGGGHHHHHHHHHHTSEEEEES
T ss_pred CEEEEECH------HHcCEEECCCCCcHHHhhhhcCeEEEEcC
Confidence 35677774 79999999999999999999999999954
No 11
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=97.82 E-value=4.3e-05 Score=57.60 Aligned_cols=37 Identities=27% Similarity=0.456 Sum_probs=31.9
Q ss_pred EEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecC
Q psy12968 73 VKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGK 115 (402)
Q Consensus 73 eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGK 115 (402)
++|.||. .++|.|||++|.++++|+++|||+|.|-..
T Consensus 2 ~~i~Vp~------~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~ 38 (62)
T cd02394 2 EEVEIPK------KLHRFIIGKKGSNIRKIMEETGVKIRFPDP 38 (62)
T ss_pred eEEEeCH------HHhhhccCCCCCcHHHHHHHhCCEEEcCCC
Confidence 3566765 678999999999999999999999999754
No 12
>KOG1960|consensus
Probab=97.21 E-value=0.00021 Score=74.05 Aligned_cols=86 Identities=16% Similarity=-0.017 Sum_probs=68.2
Q ss_pred ceEEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEe
Q psy12968 69 ILVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSA 148 (402)
Q Consensus 69 vkl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA 148 (402)
++...|++|++| .|.||.-+..=|++-.+|..+|.||+.+++||||||+...--+ + +..+|||.++|+.
T Consensus 208 ~~Y~~k~~v~~~-~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~---------G-~EsnEPMYI~i~h 276 (531)
T KOG1960|consen 208 RYYPNKALATDK-DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNE---------G-NESNEPMYIFSTH 276 (531)
T ss_pred ccchhheecccC-CcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCccc---------c-cccCCceeEEeec
Confidence 455568999998 7999999999999999999999999999999999998864321 2 2379999999999
Q ss_pred cCChhHHHHHHHHHHHHHHhhc
Q psy12968 149 LAPPAEAHARIAYALSELRKYI 170 (402)
Q Consensus 149 ~~~~~~A~~rLa~AveeIeklL 170 (402)
..... +..|+.++..++
T Consensus 277 ~~~~g-----~~~A~r~~~nl~ 293 (531)
T KOG1960|consen 277 GNGNG-----ENGAPRRKWNLE 293 (531)
T ss_pred CCchh-----hccchhHHHhHH
Confidence 87633 345555554444
No 13
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.01 E-value=0.0014 Score=60.44 Aligned_cols=52 Identities=23% Similarity=0.370 Sum_probs=40.9
Q ss_pred eeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecCChhHHHHHHHHHHHHH
Q psy12968 87 FVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALAPPAEAHARIAYALSEL 166 (402)
Q Consensus 87 FVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~~~~~A~~rLa~AveeI 166 (402)
.+|+|||+.|.|.|.||..|||+|.|-|+ .|.|.++ ..+++.|.+.|
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~---------------------------~v~i~G~------~~~~~~A~~~I 151 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGK---------------------------TVAIIGD------PEQVEIAREAI 151 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCC---------------------------EEEEEeC------HHHHHHHHHHH
Confidence 69999999999999999999999998531 1556653 35567777778
Q ss_pred HhhcC
Q psy12968 167 RKYII 171 (402)
Q Consensus 167 eklL~ 171 (402)
+.|+.
T Consensus 152 ~~li~ 156 (180)
T PRK13763 152 EMLIE 156 (180)
T ss_pred HHHHc
Confidence 87774
No 14
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=96.96 E-value=0.0012 Score=60.31 Aligned_cols=52 Identities=21% Similarity=0.328 Sum_probs=42.0
Q ss_pred eeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecCChhHHHHHHHHHHHHH
Q psy12968 87 FVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALAPPAEAHARIAYALSEL 166 (402)
Q Consensus 87 FVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~~~~~A~~rLa~AveeI 166 (402)
.+|||+|+.|.|++.||..|||+|.|-| =.|.|.++ ...++.|.+.|
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~---------------------------~~v~i~G~------~~~~~~A~~~i 145 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYG---------------------------KTVGIIGD------PEQVQIAREAI 145 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcC---------------------------CEEEEECC------HHHHHHHHHHH
Confidence 6999999999999999999999999853 03667763 35677788888
Q ss_pred HhhcC
Q psy12968 167 RKYII 171 (402)
Q Consensus 167 eklL~ 171 (402)
+.|+.
T Consensus 146 ~~li~ 150 (172)
T TIGR03665 146 EMLIE 150 (172)
T ss_pred HHHHc
Confidence 88884
No 15
>KOG1676|consensus
Probab=96.81 E-value=0.0032 Score=67.72 Aligned_cols=100 Identities=17% Similarity=0.324 Sum_probs=70.6
Q ss_pred hHHHHHHHHHHHHhhhhcCCCCCCCCccccccCCCceEEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEe
Q psy12968 34 HSYTLKLLDDEINKAMASNKKKYDSPYLDLFREKPILVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSIL 113 (402)
Q Consensus 34 F~ha~rLLd~EI~RV~~~~~p~~~~~y~D~~~ekpvkl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IR 113 (402)
-.-+++||++.+.|.+.... |.+.- ..++.+.+|.||- |=+|+|||=.|.|+|+|++.+|||+.+-
T Consensus 110 v~~aK~li~evv~r~~~~~~------~~~~q--~~~~ttqeI~IPa------~k~GlIIGKgGETikqlqe~sg~k~i~i 175 (600)
T KOG1676|consen 110 VEVAKQLIGEVVSRGRPPGG------FPDNQ--GSVETTQEILIPA------NKCGLIIGKGGETIKQLQEQSGVKMILV 175 (600)
T ss_pred HHHHHHhhhhhhhccCCCCC------ccccC--CccceeeeeccCc------cceeeEeccCccHHHHHHhhcCCceEEE
Confidence 34678899999998883221 11111 1567888999996 7799999999999999999999999887
Q ss_pred cCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecCChhHHHHHHHHHHHHHHhhcC
Q psy12968 114 GKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALAPPAEAHARIAYALSELRKYII 171 (402)
Q Consensus 114 GKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~~~~~A~~rLa~AveeIeklL~ 171 (402)
=-|+.-++ .+.|| .|+++. .+++.|.+.|-++|.
T Consensus 176 qd~~~~~~----------------~~Kpl--ritGdp------~~ve~a~~lV~dil~ 209 (600)
T KOG1676|consen 176 QDGSIATG----------------ADKPL--RITGDP------DKVEQAKQLVADILR 209 (600)
T ss_pred ecCCcCCC----------------CCCce--eecCCH------HHHHHHHHHHHHHHH
Confidence 65554332 22344 455543 467777777877775
No 16
>PRK13763 putative RNA-processing protein; Provisional
Probab=96.48 E-value=0.0053 Score=56.66 Aligned_cols=65 Identities=20% Similarity=0.213 Sum_probs=49.3
Q ss_pred EEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEE---e
Q psy12968 72 KVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVS---A 148 (402)
Q Consensus 72 ~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIs---A 148 (402)
...+.||. +-+|.|+|+.|.|.|.|+++|||+|.|--. .=.|.|. +
T Consensus 4 ~~~i~IP~------~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-------------------------~g~V~I~~~~~ 52 (180)
T PRK13763 4 MEYVKIPK------DRIGVLIGKKGETKKEIEERTGVKLEIDSE-------------------------TGEVIIEPTDG 52 (180)
T ss_pred eEEEEcCH------HHhhhHhccchhHHHHHHHHHCcEEEEECC-------------------------CCeEEEEeCCC
Confidence 34566664 679999999999999999999999999742 1246665 3
Q ss_pred cCChhHHHHHHHHHHHHHHhhcCC
Q psy12968 149 LAPPAEAHARIAYALSELRKYIIP 172 (402)
Q Consensus 149 ~~~~~~A~~rLa~AveeIeklL~P 172 (402)
.+ ...+.+|.+.|+.++..
