Query 029290
Match_columns 196
No_of_seqs 180 out of 353
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 10:32:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029290.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029290hhsearch_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 2.2E-38 4.7E-43 276.6 13.4 125 28-196 21-145 (259)
2 KOG0119 Splicing factor 1/bran 100.0 1.5E-31 3.2E-36 249.6 8.4 132 60-194 52-189 (554)
3 COG5176 MSL5 Splicing factor ( 99.9 1.9E-27 4.1E-32 204.1 6.7 124 67-193 70-198 (269)
4 cd02395 SF1_like-KH Splicing f 99.9 2.8E-22 6E-27 158.0 5.8 53 144-196 1-53 (120)
5 PF13014 KH_3: KH domain 98.2 1.7E-06 3.7E-11 56.0 3.1 28 159-186 1-28 (43)
6 cd02393 PNPase_KH Polynucleoti 98.1 4.9E-06 1.1E-10 58.0 4.5 39 144-188 3-41 (61)
7 cd00105 KH-I K homology RNA-bi 98.1 4.7E-06 1E-10 56.4 4.1 39 145-189 2-40 (64)
8 smart00322 KH K homology RNA-b 97.8 2.9E-05 6.3E-10 51.5 4.6 39 144-188 4-42 (69)
9 PF00013 KH_1: KH domain syndr 97.8 6.3E-06 1.4E-10 56.1 0.7 38 144-187 1-38 (60)
10 cd02396 PCBP_like_KH K homolog 97.8 3.8E-05 8.1E-10 53.6 4.1 39 145-189 2-40 (65)
11 cd02394 vigilin_like_KH K homo 97.7 1.8E-05 4E-10 54.1 2.1 38 145-188 2-39 (62)
12 PRK13763 putative RNA-processi 96.7 0.00096 2.1E-08 55.7 2.6 29 159-187 105-133 (180)
13 KOG2193 IGF-II mRNA-binding pr 96.6 0.00061 1.3E-08 64.7 0.6 39 147-185 278-316 (584)
14 TIGR03665 arCOG04150 arCOG0415 96.6 0.0013 2.7E-08 54.6 2.1 28 159-186 99-126 (172)
15 COG1094 Predicted RNA-binding 96.2 0.0039 8.5E-08 53.5 3.2 29 159-187 112-140 (194)
16 TIGR03591 polynuc_phos polyrib 95.0 0.013 2.7E-07 58.2 2.1 42 143-190 551-592 (684)
17 KOG2874 rRNA processing protei 94.9 0.015 3.3E-07 53.0 2.2 27 161-187 161-187 (356)
18 KOG1960 Predicted RNA-binding 94.4 0.015 3.2E-07 55.2 0.9 50 141-191 208-257 (531)
19 TIGR02696 pppGpp_PNP guanosine 94.0 0.052 1.1E-06 54.5 3.7 44 141-190 576-619 (719)
20 KOG1676 K-homology type RNA bi 93.4 0.087 1.9E-06 51.8 4.1 28 158-185 239-266 (600)
21 KOG1676 K-homology type RNA bi 92.9 0.17 3.6E-06 49.9 5.0 47 140-192 136-182 (600)
22 KOG2191 RNA-binding protein NO 92.8 0.12 2.6E-06 48.1 3.8 37 143-185 39-75 (402)
23 KOG2193 IGF-II mRNA-binding pr 89.3 0.23 5E-06 47.7 2.1 36 146-187 202-237 (584)
24 KOG2814 Transcription coactiva 89.3 0.19 4.1E-06 46.5 1.5 35 158-192 66-100 (345)
25 KOG2190 PolyC-binding proteins 89.0 0.51 1.1E-05 45.5 4.2 39 143-187 138-176 (485)
26 PLN00207 polyribonucleotide nu 88.8 0.12 2.7E-06 53.0 -0.0 43 143-191 685-728 (891)
27 PRK04163 exosome complex RNA-b 88.6 0.19 4.1E-06 43.6 0.9 31 158-188 154-184 (235)
28 cd02134 NusA_KH NusA_K homolog 88.4 1 2.3E-05 31.1 4.4 35 144-184 26-60 (61)
29 KOG2191 RNA-binding protein NO 88.0 0.59 1.3E-05 43.7 3.8 37 143-185 132-168 (402)
30 PRK11824 polynucleotide phosph 85.9 0.22 4.8E-06 49.6 -0.2 34 158-191 563-596 (693)
31 KOG2190 PolyC-binding proteins 84.9 0.92 2E-05 43.7 3.5 42 141-188 336-377 (485)
32 KOG0336 ATP-dependent RNA heli 83.8 0.54 1.2E-05 45.5 1.4 29 157-185 55-83 (629)
33 PF13184 KH_5: NusA-like KH do 76.0 1.6 3.5E-05 31.3 1.5 31 155-185 14-45 (69)
34 TIGR03319 YmdA_YtgF conserved 75.8 1.9 4.2E-05 41.7 2.3 35 146-185 207-241 (514)
35 PRK12704 phosphodiesterase; Pr 75.5 2.2 4.8E-05 41.3 2.6 35 146-185 213-247 (520)
36 PRK00106 hypothetical protein; 73.8 2.4 5.1E-05 41.5 2.4 34 146-184 228-261 (535)
37 COG1185 Pnp Polyribonucleotide 73.3 1.6 3.6E-05 43.8 1.2 43 144-192 553-595 (692)
38 cd02409 KH-II KH-II (K homolo 72.4 3.3 7.2E-05 27.3 2.2 23 160-182 36-58 (68)
39 PRK12705 hypothetical protein; 67.6 3.2 6.8E-05 40.4 1.7 31 155-185 205-235 (508)
40 COG1097 RRP4 RNA-binding prote 66.1 5 0.00011 35.7 2.5 31 158-188 155-185 (239)
41 cd02414 jag_KH jag_K homology 63.0 4.7 0.0001 28.9 1.5 20 160-179 35-54 (77)
42 PRK08406 transcription elongat 61.2 7.2 0.00016 31.5 2.5 28 158-185 41-68 (140)
43 PF00126 HTH_1: Bacterial regu 52.3 12 0.00025 25.3 2.0 20 170-189 33-52 (60)
44 KOG2208 Vigilin [Lipid transpo 49.1 12 0.00025 38.2 2.2 38 142-185 708-745 (753)
45 KOG2113 Predicted RNA binding 46.9 11 0.00023 35.3 1.5 37 141-183 24-60 (394)
