Query psy1580
Match_columns 267
No_of_seqs 149 out of 371
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 21:39:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1580.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1580hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1588|consensus 100.0 1.9E-50 4E-55 368.1 14.0 140 5-153 75-214 (259)
2 KOG0119|consensus 100.0 2.8E-48 6.1E-53 377.0 14.5 180 9-200 124-311 (554)
3 cd02395 SF1_like-KH Splicing f 100.0 6.3E-41 1.4E-45 275.9 12.8 120 23-152 1-120 (120)
4 COG5176 MSL5 Splicing factor ( 100.0 1.1E-30 2.4E-35 233.7 7.2 134 10-154 135-269 (269)
5 cd00105 KH-I K homology RNA-bi 98.4 6.6E-07 1.4E-11 63.5 6.6 62 24-117 2-63 (64)
6 cd02393 PNPase_KH Polynucleoti 98.4 1.2E-06 2.7E-11 64.0 7.2 59 23-118 3-61 (61)
7 smart00322 KH K homology RNA-b 98.4 2.6E-06 5.6E-11 59.3 7.7 66 22-121 3-68 (69)
8 PF00013 KH_1: KH domain syndr 98.2 1.1E-06 2.3E-11 62.7 2.8 60 23-117 1-60 (60)
9 PF13014 KH_3: KH domain 98.1 1.8E-06 3.8E-11 58.6 3.0 28 38-65 1-28 (43)
10 cd02396 PCBP_like_KH K homolog 98.1 1E-05 2.2E-10 59.2 6.5 63 24-117 2-64 (65)
11 cd02394 vigilin_like_KH K homo 98.1 6.6E-06 1.4E-10 59.0 4.7 60 24-117 2-61 (62)
12 KOG1960|consensus 97.8 1.5E-05 3.3E-10 78.2 3.4 90 19-124 207-296 (531)
13 COG5082 AIR1 Arginine methyltr 97.5 3E-05 6.4E-10 69.3 0.4 52 145-196 55-120 (190)
14 TIGR03665 arCOG04150 arCOG0415 97.4 0.00029 6.2E-09 61.3 5.2 53 38-123 99-151 (172)
15 PRK13763 putative RNA-processi 97.3 0.00036 7.8E-09 61.1 5.6 53 38-123 105-157 (180)
16 PRK13763 putative RNA-processi 97.0 0.0012 2.5E-08 57.9 5.4 65 23-123 4-71 (180)
17 TIGR03665 arCOG04150 arCOG0415 97.0 0.00064 1.4E-08 59.1 3.6 57 37-123 7-65 (172)
18 COG1094 Predicted RNA-binding 96.9 0.0024 5.1E-08 57.4 6.0 54 38-124 112-165 (194)
19 TIGR02696 pppGpp_PNP guanosine 96.7 0.0041 8.9E-08 65.1 7.5 72 13-123 571-642 (719)
20 KOG1676|consensus 96.6 0.0037 8E-08 63.9 6.2 74 19-122 136-209 (600)
21 PTZ00368 universal minicircle 96.4 0.0027 5.9E-08 53.2 3.0 43 151-193 78-122 (148)
22 TIGR03591 polynuc_phos polyrib 96.3 0.0055 1.2E-07 63.7 5.6 62 24-122 553-614 (684)
23 KOG1676|consensus 96.1 0.011 2.5E-07 60.4 6.1 63 37-124 239-301 (600)
24 KOG2193|consensus 95.8 0.003 6.6E-08 62.8 0.6 38 27-64 279-316 (584)
25 PTZ00368 universal minicircle 95.6 0.016 3.5E-07 48.6 4.2 43 151-193 53-96 (148)
26 PF00098 zf-CCHC: Zinc knuckle 95.5 0.0093 2E-07 34.4 1.7 16 176-191 2-17 (18)
27 PRK04163 exosome complex RNA-b 95.3 0.03 6.6E-07 50.9 5.1 68 37-138 154-221 (235)
28 PLN00207 polyribonucleotide nu 95.0 0.016 3.6E-07 62.0 3.0 64 23-123 686-750 (891)
29 KOG4400|consensus 95.0 0.019 4.2E-07 52.4 2.9 39 153-194 146-184 (261)
30 KOG2190|consensus 94.5 0.16 3.5E-06 51.3 8.5 82 8-121 123-206 (485)
31 PRK11824 polynucleotide phosph 94.3 0.031 6.7E-07 58.3 3.0 56 37-123 563-618 (693)
32 KOG2874|consensus 93.6 0.038 8.3E-07 52.7 2.0 27 40-66 161-187 (356)
33 KOG2814|consensus 93.3 0.12 2.6E-06 50.1 4.7 31 37-67 66-96 (345)
34 COG5082 AIR1 Arginine methyltr 92.8 0.091 2E-06 47.3 2.9 42 153-196 100-142 (190)
35 PF13696 zf-CCHC_2: Zinc knuck 92.6 0.075 1.6E-06 35.1 1.6 21 174-194 8-28 (32)
36 KOG2191|consensus 92.5 0.2 4.4E-06 48.8 5.1 37 22-64 39-75 (402)
37 KOG2193|consensus 92.2 0.26 5.5E-06 49.6 5.4 71 22-123 199-269 (584)
38 KOG1960|consensus 90.6 0.19 4.2E-06 50.1 2.8 62 41-118 107-168 (531)
39 KOG4400|consensus 89.9 0.25 5.3E-06 45.2 2.7 40 153-193 121-162 (261)
40 TIGR03319 YmdA_YtgF conserved 89.6 0.84 1.8E-05 46.3 6.5 63 25-122 207-269 (514)
41 KOG2191|consensus 89.1 1.9 4.1E-05 42.3 8.1 38 22-65 132-169 (402)
42 PF00098 zf-CCHC: Zinc knuckle 88.8 0.31 6.8E-06 28.0 1.6 17 152-168 2-18 (18)
43 COG1185 Pnp Polyribonucleotide 88.7 0.61 1.3E-05 49.0 4.9 61 26-123 556-616 (692)
44 PRK00106 hypothetical protein; 88.7 0.87 1.9E-05 46.6 5.9 64 25-123 228-291 (535)
45 cd02134 NusA_KH NusA_K homolog 88.4 0.94 2E-05 33.0 4.4 36 22-63 25-60 (61)
46 PF13917 zf-CCHC_3: Zinc knuck 88.3 0.26 5.6E-06 34.4 1.3 18 175-192 5-22 (42)
47 PF15288 zf-CCHC_6: Zinc knuck 87.5 0.47 1E-05 32.9 2.2 20 175-194 2-23 (40)
48 PRK12704 phosphodiesterase; Pr 86.9 3.3 7.2E-05 42.1 8.8 48 25-102 213-260 (520)
49 KOG0336|consensus 86.9 0.34 7.3E-06 49.0 1.6 30 35-64 54-83 (629)
50 PF13917 zf-CCHC_3: Zinc knuck 83.8 0.64 1.4E-05 32.4 1.4 20 148-167 2-21 (42)
51 KOG2190|consensus 83.2 1.4 3.1E-05 44.6 4.2 42 19-66 335-376 (485)
52 PF12353 eIF3g: Eukaryotic tra 82.9 0.63 1.4E-05 39.1 1.3 21 173-194 105-125 (128)
53 KOG2113|consensus 81.8 1.4 3.1E-05 42.9 3.4 49 8-62 12-60 (394)
54 PF13184 KH_5: NusA-like KH do 81.7 0.76 1.6E-05 34.7 1.2 33 34-66 14-47 (69)
55 cd02409 KH-II KH-II (K homolo 74.8 2.8 6.1E-05 29.1 2.4 24 38-61 35-58 (68)
56 PF14392 zf-CCHC_4: Zinc knuck 72.4 1.7 3.6E-05 30.5 0.7 24 169-192 26-49 (49)
57 smart00343 ZnF_C2HC zinc finge 69.8 2.5 5.5E-05 25.6 1.1 17 176-192 1-17 (26)
58 PRK08406 transcription elongat 68.4 3.7 8.1E-05 34.9 2.1 30 37-66 41-70 (140)
59 cd02414 jag_KH jag_K homology 64.9 4.3 9.3E-05 30.6 1.7 22 39-60 35-56 (77)
60 PF13696 zf-CCHC_2: Zinc knuck 61.1 4.7 0.0001 26.7 1.1 20 150-169 8-27 (32)
61 PRK12705 hypothetical protein; 60.7 15 0.00033 37.6 5.2 30 34-63 205-234 (508)
62 COG1097 RRP4 RNA-binding prote 60.4 8.9 0.00019 35.8 3.2 28 37-64 155-182 (239)
63 PRK04023 DNA polymerase II lar 60.1 13 0.00028 41.3 4.7 48 151-200 627-676 (1121)
64 KOG1067|consensus 59.6 7.5 0.00016 40.8 2.8 54 38-123 607-660 (760)
65 PF07295 DUF1451: Protein of u 53.8 5.6 0.00012 34.3 0.7 29 149-183 111-139 (146)
66 KOG0122|consensus 52.3 5.7 0.00012 37.5 0.6 24 173-197 118-141 (270)
67 PRK12327 nusA transcription el 50.6 15 0.00033 35.9 3.2 42 24-66 233-275 (362)
68 PRK06418 transcription elongat 48.9 11 0.00024 33.3 1.8 52 11-67 48-99 (166)
69 COG0195 NusA Transcription elo 47.8 14 0.0003 33.2 2.2 34 34-67 82-115 (190)
70 TIGR01953 NusA transcription t 47.3 21 0.00045 34.7 3.6 42 24-66 231-273 (341)
71 KOG0334|consensus 46.8 15 0.00033 40.4 2.8 77 27-123 901-977 (997)
72 TIGR01952 nusA_arch NusA famil 46.0 16 0.00034 31.4 2.2 38 25-66 34-71 (141)
73 KOG2208|consensus 45.3 9 0.00019 40.9 0.8 38 22-65 709-746 (753)
74 KOG2113|consensus 43.2 21 0.00045 35.1 2.8 31 36-66 123-153 (394)
75 PRK11032 hypothetical protein; 43.0 10 0.00022 33.4 0.6 29 149-183 123-151 (160)
76 COG1094 Predicted RNA-binding 42.5 22 0.00047 32.4 2.6 28 39-66 19-46 (194)
77 KOG0720|consensus 41.7 38 0.00083 34.7 4.5 78 103-189 273-363 (490)
78 PF13083 KH_4: KH domain; PDB: 39.1 5.6 0.00012 29.4 -1.4 20 39-58 40-59 (73)
79 PF11598 COMP: Cartilage oligo 35.8 40 0.00088 23.9 2.6 41 108-157 4-45 (45)
80 PRK12328 nusA transcription el 34.2 26 0.00057 34.7 2.0 42 24-66 239-281 (374)
81 COG2956 Predicted N-acetylgluc 33.6 21 0.00046 35.3 1.3 21 148-168 352-373 (389)
82 PRK12329 nusA transcription el 33.3 33 0.00071 34.9 2.5 43 23-66 264-307 (449)
83 PRK02821 hypothetical protein; 31.5 28 0.0006 27.0 1.4 22 37-58 40-61 (77)
84 KOG3799|consensus 30.9 56 0.0012 28.6 3.2 46 132-183 31-98 (169)
85 KOG1244|consensus 30.7 34 0.00073 33.1 2.0 19 132-150 208-226 (336)
86 PRK00468 hypothetical protein; 30.4 29 0.00064 26.7 1.3 19 38-56 40-58 (75)
87 PF00381 PTS-HPr: PTS HPr comp 30.4 1E+02 0.0023 23.2 4.4 59 51-121 23-81 (84)
88 PRK01064 hypothetical protein; 30.3 38 0.00083 26.3 1.9 20 39-58 41-60 (78)
89 TIGR01170 rplA_mito ribosomal 30.0 9.5 0.0002 32.6 -1.6 23 26-48 96-118 (141)
90 PF14787 zf-CCHC_5: GAG-polypr 29.7 43 0.00093 22.8 1.9 19 176-194 4-22 (36)
91 KOG4718|consensus 29.6 52 0.0011 30.6 3.0 61 112-183 164-225 (235)
92 KOG4165|consensus 29.2 65 0.0014 32.1 3.7 41 37-102 190-232 (433)
93 PF00126 HTH_1: Bacterial regu 28.6 41 0.00089 23.8 1.8 19 49-67 33-51 (60)
94 PRK08406 transcription elongat 28.4 26 0.00056 29.8 0.8 26 38-63 109-134 (140)
95 PRK14714 DNA polymerase II lar 28.1 82 0.0018 36.1 4.7 44 150-194 667-716 (1337)
96 PRK09202 nusA transcription el 28.0 43 0.00094 33.9 2.4 42 24-66 233-275 (470)
97 COG1837 Predicted RNA-binding 26.4 38 0.00083 26.4 1.3 18 38-55 40-57 (76)
98 COG1702 PhoH Phosphate starvat 26.4 49 0.0011 32.6 2.4 30 37-66 24-53 (348)
99 PRK13782 phosphocarrier protei 26.0 1.8E+02 0.0039 22.0 5.0 56 54-121 26-81 (82)
100 PRK04023 DNA polymerase II lar 25.8 52 0.0011 36.8 2.6 118 45-184 551-673 (1121)
101 KOG2192|consensus 24.9 1.3E+02 0.0029 29.2 4.9 38 21-64 47-84 (390)
102 KOG0341|consensus 24.7 36 0.00078 34.8 1.1 22 176-197 572-594 (610)
103 PRK05424 rplA 50S ribosomal pr 24.5 2.2E+02 0.0048 26.1 6.2 31 91-121 168-199 (230)
104 PRK13348 chromosome replicatio 24.1 50 0.0011 29.4 1.9 24 48-71 35-58 (294)
105 TIGR01169 rplA_bact ribosomal 22.7 17 0.00036 33.3 -1.5 13 36-48 122-134 (227)
106 COG1198 PriA Primosomal protei 21.5 73 0.0016 34.2 2.7 39 152-194 437-482 (730)
107 KOG2192|consensus 21.4 99 0.0021 30.1 3.3 40 18-64 312-351 (390)
108 COG1997 RPL43A Ribosomal prote 21.2 1.2E+02 0.0027 24.5 3.3 33 144-182 29-61 (89)
109 COG5179 TAF1 Transcription ini 20.3 1E+02 0.0022 33.2 3.4 26 173-198 936-963 (968)
110 CHL00129 rpl1 ribosomal protei 20.2 35 0.00076 31.4 0.0 10 39-48 126-135 (229)
111 TIGR00436 era GTP-binding prot 20.2 2E+02 0.0043 26.0 5.0 39 20-63 219-265 (270)
112 COG5179 TAF1 Transcription ini 20.1 68 0.0015 34.5 2.1 19 150-168 937-957 (968)
No 1
>KOG1588|consensus
Probab=100.00 E-value=1.9e-50 Score=368.15 Aligned_cols=140 Identities=54% Similarity=0.857 Sum_probs=132.8
Q ss_pred CCCCCCccccCCCCCcceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCC
Q psy1580 5 EPHGRKMVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDP 84 (267)
Q Consensus 5 ~~~~~~~~d~~~~kp~k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp 84 (267)
+++.+.|.|+++.+++|+++||+|||++||+||||||||||||||+||||++|||||+||||||+||..+|++|| +||
T Consensus 75 ~~~~~~~~~~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR--~~p 152 (259)
T KOG1588|consen 75 EPEELPYADVYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELR--GDP 152 (259)
T ss_pred CchhcccccCccCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhh--cCc
Confidence 678888889999999999999999999999999999999999999999999999999999999999999999999 499
Q ss_pred ccCCCCCccEEEEEecCChhHHHHHHHHHHHHHHHhhcCCCcCCCCcchhHHHHHHHHHHHHhhCCCCC
Q psy1580 85 KFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQILKEDGGA 153 (267)
Q Consensus 85 ~~~hl~EpLHVlIsa~~~~~~a~~rl~~Av~~I~~lL~P~~~s~~~d~~DelK~~QL~ELA~lNGt~r~ 153 (267)
+|+||++||||+|++++++++|+.||++|+++|++||+|.. +|+.|++||+|||++||||..
