Query 031032
Match_columns 167
No_of_seqs 141 out of 570
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 08:13:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031032.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031032hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1588 RNA-binding protein Sa 100.0 5.7E-50 1.2E-54 336.9 13.9 155 11-167 84-242 (259)
2 cd02395 SF1_like-KH Splicing f 100.0 1.8E-42 3.8E-47 263.8 12.8 119 20-142 1-120 (120)
3 KOG0119 Splicing factor 1/bran 100.0 1.2E-35 2.6E-40 266.9 10.4 131 8-146 127-261 (554)
4 COG5176 MSL5 Splicing factor ( 99.9 2.5E-28 5.5E-33 201.3 7.3 128 13-144 142-269 (269)
5 cd02393 PNPase_KH Polynucleoti 99.4 1.3E-12 2.8E-17 88.3 7.0 61 18-113 1-61 (61)
6 TIGR02696 pppGpp_PNP guanosine 99.1 1.7E-10 3.8E-15 109.5 7.9 73 11-118 570-642 (719)
7 TIGR03591 polynuc_phos polyrib 98.9 1.2E-09 2.7E-14 103.5 6.0 73 11-118 543-615 (684)
8 cd02394 vigilin_like_KH K homo 98.9 1.6E-09 3.4E-14 72.2 4.7 61 21-113 2-62 (62)
9 PF00013 KH_1: KH domain syndr 98.9 3.9E-10 8.5E-15 74.7 1.7 59 21-112 2-60 (60)
10 cd00105 KH-I K homology RNA-bi 98.9 6.7E-09 1.5E-13 68.6 7.2 62 21-112 2-63 (64)
11 smart00322 KH K homology RNA-b 98.8 3.4E-08 7.3E-13 64.3 7.5 66 19-116 3-68 (69)
12 PLN00207 polyribonucleotide nu 98.8 3.6E-09 7.9E-14 102.6 3.7 73 12-119 678-751 (891)
13 PRK13763 putative RNA-processi 98.7 1.2E-08 2.6E-13 82.4 5.1 64 20-118 4-71 (180)
14 cd02396 PCBP_like_KH K homolog 98.7 3.2E-08 7E-13 67.0 6.3 63 21-112 2-64 (65)
15 TIGR03665 arCOG04150 arCOG0415 98.7 1.5E-08 3.2E-13 81.2 3.5 61 23-118 2-65 (172)
16 KOG1960 Predicted RNA-binding 98.6 2.4E-08 5.3E-13 89.6 2.9 92 22-127 213-304 (531)
17 PF13014 KH_3: KH domain 98.6 1.2E-07 2.7E-12 59.3 5.0 28 35-62 1-28 (43)
18 PRK11824 polynucleotide phosph 98.5 4.7E-08 1E-12 92.9 3.3 75 9-118 544-618 (693)
19 COG1185 Pnp Polyribonucleotide 98.5 1.2E-07 2.5E-12 89.6 5.0 72 13-119 546-617 (692)
20 TIGR03665 arCOG04150 arCOG0415 98.4 2.2E-07 4.7E-12 74.5 4.6 53 35-118 99-151 (172)
21 PRK13763 putative RNA-processi 98.4 4.4E-07 9.6E-12 73.3 5.4 53 35-118 105-157 (180)
22 PRK04163 exosome complex RNA-b 98.2 3.4E-06 7.3E-11 70.7 5.9 64 22-120 148-211 (235)
23 COG1094 Predicted RNA-binding 98.0 1.5E-05 3.2E-10 65.6 6.3 55 35-120 112-166 (194)
24 KOG1676 K-homology type RNA bi 97.8 4.6E-05 9.9E-10 71.3 7.3 74 17-118 137-210 (600)
25 KOG1676 K-homology type RNA bi 97.7 0.00011 2.4E-09 68.7 7.4 71 20-119 231-301 (600)
26 KOG2193 IGF-II mRNA-binding pr 97.6 0.00011 2.5E-09 66.9 5.9 70 21-119 201-270 (584)
27 KOG1067 Predicted RNA-binding 97.4 0.00016 3.6E-09 67.8 4.8 72 12-119 590-661 (760)
28 KOG2191 RNA-binding protein NO 97.0 0.0032 7E-08 56.0 8.2 37 19-61 132-168 (402)
29 KOG2874 rRNA processing protei 97.0 0.0022 4.8E-08 55.9 6.6 68 37-135 161-228 (356)
30 PRK00106 hypothetical protein; 96.9 0.002 4.4E-08 60.2 6.2 66 20-118 226-291 (535)
31 TIGR03319 YmdA_YtgF conserved 96.9 0.002 4.2E-08 59.9 5.8 66 20-118 205-270 (514)
32 PRK12704 phosphodiesterase; Pr 96.8 0.007 1.5E-07 56.3 9.0 65 20-117 211-275 (520)
33 KOG2191 RNA-binding protein NO 96.7 0.0035 7.5E-08 55.8 5.6 38 18-61 38-75 (402)
34 KOG2190 PolyC-binding proteins 96.6 0.0052 1.1E-07 56.9 6.8 72 18-118 137-208 (485)
35 KOG2193 IGF-II mRNA-binding pr 96.4 0.001 2.2E-08 60.8 0.6 38 24-61 279-316 (584)
36 KOG2814 Transcription coactiva 96.3 0.0046 1E-07 54.7 4.0 59 34-117 66-124 (345)
37 cd02134 NusA_KH NusA_K homolog 96.1 0.012 2.5E-07 39.5 4.4 36 19-60 25-60 (61)
38 COG1094 Predicted RNA-binding 95.5 0.049 1.1E-06 45.0 6.7 69 18-120 7-79 (194)
39 PRK12705 hypothetical protein; 94.6 0.043 9.4E-07 51.1 4.4 66 20-118 199-264 (508)
40 COG1097 RRP4 RNA-binding prote 94.6 0.17 3.7E-06 43.1 7.5 41 34-98 155-195 (239)
41 KOG1960 Predicted RNA-binding 94.1 0.022 4.8E-07 51.9 1.2 76 38-126 308-383 (531)
42 KOG0336 ATP-dependent RNA heli 93.5 0.13 2.8E-06 47.7 5.0 29 33-61 55-83 (629)
43 KOG2190 PolyC-binding proteins 93.5 0.099 2.1E-06 48.5 4.3 42 16-63 335-376 (485)
44 PF13184 KH_5: NusA-like KH do 92.7 0.045 9.7E-07 37.9 0.7 32 30-61 13-45 (69)
45 cd02409 KH-II KH-II (K homolo 90.1 0.29 6.2E-06 31.6 2.5 23 36-58 36-58 (68)
46 PRK08406 transcription elongat 89.3 0.47 1E-05 37.0 3.5 28 35-62 42-69 (140)
47 KOG2192 PolyC-binding hnRNP-K 89.0 1.4 3.1E-05 38.7 6.6 37 20-62 49-85 (390)
48 KOG2192 PolyC-binding hnRNP-K 86.8 1.4 2.9E-05 38.8 5.1 37 20-62 316-352 (390)
49 KOG2113 Predicted RNA binding 84.6 1.5 3.3E-05 39.2 4.4 38 17-60 24-61 (394)
50 cd02414 jag_KH jag_K homology 83.5 0.73 1.6E-05 31.9 1.6 27 35-61 34-60 (77)
51 COG1855 ATPase (PilT family) [ 83.0 1.1 2.4E-05 42.0 3.1 39 21-65 488-526 (604)
52 PRK08406 transcription elongat 82.1 1.2 2.5E-05 34.8 2.5 36 20-61 100-135 (140)
53 COG0195 NusA Transcription elo 82.1 1.1 2.3E-05 36.9 2.3 32 32-63 83-114 (190)
54 PRK12327 nusA transcription el 81.4 1.6 3.4E-05 39.2 3.3 34 29-62 240-274 (362)
55 TIGR01953 NusA transcription t 80.7 1.9 4.2E-05 38.3 3.7 33 30-62 239-272 (341)
56 TIGR01952 nusA_arch NusA famil 80.6 1.4 2.9E-05 34.6 2.4 29 34-62 42-70 (141)
57 PRK12329 nusA transcription el 80.5 2.9 6.4E-05 38.6 4.8 33 30-62 273-306 (449)
58 PRK02821 hypothetical protein; 80.3 0.97 2.1E-05 32.0 1.3 22 35-56 41-62 (77)
59 PRK00468 hypothetical protein; 80.1 0.99 2.1E-05 31.8 1.3 26 22-53 33-58 (75)
60 COG1702 PhoH Phosphate starvat 79.7 3.8 8.2E-05 36.8 5.1 30 34-63 24-53 (348)
61 KOG2208 Vigilin [Lipid transpo 79.3 1.3 2.8E-05 43.3 2.3 40 16-61 706-745 (753)
62 PRK13764 ATPase; Provisional 77.5 1.6 3.5E-05 41.6 2.3 40 20-65 482-521 (602)
63 PF13083 KH_4: KH domain; PDB: 77.1 0.44 9.5E-06 32.5 -1.2 21 35-55 39-59 (73)
64 COG1837 Predicted RNA-binding 76.1 1.5 3.3E-05 31.1 1.3 19 35-53 40-58 (76)
65 PRK06418 transcription elongat 75.1 2.4 5.1E-05 34.3 2.3 27 37-63 72-98 (166)
66 PRK01064 hypothetical protein; 73.6 5.2 0.00011 28.3 3.5 21 35-55 40-60 (78)
67 PRK12328 nusA transcription el 72.9 2.4 5.2E-05 38.3 2.1 34 29-62 246-280 (374)
68 PRK12328 nusA transcription el 72.8 4.8 0.0001 36.4 3.9 44 19-68 308-351 (374)
69 KOG3273 Predicted RNA-binding 70.9 3.3 7.1E-05 35.0 2.3 28 35-62 179-206 (252)
70 KOG4165 Gamma-glutamyl phospha 69.2 6.5 0.00014 35.6 3.9 62 34-118 190-260 (433)
71 KOG2208 Vigilin [Lipid transpo 68.7 6.5 0.00014 38.5 4.1 32 35-66 357-388 (753)
72 PRK09202 nusA transcription el 68.7 4 8.6E-05 37.9 2.6 34 29-62 240-274 (470)
73 KOG2279 Kinase anchor protein 65.7 4.5 9.7E-05 38.5 2.3 42 17-64 66-107 (608)
74 TIGR00436 era GTP-binding prot 61.3 20 0.00043 29.9 5.2 40 17-61 219-266 (270)
75 cd02410 archeal_CPSF_KH The ar 59.0 11 0.00024 29.9 3.1 27 35-61 86-112 (145)
76 TIGR01953 NusA transcription t 58.9 10 0.00022 33.8 3.2 38 19-62 301-338 (341)
77 COG3967 DltE Short-chain dehyd 56.0 7.2 0.00016 33.2 1.7 69 52-135 2-72 (245)
78 PF14611 SLS: Mitochondrial in 52.8 39 0.00086 27.1 5.5 80 35-143 36-130 (210)
79 PRK00089 era GTPase Era; Revie 52.0 31 0.00068 28.8 5.0 39 18-61 225-271 (292)
80 KOG1423 Ras-like GTPase ERA [C 51.7 17 0.00036 32.8 3.3 39 23-61 326-373 (379)
81 PRK09986 DNA-binding transcrip 50.7 20 0.00043 29.2 3.5 19 45-63 40-58 (294)
82 PRK15494 era GTPase Era; Provi 47.8 38 0.00081 29.6 4.9 38 19-61 273-318 (339)
83 PRK09202 nusA transcription el 46.2 18 0.00039 33.6 2.8 37 20-62 303-339 (470)
84 PRK05424 rplA 50S ribosomal pr 46.1 61 0.0013 27.2 5.7 64 33-116 123-199 (230)
85 PRK12327 nusA transcription el 46.0 23 0.0005 31.8 3.4 39 19-63 303-341 (362)
86 PF07650 KH_2: KH domain syndr 43.4 4.5 9.8E-05 27.6 -1.2 24 35-58 35-58 (78)
87 TIGR01169 rplA_bact ribosomal 43.0 40 0.00087 28.2 4.2 30 33-62 122-163 (227)
88 COG0081 RplA Ribosomal protein 42.7 33 0.00071 29.2 3.6 76 22-117 114-202 (228)
89 PTZ00225 60S ribosomal protein 42.1 68 0.0015 26.7 5.4 61 36-116 117-191 (214)
90 TIGR01952 nusA_arch NusA famil 42.0 18 0.00038 28.4 1.8 37 19-61 100-136 (141)
91 PF00126 HTH_1: Bacterial regu 40.5 23 0.00051 22.8 2.0 19 46-64 33-51 (60)
92 KOG2113 Predicted RNA binding 40.0 14 0.0003 33.2 1.0 31 33-63 123-153 (394)
93 PRK10837 putative DNA-binding 37.5 42 0.00091 27.3 3.5 20 45-64 36-55 (290)
94 PRK11716 DNA-binding transcrip 35.8 45 0.00098 26.5 3.3 18 46-63 11-28 (269)
95 cd02412 30S_S3_KH K homology R 34.5 22 0.00048 26.2 1.2 21 35-55 71-91 (109)
96 COG0080 RplK Ribosomal protein 32.7 1.7E+02 0.0037 23.2 5.9 40 18-57 5-44 (141)
97 PRK09906 DNA-binding transcrip 32.4 55 0.0012 26.8 3.4 20 45-64 34-53 (296)
98 PRK11013 DNA-binding transcrip 32.3 37 0.0008 28.3 2.4 19 46-64 38-56 (309)
99 PRK11242 DNA-binding transcrip 32.3 62 0.0014 26.3 3.7 18 45-62 34-51 (296)
100 PF00381 PTS-HPr: PTS HPr comp 31.9 36 0.00077 23.5 1.9 59 47-117 22-82 (84)
101 PRK12329 nusA transcription el 30.9 39 0.00084 31.4 2.4 38 20-63 336-373 (449)
102 PRK09791 putative DNA-binding 30.9 71 0.0015 26.3 3.8 19 46-64 39-57 (302)
103 PRK15421 DNA-binding transcrip 30.8 60 0.0013 27.4 3.4 18 45-62 35-52 (317)
104 COG0195 NusA Transcription elo 30.8 46 0.00099 27.4 2.6 37 20-62 143-179 (190)
105 COG1847 Jag Predicted RNA-bind 30.7 21 0.00045 30.0 0.6 26 36-61 102-127 (208)
106 PRK03601 transcriptional regul 29.8 62 0.0014 26.5 3.3 17 46-62 35-51 (275)
107 TIGR02036 dsdC D-serine deamin 29.7 58 0.0013 27.1 3.1 19 46-64 42-60 (302)
108 COG0026 PurK Phosphoribosylami 29.6 92 0.002 28.4 4.5 49 35-98 305-355 (375)
109 TIGR01170 rplA_mito ribosomal 29.4 9.8 0.00021 29.7 -1.5 19 27-45 100-118 (141)
110 PRK11074 putative DNA-binding 28.7 76 0.0016 26.2 3.7 18 45-62 35-52 (300)
111 KOG4797 Transcriptional regula 28.5 16 0.00034 27.9 -0.4 43 102-145 47-90 (123)
112 PRK13348 chromosome replicatio 28.4 43 0.00093 27.5 2.1 21 45-65 35-55 (294)
113 PRK10094 DNA-binding transcrip 27.6 72 0.0016 26.7 3.4 18 46-63 36-53 (308)
114 KOG0334 RNA helicase [RNA proc 27.4 35 0.00076 34.7 1.6 78 22-117 899-976 (997)
115 cd02413 40S_S3_KH K homology R 27.0 51 0.0011 23.2 2.0 21 35-55 40-60 (81)
116 PRK13782 phosphocarrier protei 26.8 86 0.0019 21.7 3.1 54 51-116 26-81 (82)
117 PRK12680 transcriptional regul 26.3 67 0.0015 27.4 3.0 21 46-66 36-56 (327)
118 PRK06019 phosphoribosylaminoim 26.0 1.8E+02 0.0038 25.5 5.6 49 35-98 305-355 (372)
119 PRK00394 transcription factor; 25.2 2.6E+02 0.0056 22.5 6.0 31 89-119 56-86 (179)
120 PRK15092 DNA-binding transcrip 25.0 74 0.0016 26.9 3.0 19 45-63 44-62 (310)
121 PRK14997 LysR family transcrip 24.5 87 0.0019 25.7 3.3 18 46-63 36-53 (301)
122 PRK11151 DNA-binding transcrip 24.5 87 0.0019 25.8 3.3 18 45-62 34-51 (305)
123 TIGR02424 TF_pcaQ pca operon t 24.5 75 0.0016 26.0 2.9 20 45-64 36-55 (300)
124 cd04516 TBP_eukaryotes eukaryo 24.0 2.8E+02 0.006 22.3 6.0 50 26-117 123-172 (174)
125 TIGR03298 argP transcriptional 22.8 50 0.0011 27.0 1.5 20 46-65 35-54 (292)
126 PRK10086 DNA-binding transcrip 22.7 75 0.0016 26.5 2.6 20 45-64 47-66 (311)
127 TIGR03418 chol_sulf_TF putativ 22.0 57 0.0012 26.6 1.7 17 46-62 35-51 (291)
128 TIGR01632 L11_bact 50S ribosom 21.9 1.2E+02 0.0026 23.7 3.4 40 19-58 5-44 (140)
129 PF03946 Ribosomal_L11_N: Ribo 21.6 21 0.00045 24.0 -0.8 21 35-55 16-36 (60)
130 PRK11482 putative DNA-binding 21.4 69 0.0015 27.1 2.1 20 45-64 62-81 (317)
131 PF00408 PGM_PMM_IV: Phosphogl 20.7 1.3E+02 0.0029 20.0 3.0 23 88-115 49-71 (73)
132 cd00652 TBP_TLF TATA box bindi 20.6 4.1E+02 0.0088 21.2 6.3 31 89-119 57-87 (174)
133 PRK10082 cell density-dependen 20.5 81 0.0018 26.1 2.3 19 45-63 44-62 (303)
134 KOG2944 Glyoxalase [Carbohydra 20.5 1.2E+02 0.0025 24.8 3.1 19 89-115 118-136 (170)
135 PRK03635 chromosome replicatio 20.4 79 0.0017 26.0 2.2 21 45-65 35-55 (294)
No 1
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=100.00 E-value=5.7e-50 Score=336.87 Aligned_cols=155 Identities=55% Similarity=0.895 Sum_probs=145.9
Q ss_pred CCCCcccceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEE
Q 031032 11 SPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHI 90 (167)
Q Consensus 11 ~~~g~~~~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV 90 (167)
.++++.++.+.||+||+++||+||||||||||+|+|+|+||++|||||.|||+||+||..+|++++++|+|+|+++||||
T Consensus 84 ~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHV 163 (259)
T KOG1588|consen 84 VYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHV 163 (259)
T ss_pred CccCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEE
Confidence 68899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCcchHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHhcCc-cCCCCCCCCC---CCCCCCcccccccccC
Q 031032 91 LIEADLPANIVDIRLRQAQEIIEELLKPVDESQDYIKRQQLRELAMLNSN-FREDSPGPSG---SVSPFNSSGMKRAKTG 166 (167)
Q Consensus 91 ~Isa~~~~~~a~~~l~~A~~~Ie~LL~~~~~~~d~~k~~QL~elA~lnGt-~r~~~~~~~~---~~~~~~~~~~~~~~~~ 166 (167)
+|++.+++++|+.+|.+|++.|++||.|.+++.| |++||+|||++||| +++.+..++| ..+||++.+++|++||
T Consensus 164 lIe~~~p~~ea~~rl~~AleeI~klL~P~~e~~d--k~~QL~ELa~lngt~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~ 241 (259)
T KOG1588|consen 164 LIETEAPPAEAYARLAYALEEIKKLLVPDHEDED--KREQLRELAILNGTYLRSESRKPSGGNGRGVPGNSAGGKRGKTG 241 (259)
T ss_pred EEEEeCCHHHHHHHHHHHHHHHHHhcCCCCCCch--HHHHHHHHhhcCCccccccccccCCCCCcCCCCCCCCcccccCC
Confidence 9999999999999999999999999999988777 99999999999999 5555544555 7899999999999987
Q ss_pred C
Q 031032 167 R 167 (167)
Q Consensus 167 ~ 167 (167)
.