46 PF13083 KH_4: KH domain; PDB: 44.8 4.8 0.0001 28.3 -0.9 20 160-179 40-59 (73)
47 PRK13348 chromosome replicatio 44.3 17 0.00036 30.8 2.1 20 169-188 35-54 (294)
48 PRK12327 nusA transcription el 39.9 30 0.00066 32.3 3.3 38 146-184 234-272 (362)
49 PRK02821 hypothetical protein; 39.6 17 0.00036 26.9 1.3 20 158-177 40-59 (77)
50 PRK06418 transcription elongat 38.8 26 0.00057 29.4 2.4 26 161-186 72-97 (166)
51 TIGR00436 era GTP-binding prot 38.2 37 0.00081 29.2 3.4 40 141-185 219-266 (270)
52 TIGR01953 NusA transcription t 37.3 39 0.00085 31.2 3.6 38 146-184 232-270 (341)
53 COG0195 NusA Transcription elo 37.0 28 0.00061 29.7 2.4 30 155-184 82-111 (190)
54 PRK00468 hypothetical protein; 36.8 20 0.00044 26.2 1.3 17 160-176 41-57 (75)
55 TIGR01952 nusA_arch NusA famil 36.5 30 0.00065 28.2 2.4 28 158-185 42-69 (141)
56 TIGR03298 argP transcriptional 36.3 21 0.00046 30.1 1.5 19 170-188 35-53 (292)
57 COG1702 PhoH Phosphate starvat 35.7 29 0.00063 32.5 2.4 31 158-188 24-54 (348)
58 PRK09791 putative DNA-binding 34.9 35 0.00075 29.0 2.7 21 170-190 39-59 (302)
59 PRK03635 chromosome replicatio 34.3 31 0.00066 29.4 2.2 20 169-188 35-54 (294)
60 PRK09986 DNA-binding transcrip 33.2 36 0.00077 28.6 2.4 22 169-190 40-61 (294)
61 PRK12684 transcriptional regul 32.5 37 0.0008 29.4 2.5 19 170-188 36-55 (313)
62 PRK12329 nusA transcription el 32.1 67 0.0014 31.2 4.3 40 144-184 264-304 (449)
63 PRK00089 era GTPase Era; Revie 32.1 53 0.0012 28.3 3.4 40 141-185 224-271 (292)
64 PRK01064 hypothetical protein; 32.0 35 0.00075 25.2 1.9 19 160-178 41-59 (78)
65 COG1837 Predicted RNA-binding 31.3 29 0.00062 25.7 1.3 17 160-176 41-57 (76)
66 PRK12683 transcriptional regul 30.9 40 0.00088 29.2 2.5 20 169-188 35-55 (309)
67 PRK05465 ethanolamine ammonia- 30.7 73 0.0016 28.8 4.0 48 7-54 190-239 (260)
68 KOG2113 Predicted RNA binding 30.6 26 0.00056 32.9 1.2 30 157-186 123-152 (394)
69 PRK12682 transcriptional regul 30.5 42 0.00091 28.8 2.5 19 170-188 36-55 (309)
70 PRK11013 DNA-binding transcrip 29.3 44 0.00095 28.7 2.4 21 170-190 38-58 (309)
71 PRK11242 DNA-binding transcrip 28.8 47 0.001 27.9 2.4 20 169-188 34-53 (296)
72 TIGR01170 rplA_mito ribosomal 28.2 10 0.00023 30.8 -1.5 18 152-169 101-118 (141)
73 PRK09906 DNA-binding transcrip 27.9 49 0.0011 27.9 2.4 22 169-190 34-55 (296)
74 PRK10837 putative DNA-binding 27.6 45 0.00097 27.9 2.1 20 170-189 37-56 (290)
75 PRK10216 DNA-binding transcrip 27.1 57 0.0012 28.2 2.7 22 169-190 41-62 (319)
76 PRK15494 era GTPase Era; Provi 27.0 71 0.0015 28.9 3.4 40 141-185 271-318 (339)
77 TIGR02424 TF_pcaQ pca operon t 27.0 59 0.0013 27.5 2.7 22 170-191 37-58 (300)
78 PRK10094 DNA-binding transcrip 26.8 52 0.0011 28.4 2.4 22 169-190 35-56 (308)
79 PRK12328 nusA transcription el 26.1 94 0.002 29.4 4.1 42 145-192 310-351 (374)
80 PRK11139 DNA-binding transcrip 25.5 47 0.001 28.2 1.9 22 169-190 39-60 (297)
81 PRK12680 transcriptional regul 24.8 68 0.0015 28.2 2.8 23 169-191 35-57 (327)
82 PRK12328 nusA transcription el 24.3 52 0.0011 31.1 2.0 38 146-184 240-278 (374)
83 PF08285 DPM3: Dolichol-phosph 24.1 78 0.0017 24.0 2.6 26 56-81 64-89 (91)
84 PRK15092 DNA-binding transcrip 24.0 59 0.0013 28.4 2.3 20 169-188 44-63 (310)
85 PRK09801 transcriptional activ 22.9 76 0.0017 27.5 2.7 22 169-190 39-60 (310)
86 TIGR00637 ModE_repress ModE mo 22.9 72 0.0016 24.0 2.3 18 170-187 36-53 (99)
87 PRK08406 transcription elongat 22.7 44 0.00096 27.0 1.1 25 160-184 110-134 (140)
88 TIGR02036 dsdC D-serine deamin 22.2 69 0.0015 27.5 2.3 21 170-190 42-62 (302)
89 PRK12681 cysB transcriptional 21.6 79 0.0017 27.7 2.6 20 169-188 35-54 (324)
90 KOG1067 Predicted RNA-binding 20.9 25 0.00054 35.5 -0.8 24 160-183 608-631 (760)
91 PRK10082 cell density-dependen 20.7 89 0.0019 26.7 2.6 22 169-190 44-65 (303)
92 PRK14997 LysR family transcrip 20.7 77 0.0017 26.8 2.3 20 170-189 36-55 (301)
93 PRK11062 nhaR transcriptional 20.6 70 0.0015 27.3 2.0 21 170-190 38-58 (296)
94 PRK09202 nusA transcription el 20.3 80 0.0017 30.5 2.5 38 146-184 234-272 (470)