T Consensus 153 ~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~P~~-------e~~dk~~QL~ELa~lngt~~~ 214 (259)
T KOG1588|consen 153 GYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLVPDH-------EDEDKREQLRELAILNGTYLR 214 (259)
T ss_pred chHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcCCCC-------CCchHHHHHHHHhhcCCcccc
Confidence 99999999999999999999999999999999999999954 455599999999999999543
No 2
>KOG0119|consensus
Probab=100.00 E-value=2.8e-48 Score=377.01 Aligned_cols=180 Identities=25% Similarity=0.395 Sum_probs=155.0
Q ss_pred CCccccCCCCCc-ceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccC
Q psy1580 9 RKMVDITRDKPI-KVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFL 87 (267)
Q Consensus 9 ~~~~d~~~~kp~-k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~ 87 (267)
..|-.+.+||+. +++.||||||++||+||||||||||||+|||+||+||||||+||||||+|+++. + +.|..|.
T Consensus 124 P~fkpP~DYk~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~----~-~~d~~~~ 198 (554)
T KOG0119|consen 124 PGFKPPADYKPPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKG----R-SDDLSYI 198 (554)
T ss_pred cCCCCCcccCcccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEecccccccccc----C-Ccccccc
Confidence 467788899998 999999999999999999999999999999999999999999999999999872 2 1233332
Q ss_pred -CCCCccEEEEEecCChhHHHHHHHHHHHHHHHhhcCCCcCCCCcchhHHHHHHHHHHHHhhCCCC------CCCCCCCC
Q psy1580 88 -HLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQILKEDGG------AASCSESS 160 (267)
Q Consensus 88 -hl~EpLHVlIsa~~~~~~a~~rl~~Av~~I~~lL~P~~~s~~~d~~DelK~~QL~ELA~lNGt~r------~~~cg~~~ 160 (267)
..+||||++|+|++ +++|++|++.|+.||.-.. +++|+++++|+.||+|||.+|||+| |.+||+++
T Consensus 199 ~~~~epLH~~Isadt-----~eki~~Ai~vienli~~av--~~~e~~n~l~~~Qlrela~lNgt~r~~d~~~c~~cg~~~ 271 (554)
T KOG0119|consen 199 PKENEPLHCLISADT-----QEKIKKAIAVIENLIQSAV--SVPEGQNDLKRLQLRELARLNGTLRDDDNRACRNCGSTG 271 (554)
T ss_pred cccccceeEEEecch-----HHHHHHHHHHHHHHHHhhc--cCccccccccHHHHHHHHHhCCCCCccccccccccCCCc
Confidence 46899999999986 6999999999999997533 3459999999999999999999987 56899999
Q ss_pred CCCCCCccccccCCCccccCCCCCCCCCCCCCCCccCCcc
Q psy1580 161 ESSVNNPLLYAENTSPVENLTPPEYTLVDPAFNRIQPATE 200 (267)
Q Consensus 161 h~~~~cp~~~~~~~~~c~~cg~~gh~t~dc~~~~~~~~~~ 200 (267)
|+.|+||.++......|.+||..||+++||++++.+..-+
T Consensus 272 H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~~~q~~~~~ 311 (554)
T KOG0119|consen 272 HKQYDCPGRIPNTTNVCKICGPLGHISIDCKVNDQQMPMS 311 (554)
T ss_pred cccccCCcccccccccccccCCcccccccCCCcccccchh
Confidence 9999999974333228999999999999999996554333
No 3
>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=6.3e-41 Score=275.86 Aligned_cols=120 Identities=44% Similarity=0.730 Sum_probs=110.7
Q ss_pred EEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCC
Q psy1580 23 TIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAP 102 (267)
Q Consensus 23 ~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~ 102 (267)
++|||||+++||+|||||+||||+|+|+|+||++|||+|.|||+||+++++++.+++. |.|+|++|||||+|+|+++
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 4799999999999999999999999999999999999999999999999999877763 7899999999999999986
Q ss_pred hhHHHHHHHHHHHHHHHhhcCCCcCCCCcchhHHHHHHHHHHHHhhCCCC
Q psy1580 103 PAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQILKEDGG 152 (267)
Q Consensus 103 ~~~a~~rl~~Av~~I~~lL~P~~~s~~~d~~DelK~~QL~ELA~lNGt~r 152 (267)
+.+++++|+++|+.||.+..+ ++.|++|++||+|||++||||+
T Consensus 78 ---~~e~~~~A~~~I~~ll~~~~~----~~~~~~k~~ql~~la~~nGt~~ 120 (120)
T cd02395 78 ---PEEALAKAVEAIEELLKPAIE----GGNDELKREQLRELALLNGTYR 120 (120)
T ss_pred ---HHHHHHHHHHHHHHHhccCCC----ccchHHHHHHHHHHHHhcccCC
Confidence 568899999999999998751 2489999999999999999986
No 4
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.96 E-value=1.1e-30 Score=233.69 Aligned_cols=134 Identities=23% Similarity=0.350 Sum_probs=109.5
Q ss_pred Ccccc-CCCCCcceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCC
Q psy1580 10 KMVDI-TRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLH 88 (267)
Q Consensus 10 ~~~d~-~~~kp~k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~h 88 (267)
.|+-+ +.-+|.|.+.||||||++||+.||||+||||||+|+|+||+.|+|||.|||+||+|+++-..++. +..-.
T Consensus 135 ~fv~p~dy~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p----~~~~N 210 (269)
T COG5176 135 RFVLPNDYIRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTP----ESLKN 210 (269)
T ss_pred cccCCccccCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCc----hhhhh
Confidence 44444 44679999999999999999999999999999999999999999999999999999987543322 12224
Q ss_pred CCCccEEEEEecCChhHHHHHHHHHHHHHHHhhcCCCcCCCCcchhHHHHHHHHHHHHhhCCCCCC
Q psy1580 89 LLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQILKEDGGAA 154 (267)
Q Consensus 89 l~EpLHVlIsa~~~~~~a~~rl~~Av~~I~~lL~P~~~s~~~d~~DelK~~QL~ELA~lNGt~r~~ 154 (267)
..++||+||+++. +.++.+++..+..++.-...+| ++++++|+-||++||.+|||++++
T Consensus 211 ~e~~lhcLI~ads-----edki~~~ik~~~n~I~~a~~~P--eGqnDlkR~qlr~la~lngtlr~d 269 (269)
T COG5176 211 AEAVLHCLIEADS-----EDKICRLIKSQLNAIREARRNP--EGQNDLKRFQLRWLAHLNGTLRAD 269 (269)
T ss_pred hHHhHHHHhhcch-----hhhHHHHHHHHHHHHHHHhcCC--cccchHHHHHHHHHHHhcceecCC
Confidence 6789999999974 5778888776666554433332 899999999999999999999863
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=98.45 E-value=6.6e-07 Score=63.52 Aligned_cols=62 Identities=32% Similarity=0.482 Sum_probs=48.7
Q ss_pred EEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCCh
Q psy1580 24 IRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPP 103 (267)
Q Consensus 24 eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~ 103 (267)
.+|.||. +++|+||||+|+++++|+++|||+|.|...++ ...+-.|.|.+.
T Consensus 2 ~~i~ip~------~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~--------------------~~~~~~v~i~G~--- 52 (64)
T cd00105 2 ERVLVPS------SLVGRIIGKGGSTIKEIREETGAKIKIPDSGS--------------------GSEERIVTITGT--- 52 (64)
T ss_pred EEEEEch------hhcceeECCCCHHHHHHHHHHCCEEEEcCCCC--------------------CCCceEEEEEcC---
Confidence 4688885 78999999999999999999999999986542 124455888876
Q ss_pred hHHHHHHHHHHHHH
Q psy1580 104 AEAHARIAYALAEV 117 (267)
Q Consensus 104 ~~a~~rl~~Av~~I 117 (267)
.+.+..|..+|
T Consensus 53 ---~~~v~~a~~~i 63 (64)
T cd00105 53 ---PEAVEKAKELI 63 (64)
T ss_pred ---HHHHHHHHHHh
Confidence 36777777665
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=98.40 E-value=1.2e-06 Score=63.95 Aligned_cols=59 Identities=20% Similarity=0.290 Sum_probs=45.7
Q ss_pred EEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCC
Q psy1580 23 TIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAP 102 (267)
Q Consensus 23 ~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~ 102 (267)
.+.|.||. .++|+|||++|+|+|+||++|||+|.|--. -.|.|++.+.
T Consensus 3 ~~~i~Ip~------~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~--------------------------g~v~I~G~~~ 50 (61)
T cd02393 3 IETMKIPP------DKIRDVIGPGGKTIKKIIEETGVKIDIEDD--------------------------GTVYIAASDK 50 (61)
T ss_pred EEEEEeCh------hheeeeECCCchHHHHHHHHHCCEEEeCCC--------------------------CEEEEEeCCH
Confidence 35677773 689999999999999999999999986320 1388898653
Q ss_pred hhHHHHHHHHHHHHHH
Q psy1580 103 PAEAHARIAYALAEVR 118 (267)
Q Consensus 103 ~~~a~~rl~~Av~~I~ 118 (267)
+.++.|.++|+
T Consensus 51 -----~~v~~A~~~I~ 61 (61)
T cd02393 51 -----EAAEKAKKMIE 61 (61)
T ss_pred -----HHHHHHHHHhC
Confidence 67788877763
No 7
>smart00322 KH K homology RNA-binding domain.
Probab=98.35 E-value=2.6e-06 Score=59.30 Aligned_cols=66 Identities=35% Similarity=0.529 Sum_probs=50.6
Q ss_pred eEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecC
Q psy1580 22 VTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFA 101 (267)
Q Consensus 22 ~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~ 101 (267)
...+|.||. +++|+|||++|.+++.|+++|||+|.+.+.++ ..-.|.|.+.
T Consensus 3 ~~~~i~i~~------~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~----------------------~~~~v~i~g~- 53 (69)
T smart00322 3 VTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS----------------------EERVVEITGP- 53 (69)
T ss_pred eEEEEEEcc------hhcceeECCCchHHHHHHHHHCCEEEECCCCC----------------------CccEEEEEcC-
Confidence 456788875 78999999999999999999999999975432 2334777775
Q ss_pred ChhHHHHHHHHHHHHHHHhh
Q psy1580 102 PPAEAHARIAYALAEVRRFL 121 (267)
Q Consensus 102 ~~~~a~~rl~~Av~~I~~lL 121 (267)
...+..|...|.+.+
T Consensus 54 -----~~~v~~a~~~i~~~~ 68 (69)
T smart00322 54 -----PENVEKAAELILEIL 68 (69)
T ss_pred -----HHHHHHHHHHHHHHh
Confidence 256777777776654
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=98.19 E-value=1.1e-06 Score=62.73 Aligned_cols=60 Identities=28% Similarity=0.431 Sum_probs=47.0
Q ss_pred EEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCC
Q psy1580 23 TIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAP 102 (267)
Q Consensus 23 ~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~ 102 (267)
+.+|.|| ..++|+|||++|.++|+||++|||+|.|... ++.-.|.|++.
T Consensus 1 T~~i~vp------~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-----------------------~~~~~v~I~G~-- 49 (60)
T PF00013_consen 1 TERIEVP------SSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-----------------------DERDIVTISGS-- 49 (60)
T ss_dssp EEEEEEE------HHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-----------------------TEEEEEEEEES--
T ss_pred CEEEEEC------HHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-----------------------CCcEEEEEEeC--
Confidence 3577888 3689999999999999999999999999443 13346788883
Q ss_pred hhHHHHHHHHHHHHH
Q psy1580 103 PAEAHARIAYALAEV 117 (267)
Q Consensus 103 ~~~a~~rl~~Av~~I 117 (267)
.+.+++|.++|
T Consensus 50 ----~~~v~~A~~~I 60 (60)
T PF00013_consen 50 ----PEQVEKAKKMI 60 (60)
T ss_dssp ----HHHHHHHHHHH
T ss_pred ----HHHHHHHHhhC
Confidence 37788887765
No 9
>PF13014 KH_3: KH domain
Probab=98.15 E-value=1.8e-06 Score=58.57 Aligned_cols=28 Identities=32% Similarity=0.725 Sum_probs=26.9
Q ss_pred eeeEEeCCCcchHHHHHHhhCceEEEee
Q psy1580 38 FVGKLLGPKGNSLKRLQEDTMTRMAILG 65 (267)
Q Consensus 38 FvGrILGPrG~TlKrLE~eTgcKI~IRG 65 (267)
|+|+|||++|.|+++|+++|||+|.|--
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 7899999999999999999999999976
No 10
>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=98.11 E-value=1e-05 Score=59.22 Aligned_cols=63 Identities=24% Similarity=0.418 Sum_probs=46.3
Q ss_pred EEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCCh
Q psy1580 24 IRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPP 103 (267)
Q Consensus 24 eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~ 103 (267)
.+++||. +.+|+|||.+|.++++|+++|||+|.|--... + ..++. -|.|++.
T Consensus 2 ~r~~ip~------~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~---------------~---~~~~r-~v~I~G~--- 53 (65)
T cd02396 2 LRLLVPS------SQAGSIIGKGGSTIKEIREETGAKIRVSKSVL---------------P---GSTER-VVTISGK--- 53 (65)
T ss_pred EEEEECH------HHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC---------------C---CCCce-EEEEEeC---
Confidence 4678883 68999999999999999999999999943211 0 11233 3777775
Q ss_pred hHHHHHHHHHHHHH
Q psy1580 104 AEAHARIAYALAEV 117 (267)
Q Consensus 104 ~~a~~rl~~Av~~I 117 (267)
.+.+.+|+.+|
T Consensus 54 ---~~~v~~A~~~I 64 (65)
T cd02396 54 ---PSAVQKALLLI 64 (65)
T ss_pred ---HHHHHHHHHhh
Confidence 36788888776
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=98.06 E-value=6.6e-06 Score=59.00 Aligned_cols=60 Identities=20% Similarity=0.344 Sum_probs=45.9
Q ss_pred EEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCCh
Q psy1580 24 IRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPP 103 (267)
Q Consensus 24 eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~ 103 (267)
++|.||. .++|.|||++|.++++|+++|||+|.|-..+ +.+=.|.|++.