T Consensus 53 ~d-----~~~i~kA~~~I~ai~~g 71 (180)
T PRK13763 53 ED-----PLAVLKARDIVKAIGRG 71 (180)
T ss_pred CC-----HHHHHHHHHHHHHHhcC
Confidence 33 25577889999888864
No 17
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=96.21 E-value=0.013 Score=64.64 Aligned_cols=65 Identities=28% Similarity=0.425 Sum_probs=52.9
Q ss_pred EEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecC
Q psy12968 71 VKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALA 150 (402)
Q Consensus 71 l~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~ 150 (402)
....+.||. +-||.||||+|.|+|.|+++|||+|-|-- +=+|.|.+.+
T Consensus 578 ~~~~~~I~~------~ki~~vIG~gGk~I~~i~~~tg~~Idi~d--------------------------~G~V~I~a~d 625 (719)
T TIGR02696 578 RIITVKIPV------DKIGEVIGPKGKMINQIQDETGAEISIED--------------------------DGTVYIGAAD 625 (719)
T ss_pred eeEEEEeCh------HHhhheeCCCcHhHHHHHHHHCCEEEEec--------------------------CcEEEEEeCC
Confidence 344667775 57999999999999999999999998852 3468888877
Q ss_pred ChhHHHHHHHHHHHHHHhhcCC
Q psy12968 151 PPAEAHARIAYALSELRKYIIP 172 (402)
Q Consensus 151 ~~~~A~~rLa~AveeIeklL~P 172 (402)
..++++|++.|+.++.+
T Consensus 626 -----~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 626 -----GPSAEAARAMINAIANP 642 (719)
T ss_pred -----HHHHHHHHHHHHHhhCc
Confidence 46788999999988874
No 18
>KOG1676|consensus
Probab=96.04 E-value=0.019 Score=62.03 Aligned_cols=28 Identities=32% Similarity=0.547 Sum_probs=27.0
Q ss_pred ceeeEEeCCCchhHHHHHHhhCceEEEe
Q psy12968 86 NFVGKLLGPKGNSLRRLQEETMTKMSIL 113 (402)
Q Consensus 86 NFVGrILGPRGnTlKrLE~ETGcKI~IR 113 (402)
+=||.|||=.|.|+|+|+.+||+||.++
T Consensus 239 ~~VG~IIGkgGE~IKklq~etG~KIQfk 266 (600)
T KOG1676|consen 239 SKVGIIIGKGGEMIKKLQNETGAKIQFK 266 (600)
T ss_pred cceeeEEecCchHHHHHhhccCceeEee
Confidence 6799999999999999999999999997
No 19
>KOG2193|consensus
Probab=96.00 E-value=0.0021 Score=67.29 Aligned_cols=38 Identities=34% Similarity=0.661 Sum_probs=34.4
Q ss_pred EccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEe
Q psy12968 76 LVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSIL 113 (402)
Q Consensus 76 ~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IR 113 (402)
.||++-.-.-||||||||-.|.++|.||++||+||.|-
T Consensus 279 e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis 316 (584)
T KOG2193|consen 279 EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITIS 316 (584)
T ss_pred hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeee
Confidence 47777767779999999999999999999999999995
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=95.79 E-value=0.016 Score=63.37 Aligned_cols=63 Identities=21% Similarity=0.289 Sum_probs=48.3
Q ss_pred EEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecC
Q psy12968 71 VKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALA 150 (402)
Q Consensus 71 l~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~ 150 (402)
....+-||. ..||.||||+|.|+|.|+++|||+|.|-- +=+|.|.+.+
T Consensus 551 ~~~~~~I~~------~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d--------------------------dG~V~i~~~~ 598 (684)
T TIGR03591 551 RIETIKINP------DKIRDVIGPGGKVIREITEETGAKIDIED--------------------------DGTVKIAASD 598 (684)
T ss_pred eEEEEecCH------HHHHhhcCCCcHHHHHHHHHHCCEEEEec--------------------------CeEEEEEECc
Confidence 344566775 67999999999999999999999999931 2357777766
Q ss_pred ChhHHHHHHHHHHHHHHhhc
Q psy12968 151 PPAEAHARIAYALSELRKYI 170 (402)
Q Consensus 151 ~~~~A~~rLa~AveeIeklL 170 (402)
...+++|.+.|+.+.
T Consensus 599 -----~~~~~~a~~~I~~~~ 613 (684)
T TIGR03591 599 -----GEAAEAAIKMIEGIT 613 (684)
T ss_pred -----HHHHHHHHHHHHhhh
Confidence 355777877777664
No 21
>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=95.64 E-value=0.0046 Score=56.62 Aligned_cols=29 Identities=28% Similarity=0.496 Sum_probs=27.4
Q ss_pred ceeeEEeCCCchhHHHHHHhhCceEEEec
Q psy12968 86 NFVGKLLGPKGNSLRRLQEETMTKMSILG 114 (402)
Q Consensus 86 NFVGrILGPRGnTlKrLE~ETGcKI~IRG 114 (402)
+.+|.||||+|.|.|+||++|||+|.|--
T Consensus 7 ~kig~vIG~gG~~Ik~I~~~tgv~I~Id~ 35 (172)
T TIGR03665 7 DRIGVLIGKGGETKKEIEERTGVKLDIDS 35 (172)
T ss_pred HHhhhHhCCchhHHHHHHHHhCcEEEEEc
Confidence 78999999999999999999999999973
No 22
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=95.49 E-value=0.011 Score=56.10 Aligned_cols=29 Identities=31% Similarity=0.595 Sum_probs=27.5
Q ss_pred eeeEEeCCCchhHHHHHHhhCceEEEecC
Q psy12968 87 FVGKLLGPKGNSLRRLQEETMTKMSILGK 115 (402)
Q Consensus 87 FVGrILGPRGnTlKrLE~ETGcKI~IRGK 115 (402)
..|||+|+.|.|.+.||.-|||.|.|.|+
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~ 140 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK 140 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc
Confidence 57999999999999999999999999984
No 23
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=95.17 E-value=0.031 Score=63.07 Aligned_cols=64 Identities=16% Similarity=0.223 Sum_probs=51.6
Q ss_pred EEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCce-EEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEec
Q psy12968 71 VKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTK-MSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSAL 149 (402)
Q Consensus 71 l~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcK-I~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~ 149 (402)
....+-||. +-||.||||+|.|+|.|+++||++ |-|+ |+-+|.|.+.
T Consensus 685 ~i~~~~i~~------~ki~~vIG~GGktIk~I~eetg~~~Idi~--------------------------ddg~V~I~a~ 732 (891)
T PLN00207 685 LIHIMKVKP------EKVNMIIGSGGKKVKSIIEETGVEAIDTQ--------------------------DDGTVKITAK 732 (891)
T ss_pred eeEEEEcCH------HHHHHHhcCCchhHHHHHHHHCCCccCcC--------------------------CCeeEEEEeC
Confidence 344566764 689999999999999999999998 7654 3478889888
Q ss_pred CChhHHHHHHHHHHHHHHhhcC
Q psy12968 150 APPAEAHARIAYALSELRKYII 171 (402)
Q Consensus 150 ~~~~~A~~rLa~AveeIeklL~ 171 (402)
+ ..+|+.|++.|+.+..
T Consensus 733 d-----~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 733 D-----LSSLEKSKAIISSLTM 749 (891)
T ss_pred C-----HHHHHHHHHHHHHHhc
Confidence 7 3578899988888764
No 24
>KOG2190|consensus
Probab=94.31 E-value=0.2 Score=53.33 Aligned_cols=70 Identities=29% Similarity=0.468 Sum_probs=52.0
Q ss_pred eEEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEec
Q psy12968 70 LVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSAL 149 (402)
Q Consensus 70 kl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~ 149 (402)
....+++||- +-+|-|||=+|..+|.|.++|||+|.|.+. + -|.. .|.+ |.|+++
T Consensus 137 ~v~~RLlVp~------sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~--~-------------lP~s---ter~-V~IsG~ 191 (485)
T KOG2190|consen 137 EVTCRLLVPS------SQVGSLIGKGGSLIKEIREETGAKIRVSSD--M-------------LPNS---TERA-VTISGE 191 (485)
T ss_pred ceEEEEEech------hheeeeeccCcHHHHHHHHhcCceEEecCC--C-------------CCcc---ccee-EEEcCc
Confidence 5778999995 789999999999999999999999999985 1 1322 2333 777765
Q ss_pred CChhHHHHHHHHHHHHHHhhc
Q psy12968 150 APPAEAHARIAYALSELRKYI 170 (402)
Q Consensus 150 ~~~~~A~~rLa~AveeIeklL 170 (402)
. ..+.+|+..|-.+|
T Consensus 192 ~------~av~~al~~Is~~L 206 (485)
T KOG2190|consen 192 P------DAVKKALVQISSRL 206 (485)
T ss_pred h------HHHHHHHHHHHHHH
Confidence 3 33556666665555
No 25
>PRK12704 phosphodiesterase; Provisional
Probab=94.28 E-value=0.42 Score=51.08 Aligned_cols=50 Identities=24% Similarity=0.347 Sum_probs=41.4
Q ss_pred EEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecCChh
Q psy12968 74 KVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALAPPA 153 (402)
Q Consensus 74 KI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~~~~ 153 (402)
-|.+|-+ .+-|||||--|-++|.||.-||+-|.|= +.|=-|+||+.++..
T Consensus 213 ~v~lp~d-----~mkgriigreGrnir~~e~~tgvd~iid-------------------------dtp~~v~ls~~~~~r 262 (520)
T PRK12704 213 VVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIID-------------------------DTPEAVILSGFDPIR 262 (520)
T ss_pred eeecCCc-----hhhcceeCCCcchHHHHHHHhCCeEEEc-------------------------CCCCeEEEecCChhh
Confidence 4567765 5779999999999999999999999983 234569999999865
No 26
>KOG2814|consensus
Probab=93.87 E-value=0.088 Score=53.83 Aligned_cols=61 Identities=26% Similarity=0.444 Sum_probs=46.9
Q ss_pred ceeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecCC--hhHHHHHHHHHH
Q psy12968 86 NFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALAP--PAEAHARIAYAL 163 (402)
Q Consensus 86 NFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~~--~~~A~~rLa~Av 163 (402)
-|+|.|+|=+|.|.|+||+||+|+|.+=-.+..+ =|+-|++-.- ...|..||++++
T Consensus 66 ~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~----------------------~~i~i~~~~~~~V~~a~~Ri~~~i 123 (345)
T KOG2814|consen 66 SFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNK----------------------EEIKIIGISRNCVIQALERIAKLI 123 (345)
T ss_pred HHhhhhhcccchHHHHHHHhhccceEccCCCCCc----------------------ceEEEeehhHHHHHHHHHHHHHHH
Confidence 6899999999999999999999999986433221 2555655443 456788999999
Q ss_pred HHHHh
Q psy12968 164 SELRK 168 (402)
Q Consensus 164 eeIek 168 (402)
....+
T Consensus 124 ds~r~ 128 (345)
T KOG2814|consen 124 DSDRK 128 (345)
T ss_pred Hhhhh
Confidence 88774
No 27
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=93.02 E-value=0.14 Score=49.03 Aligned_cols=54 Identities=19% Similarity=0.244 Sum_probs=42.0
Q ss_pred ceeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecCChhHHHHHHHHHHHH
Q psy12968 86 NFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALAPPAEAHARIAYALSE 165 (402)
Q Consensus 86 NFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~~~~~A~~rLa~Avee 165 (402)
+.+++||||+|.+++.|.++|+|+|.|- . .=.|+|.+.+. ..+..|++.