95 TIGR01169 rplA_bact ribosomal 20.0 20 0.00044 31.1 -1.4 14 155-168 120-133 (227)
No 1
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=100.00 E-value=2.2e-38 Score=276.61 Aligned_cols=125 Identities=51% Similarity=0.789 Sum_probs=104.2
Q ss_pred cCCcccchhHHHHHHHHHHHHhhcCCCCCChhhHHHHHHHHHHHHHHhhcCCccCCCCCCCCCCCCCCCCCcCCCCCCcc
Q 029290 28 RSASSAILDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTN 107 (196)
Q Consensus 28 r~~~~~~~~~~~YL~ELl~Ek~kL~pf~~vlph~~rLLnqEI~RV~~~l~~~~~~~~d~~~~~SP~~s~g~~~N~~~~~~ 107 (196)
+.++......++||.||++|+++|++|+. |+||.|||++||.||...+++.+ ...|
T Consensus 21 ~~~~~~~~~~~~yl~el~~e~~~l~~~~~-~~~~~rLL~~Ei~rv~~~~~~~~--------~~~~--------------- 76 (259)
T KOG1588|consen 21 RYQPQLNEKASKYLSELLAERKSLSPFFP-FPHAERLLDEEIERVQTSGRQHG--------SKEP--------------- 76 (259)
T ss_pred ccccchhhHHHHHHHHHHhhHHhcCcccc-hHHHHHHHHHHHHHHHhhhhhcc--------CCCc---------------
Confidence 44455566788999999999999999987 88999999999999998876542 0000
Q ss_pred chhhhhhHHhhhhhhccccCCCCCCCCCCCCCceeeEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecc
Q 029290 108 GLASRFQSEISGLMQSSSAQNWLSSQGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (196)
Q Consensus 108 ~~~~~~~~Er~~li~~~~~~~~~~pp~~~~~p~vk~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGk 187 (196)
++. + -.+.++.+++|+++||+|||++||+||||||||||||||+||||++|||||+||||
T Consensus 77 --------~~~----------~--~~~~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr 136 (259)
T KOG1588|consen 77 --------EEL----------P--YADVYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR 136 (259)
T ss_pred --------hhc----------c--cccCccCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence 100 0 00234567899999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCC
Q 029290 188 GSIKDPARK 196 (196)
Q Consensus 188 GS~kd~~KE 196 (196)
|||||+.||
T Consensus 137 gSmrD~~KE 145 (259)
T KOG1588|consen 137 GSMRDKAKE 145 (259)
T ss_pred CcccchHHH
Confidence 999999997
No 2
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=99.97 E-value=1.5e-31 Score=249.59 Aligned_cols=132 Identities=29% Similarity=0.423 Sum_probs=110.9
Q ss_pred hHHHHHHHHHHHHHHhhcCCccC-CCCC-CCCCCC---CCCCCCcCCCCCCccchhhhhhHHhhhhhhccccCCC-CCCC
Q 029290 60 NAYRLLNQEIMRVTTLLGNASVL-GQSG-LEHASP---LTSGGIFSNGGADTNGLASRFQSEISGLMQSSSAQNW-LSSQ 133 (196)
Q Consensus 60 h~~rLLnqEI~RV~~~l~~~~~~-~~d~-~~~~SP---~~s~g~~~N~~~~~~~~~~~~~~Er~~li~~~~~~~~-~~pp 133 (196)
.-.-+|+-+|++++.+|+.++|. ++.+ .+++|| ++..|.+.|||+ ..+++++++||+++|+.++..+. +.+|
T Consensus 52 ~~~y~l~~~iee~t~kLrt~d~~~p~~~e~rSPsp~p~yda~g~R~ntRe--~R~r~~Le~er~e~I~~~lk~nP~fkpP 129 (554)
T KOG0119|consen 52 KESYSLNLRIEEITRKLRTGDVGVPPPRELRSPSPEPVYDAKGKRLNTRE--QRARKKLEDERHEIIEEILKLNPGFKPP 129 (554)
T ss_pred hhhhhHHHHHHHhhhhhccccCCCCCCccccCCCcchhhhhhccchhhHH--HHHHHHHHHHHHHHHHHHHHhCcCCCCC
Confidence 34567889999999999999994 3333 467776 367788899885 34678999999999999876544 4566
Q ss_pred CCCCCCceeeEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecccCCCCCC
Q 029290 134 GSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPA 194 (196)
Q Consensus 134 ~~~~~p~vk~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkGS~kd~~ 194 (196)
+||+.+ .|++.|||||||+||+|||||+||||||+|+|+||+||||||+||||||+|+.+
T Consensus 130 ~DYk~p-~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk 189 (554)
T KOG0119|consen 130 ADYKPP-AKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGK 189 (554)
T ss_pred cccCcc-cccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccc
Confidence 677655 499999999999999999999999999999999999999999999999999975
No 3
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.94 E-value=1.9e-27 Score=204.14 Aligned_cols=124 Identities=27% Similarity=0.378 Sum_probs=106.1
Q ss_pred HHHHHHHHhhcCCccCCCCC-CCCCCCC---CCCCCcCCCCCCccchhhhhhHHhhhhhhcccc-CCCCCCCCCCCCCce
Q 029290 67 QEIMRVTTLLGNASVLGQSG-LEHASPL---TSGGIFSNGGADTNGLASRFQSEISGLMQSSSA-QNWLSSQGSSSGLIV 141 (196)
Q Consensus 67 qEI~RV~~~l~~~~~~~~d~-~~~~SP~---~s~g~~~N~~~~~~~~~~~~~~Er~~li~~~~~-~~~~~pp~~~~~p~v 141 (196)
-.+.++..+++..+++++.+ +|++||. +..|.+.||++ -.|++++++||+.|++.+.. ..++-+|.++..| .