T Consensus 2 ~~i~Vp~------~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~----------------------~~~~~v~I~G~--- 50 (62)
T cd02394 2 EEVEIPK------KLHRFIIGKKGSNIRKIMEETGVKIRFPDPG----------------------SKSDTITITGP--- 50 (62)
T ss_pred eEEEeCH------HHhhhccCCCCCcHHHHHHHhCCEEEcCCCC----------------------CCCCEEEEEcC---
Confidence 4567774 5779999999999999999999999987643 12234788886
Q ss_pred hHHHHHHHHHHHHH
Q psy1580 104 AEAHARIAYALAEV 117 (267)
Q Consensus 104 ~~a~~rl~~Av~~I 117 (267)
.+.+..|.++|
T Consensus 51 ---~~~v~~A~~~i 61 (62)
T cd02394 51 ---KENVEKAKEEI 61 (62)
T ss_pred ---HHHHHHHHHHh
Confidence 25777887765
No 12
>KOG1960|consensus
Probab=97.79 E-value=1.5e-05 Score=78.17 Aligned_cols=90 Identities=13% Similarity=-0.030 Sum_probs=75.6
Q ss_pred CcceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEE
Q psy1580 19 PIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEIT 98 (267)
Q Consensus 19 p~k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIs 98 (267)
=++...|++|+++ -|.||.-+..=||+-.+|..+|.||+.++.||||||+.-.-- +|. ..+|||+++|+
T Consensus 207 G~~Y~~k~~v~~~-~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~------~G~----EsnEPMYI~i~ 275 (531)
T KOG1960|consen 207 GRYYPNKALATDK-DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPN------EGN----ESNEPMYIFST 275 (531)
T ss_pred cccchhheecccC-CcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCcc------ccc----ccCCceeEEee
Confidence 3445558999998 889999999999999999999999999999999999886431 232 36899999999
Q ss_pred ecCChhHHHHHHHHHHHHHHHhhcCC
Q psy1580 99 AFAPPAEAHARIAYALAEVRRFLVPF 124 (267)
Q Consensus 99 a~~~~~~a~~rl~~Av~~I~~lL~P~ 124 (267)
.... .-+.+|+.++..|+.-+
T Consensus 276 h~~~-----~g~~~A~r~~~nl~~~v 296 (531)
T KOG1960|consen 276 HGNG-----NGENGAPRRKWNLEEKV 296 (531)
T ss_pred cCCc-----hhhccchhHHHhHHHHH
Confidence 9876 66788999998888764
No 13
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=97.47 E-value=3e-05 Score=69.26 Aligned_cols=52 Identities=13% Similarity=0.024 Sum_probs=37.4
Q ss_pred HHhhCCCCCCCCCCCCCCCCCCc---------c--ccc--cCCCccccCCCCCCCCCCC-CCCCcc
Q psy1580 145 QILKEDGGAASCSESSESSVNNP---------L--LYA--ENTSPVENLTPPEYTLVDP-AFNRIQ 196 (267)
Q Consensus 145 A~lNGt~r~~~cg~~~h~~~~cp---------~--~~~--~~~~~c~~cg~~gh~t~dc-~~~~~~ 196 (267)
++.+-.-.|-+||+.||...+|| . +-. .-..+|-+||..||+.+|| |....+
T Consensus 55 ~~~~~~~~C~nCg~~GH~~~DCP~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~~~~ 120 (190)
T COG5082 55 AIREENPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKDQQ 120 (190)
T ss_pred cccccccccchhcccCcccccCChhHhhhcCCCCcccccCCcccccccccccCccccccCcccccC
Confidence 34444456789999999999999 2 111 1226899999999999999 454433
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=97.36 E-value=0.00029 Score=61.25 Aligned_cols=53 Identities=17% Similarity=0.333 Sum_probs=44.9
Q ss_pred eeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCChhHHHHHHHHHHHHH
Q psy1580 38 FVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEV 117 (267)
Q Consensus 38 FvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~~~a~~rl~~Av~~I 117 (267)
.+|+|||+.|.|.+.||..|||+|.|-|+ .|.|.++ .++++.|.+.|
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~~---------------------------~v~i~G~------~~~~~~A~~~i 145 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYGK---------------------------TVGIIGD------PEQVQIAREAI 145 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcCC---------------------------EEEEECC------HHHHHHHHHHH
Confidence 59999999999999999999999998541 2677773 47899999999
Q ss_pred HHhhcC
Q psy1580 118 RRFLVP 123 (267)
Q Consensus 118 ~~lL~P 123 (267)
+.|+.-
T Consensus 146 ~~li~~ 151 (172)
T TIGR03665 146 EMLIEG 151 (172)
T ss_pred HHHHcC
Confidence 999854
No 15
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.34 E-value=0.00036 Score=61.13 Aligned_cols=53 Identities=17% Similarity=0.338 Sum_probs=44.1
Q ss_pred eeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCChhHHHHHHHHHHHHH
Q psy1580 38 FVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEV 117 (267)
Q Consensus 38 FvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~~~a~~rl~~Av~~I 117 (267)
.+|+|||+.|.|.|.||..|||+|.|-++ .|.|.++ ..++..|.+.|
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 1666763 37888999999
Q ss_pred HHhhcC
Q psy1580 118 RRFLVP 123 (267)
Q Consensus 118 ~~lL~P 123 (267)
+.|+.-
T Consensus 152 ~~li~g 157 (180)
T PRK13763 152 EMLIEG 157 (180)
T ss_pred HHHHcC
Confidence 998855
No 16
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.01 E-value=0.0012 Score=57.92 Aligned_cols=65 Identities=25% Similarity=0.252 Sum_probs=50.5
Q ss_pred EEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEE---e
Q psy1580 23 TIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEIT---A 99 (267)
Q Consensus 23 ~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIs---a 99 (267)
...+.||. +-+|.|+||.|.|.|.|+++|||+|.|--.. =.|.|. +
T Consensus 4 ~~~i~IP~------~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~-------------------------g~V~I~~~~~ 52 (180)
T PRK13763 4 MEYVKIPK------DRIGVLIGKKGETKKEIEERTGVKLEIDSET-------------------------GEVIIEPTDG 52 (180)
T ss_pred eEEEEcCH------HHhhhHhccchhHHHHHHHHHCcEEEEECCC-------------------------CeEEEEeCCC
Confidence 34566663 5789999999999999999999999997540 135555 3
Q ss_pred cCChhHHHHHHHHHHHHHHHhhcC
Q psy1580 100 FAPPAEAHARIAYALAEVRRFLVP 123 (267)
Q Consensus 100 ~~~~~~a~~rl~~Av~~I~~lL~P 123 (267)
.++ ..+.+|.+.|+.|+..
T Consensus 53 ~d~-----~~i~kA~~~I~ai~~g 71 (180)
T PRK13763 53 EDP-----LAVLKARDIVKAIGRG 71 (180)
T ss_pred CCH-----HHHHHHHHHHHHHhcC
Confidence 343 6789999999999885
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=97.00 E-value=0.00064 Score=59.08 Aligned_cols=57 Identities=23% Similarity=0.264 Sum_probs=44.9
Q ss_pred CeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEE--EecCChhHHHHHHHHHH
Q psy1580 37 NFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEI--TAFAPPAEAHARIAYAL 114 (267)
Q Consensus 37 NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlI--sa~~~~~~a~~rl~~Av 114 (267)
+.+|.||||+|.|.|+||++|||+|.|--. .=.|.| .+.++ ..+.+|.
T Consensus 7 ~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-------------------------~g~V~I~~~t~d~-----~~i~kA~ 56 (172)
T TIGR03665 7 DRIGVLIGKGGETKKEIEERTGVKLDIDSE-------------------------TGEVKIEEEDEDP-----LAVMKAR 56 (172)
T ss_pred HHhhhHhCCchhHHHHHHHHhCcEEEEEcC-------------------------CceEEEecCCCCH-----HHHHHHH
Confidence 689999999999999999999999999742 012455 23332 6788999
Q ss_pred HHHHHhhcC
Q psy1580 115 AEVRRFLVP 123 (267)
Q Consensus 115 ~~I~~lL~P 123 (267)
+.|+.|...
T Consensus 57 ~~I~~i~~g 65 (172)
T TIGR03665 57 EVVKAIGRG 65 (172)
T ss_pred HHHHHHHcC
Confidence 999998875
No 18
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.85 E-value=0.0024 Score=57.42 Aligned_cols=54 Identities=19% Similarity=0.333 Sum_probs=44.9
Q ss_pred eeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCChhHHHHHHHHHHHHH
Q psy1580 38 FVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEV 117 (267)
Q Consensus 38 FvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~~~a~~rl~~Av~~I 117 (267)
..|||||+.|.|.+.||+-|||.|+|.|+ +|.|-+. +..++.|-+.|
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~---------------------------tVaiiG~------~~~v~iAr~AV 158 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK---------------------------TVAIIGG------FEQVEIAREAV 158 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc---------------------------EEEEecC------hhhhHHHHHHH
Confidence 47999999999999999999999999996 2445553 47788888888
Q ss_pred HHhhcCC
Q psy1580 118 RRFLVPF 124 (267)
Q Consensus 118 ~~lL~P~ 124 (267)
+.|+.-.
T Consensus 159 emli~G~ 165 (194)
T COG1094 159 EMLINGA 165 (194)
T ss_pred HHHHcCC
Confidence 8888654
No 19
>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=96.73 E-value=0.0041 Score=65.14 Aligned_cols=72 Identities=26% Similarity=0.400 Sum_probs=56.4
Q ss_pred ccCCCCCcceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCc
Q psy1580 13 DITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEE 92 (267)
Q Consensus 13 d~~~~kp~k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~Ep 92 (267)
++..+-|.- ..+.||. .-+|.||||+|.|.|.|+++||++|.|--.
T Consensus 571 ~~s~~aP~~--~~~~I~~------~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~-------------------------- 616 (719)
T TIGR02696 571 EMSPYAPRI--ITVKIPV------DKIGEVIGPKGKMINQIQDETGAEISIEDD-------------------------- 616 (719)
T ss_pred ccccCCCee--EEEEeCh------HHhhheeCCCcHhHHHHHHHHCCEEEEecC--------------------------
Confidence 344445543 4566763 578999999999999999999999988543
Q ss_pred cEEEEEecCChhHHHHHHHHHHHHHHHhhcC
Q psy1580 93 LHVEITAFAPPAEAHARIAYALAEVRRFLVP 123 (267)
Q Consensus 93 LHVlIsa~~~~~~a~~rl~~Av~~I~~lL~P 123 (267)
=+|.|.+.+. +++++|++.|+.+..+
T Consensus 617 G~V~I~a~d~-----~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 617 GTVYIGAADG-----PSAEAARAMINAIANP 642 (719)
T ss_pred cEEEEEeCCH-----HHHHHHHHHHHHhhCc
Confidence 3578888764 7899999999999985
No 20
>KOG1676|consensus
Probab=96.63 E-value=0.0037 Score=63.93 Aligned_cols=74 Identities=27% Similarity=0.425 Sum_probs=58.8
Q ss_pred CcceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEE
Q psy1580 19 PIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEIT 98 (267)
Q Consensus 19 p~k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIs 98 (267)
+++.+.+|.||. |=+|+|||=.|.|.|+|++.||||+.+-=.|+.-++. +.|| .|+
T Consensus 136 ~~~ttqeI~IPa------~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~----------------~Kpl--rit 191 (600)
T KOG1676|consen 136 SVETTQEILIPA------NKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGA----------------DKPL--RIT 191 (600)
T ss_pred ccceeeeeccCc------cceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCC----------------CCce--eec
Confidence 677888999994 5689999999999999999999999988777655531 2232 345
Q ss_pred ecCChhHHHHHHHHHHHHHHHhhc
Q psy1580 99 AFAPPAEAHARIAYALAEVRRFLV 122 (267)
Q Consensus 99 a~~~~~~a~~rl~~Av~~I~~lL~ 122 (267)
++. .+|+.|.++|-++|.
T Consensus 192 Gdp------~~ve~a~~lV~dil~ 209 (600)
T KOG1676|consen 192 GDP------DKVEQAKQLVADILR 209 (600)
T ss_pred CCH------HHHHHHHHHHHHHHH
Confidence 543 688999999999997
No 21
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=96.38 E-value=0.0027 Score=53.21 Aligned_cols=43 Identities=12% Similarity=-0.008 Sum_probs=25.6
Q ss_pred CCCCCCCCCCCCCCCCccccc--cCCCccccCCCCCCCCCCCCCC
Q psy1580 151 GGAASCSESSESSVNNPLLYA--ENTSPVENLTPPEYTLVDPAFN 193 (267)
Q Consensus 151 ~r~~~cg~~~h~~~~cp~~~~--~~~~~c~~cg~~gh~t~dc~~~ 193 (267)
..|.+||+.+|...+||+... .....|..||..||+..||+..
T Consensus 78 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~ 122 (148)
T PTZ00368 78 RSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNA 122 (148)
T ss_pred cccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCc
Confidence 346666666666666666321 2334566666666666666654
No 22
>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=96.34 E-value=0.0055 Score=63.67 Aligned_cols=62 Identities=16% Similarity=0.261 Sum_probs=48.6
Q ss_pred EEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCCh
Q psy1580 24 IRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPP 103 (267)
Q Consensus 24 eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~ 103 (267)
..+.||. ..+|.||||+|.|+|.|+++|||+|.|--. =.|.|.+.+.
T Consensus 553 ~~~~I~~------~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd--------------------------G~V~i~~~~~- 599 (684)
T TIGR03591 553 ETIKINP------DKIRDVIGPGGKVIREITEETGAKIDIEDD--------------------------GTVKIAASDG- 599 (684)
T ss_pred EEEecCH------HHHHhhcCCCcHHHHHHHHHHCCEEEEecC--------------------------eEEEEEECcH-
Confidence 4566663 578999999999999999999999999432 2466777663
Q ss_pred hHHHHHHHHHHHHHHHhhc
Q psy1580 104 AEAHARIAYALAEVRRFLV 122 (267)
Q Consensus 104 ~~a~~rl~~Av~~I~~lL~ 122 (267)
..+++|.+.|+.+..
T Consensus 600 ----~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 600 ----EAAEAAIKMIEGITA 614 (684)
T ss_pred ----HHHHHHHHHHHhhhc
Confidence 678899999888754
No 23
>KOG1676|consensus
Probab=96.06 E-value=0.011 Score=60.44 Aligned_cols=63 Identities=22% Similarity=0.323 Sum_probs=47.6
Q ss_pred CeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCChhHHHHHHHHHHHH
Q psy1580 37 NFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAE 116 (267)
Q Consensus 37 NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~~~a~~rl~~Av~~ 116 (267)
+=||.|||=.|.|+|+|+.+||+||.++=- .+|. ..+=-+.|.+. -.+|.+|.++
T Consensus 239 ~~VG~IIGkgGE~IKklq~etG~KIQfkpD---------------d~p~----speR~~~IiG~------~d~ie~Aa~l 293 (600)
T KOG1676|consen 239 SKVGIIIGKGGEMIKKLQNETGAKIQFKPD---------------DDPS----SPERPAQIIGT------VDQIEHAAEL 293 (600)
T ss_pred cceeeEEecCchHHHHHhhccCceeEeecC---------------CCCC----CccceeeeecC------HHHHHHHHHH
Confidence 569999999999999999999999999742 1221 12223445554 3789999999
Q ss_pred HHHhhcCC
Q psy1580 117 VRRFLVPF 124 (267)
Q Consensus 117 I~~lL~P~ 124 (267)
|.+||.-.
T Consensus 294 I~eii~~~ 301 (600)
T KOG1676|consen 294 INEIIAEA 301 (600)
T ss_pred HHHHHHHH
Confidence 99998764
No 24
>KOG2193|consensus
Probab=95.78 E-value=0.003 Score=62.83 Aligned_cols=38 Identities=34% Similarity=0.657 Sum_probs=32.5
Q ss_pred EecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEe
Q psy1580 27 IVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAIL 64 (267)
Q Consensus 27 ~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IR 64 (267)
-||++-.---||+|||||-.|.++|.||.+||+||.|-
T Consensus 279 e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis 316 (584)
T KOG2193|consen 279 EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITIS 316 (584)
T ss_pred hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeee
Confidence 35555445569999999999999999999999999984
No 25
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=95.59 E-value=0.016 Score=48.58 Aligned_cols=43 Identities=9% Similarity=0.008 Sum_probs=29.9
Q ss_pred CCCCCCCCCCCCCCCCccccc-cCCCccccCCCCCCCCCCCCCC
Q psy1580 151 GGAASCSESSESSVNNPLLYA-ENTSPVENLTPPEYTLVDPAFN 193 (267)
Q Consensus 151 ~r~~~cg~~~h~~~~cp~~~~-~~~~~c~~cg~~gh~t~dc~~~ 193 (267)
..|.+|+..+|...+||.... .....|.+||..||+.+||+..