T Consensus 242 ~ 242 (259)
T KOG1588|consen 242 P 242 (259)
T ss_pred C
Confidence 3
No 2
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=100.00 E-value=1.8e-42 Score=263.76 Aligned_cols=119 Identities=57% Similarity=0.969 Sum_probs=111.9
Q ss_pred EEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcc
Q 031032 20 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 99 (167)
Q Consensus 20 ~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~ 99 (167)
++||+||+++||+|||||+||||+|+|+|+||++|||+|.|||+||+++.+++.++++ |.++|++|||||+|++.++
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 3689999999999999999999999999999999999999999999999999988887 8899999999999999984
Q ss_pred hHHHHHHHHHHHHHhccCCCCcc-hHHHHHHHHHHHHHhcCccC
Q 031032 100 IVDIRLRQAQEIIEELLKPVDES-QDYIKRQQLRELAMLNSNFR 142 (167)
Q Consensus 100 ~a~~~l~~A~~~Ie~LL~~~~~~-~d~~k~~QL~elA~lnGt~r 142 (167)
+..++++|+++|+.||.+.+++ .|++|++||+|||++|||||
T Consensus 78 -~~e~~~~A~~~I~~ll~~~~~~~~~~~k~~ql~~la~~nGt~~ 120 (120)
T cd02395 78 -PEEALAKAVEAIEELLKPAIEGGNDELKREQLRELALLNGTYR 120 (120)
T ss_pred -HHHHHHHHHHHHHHHhccCCCccchHHHHHHHHHHHHhcccCC
Confidence 2348999999999999998877 99999999999999999997
No 3
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=100.00 E-value=1.2e-35 Score=266.85 Aligned_cols=131 Identities=42% Similarity=0.688 Sum_probs=113.4
Q ss_pred CCCCCCCcccceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCC-CCCC
Q 031032 8 APASPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYE-HLND 86 (167)
Q Consensus 8 ~p~~~~g~~~~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~-~~~e 86 (167)
.||.=.-+.+++..||||||++||+|||||+||||||+|+|+||+||||||.|||+||+|+++. .+++..+. ..+|
T Consensus 127 kpP~DYk~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~---~~~d~~~~~~~~e 203 (554)
T KOG0119|consen 127 KPPADYKPPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKG---RSDDLSYIPKENE 203 (554)
T ss_pred CCCcccCcccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEecccccccccc---CCccccccccccc
Confidence 3333333444889999999999999999999999999999999999999999999999999872 12233332 5789
Q ss_pred CcEEEEEecCCcchHHHHHHHHHHHHHhccC---CCCcchHHHHHHHHHHHHHhcCccCCCCC
Q 031032 87 PLHILIEADLPANIVDIRLRQAQEIIEELLK---PVDESQDYIKRQQLRELAMLNSNFREDSP 146 (167)
Q Consensus 87 pLHV~Isa~~~~~~a~~~l~~A~~~Ie~LL~---~~~~~~d~~k~~QL~elA~lnGt~r~~~~ 146 (167)
|||++|++++++ +|++|+++|+.||. .++|+++++|+.||+|||-+|||+|++++
T Consensus 204 pLH~~Isadt~e-----ki~~Ai~vienli~~av~~~e~~n~l~~~Qlrela~lNgt~r~~d~ 261 (554)
T KOG0119|consen 204 PLHCLISADTQE-----KIKKAIAVIENLIQSAVSVPEGQNDLKRLQLRELARLNGTLRDDDN 261 (554)
T ss_pred ceeEEEecchHH-----HHHHHHHHHHHHHHhhccCccccccccHHHHHHHHHhCCCCCcccc
Confidence 999999999987 89999999999998 57899999999999999999999999983
No 4
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.95 E-value=2.5e-28 Score=201.29 Aligned_cols=128 Identities=37% Similarity=0.529 Sum_probs=100.3
Q ss_pred CCcccceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEE
Q 031032 13 SSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILI 92 (167)
Q Consensus 13 ~g~~~~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~I 92 (167)
+-.+.+.+.|+||||++||+.||||+||||+|+|+|+||+.|+|||.|||+||.|+++-..++... .-...++||++|
T Consensus 142 y~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~--~~N~e~~lhcLI 219 (269)
T COG5176 142 YIRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPES--LKNAEAVLHCLI 219 (269)
T ss_pred ccCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchh--hhhhHHhHHHHh
Confidence 344567789999999999999999999999999999999999999999999999987654443211 113678999999
Q ss_pred EecCCcchHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHhcCccCCC
Q 031032 93 EADLPANIVDIRLRQAQEIIEELLKPVDESQDYIKRQQLRELAMLNSNFRED 144 (167)
Q Consensus 93 sa~~~~~~a~~~l~~A~~~Ie~LL~~~~~~~d~~k~~QL~elA~lnGt~r~~ 144 (167)
++++....+. .+.-....|..... .+++++++|+-||.+||-+|||+|++
T Consensus 220 ~adsedki~~-~ik~~~n~I~~a~~-~PeGqnDlkR~qlr~la~lngtlr~d 269 (269)
T COG5176 220 EADSEDKICR-LIKSQLNAIREARR-NPEGQNDLKRFQLRWLAHLNGTLRAD 269 (269)
T ss_pred hcchhhhHHH-HHHHHHHHHHHHhc-CCcccchHHHHHHHHHHHhcceecCC
Confidence 9987552221 22223334444444 57889999999999999999999875
No 5
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.39 E-value=1.3e-12 Score=88.27 Aligned_cols=61 Identities=30% Similarity=0.557 Sum_probs=53.4
Q ss_pred ceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCC
Q 031032 18 KRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLP 97 (167)
Q Consensus 18 ~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~ 97 (167)
|+...+.||.+ ++|+|||++|+|+|+|+++|||+|.|...| .|.|++.+.
T Consensus 1 P~~~~i~Ip~~------~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g------------------------~v~I~G~~~ 50 (61)
T cd02393 1 PRIETMKIPPD------KIRDVIGPGGKTIKKIIEETGVKIDIEDDG------------------------TVYIAASDK 50 (61)
T ss_pred CeEEEEEeChh------heeeeECCCchHHHHHHHHHCCEEEeCCCC------------------------EEEEEeCCH
Confidence 46788999997 999999999999999999999999998543 799999876
Q ss_pred cchHHHHHHHHHHHHH
Q 031032 98 ANIVDIRLRQAQEIIE 113 (167)
Q Consensus 98 ~~~a~~~l~~A~~~Ie 113 (167)
+ ++++|+++|+
T Consensus 51 ~-----~v~~A~~~I~ 61 (61)
T cd02393 51 E-----AAEKAKKMIE 61 (61)
T ss_pred H-----HHHHHHHHhC
Confidence 5 7888988874
No 6
>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=99.11 E-value=1.7e-10 Score=109.53 Aligned_cols=73 Identities=27% Similarity=0.543 Sum_probs=68.3
Q ss_pred CCCCcccceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEE
Q 031032 11 SPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHI 90 (167)
Q Consensus 11 ~~~g~~~~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV 90 (167)
..-.+++|++.++.||++ .||.||||+|+|+|.|+++|||+|.|...| +|
T Consensus 570 ~~~s~~aP~~~~~~I~~~------ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G------------------------~V 619 (719)
T TIGR02696 570 DEMSPYAPRIITVKIPVD------KIGEVIGPKGKMINQIQDETGAEISIEDDG------------------------TV 619 (719)
T ss_pred cccccCCCeeEEEEeChH------HhhheeCCCcHhHHHHHHHHCCEEEEecCc------------------------EE
Confidence 456789999999999998 999999999999999999999999999988 99
Q ss_pred EEEecCCcchHHHHHHHHHHHHHhccCC
Q 031032 91 LIEADLPANIVDIRLRQAQEIIEELLKP 118 (167)
Q Consensus 91 ~Isa~~~~~~a~~~l~~A~~~Ie~LL~~ 118 (167)
.|++.+.+ ++++|+++|+.++.+
T Consensus 620 ~I~a~d~~-----~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 620 YIGAADGP-----SAEAARAMINAIANP 642 (719)
T ss_pred EEEeCCHH-----HHHHHHHHHHHhhCc
Confidence 99999876 899999999999994
No 7
>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=98.93 E-value=1.2e-09 Score=103.49 Aligned_cols=73 Identities=23% Similarity=0.360 Sum_probs=66.8
Q ss_pred CCCCcccceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEE
Q 031032 11 SPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHI 90 (167)
Q Consensus 11 ~~~g~~~~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV 90 (167)
..-.+++|++.++.||++ +||.||||+|+|+|.|+++|||+|.|...| +|
T Consensus 543 ~~~~~~~p~~~~~~I~~~------kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG------------------------~V 592 (684)
T TIGR03591 543 AELSPYAPRIETIKINPD------KIRDVIGPGGKVIREITEETGAKIDIEDDG------------------------TV 592 (684)
T ss_pred ccccccCCeEEEEecCHH------HHHhhcCCCcHHHHHHHHHHCCEEEEecCe------------------------EE
Confidence 446789999999999998 999999999999999999999999999887 99
Q ss_pred EEEecCCcchHHHHHHHHHHHHHhccCC
Q 031032 91 LIEADLPANIVDIRLRQAQEIIEELLKP 118 (167)
Q Consensus 91 ~Isa~~~~~~a~~~l~~A~~~Ie~LL~~ 118 (167)
.|.+.+.+ .+++|.+.|+.+...
T Consensus 593 ~i~~~~~~-----~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 593 KIAASDGE-----AAEAAIKMIEGITAE 615 (684)
T ss_pred EEEECcHH-----HHHHHHHHHHhhhcc
Confidence 99998866 899999999998764
No 8
>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=98.93 E-value=1.6e-09 Score=72.19 Aligned_cols=61 Identities=23% Similarity=0.411 Sum_probs=48.7
Q ss_pred EEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcch
Q 031032 21 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANI 100 (167)
Q Consensus 21 ~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~ 100 (167)
.++.||.+ ++|.|||++|+++++|+++|||+|.|-...+ ..=.|.|++. .+
T Consensus 2 ~~i~Vp~~------~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~--------------------~~~~v~I~G~-~~-- 52 (62)
T cd02394 2 EEVEIPKK------LHRFIIGKKGSNIRKIMEETGVKIRFPDPGS--------------------KSDTITITGP-KE-- 52 (62)
T ss_pred eEEEeCHH------HhhhccCCCCCcHHHHHHHhCCEEEcCCCCC--------------------CCCEEEEEcC-HH--
Confidence 46788886 8999999999999999999999999987541 1117999987 33
Q ss_pred HHHHHHHHHHHHH
Q 031032 101 VDIRLRQAQEIIE 113 (167)
Q Consensus 101 a~~~l~~A~~~Ie 113 (167)
.+.+|+++|+
T Consensus 53 ---~v~~A~~~i~ 62 (62)
T cd02394 53 ---NVEKAKEEIL 62 (62)
T ss_pred ---HHHHHHHHhC
Confidence 6778887763
No 9
>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=98.92 E-value=3.9e-10 Score=74.66 Aligned_cols=59 Identities=29% Similarity=0.635 Sum_probs=48.2
Q ss_pred EEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcch
Q 031032 21 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANI 100 (167)
Q Consensus 21 ~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~ 100 (167)
.+|.||.+ ++|+|||++|+++|+|+++|||+|.|...+ +.-.|.|++ +.+
T Consensus 2 ~~i~vp~~------~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~---------------------~~~~v~I~G-~~~-- 51 (60)
T PF00013_consen 2 ERIEVPSS------LVGRIIGKKGSNIKEIEEETGVKIQIPDDD---------------------ERDIVTISG-SPE-- 51 (60)
T ss_dssp EEEEEEHH------HHHHHHTGGGHHHHHHHHHHTSEEEEESTT---------------------EEEEEEEEE-SHH--
T ss_pred EEEEECHH------HcCEEECCCCCcHHHhhhhcCeEEEEcCCC---------------------CcEEEEEEe-CHH--
Confidence 56788876 999999999999999999999999997641 112789998 554
Q ss_pred HHHHHHHHHHHH
Q 031032 101 VDIRLRQAQEII 112 (167)
Q Consensus 101 a~~~l~~A~~~I 112 (167)
.+++|+++|
T Consensus 52 ---~v~~A~~~I 60 (60)
T PF00013_consen 52 ---QVEKAKKMI 60 (60)
T ss_dssp ---HHHHHHHHH
T ss_pred ---HHHHHHhhC
Confidence 788888876
No 10
>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=98.91 E-value=6.7e-09 Score=68.59 Aligned_cols=62 Identities=29% Similarity=0.567 Sum_probs=48.7
Q ss_pred EEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcch
Q 031032 21 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANI 100 (167)
Q Consensus 21 ~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~ 100 (167)
.++.||.+ ++|+||||+|+++++|+++|||+|.|...++ ...+-.|.|.+. .
T Consensus 2 ~~i~ip~~------~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~------------------~~~~~~v~i~G~-~--- 53 (64)
T cd00105 2 ERVLVPSS------LVGRIIGKGGSTIKEIREETGAKIKIPDSGS------------------GSEERIVTITGT-P--- 53 (64)
T ss_pred EEEEEchh------hcceeECCCCHHHHHHHHHHCCEEEEcCCCC------------------CCCceEEEEEcC-H---
Confidence 46888885 9999999999999999999999999997542 122337888886 2
Q ss_pred HHHHHHHHHHHH
Q 031032 101 VDIRLRQAQEII 112 (167)
Q Consensus 101 a~~~l~~A~~~I 112 (167)
..+.+|..+|
T Consensus 54 --~~v~~a~~~i 63 (64)
T cd00105 54 --EAVEKAKELI 63 (64)
T ss_pred --HHHHHHHHHh
Confidence 2677777766
No 11
>smart00322 KH K homology RNA-binding domain.
Probab=98.79 E-value=3.4e-08 Score=64.29 Aligned_cols=66 Identities=32% Similarity=0.571 Sum_probs=52.2
Q ss_pred eEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCc
Q 031032 19 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPA 98 (167)
Q Consensus 19 ~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~ 98 (167)
...++.||.+ ++|.|||++|+++++|++.|||+|.+....+ ..-.|.|.+. ..
T Consensus 3 ~~~~i~i~~~------~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--------------------~~~~v~i~g~-~~ 55 (69)
T smart00322 3 VTIEVLIPAD------KVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--------------------EERVVEITGP-PE 55 (69)
T ss_pred eEEEEEEcch------hcceeECCCchHHHHHHHHHCCEEEECCCCC--------------------CccEEEEEcC-HH
Confidence 4567888885 8999999999999999999999999986542 1127888886 23
Q ss_pred chHHHHHHHHHHHHHhcc
Q 031032 99 NIVDIRLRQAQEIIEELL 116 (167)
Q Consensus 99 ~~a~~~l~~A~~~Ie~LL 116 (167)
.+..|.+.|.+.+
T Consensus 56 -----~v~~a~~~i~~~~ 68 (69)
T smart00322 56 -----NVEKAAELILEIL 68 (69)
T ss_pred -----HHHHHHHHHHHHh
Confidence 6778888887765
No 12
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.78 E-value=3.6e-09 Score=102.56 Aligned_cols=73 Identities=21% Similarity=0.263 Sum_probs=67.8
Q ss_pred CCCcccceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCe-EEEecccCCCCCCcccccCCCCCCCCCCCCcEE
Q 031032 12 PSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCR-VYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHI 90 (167)
Q Consensus 12 ~~g~~~~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~k-I~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV 90 (167)
.-.+++|++..+.||++ +||.||||+|+|+|.|+++||++ |.|+..| +|
T Consensus 678 ~~s~~aP~i~~~~i~~~------ki~~vIG~GGktIk~I~eetg~~~Idi~ddg------------------------~V 727 (891)
T PLN00207 678 RLSKYAPLIHIMKVKPE------KVNMIIGSGGKKVKSIIEETGVEAIDTQDDG------------------------TV 727 (891)
T ss_pred hhcccCCeeEEEEcCHH------HHHHHhcCCchhHHHHHHHHCCCccCcCCCe------------------------eE
Confidence 46789999999999997 99999999999999999999999 9999887 99
Q ss_pred EEEecCCcchHHHHHHHHHHHHHhccCCC
Q 031032 91 LIEADLPANIVDIRLRQAQEIIEELLKPV 119 (167)
Q Consensus 91 ~Isa~~~~~~a~~~l~~A~~~Ie~LL~~~ 119 (167)
.|.+.+.+ ++++|+++|+.|+..+
T Consensus 728 ~I~a~d~~-----~i~~A~~~I~~l~~~~ 751 (891)
T PLN00207 728 KITAKDLS-----SLEKSKAIISSLTMVP 751 (891)
T ss_pred EEEeCCHH-----HHHHHHHHHHHHhcCc
Confidence 99999876 8999999999998854
No 13
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.74 E-value=1.2e-08 Score=82.35 Aligned_cols=64 Identities=28% Similarity=0.572 Sum_probs=56.4
Q ss_pred EEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecc-cCCCCCCcccccCCCCCCCCCCCCcEEEEE---ec
Q 031032 20 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK-GSIKDPDKEDKLRGRPGYEHLNDPLHILIE---AD 95 (167)
Q Consensus 20 ~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~-GS~k~~~~~~~~~~~p~~~~~~epLHV~Is---a~ 95 (167)
+..+.||.+ .+|.||||+|+|+|.|+++|||+|.|..+ | .|.|. +.