T Consensus 154 ~~i~~lig~~g~~i~~l~~~~~~~I~ig-~-------------------------NG~VwI~~~~~-----~~~~~a~~~ 202 (235)
T PRK04163 154 VKVPRVIGKKGSMINMLKEETGCDIIVG-Q-------------------------NGRIWIKGPDE-----EDEEIAIEA 202 (235)
T ss_pred HHHHhhcCCCChhHhhhhhhhCcEEEEc-C-------------------------CcEEEEeeCCH-----HHHHHHHHH
Confidence 6799999999999999999999999882 1 13689999873 345566666
Q ss_pred HHhhc
Q psy12968 166 LRKYI 170 (402)
Q Consensus 166 IeklL 170 (402)
|+.+-
T Consensus 203 I~~~e 207 (235)
T PRK04163 203 IKKIE 207 (235)
T ss_pred HHHHH
Confidence 66555
No 28
>KOG2874|consensus
Probab=92.86 E-value=0.062 Score=54.22 Aligned_cols=27 Identities=30% Similarity=0.565 Sum_probs=25.5
Q ss_pred eEEeCCCchhHHHHHHhhCceEEEecC
Q psy12968 89 GKLLGPKGNSLRRLQEETMTKMSILGK 115 (402)
Q Consensus 89 GrILGPRGnTlKrLE~ETGcKI~IRGK 115 (402)
-||+||.|+|||.||--|.|-|.|.|.
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~ 187 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN 187 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc
Confidence 479999999999999999999999984
No 29
>KOG2191|consensus
Probab=92.74 E-value=0.11 Score=53.32 Aligned_cols=38 Identities=29% Similarity=0.509 Sum_probs=34.8
Q ss_pred eEEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEe
Q psy12968 70 LVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSIL 113 (402)
Q Consensus 70 kl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IR 113 (402)
....||+||- +-.|-|||-.|.|+.+||++|||+|.+-
T Consensus 38 ~y~ikvLips------~AaGsIIGKGG~ti~~lqk~tgariklS 75 (402)
T KOG2191|consen 38 QYFLKVLIPS------YAAGSIIGKGGQTIVQLQKETGARIKLS 75 (402)
T ss_pred ceEEEEEeec------ccccceeccchHHHHHHHhccCcEEEec
Confidence 3778999995 7899999999999999999999999885
No 30
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=92.13 E-value=0.13 Score=56.43 Aligned_cols=55 Identities=24% Similarity=0.374 Sum_probs=43.9
Q ss_pred ceeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecCChhHHHHHHHHHHHH
Q psy12968 86 NFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALAPPAEAHARIAYALSE 165 (402)
Q Consensus 86 NFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~~~~~A~~rLa~Avee 165 (402)
+-+|.+|||+|.|+|.|+++||++|-|+ ++-.|.|.+.+ ...+++|.+.
T Consensus 563 ~kI~~vIG~gg~~ik~I~~~~~~~idi~--------------------------d~G~v~i~~~~-----~~~~~~a~~~ 611 (693)
T PRK11824 563 DKIRDVIGPGGKTIREITEETGAKIDIE--------------------------DDGTVKIAATD-----GEAAEAAKER 611 (693)
T ss_pred HHHHHHhcCCchhHHHHHHHHCCccccC--------------------------CCceEEEEccc-----HHHHHHHHHH
Confidence 6689999999999999999999988773 23457777776 3567788888
Q ss_pred HHhhcC
Q psy12968 166 LRKYII 171 (402)
Q Consensus 166 IeklL~ 171 (402)
|+.+..
T Consensus 612 I~~~~~ 617 (693)
T PRK11824 612 IEGITA 617 (693)
T ss_pred HHHhcc
Confidence 877663
No 31
>KOG2191|consensus
Probab=91.16 E-value=1.7 Score=45.02 Aligned_cols=38 Identities=24% Similarity=0.484 Sum_probs=33.1
Q ss_pred EEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEec
Q psy12968 71 VKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILG 114 (402)
Q Consensus 71 l~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRG 114 (402)
++.||.+|.- --|.|||+.|.|+|.+++++||-|.|--
T Consensus 132 kqikivvPNs------tag~iigkggAtiK~~~Eqsga~iqisP 169 (402)
T KOG2191|consen 132 KQIKIVVPNS------TAGMIIGKGGATIKAIQEQSGAWIQISP 169 (402)
T ss_pred ceeEEeccCC------cccceecCCcchHHHHHHhhCcceEecc
Confidence 4578899863 4699999999999999999999999963
No 32
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=90.79 E-value=1.6 Score=46.77 Aligned_cols=54 Identities=24% Similarity=0.330 Sum_probs=42.8
Q ss_pred EEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecCChh
Q psy12968 74 KVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALAPPA 153 (402)
Q Consensus 74 KI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~~~~ 153 (402)
-|.+|-+ .+-|||||--|-++|.||.-||+-|.|= +.|=-|.|+++||.-
T Consensus 207 ~v~lp~d-----~~kgriigreGrnir~~e~~tgvd~iid-------------------------dtp~~v~ls~fdp~r 256 (514)
T TIGR03319 207 VVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIID-------------------------DTPEAVILSGFDPVR 256 (514)
T ss_pred eEEcCCh-----hhhccccCCCcchHHHHHHHhCceEEEc-------------------------CCCCeEEecCCchHH
Confidence 4667765 6779999999999999999999999983 234468999999864
Q ss_pred HHHH
Q psy12968 154 EAHA 157 (402)
Q Consensus 154 ~A~~ 157 (402)
+.-+
T Consensus 257 reia 260 (514)
T TIGR03319 257 REIA 260 (514)
T ss_pred HHHH
Confidence 4333
No 33
>PRK00106 hypothetical protein; Provisional
Probab=90.47 E-value=2 Score=46.53 Aligned_cols=53 Identities=25% Similarity=0.350 Sum_probs=42.8
Q ss_pred EEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecCCh
Q psy12968 73 VKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALAPP 152 (402)
Q Consensus 73 eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~~~ 152 (402)
.-|.+|-+ .+-|||||--|.+++.+|.-||+-|.|= +.|=-|.|+++||.
T Consensus 227 s~v~lp~d-----emkGriIGreGrNir~~E~~tGvdliid-------------------------dtp~~v~lS~fdpv 276 (535)
T PRK00106 227 TTVHLPDD-----NMKGRIIGREGRNIRTLESLTGIDVIID-------------------------DTPEVVVLSGFDPI 276 (535)
T ss_pred eeEEcCCh-----HhhcceeCCCcchHHHHHHHhCceEEEc-------------------------CCCCeEEEeCCChH
Confidence 34667766 5779999999999999999999999983 24456899999985
Q ss_pred hHH
Q psy12968 153 AEA 155 (402)
Q Consensus 153 ~~A 155 (402)
-+.