T Consensus 53 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~C~~~ 96 (148)
T PTZ00368 53 RSCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNR 96 (148)
T ss_pred cccCCCCCcCcCcccCCCcccCCCCcccCcCCCCCcccccCCCc
Confidence 457778888888888876321 1234688888888888888774
No 26
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=95.52 E-value=0.0093 Score=34.36 Aligned_cols=16 Identities=19% Similarity=-0.020 Sum_probs=14.5
Q ss_pred ccccCCCCCCCCCCCC
Q psy1580 176 PVENLTPPEYTLVDPA 191 (267)
Q Consensus 176 ~c~~cg~~gh~t~dc~ 191 (267)
+|-.||+.||+.+||+
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 5889999999999997
No 27
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.26 E-value=0.03 Score=50.93 Aligned_cols=68 Identities=19% Similarity=0.290 Sum_probs=50.8
Q ss_pred CeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCChhHHHHHHHHHHHH
Q psy1580 37 NFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAE 116 (267)
Q Consensus 37 NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~~~a~~rl~~Av~~ 116 (267)
+++++||||+|.+++.|.++|+++|.| |. .=.|+|.+.+. +.+..|++.
T Consensus 154 ~~i~~lig~~g~~i~~l~~~~~~~I~i-g~-------------------------NG~VwI~~~~~-----~~~~~a~~~ 202 (235)
T PRK04163 154 VKVPRVIGKKGSMINMLKEETGCDIIV-GQ-------------------------NGRIWIKGPDE-----EDEEIAIEA 202 (235)
T ss_pred HHHHhhcCCCChhHhhhhhhhCcEEEE-cC-------------------------CcEEEEeeCCH-----HHHHHHHHH
Confidence 578999999999999999999999988 21 11489999874 677788888
Q ss_pred HHHhhcCCCcCCCCcchhHHHH
Q psy1580 117 VRRFLVPFTRSLFQDYNDEIRQ 138 (267)
Q Consensus 117 I~~lL~P~~~s~~~d~~DelK~ 138 (267)
|+.+-.-.+.+ +--|.+|+
T Consensus 203 I~~~e~~~~~~---~l~~~v~~ 221 (235)
T PRK04163 203 IKKIEREAHTS---GLTDRIKE 221 (235)
T ss_pred HHHHHhhhhcc---ChHHHHHH
Confidence 88776554433 33455544
No 28
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=95.01 E-value=0.016 Score=62.01 Aligned_cols=64 Identities=20% Similarity=0.246 Sum_probs=51.2
Q ss_pred EEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCce-EEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecC
Q psy1580 23 TIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTR-MAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFA 101 (267)
Q Consensus 23 ~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcK-I~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~ 101 (267)
...+.|| | +.+|.||||+|.|+|.|+++||++ |-|+ ++-.|.|.+.+
T Consensus 686 i~~~~i~----~--~ki~~vIG~GGktIk~I~eetg~~~Idi~--------------------------ddg~V~I~a~d 733 (891)
T PLN00207 686 IHIMKVK----P--EKVNMIIGSGGKKVKSIIEETGVEAIDTQ--------------------------DDGTVKITAKD 733 (891)
T ss_pred eEEEEcC----H--HHHHHHhcCCchhHHHHHHHHCCCccCcC--------------------------CCeeEEEEeCC
Confidence 3456666 3 679999999999999999999998 6554 34567888877
Q ss_pred ChhHHHHHHHHHHHHHHHhhcC
Q psy1580 102 PPAEAHARIAYALAEVRRFLVP 123 (267)
Q Consensus 102 ~~~~a~~rl~~Av~~I~~lL~P 123 (267)
. +++++|++.|+.|..-
T Consensus 734 ~-----~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 734 L-----SSLEKSKAIISSLTMV 750 (891)
T ss_pred H-----HHHHHHHHHHHHHhcC
Confidence 4 7899999999998753
No 29
>KOG4400|consensus
Probab=94.96 E-value=0.019 Score=52.44 Aligned_cols=39 Identities=15% Similarity=0.015 Sum_probs=29.6
Q ss_pred CCCCCCCCCCCCCCccccccCCCccccCCCCCCCCCCCCCCC
Q psy1580 153 AASCSESSESSVNNPLLYAENTSPVENLTPPEYTLVDPAFNR 194 (267)
Q Consensus 153 ~~~cg~~~h~~~~cp~~~~~~~~~c~~cg~~gh~t~dc~~~~ 194 (267)
|-+||+.||...+||++ ....|-.|+.++|..+||+...
T Consensus 146 Cy~Cg~~GH~s~~C~~~---~~~~c~~c~~~~h~~~~C~~~~ 184 (261)
T KOG4400|consen 146 CYSCGEQGHISDDCPEN---KGGTCFRCGKVGHGSRDCPSKQ 184 (261)
T ss_pred cCCCCcCCcchhhCCCC---CCCccccCCCcceecccCCccc
Confidence 66778888888888877 3356888888888888888765
No 30
>KOG2190|consensus
Probab=94.52 E-value=0.16 Score=51.26 Aligned_cols=82 Identities=27% Similarity=0.413 Sum_probs=59.6
Q ss_pred CCCccccC--CCCCcceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCc
Q psy1580 8 GRKMVDIT--RDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPK 85 (267)
Q Consensus 8 ~~~~~d~~--~~kp~k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~ 85 (267)
.+..-|.. ..++ ....+++|| -+-+|-|||=+|+.+|.|.++|||+|.|.+. +- |.
T Consensus 123 ~~~~~d~~~~~~~~-~v~~RLlVp------~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~--~l-------------P~ 180 (485)
T KOG2190|consen 123 DEAAEDNGEDASGP-EVTCRLLVP------SSQVGSLIGKGGSLIKEIREETGAKIRVSSD--ML-------------PN 180 (485)
T ss_pred ccccccCCccccCC-ceEEEEEec------hhheeeeeccCcHHHHHHHHhcCceEEecCC--CC-------------Cc
Confidence 34444443 2333 467889999 3678999999999999999999999999986 11 21
Q ss_pred cCCCCCccEEEEEecCChhHHHHHHHHHHHHHHHhh
Q psy1580 86 FLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFL 121 (267)
Q Consensus 86 ~~hl~EpLHVlIsa~~~~~~a~~rl~~Av~~I~~lL 121 (267)
-.|.. |.|++.- ..|.+|+..|-.+|
T Consensus 181 ---ster~-V~IsG~~------~av~~al~~Is~~L 206 (485)
T KOG2190|consen 181 ---STERA-VTISGEP------DAVKKALVQISSRL 206 (485)
T ss_pred ---cccee-EEEcCch------HHHHHHHHHHHHHH
Confidence 12333 8888863 67888888887765
No 31
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=94.30 E-value=0.031 Score=58.28 Aligned_cols=56 Identities=18% Similarity=0.301 Sum_probs=45.2
Q ss_pred CeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCChhHHHHHHHHHHHH
Q psy1580 37 NFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAE 116 (267)
Q Consensus 37 NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~~~a~~rl~~Av~~ 116 (267)
.-+|.+|||+|.|+|.|+++||++|-|+-. -.|.|.+.+. ..+++|.+.
T Consensus 563 ~kI~~vIG~gg~~ik~I~~~~~~~idi~d~--------------------------G~v~i~~~~~-----~~~~~a~~~ 611 (693)
T PRK11824 563 DKIRDVIGPGGKTIREITEETGAKIDIEDD--------------------------GTVKIAATDG-----EAAEAAKER 611 (693)
T ss_pred HHHHHHhcCCchhHHHHHHHHCCccccCCC--------------------------ceEEEEcccH-----HHHHHHHHH
Confidence 568999999999999999999998877432 3466777653 788899999
Q ss_pred HHHhhcC
Q psy1580 117 VRRFLVP 123 (267)
Q Consensus 117 I~~lL~P 123 (267)
|+.+...
T Consensus 612 I~~~~~~ 618 (693)
T PRK11824 612 IEGITAE 618 (693)
T ss_pred HHHhccc
Confidence 9887753
No 32
>KOG2874|consensus
Probab=93.64 E-value=0.038 Score=52.72 Aligned_cols=27 Identities=33% Similarity=0.565 Sum_probs=25.7
Q ss_pred eEEeCCCcchHHHHHHhhCceEEEeec
Q psy1580 40 GKLLGPKGNSLKRLQEDTMTRMAILGR 66 (267)
Q Consensus 40 GrILGPrG~TlKrLE~eTgcKI~IRGr 66 (267)
.|||||.|+|||.||--|.|-|.|.|.
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~ 187 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN 187 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc
Confidence 589999999999999999999999996
No 33
>KOG2814|consensus
Probab=93.30 E-value=0.12 Score=50.07 Aligned_cols=31 Identities=32% Similarity=0.608 Sum_probs=27.7
Q ss_pred CeeeEEeCCCcchHHHHHHhhCceEEEeecc
Q psy1580 37 NFVGKLLGPKGNSLKRLQEDTMTRMAILGRG 67 (267)
Q Consensus 37 NFvGrILGPrG~TlKrLE~eTgcKI~IRGrG 67 (267)
-|+|.|+|=+|.|.|+||+||+|+|.+=-.+
T Consensus 66 ~~~~~lig~~g~trkkle~Etq~~i~lp~p~ 96 (345)
T KOG2814|consen 66 SFIGWLIGKQGKTRKKLEEETQTNIFLPRPN 96 (345)
T ss_pred HHhhhhhcccchHHHHHHHhhccceEccCCC
Confidence 5899999999999999999999999885443
No 34
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=92.75 E-value=0.091 Score=47.26 Aligned_cols=42 Identities=10% Similarity=-0.028 Sum_probs=32.3
Q ss_pred CCCCCCCCCCCCCCc-cccccCCCccccCCCCCCCCCCCCCCCcc
Q psy1580 153 AASCSESSESSVNNP-LLYAENTSPVENLTPPEYTLVDPAFNRIQ 196 (267)
Q Consensus 153 ~~~cg~~~h~~~~cp-~~~~~~~~~c~~cg~~gh~t~dc~~~~~~ 196 (267)
|.+||+.||.+-+|+ -.. -...|..|.-.+|.++||+..+..
T Consensus 100 C~~Cg~~GH~~~dC~P~~~--~~~~C~~C~s~~H~s~~Cp~~~k~ 142 (190)
T COG5082 100 CYNCGETGHLSRDCNPSKD--QQKSCFDCNSTRHSSEDCPSIWKH 142 (190)
T ss_pred cccccccCccccccCcccc--cCcceeccCCCccccccCcccccc
Confidence 459999999999994 322 222699999999999999987633
No 35
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=92.63 E-value=0.075 Score=35.15 Aligned_cols=21 Identities=10% Similarity=-0.100 Sum_probs=17.9
Q ss_pred CCccccCCCCCCCCCCCCCCC
Q psy1580 174 TSPVENLTPPEYTLVDPAFNR 194 (267)
Q Consensus 174 ~~~c~~cg~~gh~t~dc~~~~ 194 (267)
.-.|.+|+.+||.-.||+.+.
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~~~ 28 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPTNK 28 (32)
T ss_pred CCEeecCCCCCccHhHCCCCC
Confidence 347999999999999999853
No 36
>KOG2191|consensus
Probab=92.54 E-value=0.2 Score=48.85 Aligned_cols=37 Identities=24% Similarity=0.532 Sum_probs=33.3
Q ss_pred eEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEe
Q psy1580 22 VTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAIL 64 (267)
Q Consensus 22 ~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IR 64 (267)
+.-||+|| -+-.|-|||-.|.|+.+||++|||+|.+-
T Consensus 39 y~ikvLip------s~AaGsIIGKGG~ti~~lqk~tgariklS 75 (402)
T KOG2191|consen 39 YFLKVLIP------SYAAGSIIGKGGQTIVQLQKETGARIKLS 75 (402)
T ss_pred eEEEEEee------cccccceeccchHHHHHHHhccCcEEEec
Confidence 67799999 26789999999999999999999999875
No 37
>KOG2193|consensus
Probab=92.16 E-value=0.26 Score=49.59 Aligned_cols=71 Identities=20% Similarity=0.397 Sum_probs=50.0
Q ss_pred eEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecC
Q psy1580 22 VTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFA 101 (267)
Q Consensus 22 ~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~ 101 (267)
+--+++||- -|+|-||||.|+|+|-|-+.|.|+|-+.-+- . .|. .+..+-|+=+.+
T Consensus 199 ~PlR~lVpt------qyvgaIIGkeG~TIknItkqTqsriD~hrke----n--------~Ga-----aek~itvh~tpE- 254 (584)
T KOG2193|consen 199 WPLRLLVPT------QYVGAIIGKEGATIKNITKQTQSRIDVHRKE----N--------AGA-----AEKIITVHSTPE- 254 (584)
T ss_pred cceeeeecc------ceeEEEecCCCccccCcchhhhheeeeeecc----c--------CCc-----ccCceEEecCcc-
Confidence 334666764 5999999999999999999999999987652 1 121 245566665553
Q ss_pred ChhHHHHHHHHHHHHHHHhhcC
Q psy1580 102 PPAEAHARIAYALAEVRRFLVP 123 (267)
Q Consensus 102 ~~~~a~~rl~~Av~~I~~lL~P 123 (267)
.-.+||++|-+++.-
T Consensus 255 -------g~s~Ac~~ILeimqk 269 (584)
T KOG2193|consen 255 -------GTSKACKMILEIMQK 269 (584)
T ss_pred -------chHHHHHHHHHHHHH
Confidence 335777777777654
No 38
>KOG1960|consensus
Probab=90.58 E-value=0.19 Score=50.09 Aligned_cols=62 Identities=21% Similarity=0.174 Sum_probs=47.9
Q ss_pred EEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCChhHHHHHHHHHHHHHH
Q psy1580 41 KLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVR 118 (267)
Q Consensus 41 rILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~~~a~~rl~~Av~~I~ 118 (267)
+-+=-||.|+..||.+||+.|+.||+=- ..|+..-| ..+.+|..+|.+.+. +-+++|++.|+
T Consensus 107 ~~~~TRg~~~d~Ie~~~G~~~~~RGs~~------~~El~~vg-----~~~~pLv~hI~~~T~-----Ei~~~Ai~RIk 168 (531)
T KOG1960|consen 107 KATSTRGTSYDHIEGITGTTSASRGSAP------APELPPVG-----SSEGPLVDHIPPSTA-----EITSKAIERIK 168 (531)
T ss_pred cceeccchhHHhhhhhccceeeccCCCC------CccCCCCC-----CCCCcceeecCCccH-----HHHHHHHhhCc
Confidence 3455699999999999999999999742 22333222 247899999999875 67889999998
No 39
>KOG4400|consensus
Probab=89.91 E-value=0.25 Score=45.21 Aligned_cols=40 Identities=13% Similarity=0.050 Sum_probs=30.9
Q ss_pred CCCCCCCCCCC--CCCccccccCCCccccCCCCCCCCCCCCCC
Q psy1580 153 AASCSESSESS--VNNPLLYAENTSPVENLTPPEYTLVDPAFN 193 (267)
Q Consensus 153 ~~~cg~~~h~~--~~cp~~~~~~~~~c~~cg~~gh~t~dc~~~ 193 (267)
+-.|+..+|+. +-+|..+... ++|-.||+.||+..||+.+
T Consensus 121 ~~~c~~~gh~~~~~~~~~~~~~~-~~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 121 CYSCGKTGHRGCPDADPVDGPKP-AKCYSCGEQGHISDDCPEN 162 (261)
T ss_pred eeccCCCccccCcccccccCCCC-CccCCCCcCCcchhhCCCC
Confidence 35788888888 2333456666 8899999999999999943
No 40
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=89.59 E-value=0.84 Score=46.32 Aligned_cols=63 Identities=21% Similarity=0.341 Sum_probs=45.5
Q ss_pred EEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCChh
Q psy1580 25 RVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPA 104 (267)
Q Consensus 25 KI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~~ 104 (267)
-|.+|-+ .+-|||||--|-+.|.+|.-||+-|.|= +.|=-|.||++||
T Consensus 207 ~v~lp~d-----~~kgriigreGrnir~~e~~tgvd~iid-------------------------dtp~~v~ls~fdp-- 254 (514)
T TIGR03319 207 VVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIID-------------------------DTPEAVILSGFDP-- 254 (514)
T ss_pred eEEcCCh-----hhhccccCCCcchHHHHHHHhCceEEEc-------------------------CCCCeEEecCCch--
Confidence 4566655 6779999999999999999999999882 2344588899988
Q ss_pred HHHHHHHHHHHHHHHhhc
Q psy1580 105 EAHARIAYALAEVRRFLV 122 (267)
Q Consensus 105 ~a~~rl~~Av~~I~~lL~ 122 (267)
.|=+-|..-+++|+.