T Consensus 4 ~~~i~IP~~------kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g------------------------~V~I~~~~~~ 53 (180)
T PRK13763 4 MEYVKIPKD------RIGVLIGKKGETKKEIEERTGVKLEIDSETG------------------------EVIIEPTDGE 53 (180)
T ss_pred eEEEEcCHH------HhhhHhccchhHHHHHHHHHCcEEEEECCCC------------------------eEEEEeCCCC
Confidence 567888887 99999999999999999999999999976 4 78888 56
Q ss_pred CCcchHHHHHHHHHHHHHhccCC
Q 031032 96 LPANIVDIRLRQAQEIIEELLKP 118 (167)
Q Consensus 96 ~~~~~a~~~l~~A~~~Ie~LL~~ 118 (167)
++. .+++|+++|+.|+..
T Consensus 54 d~~-----~i~kA~~~I~ai~~g 71 (180)
T PRK13763 54 DPL-----AVLKARDIVKAIGRG 71 (180)
T ss_pred CHH-----HHHHHHHHHHHHhcC
Confidence 655 899999999999984
No 14
>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=98.74 E-value=3.2e-08 Score=66.97 Aligned_cols=63 Identities=22% Similarity=0.422 Sum_probs=47.7
Q ss_pred EEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcch
Q 031032 21 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANI 100 (167)
Q Consensus 21 ~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~ 100 (167)
.++.||.+ .+|+|||.+|.++++|+++|||+|.|..... . ...+--|.|++. .+
T Consensus 2 ~r~~ip~~------~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----------------~-~~~~r~v~I~G~-~~-- 55 (65)
T cd02396 2 LRLLVPSS------QAGSIIGKGGSTIKEIREETGAKIRVSKSVL----------------P-GSTERVVTISGK-PS-- 55 (65)
T ss_pred EEEEECHH------HcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----------------C-CCCceEEEEEeC-HH--
Confidence 47889986 9999999999999999999999999975331 0 111225778775 33
Q ss_pred HHHHHHHHHHHH
Q 031032 101 VDIRLRQAQEII 112 (167)
Q Consensus 101 a~~~l~~A~~~I 112 (167)
.+.+|+.+|
T Consensus 56 ---~v~~A~~~I 64 (65)
T cd02396 56 ---AVQKALLLI 64 (65)
T ss_pred ---HHHHHHHhh
Confidence 677888876
No 15
>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=98.67 E-value=1.5e-08 Score=81.24 Aligned_cols=61 Identities=30% Similarity=0.562 Sum_probs=51.9
Q ss_pred EecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecc-cCCCCCCcccccCCCCCCCCCCCCcEEEE--EecCCcc
Q 031032 23 LEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK-GSIKDPDKEDKLRGRPGYEHLNDPLHILI--EADLPAN 99 (167)
Q Consensus 23 i~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~-GS~k~~~~~~~~~~~p~~~~~~epLHV~I--sa~~~~~ 99 (167)
+.||.+ .+|.||||+|+|+|.|+++|||+|.|..+ | .|.| .+.|+.
T Consensus 2 i~Ip~~------kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g------------------------~V~I~~~t~d~~- 50 (172)
T TIGR03665 2 VKIPKD------RIGVLIGKGGETKKEIEERTGVKLDIDSETG------------------------EVKIEEEDEDPL- 50 (172)
T ss_pred ccCCHH------HhhhHhCCchhHHHHHHHHhCcEEEEEcCCc------------------------eEEEecCCCCHH-
Confidence 456765 99999999999999999999999999965 3 6888 455555
Q ss_pred hHHHHHHHHHHHHHhccCC
Q 031032 100 IVDIRLRQAQEIIEELLKP 118 (167)
Q Consensus 100 ~a~~~l~~A~~~Ie~LL~~ 118 (167)
.+.+|+++|+.|...
T Consensus 51 ----~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 51 ----AVMKAREVVKAIGRG 65 (172)
T ss_pred ----HHHHHHHHHHHHHcC
Confidence 899999999999885
No 16
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=98.59 E-value=2.4e-08 Score=89.63 Aligned_cols=92 Identities=14% Similarity=-0.012 Sum_probs=80.0
Q ss_pred EEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcchH
Q 031032 22 RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIV 101 (167)
Q Consensus 22 ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~a 101 (167)
|.+|++| .|.||.-+..=||+..++..+|.++++++.||||+|++-+.-++ ++.+||++++|++.+.+
T Consensus 213 k~~v~~~-~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G--------~EsnEPMYI~i~h~~~~--- 280 (531)
T KOG1960|consen 213 KALATDK-DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEG--------NESNEPMYIFSTHGNGN--- 280 (531)
T ss_pred heecccC-CcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCcccc--------cccCCceeEEeecCCch---
Confidence 7889998 89999999999999999999999999999999999988764332 25899999999999887
Q ss_pred HHHHHHHHHHHHhccCCCCcchHHHH
Q 031032 102 DIRLRQAQEIIEELLKPVDESQDYIK 127 (167)
Q Consensus 102 ~~~l~~A~~~Ie~LL~~~~~~~d~~k 127 (167)
.+.+|+.++.+|+..++.++..+-
T Consensus 281 --g~~~A~r~~~nl~~~v~~~~sr~~ 304 (531)
T KOG1960|consen 281 --GENGAPRRKWNLEEKVYINLSRGF 304 (531)
T ss_pred --hhccchhHHHhHHHHHHHHhhhhh
Confidence 788999999999998865555444
No 17
>PF13014 KH_3: KH domain
Probab=98.57 E-value=1.2e-07 Score=59.27 Aligned_cols=28 Identities=36% Similarity=0.789 Sum_probs=26.9
Q ss_pred eeeEEeCCCcchHHHHHHHhCCeEEEec
Q 031032 35 FVGRLLGPRGNSLKRVEATTGCRVYIRG 62 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG~kI~IrG 62 (167)
|+|+|||++|+|+++|+++|||+|.|-.
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC
Confidence 6899999999999999999999999986
No 18
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.54 E-value=4.7e-08 Score=92.94 Aligned_cols=75 Identities=27% Similarity=0.432 Sum_probs=66.4
Q ss_pred CCCCCCcccceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCc
Q 031032 9 PASPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPL 88 (167)
Q Consensus 9 p~~~~g~~~~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epL 88 (167)
|-..-.++++++..+.||++ .|+.+|||+|+|+|.|+++||++|.|+..|
T Consensus 544 ~r~~~~~~ap~~~~~~I~~~------kI~~vIG~gg~~ik~I~~~~~~~idi~d~G------------------------ 593 (693)
T PRK11824 544 PRAELSPYAPRIETIKIPPD------KIRDVIGPGGKTIREITEETGAKIDIEDDG------------------------ 593 (693)
T ss_pred ChhhhcccCchheeecCCHH------HHHHHhcCCchhHHHHHHHHCCccccCCCc------------------------
Confidence 33445678899999999876 899999999999999999999999999887
Q ss_pred EEEEEecCCcchHHHHHHHHHHHHHhccCC
Q 031032 89 HILIEADLPANIVDIRLRQAQEIIEELLKP 118 (167)
Q Consensus 89 HV~Isa~~~~~~a~~~l~~A~~~Ie~LL~~ 118 (167)
+|.|++.+.+ .+++|.+.|+.+...
T Consensus 594 ~v~i~~~~~~-----~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 594 TVKIAATDGE-----AAEAAKERIEGITAE 618 (693)
T ss_pred eEEEEcccHH-----HHHHHHHHHHHhccc
Confidence 8999998876 899999999999864
No 19
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.51 E-value=1.2e-07 Score=89.65 Aligned_cols=72 Identities=28% Similarity=0.428 Sum_probs=65.8
Q ss_pred CCcccceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEE
Q 031032 13 SSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILI 92 (167)
Q Consensus 13 ~g~~~~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~I 92 (167)
-.+++|++..+.|+++ .|+.+|||+|+|++.|.++|||+|.|..+| .|.|
T Consensus 546 ls~~aPri~t~~i~~d------KI~dvIG~gGk~I~~I~eetg~~IdieddG------------------------tv~i 595 (692)
T COG1185 546 LSPYAPRIETIKIDPD------KIRDVIGPGGKTIKAITEETGVKIDIEDDG------------------------TVKI 595 (692)
T ss_pred hhccCCceEEEccCHH------HHhhccCCcccchhhhhhhhCcEEEecCCC------------------------cEEE
Confidence 4678999999999998 899999999999999999999999999988 7899
Q ss_pred EecCCcchHHHHHHHHHHHHHhccCCC
Q 031032 93 EADLPANIVDIRLRQAQEIIEELLKPV 119 (167)
Q Consensus 93 sa~~~~~~a~~~l~~A~~~Ie~LL~~~ 119 (167)
++.+.+ ++.+|++.|+.++..+
T Consensus 596 ~~s~~~-----~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 596 AASDGE-----SAKKAKERIEAITREV 617 (692)
T ss_pred EecchH-----HHHHHHHHHHHHHhhc
Confidence 998876 7899999999999654
No 20
>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=98.45 E-value=2.2e-07 Score=74.51 Aligned_cols=53 Identities=30% Similarity=0.506 Sum_probs=47.2
Q ss_pred eeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcchHHHHHHHHHHHHHh
Q 031032 35 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEE 114 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~a~~~l~~A~~~Ie~ 114 (167)
.+|||||++|.|++.||..|||+|.|-|+ .|.|.+ +++ .++.|.+.|+.
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~~-------------------------~v~i~G-~~~-----~~~~A~~~i~~ 147 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYGK-------------------------TVGIIG-DPE-----QVQIAREAIEM 147 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcCC-------------------------EEEEEC-CHH-----HHHHHHHHHHH
Confidence 69999999999999999999999999862 789999 555 78999999999
Q ss_pred ccCC
Q 031032 115 LLKP 118 (167)
Q Consensus 115 LL~~ 118 (167)
|+..
T Consensus 148 li~~ 151 (172)
T TIGR03665 148 LIEG 151 (172)
T ss_pred HHcC
Confidence 9965
No 21
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.40 E-value=4.4e-07 Score=73.26 Aligned_cols=53 Identities=30% Similarity=0.518 Sum_probs=46.1
Q ss_pred eeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcchHHHHHHHHHHHHHh
Q 031032 35 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEE 114 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~a~~~l~~A~~~Ie~ 114 (167)
.+|+|||++|+|+|.||+.|||+|.|-++ .|.|.+ +++ .++.|.+.|+.
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~-------------------------~v~i~G-~~~-----~~~~A~~~I~~ 153 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGK-------------------------TVAIIG-DPE-----QVEIAREAIEM 153 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCC-------------------------EEEEEe-CHH-----HHHHHHHHHHH
Confidence 69999999999999999999999999753 577877 454 78999999999
Q ss_pred ccCC
Q 031032 115 LLKP 118 (167)
Q Consensus 115 LL~~ 118 (167)
|+..
T Consensus 154 li~g 157 (180)
T PRK13763 154 LIEG 157 (180)
T ss_pred HHcC
Confidence 9965
No 22
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.18 E-value=3.4e-06 Score=70.69 Aligned_cols=64 Identities=23% Similarity=0.379 Sum_probs=55.6
Q ss_pred EEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcchH
Q 031032 22 RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIV 101 (167)
Q Consensus 22 ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~a 101 (167)
.+.||.+ ++++||||+|.+++.|.++|+|+|.|--.| .|+|++.+.+
T Consensus 148 ~~~V~~~------~i~~lig~~g~~i~~l~~~~~~~I~ig~NG------------------------~VwI~~~~~~--- 194 (235)
T PRK04163 148 IVEIKPV------KVPRVIGKKGSMINMLKEETGCDIIVGQNG------------------------RIWIKGPDEE--- 194 (235)
T ss_pred EEEECHH------HHHhhcCCCChhHhhhhhhhCcEEEEcCCc------------------------EEEEeeCCHH---
Confidence 3566665 899999999999999999999999998777 9999999876
Q ss_pred HHHHHHHHHHHHhccCCCC
Q 031032 102 DIRLRQAQEIIEELLKPVD 120 (167)
Q Consensus 102 ~~~l~~A~~~Ie~LL~~~~ 120 (167)
.+++|+++|+.+-...|
T Consensus 195 --~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 195 --DEEIAIEAIKKIEREAH 211 (235)
T ss_pred --HHHHHHHHHHHHHhhhh
Confidence 78899999998877654
No 23
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.00 E-value=1.5e-05 Score=65.58 Aligned_cols=55 Identities=25% Similarity=0.452 Sum_probs=48.6
Q ss_pred eeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcchHHHHHHHHHHHHHh
Q 031032 35 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEE 114 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~a~~~l~~A~~~Ie~ 114 (167)
..|||||+.|.|.+.||+-|||.|.|.|+ +|.|-+. ++ .++.|.+.|+.
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~-------------------------tVaiiG~-~~-----~v~iAr~AVem 160 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK-------------------------TVAIIGG-FE-----QVEIAREAVEM 160 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc-------------------------EEEEecC-hh-----hhHHHHHHHHH
Confidence 57999999999999999999999999985 8889884 44 68899999999
Q ss_pred ccCCCC
Q 031032 115 LLKPVD 120 (167)
Q Consensus 115 LL~~~~ 120 (167)
|+.-.+
T Consensus 161 li~G~~ 166 (194)
T COG1094 161 LINGAP 166 (194)
T ss_pred HHcCCC
Confidence 998643
No 24
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=97.84 E-value=4.6e-05 Score=71.26 Aligned_cols=74 Identities=26% Similarity=0.582 Sum_probs=59.0
Q ss_pred cceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecC
Q 031032 17 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADL 96 (167)
Q Consensus 17 ~~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~ 96 (167)
...+..|.||.. .+|+|||-+|.|+|+|++.+|||+.+--+|+.... ...|| .|+++
T Consensus 137 ~~ttqeI~IPa~------k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~--------------~~Kpl--ritGd- 193 (600)
T KOG1676|consen 137 VETTQEILIPAN------KCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG--------------ADKPL--RITGD- 193 (600)
T ss_pred cceeeeeccCcc------ceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC--------------CCCce--eecCC-
Confidence 345777888875 99999999999999999999999999888865443 23333 56664
Q ss_pred CcchHHHHHHHHHHHHHhccCC
Q 031032 97 PANIVDIRLRQAQEIIEELLKP 118 (167)
Q Consensus 97 ~~~~a~~~l~~A~~~Ie~LL~~ 118 (167)
+. +++.|+++|.++|..
T Consensus 194 p~-----~ve~a~~lV~dil~e 210 (600)
T KOG1676|consen 194 PD-----KVEQAKQLVADILRE 210 (600)
T ss_pred HH-----HHHHHHHHHHHHHHh
Confidence 33 799999999999985
No 25
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=97.69 E-value=0.00011 Score=68.71 Aligned_cols=71 Identities=21% Similarity=0.439 Sum_probs=51.7
Q ss_pred EEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcc
Q 031032 20 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 99 (167)
Q Consensus 20 ~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~ 99 (167)
...|.||-. .||.|||-+|.|||+|+.+||+||.++=+- + |. ...=-+.|.+..
T Consensus 231 ~~~V~VPr~------~VG~IIGkgGE~IKklq~etG~KIQfkpDd---~----------p~----speR~~~IiG~~--- 284 (600)
T KOG1676|consen 231 TREVKVPRS------KVGIIIGKGGEMIKKLQNETGAKIQFKPDD---D----------PS----SPERPAQIIGTV--- 284 (600)
T ss_pred eeEEecccc------ceeeEEecCchHHHHHhhccCceeEeecCC---C----------CC----CccceeeeecCH---
Confidence 455666664 899999999999999999999999998431 0 10 011134555542
Q ss_pred hHHHHHHHHHHHHHhccCCC
Q 031032 100 IVDIRLRQAQEIIEELLKPV 119 (167)
Q Consensus 100 ~a~~~l~~A~~~Ie~LL~~~ 119 (167)
.++.+|.++|.+||...
T Consensus 285 ---d~ie~Aa~lI~eii~~~ 301 (600)
T KOG1676|consen 285 ---DQIEHAAELINEIIAEA 301 (600)
T ss_pred ---HHHHHHHHHHHHHHHHH
Confidence 28999999999999754
No 26
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.61 E-value=0.00011 Score=66.85 Aligned_cols=70 Identities=24% Similarity=0.462 Sum_probs=50.0
Q ss_pred EEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcch
Q 031032 21 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANI 100 (167)
Q Consensus 21 ~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~ 100 (167)
.++.+|.. |+|.||||.|.|+|.|-+.|.|+|.+.-+- .+ + -.+..|.|+= .+|
T Consensus 201 lR~lVptq------yvgaIIGkeG~TIknItkqTqsriD~hrke-n~------------G--aaek~itvh~---tpE-- 254 (584)
T KOG2193|consen 201 LRLLVPTQ------YVGAIIGKEGATIKNITKQTQSRIDVHRKE-NA------------G--AAEKIITVHS---TPE-- 254 (584)
T ss_pred eeeeeccc------eeEEEecCCCccccCcchhhhheeeeeecc-cC------------C--cccCceEEec---Ccc--
Confidence 36777876 999999999999999999999999998531 11 1 1223344332 344
Q ss_pred HHHHHHHHHHHHHhccCCC
Q 031032 101 VDIRLRQAQEIIEELLKPV 119 (167)
Q Consensus 101 a~~~l~~A~~~Ie~LL~~~ 119 (167)
...+||.+|.+++...
T Consensus 255 ---g~s~Ac~~ILeimqkE 270 (584)
T KOG2193|consen 255 ---GTSKACKMILEIMQKE 270 (584)
T ss_pred ---chHHHHHHHHHHHHHh
Confidence 4567888888888753
No 27
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=97.44 E-value=0.00016 Score=67.81 Aligned_cols=72 Identities=24% Similarity=0.317 Sum_probs=61.7
Q ss_pred CCCcccceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEE
Q 031032 12 PSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHIL 91 (167)
Q Consensus 12 ~~g~~~~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~ 91 (167)
..+.+.|+.+.+.++.+ ....+|||+|..+|.|+.|||+.-.+. .| |+.