T Consensus 277 RRe 279 (535)
T PRK00106 277 RRE 279 (535)
T ss_pred HHH
Confidence 443
No 34
>KOG2193|consensus
Probab=87.34 E-value=0.35 Score=51.35 Aligned_cols=38 Identities=21% Similarity=0.654 Sum_probs=32.4
Q ss_pred EEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEec
Q psy12968 71 VKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILG 114 (402)
Q Consensus 71 l~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRG 114 (402)
+-.+++||. -|||-||||.|.|+|-|-+.|-|||-|.-
T Consensus 199 ~PlR~lVpt------qyvgaIIGkeG~TIknItkqTqsriD~hr 236 (584)
T KOG2193|consen 199 WPLRLLVPT------QYVGAIIGKEGATIKNITKQTQSRIDVHR 236 (584)
T ss_pred cceeeeecc------ceeEEEecCCCccccCcchhhhheeeeee
Confidence 344566664 69999999999999999999999999874
No 35
>KOG2190|consensus
Probab=84.49 E-value=0.9 Score=48.48 Aligned_cols=41 Identities=29% Similarity=0.575 Sum_probs=36.1
Q ss_pred ceEEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecC
Q psy12968 69 ILVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGK 115 (402)
Q Consensus 69 vkl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGK 115 (402)
...+.++.||- +|+|.|||..|+.+-.|++.|||.|.|.++
T Consensus 336 ~~v~~~l~vps------~~igciiGk~G~~iseir~~tgA~I~I~~~ 376 (485)
T KOG2190|consen 336 QTVTQRLLVPS------DLIGCIIGKGGAKISEIRQRTGASISILNK 376 (485)
T ss_pred ceeeeeeccCc------cccceeecccccchHHHHHhcCCceEEccc
Confidence 34667788874 899999999999999999999999999874
No 36
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=84.32 E-value=1.1 Score=34.57 Aligned_cols=36 Identities=25% Similarity=0.415 Sum_probs=30.7
Q ss_pred EEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEE
Q psy12968 71 VKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSI 112 (402)
Q Consensus 71 l~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~I 112 (402)
...+|.|+. .-+|+.||.+|.+++.++..+|.+|-|
T Consensus 25 ~~~~v~V~~------~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPD------DQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECc------ccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 455677776 558999999999999999999999876
No 37
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=82.88 E-value=1.8 Score=48.19 Aligned_cols=37 Identities=24% Similarity=0.564 Sum_probs=30.0
Q ss_pred EEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCCC
Q psy12968 75 VLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGS 117 (402)
Q Consensus 75 I~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS 117 (402)
+-|+.+. ++-+|||.|.|.+.|.++|||+|.|--.|+
T Consensus 556 ~~i~~dK------I~dvIG~gGk~I~~I~eetg~~IdieddGt 592 (692)
T COG1185 556 IKIDPDK------IRDVIGPGGKTIKAITEETGVKIDIEDDGT 592 (692)
T ss_pred EccCHHH------HhhccCCcccchhhhhhhhCcEEEecCCCc
Confidence 4466554 556899999999999999999999975554
No 38
>KOG0336|consensus
Probab=81.66 E-value=0.73 Score=49.23 Aligned_cols=29 Identities=34% Similarity=0.736 Sum_probs=26.7
Q ss_pred CceeeEEeCCCchhHHHHHHhhCceEEEe
Q psy12968 85 FNFVGKLLGPKGNSLRRLQEETMTKMSIL 113 (402)
Q Consensus 85 fNFVGrILGPRGnTlKrLE~ETGcKI~IR 113 (402)
-||||.+||=.|+.+|+||..|+++|.|-
T Consensus 55 s~mvg~vigrggskik~iq~~tnt~iqii 83 (629)
T KOG0336|consen 55 SEMVGKVIGRGGSKIKRIQNDTNTRIQII 83 (629)
T ss_pred hhhhheeeccCcchhhhhhcccceeEEEe
Confidence 48999999999999999999999988763
No 39
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=76.84 E-value=1.4 Score=35.33 Aligned_cols=32 Identities=28% Similarity=0.576 Sum_probs=26.2
Q ss_pred CCCceeeEEeCCCchhHHHHHHhh-CceEEEec
Q psy12968 83 PRFNFVGKLLGPKGNSLRRLQEET-MTKMSILG 114 (402)
Q Consensus 83 P~fNFVGrILGPRGnTlKrLE~ET-GcKI~IRG 114 (402)
++++-+|.++|.+|...|.|+++. |-||.|=.
T Consensus 14 ~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 14 PNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp TTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred CCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 889999999999999999999999 77776654
No 40
>PRK12705 hypothetical protein; Provisional
Probab=74.55 E-value=5.3 Score=43.11 Aligned_cols=35 Identities=23% Similarity=0.442 Sum_probs=29.8
Q ss_pred EEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEe
Q psy12968 74 KVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSIL 113 (402)
Q Consensus 74 KI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IR 113 (402)
-|.+|-+ .+-|||||--|..++.+|..||+-|.|=
T Consensus 201 ~v~lp~d-----emkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 201 VVPIPSD-----AMKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred eeecCCh-----HhhccccCccchhHHHHHHhhCCceEec
Confidence 4556654 6779999999999999999999998884
No 41
>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=72.61 E-value=13 Score=35.64 Aligned_cols=41 Identities=10% Similarity=0.123 Sum_probs=31.5
Q ss_pred CceEEEEEEccCCCCCCCceeeEEeCCCchhHHHH--------HHhhCceEEEe
Q psy12968 68 PILVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRL--------QEETMTKMSIL 113 (402)
Q Consensus 68 pvkl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrL--------E~ETGcKI~IR 113 (402)
.+.+...|+|.-+. --|-|||-+|.++|+| |+-.||||.+.
T Consensus 218 ~~~i~~~i~v~~~s-----~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l~ 266 (270)
T TIGR00436 218 LLKIHALISVERES-----QKKIIIGKNGSMIKAIGIAARKDILELFDCDVFLE 266 (270)
T ss_pred eEEEEEEEEECcCC-----ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 35577778888764 4589999999999986 66678888763
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=70.14 E-value=4 Score=29.95 Aligned_cols=24 Identities=29% Similarity=0.454 Sum_probs=21.0
Q ss_pred eeeEEeCCCchhHHHHHHhhCceE
Q psy12968 87 FVGKLLGPKGNSLRRLQEETMTKM 110 (402)
Q Consensus 87 FVGrILGPRGnTlKrLE~ETGcKI 110 (402)
-.|+++|.+|.+++.||..++-.+
T Consensus 35 ~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 35 QPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CCceEECCCCccHHHHHHHHHHHc
Confidence 369999999999999999998554
No 43
>KOG1960|consensus
Probab=68.96 E-value=7 Score=41.69 Aligned_cols=62 Identities=16% Similarity=0.142 Sum_probs=44.6
Q ss_pred EEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecCChhHHHHHHHHHHHHHH
Q psy12968 90 KLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALAPPAEAHARIAYALSELR 167 (402)
Q Consensus 90 rILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~~~~~A~~rLa~AveeIe 167 (402)
+-+==||.|+-.||.+||+.|..||+--.- +|.. + -..+++|-.+|.+.+. .-+++||+.|+
T Consensus 107 ~~~~TRg~~~d~Ie~~~G~~~~~RGs~~~~------El~~--v---g~~~~pLv~hI~~~T~-----Ei~~~Ai~RIk 168 (531)
T KOG1960|consen 107 KATSTRGTSYDHIEGITGTTSASRGSAPAP------ELPP--V---GSSEGPLVDHIPPSTA-----EITSKAIERIK 168 (531)
T ss_pred cceeccchhHHhhhhhccceeeccCCCCCc------cCCC--C---CCCCCcceeecCCccH-----HHHHHHHhhCc
Confidence 344459999999999999999999974422 2322 1 1257899999998874 34667777776
No 44
>PRK15494 era GTPase Era; Provisional
Probab=65.14 E-value=20 Score=36.07 Aligned_cols=41 Identities=10% Similarity=0.296 Sum_probs=31.8
Q ss_pred CceEEEEEEccCCCCCCCceeeEEeCCCchhHHHH--------HHhhCceEEEe
Q psy12968 68 PILVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRL--------QEETMTKMSIL 113 (402)
Q Consensus 68 pvkl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrL--------E~ETGcKI~IR 113 (402)
.+.+...|+|.-+. --|-|||-+|..+|+| |+-.||||.+.
T Consensus 270 ~~~i~~~i~v~~~s-----qk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 270 SVKINQVIVVSRES-----YKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred eEEEEEEEEECCCC-----ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 35567788888764 4589999999999986 67778887765
No 45
>KOG1924|consensus
Probab=62.23 E-value=16 Score=42.01 Aligned_cols=17 Identities=6% Similarity=0.094 Sum_probs=8.3
Q ss_pred chhHHHHHHhhCceEEEe
Q psy12968 96 GNSLRRLQEETMTKMSIL 113 (402)
Q Consensus 96 GnTlKrLE~ETGcKI~IR 113 (402)
-...|-||++.- .|.+.
T Consensus 422 pqYykLIEecIS-qIvlH 438 (1102)
T KOG1924|consen 422 PQYYKLIEECIS-QIVLH 438 (1102)
T ss_pred HHHHHHHHHHHH-HHHHh
Confidence 345566665543 44443
No 46
>PRK00089 era GTPase Era; Reviewed
Probab=60.47 E-value=31 Score=33.00 Aligned_cols=41 Identities=15% Similarity=0.301 Sum_probs=31.3
Q ss_pred CceEEEEEEccCCCCCCCceeeEEeCCCchhHHHH--------HHhhCceEEEe
Q psy12968 68 PILVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRL--------QEETMTKMSIL 113 (402)
Q Consensus 68 pvkl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrL--------E~ETGcKI~IR 113 (402)
.+++...|+|.-+.+ .+-|||-+|.++|+| |+-+||||.+.
T Consensus 223 ~~~i~~~i~v~~~~~-----k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 223 LVRIEATIYVERDSQ-----KGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred eEEEEEEEEEccCCc-----eeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 355677788877644 689999999999976 66678887764
No 47
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=60.47 E-value=6.9 Score=35.26 Aligned_cols=29 Identities=21% Similarity=0.448 Sum_probs=27.2
Q ss_pred ceeeEEeCCCchhHHHHHHhhCceEEEec
Q psy12968 86 NFVGKLLGPKGNSLRRLQEETMTKMSILG 114 (402)
Q Consensus 86 NFVGrILGPRGnTlKrLE~ETGcKI~IRG 114 (402)
+.+|..+|.+|...|.|++..|-||-|=.