T Consensus 255 ---~rreia~~~l~~li~ 269 (514)
T TIGR03319 255 ---VRREIARMALEKLIQ 269 (514)
T ss_pred ---HHHHHHHHHHHHHHH
Confidence 333344444444443
No 41
>KOG2191|consensus
Probab=89.12 E-value=1.9 Score=42.34 Aligned_cols=38 Identities=26% Similarity=0.494 Sum_probs=32.4
Q ss_pred eEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEee
Q psy1580 22 VTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILG 65 (267)
Q Consensus 22 ~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRG 65 (267)
.+.||.+|-. --|.|||+.|.|+|.+.+++||-|+|--
T Consensus 132 kqikivvPNs------tag~iigkggAtiK~~~Eqsga~iqisP 169 (402)
T KOG2191|consen 132 KQIKIVVPNS------TAGMIIGKGGATIKAIQEQSGAWIQISP 169 (402)
T ss_pred ceeEEeccCC------cccceecCCcchHHHHHHhhCcceEecc
Confidence 3468888843 4699999999999999999999999964
No 42
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=88.76 E-value=0.31 Score=27.99 Aligned_cols=17 Identities=18% Similarity=0.352 Sum_probs=15.1
Q ss_pred CCCCCCCCCCCCCCCcc
Q psy1580 152 GAASCSESSESSVNNPL 168 (267)
Q Consensus 152 r~~~cg~~~h~~~~cp~ 168 (267)
.|-+||+.||.+.+||.
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 46799999999999984
No 43
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=88.73 E-value=0.61 Score=49.02 Aligned_cols=61 Identities=18% Similarity=0.351 Sum_probs=46.2
Q ss_pred EEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCChhH
Q psy1580 26 VIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAE 105 (267)
Q Consensus 26 I~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~~~ 105 (267)
+-|+.+. ++-+|||.|.|.+.|.++||++|.|--.|+++ |.+.+.
T Consensus 556 ~~i~~dK------I~dvIG~gGk~I~~I~eetg~~IdieddGtv~--------------------------i~~s~~--- 600 (692)
T COG1185 556 IKIDPDK------IRDVIGPGGKTIKAITEETGVKIDIEDDGTVK--------------------------IAASDG--- 600 (692)
T ss_pred EccCHHH------HhhccCCcccchhhhhhhhCcEEEecCCCcEE--------------------------EEecch---
Confidence 4556554 45689999999999999999999998766544 344432
Q ss_pred HHHHHHHHHHHHHHhhcC
Q psy1580 106 AHARIAYALAEVRRFLVP 123 (267)
Q Consensus 106 a~~rl~~Av~~I~~lL~P 123 (267)
.++.+|.+.|+.++.-
T Consensus 601 --~~~~~ak~~I~~i~~e 616 (692)
T COG1185 601 --ESAKKAKERIEAITRE 616 (692)
T ss_pred --HHHHHHHHHHHHHHhh
Confidence 6778888888887743
No 44
>PRK00106 hypothetical protein; Provisional
Probab=88.72 E-value=0.87 Score=46.65 Aligned_cols=64 Identities=22% Similarity=0.326 Sum_probs=48.1
Q ss_pred EEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCChh
Q psy1580 25 RVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPA 104 (267)
Q Consensus 25 KI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~~ 104 (267)
-|.+|-+ .+-|||||--|-+.+.+|.-||+-|.|= +.|=-|.||++||
T Consensus 228 ~v~lp~d-----emkGriIGreGrNir~~E~~tGvdliid-------------------------dtp~~v~lS~fdp-- 275 (535)
T PRK00106 228 TVHLPDD-----NMKGRIIGREGRNIRTLESLTGIDVIID-------------------------DTPEVVVLSGFDP-- 275 (535)
T ss_pred eEEcCCh-----HhhcceeCCCcchHHHHHHHhCceEEEc-------------------------CCCCeEEEeCCCh--
Confidence 4566655 6779999999999999999999999882 3455688999998
Q ss_pred HHHHHHHHHHHHHHHhhcC
Q psy1580 105 EAHARIAYALAEVRRFLVP 123 (267)
Q Consensus 105 ~a~~rl~~Av~~I~~lL~P 123 (267)
.|-+-|..-+++|+..
T Consensus 276 ---vRReiAr~~le~Li~d 291 (535)
T PRK00106 276 ---IRREIARMTLESLIKD 291 (535)
T ss_pred ---HHHHHHHHHHHHHHHc
Confidence 4445555555665543
No 45
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=88.38 E-value=0.94 Score=32.97 Aligned_cols=36 Identities=22% Similarity=0.369 Sum_probs=30.2
Q ss_pred eEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEE
Q psy1580 22 VTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAI 63 (267)
Q Consensus 22 ~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~I 63 (267)
...+|+||. .-+|+.||.+|.+++.++..+|-+|-|
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 455677775 457999999999999999999988876
No 46
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=88.28 E-value=0.26 Score=34.36 Aligned_cols=18 Identities=0% Similarity=-0.272 Sum_probs=12.0
Q ss_pred CccccCCCCCCCCCCCCC
Q psy1580 175 SPVENLTPPEYTLVDPAF 192 (267)
Q Consensus 175 ~~c~~cg~~gh~t~dc~~ 192 (267)
..|..||..||.+..|+-
T Consensus 5 ~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 5 VRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CcCcccCCCCcchhhCCC
Confidence 456777777777777764
No 47
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=87.47 E-value=0.47 Score=32.87 Aligned_cols=20 Identities=5% Similarity=-0.252 Sum_probs=17.6
Q ss_pred CccccCCCCCCCC--CCCCCCC
Q psy1580 175 SPVENLTPPEYTL--VDPAFNR 194 (267)
Q Consensus 175 ~~c~~cg~~gh~t--~dc~~~~ 194 (267)
++|..||..||.. +.||+..
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred ccccccccccccccCccCCCCC
Confidence 6899999999994 7899987
No 48
>PRK12704 phosphodiesterase; Provisional
Probab=86.91 E-value=3.3 Score=42.14 Aligned_cols=48 Identities=23% Similarity=0.381 Sum_probs=39.5
Q ss_pred EEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCC
Q psy1580 25 RVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAP 102 (267)
Q Consensus 25 KI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~ 102 (267)
-|.+|-+ .+-|||||--|-+.|.||.-||+-|.|= +.|=-|+||++++
T Consensus 213 ~v~lp~d-----~mkgriigreGrnir~~e~~tgvd~iid-------------------------dtp~~v~ls~~~~ 260 (520)
T PRK12704 213 VVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIID-------------------------DTPEAVILSGFDP 260 (520)
T ss_pred eeecCCc-----hhhcceeCCCcchHHHHHHHhCCeEEEc-------------------------CCCCeEEEecCCh
Confidence 4566655 6779999999999999999999999882 3455689999988
No 49
>KOG0336|consensus
Probab=86.90 E-value=0.34 Score=49.00 Aligned_cols=30 Identities=47% Similarity=0.792 Sum_probs=27.1
Q ss_pred CCCeeeEEeCCCcchHHHHHHhhCceEEEe
Q psy1580 35 KFNFVGKLLGPKGNSLKRLQEDTMTRMAIL 64 (267)
Q Consensus 35 ~~NFvGrILGPrG~TlKrLE~eTgcKI~IR 64 (267)
+-||||.+||=.|+.+|+||..|+++|.|-
T Consensus 54 ks~mvg~vigrggskik~iq~~tnt~iqii 83 (629)
T KOG0336|consen 54 KSEMVGKVIGRGGSKIKRIQNDTNTRIQII 83 (629)
T ss_pred hhhhhheeeccCcchhhhhhcccceeEEEe
Confidence 458999999999999999999999988763
No 50
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=83.81 E-value=0.64 Score=32.40 Aligned_cols=20 Identities=10% Similarity=0.250 Sum_probs=17.4
Q ss_pred hCCCCCCCCCCCCCCCCCCc
Q psy1580 148 KEDGGAASCSESSESSVNNP 167 (267)
Q Consensus 148 NGt~r~~~cg~~~h~~~~cp 167 (267)
|....|..|+..||.+|+||
T Consensus 2 ~~~~~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 2 NARVRCQKCGQKGHWTYECP 21 (42)
T ss_pred CCCCcCcccCCCCcchhhCC
Confidence 45667999999999999996
No 51
>KOG2190|consensus
Probab=83.20 E-value=1.4 Score=44.57 Aligned_cols=42 Identities=26% Similarity=0.563 Sum_probs=37.1
Q ss_pred CcceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeec
Q psy1580 19 PIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGR 66 (267)
Q Consensus 19 p~k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGr 66 (267)
....+.++.|| .+|+|.|||..|+.+-.|++.|||.|.|.++
T Consensus 335 ~~~v~~~l~vp------s~~igciiGk~G~~iseir~~tgA~I~I~~~ 376 (485)
T KOG2190|consen 335 TQTVTQRLLVP------SDLIGCIIGKGGAKISEIRQRTGASISILNK 376 (485)
T ss_pred cceeeeeeccC------ccccceeecccccchHHHHHhcCCceEEccc
Confidence 44566788888 4799999999999999999999999999886
No 52
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=82.95 E-value=0.63 Score=39.12 Aligned_cols=21 Identities=0% Similarity=-0.124 Sum_probs=18.1
Q ss_pred CCCccccCCCCCCCCCCCCCCC
Q psy1580 173 NTSPVENLTPPEYTLVDPAFNR 194 (267)
Q Consensus 173 ~~~~c~~cg~~gh~t~dc~~~~ 194 (267)
..++|.+|+ ..|+|..|||++
T Consensus 105 ~~v~CR~Ck-GdH~T~~CPyKd 125 (128)
T PF12353_consen 105 SKVKCRICK-GDHWTSKCPYKD 125 (128)
T ss_pred ceEEeCCCC-CCcccccCCccc
Confidence 347899997 899999999986
No 53
>KOG2113|consensus
Probab=81.75 E-value=1.4 Score=42.89 Aligned_cols=49 Identities=24% Similarity=0.307 Sum_probs=41.1
Q ss_pred CCCccccCCCCCcceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEE
Q psy1580 8 GRKMVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMA 62 (267)
Q Consensus 8 ~~~~~d~~~~kp~k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~ 62 (267)
...++|+.-..|..+++.+-+| +-||+.|.||+|.+.|.|+.+|.+.|.
T Consensus 12 ~v~~ms~~~~~p~nvt~sv~vp------s~~v~~ivg~qg~kikalr~KTqtyi~ 60 (394)
T KOG2113|consen 12 IAQFMSYRTSIGQNVTESVEVP------SEHVAEIVGRQGCKIKALRAKTQTYIK 60 (394)
T ss_pred cccccccCCCCCCccceeeecC------cccceeecccCccccchhhhhhcceec
Confidence 3456777777778888888777 459999999999999999999999886
No 54
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=81.69 E-value=0.76 Score=34.72 Aligned_cols=33 Identities=24% Similarity=0.528 Sum_probs=26.1
Q ss_pred CCCCeeeEEeCCCcchHHHHHHhh-CceEEEeec
Q psy1580 34 PKFNFVGKLLGPKGNSLKRLQEDT-MTRMAILGR 66 (267)
Q Consensus 34 P~~NFvGrILGPrG~TlKrLE~eT-gcKI~IRGr 66 (267)
|+++-+|..+|++|...|.|+++. |-+|-|=.-
T Consensus 14 ~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 14 PNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp TTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred CCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 889999999999999999999999 777766553
No 55
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=74.80 E-value=2.8 Score=29.14 Aligned_cols=24 Identities=25% Similarity=0.408 Sum_probs=21.0
Q ss_pred eeeEEeCCCcchHHHHHHhhCceE
Q psy1580 38 FVGKLLGPKGNSLKRLQEDTMTRM 61 (267)
Q Consensus 38 FvGrILGPrG~TlKrLE~eTgcKI 61 (267)
-.|++||.+|.+++.|+..++-.+
T Consensus 35 ~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 35 QPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CCceEECCCCccHHHHHHHHHHHc
Confidence 369999999999999999998554
No 56
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=72.41 E-value=1.7 Score=30.47 Aligned_cols=24 Identities=4% Similarity=-0.277 Sum_probs=20.5
Q ss_pred ccccCCCccccCCCCCCCCCCCCC
Q psy1580 169 LYAENTSPVENLTPPEYTLVDPAF 192 (267)
Q Consensus 169 ~~~~~~~~c~~cg~~gh~t~dc~~ 192 (267)
.|...+..|..||-.||...+|+.
T Consensus 26 ~YE~lp~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 26 KYERLPRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred EECCcChhhcCCCCcCcCHhHcCC
Confidence 566777789999999999999974
No 57
>smart00343 ZnF_C2HC zinc finger.
Probab=69.85 E-value=2.5 Score=25.61 Aligned_cols=17 Identities=12% Similarity=-0.220 Sum_probs=14.8
Q ss_pred ccccCCCCCCCCCCCCC
Q psy1580 176 PVENLTPPEYTLVDPAF 192 (267)
Q Consensus 176 ~c~~cg~~gh~t~dc~~ 192 (267)
+|..||..||..++|+.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 48889999999999983
No 58
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=68.35 E-value=3.7 Score=34.88 Aligned_cols=30 Identities=23% Similarity=0.400 Sum_probs=27.5
Q ss_pred CeeeEEeCCCcchHHHHHHhhCceEEEeec
Q psy1580 37 NFVGKLLGPKGNSLKRLQEDTMTRMAILGR 66 (267)
Q Consensus 37 NFvGrILGPrG~TlKrLE~eTgcKI~IRGr 66 (267)
+.+|..+|++|+..|.|++..|-+|-|=.=
T Consensus 41 ~~vG~~IG~~G~rI~~i~e~lgekIdVve~ 70 (140)
T PRK08406 41 GDMGLAIGKGGENVKRLEEKLGKDIELVEY 70 (140)
T ss_pred CCccccCCcCchHHHHHHHHhCCceEEEEc
Confidence 578999999999999999999999998873
No 59
>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=64.86 E-value=4.3 Score=30.59 Aligned_cols=22 Identities=32% Similarity=0.471 Sum_probs=19.4
Q ss_pred eeEEeCCCcchHHHHHHhhCce
Q psy1580 39 VGKLLGPKGNSLKRLQEDTMTR 60 (267)
Q Consensus 39 vGrILGPrG~TlKrLE~eTgcK 60 (267)
.|+|||-+|.|+..||--++.-
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~~ 56 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANLV 56 (77)
T ss_pred CCeEECCCCccHHHHHHHHHHH
Confidence 5999999999999999887743
No 60
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=61.05 E-value=4.7 Score=26.69 Aligned_cols=20 Identities=10% Similarity=0.067 Sum_probs=17.9
Q ss_pred CCCCCCCCCCCCCCCCCccc
Q psy1580 150 DGGAASCSESSESSVNNPLL 169 (267)
Q Consensus 150 t~r~~~cg~~~h~~~~cp~~ 169 (267)
.|.|-.|+..||...+||.+
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCEeecCCCCCccHhHCCCC
Confidence 57789999999999999984
No 61
>PRK12705 hypothetical protein; Provisional
Probab=60.70 E-value=15 Score=37.56 Aligned_cols=30 Identities=20% Similarity=0.455 Sum_probs=26.5
Q ss_pred CCCCeeeEEeCCCcchHHHHHHhhCceEEE
Q psy1580 34 PKFNFVGKLLGPKGNSLKRLQEDTMTRMAI 63 (267)
Q Consensus 34 P~~NFvGrILGPrG~TlKrLE~eTgcKI~I 63 (267)
|+=.+-|||||--|.+.+.+|..||.-|.|
T Consensus 205 p~demkGriIGreGrNir~~E~~tGvdlii 234 (508)
T PRK12705 205 PSDAMKGRIIGREGRNIRAFEGLTGVDLII 234 (508)
T ss_pred CChHhhccccCccchhHHHHHHhhCCceEe
Confidence 334678999999999999999999998887
No 62
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=60.39 E-value=8.9 Score=35.82 Aligned_cols=28 Identities=29% Similarity=0.406 Sum_probs=26.1
Q ss_pred CeeeEEeCCCcchHHHHHHhhCceEEEe
Q psy1580 37 NFVGKLLGPKGNSLKRLQEDTMTRMAIL 64 (267)
Q Consensus 37 NFvGrILGPrG~TlKrLE~eTgcKI~IR 64 (267)
++|=|+||.+|+-++.|.++|+|.|.|=
T Consensus 155 ~kVpRvig~~~sm~~~l~~~~~~~I~VG 182 (239)
T COG1097 155 SKVPRVIGKKGSMLNMLKEKTGCEIIVG 182 (239)
T ss_pred hhcceEecCCCcHHHHhhhhcCeEEEEe
Confidence 7788999999999999999999999884
No 63
>PRK04023 DNA polymerase II large subunit; Validated
Probab=60.06 E-value=13 Score=41.30 Aligned_cols=48 Identities=10% Similarity=-0.044 Sum_probs=30.9
Q ss_pred CCCCCCCCCCCCCCCCcc--ccccCCCccccCCCCCCCCCCCCCCCccCCcc
Q psy1580 151 GGAASCSESSESSVNNPL--LYAENTSPVENLTPPEYTLVDPAFNRIQPATE 200 (267)
Q Consensus 151 ~r~~~cg~~~h~~~~cp~--~~~~~~~~c~~cg~~gh~t~dc~~~~~~~~~~ 200 (267)
..|..||..+ ..+-||. ......-.|..||..+.... |+--|....+.