T Consensus 590 ~~~~y~P~~~tlkv~~s------k~~~lIGp~G~~~kki~~EtGai~~vD-e~------------------------t~~ 638 (760)
T KOG1067|consen 590 SDKEYSPVLETLKVSPS------KRATLIGPGGVLKKKIEVETGAISQVD-EG------------------------TFS 638 (760)
T ss_pred CccccCceeeEEeecch------hhheeecCccceeeeEeeeccceeeec-Cc------------------------eEE
Confidence 67889999999999987 788999999999999999999444443 33 999
Q ss_pred EEecCCcchHHHHHHHHHHHHHhccCCC
Q 031032 92 IEADLPANIVDIRLRQAQEIIEELLKPV 119 (167)
Q Consensus 92 Isa~~~~~~a~~~l~~A~~~Ie~LL~~~ 119 (167)
|.+.++. .+++|.+.|..++..+
T Consensus 639 i~A~~~~-----am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 639 IFAPTQA-----AMEEAKEFIDGIIKDD 661 (760)
T ss_pred EEecCHH-----HHHHHHHHHHHHhcCc
Confidence 9999876 8999999999999854
No 28
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.02 E-value=0.0032 Score=55.96 Aligned_cols=37 Identities=19% Similarity=0.539 Sum_probs=33.6
Q ss_pred eEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEe
Q 031032 19 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 61 (167)
Q Consensus 19 ~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~Ir 61 (167)
++.||.+|-. -.|.|||++|.|+|.|++++||-|.|.
T Consensus 132 kqikivvPNs------tag~iigkggAtiK~~~Eqsga~iqis 168 (402)
T KOG2191|consen 132 KQIKIVVPNS------TAGMIIGKGGATIKAIQEQSGAWIQIS 168 (402)
T ss_pred ceeEEeccCC------cccceecCCcchHHHHHHhhCcceEec
Confidence 4578888876 689999999999999999999999998
No 29
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=96.97 E-value=0.0022 Score=55.91 Aligned_cols=68 Identities=28% Similarity=0.500 Sum_probs=51.6
Q ss_pred eEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcchHHHHHHHHHHHHHhcc
Q 031032 37 GRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELL 116 (167)
Q Consensus 37 G~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~a~~~l~~A~~~Ie~LL 116 (167)
-|||||.|+|+|.||--|.|-|.|.|. .|.+.|.- ..|..+..+|++.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~-------------------------TVsaiGpf------kGlkevr~IV~DcM 209 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN-------------------------TVSAIGPF------KGLKEVRKIVEDCM 209 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc-------------------------EEEeecCc------chHHHHHHHHHHHH
Confidence 489999999999999999999999985 56666642 37888999999998
Q ss_pred CCCCcchHHHHHHHHHHHH
Q 031032 117 KPVDESQDYIKRQQLRELA 135 (167)
Q Consensus 117 ~~~~~~~d~~k~~QL~elA 135 (167)
...|.-++.-.-+--+||+
T Consensus 210 ~NiHPiY~IK~LmiKRel~ 228 (356)
T KOG2874|consen 210 KNIHPIYNIKTLMIKRELA 228 (356)
T ss_pred hccchHHHHHHHHHHHHhh
Confidence 8887666533223333443
No 30
>PRK00106 hypothetical protein; Provisional
Probab=96.90 E-value=0.002 Score=60.19 Aligned_cols=66 Identities=30% Similarity=0.526 Sum_probs=55.4
Q ss_pred EEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcc
Q 031032 20 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 99 (167)
Q Consensus 20 ~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~ 99 (167)
+..|.+|-+ .+-|||||.-|.++|.+|..||+.|.|... |=-|.||++|+-
T Consensus 226 vs~v~lp~d-----emkGriIGreGrNir~~E~~tGvdliiddt-----------------------p~~v~lS~fdpv- 276 (535)
T PRK00106 226 ITTVHLPDD-----NMKGRIIGREGRNIRTLESLTGIDVIIDDT-----------------------PEVVVLSGFDPI- 276 (535)
T ss_pred eeeEEcCCh-----HhhcceeCCCcchHHHHHHHhCceEEEcCC-----------------------CCeEEEeCCChH-
Confidence 456677877 488999999999999999999999999853 227999999997
Q ss_pred hHHHHHHHHHHHHHhccCC
Q 031032 100 IVDIRLRQAQEIIEELLKP 118 (167)
Q Consensus 100 ~a~~~l~~A~~~Ie~LL~~ 118 (167)
+-+-|..-++.|+.+
T Consensus 277 ----RReiAr~~le~Li~d 291 (535)
T PRK00106 277 ----RREIARMTLESLIKD 291 (535)
T ss_pred ----HHHHHHHHHHHHHHc
Confidence 667788888888875
No 31
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.87 E-value=0.002 Score=59.89 Aligned_cols=66 Identities=24% Similarity=0.503 Sum_probs=53.9
Q ss_pred EEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcc
Q 031032 20 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 99 (167)
Q Consensus 20 ~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~ 99 (167)
+..|.+|-+ .+-|||||--|.++|.+|..||+.|.|... |=-|.||++|+-
T Consensus 205 ~~~v~lp~d-----~~kgriigreGrnir~~e~~tgvd~iiddt-----------------------p~~v~ls~fdp~- 255 (514)
T TIGR03319 205 VSVVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIIDDT-----------------------PEAVILSGFDPV- 255 (514)
T ss_pred eeeEEcCCh-----hhhccccCCCcchHHHHHHHhCceEEEcCC-----------------------CCeEEecCCchH-
Confidence 456678877 488999999999999999999999999853 227999999987
Q ss_pred hHHHHHHHHHHHHHhccCC
Q 031032 100 IVDIRLRQAQEIIEELLKP 118 (167)
Q Consensus 100 ~a~~~l~~A~~~Ie~LL~~ 118 (167)
+=+-|..-++.|+.+
T Consensus 256 ----rreia~~~l~~li~d 270 (514)
T TIGR03319 256 ----RREIARMALEKLIQD 270 (514)
T ss_pred ----HHHHHHHHHHHHHHc
Confidence 556677777777764
No 32
>PRK12704 phosphodiesterase; Provisional
Probab=96.81 E-value=0.007 Score=56.31 Aligned_cols=65 Identities=23% Similarity=0.473 Sum_probs=49.6
Q ss_pred EEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcc
Q 031032 20 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 99 (167)
Q Consensus 20 ~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~ 99 (167)
+..|.+|-++ +-|||||--|-++|.+|..||+.|.|... |=-|.||++|+..
T Consensus 211 ~~~v~lp~d~-----mkgriigreGrnir~~e~~tgvd~iiddt-----------------------p~~v~ls~~~~~r 262 (520)
T PRK12704 211 VSVVNLPNDE-----MKGRIIGREGRNIRALETLTGVDLIIDDT-----------------------PEAVILSGFDPIR 262 (520)
T ss_pred eeeeecCCch-----hhcceeCCCcchHHHHHHHhCCeEEEcCC-----------------------CCeEEEecCChhh
Confidence 4556778774 88999999999999999999999999853 2279999999873
Q ss_pred hHHHHHHHHHHHHHhccC
Q 031032 100 IVDIRLRQAQEIIEELLK 117 (167)
Q Consensus 100 ~a~~~l~~A~~~Ie~LL~ 117 (167)
-+-|...++.|+.
T Consensus 263 -----re~a~~~l~~l~~ 275 (520)
T PRK12704 263 -----REIARLALEKLVQ 275 (520)
T ss_pred -----HHHHHHHHHHHHh
Confidence 3344445544443
No 33
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.68 E-value=0.0035 Score=55.76 Aligned_cols=38 Identities=24% Similarity=0.538 Sum_probs=34.5
Q ss_pred ceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEe
Q 031032 18 KRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 61 (167)
Q Consensus 18 ~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~Ir 61 (167)
....||+||-- -.|-|||-+|.|+.+||++|||+|.+-
T Consensus 38 ~y~ikvLips~------AaGsIIGKGG~ti~~lqk~tgariklS 75 (402)
T KOG2191|consen 38 QYFLKVLIPSY------AAGSIIGKGGQTIVQLQKETGARIKLS 75 (402)
T ss_pred ceEEEEEeecc------cccceeccchHHHHHHHhccCcEEEec
Confidence 36778999974 899999999999999999999999987
No 34
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.65 E-value=0.0052 Score=56.88 Aligned_cols=72 Identities=22% Similarity=0.367 Sum_probs=53.8
Q ss_pred ceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCC
Q 031032 18 KRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLP 97 (167)
Q Consensus 18 ~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~ 97 (167)
+...++.||-. -+|-|||-+|+.||.|.++|||+|.|-++ .. |. ..+.. |.|++.-
T Consensus 137 ~v~~RLlVp~s------q~GslIGK~G~~Ik~Ire~TgA~I~v~~~---~l----------P~---ster~-V~IsG~~- 192 (485)
T KOG2190|consen 137 EVTCRLLVPSS------QVGSLIGKGGSLIKEIREETGAKIRVSSD---ML----------PN---STERA-VTISGEP- 192 (485)
T ss_pred ceEEEEEechh------heeeeeccCcHHHHHHHHhcCceEEecCC---CC----------Cc---cccee-EEEcCch-
Confidence 56789999986 89999999999999999999999999975 11 11 12222 8887753
Q ss_pred cchHHHHHHHHHHHHHhccCC
Q 031032 98 ANIVDIRLRQAQEIIEELLKP 118 (167)
Q Consensus 98 ~~~a~~~l~~A~~~Ie~LL~~ 118 (167)
+ .+.+|+..|-.+|..
T Consensus 193 ~-----av~~al~~Is~~L~~ 208 (485)
T KOG2190|consen 193 D-----AVKKALVQISSRLLE 208 (485)
T ss_pred H-----HHHHHHHHHHHHHHh
Confidence 2 566777777666654
No 35
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.40 E-value=0.001 Score=60.79 Aligned_cols=38 Identities=42% Similarity=0.785 Sum_probs=33.7
Q ss_pred ecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEe
Q 031032 24 EIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 61 (167)
Q Consensus 24 ~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~Ir 61 (167)
.||.+-.-.-||+|||||-.|.++|.|+.+||+||.|-
T Consensus 279 e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis 316 (584)
T KOG2193|consen 279 EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITIS 316 (584)
T ss_pred hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeee
Confidence 35666566679999999999999999999999999997
No 36
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.28 E-value=0.0046 Score=54.70 Aligned_cols=59 Identities=27% Similarity=0.421 Sum_probs=42.9
Q ss_pred ceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcchHHHHHHHHHHHHH
Q 031032 34 NFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIE 113 (167)
Q Consensus 34 NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~a~~~l~~A~~~Ie 113 (167)
.|+|-|||-+|.|.+.||+||+|+|.+-=.+..++ |+.|++-... .+-+|.+.|.
T Consensus 66 ~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~--------------------~i~i~~~~~~-----~V~~a~~Ri~ 120 (345)
T KOG2814|consen 66 SFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKE--------------------EIKIIGISRN-----CVIQALERIA 120 (345)
T ss_pred HHhhhhhcccchHHHHHHHhhccceEccCCCCCcc--------------------eEEEeehhHH-----HHHHHHHHHH
Confidence 39999999999999999999999999874432111 8888887655 3444445444
Q ss_pred hccC
Q 031032 114 ELLK 117 (167)
Q Consensus 114 ~LL~ 117 (167)
.|+.
T Consensus 121 ~~id 124 (345)
T KOG2814|consen 121 KLID 124 (345)
T ss_pred HHHH
Confidence 4443
No 37
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=96.10 E-value=0.012 Score=39.50 Aligned_cols=36 Identities=22% Similarity=0.416 Sum_probs=31.5
Q ss_pred eEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEE
Q 031032 19 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYI 60 (167)
Q Consensus 19 ~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~I 60 (167)
....+.++.+ -+|+.||.+|.+++.+++.+|.+|.|
T Consensus 25 ~~~~v~V~~~------~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDD------QLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcc------cceeeECCCCHHHHHHHHHHCCCeEE
Confidence 4566777876 78999999999999999999998876
No 38
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=95.52 E-value=0.049 Score=45.00 Aligned_cols=69 Identities=26% Similarity=0.426 Sum_probs=54.0
Q ss_pred ceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEec--
Q 031032 18 KRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEAD-- 95 (167)
Q Consensus 18 ~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~-- 95 (167)
...+.+.||.+ -+|-|||+.|.+.+.|++.++|+|.|..+.. -|.|...
T Consensus 7 ~~~~~v~iPk~------R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~-----------------------~V~i~~~~~ 57 (194)
T COG1094 7 KSSEAVKIPKD------RIGVLIGKWGEVKKAIEEKTGVKLRIDSKTG-----------------------SVTIRTTRK 57 (194)
T ss_pred cceeeeecCch------hheeeecccccchHHHHhhcCeEEEEECCCC-----------------------eEEEEecCC
Confidence 34566788887 7999999999999999999999999997631 4555554
Q ss_pred --CCcchHHHHHHHHHHHHHhccCCCC
Q 031032 96 --LPANIVDIRLRQAQEIIEELLKPVD 120 (167)
Q Consensus 96 --~~~~~a~~~l~~A~~~Ie~LL~~~~ 120 (167)
|+- .+.+|.++|+.+-.-.+
T Consensus 58 t~Dp~-----~~~ka~d~VkAIgrGF~ 79 (194)
T COG1094 58 TEDPL-----ALLKARDVVKAIGRGFP 79 (194)
T ss_pred CCChH-----HHHHHHHHHHHHhcCCC
Confidence 333 78889999988876654
No 39
>PRK12705 hypothetical protein; Provisional
Probab=94.62 E-value=0.043 Score=51.15 Aligned_cols=66 Identities=27% Similarity=0.445 Sum_probs=48.2
Q ss_pred EEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcc
Q 031032 20 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN 99 (167)
Q Consensus 20 ~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~ 99 (167)
+..|.+|-+ .+-|||||--|.++|.+|..||+.|.|...- =-|.|+++++.
T Consensus 199 vs~v~lp~d-----emkGriIGreGrNir~~E~~tGvdliiddtp-----------------------~~V~ls~fdp~- 249 (508)
T PRK12705 199 VSVVPIPSD-----AMKGRIIGREGRNIRAFEGLTGVDLIIDDTP-----------------------EAVVISSFNPI- 249 (508)
T ss_pred eeeeecCCh-----HhhccccCccchhHHHHHHhhCCceEecCCc-----------------------cchhhcccCcc-
Confidence 345567766 4889999999999999999999999998531 14777888776
Q ss_pred hHHHHHHHHHHHHHhccCC
Q 031032 100 IVDIRLRQAQEIIEELLKP 118 (167)
Q Consensus 100 ~a~~~l~~A~~~Ie~LL~~ 118 (167)
+=+.|...++.|+..
T Consensus 250 ----rreia~~~l~~Li~d 264 (508)
T PRK12705 250 ----RREIARLTLEKLLAD 264 (508)
T ss_pred ----chHHHHHHHHHHHhc
Confidence 334455555555544
No 40
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=94.58 E-value=0.17 Score=43.10 Aligned_cols=41 Identities=24% Similarity=0.587 Sum_probs=36.9
Q ss_pred ceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCc
Q 031032 34 NFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPA 98 (167)
Q Consensus 34 NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~ 98 (167)
.++-|+||++|+.++.|.+.|+|.|.|=-.| .|+|.+.+..
T Consensus 155 ~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG------------------------~IWV~~~~~~ 195 (239)
T COG1097 155 SKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG------------------------RIWVDGENES 195 (239)
T ss_pred hhcceEecCCCcHHHHhhhhcCeEEEEecCC------------------------EEEecCCCcc
Confidence 3888999999999999999999999998777 8999988763
No 41
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=94.07 E-value=0.022 Score=51.93 Aligned_cols=76 Identities=25% Similarity=0.460 Sum_probs=63.1
Q ss_pred EEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcchHHHHHHHHHHHHHhccC
Q 031032 38 RLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLK 117 (167)
Q Consensus 38 ~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~a~~~l~~A~~~Ie~LL~ 117 (167)
.|.||.|-++|.++.++-..+.|.|-||..-.. +.....++|.||.|.+.++. .|+.|+-+++.++.
T Consensus 308 ~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i~p--------~~~~~~~~p~~~~~~~~~~~-----~~~~~~~~~~~~i~ 374 (531)
T KOG1960|consen 308 AIVGPQGAYVKHIQQETRTRVQIKGQGSAFIEP--------STNRESDEPIHLCIMSHDPN-----AIQRAKVLCEDLIA 374 (531)
T ss_pred ccccCCcccccccCCCCCcceeccCccceeecC--------CCCCCCCCCcccccccCChh-----hhhhhhhcccccCC
Confidence 478999999999999999999999999987543 23346789999999998876 67789999999999
Q ss_pred CCCcchHHH
Q 031032 118 PVDESQDYI 126 (167)
Q Consensus 118 ~~~~~~d~~ 126 (167)
+++-.+-.-
T Consensus 375 ~v~~qy~~~ 383 (531)
T KOG1960|consen 375 SVHQQYKAW 383 (531)
T ss_pred cccccCccc
Confidence 987554433
No 42
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=93.52 E-value=0.13 Score=47.66 Aligned_cols=29 Identities=31% Similarity=0.628 Sum_probs=27.5
Q ss_pred CceeeEEeCCCcchHHHHHHHhCCeEEEe
Q 031032 33 FNFVGRLLGPRGNSLKRVEATTGCRVYIR 61 (167)
Q Consensus 33 ~NfiG~IIGP~G~tiK~Iq~eTG~kI~Ir 61 (167)
-++||.+||-+|+.+|+||..|+++|.|-
T Consensus 55 s~mvg~vigrggskik~iq~~tnt~iqii 83 (629)
T KOG0336|consen 55 SEMVGKVIGRGGSKIKRIQNDTNTRIQII 83 (629)
T ss_pred hhhhheeeccCcchhhhhhcccceeEEEe
Confidence 36999999999999999999999999997
No 43
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=93.47 E-value=0.099 Score=48.52 Aligned_cols=42 Identities=29% Similarity=0.525 Sum_probs=36.7
Q ss_pred ccceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecc
Q 031032 16 TVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 63 (167)
Q Consensus 16 ~~~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~ 63 (167)
..-...++.||.+ ++|.|||..|..+-.|++.|||.|.|-++
T Consensus 335 ~~~v~~~l~vps~------~igciiGk~G~~iseir~~tgA~I~I~~~ 376 (485)
T KOG2190|consen 335 TQTVTQRLLVPSD------LIGCIIGKGGAKISEIRQRTGASISILNK 376 (485)
T ss_pred cceeeeeeccCcc------ccceeecccccchHHHHHhcCCceEEccc
Confidence 4445577888876 99999999999999999999999999874
No 44
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=92.66 E-value=0.045 Score=37.90 Aligned_cols=32 Identities=25% Similarity=0.518 Sum_probs=25.2
Q ss_pred CCCCceeeEEeCCCcchHHHHHHHh-CCeEEEe
Q 031032 30 YPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIR 61 (167)
Q Consensus 30 ~P~~NfiG~IIGP~G~tiK~Iq~eT-G~kI~Ir 61 (167)
.|+++-+|..||++|+.+|.|+++. |-+|.|=
T Consensus 13 ~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 13 DPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp STTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred CCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 3788999999999999999999999 6666555
No 45
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=90.07 E-value=0.29 Score=31.62 Aligned_cols=23 Identities=13% Similarity=0.368 Sum_probs=20.7
Q ss_pred eeEEeCCCcchHHHHHHHhCCeE
Q 031032 36 VGRLLGPRGNSLKRVEATTGCRV 58 (167)
Q Consensus 36 iG~IIGP~G~tiK~Iq~eTG~kI 58 (167)
.|++||.+|.+++.|+..++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 69999999999999999998554
No 46
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=89.26 E-value=0.47 Score=36.97 Aligned_cols=28 Identities=25% Similarity=0.410 Sum_probs=26.6
Q ss_pred eeeEEeCCCcchHHHHHHHhCCeEEEec
Q 031032 35 FVGRLLGPRGNSLKRVEATTGCRVYIRG 62 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG~kI~IrG 62 (167)
.+|..||++|+.+|.|++..|-+|.|=.