T Consensus 41 ~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 41 GDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 57899999999999999999999999887
No 48
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=57.30 E-value=8.6 Score=38.06 Aligned_cols=29 Identities=28% Similarity=0.348 Sum_probs=26.9
Q ss_pred CceeeEEeCCCchhHHHHHHhhCceEEEe
Q psy12968 85 FNFVGKLLGPKGNSLRRLQEETMTKMSIL 113 (402)
Q Consensus 85 fNFVGrILGPRGnTlKrLE~ETGcKI~IR 113 (402)
.++|-|+||.+|+-++.|.+.|+|.|.|=
T Consensus 154 p~kVpRvig~~~sm~~~l~~~~~~~I~VG 182 (239)
T COG1097 154 PSKVPRVIGKKGSMLNMLKEKTGCEIIVG 182 (239)
T ss_pred hhhcceEecCCCcHHHHhhhhcCeEEEEe
Confidence 47888999999999999999999999983
No 49
>KOG1924|consensus
Probab=50.72 E-value=31 Score=39.79 Aligned_cols=8 Identities=25% Similarity=0.214 Sum_probs=4.0
Q ss_pred ccCCCCCC
Q psy12968 129 KEGDPKNA 136 (402)
Q Consensus 129 ~sgdP~~e 136 (402)
++.||++.
T Consensus 440 ~~~DPdf~ 447 (1102)
T KOG1924|consen 440 TGMDPDFK 447 (1102)
T ss_pred CCCCCCcc
Confidence 44456543
No 50
>PF08926 DUF1908: Domain of unknown function (DUF1908); InterPro: IPR015022 This domain is found in microtubule-associated serine/threonine-protein kinases. ; GO: 0000287 magnesium ion binding, 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1V9V_A.
Probab=50.33 E-value=5.3 Score=40.35 Aligned_cols=32 Identities=41% Similarity=0.668 Sum_probs=0.0
Q ss_pred CCCCCCCC----CCCCccccCCCCCCCCCCccccCccccc
Q psy12968 322 RTGGSGWK----SSSGYAEHHSSSRSKSSAPIRSSSSEKV 357 (402)
Q Consensus 322 ~~~~~~wk----~~~~y~~~~~~~~~~~~~~~~~~~~~~~ 357 (402)
+..||.|- |||||+|.++|+.-.| ..||.|++
T Consensus 28 ~~D~RRWSlASLPSSGYgT~~~sS~vSS----scSSQE~L 63 (282)
T PF08926_consen 28 RADGRRWSLASLPSSGYGTNTPSSTVSS----SCSSQERL 63 (282)
T ss_dssp ----------------------------------------
T ss_pred ccCCCccccccCCCCCCCcCCCCCeeec----chhhHHHh
Confidence 57899997 8999999987654322 24566766
No 51
>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=49.79 E-value=10 Score=30.23 Aligned_cols=21 Identities=33% Similarity=0.531 Sum_probs=18.9
Q ss_pred eeEEeCCCchhHHHHHHhhCc
Q psy12968 88 VGKLLGPKGNSLRRLQEETMT 108 (402)
Q Consensus 88 VGrILGPRGnTlKrLE~ETGc 108 (402)
.|+|||-+|.|++-||--++.
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~ 55 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANL 55 (77)
T ss_pred CCeEECCCCccHHHHHHHHHH
Confidence 599999999999999988773
No 52
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=45.51 E-value=27 Score=36.63 Aligned_cols=71 Identities=17% Similarity=0.244 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHhhhhcCCCCCCCCccccccCCCceEEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhh-CceEEEec
Q psy12968 36 YTLKLLDDEINKAMASNKKKYDSPYLDLFREKPILVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEET-MTKMSILG 114 (402)
Q Consensus 36 ha~rLLd~EI~RV~~~~~p~~~~~y~D~~~ekpvkl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ET-GcKI~IRG 114 (402)
...+|+..||--|..+.- .-..+-|+.- ...||-|= ..-|+++-||..+|++|..++.|.++. |=||-|=-
T Consensus 209 ~v~~Lfe~EVPEI~dG~V-----eIk~IARepG--~RtKVAV~-S~d~~iDPvGacIG~~G~rI~~I~~eL~gEkIDvI~ 280 (374)
T PRK12328 209 FLEALLELEVPEIKDGEV-----IIIHSARIPG--ERAKVALF-SNNPNIDPIGATVGVKGVRINAVSKELNGENIDCIE 280 (374)
T ss_pred HHHHHHHHhCccccCCeE-----EEEEEeccCc--ceeEEEEE-cCCCCCChHHhhcCCCcchHHHHHHHhCCCeEEEEE
Confidence 678999999887775420 0011122221 12244433 234899999999999999999999999 77777654
No 53
>KOG1067|consensus
Probab=44.79 E-value=16 Score=40.59 Aligned_cols=53 Identities=19% Similarity=0.201 Sum_probs=39.1
Q ss_pred eeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecCChhHHHHHHHHHHHHHH
Q psy12968 88 VGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALAPPAEAHARIAYALSELR 167 (402)
Q Consensus 88 VGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~~~~~A~~rLa~AveeIe 167 (402)
+..+|||.|-.+|+||.|||+.-+| ++=|+-|-|.++ +-|.+|.+.|.
T Consensus 608 ~~~lIGp~G~~~kki~~EtGai~~v---------------------------De~t~~i~A~~~-----~am~~Ak~~I~ 655 (760)
T KOG1067|consen 608 RATLIGPGGVLKKKIEVETGAISQV---------------------------DEGTFSIFAPTQ-----AAMEEAKEFID 655 (760)
T ss_pred hheeecCccceeeeEeeeccceeee---------------------------cCceEEEEecCH-----HHHHHHHHHHH
Confidence 5679999999999999999943222 334677777773 45778888887
Q ss_pred hhcCC
Q psy12968 168 KYIIP 172 (402)
Q Consensus 168 klL~P 172 (402)
.+..-
T Consensus 656 ~i~~~ 660 (760)
T KOG1067|consen 656 GIIKD 660 (760)
T ss_pred HHhcC
Confidence 76653
No 54
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=42.17 E-value=25 Score=36.54 Aligned_cols=33 Identities=27% Similarity=0.559 Sum_probs=30.1
Q ss_pred CCCCceeeEEeCCCchhHHHHHHhh-CceEEEec
Q psy12968 82 HPRFNFVGKLLGPKGNSLRRLQEET-MTKMSILG 114 (402)
Q Consensus 82 yP~fNFVGrILGPRGnTlKrLE~ET-GcKI~IRG 114 (402)
-|+++-||..+|++|..++.+.++. |=||-|=-
T Consensus 241 ~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv~ 274 (362)
T PRK12327 241 NPNVDAKGACVGPKGQRVQNIVSELKGEKIDIID 274 (362)
T ss_pred CCCCCchheeECCCChhHHHHHHHhCCCeEEEEE
Confidence 4999999999999999999999999 88887764
No 55
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=41.85 E-value=20 Score=34.52 Aligned_cols=38 Identities=29% Similarity=0.413 Sum_probs=31.6
Q ss_pred EEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecC
Q psy12968 72 KVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGK 115 (402)
Q Consensus 72 ~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGK 115 (402)
.+.|.||-+ =+|-|+|+.|.+.|.||+.|||+|.|=.+
T Consensus 9 ~~~v~iPk~------R~~~lig~~g~v~k~ie~~~~~~~~iD~~ 46 (194)
T COG1094 9 SEAVKIPKD------RIGVLIGKWGEVKKAIEEKTGVKLRIDSK 46 (194)
T ss_pred eeeeecCch------hheeeecccccchHHHHhhcCeEEEEECC
Confidence 345666643 37999999999999999999999999876
No 56
>KOG2113|consensus
Probab=39.74 E-value=24 Score=36.74 Aligned_cols=39 Identities=26% Similarity=0.348 Sum_probs=31.8
Q ss_pred CCceEEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEE
Q psy12968 67 KPILVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMS 111 (402)
Q Consensus 67 kpvkl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~ 111 (402)
-+..+.+.|-+| +-||+.|.|++|-+.|.|+++|.+.|.