T Consensus 70 ~r~~eit~Klrt~d~Vp~~re~Rspsppp~yd~~GrRlntre--~ry~kkLeder~~l~era~k~lp~fv~p~dy~rp-s 146 (269)
T COG5176 70 MRPFEITEKLRTPDGVPSKRELRSPSPPPRYDEIGRRLNTRE--ARYNKKLEDERLWLKERAQKILPRFVLPNDYIRP-S 146 (269)
T ss_pred ccHhhhhhhhcCCCCCCchhhccCCCCCcchhHHhhhhhHHH--HHHhhhhhHHHHHHHHHHHHhcCcccCCccccCc-c
Confidence 44678888899999988766 4899875 45688888885 34889999999999998765 3446667777554 7
Q ss_pred eeEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecccCCCCC
Q 029290 142 KRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDP 193 (196)
Q Consensus 142 k~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkGS~kd~ 193 (196)
|.+.||||||++||+.||||+||||||.|+|+||+.|+|||.|||+||+|++
T Consensus 147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKeg 198 (269)
T COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEG 198 (269)
T ss_pred cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccC
Confidence 8999999999999999999999999999999999999999999999999975
No 4
>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=99.86 E-value=2.8e-22 Score=158.05 Aligned_cols=53 Identities=53% Similarity=0.988 Sum_probs=50.5
Q ss_pred EEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecccCCCCCCCC
Q 029290 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARK 196 (196)
Q Consensus 144 ~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkGS~kd~~KE 196 (196)
++|||||+++||+|||||+||||+|+|+|+||++|||+|.|||+||++|..+|
T Consensus 1 ~~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~ 53 (120)
T cd02395 1 TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKE 53 (120)
T ss_pred CCEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCccccccccc
Confidence 36999999999999999999999999999999999999999999999998765
No 5
>PF13014 KH_3: KH domain
Probab=98.16 E-value=1.7e-06 Score=55.97 Aligned_cols=28 Identities=32% Similarity=0.706 Sum_probs=26.8
Q ss_pred eeeeeecCCchhHHHHHHHhCCeEEEec
Q 029290 159 FVGRLLGPRGNSLKRVEASTECRVLIRG 186 (196)
Q Consensus 159 fvG~ilGPrG~tlK~le~eTgckI~IrG 186 (196)
|+|.|||++|.|+++|+++|||+|.|--
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 6899999999999999999999999976
No 6
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.10 E-value=4.9e-06 Score=58.05 Aligned_cols=39 Identities=23% Similarity=0.509 Sum_probs=33.0
Q ss_pred EEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEeccc
Q 029290 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRG 188 (196)
Q Consensus 144 ~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkG 188 (196)
.+.+.||. .++|+|+|+.|.|+|+||++|||+|.|--.|
T Consensus 3 ~~~i~Ip~------~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g 41 (61)
T cd02393 3 IETMKIPP------DKIRDVIGPGGKTIKKIIEETGVKIDIEDDG 41 (61)
T ss_pred EEEEEeCh------hheeeeECCCchHHHHHHHHHCCEEEeCCCC
Confidence 45677775 6899999999999999999999999886433
No 7
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.08 E-value=4.7e-06 Score=56.39 Aligned_cols=39 Identities=33% Similarity=0.651 Sum_probs=34.6
Q ss_pred EEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecccC
Q 029290 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGS 189 (196)
Q Consensus 145 ~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkGS 189 (196)
.++.||. +++|+|+||+|.++++|+++|||+|.|...++
T Consensus 2 ~~i~ip~------~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~ 40 (64)
T cd00105 2 ERVLVPS------SLVGRIIGKGGSTIKEIREETGAKIKIPDSGS 40 (64)
T ss_pred EEEEEch------hhcceeECCCCHHHHHHHHHHCCEEEEcCCCC
Confidence 4678886 88999999999999999999999999987653
No 8
>smart00322 KH K homology RNA-binding domain.
Probab=97.85 E-value=2.9e-05 Score=51.48 Aligned_cols=39 Identities=36% Similarity=0.616 Sum_probs=34.5
Q ss_pred EEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEeccc
Q 029290 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRG 188 (196)
Q Consensus 144 ~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkG 188 (196)
+.+|.||. +++|.++|++|.+++.|++.|||+|.+...+
T Consensus 4 ~~~i~i~~------~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~ 42 (69)
T smart00322 4 TIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPEDG 42 (69)
T ss_pred EEEEEEcc------hhcceeECCCchHHHHHHHHHCCEEEECCCC
Confidence 45677876 7889999999999999999999999998764
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=97.80 E-value=6.3e-06 Score=56.07 Aligned_cols=38 Identities=32% Similarity=0.723 Sum_probs=33.3
Q ss_pred EEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecc
Q 029290 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (196)
Q Consensus 144 ~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGk 187 (196)
+.+|.||. .++|+|+|++|.++|+||++|||+|.|...
T Consensus 1 T~~i~vp~------~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~ 38 (60)
T PF00013_consen 1 TERIEVPS------SLVGRIIGKKGSNIKEIEEETGVKIQIPDD 38 (60)
T ss_dssp EEEEEEEH------HHHHHHHTGGGHHHHHHHHHHTSEEEEEST
T ss_pred CEEEEECH------HHcCEEECCCCCcHHHhhhhcCeEEEEcCC
Confidence 35677774 789999999999999999999999999765
No 10
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=97.76 E-value=3.8e-05 Score=53.59 Aligned_cols=39 Identities=18% Similarity=0.441 Sum_probs=34.0
Q ss_pred EEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecccC
Q 029290 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGS 189 (196)
Q Consensus 145 ~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkGS 189 (196)
.++.||. +.+|+|+|.+|.++++|+++|||+|.|.-...