T Consensus 42 ~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 42 DMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CccccCCcCchHHHHHHHHhCCceEEEE
Confidence 7899999999999999999999999886
No 47
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=89.02 E-value=1.4 Score=38.66 Aligned_cols=37 Identities=19% Similarity=0.360 Sum_probs=31.1
Q ss_pred EEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEec
Q 031032 20 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 62 (167)
Q Consensus 20 ~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG 62 (167)
..+|++..+ -.|.|||-+|+++|+|..++++.|.|-.
T Consensus 49 e~ril~~sk------~agavigkgg~nik~lr~d~na~v~vpd 85 (390)
T KOG2192|consen 49 ELRILLQSK------NAGAVIGKGGKNIKALRTDYNASVSVPD 85 (390)
T ss_pred eEEEEEecc------cccceeccccccHHHHhhhccceeeccC
Confidence 345555555 5899999999999999999999999985
No 48
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=86.83 E-value=1.4 Score=38.82 Aligned_cols=37 Identities=24% Similarity=0.552 Sum_probs=33.8
Q ss_pred EEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEec
Q 031032 20 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 62 (167)
Q Consensus 20 ~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG 62 (167)
+..|.||.| +-|-|||-+|.-+|+|..|+||.|.|..
T Consensus 316 TaQvtip~d------lggsiigkggqri~~ir~esGA~Ikide 352 (390)
T KOG2192|consen 316 TAQVTIPKD------LGGSIIGKGGQRIKQIRHESGASIKIDE 352 (390)
T ss_pred eeeEecccc------cCcceecccchhhhhhhhccCceEEecC
Confidence 456789987 8999999999999999999999999985
No 49
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=84.61 E-value=1.5 Score=39.17 Aligned_cols=38 Identities=21% Similarity=0.355 Sum_probs=30.5
Q ss_pred cceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEE
Q 031032 17 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYI 60 (167)
Q Consensus 17 ~~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~I 60 (167)
....+.+.+|- -|++.|.|++|.++|.|+.+|...|.-
T Consensus 24 ~nvt~sv~vps------~~v~~ivg~qg~kikalr~KTqtyi~t 61 (394)
T KOG2113|consen 24 QNVTESVEVPS------EHVAEIVGRQGCKIKALRAKTQTYIKT 61 (394)
T ss_pred CccceeeecCc------ccceeecccCccccchhhhhhcceecc
Confidence 45556666662 399999999999999999999987754
No 50
>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=83.47 E-value=0.73 Score=31.90 Aligned_cols=27 Identities=22% Similarity=0.361 Sum_probs=22.0
Q ss_pred eeeEEeCCCcchHHHHHHHhCCeEEEe
Q 031032 35 FVGRLLGPRGNSLKRVEATTGCRVYIR 61 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG~kI~Ir 61 (167)
-.|+|||.+|.|+..||--+..-+.-+
T Consensus 34 ~~g~LIGk~G~tL~AlQ~L~~~~~~~~ 60 (77)
T cd02414 34 DIGLLIGKRGKTLDALQYLANLVLNRN 60 (77)
T ss_pred CCCeEECCCCccHHHHHHHHHHHHhhc
Confidence 469999999999999999877544433
No 51
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=82.97 E-value=1.1 Score=42.03 Aligned_cols=39 Identities=15% Similarity=0.486 Sum_probs=35.0
Q ss_pred EEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccC
Q 031032 21 LRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGS 65 (167)
Q Consensus 21 ~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS 65 (167)
..+++|.+ +++.+||-+|..+++|++..|-+|.|+-.+.
T Consensus 488 avv~vpe~------~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 488 AVVKVPEK------YIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred EEEEeCHH------HhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 56788877 8999999999999999999999999998664
No 52
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=82.15 E-value=1.2 Score=34.78 Aligned_cols=36 Identities=17% Similarity=0.291 Sum_probs=29.3
Q ss_pred EEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEe
Q 031032 20 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 61 (167)
Q Consensus 20 ~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~Ir 61 (167)
...+.|+.+ -.|+.||.+|.|++.++.-+|-.+.|.
T Consensus 100 ~~~V~V~~~------d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 100 VAYVEVAPE------DKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred EEEEEECcc------ccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 344566665 689999999999999999999877664
No 53
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=82.11 E-value=1.1 Score=36.93 Aligned_cols=32 Identities=25% Similarity=0.406 Sum_probs=28.7
Q ss_pred CCceeeEEeCCCcchHHHHHHHhCCeEEEecc
Q 031032 32 NFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 63 (167)
Q Consensus 32 ~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~ 63 (167)
+.+-+|..||++|+.+|.|+++.|=+|.|=.-
T Consensus 83 ~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~ 114 (190)
T COG0195 83 KIDPVGACIGKRGSRVKAVSEELGEKIDVVEW 114 (190)
T ss_pred CcCchhhhccCCChHHHHHHHHhCCceEEEEe
Confidence 45689999999999999999999999988764
No 54
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=81.40 E-value=1.6 Score=39.23 Aligned_cols=34 Identities=24% Similarity=0.510 Sum_probs=30.6
Q ss_pred CCCCCceeeEEeCCCcchHHHHHHHh-CCeEEEec
Q 031032 29 TYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 62 (167)
Q Consensus 29 ~~P~~NfiG~IIGP~G~tiK~Iq~eT-G~kI~IrG 62 (167)
..|+++-+|..||++|+.++.|.++. |=+|.|=.
T Consensus 240 ~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv~ 274 (362)
T PRK12327 240 NNPNVDAKGACVGPKGQRVQNIVSELKGEKIDIID 274 (362)
T ss_pred CCCCCCchheeECCCChhHHHHHHHhCCCeEEEEE
Confidence 34889999999999999999999998 88888875
No 55
>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=80.72 E-value=1.9 Score=38.30 Aligned_cols=33 Identities=24% Similarity=0.470 Sum_probs=30.1
Q ss_pred CCCCceeeEEeCCCcchHHHHHHHh-CCeEEEec
Q 031032 30 YPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 62 (167)
Q Consensus 30 ~P~~NfiG~IIGP~G~tiK~Iq~eT-G~kI~IrG 62 (167)
.|+++-+|..||++|+.++.|.++. |=+|.|=.
T Consensus 239 ~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~ 272 (341)
T TIGR01953 239 DENIDPVGACVGPKGSRIQAISKELNGEKIDIIE 272 (341)
T ss_pred CCCCCcceeeECCCCchHHHHHHHhCCCeEEEEE
Confidence 5889999999999999999999999 88888765
No 56
>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=80.60 E-value=1.4 Score=34.63 Aligned_cols=29 Identities=24% Similarity=0.414 Sum_probs=26.9
Q ss_pred ceeeEEeCCCcchHHHHHHHhCCeEEEec
Q 031032 34 NFVGRLLGPRGNSLKRVEATTGCRVYIRG 62 (167)
Q Consensus 34 NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG 62 (167)
+-+|..||++|+.+|.|++..|=+|.|=.
T Consensus 42 g~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 42 GEMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred CCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 47999999999999999999999999886
No 57
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=80.53 E-value=2.9 Score=38.64 Aligned_cols=33 Identities=21% Similarity=0.370 Sum_probs=30.1
Q ss_pred CCCCceeeEEeCCCcchHHHHHHHh-CCeEEEec
Q 031032 30 YPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 62 (167)
Q Consensus 30 ~P~~NfiG~IIGP~G~tiK~Iq~eT-G~kI~IrG 62 (167)
.|+++-+|..||++|+.++.|.++. |=+|.|=.
T Consensus 273 d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~ 306 (449)
T PRK12329 273 ERDVDPVGACIGARGSRIQAVVNELRGEKIDVIR 306 (449)
T ss_pred CCCCChhhccCCCCcchHHHHHHHhCCCeEEEEE
Confidence 4789999999999999999999999 88998865
No 58
>PRK02821 hypothetical protein; Provisional
Probab=80.28 E-value=0.97 Score=32.04 Aligned_cols=22 Identities=14% Similarity=0.401 Sum_probs=18.7
Q ss_pred eeeEEeCCCcchHHHHHHHhCC
Q 031032 35 FVGRLLGPRGNSLKRVEATTGC 56 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG~ 56 (167)
=+|||||-+|.|++.|..--.+
T Consensus 41 D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 41 DLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred hCcceeCCCCchHHHHHHHHHH
Confidence 6999999999999999775443
No 59
>PRK00468 hypothetical protein; Provisional
Probab=80.13 E-value=0.99 Score=31.77 Aligned_cols=26 Identities=19% Similarity=0.501 Sum_probs=20.4
Q ss_pred EEecCCCCCCCCceeeEEeCCCcchHHHHHHH
Q 031032 22 RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEAT 53 (167)
Q Consensus 22 ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~e 53 (167)
.+.+..+ =+|||||-+|.|++.|..-
T Consensus 33 ~l~v~~~------D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 33 ELKVAPE------DMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred EEEEChh------hCcceecCCChhHHHHHHH
Confidence 4555554 5899999999999998764
No 60
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=79.72 E-value=3.8 Score=36.78 Aligned_cols=30 Identities=30% Similarity=0.503 Sum_probs=27.5
Q ss_pred ceeeEEeCCCcchHHHHHHHhCCeEEEecc
Q 031032 34 NFVGRLLGPRGNSLKRVEATTGCRVYIRGK 63 (167)
Q Consensus 34 NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~ 63 (167)
|-+-.|+||.+..++.|++.+|+.|.-||.
T Consensus 24 ~~~~~l~G~~~~~l~l~e~~~gv~i~~rG~ 53 (348)
T COG1702 24 NELVALFGPTDTNLSLLEIALGVSIVARGE 53 (348)
T ss_pred hhhhhhcCCCCccHHHHHHHhCcEEEeCCc
Confidence 467789999999999999999999999985
No 61
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=79.27 E-value=1.3 Score=43.25 Aligned_cols=40 Identities=23% Similarity=0.443 Sum_probs=33.3
Q ss_pred ccceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEe
Q 031032 16 TVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 61 (167)
Q Consensus 16 ~~~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~Ir 61 (167)
-.+....+.||.+ +-+.||||+|.++++++.+++|-|.+-
T Consensus 706 ~~~~~~~~~~p~~------~~~~~ig~~g~~~r~~~~~~~~~~~~~ 745 (753)
T KOG2208|consen 706 KNLVTKEIEIPRS------LHRYLIGPKGSNLRQLEKEFNVNIVVP 745 (753)
T ss_pred ccceeeEEeccHH------HhhhccCCCCccHHHHHHHhccceecC
Confidence 3445566778877 888999999999999999999988765
No 62
>PRK13764 ATPase; Provisional
Probab=77.53 E-value=1.6 Score=41.64 Aligned_cols=40 Identities=18% Similarity=0.362 Sum_probs=35.3
Q ss_pred EEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccC
Q 031032 20 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGS 65 (167)
Q Consensus 20 ~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS 65 (167)
...|+||.+ .++.+||-+|+++++|++..|..|.||-...
T Consensus 482 ~~~v~~~~~------~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 482 KAVVYVPEK------DIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred eEEEEEChh------hhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence 456889988 7889999999999999999999999998653
No 63
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=77.07 E-value=0.44 Score=32.49 Aligned_cols=21 Identities=29% Similarity=0.537 Sum_probs=18.9
Q ss_pred eeeEEeCCCcchHHHHHHHhC
Q 031032 35 FVGRLLGPRGNSLKRVEATTG 55 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG 55 (167)
-.|+|||-+|.|++.||--++
T Consensus 39 d~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 39 DAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp CCHHHCTTHHHHHHHHHHHHH
T ss_pred ccceEECCCCeeHHHHHHHHH
Confidence 589999999999999998665
No 64
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=76.12 E-value=1.5 Score=31.08 Aligned_cols=19 Identities=16% Similarity=0.586 Sum_probs=16.8
Q ss_pred eeeEEeCCCcchHHHHHHH
Q 031032 35 FVGRLLGPRGNSLKRVEAT 53 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~e 53 (167)
=+|+|||-+|.|++.|-.-
T Consensus 40 D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 40 DMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred cccceecCCChhHHHHHHH
Confidence 5899999999999999653
No 65
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=75.13 E-value=2.4 Score=34.27 Aligned_cols=27 Identities=22% Similarity=0.260 Sum_probs=25.6
Q ss_pred eEEeCCCcchHHHHHHHhCCeEEEecc
Q 031032 37 GRLLGPRGNSLKRVEATTGCRVYIRGK 63 (167)
Q Consensus 37 G~IIGP~G~tiK~Iq~eTG~kI~IrG~ 63 (167)
|.-||++|.++|++++..|-+|.|=..
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEEEc
Confidence 999999999999999999999999874
No 66
>PRK01064 hypothetical protein; Provisional
Probab=73.59 E-value=5.2 Score=28.35 Aligned_cols=21 Identities=19% Similarity=0.507 Sum_probs=18.3
Q ss_pred eeeEEeCCCcchHHHHHHHhC
Q 031032 35 FVGRLLGPRGNSLKRVEATTG 55 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG 55 (167)
-+|++||-+|.|++.|+.-..
T Consensus 40 D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 40 DIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred cceEEECCCCccHHHHHHHHH
Confidence 579999999999999988544
No 67
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=72.93 E-value=2.4 Score=38.34 Aligned_cols=34 Identities=21% Similarity=0.353 Sum_probs=30.3
Q ss_pred CCCCCceeeEEeCCCcchHHHHHHHh-CCeEEEec
Q 031032 29 TYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 62 (167)
Q Consensus 29 ~~P~~NfiG~IIGP~G~tiK~Iq~eT-G~kI~IrG 62 (167)
..|+++-+|..||++|+.++.|.++. |=+|.|=.
T Consensus 246 ~d~~iDPvGacIG~~G~rI~~I~~eL~gEkIDvI~ 280 (374)
T PRK12328 246 NNPNIDPIGATVGVKGVRINAVSKELNGENIDCIE 280 (374)
T ss_pred CCCCCChHHhhcCCCcchHHHHHHHhCCCeEEEEE
Confidence 45789999999999999999999998 78887764
No 68
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=72.81 E-value=4.8 Score=36.44 Aligned_cols=44 Identities=16% Similarity=0.271 Sum_probs=36.1
Q ss_pred eEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCC
Q 031032 19 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKD 68 (167)
Q Consensus 19 ~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~ 68 (167)
+...+.+|.+ -.++-||-+|.+++--.+-||.+|.|+.-+|.-.
T Consensus 308 ~~~~V~V~~~------qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~~~~ 351 (374)
T PRK12328 308 KKAIVTLLSD------QKSKAIGKNGINIRLASMLTGYEIELNEIGSKEN 351 (374)
T ss_pred cEEEEEEChH------HhhhhhcCCChhHHHHHHHhCCEEEEEECCCCcc
Confidence 3456677776 4579999999999999999999999999876433
No 69
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=70.92 E-value=3.3 Score=34.99 Aligned_cols=28 Identities=25% Similarity=0.453 Sum_probs=26.6
Q ss_pred eeeEEeCCCcchHHHHHHHhCCeEEEec
Q 031032 35 FVGRLLGPRGNSLKRVEATTGCRVYIRG 62 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG~kI~IrG 62 (167)
-||||.|-+|+|--.||..|.++|.|-+
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVlad 206 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIENVTRTRIVLAD 206 (252)
T ss_pred HHHHhhcCCCcceeeeeccceeEEEecC
Confidence 5899999999999999999999999986
No 70
>KOG4165 consensus Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism]
Probab=69.15 E-value=6.5 Score=35.62 Aligned_cols=62 Identities=23% Similarity=0.421 Sum_probs=40.0
Q ss_pred ceeeEEeCCCcch--HHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcchHHHH-------
Q 031032 34 NFVGRLLGPRGNS--LKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIR------- 104 (167)
Q Consensus 34 NfiG~IIGP~G~t--iK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~a~~~------- 104 (167)
++|-+|| |||++ +++|++.|. |-|.| |++.--||+|--+.....|..-
T Consensus 190 ~~IDLvI-PRGSs~LVr~Ik~~tk--IPVLG--------------------HA~GichvYvd~dad~~kA~riv~DaK~d 246 (433)
T KOG4165|consen 190 DYIDLVI-PRGSSDLVRSIKDTTK--IPVLG--------------------HAEGICHVYVDKDADLDKAKRIVRDAKCD 246 (433)
T ss_pred hheeEEe-cCCcHHHHHHHhhccc--Ccccc--------------------cccceeEEEeccccCHHHHHHHHhcccCC
Confidence 4666666 99987 789988776 88887 3455559999665433322111
Q ss_pred HHHHHHHHHhccCC
Q 031032 105 LRQAQEIIEELLKP 118 (167)
Q Consensus 105 l~~A~~~Ie~LL~~ 118 (167)
.-+||..+|-||.-
T Consensus 247 YPAaCNAmETLLIh 260 (433)
T KOG4165|consen 247 YPAACNAMETLLIH 260 (433)
T ss_pred CchhhhhHHHHhcc
Confidence 12467777777764
No 71
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=68.71 E-value=6.5 Score=38.51 Aligned_cols=32 Identities=13% Similarity=0.376 Sum_probs=28.8
Q ss_pred eeeEEeCCCcchHHHHHHHhCCeEEEecccCC
Q 031032 35 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSI 66 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~ 66 (167)
+..-++|..|..+..|.+++.|+|.++-.|+.