T Consensus 22 ~p~nvt~sv~vp------s~~v~~ivg~qg~kikalr~KTqtyi~ 60 (394)
T KOG2113|consen 22 IGQNVTESVEVP------SEHVAEIVGRQGCKIKALRAKTQTYIK 60 (394)
T ss_pred CCCccceeeecC------cccceeecccCccccchhhhhhcceec
Confidence 345666666666 459999999999999999999998875
No 57
>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=39.36 E-value=32 Score=35.41 Aligned_cols=40 Identities=28% Similarity=0.507 Sum_probs=32.8
Q ss_pred EEEccCCCCCCCceeeEEeCCCchhHHHHHHhh-CceEEEec
Q psy12968 74 KVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEET-MTKMSILG 114 (402)
Q Consensus 74 KI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ET-GcKI~IRG 114 (402)
||-|=-. -|+++-||..+|++|..++.+.++. |=||-|=-
T Consensus 232 KvAV~s~-~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~ 272 (341)
T TIGR01953 232 KIAVESN-DENIDPVGACVGPKGSRIQAISKELNGEKIDIIE 272 (341)
T ss_pred EEEEEcC-CCCCCcceeeECCCCchHHHHHHHhCCCeEEEEE
Confidence 4444333 4999999999999999999999999 88887764
No 58
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=38.68 E-value=45 Score=35.79 Aligned_cols=71 Identities=21% Similarity=0.372 Sum_probs=47.8
Q ss_pred HHHHHHHHHHHhhhhcCCCCCCCCccccccCCCceEEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhh-CceEEEec
Q psy12968 36 YTLKLLDDEINKAMASNKKKYDSPYLDLFREKPILVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEET-MTKMSILG 114 (402)
Q Consensus 36 ha~rLLd~EI~RV~~~~~p~~~~~y~D~~~ekpvkl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ET-GcKI~IRG 114 (402)
.+.+|+..||--|..+.- .-..+-|+.- ...||-|= -.-|++.-||..+|++|+.++.|.++. |=||-|=-
T Consensus 203 ~l~~Lf~~EVPEI~~G~i-----eIk~iaR~pG--~RaKvAV~-s~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~ 274 (470)
T PRK09202 203 FLKKLFEQEVPEIADGLI-----EIKAIARDPG--SRAKIAVK-SNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIIL 274 (470)
T ss_pred HHHHHHHHhCcccccCeE-----EEEEEeecCc--ceeEEEEE-cCCCCCChhHccCCCCCchHHHHHHHhCCCeEEEEE
Confidence 678899998877765420 0011112221 12244443 344899999999999999999999999 88887754
No 59
>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=38.08 E-value=24 Score=26.53 Aligned_cols=19 Identities=16% Similarity=0.144 Sum_probs=15.7
Q ss_pred hHHHHHHhhCceEEEecCC
Q psy12968 98 SLRRLQEETMTKMSILGKG 116 (402)
Q Consensus 98 TlKrLE~ETGcKI~IRGKG 116 (402)
.+++||++.|+++.+|..+
T Consensus 33 ~i~~LE~~lg~~Lf~r~~~ 51 (60)
T PF00126_consen 33 QIKQLEEELGVPLFERSGR 51 (60)
T ss_dssp HHHHHHHHHTS-SEEECSS
T ss_pred HHHHHHHHhCCeEEEECCC
Confidence 5799999999999999654
No 60
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=36.05 E-value=27 Score=33.25 Aligned_cols=34 Identities=21% Similarity=0.419 Sum_probs=29.8
Q ss_pred CCCceeeEEeCCCchhHHHHHHhhCceEEEecCC
Q psy12968 83 PRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKG 116 (402)
Q Consensus 83 P~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKG 116 (402)
++.+-+|..+|++|..+|.|.++.|=||-|=--.
T Consensus 82 ~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s 115 (190)
T COG0195 82 VKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS 115 (190)
T ss_pred cCcCchhhhccCCChHHHHHHHHhCCceEEEEeC
Confidence 4568899999999999999999999888887654
No 61
>COG1159 Era GTPase [General function prediction only]
Probab=35.95 E-value=96 Score=31.83 Aligned_cols=41 Identities=12% Similarity=0.322 Sum_probs=30.2
Q ss_pred CCceEEEEEEccCCCCCCCceeeEEeCCCchhHHHH--------HHhhCceEEE
Q psy12968 67 KPILVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRL--------QEETMTKMSI 112 (402)
Q Consensus 67 kpvkl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrL--------E~ETGcKI~I 112 (402)
.-+++..-|+|+-+.. -|-|||-+|..+|+| |+-.||||.+
T Consensus 225 ~~~~I~a~I~Ver~sQ-----K~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 225 GLLKIHATIYVERESQ-----KGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred CeEEEEEEEEEecCCc-----cceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 3467777788887644 488999999999876 5555666654
No 62
>KOG0334|consensus
Probab=35.15 E-value=31 Score=40.32 Aligned_cols=76 Identities=18% Similarity=0.235 Sum_probs=54.9
Q ss_pred EccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCCCCCCChhhHhhhccCCCCCCCCCCCcEEEEEecCChhHH
Q psy12968 76 LVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQVSALAPPAEA 155 (402)
Q Consensus 76 ~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~kd~kkEe~LR~sgdP~~ehlnEpLHVlIsA~~~~~~A 155 (402)
-+++++||. |.-+++.+=.- |.+|.+.|+|.|.+||+=--... +| ...++-||.+|++.+
T Consensus 901 ~~~inD~Pq-~~r~~vt~~~~--L~~i~e~~~~~it~rg~f~~~gk----------~p--~~gErklyl~ve~~~----- 960 (997)
T KOG0334|consen 901 ELEINDFPQ-NARWRVTYKEA--LLRISEPTAAGITTRGKFNPPGK----------EP--KPGERKLYLLVEGPD----- 960 (997)
T ss_pred eccccccch-hcceeeechhh--hhhccCccccceeeccccCCCCC----------CC--CCcchhhhhhhhcch-----
Confidence 466788885 68888887644 99999999999999997543322 23 125678999999765
Q ss_pred HHHHHHHHHHHHhhcC
Q psy12968 156 HARIAYALSELRKYII 171 (402)
Q Consensus 156 ~~rLa~AveeIeklL~ 171 (402)
+.-+..|+++++.+|.
T Consensus 961 e~~vqra~~e~~r~l~ 976 (997)
T KOG0334|consen 961 ELSVQRAIEELERLLE 976 (997)
T ss_pred hHHHHHHHHHHHHHHH
Confidence 3456677877776443
No 63
>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=34.78 E-value=31 Score=31.40 Aligned_cols=37 Identities=27% Similarity=0.495 Sum_probs=31.1
Q ss_pred EEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEec
Q psy12968 74 KVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILG 114 (402)
Q Consensus 74 KI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRG 114 (402)
||.+=|++ +-+|..+|++|...|.|++..|=||-|=.
T Consensus 34 riifvV~~----g~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 34 RVVFVVKE----GEMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred EEEEEEcC----CCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 55555553 57999999999999999999999999887
No 64
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=33.55 E-value=30 Score=32.39 Aligned_cols=24 Identities=13% Similarity=0.228 Sum_probs=19.9
Q ss_pred hhHHHHHHhhCceEEEecCCCCCC
Q psy12968 97 NSLRRLQEETMTKMSILGKGSMRD 120 (402)
Q Consensus 97 nTlKrLE~ETGcKI~IRGKGS~kd 120 (402)
..+|+||++.|+++.+||+|..-.
T Consensus 35 ~~i~~LE~~lg~~Lf~R~r~i~lT 58 (294)
T PRK13348 35 QRIKALEESLGQPLLVRGRPCRPT 58 (294)
T ss_pred HHHHHHHHHhCceeeecCCCCccC
Confidence 468999999999999999865433
No 65
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=33.02 E-value=34 Score=32.14 Aligned_cols=73 Identities=21% Similarity=0.233 Sum_probs=48.5
Q ss_pred ChHHHHHHHHH--------HHHhhhhcC-CC--CCCCCccccccCCCceEEEEEEccCCCCCCCceeeEEeCCCchhHHH
Q psy12968 33 SHSYTLKLLDD--------EINKAMASN-KK--KYDSPYLDLFREKPILVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRR 101 (402)
Q Consensus 33 ~F~ha~rLLd~--------EI~RV~~~~-~p--~~~~~y~D~~~ekpvkl~eKI~IPvkeyP~fNFVGrILGPRGnTlKr 101 (402)
.+|.|++||+. +|.|+--.. .. ..+..|.+.+ ..-.+|.+=|++ +. |..||++|.+.|+
T Consensus 15 lC~~c~~~~~~G~v~~~dv~i~~~l~~l~~~~~l~~~~~~k~~-----~~ddrvIfvV~~----gd-g~aIGk~G~~ik~ 84 (166)
T PRK06418 15 LCPRCQSLLDSGEVTELDVEVSKVLLKLEEDKELKDVEYKKAY-----EVDDLVILLVTS----GP-RIPIGKGGKIAKA 84 (166)
T ss_pred cChhHHhHhhcCceEEeehHHHHHHHHhhccccccCceEEEEE-----EeCCEEEEEEeC----CC-cccccccchHHHH
Confidence 47889999875 566654322 11 1223343332 233455555542 44 9999999999999
Q ss_pred HHHhhCceEEEecC
Q psy12968 102 LQEETMTKMSILGK 115 (402)
Q Consensus 102 LE~ETGcKI~IRGK 115 (402)
||+..|=+|.|=.-
T Consensus 85 l~~~lgk~VevVE~ 98 (166)
T PRK06418 85 LSRKLGKKVRVVEK 98 (166)
T ss_pred HHHHhCCcEEEEEc
Confidence 99999999999884
No 66
>KOG2208|consensus
Probab=32.66 E-value=19 Score=40.70 Aligned_cols=38 Identities=32% Similarity=0.578 Sum_probs=30.3
Q ss_pred eEEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEe
Q psy12968 70 LVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSIL 113 (402)
Q Consensus 70 kl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IR 113 (402)
.++..+.||. -|-+-|+||+|.++++++++++|-|.+-
T Consensus 708 ~~~~~~~~p~------~~~~~~ig~~g~~~r~~~~~~~~~~~~~ 745 (753)
T KOG2208|consen 708 LVTKEIEIPR------SLHRYLIGPKGSNLRQLEKEFNVNIVVP 745 (753)
T ss_pred ceeeEEeccH------HHhhhccCCCCccHHHHHHHhccceecC
Confidence 4455566665 4567899999999999999999998764
No 67
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=31.58 E-value=64 Score=35.54 Aligned_cols=41 Identities=20% Similarity=0.385 Sum_probs=34.0
Q ss_pred EEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEecCCCCC
Q psy12968 73 VKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMR 119 (402)
Q Consensus 73 eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IRGKGS~k 119 (402)
.-|+||-+ .++++||-+|..+++||+..|-+|.|+-.+.-.