T Consensus 627 RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~~~~~y~-CPKCG~El~~~ 676 (1121)
T PRK04023 627 RKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGIEVEEDE-CEKCGREPTPY 676 (1121)
T ss_pred ccCCCCCCcC-CcccCCCCCCCCCcceeCccccCcCCCCc-CCCCCCCCCcc
Confidence 4689999876 4457886 34455567999988776433 77665444433
No 64
>KOG1067|consensus
Probab=59.55 E-value=7.5 Score=40.81 Aligned_cols=54 Identities=20% Similarity=0.182 Sum_probs=41.0
Q ss_pred eeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCChhHHHHHHHHHHHHH
Q psy1580 38 FVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEV 117 (267)
Q Consensus 38 FvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~~~a~~rl~~Av~~I 117 (267)
=+..+|||.|-.+|+||.|||+.-+| ++=|+-|-|.++ ..+.+|.+.|
T Consensus 607 k~~~lIGp~G~~~kki~~EtGai~~v---------------------------De~t~~i~A~~~-----~am~~Ak~~I 654 (760)
T KOG1067|consen 607 KRATLIGPGGVLKKKIEVETGAISQV---------------------------DEGTFSIFAPTQ-----AAMEEAKEFI 654 (760)
T ss_pred hhheeecCccceeeeEeeeccceeee---------------------------cCceEEEEecCH-----HHHHHHHHHH
Confidence 35679999999999999999943221 333667777764 6788999999
Q ss_pred HHhhcC
Q psy1580 118 RRFLVP 123 (267)
Q Consensus 118 ~~lL~P 123 (267)
..|...
T Consensus 655 ~~i~~~ 660 (760)
T KOG1067|consen 655 DGIIKD 660 (760)
T ss_pred HHHhcC
Confidence 888765
No 65
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=53.79 E-value=5.6 Score=34.32 Aligned_cols=29 Identities=14% Similarity=0.151 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCCCCCCCCccccccCCCccccCCCC
Q psy1580 149 EDGGAASCSESSESSVNNPLLYAENTSPVENLTPP 183 (267)
Q Consensus 149 Gt~r~~~cg~~~h~~~~cp~~~~~~~~~c~~cg~~ 183 (267)
|+|.|.+||..-|... ....+.|..||..
T Consensus 111 G~l~C~~Cg~~~~~~~------~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 111 GTLVCENCGHEVELTH------PERLPPCPKCGHT 139 (146)
T ss_pred ceEecccCCCEEEecC------CCcCCCCCCCCCC
Confidence 6678999997766532 3344679999854
No 66
>KOG0122|consensus
Probab=52.31 E-value=5.7 Score=37.51 Aligned_cols=24 Identities=0% Similarity=-0.103 Sum_probs=19.5
Q ss_pred CCCccccCCCCCCCCCCCCCCCccC
Q psy1580 173 NTSPVENLTPPEYTLVDPAFNRIQP 197 (267)
Q Consensus 173 ~~~~c~~cg~~gh~t~dc~~~~~~~ 197 (267)
+...|.+| ...|.|.+|||++++-
T Consensus 118 ~~~~CR~C-~gdHwt~~CPyK~~~~ 141 (270)
T KOG0122|consen 118 SIVACRIC-KGDHWTTNCPYKDTLS 141 (270)
T ss_pred ceeeeeec-CCCeeeecCCchhhcc
Confidence 34689999 6789999999988543
No 67
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=50.62 E-value=15 Score=35.93 Aligned_cols=42 Identities=19% Similarity=0.463 Sum_probs=33.8
Q ss_pred EEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhh-CceEEEeec
Q psy1580 24 IRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDT-MTRMAILGR 66 (267)
Q Consensus 24 eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eT-gcKI~IRGr 66 (267)
.||-|=-. -|+++-||..+|++|+.++.+.++. |=+|-|=-=
T Consensus 233 tKVAV~s~-~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv~~ 275 (362)
T PRK12327 233 TKIAVRSN-NPNVDAKGACVGPKGQRVQNIVSELKGEKIDIIDW 275 (362)
T ss_pred eEEEEEcC-CCCCCchheeECCCChhHHHHHHHhCCCeEEEEEc
Confidence 35544322 3899999999999999999999999 888887654
No 68
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=48.94 E-value=11 Score=33.27 Aligned_cols=52 Identities=19% Similarity=0.227 Sum_probs=40.6
Q ss_pred ccccCCCCCcceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeecc
Q psy1580 11 MVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRG 67 (267)
Q Consensus 11 ~~d~~~~kp~k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrG 67 (267)
+.|....|-+..-.+|.+=|+ + +. |+-||++|.+.|+|++..|=+|.|-.-.
T Consensus 48 l~~~~~~k~~~~ddrvIfvV~--~--gd-g~aIGk~G~~ik~l~~~lgk~VevVE~s 99 (166)
T PRK06418 48 LKDVEYKKAYEVDDLVILLVT--S--GP-RIPIGKGGKIAKALSRKLGKKVRVVEKT 99 (166)
T ss_pred ccCceEEEEEEeCCEEEEEEe--C--CC-cccccccchHHHHHHHHhCCcEEEEEcC
Confidence 345555566666677777776 2 44 9999999999999999999999998854
No 69
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=47.75 E-value=14 Score=33.25 Aligned_cols=34 Identities=21% Similarity=0.426 Sum_probs=30.0
Q ss_pred CCCCeeeEEeCCCcchHHHHHHhhCceEEEeecc
Q psy1580 34 PKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRG 67 (267)
Q Consensus 34 P~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrG 67 (267)
++.+-+|..+|++|...|.|.++.|=+|-|---.
T Consensus 82 ~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s 115 (190)
T COG0195 82 VKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS 115 (190)
T ss_pred cCcCchhhhccCCChHHHHHHHHhCCceEEEEeC
Confidence 3567899999999999999999999888887764
No 70
>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=47.33 E-value=21 Score=34.69 Aligned_cols=42 Identities=19% Similarity=0.446 Sum_probs=33.9
Q ss_pred EEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhh-CceEEEeec
Q psy1580 24 IRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDT-MTRMAILGR 66 (267)
Q Consensus 24 eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eT-gcKI~IRGr 66 (267)
.||-|=-. -|+++-||..+|++|+.++.+.++. |=+|-|--=
T Consensus 231 tKvAV~s~-~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~ 273 (341)
T TIGR01953 231 TKIAVESN-DENIDPVGACVGPKGSRIQAISKELNGEKIDIIEY 273 (341)
T ss_pred eEEEEEcC-CCCCCcceeeECCCCchHHHHHHHhCCCeEEEEEc
Confidence 35554433 4899999999999999999999999 777777654
No 71
>KOG0334|consensus
Probab=46.82 E-value=15 Score=40.44 Aligned_cols=77 Identities=18% Similarity=0.217 Sum_probs=57.1
Q ss_pred EecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCChhHH
Q psy1580 27 IVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEA 106 (267)
Q Consensus 27 ~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~~~a 106 (267)
-++.++||- |..+++.+=.- +.+|.+.+++.|.+||+== ..++ +| ....+-||.+|++.+
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--LLRISEPTAAGITTRGKFN-PPGK---------EP--KPGERKLYLLVEGPD----- 960 (997)
T ss_pred eccccccch-hcceeeechhh--hhhccCccccceeeccccC-CCCC---------CC--CCcchhhhhhhhcch-----
Confidence 456788886 68888887644 9999999999999999731 1111 12 235788999999765
Q ss_pred HHHHHHHHHHHHHhhcC
Q psy1580 107 HARIAYALAEVRRFLVP 123 (267)
Q Consensus 107 ~~rl~~Av~~I~~lL~P 123 (267)
+..+.+|+++++.+|.-
T Consensus 961 e~~vqra~~e~~r~l~e 977 (997)
T KOG0334|consen 961 ELSVQRAIEELERLLEE 977 (997)
T ss_pred hHHHHHHHHHHHHHHHH
Confidence 47788999998886543
No 72
>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=46.00 E-value=16 Score=31.38 Aligned_cols=38 Identities=26% Similarity=0.473 Sum_probs=31.0
Q ss_pred EEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEeec
Q psy1580 25 RVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGR 66 (267)
Q Consensus 25 KI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRGr 66 (267)
||.+=|++ +-+|..+|++|...|.|++..|=||-|-.=
T Consensus 34 riifvV~~----g~vG~~IG~~G~rIk~i~el~gekIdVVey 71 (141)
T TIGR01952 34 RVVFVVKE----GEMGAAIGKGGENVKRLEELIGKSIELIEY 71 (141)
T ss_pred EEEEEEcC----CCccccCCCCchHHHHHHHhcCCeeEEEEc
Confidence 45444552 579999999999999999999999998873
No 73
>KOG2208|consensus
Probab=45.26 E-value=9 Score=40.91 Aligned_cols=38 Identities=26% Similarity=0.528 Sum_probs=29.5
Q ss_pred eEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEee
Q psy1580 22 VTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILG 65 (267)
Q Consensus 22 ~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IRG 65 (267)
.+..+.||.+ |-+-|+||+|.+++++++++++-|.+--
T Consensus 709 ~~~~~~~p~~------~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 709 VTKEIEIPRS------LHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred eeeEEeccHH------HhhhccCCCCccHHHHHHHhccceecCC
Confidence 3445566644 5567999999999999999999887643
No 74
>KOG2113|consensus
Probab=43.18 E-value=21 Score=35.12 Aligned_cols=31 Identities=42% Similarity=0.612 Sum_probs=28.2
Q ss_pred CCeeeEEeCCCcchHHHHHHhhCceEEEeec
Q psy1580 36 FNFVGKLLGPKGNSLKRLQEDTMTRMAILGR 66 (267)
Q Consensus 36 ~NFvGrILGPrG~TlKrLE~eTgcKI~IRGr 66 (267)
+-+||++.||.|+|+|++|+.++.-|.--++
T Consensus 123 ~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 123 LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred ceeeeeccccccCccchheecccceEeeecc
Confidence 6789999999999999999999999876665
No 75
>PRK11032 hypothetical protein; Provisional
Probab=42.98 E-value=10 Score=33.37 Aligned_cols=29 Identities=7% Similarity=-0.073 Sum_probs=20.3
Q ss_pred CCCCCCCCCCCCCCCCCCccccccCCCccccCCCC
Q psy1580 149 EDGGAASCSESSESSVNNPLLYAENTSPVENLTPP 183 (267)
Q Consensus 149 Gt~r~~~cg~~~h~~~~cp~~~~~~~~~c~~cg~~ 183 (267)
|++.|.+||-.-|. .+....+.|..||..
T Consensus 123 G~LvC~~Cg~~~~~------~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 123 GNLVCEKCHHHLAF------YTPEVLPLCPKCGHD 151 (160)
T ss_pred ceEEecCCCCEEEe------cCCCcCCCCCCCCCC
Confidence 56779999876655 344555679999843
No 76
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=42.46 E-value=22 Score=32.37 Aligned_cols=28 Identities=29% Similarity=0.476 Sum_probs=26.7
Q ss_pred eeEEeCCCcchHHHHHHhhCceEEEeec
Q psy1580 39 VGKLLGPKGNSLKRLQEDTMTRMAILGR 66 (267)
Q Consensus 39 vGrILGPrG~TlKrLE~eTgcKI~IRGr 66 (267)
+|-|+|+.|.+.|.||+.++|+|.|=.+
T Consensus 19 ~~~lig~~g~v~k~ie~~~~~~~~iD~~ 46 (194)
T COG1094 19 IGVLIGKWGEVKKAIEEKTGVKLRIDSK 46 (194)
T ss_pred heeeecccccchHHHHhhcCeEEEEECC
Confidence 7899999999999999999999999877
No 77
>KOG0720|consensus
Probab=41.69 E-value=38 Score=34.66 Aligned_cols=78 Identities=13% Similarity=0.154 Sum_probs=42.6
Q ss_pred hhHHHHHHHHHHHHHHHhhcCCCcCCCCcchhHHHHHHHH-------------HHHHhhCCCCCCCCCCCCCCCCCCccc
Q psy1580 103 PAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMW-------------EMQILKEDGGAASCSESSESSVNNPLL 169 (267)
Q Consensus 103 ~~~a~~rl~~Av~~I~~lL~P~~~s~~~d~~DelK~~QL~-------------ELA~lNGt~r~~~cg~~~h~~~~cp~~ 169 (267)
.++|++.|+.|-+.|-. ++.++ +..++++++-.. +++.---|..|+.||. .|..+ |..+
T Consensus 273 A~Eafk~Lq~Afevig~---~~kR~---eYd~e~~kene~~~~~~~~~~~~~~~~eEA~ntI~CskC~n-~H~r~-~T~r 344 (490)
T KOG0720|consen 273 AEEAFKKLQVAFEVIGD---SVKRK---EYDLELKKENELHRQVISSLNDLQKAVEEARNTIFCSKCGN-THFRV-LTSR 344 (490)
T ss_pred HHHHHHHHHHHHHHhcc---hhhhh---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhheehhhhcC-cceee-eecC
Confidence 46788888888777632 22222 334444433221 2333346778999985 45532 3332
Q ss_pred cccCCCccccCCCCCCCCCC
Q psy1580 170 YAENTSPVENLTPPEYTLVD 189 (267)
Q Consensus 170 ~~~~~~~c~~cg~~gh~t~d 189 (267)
-...--.|..||. -|.++|
T Consensus 345 s~s~AR~C~~C~~-~H~AKd 363 (490)
T KOG0720|consen 345 SPSQARWCAECGV-KHPAKD 363 (490)
T ss_pred ChhhhHHHHHhCc-cCcccc
Confidence 2222225999995 477666
No 78
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=39.09 E-value=5.6 Score=29.39 Aligned_cols=20 Identities=35% Similarity=0.562 Sum_probs=18.2
Q ss_pred eeEEeCCCcchHHHHHHhhC
Q psy1580 39 VGKLLGPKGNSLKRLQEDTM 58 (267)
Q Consensus 39 vGrILGPrG~TlKrLE~eTg 58 (267)
.|+|||-+|.|++.||--++
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHH
T ss_pred cceEECCCCeeHHHHHHHHH
Confidence 79999999999999997665
No 79
>PF11598 COMP: Cartilage oligomeric matrix protein; InterPro: IPR024665 Thrombospondins are adhesive glycoproteins that mediate cell-to-cell and cell-to-matrix interactions. Cartilage oligomeric matrix protein may play a role in the structural integrity of cartilage via its interaction with other extracellular matrix proteins such as collagen and fibronectin [, ]. Thrombospondin 3 and 4 and cartilage oligomeric matrix proteins contain a five-stranded coiled-coil domain represented by this entry. This domain has a binding site between two internal rings formed by Leu37 and Thr40 [].; PDB: 1MZ9_D 1FBM_A 1VDF_E.