T Consensus 2 ~r~~ip~------~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~ 40 (65)
T cd02396 2 LRLLVPS------SQAGSIIGKGGSTIKEIREETGAKIRVSKSVL 40 (65)
T ss_pred EEEEECH------HHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC
Confidence 4678886 78999999999999999999999999975543
No 11
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=97.72 E-value=1.8e-05 Score=54.09 Aligned_cols=38 Identities=18% Similarity=0.472 Sum_probs=32.6
Q ss_pred EEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEeccc
Q 029290 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRG 188 (196)
Q Consensus 145 ~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkG 188 (196)
+++.||. .++|.|+|++|.++++|+++|||+|.|-..+
T Consensus 2 ~~i~Vp~------~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~ 39 (62)
T cd02394 2 EEVEIPK------KLHRFIIGKKGSNIRKIMEETGVKIRFPDPG 39 (62)
T ss_pred eEEEeCH------HHhhhccCCCCCcHHHHHHHhCCEEEcCCCC
Confidence 3566775 5779999999999999999999999997755
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=96.75 E-value=0.00096 Score=55.72 Aligned_cols=29 Identities=24% Similarity=0.528 Sum_probs=27.0
Q ss_pred eeeeeecCCchhHHHHHHHhCCeEEEecc
Q 029290 159 FVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (196)
Q Consensus 159 fvG~ilGPrG~tlK~le~eTgckI~IrGk 187 (196)
.+|+|+|+.|.|.|.||..|||+|.|-++
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~ 133 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGK 133 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCC
Confidence 68999999999999999999999998764
No 13
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.62 E-value=0.00061 Score=64.72 Aligned_cols=39 Identities=36% Similarity=0.681 Sum_probs=35.6
Q ss_pred EecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEe
Q 029290 147 VDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (196)
Q Consensus 147 v~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~Ir 185 (196)
-.||++-...-||||||||-.|.++|.||.+||++|.|-
T Consensus 278 ~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis 316 (584)
T KOG2193|consen 278 EEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITIS 316 (584)
T ss_pred hhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeee
Confidence 468888888889999999999999999999999999873
No 14
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=96.56 E-value=0.0013 Score=54.57 Aligned_cols=28 Identities=25% Similarity=0.516 Sum_probs=26.5
Q ss_pred eeeeeecCCchhHHHHHHHhCCeEEEec
Q 029290 159 FVGRLLGPRGNSLKRVEASTECRVLIRG 186 (196)
Q Consensus 159 fvG~ilGPrG~tlK~le~eTgckI~IrG 186 (196)
.+|||+|+.|.|.+.||..|||+|.|-|
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~ 126 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYG 126 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcC
Confidence 5899999999999999999999999876
No 15
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.23 E-value=0.0039 Score=53.47 Aligned_cols=29 Identities=24% Similarity=0.543 Sum_probs=27.4
Q ss_pred eeeeeecCCchhHHHHHHHhCCeEEEecc
Q 029290 159 FVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (196)
Q Consensus 159 fvG~ilGPrG~tlK~le~eTgckI~IrGk 187 (196)
..|||+|+.|.|.+.||.-|||.|.|.|+
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~ 140 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK 140 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc
Confidence 46999999999999999999999999986
No 16
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=95.02 E-value=0.013 Score=58.20 Aligned_cols=42 Identities=19% Similarity=0.473 Sum_probs=35.2
Q ss_pred eEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecccCC
Q 029290 143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSI 190 (196)
Q Consensus 143 ~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkGS~ 190 (196)
+...+.||. ..+|.||||+|.|+|.|+++|||+|.|-=.|.+
T Consensus 551 ~~~~~~I~~------~kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG~V 592 (684)
T TIGR03591 551 RIETIKINP------DKIRDVIGPGGKVIREITEETGAKIDIEDDGTV 592 (684)
T ss_pred eEEEEecCH------HHHHhhcCCCcHHHHHHHHHHCCEEEEecCeEE
Confidence 355677875 578999999999999999999999999766644
No 17
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=94.94 E-value=0.015 Score=52.96 Aligned_cols=27 Identities=44% Similarity=0.918 Sum_probs=25.8
Q ss_pred eeeecCCchhHHHHHHHhCCeEEEecc
Q 029290 161 GRLLGPRGNSLKRVEASTECRVLIRGR 187 (196)
Q Consensus 161 G~ilGPrG~tlK~le~eTgckI~IrGk 187 (196)
-||+||.|+|||.||--|.|-|.|.|.
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~ 187 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN 187 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc
Confidence 689999999999999999999999986
No 18
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=94.44 E-value=0.015 Score=55.22 Aligned_cols=50 Identities=16% Similarity=-0.005 Sum_probs=45.4
Q ss_pred eeeEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecccCCC
Q 029290 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIK 191 (196)
Q Consensus 141 vk~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkGS~k 191 (196)
++...|.+|++| -|.+|.-+..=|++..+|..+|.||+.+++||||||..
T Consensus 208 ~~Y~~k~~v~~~-~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~ 257 (531)
T KOG1960|consen 208 RYYPNKALATDK-DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGR 257 (531)
T ss_pred ccchhheecccC-CcchhhhhhccCccchhhhhhhhhhhhhhhhccccccc
Confidence 344558999998 79999999999999999999999999999999999975
No 19
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=94.00 E-value=0.052 Score=54.47 Aligned_cols=44 Identities=30% Similarity=0.694 Sum_probs=37.2
Q ss_pred eeeEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecccCC
Q 029290 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSI 190 (196)
Q Consensus 141 vk~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkGS~ 190 (196)
.-+...+.||. .-+|.||||.|.|.|.|+++|||+|-|--.|.+
T Consensus 576 aP~~~~~~I~~------~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G~V 619 (719)
T TIGR02696 576 APRIITVKIPV------DKIGEVIGPKGKMINQIQDETGAEISIEDDGTV 619 (719)
T ss_pred CCeeEEEEeCh------HHhhheeCCCcHhHHHHHHHHCCEEEEecCcEE
Confidence 34466788886 568999999999999999999999999877754
No 20
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=93.45 E-value=0.087 Score=51.78 Aligned_cols=28 Identities=21% Similarity=0.526 Sum_probs=26.6
Q ss_pred ceeeeeecCCchhHHHHHHHhCCeEEEe
Q 029290 158 NFVGRLLGPRGNSLKRVEASTECRVLIR 185 (196)
Q Consensus 158 NfvG~ilGPrG~tlK~le~eTgckI~Ir 185 (196)
+=||.|||-.|.|+|+|+.+||+||.++
T Consensus 239 ~~VG~IIGkgGE~IKklq~etG~KIQfk 266 (600)
T KOG1676|consen 239 SKVGIIIGKGGEMIKKLQNETGAKIQFK 266 (600)
T ss_pred cceeeEEecCchHHHHHhhccCceeEee
Confidence 5699999999999999999999999986
No 21
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=92.86 E-value=0.17 Score=49.88 Aligned_cols=47 Identities=26% Similarity=0.496 Sum_probs=40.8
Q ss_pred ceeeEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecccCCCC
Q 029290 140 IVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKD 192 (196)
Q Consensus 140 ~vk~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkGS~kd 192 (196)
.++.+.+|.||- |=+|+|||-.|.|.|+|++.+||++.+-=.|+..+
T Consensus 136 ~~~ttqeI~IPa------~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~ 182 (600)
T KOG1676|consen 136 SVETTQEILIPA------NKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT 182 (600)
T ss_pred ccceeeeeccCc------cceeeEeccCccHHHHHHhhcCCceEEEecCCcCC
Confidence 366788899996 66899999999999999999999999887777655
No 22
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=92.78 E-value=0.12 Score=48.10 Aligned_cols=37 Identities=22% Similarity=0.452 Sum_probs=33.2
Q ss_pred eEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEe
Q 029290 143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (196)
Q Consensus 143 ~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~Ir 185 (196)
+..||+||- +-.|-|||-.|.|+.+||++|||+|..-
T Consensus 39 y~ikvLips------~AaGsIIGKGG~ti~~lqk~tgariklS 75 (402)
T KOG2191|consen 39 YFLKVLIPS------YAAGSIIGKGGQTIVQLQKETGARIKLS 75 (402)
T ss_pred eEEEEEeec------ccccceeccchHHHHHHHhccCcEEEec
Confidence 467999996 6789999999999999999999999864
No 23
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=89.33 E-value=0.23 Score=47.73 Aligned_cols=36 Identities=25% Similarity=0.656 Sum_probs=30.9
Q ss_pred EEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecc
Q 029290 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (196)
Q Consensus 146 kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGk 187 (196)
+++||. -|||-||||.|.|+|-|-+.|.|||-|--+
T Consensus 202 R~lVpt------qyvgaIIGkeG~TIknItkqTqsriD~hrk 237 (584)
T KOG2193|consen 202 RLLVPT------QYVGAIIGKEGATIKNITKQTQSRIDVHRK 237 (584)
T ss_pred eeeecc------ceeEEEecCCCccccCcchhhhheeeeeec
Confidence 555554 799999999999999999999999987644
No 24
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=89.32 E-value=0.19 Score=46.50 Aligned_cols=35 Identities=26% Similarity=0.597 Sum_probs=29.7
Q ss_pred ceeeeeecCCchhHHHHHHHhCCeEEEecccCCCC
Q 029290 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKD 192 (196)
Q Consensus 158 NfvG~ilGPrG~tlK~le~eTgckI~IrGkGS~kd 192 (196)
-|+|.|+|=+|.|.|+||.||+|+|.+=-.+.-++
T Consensus 66 ~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~ 100 (345)
T KOG2814|consen 66 SFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKE 100 (345)
T ss_pred HHhhhhhcccchHHHHHHHhhccceEccCCCCCcc
Confidence 68899999999999999999999999865554333
No 25
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=89.02 E-value=0.51 Score=45.50 Aligned_cols=39 Identities=26% Similarity=0.478 Sum_probs=35.4
Q ss_pred eEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecc
Q 029290 143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (196)
Q Consensus 143 ~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGk 187 (196)
...++.||- +-+|-|||=+|..+|.|.++|||+|.|.+.
T Consensus 138 v~~RLlVp~------sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~ 176 (485)
T KOG2190|consen 138 VTCRLLVPS------SQVGSLIGKGGSLIKEIREETGAKIRVSSD 176 (485)
T ss_pred eEEEEEech------hheeeeeccCcHHHHHHHHhcCceEEecCC
Confidence 457899996 668999999999999999999999999886
No 26
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=88.82 E-value=0.12 Score=52.97 Aligned_cols=43 Identities=16% Similarity=0.280 Sum_probs=36.4
Q ss_pred eEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCe-EEEecccCCC
Q 029290 143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECR-VLIRGRGSIK 191 (196)
Q Consensus 143 ~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgck-I~IrGkGS~k 191 (196)
+...+.||. +-||.||||.|.|+|.|+++||++ |-|+-.|.++
T Consensus 685 ~i~~~~i~~------~ki~~vIG~GGktIk~I~eetg~~~Idi~ddg~V~ 728 (891)
T PLN00207 685 LIHIMKVKP------EKVNMIIGSGGKKVKSIIEETGVEAIDTQDDGTVK 728 (891)
T ss_pred eeEEEEcCH------HHHHHHhcCCchhHHHHHHHHCCCccCcCCCeeEE
Confidence 456677775 678999999999999999999999 8888777654
No 27
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=88.62 E-value=0.19 Score=43.62 Aligned_cols=31 Identities=23% Similarity=0.563 Sum_probs=27.4
Q ss_pred ceeeeeecCCchhHHHHHHHhCCeEEEeccc
Q 029290 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRG 188 (196)
Q Consensus 158 NfvG~ilGPrG~tlK~le~eTgckI~IrGkG 188 (196)
+.++++|||+|.+++.|.++|+|+|.|-=.|
T Consensus 154 ~~i~~lig~~g~~i~~l~~~~~~~I~ig~NG 184 (235)
T PRK04163 154 VKVPRVIGKKGSMINMLKEETGCDIIVGQNG 184 (235)