T Consensus 488 avv~vpe~------~i~~vigk~g~~i~~ie~klgi~I~v~~~e~~~ 528 (604)
T COG1855 488 AVVKVPEK------YIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEE 528 (604)
T ss_pred EEEEeCHH------HhhHHhhcccchHHHHHHHhCCceEEEEccccc
Confidence 34677754 577899999999999999999999999876533
No 68
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=29.54 E-value=12 Score=29.38 Aligned_cols=20 Identities=35% Similarity=0.574 Sum_probs=18.3
Q ss_pred eeEEeCCCchhHHHHHHhhC
Q psy12968 88 VGKLLGPKGNSLRRLQEETM 107 (402)
Q Consensus 88 VGrILGPRGnTlKrLE~ETG 107 (402)
.|+|||-+|.|++-||--++
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 79999999999999997765
No 69
>KOG2236|consensus
Probab=28.86 E-value=4e+02 Score=29.23 Aligned_cols=30 Identities=20% Similarity=-0.044 Sum_probs=20.2
Q ss_pred CCCCCCCCCCcEEEEEecCChhHHHHHHHH
Q psy12968 132 DPKNAHLVEDLHVQVSALAPPAEAHARIAY 161 (402)
Q Consensus 132 dP~~ehlnEpLHVlIsA~~~~~~A~~rLa~ 161 (402)
|.-|.+..|.+-=.++-.+.+.+|.+|..+
T Consensus 305 DASn~~DeE~p~~e~dfSDDEkEaeak~~k 334 (483)
T KOG2236|consen 305 DASNRYDEEIPPREQDFSDDEKEAEAKQMK 334 (483)
T ss_pred cccccccccCChhhhccchHHHHHHHHHHH
Confidence 667777777776667666766666666543
No 70
>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=27.85 E-value=35 Score=31.98 Aligned_cols=24 Identities=8% Similarity=0.108 Sum_probs=19.6
Q ss_pred hHHHHHHhhCceEEEecCCCCCCC
Q psy12968 98 SLRRLQEETMTKMSILGKGSMRDR 121 (402)
Q Consensus 98 TlKrLE~ETGcKI~IRGKGS~kd~ 121 (402)
.+|+||++.|+++.+|++|-.-..
T Consensus 35 ~I~~LE~~lg~~Lf~R~r~~~lT~ 58 (292)
T TIGR03298 35 RIKALEERLGQPLLVRTQPCRATE 58 (292)
T ss_pred HHHHHHHHhCchheecCCCCcCCH
Confidence 479999999999999997654433
No 71
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=27.40 E-value=1.7e+02 Score=28.54 Aligned_cols=30 Identities=7% Similarity=0.169 Sum_probs=18.4
Q ss_pred CcEEEEEecCC-hhHHHHHHHHHHHHHHhhc
Q psy12968 141 DLHVQVSALAP-PAEAHARIAYALSELRKYI 170 (402)
Q Consensus 141 pLHVlIsA~~~-~~~A~~rLa~AveeIeklL 170 (402)
-+|+-|=-.+- .++..+.|...++.|.+.+
T Consensus 169 ~i~~~IG~~~m~~e~i~eNi~a~l~~i~~~~ 199 (230)
T PRK05424 169 IIHAPIGKVSFDAEKLKENLKALIDAIKKAK 199 (230)
T ss_pred EEEEEEeCCCCCHHHHHHHHHHHHHHHHHhC
Confidence 47887755443 4556666766666666544
No 72
>KOG2113|consensus
Probab=27.40 E-value=29 Score=36.15 Aligned_cols=31 Identities=32% Similarity=0.575 Sum_probs=28.1
Q ss_pred CceeeEEeCCCchhHHHHHHhhCceEEEecC
Q psy12968 85 FNFVGKLLGPKGNSLRRLQEETMTKMSILGK 115 (402)
Q Consensus 85 fNFVGrILGPRGnTlKrLE~ETGcKI~IRGK 115 (402)
+-+||++.||.|+|+|++|+.|+.-|.--++
T Consensus 123 ~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 123 LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred ceeeeeccccccCccchheecccceEeeecc
Confidence 6899999999999999999999998876664
No 73
>PRK02821 hypothetical protein; Provisional
Probab=27.07 E-value=36 Score=28.20 Aligned_cols=22 Identities=23% Similarity=0.421 Sum_probs=17.9
Q ss_pred ceeeEEeCCCchhHHHHHHhhC
Q psy12968 86 NFVGKLLGPKGNSLRRLQEETM 107 (402)
Q Consensus 86 NFVGrILGPRGnTlKrLE~ETG 107 (402)
.=+|||||=+|.|++-|-.-..
T Consensus 40 ~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 40 DDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred hhCcceeCCCCchHHHHHHHHH
Confidence 4589999999999998865443
No 74
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=26.92 E-value=48 Score=35.66 Aligned_cols=41 Identities=20% Similarity=0.369 Sum_probs=33.4
Q ss_pred EEEEccCCCCCCCceeeEEeCCCchhHHHHHHhh-CceEEEec
Q psy12968 73 VKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEET-MTKMSILG 114 (402)
Q Consensus 73 eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ET-GcKI~IRG 114 (402)
.||-|=- .-|+++-||..+|++|..++.|.++. |=||-|=-
T Consensus 265 tKVAV~S-~d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~ 306 (449)
T PRK12329 265 TKIAVDT-LERDVDPVGACIGARGSRIQAVVNELRGEKIDVIR 306 (449)
T ss_pred eEEEEEc-CCCCCChhhccCCCCcchHHHHHHHhCCCeEEEEE
Confidence 3554433 23899999999999999999999999 88887764
No 75
>TIGR01169 rplA_bact ribosomal protein L1, bacterial/chloroplast. This model describes bacterial (and chloroplast) ribosomal protein L1. The apparent mitochondrial L1 is sufficiently diverged to be the subject of a separate model.
Probab=26.71 E-value=1e+02 Score=29.90 Aligned_cols=29 Identities=10% Similarity=0.291 Sum_probs=17.0
Q ss_pred CcEEEEEecCC-hhHHHHHHHHHHHHHHhh
Q psy12968 141 DLHVQVSALAP-PAEAHARIAYALSELRKY 169 (402)
Q Consensus 141 pLHVlIsA~~~-~~~A~~rLa~AveeIekl 169 (402)
-+|+-|=-.+- .++..+.|...++.|.+.
T Consensus 168 ~i~~~VG~~~m~~e~i~eNi~a~l~~i~~~ 197 (227)
T TIGR01169 168 NIHASIGKVSFDSEKLKENLEALLDAIKKA 197 (227)
T ss_pred EEEEEEecCCCCHHHHHHHHHHHHHHHHHh
Confidence 47777754443 455556666666655543
No 76
>PRK00468 hypothetical protein; Provisional
Probab=25.34 E-value=41 Score=27.61 Aligned_cols=19 Identities=21% Similarity=0.559 Sum_probs=16.0
Q ss_pred eeEEeCCCchhHHHHHHhh
Q psy12968 88 VGKLLGPKGNSLRRLQEET 106 (402)
Q Consensus 88 VGrILGPRGnTlKrLE~ET 106 (402)
+|||||=+|.|++-|-.-.
T Consensus 41 ~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CcceecCCChhHHHHHHHH
Confidence 6999999999999886543
No 77
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=24.64 E-value=56 Score=34.13 Aligned_cols=30 Identities=23% Similarity=0.290 Sum_probs=27.6
Q ss_pred ceeeEEeCCCchhHHHHHHhhCceEEEecC
Q psy12968 86 NFVGKLLGPKGNSLRRLQEETMTKMSILGK 115 (402)
Q Consensus 86 NFVGrILGPRGnTlKrLE~ETGcKI~IRGK 115 (402)
|-+--|+||.|..++.||+.+|+.|.-||.
T Consensus 24 ~~~~~l~G~~~~~l~l~e~~~gv~i~~rG~ 53 (348)
T COG1702 24 NELVALFGPTDTNLSLLEIALGVSIVARGE 53 (348)
T ss_pred hhhhhhcCCCCccHHHHHHHhCcEEEeCCc
Confidence 667789999999999999999999999984
No 78
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=24.46 E-value=55 Score=30.91 Aligned_cols=24 Identities=8% Similarity=0.110 Sum_probs=19.8
Q ss_pred hhHHHHHHhhCceEEEecCCCCCC
Q psy12968 97 NSLRRLQEETMTKMSILGKGSMRD 120 (402)
Q Consensus 97 nTlKrLE~ETGcKI~IRGKGS~kd 120 (402)
..+|+||++.||+++.|++|-.-.
T Consensus 35 ~~I~~LE~~lg~~LF~R~~~~~lT 58 (294)
T PRK03635 35 QRIKALEERVGQVLLVRTQPCRPT 58 (294)
T ss_pred HHHHHHHHHhCceeeecCCCCccC
Confidence 358999999999999999765443
No 79
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=24.22 E-value=62 Score=30.69 Aligned_cols=19 Identities=16% Similarity=0.094 Sum_probs=16.6
Q ss_pred hhHHHHHHhhCceEEEecC
Q psy12968 97 NSLRRLQEETMTKMSILGK 115 (402)
Q Consensus 97 nTlKrLE~ETGcKI~IRGK 115 (402)
..+|+||++.|+.+++|..