T Consensus 357 ~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~ 388 (753)
T KOG2208|consen 357 ELKFVIGKKGANIEKIREESQVKIDLPKQGSN 388 (753)
T ss_pred hhhhhcCCCCccHHHHHHhhhhceecccccCC
Confidence 67789999999999999999999999987653
No 72
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=68.69 E-value=4 Score=37.88 Aligned_cols=34 Identities=24% Similarity=0.393 Sum_probs=30.5
Q ss_pred CCCCCceeeEEeCCCcchHHHHHHHh-CCeEEEec
Q 031032 29 TYPNFNFVGRLLGPRGNSLKRVEATT-GCRVYIRG 62 (167)
Q Consensus 29 ~~P~~NfiG~IIGP~G~tiK~Iq~eT-G~kI~IrG 62 (167)
..|+++-+|..||++|+.++.|.++. |=+|.|--
T Consensus 240 ~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~ 274 (470)
T PRK09202 240 NDPRIDPVGACVGMRGSRIQAISNELGGEKIDIIL 274 (470)
T ss_pred CCCCCChhHccCCCCCchHHHHHHHhCCCeEEEEE
Confidence 56889999999999999999999998 88888764
No 73
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=65.67 E-value=4.5 Score=38.48 Aligned_cols=42 Identities=17% Similarity=0.424 Sum_probs=36.3
Q ss_pred cceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEeccc
Q 031032 17 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKG 64 (167)
Q Consensus 17 ~~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~G 64 (167)
.+...++.+|++ ++=+|+|-.|+++|.|...|++||.++-+-
T Consensus 66 k~v~~e~Vv~~e------~vkli~gr~gsnik~l~~~t~aKi~L~~ed 107 (608)
T KOG2279|consen 66 KDIEIEMVVPQE------AVKLIIGRQGSNIKQLRKQTGAKIDLDTED 107 (608)
T ss_pred hheeeeEeeccc------ceeeeeccccCCcchhhcccccceecCccc
Confidence 344567788887 899999999999999999999999999653
No 74
>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=61.28 E-value=20 Score=29.92 Aligned_cols=40 Identities=15% Similarity=0.346 Sum_probs=29.3
Q ss_pred cceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHH--------HhCCeEEEe
Q 031032 17 VKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEA--------TTGCRVYIR 61 (167)
Q Consensus 17 ~~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~--------eTG~kI~Ir 61 (167)
..-...|++..+. --+-|||.+|+++|+|.. -.||+|.+.
T Consensus 219 ~~i~~~i~v~~~s-----~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l~ 266 (270)
T TIGR00436 219 LKIHALISVERES-----QKKIIIGKNGSMIKAIGIAARKDILELFDCDVFLE 266 (270)
T ss_pred EEEEEEEEECcCC-----ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 3445667777763 568999999999998755 457777764
No 75
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. 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 domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=59.01 E-value=11 Score=29.92 Aligned_cols=27 Identities=22% Similarity=0.396 Sum_probs=24.5
Q ss_pred eeeEEeCCCcchHHHHHHHhCCeEEEe
Q 031032 35 FVGRLLGPRGNSLKRVEATTGCRVYIR 61 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG~kI~Ir 61 (167)
.-|++||.+|.|++.|-.+||-...|.
T Consensus 86 KPG~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 86 KPGLVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred CCeEEEecCchhHHHHHHHhCCeeEEE
Confidence 569999999999999999999887776
No 76
>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=58.95 E-value=10 Score=33.77 Aligned_cols=38 Identities=16% Similarity=0.325 Sum_probs=32.0
Q ss_pred eEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEec
Q 031032 19 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 62 (167)
Q Consensus 19 ~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG 62 (167)
+...+.+|.+ -.++.||-+|.+++--.+-||++|.|+-
T Consensus 301 ~~~~v~V~~~------~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 301 HSAEVVVPDD------QLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cEEEEEEChH------HcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 3456677776 4679999999999999999999999984
No 77
>COG3967 DltE Short-chain dehydrogenase involved in D-alanine esterification of lipoteichoic acid and wall teichoic acid (D-alanine transfer protein) [Cell envelope biogenesis, outer membrane]
Probab=56.01 E-value=7.2 Score=33.24 Aligned_cols=69 Identities=25% Similarity=0.246 Sum_probs=49.6
Q ss_pred HHhCCeEEEecccCCCCCCcccccC--CCCCCCCCCCCcEEEEEecCCcchHHHHHHHHHHHHHhccCCCCcchHHHHHH
Q 031032 52 ATTGCRVYIRGKGSIKDPDKEDKLR--GRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLKPVDESQDYIKRQ 129 (167)
Q Consensus 52 ~eTG~kI~IrG~GS~k~~~~~~~~~--~~p~~~~~~epLHV~Isa~~~~~~a~~~l~~A~~~Ie~LL~~~~~~~d~~k~~ 129 (167)
+.||-.|.|-|-+|+=.-.-..++. |. .|.|.+...+ +|+.|++..-.+...+-|-.|...++
T Consensus 2 k~tgnTiLITGG~sGIGl~lak~f~elgN----------~VIi~gR~e~-----~L~e~~~~~p~~~t~v~Dv~d~~~~~ 66 (245)
T COG3967 2 KTTGNTILITGGASGIGLALAKRFLELGN----------TVIICGRNEE-----RLAEAKAENPEIHTEVCDVADRDSRR 66 (245)
T ss_pred cccCcEEEEeCCcchhhHHHHHHHHHhCC----------EEEEecCcHH-----HHHHHHhcCcchheeeecccchhhHH
Confidence 3578899999987754432222221 22 7999998865 99999999999998887777777777
Q ss_pred HHHHHH
Q 031032 130 QLRELA 135 (167)
Q Consensus 130 QL~elA 135 (167)
+|.|-.
T Consensus 67 ~lvewL 72 (245)
T COG3967 67 ELVEWL 72 (245)
T ss_pred HHHHHH
Confidence 776653
No 78
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=52.84 E-value=39 Score=27.11 Aligned_cols=80 Identities=19% Similarity=0.225 Sum_probs=52.0
Q ss_pred eeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcchHHHHHHHHHHHHHh
Q 031032 35 FVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEE 114 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~a~~~l~~A~~~Ie~ 114 (167)
.+-+|+.++|..++.|-...||+|.+.-.- -.+.|+|... .++.+.+.|.+
T Consensus 36 ~~~LLl~~~~~~L~~l~~~~~~~I~~~~~~-----------------------~~i~I~g~k~------~~~~i~~~i~~ 86 (210)
T PF14611_consen 36 EFFLLLTGNGRILENLAARNGAKIEVSRSE-----------------------NRIRITGTKS------TAEYIEASINE 86 (210)
T ss_pred heeeeecCCchHHHHHHHhcCceEEEecCC-----------------------cEEEEEccHH------HHHHHHHHHHH
Confidence 566899999999999988889999997421 1788888543 34445555555
Q ss_pred ccCC-------CCc--------chHHHHHHHHHHHHHhcCccCC
Q 031032 115 LLKP-------VDE--------SQDYIKRQQLRELAMLNSNFRE 143 (167)
Q Consensus 115 LL~~-------~~~--------~~d~~k~~QL~elA~lnGt~r~ 143 (167)
+|.. .+. ....+...=|.+++-+.++|-.
T Consensus 87 ~l~~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie 130 (210)
T PF14611_consen 87 ILSNIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIE 130 (210)
T ss_pred HHhhcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEE
Confidence 5533 211 1112334557788888888744
No 79
>PRK00089 era GTPase Era; Reviewed
Probab=52.04 E-value=31 Score=28.77 Aligned_cols=39 Identities=21% Similarity=0.402 Sum_probs=29.0
Q ss_pred ceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHH--------HhCCeEEEe
Q 031032 18 KRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEA--------TTGCRVYIR 61 (167)
Q Consensus 18 ~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~--------eTG~kI~Ir 61 (167)
.....|++.-+. -.+-|||-+|+++|+|.. -+||+|.+.
T Consensus 225 ~i~~~i~v~~~~-----~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 225 RIEATIYVERDS-----QKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEEccCC-----ceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 344566776663 568999999999998654 568888776
No 80
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=51.71 E-value=17 Score=32.81 Aligned_cols=39 Identities=23% Similarity=0.434 Sum_probs=27.2
Q ss_pred EecCCC-CCCCCceeeEEeCCCcchHHHHHHHh--------CCeEEEe
Q 031032 23 LEIPVD-TYPNFNFVGRLLGPRGNSLKRVEATT--------GCRVYIR 61 (167)
Q Consensus 23 i~IPv~-~~P~~NfiG~IIGP~G~tiK~Iq~eT--------G~kI~Ir 61 (167)
++|-++ ..|+-...-+|||++|+-+++|-++. +|++.+|
T Consensus 326 l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~dL~~if~r~V~l~ 373 (379)
T KOG1423|consen 326 LFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRANEDLEDIFQRKVFLR 373 (379)
T ss_pred EEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHHHHHHHHhhceeeEE
Confidence 344444 35555678899999999999987654 5555554
No 81
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=50.67 E-value=20 Score=29.24 Aligned_cols=19 Identities=26% Similarity=0.469 Sum_probs=17.1
Q ss_pred chHHHHHHHhCCeEEEecc
Q 031032 45 NSLKRVEATTGCRVYIRGK 63 (167)
Q Consensus 45 ~tiK~Iq~eTG~kI~IrG~ 63 (167)
..+|+||++.|+++.+|..
T Consensus 40 ~~i~~LE~~lg~~Lf~R~~ 58 (294)
T PRK09986 40 IHIKELEDQLGTPLFIRHS 58 (294)
T ss_pred HHHHHHHHHhCCeeEeeCC
Confidence 4689999999999999974
No 82
>PRK15494 era GTPase Era; Provisional
Probab=47.79 E-value=38 Score=29.61 Aligned_cols=38 Identities=16% Similarity=0.245 Sum_probs=29.4
Q ss_pred eEEEEecCCCCCCCCceeeEEeCCCcchHHHHH--------HHhCCeEEEe
Q 031032 19 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVE--------ATTGCRVYIR 61 (167)
Q Consensus 19 ~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq--------~eTG~kI~Ir 61 (167)
....|++.-+. --+-|||-+|+.+|+|- +-+||+|.+.
T Consensus 273 i~~~i~v~~~s-----qk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 273 INQVIVVSRES-----YKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred EEEEEEECCCC-----ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 44677777763 56899999999999864 4568888876
No 83
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=46.23 E-value=18 Score=33.63 Aligned_cols=37 Identities=19% Similarity=0.324 Sum_probs=32.0
Q ss_pred EEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEec
Q 031032 20 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 62 (167)
Q Consensus 20 ~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG 62 (167)
...+.+|.+ -.++-||.+|.++|...+-||.+|.|.-
T Consensus 303 ~~~v~V~~~------~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 303 SADVVVPDD------QLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred EEEEEECcc------hHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 455667766 5789999999999999999999999986
No 84
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=46.08 E-value=61 Score=27.18 Aligned_cols=64 Identities=20% Similarity=0.270 Sum_probs=34.3
Q ss_pred CceeeEEeCCCc-----------chHHHHHHHhCC-eEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCc-c
Q 031032 33 FNFVGRLLGPRG-----------NSLKRVEATTGC-RVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPA-N 99 (167)
Q Consensus 33 ~NfiG~IIGP~G-----------~tiK~Iq~eTG~-kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~-~ 99 (167)
+..+|+||||+| ..+..+-++.-. ++.+|-+- ..-+|+-|--.+.. .
T Consensus 123 l~~Lg~iLGPrGlMP~pk~gTv~~di~~~I~~~k~g~v~~r~~k--------------------~g~i~~~IG~~~m~~e 182 (230)
T PRK05424 123 VGKLGRILGPRGLMPNPKTGTVTMDVAKAVKEAKAGKVEFRVDK--------------------AGIIHAPIGKVSFDAE 182 (230)
T ss_pred HHHhccccccccCCCCCCCCCcchhHHHHHHHHhcCcEEEEecC--------------------CCEEEEEEeCCCCCHH
Confidence 344799999998 234444444432 45555321 22357777655543 2
Q ss_pred hHHHHHHHHHHHHHhcc
Q 031032 100 IVDIRLRQAQEIIEELL 116 (167)
Q Consensus 100 ~a~~~l~~A~~~Ie~LL 116 (167)
...+.+...++.|...+
T Consensus 183 ~i~eNi~a~l~~i~~~~ 199 (230)
T PRK05424 183 KLKENLKALIDAIKKAK 199 (230)
T ss_pred HHHHHHHHHHHHHHHhC
Confidence 33445555555555544
No 85
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=46.02 E-value=23 Score=31.85 Aligned_cols=39 Identities=18% Similarity=0.350 Sum_probs=33.1
Q ss_pred eEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecc
Q 031032 19 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 63 (167)
Q Consensus 19 ~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~ 63 (167)
+...+.+|.+ -.++-||-+|.+++.-.+-||++|.|.-.
T Consensus 303 ~~~~v~V~~~------~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 303 KAARVVVPDY------QLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred cEEEEEEChh------hcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 3456777776 57899999999999999999999999953
No 86
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=43.41 E-value=4.5 Score=27.58 Aligned_cols=24 Identities=17% Similarity=0.428 Sum_probs=20.5
Q ss_pred eeeEEeCCCcchHHHHHHHhCCeE
Q 031032 35 FVGRLLGPRGNSLKRVEATTGCRV 58 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG~kI 58 (167)
..|.+||-+|++++.|..+.+-.+
T Consensus 35 ~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 35 QPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CccHhHHhhhHHHHHHHHHHHHHH
Confidence 568999999999999998876554
No 87
>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=43.02 E-value=40 Score=28.21 Aligned_cols=30 Identities=30% Similarity=0.560 Sum_probs=18.1
Q ss_pred CceeeEEeCCCc-----------chHHHHHHHhCC-eEEEec
Q 031032 33 FNFVGRLLGPRG-----------NSLKRVEATTGC-RVYIRG 62 (167)
Q Consensus 33 ~NfiG~IIGP~G-----------~tiK~Iq~eTG~-kI~IrG 62 (167)
...+|+|+||+| ..+..+-++... ++.+|-
T Consensus 122 l~~Lg~iLGPrGlMP~~k~gtv~~di~~~I~~~k~g~v~~r~ 163 (227)
T TIGR01169 122 VGKLGRILGPRGLMPNPKTGTVTADVAKAVKNAKKGQVEFRA 163 (227)
T ss_pred HHHhccccccccCCCCCCCCCccccHHHHHHHHHcCcEEEEe
Confidence 334699999996 234555455432 566663
No 88
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=42.71 E-value=33 Score=29.16 Aligned_cols=76 Identities=17% Similarity=0.185 Sum_probs=43.9
Q ss_pred EEecCCCCCCCCceeeEEeCCCcch-----------HHHHHHHhCC-eEEEecccCCCCCCcccccCCCCCCCCCCCCcE
Q 031032 22 RLEIPVDTYPNFNFVGRLLGPRGNS-----------LKRVEATTGC-RVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLH 89 (167)
Q Consensus 22 ki~IPv~~~P~~NfiG~IIGP~G~t-----------iK~Iq~eTG~-kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLH 89 (167)
.+.-.++-.|.+-.+|++|||||.. +...-++... +|..|=+. .--+|
T Consensus 114 ~~IAtpdmM~~v~~LG~vLGPRGlMP~Pk~gTvt~Dv~~av~~~K~g~v~~R~dk--------------------~g~ih 173 (228)
T COG0081 114 VFIATPDMMPLVGKLGKVLGPRGLMPNPKTGTVTDDVAKAVEELKKGTVEFRADK--------------------AGVIH 173 (228)
T ss_pred EEEECchHHHHHHHHhhhcCCCCCCCCCCCCCCCcCHHHHHHHHhcCcEEEEECC--------------------CceEE
Confidence 3444555566666799999999962 3444444444 67776432 23359
Q ss_pred EEEEecCCcc-hHHHHHHHHHHHHHhccC
Q 031032 90 ILIEADLPAN-IVDIRLRQAQEIIEELLK 117 (167)
Q Consensus 90 V~Isa~~~~~-~a~~~l~~A~~~Ie~LL~ 117 (167)
+.|-..+.+. ...+.+...++.|...+-
T Consensus 174 ~~iGk~sf~~e~L~eNi~a~l~~i~~~~p 202 (228)
T COG0081 174 VPIGKVSFDDEKLAENIEALLNAIVKAKP 202 (228)
T ss_pred EEecCCCCCHHHHHHHHHHHHHHHHHhCc
Confidence 9887665542 223345555555555543
No 89
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=42.10 E-value=68 Score=26.65 Aligned_cols=61 Identities=21% Similarity=0.131 Sum_probs=35.5
Q ss_pred eeEEeCCC-------------cchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcc-hH
Q 031032 36 VGRLLGPR-------------GNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPAN-IV 101 (167)
Q Consensus 36 iG~IIGP~-------------G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~-~a 101 (167)
+|++|||+ ...+....+++.+++.+|=+- .--+|+.|-..+.+. ..
T Consensus 117 lgk~LGp~~~p~gK~P~~~~~~~dl~~~i~~~k~~v~~r~~k--------------------~~~~~~~VGk~~m~~e~i 176 (214)
T PTZ00225 117 VPRLVGPHMHRMGKFPTVCSPSESLPDKVVELRSTVKFQLKK--------------------VLCLGTCVGHVEMTEEQL 176 (214)
T ss_pred hhhhcCCCCCcCCCCCcccCCccCHHHHHHHHhheeEEEecC--------------------ccEEEeEEccCCCCHHHH
Confidence 59999998 344666666776666666221 113488886665442 23
Q ss_pred HHHHHHHHHHHHhcc
Q 031032 102 DIRLRQAQEIIEELL 116 (167)
Q Consensus 102 ~~~l~~A~~~Ie~LL 116 (167)
.+.+.++++.|...+
T Consensus 177 ~eNi~a~l~~l~~~~ 191 (214)
T PTZ00225 177 RQNVVMAINFLVSLL 191 (214)
T ss_pred HHHHHHHHHHHHHhC
Confidence 334555555555554
No 90
>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=41.98 E-value=18 Score=28.36 Aligned_cols=37 Identities=16% Similarity=0.240 Sum_probs=30.2
Q ss_pred eEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEe
Q 031032 19 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIR 61 (167)
Q Consensus 19 ~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~Ir 61 (167)
+...+.||.+ -.++.||-+|.+++...+-+|-++.|.