T ss_pred HHHHhhcCCCChhHhhhhhhhCcEEEEcCCc
Confidence 6799999999999999999999999884333
No 28
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=88.43 E-value=1 Score=31.13 Aligned_cols=35 Identities=20% Similarity=0.320 Sum_probs=29.9
Q ss_pred EEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEE
Q 029290 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLI 184 (196)
Q Consensus 144 ~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~I 184 (196)
..+|.||. .-+|+.||.+|.+++.++..+|.+|-|
T Consensus 26 ~~~v~V~~------~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 26 RARVVVPD------DQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred EEEEEECc------ccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 45677776 457999999999999999999998876
No 29
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=88.00 E-value=0.59 Score=43.66 Aligned_cols=37 Identities=19% Similarity=0.515 Sum_probs=32.5
Q ss_pred eEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEe
Q 029290 143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (196)
Q Consensus 143 ~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~Ir 185 (196)
++.||.+|-.. -|.|||+.|.|+|.+.+++||-|.|-
T Consensus 132 kqikivvPNst------ag~iigkggAtiK~~~Eqsga~iqis 168 (402)
T KOG2191|consen 132 KQIKIVVPNST------AGMIIGKGGATIKAIQEQSGAWIQIS 168 (402)
T ss_pred ceeEEeccCCc------ccceecCCcchHHHHHHhhCcceEec
Confidence 46789999643 48999999999999999999999986
No 30
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=85.94 E-value=0.22 Score=49.59 Aligned_cols=34 Identities=21% Similarity=0.580 Sum_probs=30.5
Q ss_pred ceeeeeecCCchhHHHHHHHhCCeEEEecccCCC
Q 029290 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIK 191 (196)
Q Consensus 158 NfvG~ilGPrG~tlK~le~eTgckI~IrGkGS~k 191 (196)
.-++.+|||.|.|+|.|+++||++|-|+-.|.++
T Consensus 563 ~kI~~vIG~gg~~ik~I~~~~~~~idi~d~G~v~ 596 (693)
T PRK11824 563 DKIRDVIGPGGKTIREITEETGAKIDIEDDGTVK 596 (693)
T ss_pred HHHHHHhcCCchhHHHHHHHHCCccccCCCceEE
Confidence 5689999999999999999999999998777654
No 31
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=84.86 E-value=0.92 Score=43.75 Aligned_cols=42 Identities=19% Similarity=0.411 Sum_probs=36.7
Q ss_pred eeeEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEeccc
Q 029290 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRG 188 (196)
Q Consensus 141 vk~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkG 188 (196)
...+.++.||. +++|.|+|..|+..-.|++.|||.|.|.++-
T Consensus 336 ~~v~~~l~vps------~~igciiGk~G~~iseir~~tgA~I~I~~~~ 377 (485)
T KOG2190|consen 336 QTVTQRLLVPS------DLIGCIIGKGGAKISEIRQRTGASISILNKE 377 (485)
T ss_pred ceeeeeeccCc------cccceeecccccchHHHHHhcCCceEEcccc
Confidence 34567888885 8999999999999999999999999998764
No 32
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=83.77 E-value=0.54 Score=45.48 Aligned_cols=29 Identities=31% Similarity=0.641 Sum_probs=26.9
Q ss_pred CceeeeeecCCchhHHHHHHHhCCeEEEe
Q 029290 157 FNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (196)
Q Consensus 157 ~NfvG~ilGPrG~tlK~le~eTgckI~Ir 185 (196)
-||||.+||=.|+.+|+||..|+++|.|-
T Consensus 55 s~mvg~vigrggskik~iq~~tnt~iqii 83 (629)
T KOG0336|consen 55 SEMVGKVIGRGGSKIKRIQNDTNTRIQII 83 (629)
T ss_pred hhhhheeeccCcchhhhhhcccceeEEEe
Confidence 48999999999999999999999998763
No 33
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=76.04 E-value=1.6 Score=31.33 Aligned_cols=31 Identities=23% Similarity=0.476 Sum_probs=25.9
Q ss_pred CCCceeeeeecCCchhHHHHHHHh-CCeEEEe
Q 029290 155 PNFNFVGRLLGPRGNSLKRVEAST-ECRVLIR 185 (196)
Q Consensus 155 P~~NfvG~ilGPrG~tlK~le~eT-gckI~Ir 185 (196)
++++-+|..+|.+|...|.|+++. |-+|-|=
T Consensus 14 ~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 14 PNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp TTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred CCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 889999999999999999999999 8888764
No 34
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=75.82 E-value=1.9 Score=41.66 Aligned_cols=35 Identities=26% Similarity=0.616 Sum_probs=30.1
Q ss_pred EEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEe
Q 029290 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (196)
Q Consensus 146 kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~Ir 185 (196)
-|.+|-+ .+-|||||-.|.+.|.+|+-||+-|.|=
T Consensus 207 ~v~lp~d-----~~kgriigreGrnir~~e~~tgvd~iid 241 (514)
T TIGR03319 207 VVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIID 241 (514)
T ss_pred eEEcCCh-----hhhccccCCCcchHHHHHHHhCceEEEc
Confidence 4566665 5679999999999999999999999873
No 35
>PRK12704 phosphodiesterase; Provisional
Probab=75.51 E-value=2.2 Score=41.34 Aligned_cols=35 Identities=26% Similarity=0.616 Sum_probs=30.0
Q ss_pred EEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEe
Q 029290 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (196)
Q Consensus 146 kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~Ir 185 (196)
-|.+|-+ .+-|||||-.|.+.|.+|+-||+-|.|=
T Consensus 213 ~v~lp~d-----~mkgriigreGrnir~~e~~tgvd~iid 247 (520)
T PRK12704 213 VVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIID 247 (520)
T ss_pred eeecCCc-----hhhcceeCCCcchHHHHHHHhCCeEEEc
Confidence 4566665 5679999999999999999999999873
No 36
>PRK00106 hypothetical protein; Provisional
Probab=73.85 E-value=2.4 Score=41.52 Aligned_cols=34 Identities=32% Similarity=0.672 Sum_probs=29.8
Q ss_pred EEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEE
Q 029290 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLI 184 (196)
Q Consensus 146 kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~I 184 (196)
-|.+|-+ .+-|||||-.|.+.+.+|+-||+-|.|
T Consensus 228 ~v~lp~d-----emkGriIGreGrNir~~E~~tGvdlii 261 (535)