Probab=35.79 E-value=40 Score=23.86 Aligned_cols=41 Identities=17% Similarity=0.389 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHhhcCCCcCCCCcchhHHHHHHHHHHHHhhCCC-CCCCCC
Q psy1580 108 ARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWEMQILKEDG-GAASCS 157 (267)
Q Consensus 108 ~rl~~Av~~I~~lL~P~~~s~~~d~~DelK~~QL~ELA~lNGt~-r~~~cg 157 (267)
..|...+.+...+|.- -.+++ ++|..|.+.|..|+ +|.-||
T Consensus 4 ~~l~~ql~~l~~~l~e--------lk~~l-~~Q~kE~~~LRntI~eC~aCg 45 (45)
T PF11598_consen 4 SQLIKQLSELNQMLQE--------LKELL-RQQIKETRFLRNTIMECQACG 45 (45)
T ss_dssp HHHHHHHHHHHHHHHH--------HHHHH-HHHHHHHHHHHHHHHT-TTG-
T ss_pred HHHHHHHHHHHHHHHH--------HHHHH-HHHHHHHHHHHHHHHHhcccC
Confidence 3455666666666653 34555 55999999999885 577776
No 80
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=34.24 E-value=26 Score=34.71 Aligned_cols=42 Identities=14% Similarity=0.321 Sum_probs=32.9
Q ss_pred EEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhh-CceEEEeec
Q psy1580 24 IRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDT-MTRMAILGR 66 (267)
Q Consensus 24 eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eT-gcKI~IRGr 66 (267)
.||-|=- .-|+++-||..+|++|+.++.|.++. |=+|-|--=
T Consensus 239 tKVAV~S-~d~~iDPvGacIG~~G~rI~~I~~eL~gEkIDvI~~ 281 (374)
T PRK12328 239 AKVALFS-NNPNIDPIGATVGVKGVRINAVSKELNGENIDCIEY 281 (374)
T ss_pred eEEEEEc-CCCCCChHHhhcCCCcchHHHHHHHhCCCeEEEEEc
Confidence 3554432 34899999999999999999999999 777766543
No 81
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=33.62 E-value=21 Score=35.32 Aligned_cols=21 Identities=14% Similarity=0.181 Sum_probs=17.7
Q ss_pred hCCCCCCCCCCCCCCC-CCCcc
Q psy1580 148 KEDGGAASCSESSESS-VNNPL 168 (267)
Q Consensus 148 NGt~r~~~cg~~~h~~-~~cp~ 168 (267)
|-.|||.+||.+.|.. |.||.
T Consensus 352 ~~~YRC~~CGF~a~~l~W~CPs 373 (389)
T COG2956 352 KPRYRCQNCGFTAHTLYWHCPS 373 (389)
T ss_pred cCCceecccCCcceeeeeeCCC
Confidence 4458999999999995 69997
No 82
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=33.29 E-value=33 Score=34.88 Aligned_cols=43 Identities=12% Similarity=0.326 Sum_probs=34.6
Q ss_pred EEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhh-CceEEEeec
Q psy1580 23 TIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDT-MTRMAILGR 66 (267)
Q Consensus 23 ~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eT-gcKI~IRGr 66 (267)
..||-|=-. -|+++-||..+|++|+.++.|.++. |=||-|=-=
T Consensus 264 RtKVAV~S~-d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~y 307 (449)
T PRK12329 264 RTKIAVDTL-ERDVDPVGACIGARGSRIQAVVNELRGEKIDVIRW 307 (449)
T ss_pred eeEEEEEcC-CCCCChhhccCCCCcchHHHHHHHhCCCeEEEEEc
Confidence 346655432 3899999999999999999999999 888887654
No 83
>PRK02821 hypothetical protein; Provisional
Probab=31.49 E-value=28 Score=27.04 Aligned_cols=22 Identities=23% Similarity=0.410 Sum_probs=18.0
Q ss_pred CeeeEEeCCCcchHHHHHHhhC
Q psy1580 37 NFVGKLLGPKGNSLKRLQEDTM 58 (267)
Q Consensus 37 NFvGrILGPrG~TlKrLE~eTg 58 (267)
.=+|||||=+|.|.+.|-.--.
T Consensus 40 ~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 40 DDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred hhCcceeCCCCchHHHHHHHHH
Confidence 4589999999999998865543
No 84
>KOG3799|consensus
Probab=30.88 E-value=56 Score=28.64 Aligned_cols=46 Identities=22% Similarity=0.211 Sum_probs=28.8
Q ss_pred chhHHHHHHHHHHHHhh-------------CCCCCCCC---CCC------CCCCCCCccccccCCCccccCCCC
Q psy1580 132 YNDEIRQEQMWEMQILK-------------EDGGAASC---SES------SESSVNNPLLYAENTSPVENLTPP 183 (267)
Q Consensus 132 ~~DelK~~QL~ELA~lN-------------Gt~r~~~c---g~~------~h~~~~cp~~~~~~~~~c~~cg~~ 183 (267)
.+.++-++|..||..|. |+-.++.| ..+ ||.-+-|..+| |..||..
T Consensus 31 kq~ei~~~~~~e~~el~~Qi~erkEqqKKaGv~ddatC~IC~KTKFADG~GH~C~YCq~r~------CARCGGr 98 (169)
T KOG3799|consen 31 KQFEIYKEQVKEMGELSQQIQERKEQQKKAGVGDDATCGICHKTKFADGCGHNCSYCQTRF------CARCGGR 98 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCcCcchhhhhhcccccccCcccchhhhhH------HHhcCCe
Confidence 34555566666665555 55554444 333 77777787777 9999944
No 85
>KOG1244|consensus
Probab=30.70 E-value=34 Score=33.11 Aligned_cols=19 Identities=5% Similarity=-0.022 Sum_probs=10.7
Q ss_pred chhHHHHHHHHHHHHhhCC
Q psy1580 132 YNDEIRQEQMWEMQILKED 150 (267)
Q Consensus 132 ~~DelK~~QL~ELA~lNGt 150 (267)
+++..|+.--+.+|+-|+.
T Consensus 208 ge~~vkqr~kkd~a~Pn~Y 226 (336)
T KOG1244|consen 208 GEAKVKQRVKKDIAQPNPY 226 (336)
T ss_pred chhhHHHhhhcccccCCcc
Confidence 4455554444456777755
No 86
>PRK00468 hypothetical protein; Provisional
Probab=30.39 E-value=29 Score=26.66 Aligned_cols=19 Identities=26% Similarity=0.471 Sum_probs=16.1
Q ss_pred eeeEEeCCCcchHHHHHHh
Q psy1580 38 FVGKLLGPKGNSLKRLQED 56 (267)
Q Consensus 38 FvGrILGPrG~TlKrLE~e 56 (267)
=+|||||=+|.|.+.|-.-
T Consensus 40 D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 40 DMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred hCcceecCCChhHHHHHHH
Confidence 3799999999999987653
No 87
>PF00381 PTS-HPr: PTS HPr component phosphorylation site; InterPro: IPR005698 The histidine-containing phosphocarrier protein (HPr) is a central component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), which transfers metabolic carbohydrates across the cell membrane in many bacterial species [, ]. PTS catalyses the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is as follows: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to Enzyme I (EI) of the PTS, which in turn transfers it to the phosphoryl carrier protein (HPr) [, ]. Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease complex (enzymes EII/EIII). HPr [, ] is a small cytoplasmic protein of 70 to 90 amino acid residues. In some bacteria, HPr is a domain in a larger protein that includes a EIII(Fru) (IIA) domain and in some cases also the EI domain. A conserved histidine in the N-terminal section of HPr serves as an acceptor for the phosphoryl group of EI. In the central part of HPr, there is a conserved serine which (in Gram-positive bacteria only) is phosphorylated by an ATP-dependent protein kinase; a process which probably play a regulatory role in sugar transport. The overall architecture of the HPr domain has been described as an open faced beta-sandwich in which a beta-sheet is packed against three alpha-helices. Regulatory phosphorylation at the conserved Ser residue does not appear to induce large structural changes to the HPr domain, in particular in the region of the active site [, ].; GO: 0005351 sugar:hydrogen symporter activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TXE_A 1QR5_A 1RZR_S 2NZU_L 2OEN_L 2NZV_L 1Y51_B 1Y4Y_A 1Y50_A 2HPR_A ....
Probab=30.39 E-value=1e+02 Score=23.16 Aligned_cols=59 Identities=19% Similarity=0.183 Sum_probs=38.1
Q ss_pred HHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCChhHHHHHHHHHHHHHHHhh
Q psy1580 51 KRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFL 121 (267)
Q Consensus 51 KrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~~~a~~rl~~Av~~I~~lL 121 (267)
-++=+..+|.|.|+-.|..-|.++--.+-.-|- .-.+.++|.+++++. +.|++.|.++|
T Consensus 23 v~~a~~~~~~i~i~~~~~~vdakSil~l~~L~~----~~G~~i~i~~~G~de--------~~a~~~i~~~~ 81 (84)
T PF00381_consen 23 VQIASKFDSDITIRKGGKTVDAKSILGLMSLGA----KKGDEIEIEAEGEDE--------EEALEAIAEFL 81 (84)
T ss_dssp HHHHHTSSSEEEEEETTEEEETTSHHHHHHHTB----STTEEEEEEEESTTH--------HHHHHHHHHHH
T ss_pred HHHHhhCCCEEEEEeCceeEecCCHHHHhhhhc----CCCCEEEEEEECcCH--------HHHHHHHHHHH
Confidence 355567799999998876666655444432121 135788888888763 35666666665
No 88
>PRK01064 hypothetical protein; Provisional
Probab=30.30 E-value=38 Score=26.31 Aligned_cols=20 Identities=25% Similarity=0.667 Sum_probs=17.6
Q ss_pred eeEEeCCCcchHHHHHHhhC
Q psy1580 39 VGKLLGPKGNSLKRLQEDTM 58 (267)
Q Consensus 39 vGrILGPrG~TlKrLE~eTg 58 (267)
+|++||=+|.|++.|..-..
T Consensus 41 ~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred ceEEECCCCccHHHHHHHHH
Confidence 79999999999999987544
No 89
>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=30.01 E-value=9.5 Score=32.63 Aligned_cols=23 Identities=35% Similarity=0.541 Sum_probs=16.8
Q ss_pred EEecCCCCCCCCeeeEEeCCCcc
Q psy1580 26 VIVPVRDHPKFNFVGKLLGPKGN 48 (267)
Q Consensus 26 I~IPvkeyP~~NFvGrILGPrG~ 48 (267)
++--.+-.|.+..+|+||||||.
T Consensus 96 ~iA~~~~m~~l~~Lg~iLGprGl 118 (141)
T TIGR01170 96 LIAHPDIVPELAQLRRLLGPKGL 118 (141)
T ss_pred EEECHHHHHHHHHhhcccccCcC
Confidence 33334455777889999999986
No 90
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=29.73 E-value=43 Score=22.84 Aligned_cols=19 Identities=0% Similarity=-0.387 Sum_probs=12.4
Q ss_pred ccccCCCCCCCCCCCCCCC
Q psy1580 176 PVENLTPPEYTLVDPAFNR 194 (267)
Q Consensus 176 ~c~~cg~~gh~t~dc~~~~ 194 (267)
.|..||...|.++||....
T Consensus 4 ~CprC~kg~Hwa~~C~sk~ 22 (36)
T PF14787_consen 4 LCPRCGKGFHWASECRSKT 22 (36)
T ss_dssp C-TTTSSSCS-TTT---TC
T ss_pred cCcccCCCcchhhhhhhhh
Confidence 5999999999999999864
No 91
>KOG4718|consensus
Probab=29.58 E-value=52 Score=30.65 Aligned_cols=61 Identities=18% Similarity=0.235 Sum_probs=41.3
Q ss_pred HHHHHHHHhhcCCCcCCCCcchhHHHHHHH-HHHHHhhCCCCCCCCCCCCCCCCCCccccccCCCccccCCCC
Q psy1580 112 YALAEVRRFLVPFTRSLFQDYNDEIRQEQM-WEMQILKEDGGAASCSESSESSVNNPLLYAENTSPVENLTPP 183 (267)
Q Consensus 112 ~Av~~I~~lL~P~~~s~~~d~~DelK~~QL-~ELA~lNGt~r~~~cg~~~h~~~~cp~~~~~~~~~c~~cg~~ 183 (267)
+|+++++.+|.. ...|-+|-=|+ .+|++ -| .||.+||-.-|.. |=+.|......|..||+-
T Consensus 164 ralaELe~YL~s-------~y~dnlk~Cn~Ch~LvI-qg-~rCg~c~i~~h~~--c~qty~q~~~~cphc~d~ 225 (235)
T KOG4718|consen 164 RALAELEFYLSS-------NYADNLKNCNLCHCLVI-QG-IRCGSCNIQYHRG--CIQTYLQRRDICPHCGDL 225 (235)
T ss_pred HHHHHHHHHHHh-------hhHHHHHHHhHhHHHhh-ee-eccCcccchhhhH--HHHHHhcccCcCCchhcc
Confidence 778888888877 56778887777 44544 33 4788888655543 333666667889999863
No 92
>KOG4165|consensus
Probab=29.19 E-value=65 Score=32.15 Aligned_cols=41 Identities=22% Similarity=0.489 Sum_probs=28.6
Q ss_pred CeeeEEeCCCcch--HHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCC
Q psy1580 37 NFVGKLLGPKGNS--LKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAP 102 (267)
Q Consensus 37 NFvGrILGPrG~T--lKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~ 102 (267)
++|-+|| |||++ +++|+..|. |-+.|- .+.-.||+|--++.