T Consensus 35 ~~I~~LE~~lg~~LF~R~~ 53 (300)
T PRK11074 35 YTVRQLEEWLAVPLFERRH 53 (300)
T ss_pred HHHHHHHHHhCCeeEEeCC
Confidence 4689999999999999943
No 80
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=24.07 E-value=57 Score=30.65 Aligned_cols=17 Identities=12% Similarity=0.176 Sum_probs=15.6
Q ss_pred hHHHHHHhhCceEEEec
Q psy12968 98 SLRRLQEETMTKMSILG 114 (402)
Q Consensus 98 TlKrLE~ETGcKI~IRG 114 (402)
.+|+||++.||+++.|.
T Consensus 35 ~I~~LE~~lG~~LF~R~ 51 (275)
T PRK03601 35 RIRQLENQLGVNLFTRH 51 (275)
T ss_pred HHHHHHHHhCCceEEEC
Confidence 58999999999999994
No 81
>PRK01064 hypothetical protein; Provisional
Probab=23.13 E-value=59 Score=26.94 Aligned_cols=20 Identities=20% Similarity=0.679 Sum_probs=17.7
Q ss_pred eeEEeCCCchhHHHHHHhhC
Q psy12968 88 VGKLLGPKGNSLRRLQEETM 107 (402)
Q Consensus 88 VGrILGPRGnTlKrLE~ETG 107 (402)
+|++||=+|.|++.|..-..
T Consensus 41 ~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred ceEEECCCCccHHHHHHHHH
Confidence 69999999999999987654
No 82
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=22.97 E-value=66 Score=29.92 Aligned_cols=23 Identities=17% Similarity=0.167 Sum_probs=19.1
Q ss_pred hhHHHHHHhhCceEEEecCCCCC
Q psy12968 97 NSLRRLQEETMTKMSILGKGSMR 119 (402)
Q Consensus 97 nTlKrLE~ETGcKI~IRGKGS~k 119 (402)
..+|+||++.||++.+|+.+...
T Consensus 40 ~~i~~LE~~lg~~Lf~R~~r~~~ 62 (294)
T PRK09986 40 IHIKELEDQLGTPLFIRHSRSVV 62 (294)
T ss_pred HHHHHHHHHhCCeeEeeCCCcee
Confidence 46899999999999999854443
No 83
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=22.53 E-value=72 Score=30.11 Aligned_cols=22 Identities=14% Similarity=0.215 Sum_probs=19.3
Q ss_pred hHHHHHHhhCceEEEecCCCCC
Q psy12968 98 SLRRLQEETMTKMSILGKGSMR 119 (402)
Q Consensus 98 TlKrLE~ETGcKI~IRGKGS~k 119 (402)
.+|+||++.||++.+|.++.+.
T Consensus 39 ~i~~LE~~lG~~LF~R~~r~~~ 60 (302)
T PRK09791 39 SIQELEEGLAAQLFFRRSKGVT 60 (302)
T ss_pred HHHHHHHHhCCeEEEEcCCCce
Confidence 5899999999999999877654
No 84
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=22.52 E-value=67 Score=31.15 Aligned_cols=19 Identities=5% Similarity=0.113 Sum_probs=16.6
Q ss_pred hhHHHHHHhhCceEEEecC
Q psy12968 97 NSLRRLQEETMTKMSILGK 115 (402)
Q Consensus 97 nTlKrLE~ETGcKI~IRGK 115 (402)
..+|+||++.|+++.+|..
T Consensus 35 ~~Ik~LE~~lg~~LF~R~~ 53 (317)
T PRK15421 35 HQFSDLEQRLGFRLFVRKS 53 (317)
T ss_pred HHHHHHHHHhCCEEEEecC
Confidence 4589999999999999953
No 85
>KOG2192|consensus
Probab=22.47 E-value=1.7e+02 Score=30.21 Aligned_cols=39 Identities=21% Similarity=0.473 Sum_probs=32.6
Q ss_pred ceEEEEEEccCCCCCCCceeeEEeCCCchhHHHHHHhhCceEEEe
Q psy12968 69 ILVKVKVLVPVKEHPRFNFVGKLLGPKGNSLRRLQEETMTKMSIL 113 (402)
Q Consensus 69 vkl~eKI~IPvkeyP~fNFVGrILGPRGnTlKrLE~ETGcKI~IR 113 (402)
-++..+|++--|. -|-|+|-.|..+|+|-.+.++.|+|-
T Consensus 46 ~r~e~ril~~sk~------agavigkgg~nik~lr~d~na~v~vp 84 (390)
T KOG2192|consen 46 SRVELRILLQSKN------AGAVIGKGGKNIKALRTDYNASVSVP 84 (390)
T ss_pred cceeEEEEEeccc------ccceeccccccHHHHhhhccceeecc
Confidence 4566677777653 58999999999999999999999875
No 86
>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=22.25 E-value=18 Score=32.87 Aligned_cols=18 Identities=39% Similarity=0.656 Sum_probs=15.2
Q ss_pred CCCCCCceeeEEeCCCch
Q psy12968 80 KEHPRFNFVGKLLGPKGN 97 (402)
Q Consensus 80 keyP~fNFVGrILGPRGn 97 (402)
+-.|..+.+|+||||||.
T Consensus 101 ~~m~~l~~Lg~iLGprGl 118 (141)
T TIGR01170 101 DIVPELAQLRRLLGPKGL 118 (141)
T ss_pred HHHHHHHHhhcccccCcC
Confidence 456778899999999986
No 87
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=22.15 E-value=68 Score=30.82 Aligned_cols=21 Identities=19% Similarity=0.235 Sum_probs=17.6
Q ss_pred hhHHHHHHhhCceEEEe-cCCC
Q psy12968 97 NSLRRLQEETMTKMSIL-GKGS 117 (402)
Q Consensus 97 nTlKrLE~ETGcKI~IR-GKGS 117 (402)
..+|+||++.||++.+| |||-
T Consensus 35 ~~ik~LE~~lg~~Lf~R~~r~~ 56 (313)
T PRK12684 35 KAIIELEDELGVEIFTRHGKRL 56 (313)
T ss_pred HHHHHHHHHhCCeeEEEcCCcc
Confidence 35899999999999999 4553
No 88
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=22.07 E-value=52 Score=27.40 Aligned_cols=17 Identities=24% Similarity=0.780 Sum_probs=15.2
Q ss_pred eeEEeCCCchhHHHHHH
Q psy12968 88 VGKLLGPKGNSLRRLQE 104 (402)
Q Consensus 88 VGrILGPRGnTlKrLE~ 104 (402)
+|++||=+|.|++.|-.
T Consensus 41 ~GkvIGk~GRti~AIRT 57 (76)
T COG1837 41 MGKVIGKQGRTIQAIRT 57 (76)
T ss_pred ccceecCCChhHHHHHH
Confidence 89999999999998853
No 89
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=21.88 E-value=70 Score=30.77 Aligned_cols=21 Identities=24% Similarity=0.363 Sum_probs=17.9
Q ss_pred hhHHHHHHhhCceEEEe-cCCC
Q psy12968 97 NSLRRLQEETMTKMSIL-GKGS 117 (402)
Q Consensus 97 nTlKrLE~ETGcKI~IR-GKGS 117 (402)
..+|+||++.|+++++| |+|-
T Consensus 35 ~~I~~LE~~lg~~Lf~R~~r~~ 56 (309)
T PRK12683 35 KQIKDLEDELGVEIFIRRGKRL 56 (309)
T ss_pred HHHHHHHHHhCCeeEeeCCCCc
Confidence 35899999999999999 5664
No 90
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=21.21 E-value=77 Score=30.20 Aligned_cols=20 Identities=25% Similarity=0.182 Sum_probs=17.2
Q ss_pred hHHHHHHhhCceEEEec-CCC
Q psy12968 98 SLRRLQEETMTKMSILG-KGS 117 (402)
Q Consensus 98 TlKrLE~ETGcKI~IRG-KGS 117 (402)
.+|+||++.||++++|. +|-
T Consensus 36 ~I~~LE~~lg~~LF~R~~~~~ 56 (309)
T PRK12682 36 AIIELEEELGIEIFIRHGKRL 56 (309)
T ss_pred HHHHHHHHhCCeeEEECCCCc
Confidence 58999999999999995 554
No 91
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=20.68 E-value=78 Score=29.49 Aligned_cols=19 Identities=16% Similarity=0.167 Sum_probs=16.9
Q ss_pred hhHHHHHHhhCceEEEecC
Q psy12968 97 NSLRRLQEETMTKMSILGK 115 (402)
Q Consensus 97 nTlKrLE~ETGcKI~IRGK 115 (402)
..+|+||++.|+++.+|+.
T Consensus 34 ~~i~~LE~~lg~~Lf~R~~ 52 (296)
T PRK11242 34 QQIRQLEESLGVQLFDRSG 52 (296)
T ss_pred HHHHHHHHHhCCeeEeEcC
Confidence 4689999999999999963
No 92
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=20.45 E-value=49 Score=29.83 Aligned_cols=26 Identities=19% Similarity=0.370 Sum_probs=22.6
Q ss_pred eeeEEeCCCchhHHHHHHhhCceEEE
Q psy12968 87 FVGKLLGPKGNSLRRLQEETMTKMSI 112 (402)
Q Consensus 87 FVGrILGPRGnTlKrLE~ETGcKI~I 112 (402)
-+|++||.+|.+++.++.-+|-++-|
T Consensus 109 d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 109 DKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred ccchhhCCCCHHHHHHHHHhCCccCC
Confidence 47999999999999999999876644
Done!