T Consensus 100 ~~a~V~V~~~------d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 100 KVAYVEVHPR------DKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred EEEEEEEChh------hhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 4456677776 458999999999999999999887765
No 91
>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=40.52 E-value=23 Score=22.84 Aligned_cols=19 Identities=21% Similarity=0.433 Sum_probs=15.7
Q ss_pred hHHHHHHHhCCeEEEeccc
Q 031032 46 SLKRVEATTGCRVYIRGKG 64 (167)
Q Consensus 46 tiK~Iq~eTG~kI~IrG~G 64 (167)
.+++||++.|+++.+|..+
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 5899999999999999654
No 92
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=40.03 E-value=14 Score=33.24 Aligned_cols=31 Identities=26% Similarity=0.549 Sum_probs=26.7
Q ss_pred CceeeEEeCCCcchHHHHHHHhCCeEEEecc
Q 031032 33 FNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 63 (167)
Q Consensus 33 ~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~ 63 (167)
+-++|++.||.|.|+|+||+.+..-|.--.+
T Consensus 123 ~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 123 LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred ceeeeeccccccCccchheecccceEeeecc
Confidence 4599999999999999999999987765543
No 93
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=37.52 E-value=42 Score=27.25 Aligned_cols=20 Identities=20% Similarity=0.328 Sum_probs=17.1
Q ss_pred chHHHHHHHhCCeEEEeccc
Q 031032 45 NSLKRVEATTGCRVYIRGKG 64 (167)
Q Consensus 45 ~tiK~Iq~eTG~kI~IrG~G 64 (167)
..+|+||++.||++.+|...
T Consensus 36 ~~I~~LE~~lg~~Lf~R~~r 55 (290)
T PRK10837 36 AALTDLEGQLGVQLFDRVGK 55 (290)
T ss_pred HHHHHHHHHhCCccEeecCC
Confidence 35899999999999999643
No 94
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=35.78 E-value=45 Score=26.45 Aligned_cols=18 Identities=22% Similarity=0.595 Sum_probs=16.2
Q ss_pred hHHHHHHHhCCeEEEecc
Q 031032 46 SLKRVEATTGCRVYIRGK 63 (167)
Q Consensus 46 tiK~Iq~eTG~kI~IrG~ 63 (167)
.||.||++.|+++.+|..
T Consensus 11 ~I~~LE~~lg~~Lf~R~~ 28 (269)
T PRK11716 11 QIQRLEEELGQPLFVRDN 28 (269)
T ss_pred HHHHHHHHhCCeeEEecC
Confidence 589999999999999963
No 95
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. 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=34.49 E-value=22 Score=26.19 Aligned_cols=21 Identities=14% Similarity=0.419 Sum_probs=18.3
Q ss_pred eeeEEeCCCcchHHHHHHHhC
Q 031032 35 FVGRLLGPRGNSLKRVEATTG 55 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG 55 (167)
+-|.|||-+|.++++|++...
T Consensus 71 rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 71 RPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred CCCcccCCchHHHHHHHHHHH
Confidence 568999999999999998754
No 96
>COG0080 RplK Ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=32.68 E-value=1.7e+02 Score=23.17 Aligned_cols=40 Identities=20% Similarity=0.282 Sum_probs=26.9
Q ss_pred ceEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCe
Q 031032 18 KRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCR 57 (167)
Q Consensus 18 ~~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~k 57 (167)
..+.++.||-=+-.-=--+|-=|||.|-++.+..++++.+
T Consensus 5 ~~~ikl~v~aGkA~p~PpvGPALG~~Gvni~~f~k~fN~~ 44 (141)
T COG0080 5 VKIIKLQVPAGKANPSPPVGPALGQLGVNIMEFCKEFNAA 44 (141)
T ss_pred ceEEEEEecccccCCCCCCCccccccCCCHHHHHHHHHHH
Confidence 3455566654432112257889999999999988888744
No 97
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=32.41 E-value=55 Score=26.77 Aligned_cols=20 Identities=25% Similarity=0.481 Sum_probs=17.2
Q ss_pred chHHHHHHHhCCeEEEeccc
Q 031032 45 NSLKRVEATTGCRVYIRGKG 64 (167)
Q Consensus 45 ~tiK~Iq~eTG~kI~IrG~G 64 (167)
..++.||++.||++.+|-.+
T Consensus 34 r~i~~LE~~lg~~Lf~R~~~ 53 (296)
T PRK09906 34 QQIKDLENCVGVPLLVRDKR 53 (296)
T ss_pred HHHHHHHHHhCCeeeeeCCC
Confidence 36899999999999999643
No 98
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=32.31 E-value=37 Score=28.30 Aligned_cols=19 Identities=32% Similarity=0.595 Sum_probs=17.1
Q ss_pred hHHHHHHHhCCeEEEeccc
Q 031032 46 SLKRVEATTGCRVYIRGKG 64 (167)
Q Consensus 46 tiK~Iq~eTG~kI~IrG~G 64 (167)
.+|+||++.|+++.+|..+
T Consensus 38 ~Ik~LE~~lg~~Lf~R~~~ 56 (309)
T PRK11013 38 ELARFEKVIGLKLFERVRG 56 (309)
T ss_pred HHHHHHHHhCceeeeecCC
Confidence 5899999999999999754
No 99
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=32.29 E-value=62 Score=26.31 Aligned_cols=18 Identities=17% Similarity=0.553 Sum_probs=16.4
Q ss_pred chHHHHHHHhCCeEEEec
Q 031032 45 NSLKRVEATTGCRVYIRG 62 (167)
Q Consensus 45 ~tiK~Iq~eTG~kI~IrG 62 (167)
..+++||++.|+++.+|.
T Consensus 34 ~~i~~LE~~lg~~Lf~R~ 51 (296)
T PRK11242 34 QQIRQLEESLGVQLFDRS 51 (296)
T ss_pred HHHHHHHHHhCCeeEeEc
Confidence 368999999999999996
No 100
>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=31.89 E-value=36 Score=23.51 Aligned_cols=59 Identities=25% Similarity=0.312 Sum_probs=34.3
Q ss_pred HHHHHHHhCCeEEEecccCCCCCCccccc-C-CCCCCCCCCCCcEEEEEecCCcchHHHHHHHHHHHHHhccC
Q 031032 47 LKRVEATTGCRVYIRGKGSIKDPDKEDKL-R-GRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLK 117 (167)
Q Consensus 47 iK~Iq~eTG~kI~IrG~GS~k~~~~~~~~-~-~~p~~~~~~epLHV~Isa~~~~~~a~~~l~~A~~~Ie~LL~ 117 (167)
+-++-+.+.|.|.|+-.+..-+.++--.+ . +- ...+.++|.+++++. +.|++.|..++.
T Consensus 22 lv~~a~~~~~~i~i~~~~~~vdakSil~l~~L~~----~~G~~i~i~~~G~de--------~~a~~~i~~~~~ 82 (84)
T PF00381_consen 22 LVQIASKFDSDITIRKGGKTVDAKSILGLMSLGA----KKGDEIEIEAEGEDE--------EEALEAIAEFLE 82 (84)
T ss_dssp HHHHHHTSSSEEEEEETTEEEETTSHHHHHHHTB----STTEEEEEEEESTTH--------HHHHHHHHHHHH
T ss_pred HHHHHhhCCCEEEEEeCceeEecCCHHHHhhhhc----CCCCEEEEEEECcCH--------HHHHHHHHHHHh
Confidence 34556778999999976644444432221 1 11 134566777777654 356666666653
No 101
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=30.91 E-value=39 Score=31.45 Aligned_cols=38 Identities=18% Similarity=0.369 Sum_probs=32.2
Q ss_pred EEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecc
Q 031032 20 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGK 63 (167)
Q Consensus 20 ~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~ 63 (167)
...+.+|.+ -.++-||-+|.+++--.+-||.+|.|...
T Consensus 336 ~a~V~V~~~------qlslAIGK~GqNvrLAs~Ltg~~idI~s~ 373 (449)
T PRK12329 336 HAHVLVPPD------QLSLAIGKEGQNVRLAARLTGWKIDIKDS 373 (449)
T ss_pred EEEEEEChH------hcchhhcCCChhHHHHHHHHCCEeccccH
Confidence 456777776 46799999999999999999999999853
No 102
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=30.85 E-value=71 Score=26.30 Aligned_cols=19 Identities=16% Similarity=0.405 Sum_probs=17.0
Q ss_pred hHHHHHHHhCCeEEEeccc
Q 031032 46 SLKRVEATTGCRVYIRGKG 64 (167)
Q Consensus 46 tiK~Iq~eTG~kI~IrG~G 64 (167)
.+|+||++.|+++..|..+
T Consensus 39 ~i~~LE~~lG~~LF~R~~r 57 (302)
T PRK09791 39 SIQELEEGLAAQLFFRRSK 57 (302)
T ss_pred HHHHHHHHhCCeEEEEcCC
Confidence 5899999999999999754
No 103
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=30.84 E-value=60 Score=27.44 Aligned_cols=18 Identities=22% Similarity=0.575 Sum_probs=16.3
Q ss_pred chHHHHHHHhCCeEEEec
Q 031032 45 NSLKRVEATTGCRVYIRG 62 (167)
Q Consensus 45 ~tiK~Iq~eTG~kI~IrG 62 (167)
..||+||++.|+++.+|.
T Consensus 35 ~~Ik~LE~~lg~~LF~R~ 52 (317)
T PRK15421 35 HQFSDLEQRLGFRLFVRK 52 (317)
T ss_pred HHHHHHHHHhCCEEEEec
Confidence 368999999999999995
No 104
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=30.80 E-value=46 Score=27.36 Aligned_cols=37 Identities=19% Similarity=0.347 Sum_probs=31.5
Q ss_pred EEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEec
Q 031032 20 ILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRG 62 (167)
Q Consensus 20 ~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG 62 (167)
...+.||.+ -.++.||-+|.+++...+-||-+|.|..
T Consensus 143 ~~~v~V~~~------~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPD------QLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHH------HHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 455667776 5689999999999999999999999985
No 105
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=30.70 E-value=21 Score=29.98 Aligned_cols=26 Identities=23% Similarity=0.401 Sum_probs=22.6
Q ss_pred eeEEeCCCcchHHHHHHHhCCeEEEe
Q 031032 36 VGRLLGPRGNSLKRVEATTGCRVYIR 61 (167)
Q Consensus 36 iG~IIGP~G~tiK~Iq~eTG~kI~Ir 61 (167)
+|+|||-+|+|+..||--+..-+.-.
T Consensus 102 ~~~LIG~~Gk~LdALQ~L~n~~l~~~ 127 (208)
T COG1847 102 AGRLIGKHGKTLDALQYLANLYLNKI 127 (208)
T ss_pred hhhhhccCCcchHHHHHHHHHHhhhh
Confidence 89999999999999999888666553
No 106
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=29.81 E-value=62 Score=26.49 Aligned_cols=17 Identities=18% Similarity=0.532 Sum_probs=15.8
Q ss_pred hHHHHHHHhCCeEEEec
Q 031032 46 SLKRVEATTGCRVYIRG 62 (167)
Q Consensus 46 tiK~Iq~eTG~kI~IrG 62 (167)
.+|+||++.|+++..|.
T Consensus 35 ~I~~LE~~lG~~LF~R~ 51 (275)
T PRK03601 35 RIRQLENQLGVNLFTRH 51 (275)
T ss_pred HHHHHHHHhCCceEEEC
Confidence 58999999999999995
No 107
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=29.66 E-value=58 Score=27.06 Aligned_cols=19 Identities=16% Similarity=0.538 Sum_probs=16.9
Q ss_pred hHHHHHHHhCCeEEEeccc
Q 031032 46 SLKRVEATTGCRVYIRGKG 64 (167)
Q Consensus 46 tiK~Iq~eTG~kI~IrG~G 64 (167)
.|++||++.|+++..|...
T Consensus 42 ~I~~LE~~lg~~Lf~R~~r 60 (302)
T TIGR02036 42 RINQLEEELGIQLFVRSHR 60 (302)
T ss_pred HHHHHHHHhCCceEEECCC
Confidence 5899999999999999754
No 108
>COG0026 PurK Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) [Nucleotide transport and metabolism]
Probab=29.63 E-value=92 Score=28.40 Aligned_cols=49 Identities=22% Similarity=0.227 Sum_probs=35.0
Q ss_pred eeeEEeCCCcc--hHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCc
Q 031032 35 FVGRLLGPRGN--SLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPA 98 (167)
Q Consensus 35 fiG~IIGP~G~--tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~ 98 (167)
.+--|||-.-. ..+.+-+.-+|++...||.-.|.+.+-+ ||.+.+.+.+
T Consensus 305 vMvNlLG~~~~~~~~~~~l~~p~~~lH~YGK~e~R~gRKmG---------------Hvn~~~~~~~ 355 (375)
T COG0026 305 VMVNLLGDDVPPDDVKAVLALPGAHLHWYGKAEARPGRKMG---------------HVNVLGSDSD 355 (375)
T ss_pred EEEEecCCCCchhhhHHHHhCCCCEEEEecCccCCCCCeee---------------eEEeecCCHH
Confidence 33344453322 4689999999999999997666665544 9999998833
No 109
>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=29.37 E-value=9.8 Score=29.74 Aligned_cols=19 Identities=42% Similarity=0.751 Sum_probs=14.7
Q ss_pred CCCCCCCceeeEEeCCCcc
Q 031032 27 VDTYPNFNFVGRLLGPRGN 45 (167)
Q Consensus 27 v~~~P~~NfiG~IIGP~G~ 45 (167)
.+-.|.+..+|+||||+|.
T Consensus 100 ~~~m~~l~~Lg~iLGprGl 118 (141)
T TIGR01170 100 PDIVPELAQLRRLLGPKGL 118 (141)
T ss_pred HHHHHHHHHhhcccccCcC
Confidence 3345666789999999986
No 110
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=28.68 E-value=76 Score=26.22 Aligned_cols=18 Identities=11% Similarity=0.265 Sum_probs=16.2
Q ss_pred chHHHHHHHhCCeEEEec
Q 031032 45 NSLKRVEATTGCRVYIRG 62 (167)
Q Consensus 45 ~tiK~Iq~eTG~kI~IrG 62 (167)
..||+||++.|+.+.+|.
T Consensus 35 ~~I~~LE~~lg~~LF~R~ 52 (300)
T PRK11074 35 YTVRQLEEWLAVPLFERR 52 (300)
T ss_pred HHHHHHHHHhCCeeEEeC
Confidence 358999999999999995
No 111
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=28.46 E-value=16 Score=27.94 Aligned_cols=43 Identities=26% Similarity=0.461 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHhc-cCCCCcchHHHHHHHHHHHHHhcCccCCCC
Q 031032 102 DIRLRQAQEIIEEL-LKPVDESQDYIKRQQLRELAMLNSNFREDS 145 (167)
Q Consensus 102 ~~~l~~A~~~Ie~L-L~~~~~~~d~~k~~QL~elA~lnGt~r~~~ 145 (167)
+.||+.|+.+|+.- +..+-++-+-+ +.|.+||.-.|..++..+
T Consensus 47 DNKIeQAMDLVKtHLmfAVREEVe~L-k~qI~eL~er~~~Le~EN 90 (123)
T KOG4797|consen 47 DNKIEQAMDLVKTHLMFAVREEVEVL-KEQIRELEERNSALEREN 90 (123)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence 45899999999874 44454444444 589999988877765443
No 112
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=28.35 E-value=43 Score=27.46 Aligned_cols=21 Identities=24% Similarity=0.512 Sum_probs=18.3
Q ss_pred chHHHHHHHhCCeEEEecccC
Q 031032 45 NSLKRVEATTGCRVYIRGKGS 65 (167)
Q Consensus 45 ~tiK~Iq~eTG~kI~IrG~GS 65 (167)
..+|+||++.|+++..|++|.
T Consensus 35 ~~i~~LE~~lg~~Lf~R~r~i 55 (294)
T PRK13348 35 QRIKALEESLGQPLLVRGRPC 55 (294)
T ss_pred HHHHHHHHHhCceeeecCCCC
Confidence 368999999999999998653
No 113
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=27.59 E-value=72 Score=26.70 Aligned_cols=18 Identities=28% Similarity=0.549 Sum_probs=16.3
Q ss_pred hHHHHHHHhCCeEEEecc
Q 031032 46 SLKRVEATTGCRVYIRGK 63 (167)
Q Consensus 46 tiK~Iq~eTG~kI~IrG~ 63 (167)
.+|+||++.|+++..|..
T Consensus 36 ~I~~LE~~lg~~Lf~R~~ 53 (308)
T PRK10094 36 RIKLLEENTGVALFFRTT 53 (308)
T ss_pred HHHHHHHHhCCEEEeeCC
Confidence 589999999999999964
No 114
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=27.40 E-value=35 Score=34.72 Aligned_cols=78 Identities=27% Similarity=0.386 Sum_probs=54.3
Q ss_pred EEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcchH
Q 031032 22 RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIV 101 (167)
Q Consensus 22 ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~a 101 (167)
..-.+.+.+|. |.-+++.+-. ++.+|.+.++|.|.+||+=- ...+ .| ...+..||.+|.+.+.-
T Consensus 899 ~~~~~inD~Pq-~~r~~vt~~~--~L~~i~e~~~~~it~rg~f~--~~gk------~p--~~gErklyl~ve~~~e~--- 962 (997)
T KOG0334|consen 899 EAELEINDFPQ-NARWRVTYKE--ALLRISEPTAAGITTRGKFN--PPGK------EP--KPGERKLYLLVEGPDEL--- 962 (997)
T ss_pred eeeccccccch-hcceeeechh--hhhhccCccccceeeccccC--CCCC------CC--CCcchhhhhhhhcchhH---
Confidence 33455666774 4677777654 49999999999999999631 1110 11 23577899999977644
Q ss_pred HHHHHHHHHHHHhccC
Q 031032 102 DIRLRQAQEIIEELLK 117 (167)
Q Consensus 102 ~~~l~~A~~~Ie~LL~ 117 (167)
.+.+|++.++.++.