T Consensus 190 ~~IDLvI-PRGSs~LVr~Ik~~tk--IPVLGH----------------------A~GichvYvd~dad 232 (433)
T KOG4165|consen 190 DYIDLVI-PRGSSDLVRSIKDTTK--IPVLGH----------------------AEGICHVYVDKDAD 232 (433)
T ss_pred hheeEEe-cCCcHHHHHHHhhccc--Cccccc----------------------ccceeEEEeccccC
Confidence 4555655 99987 577777664 777773 46678999976654
No 93
>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=28.61 E-value=41 Score=23.78 Aligned_cols=19 Identities=16% Similarity=0.142 Sum_probs=15.7
Q ss_pred hHHHHHHhhCceEEEeecc
Q psy1580 49 SLKRLQEDTMTRMAILGRG 67 (267)
Q Consensus 49 TlKrLE~eTgcKI~IRGrG 67 (267)
.+++||++.|+++.+|..+
T Consensus 33 ~i~~LE~~lg~~Lf~r~~~ 51 (60)
T PF00126_consen 33 QIKQLEEELGVPLFERSGR 51 (60)
T ss_dssp HHHHHHHHHTS-SEEECSS
T ss_pred HHHHHHHHhCCeEEEECCC
Confidence 4799999999999999654
No 94
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=28.35 E-value=26 Score=29.80 Aligned_cols=26 Identities=19% Similarity=0.355 Sum_probs=22.5
Q ss_pred eeeEEeCCCcchHHHHHHhhCceEEE
Q psy1580 38 FVGKLLGPKGNSLKRLQEDTMTRMAI 63 (267)
Q Consensus 38 FvGrILGPrG~TlKrLE~eTgcKI~I 63 (267)
-+|++||.+|.+++.++.-+|-++-|
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
No 95
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=28.07 E-value=82 Score=36.06 Aligned_cols=44 Identities=11% Similarity=-0.016 Sum_probs=27.9
Q ss_pred CCCCCCCCCCCCCCCCCcc--ccccCCCccccCCCCCCC----CCCCCCCC
Q psy1580 150 DGGAASCSESSESSVNNPL--LYAENTSPVENLTPPEYT----LVDPAFNR 194 (267)
Q Consensus 150 t~r~~~cg~~~h~~~~cp~--~~~~~~~~c~~cg~~gh~----t~dc~~~~ 194 (267)
..+|..||..... .-||. ........|..||..-.. +..|++=|
T Consensus 667 ~rkCPkCG~~t~~-~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CG 716 (1337)
T PRK14714 667 RRRCPSCGTETYE-NRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCD 716 (1337)
T ss_pred EEECCCCCCcccc-ccCcccCCcCCCceeCccCCCccCCCccccccCCCCC
Confidence 4789999987765 36776 222334478888864222 33577755
No 96
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=28.05 E-value=43 Score=33.95 Aligned_cols=42 Identities=17% Similarity=0.432 Sum_probs=33.9
Q ss_pred EEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhh-CceEEEeec
Q psy1580 24 IRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDT-MTRMAILGR 66 (267)
Q Consensus 24 eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eT-gcKI~IRGr 66 (267)
.||-|= ..-|++.-||..+|++|+.++.+.++. |=+|-|--=
T Consensus 233 aKvAV~-s~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~ 275 (470)
T PRK09202 233 AKIAVK-SNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILW 275 (470)
T ss_pred eEEEEE-cCCCCCChhHccCCCCCchHHHHHHHhCCCeEEEEEc
Confidence 355444 334899999999999999999999999 788877654
No 97
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=26.38 E-value=38 Score=26.38 Aligned_cols=18 Identities=22% Similarity=0.654 Sum_probs=15.7
Q ss_pred eeeEEeCCCcchHHHHHH
Q psy1580 38 FVGKLLGPKGNSLKRLQE 55 (267)
Q Consensus 38 FvGrILGPrG~TlKrLE~ 55 (267)
=+|++||=+|.|.+.|-.
T Consensus 40 D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 40 DMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred cccceecCCChhHHHHHH
Confidence 389999999999998854
No 98
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=26.36 E-value=49 Score=32.61 Aligned_cols=30 Identities=23% Similarity=0.290 Sum_probs=27.6
Q ss_pred CeeeEEeCCCcchHHHHHHhhCceEEEeec
Q psy1580 37 NFVGKLLGPKGNSLKRLQEDTMTRMAILGR 66 (267)
Q Consensus 37 NFvGrILGPrG~TlKrLE~eTgcKI~IRGr 66 (267)
|-+--|+||.|..++.||+..|+.|.-||.
T Consensus 24 ~~~~~l~G~~~~~l~l~e~~~gv~i~~rG~ 53 (348)
T COG1702 24 NELVALFGPTDTNLSLLEIALGVSIVARGE 53 (348)
T ss_pred hhhhhhcCCCCccHHHHHHHhCcEEEeCCc
Confidence 667779999999999999999999999986
No 99
>PRK13782 phosphocarrier protein Chr; Provisional
Probab=26.05 E-value=1.8e+02 Score=22.04 Aligned_cols=56 Identities=9% Similarity=-0.040 Sum_probs=33.3
Q ss_pred HHhhCceEEEeeccccCCcchhhhhhcCCCCccCCCCCccEEEEEecCChhHHHHHHHHHHHHHHHhh
Q psy1580 54 QEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFL 121 (267)
Q Consensus 54 E~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~hl~EpLHVlIsa~~~~~~a~~rl~~Av~~I~~lL 121 (267)
=+...|.|.|+-.|-.-+.++=-.+-.-|-. -.+.+.|.++++|. +.|++.|.++|
T Consensus 26 a~~f~~~i~l~~~~~~vdaKSil~llsLg~~----~g~~v~v~~~G~de--------~~a~~~l~~~~ 81 (82)
T PRK13782 26 ANRFHADIFIEKDGKKVNAKSIMGLMSLAIG----TGSMITIITEGSDE--------EEALEALAAYV 81 (82)
T ss_pred HHhCCCEEEEEECCeEEecHhHHHHHhcCCC----CCCEEEEEEeCcCH--------HHHHHHHHHHh
Confidence 3467899999866555555544343322211 35678888777653 35666666665
No 100
>PRK04023 DNA polymerase II large subunit; Validated
Probab=25.76 E-value=52 Score=36.82 Aligned_cols=118 Identities=14% Similarity=0.060 Sum_probs=66.0
Q ss_pred CCcchHHHHHHhhCceEEEeeccccCCcchhhhhhcCCCCccC---CCCCccEEEEEecCChhHHHHHHHHHHHHHHHhh
Q psy1580 45 PKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFL---HLLEELHVEITAFAPPAEAHARIAYALAEVRRFL 121 (267)
Q Consensus 45 PrG~TlKrLE~eTgcKI~IRGrGS~kd~~ke~elr~sgdp~~~---hl~EpLHVlIsa~~~~~~a~~rl~~Av~~I~~lL 121 (267)
...++++-+-+-+| |.||-|+.++-+.+= |.|+-+ .+.-|.|+|.=.-.. --+...|.+|.+.-..+-
T Consensus 551 ~~~~~~~~vn~~s~--~~ir~ra~trIG~Rm------GRPEKa~~RkMkP~~h~LFPiG~~-GG~~R~i~~A~~~~g~~e 621 (1121)
T PRK04023 551 DGSNVLEAVNELSG--FEIRPKAPTRIGARM------GRPEKAKERKMKPPVHVLFPIGNA-GGSTRDINKAAKYKGTIE 621 (1121)
T ss_pred ccccHHHHHHHhCC--cEEeccCCceeeccc------CCCcccccccCCCCCccccccccc-CcccccHHHHHhcCCcee
Confidence 33467777777776 557777777776532 344222 356788998754321 122345777765311121
Q ss_pred cCCC-cCCCCcchhHHHHHHHHHHHHhhCCCCCCCCCCCCCCCCCCcc-ccccCCCccccCCCCC
Q psy1580 122 VPFT-RSLFQDYNDEIRQEQMWEMQILKEDGGAASCSESSESSVNNPL-LYAENTSPVENLTPPE 184 (267)
Q Consensus 122 ~P~~-~s~~~d~~DelK~~QL~ELA~lNGt~r~~~cg~~~h~~~~cp~-~~~~~~~~c~~cg~~g 184 (267)
+++. ..+..=+.. -...+|.+||......+-||. .-..+.-.|..||-..
T Consensus 622 VEVg~RfCpsCG~~-------------t~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El 673 (1121)
T PRK04023 622 VEIGRRKCPSCGKE-------------TFYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREP 673 (1121)
T ss_pred ecccCccCCCCCCc-------------CCcccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCC
Confidence 2211 001101111 144789999988777788887 4444445699999653
No 101
>KOG2192|consensus
Probab=24.91 E-value=1.3e+02 Score=29.21 Aligned_cols=38 Identities=21% Similarity=0.565 Sum_probs=30.5
Q ss_pred ceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEe
Q psy1580 21 KVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAIL 64 (267)
Q Consensus 21 k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IR 64 (267)
++.-+|++--+. -|.|+|-.|.++|+|-.+.++.|+|-
T Consensus 47 r~e~ril~~sk~------agavigkgg~nik~lr~d~na~v~vp 84 (390)
T KOG2192|consen 47 RVELRILLQSKN------AGAVIGKGGKNIKALRTDYNASVSVP 84 (390)
T ss_pred ceeEEEEEeccc------ccceeccccccHHHHhhhccceeecc
Confidence 455566665442 58999999999999999999999874
No 102
>KOG0341|consensus
Probab=24.66 E-value=36 Score=34.76 Aligned_cols=22 Identities=9% Similarity=-0.165 Sum_probs=14.8
Q ss_pred ccccCCCCCCCCCCCCC-CCccC
Q psy1580 176 PVENLTPPEYTLVDPAF-NRIQP 197 (267)
Q Consensus 176 ~c~~cg~~gh~t~dc~~-~~~~~ 197 (267)
-|..||.-||--.|||- ..+|+
T Consensus 572 GCayCgGLGHRItdCPKle~~~~ 594 (610)
T KOG0341|consen 572 GCAYCGGLGHRITDCPKLEAQQN 594 (610)
T ss_pred ccccccCCCcccccCchhhhhcc
Confidence 37888888888778764 33443
No 103
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=24.52 E-value=2.2e+02 Score=26.06 Aligned_cols=31 Identities=6% Similarity=0.116 Sum_probs=18.1
Q ss_pred CccEEEEEecCCh-hHHHHHHHHHHHHHHHhh
Q psy1580 91 EELHVEITAFAPP-AEAHARIAYALAEVRRFL 121 (267)
Q Consensus 91 EpLHVlIsa~~~~-~~a~~rl~~Av~~I~~lL 121 (267)
--+|+-|=-.+-+ ++-.+.+...++.|.+.+
T Consensus 168 g~i~~~IG~~~m~~e~i~eNi~a~l~~i~~~~ 199 (230)
T PRK05424 168 GIIHAPIGKVSFDAEKLKENLKALIDAIKKAK 199 (230)
T ss_pred CEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhC
Confidence 4566666544432 455566666666666654
No 104
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=24.12 E-value=50 Score=29.36 Aligned_cols=24 Identities=21% Similarity=0.266 Sum_probs=19.6
Q ss_pred chHHHHHHhhCceEEEeeccccCC
Q psy1580 48 NSLKRLQEDTMTRMAILGRGSIRD 71 (267)
Q Consensus 48 ~TlKrLE~eTgcKI~IRGrGS~kd 71 (267)
..+|+||++.|+++.+|++|..-.
T Consensus 35 ~~i~~LE~~lg~~Lf~R~r~i~lT 58 (294)
T PRK13348 35 QRIKALEESLGQPLLVRGRPCRPT 58 (294)
T ss_pred HHHHHHHHHhCceeeecCCCCccC
Confidence 358999999999999999864433
No 105
>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=22.69 E-value=17 Score=33.28 Aligned_cols=13 Identities=38% Similarity=0.912 Sum_probs=9.9
Q ss_pred CCeeeEEeCCCcc
Q psy1580 36 FNFVGKLLGPKGN 48 (267)
Q Consensus 36 ~NFvGrILGPrG~ 48 (267)
...+|+||||||.
T Consensus 122 l~~Lg~iLGPrGl 134 (227)
T TIGR01169 122 VGKLGRILGPRGL 134 (227)
T ss_pred HHHhccccccccC
Confidence 3445999999973
No 106
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=21.47 E-value=73 Score=34.25 Aligned_cols=39 Identities=10% Similarity=-0.130 Sum_probs=28.3
Q ss_pred CCCCCCCCCCCCCCCcc-----c--cccCCCccccCCCCCCCCCCCCCCC
Q psy1580 152 GAASCSESSESSVNNPL-----L--YAENTSPVENLTPPEYTLVDPAFNR 194 (267)
Q Consensus 152 r~~~cg~~~h~~~~cp~-----~--~~~~~~~c~~cg~~gh~t~dc~~~~ 194 (267)
-|..|| ....||. . -..+...|+.||-...+...||-=|
T Consensus 437 ~C~~Cg----~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cg 482 (730)
T COG1198 437 LCRDCG----YIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECG 482 (730)
T ss_pred ecccCC----CcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCC
Confidence 477777 4566775 2 2246678999999999999998744
No 107
>KOG2192|consensus
Probab=21.44 E-value=99 Score=30.06 Aligned_cols=40 Identities=25% Similarity=0.532 Sum_probs=32.5
Q ss_pred CCcceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHHhhCceEEEe
Q psy1580 18 KPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAIL 64 (267)
Q Consensus 18 kp~k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~eTgcKI~IR 64 (267)
-|+. +..|-||-+ +-|-|||-.|.-+|||-.|+|+.|.|-
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 3443 446788844 679999999999999999999999874
No 108
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=21.17 E-value=1.2e+02 Score=24.47 Aligned_cols=33 Identities=6% Similarity=-0.013 Sum_probs=25.6
Q ss_pred HHHhhCCCCCCCCCCCCCCCCCCccccccCCCccccCCC
Q psy1580 144 MQILKEDGGAASCSESSESSVNNPLLYAENTSPVENLTP 182 (267)
Q Consensus 144 LA~lNGt~r~~~cg~~~h~~~~cp~~~~~~~~~c~~cg~ 182 (267)
.+..+..+.|..||.+.++ +.+..+-.|..||-
T Consensus 29 e~~~~~~~~Cp~C~~~~Vk------R~a~GIW~C~kCg~ 61 (89)
T COG1997 29 EAQQRAKHVCPFCGRTTVK------RIATGIWKCRKCGA 61 (89)
T ss_pred HHHHhcCCcCCCCCCccee------eeccCeEEcCCCCC
Confidence 3666778899999988777 56666668988883
No 109
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=20.25 E-value=1e+02 Score=33.17 Aligned_cols=26 Identities=8% Similarity=-0.227 Sum_probs=19.6
Q ss_pred CCCccccCCCCCCC--CCCCCCCCccCC
Q psy1580 173 NTSPVENLTPPEYT--LVDPAFNRIQPA 198 (267)
Q Consensus 173 ~~~~c~~cg~~gh~--t~dc~~~~~~~~ 198 (267)
..-+|..||+.||+ -+-||.-+....
T Consensus 936 Ttr~C~nCGQvGHmkTNK~CP~f~s~~~ 963 (968)
T COG5179 936 TTRTCGNCGQVGHMKTNKACPKFSSKDN 963 (968)
T ss_pred cceecccccccccccccccCccccCCCC
Confidence 34589999999999 567988764444
No 110
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=20.17 E-value=35 Score=31.38 Aligned_cols=10 Identities=50% Similarity=1.245 Sum_probs=8.7
Q ss_pred eeEEeCCCcc
Q psy1580 39 VGKLLGPKGN 48 (267)
Q Consensus 39 vGrILGPrG~ 48 (267)
+|+||||||.
T Consensus 126 LgriLGprGl 135 (229)
T CHL00129 126 LGRVLGPRGL 135 (229)
T ss_pred hcCcccccCC
Confidence 5999999975
No 111
>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=20.16 E-value=2e+02 Score=26.01 Aligned_cols=39 Identities=13% Similarity=0.143 Sum_probs=28.3
Q ss_pred cceEEEEEecCCCCCCCCeeeEEeCCCcchHHHHHH--------hhCceEEE
Q psy1580 20 IKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQE--------DTMTRMAI 63 (267)
Q Consensus 20 ~k~~eKI~IPvkeyP~~NFvGrILGPrG~TlKrLE~--------eTgcKI~I 63 (267)
+.+...|++.-+. --|-|||-+|..+|+|.. -.||+|.+
T Consensus 219 ~~i~~~i~v~~~s-----~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l 265 (270)
T TIGR00436 219 LKIHALISVERES-----QKKIIIGKNGSMIKAIGIAARKDILELFDCDVFL 265 (270)
T ss_pred EEEEEEEEECcCC-----ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 4566778887663 458999999999998644 45666654
No 112
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=20.06 E-value=68 Score=34.48 Aligned_cols=19 Identities=11% Similarity=0.270 Sum_probs=15.6
Q ss_pred CCCCCCCCCCCCCCC--CCcc
Q psy1580 150 DGGAASCSESSESSV--NNPL 168 (267)
Q Consensus 150 t~r~~~cg~~~h~~~--~cp~ 168 (267)
|.+|.+||+-||... .||.
T Consensus 937 tr~C~nCGQvGHmkTNK~CP~ 957 (968)
T COG5179 937 TRTCGNCGQVGHMKTNKACPK 957 (968)
T ss_pred ceecccccccccccccccCcc
Confidence 567999999999864 6885
Done!