T Consensus 963 --~vqra~~e~~r~l~ 976 (997)
T KOG0334|consen 963 --SVQRAIEELERLLE 976 (997)
T ss_pred --HHHHHHHHHHHHHH
Confidence 68889999888664
No 115
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. 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=26.95 E-value=51 Score=23.18 Aligned_cols=21 Identities=14% Similarity=0.379 Sum_probs=18.2
Q ss_pred eeeEEeCCCcchHHHHHHHhC
Q 031032 35 FVGRLLGPRGNSLKRVEATTG 55 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG 55 (167)
.-|.|||-+|.++++|.++..
T Consensus 40 rPg~vIG~~G~~i~~L~~~L~ 60 (81)
T cd02413 40 RTQNVLGEKGRRIRELTSLVQ 60 (81)
T ss_pred CCceEECCCchhHHHHHHHHH
Confidence 569999999999999988754
No 116
>PRK13782 phosphocarrier protein Chr; Provisional
Probab=26.80 E-value=86 Score=21.70 Aligned_cols=54 Identities=13% Similarity=0.151 Sum_probs=29.1
Q ss_pred HHHhCCeEEEecccCCCCCCccccc-C-CCCCCCCCCCCcEEEEEecCCcchHHHHHHHHHHHHHhcc
Q 031032 51 EATTGCRVYIRGKGSIKDPDKEDKL-R-GRPGYEHLNDPLHILIEADLPANIVDIRLRQAQEIIEELL 116 (167)
Q Consensus 51 q~eTG~kI~IrG~GS~k~~~~~~~~-~-~~p~~~~~~epLHV~Isa~~~~~~a~~~l~~A~~~Ie~LL 116 (167)
-..+.|+|.|+-.|-.-+.++--.+ . +- .-.+.+.|.++++|. +.|++.|..+|
T Consensus 26 a~~f~~~i~l~~~~~~vdaKSil~llsLg~----~~g~~v~v~~~G~de--------~~a~~~l~~~~ 81 (82)
T PRK13782 26 ANRFHADIFIEKDGKKVNAKSIMGLMSLAI----GTGSMITIITEGSDE--------EEALEALAAYV 81 (82)
T ss_pred HHhCCCEEEEEECCeEEecHhHHHHHhcCC----CCCCEEEEEEeCcCH--------HHHHHHHHHHh
Confidence 4568899999855433333332211 1 11 234566777666653 35666666655
No 117
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=26.33 E-value=67 Score=27.36 Aligned_cols=21 Identities=29% Similarity=0.520 Sum_probs=18.2
Q ss_pred hHHHHHHHhCCeEEEecccCC
Q 031032 46 SLKRVEATTGCRVYIRGKGSI 66 (167)
Q Consensus 46 tiK~Iq~eTG~kI~IrG~GS~ 66 (167)
.||+||++.|+++..|..+..
T Consensus 36 ~I~~LE~~lG~~LF~R~~r~v 56 (327)
T PRK12680 36 QLKQLEDELGFLLFVRKGRSL 56 (327)
T ss_pred HHHHHHHHhCCeEEEECCCcC
Confidence 589999999999999986544
No 118
>PRK06019 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed
Probab=26.00 E-value=1.8e+02 Score=25.49 Aligned_cols=49 Identities=20% Similarity=0.230 Sum_probs=31.9
Q ss_pred eeeEEeCCCc--chHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCc
Q 031032 35 FVGRLLGPRG--NSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPA 98 (167)
Q Consensus 35 fiG~IIGP~G--~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~ 98 (167)
.+--|||-.. .....+....|+++.+.||...+...+-+ ||.+.+.+.+
T Consensus 305 ~m~nilg~~~~~~~~~~~~~~~~~~~~~ygk~~~~~~rk~G---------------hv~~~~~~~~ 355 (372)
T PRK06019 305 VMVNLLGDDWLEPRWDALLALPGAHLHLYGKAEARPGRKMG---------------HVTVLGDDVE 355 (372)
T ss_pred EEEEEECchhhhhHHHHHhhCCCCEEEECCCCCCCCCCceE---------------EEEeecCCHH
Confidence 3445555431 22334445689999999997666665543 9999987654
No 119
>PRK00394 transcription factor; Reviewed
Probab=25.24 E-value=2.6e+02 Score=22.52 Aligned_cols=31 Identities=10% Similarity=0.065 Sum_probs=21.0
Q ss_pred EEEEEecCCcchHHHHHHHHHHHHHhccCCC
Q 031032 89 HILIEADLPANIVDIRLRQAQEIIEELLKPV 119 (167)
Q Consensus 89 HV~Isa~~~~~~a~~~l~~A~~~Ie~LL~~~ 119 (167)
.+.|+|...+..++..+++....++++=.++
T Consensus 56 Kiv~tGa~S~~~a~~a~~~~~~~l~~~g~~~ 86 (179)
T PRK00394 56 KVVCTGAKSVEDLHEAVKIIIKKLKELGIKV 86 (179)
T ss_pred cEEEEccCCHHHHHHHHHHHHHHHHHcCCCc
Confidence 6788886666566666777777777765443
No 120
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=25.01 E-value=74 Score=26.88 Aligned_cols=19 Identities=21% Similarity=0.462 Sum_probs=16.8
Q ss_pred chHHHHHHHhCCeEEEecc
Q 031032 45 NSLKRVEATTGCRVYIRGK 63 (167)
Q Consensus 45 ~tiK~Iq~eTG~kI~IrG~ 63 (167)
..||+||++.||++..|..
T Consensus 44 ~~I~~LE~~lG~~LF~R~~ 62 (310)
T PRK15092 44 QQMQRLEQLVGKELFARHG 62 (310)
T ss_pred HHHHHHHHHhCcceEEECC
Confidence 3589999999999999964
No 121
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=24.54 E-value=87 Score=25.71 Aligned_cols=18 Identities=22% Similarity=0.405 Sum_probs=16.4
Q ss_pred hHHHHHHHhCCeEEEecc
Q 031032 46 SLKRVEATTGCRVYIRGK 63 (167)
Q Consensus 46 tiK~Iq~eTG~kI~IrG~ 63 (167)
.+++||++.|+++..|..
T Consensus 36 ~I~~LE~~lG~~LF~R~~ 53 (301)
T PRK14997 36 RIAQLEERLGVRLIQRTT 53 (301)
T ss_pred HHHHHHHHhCCEeeeecc
Confidence 589999999999999974
No 122
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=24.52 E-value=87 Score=25.82 Aligned_cols=18 Identities=17% Similarity=0.374 Sum_probs=16.4
Q ss_pred chHHHHHHHhCCeEEEec
Q 031032 45 NSLKRVEATTGCRVYIRG 62 (167)
Q Consensus 45 ~tiK~Iq~eTG~kI~IrG 62 (167)
..+|+||++.||++.+|.
T Consensus 34 ~~i~~LE~~lg~~LF~R~ 51 (305)
T PRK11151 34 GQIRKLEDELGVMLLERT 51 (305)
T ss_pred HHHHHHHHHhCchheeeC
Confidence 468999999999999995
No 123
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=24.47 E-value=75 Score=26.00 Aligned_cols=20 Identities=20% Similarity=0.481 Sum_probs=17.5
Q ss_pred chHHHHHHHhCCeEEEeccc
Q 031032 45 NSLKRVEATTGCRVYIRGKG 64 (167)
Q Consensus 45 ~tiK~Iq~eTG~kI~IrG~G 64 (167)
..||+||++.|+++..|..+
T Consensus 36 ~~I~~LE~~lg~~LF~R~~~ 55 (300)
T TIGR02424 36 KTLRELEEILGTPLFERDRR 55 (300)
T ss_pred HHHHHHHHHhCCeEEEEcCC
Confidence 36899999999999999754
No 124
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=23.97 E-value=2.8e+02 Score=22.27 Aligned_cols=50 Identities=22% Similarity=0.353 Sum_probs=33.1
Q ss_pred CCCCCCCCceeeEEeCCCcchHHHHHHHhCCeEEEecccCCCCCCcccccCCCCCCCCCCCCcEEEEEecCCcchHHHHH
Q 031032 26 PVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGYEHLNDPLHILIEADLPANIVDIRL 105 (167)
Q Consensus 26 Pv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI~IrG~GS~k~~~~~~~~~~~p~~~~~~epLHV~Isa~~~~~~a~~~l 105 (167)
-++.||+ .+-|+-+|+ +.+.|-..| .|.|++...++ .+
T Consensus 123 ePE~fPg--liyr~~~pk------------~~~liF~sG------------------------kvvitGaks~~----~~ 160 (174)
T cd04516 123 EPELFPG--LIYRMVKPK------------IVLLIFVSG------------------------KIVLTGAKSRE----EI 160 (174)
T ss_pred CCccCce--EEEEecCCc------------EEEEEeCCC------------------------EEEEEecCCHH----HH
Confidence 3456665 455555543 777888776 78888765442 57
Q ss_pred HHHHHHHHhccC
Q 031032 106 RQAQEIIEELLK 117 (167)
Q Consensus 106 ~~A~~~Ie~LL~ 117 (167)
.+|++.|..+|.
T Consensus 161 ~~a~~~i~p~L~ 172 (174)
T cd04516 161 YQAFENIYPILL 172 (174)
T ss_pred HHHHHHHHHHHh
Confidence 788888877764
No 125
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=22.76 E-value=50 Score=27.00 Aligned_cols=20 Identities=20% Similarity=0.350 Sum_probs=17.5
Q ss_pred hHHHHHHHhCCeEEEecccC
Q 031032 46 SLKRVEATTGCRVYIRGKGS 65 (167)
Q Consensus 46 tiK~Iq~eTG~kI~IrG~GS 65 (167)
.+++||++.|+++..|++|-
T Consensus 35 ~I~~LE~~lg~~Lf~R~r~~ 54 (292)
T TIGR03298 35 RIKALEERLGQPLLVRTQPC 54 (292)
T ss_pred HHHHHHHHhCchheecCCCC
Confidence 58999999999999998653
No 126
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=22.67 E-value=75 Score=26.51 Aligned_cols=20 Identities=15% Similarity=0.551 Sum_probs=17.2
Q ss_pred chHHHHHHHhCCeEEEeccc
Q 031032 45 NSLKRVEATTGCRVYIRGKG 64 (167)
Q Consensus 45 ~tiK~Iq~eTG~kI~IrG~G 64 (167)
..|++||++.||.+..|...
T Consensus 47 ~~I~~LE~~lG~~LF~R~~r 66 (311)
T PRK10086 47 HRINQLEEELGIKLFVRSHR 66 (311)
T ss_pred HHHHHHHHHhCCeeEEEcCC
Confidence 35899999999999999643
No 127
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=22.01 E-value=57 Score=26.59 Aligned_cols=17 Identities=35% Similarity=0.679 Sum_probs=15.8
Q ss_pred hHHHHHHHhCCeEEEec
Q 031032 46 SLKRVEATTGCRVYIRG 62 (167)
Q Consensus 46 tiK~Iq~eTG~kI~IrG 62 (167)
.||+||++.||++..|.
T Consensus 35 ~Ik~LE~~lg~~LF~R~ 51 (291)
T TIGR03418 35 QVKRLEEELGTPLFERG 51 (291)
T ss_pred HHHHHHHHhCcHHhhcC
Confidence 58999999999999996
No 128
>TIGR01632 L11_bact 50S ribosomal protein L11. This model represents bacterial, chloroplast, and most mitochondrial forms of 50S ribosomal protein L11.
Probab=21.85 E-value=1.2e+02 Score=23.71 Aligned_cols=40 Identities=25% Similarity=0.370 Sum_probs=26.9
Q ss_pred eEEEEecCCCCCCCCceeeEEeCCCcchHHHHHHHhCCeE
Q 031032 19 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRV 58 (167)
Q Consensus 19 ~~~ki~IPv~~~P~~NfiG~IIGP~G~tiK~Iq~eTG~kI 58 (167)
...++.||--+-.-=--+|-.|||.|-++.+..++++.+.
T Consensus 5 ~~ikl~v~aG~A~p~PplGP~LG~~Gini~~f~k~fN~~T 44 (140)
T TIGR01632 5 GIIKLQVPAGQANPAPPVGPALGQRGVNIMEFCKQFNART 44 (140)
T ss_pred EEEEEEEeccccCCCCCCcccccccCCCHHHHHHHHHHHH
Confidence 3456666533221112689999999999999988877443
No 129
>PF03946 Ribosomal_L11_N: Ribosomal protein L11, N-terminal domain; InterPro: IPR020784 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacteria, plant chloroplast, red algal chloroplast, cyanelle and archaeabacterial L11; and mammalian, plant and yeast L12 (YL15). L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown [] to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure.; PDB: 2ZJQ_F 2ZJP_F 3CF5_F 2WRJ_K 2WH4_K 2WRL_K 3FIN_L 2X9U_K 3I8I_L 2XUX_K ....
Probab=21.61 E-value=21 Score=23.97 Aligned_cols=21 Identities=29% Similarity=0.426 Sum_probs=17.8
Q ss_pred eeeEEeCCCcchHHHHHHHhC
Q 031032 35 FVGRLLGPRGNSLKRVEATTG 55 (167)
Q Consensus 35 fiG~IIGP~G~tiK~Iq~eTG 55 (167)
-+|-.|||.|-++++.-++..
T Consensus 16 plgp~LG~~Gin~~~f~k~fN 36 (60)
T PF03946_consen 16 PLGPALGPLGINIKKFCKDFN 36 (60)
T ss_dssp TSTHHHHTTTS-HHHHHHHHH
T ss_pred CcCcccccCCCCHHHHHHHHH
Confidence 578899999999999988876
No 130
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=21.43 E-value=69 Score=27.05 Aligned_cols=20 Identities=15% Similarity=0.270 Sum_probs=17.3
Q ss_pred chHHHHHHHhCCeEEEeccc
Q 031032 45 NSLKRVEATTGCRVYIRGKG 64 (167)
Q Consensus 45 ~tiK~Iq~eTG~kI~IrG~G 64 (167)
..+|+||++.|+.+.+|...
T Consensus 62 ~~I~~LE~~lG~~LF~R~~r 81 (317)
T PRK11482 62 QSIQKLRVIFPDPLFIRKGQ 81 (317)
T ss_pred HHHHHHHHHhCCcceEecCC
Confidence 36899999999999999744
No 131
>PF00408 PGM_PMM_IV: Phosphoglucomutase/phosphomannomutase, C-terminal domain; InterPro: IPR005843 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1KFQ_B 1KFI_A 3PDK_B 2F7L_A 1TUO_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=20.73 E-value=1.3e+02 Score=19.99 Aligned_cols=23 Identities=26% Similarity=0.338 Sum_probs=14.0
Q ss_pred cEEEEEecCCcchHHHHHHHHHHHHHhc
Q 031032 88 LHILIEADLPANIVDIRLRQAQEIIEEL 115 (167)
Q Consensus 88 LHV~Isa~~~~~~a~~~l~~A~~~Ie~L 115 (167)
|.|++++.+.+ .+++.++.|..+
T Consensus 49 iRv~~Ea~~~~-----~~~~~~~~i~~~ 71 (73)
T PF00408_consen 49 IRVYVEAPDEE-----ELEEIAEEIAEA 71 (73)
T ss_dssp EEEEEEESSHH-----HHHHHHHHHHHH
T ss_pred EEEEEEeCCHH-----HHHHHHHHHHHh
Confidence 67888888654 455555555443
No 132
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=20.59 E-value=4.1e+02 Score=21.16 Aligned_cols=31 Identities=19% Similarity=0.294 Sum_probs=21.5
Q ss_pred EEEEEecCCcchHHHHHHHHHHHHHhccCCC
Q 031032 89 HILIEADLPANIVDIRLRQAQEIIEELLKPV 119 (167)
Q Consensus 89 HV~Isa~~~~~~a~~~l~~A~~~Ie~LL~~~ 119 (167)
.+.|+|-..+..++..+++.+..++++-..+
T Consensus 57 KivitGaks~~~~~~a~~~~~~~L~~~g~~~ 87 (174)
T cd00652 57 KMVITGAKSEEDAKLAARKYARILQKLGFPV 87 (174)
T ss_pred EEEEEecCCHHHHHHHHHHHHHHHHHcCCCc
Confidence 7888886555566667777777777776544
No 133
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=20.54 E-value=81 Score=26.08 Aligned_cols=19 Identities=16% Similarity=0.410 Sum_probs=16.8
Q ss_pred chHHHHHHHhCCeEEEecc
Q 031032 45 NSLKRVEATTGCRVYIRGK 63 (167)
Q Consensus 45 ~tiK~Iq~eTG~kI~IrG~ 63 (167)
..||+||++.|+++..|..
T Consensus 44 ~~I~~LE~~lG~~Lf~R~~ 62 (303)
T PRK10082 44 RRIRALEQAIGVELFNRQV 62 (303)
T ss_pred HHHHHHHHHcCCEEEEecC
Confidence 3689999999999999973
No 134
>KOG2944 consensus Glyoxalase [Carbohydrate transport and metabolism]
Probab=20.46 E-value=1.2e+02 Score=24.79 Aligned_cols=19 Identities=42% Similarity=0.473 Sum_probs=15.0
Q ss_pred EEEEEecCCcchHHHHHHHHHHHHHhc
Q 031032 89 HILIEADLPANIVDIRLRQAQEIIEEL 115 (167)
Q Consensus 89 HV~Isa~~~~~~a~~~l~~A~~~Ie~L 115 (167)
|++|+++| +..||+.+++.
T Consensus 118 HIci~V~d--------i~sac~~lkek 136 (170)
T KOG2944|consen 118 HICIEVDD--------INSACERLKEK 136 (170)
T ss_pred eEEEEeCC--------HHHHHHHHHHh
Confidence 99999986 56777777764
No 135
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=20.37 E-value=79 Score=26.02 Aligned_cols=21 Identities=19% Similarity=0.347 Sum_probs=18.2
Q ss_pred chHHHHHHHhCCeEEEecccC
Q 031032 45 NSLKRVEATTGCRVYIRGKGS 65 (167)
Q Consensus 45 ~tiK~Iq~eTG~kI~IrG~GS 65 (167)
..+|+||++.|+++..|++|-
T Consensus 35 ~~I~~LE~~lg~~LF~R~~~~ 55 (294)
T PRK03635 35 QRIKALEERVGQVLLVRTQPC 55 (294)
T ss_pred HHHHHHHHHhCceeeecCCCC
Confidence 368999999999999998653
Done!