T PRK00106 228 TVHLPDD-----NMKGRIIGREGRNIRTLESLTGIDVII 261 (535)
T ss_pred eEEcCCh-----HhhcceeCCCcchHHHHHHHhCceEEE
Confidence 4667665 567999999999999999999999987
No 37
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=73.32 E-value=1.6 Score=43.81 Aligned_cols=43 Identities=23% Similarity=0.489 Sum_probs=35.6
Q ss_pred EEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecccCCCC
Q 029290 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKD 192 (196)
Q Consensus 144 ~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkGS~kd 192 (196)
.+.+-|+.+. ++-++||.|.|.+.|.++|||+|-|--.|+++-
T Consensus 553 i~t~~i~~dK------I~dvIG~gGk~I~~I~eetg~~IdieddGtv~i 595 (692)
T COG1185 553 IETIKIDPDK------IRDVIGPGGKTIKAITEETGVKIDIEDDGTVKI 595 (692)
T ss_pred eEEEccCHHH------HhhccCCcccchhhhhhhhCcEEEecCCCcEEE
Confidence 4455677665 467899999999999999999999998888763
No 38
>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=72.39 E-value=3.3 Score=27.33 Aligned_cols=23 Identities=13% Similarity=0.395 Sum_probs=20.2
Q ss_pred eeeeecCCchhHHHHHHHhCCeE
Q 029290 160 VGRLLGPRGNSLKRVEASTECRV 182 (196)
Q Consensus 160 vG~ilGPrG~tlK~le~eTgckI 182 (196)
.|+++|.+|.+++.|+..++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 59999999999999999998443
No 39
>PRK12705 hypothetical protein; Provisional
Probab=67.60 E-value=3.2 Score=40.42 Aligned_cols=31 Identities=26% Similarity=0.550 Sum_probs=27.1
Q ss_pred CCCceeeeeecCCchhHHHHHHHhCCeEEEe
Q 029290 155 PNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (196)
Q Consensus 155 P~~NfvG~ilGPrG~tlK~le~eTgckI~Ir 185 (196)
|+-..-|||||-.|.+.+.+|..||+-|.|-
T Consensus 205 p~demkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 205 PSDAMKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred CChHhhccccCccchhHHHHHHhhCCceEec
Confidence 3346789999999999999999999999873
No 40
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=66.10 E-value=5 Score=35.69 Aligned_cols=31 Identities=26% Similarity=0.616 Sum_probs=27.5
Q ss_pred ceeeeeecCCchhHHHHHHHhCCeEEEeccc
Q 029290 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRG 188 (196)
Q Consensus 158 NfvG~ilGPrG~tlK~le~eTgckI~IrGkG 188 (196)
++|-|++|.+|+-++-|.+.|+|.|.|==.|
T Consensus 155 ~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG 185 (239)
T COG1097 155 SKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG 185 (239)
T ss_pred hhcceEecCCCcHHHHhhhhcCeEEEEecCC
Confidence 7788999999999999999999999885444
No 41
>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=62.96 E-value=4.7 Score=28.89 Aligned_cols=20 Identities=30% Similarity=0.642 Sum_probs=17.4
Q ss_pred eeeeecCCchhHHHHHHHhC
Q 029290 160 VGRLLGPRGNSLKRVEASTE 179 (196)
Q Consensus 160 vG~ilGPrG~tlK~le~eTg 179 (196)
.|+|||-+|.||+.||--+.
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~ 54 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLAN 54 (77)
T ss_pred CCeEECCCCccHHHHHHHHH
Confidence 49999999999999986554
No 42
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=61.18 E-value=7.2 Score=31.52 Aligned_cols=28 Identities=21% Similarity=0.335 Sum_probs=25.2
Q ss_pred ceeeeeecCCchhHHHHHHHhCCeEEEe
Q 029290 158 NFVGRLLGPRGNSLKRVEASTECRVLIR 185 (196)
Q Consensus 158 NfvG~ilGPrG~tlK~le~eTgckI~Ir 185 (196)
+.+|..+|.+|...|.|++..|-+|-|=
T Consensus 41 ~~vG~~IG~~G~rI~~i~e~lgekIdVv 68 (140)
T PRK08406 41 GDMGLAIGKGGENVKRLEEKLGKDIELV 68 (140)
T ss_pred CCccccCCcCchHHHHHHHHhCCceEEE
Confidence 5789999999999999999999888763
No 43
>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=52.33 E-value=12 Score=25.31 Aligned_cols=20 Identities=15% Similarity=0.250 Sum_probs=16.1
Q ss_pred hHHHHHHHhCCeEEEecccC
Q 029290 170 SLKRVEASTECRVLIRGRGS 189 (196)
Q Consensus 170 tlK~le~eTgckI~IrGkGS 189 (196)
.+++||++.|+++++|..+.
T Consensus 33 ~i~~LE~~lg~~Lf~r~~~~ 52 (60)
T PF00126_consen 33 QIKQLEEELGVPLFERSGRG 52 (60)
T ss_dssp HHHHHHHHHTS-SEEECSSS
T ss_pred HHHHHHHHhCCeEEEECCCC
Confidence 47999999999999996553
No 44
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=49.06 E-value=12 Score=38.16 Aligned_cols=38 Identities=24% Similarity=0.537 Sum_probs=30.6
Q ss_pred eeEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEe
Q 029290 142 KRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (196)
Q Consensus 142 k~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~Ir 185 (196)
..+..+.||.+ |-.-|+||.|.++++++.+++|.|.+-
T Consensus 708 ~~~~~~~~p~~------~~~~~ig~~g~~~r~~~~~~~~~~~~~ 745 (753)
T KOG2208|consen 708 LVTKEIEIPRS------LHRYLIGPKGSNLRQLEKEFNVNIVVP 745 (753)
T ss_pred ceeeEEeccHH------HhhhccCCCCccHHHHHHHhccceecC
Confidence 34556777765 446799999999999999999998764
No 45
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=46.94 E-value=11 Score=35.34 Aligned_cols=37 Identities=24% Similarity=0.413 Sum_probs=30.2
Q ss_pred eeeEEEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEE
Q 029290 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVL 183 (196)
Q Consensus 141 vk~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~ 183 (196)
..+++-|-+| +-||+.|.|++|.+.|.|+++|.+.|.
T Consensus 24 ~nvt~sv~vp------s~~v~~ivg~qg~kikalr~KTqtyi~ 60 (394)
T KOG2113|consen 24 QNVTESVEVP------SEHVAEIVGRQGCKIKALRAKTQTYIK 60 (394)
T ss_pred CccceeeecC------cccceeecccCccccchhhhhhcceec
Confidence 3445556565 358999999999999999999999886
No 46
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=44.83 E-value=4.8 Score=28.30 Aligned_cols=20 Identities=30% Similarity=0.634 Sum_probs=17.6
Q ss_pred eeeeecCCchhHHHHHHHhC
Q 029290 160 VGRLLGPRGNSLKRVEASTE 179 (196)
Q Consensus 160 vG~ilGPrG~tlK~le~eTg 179 (196)
.|+|||-+|.|++.||--++
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHH
T ss_pred cceEECCCCeeHHHHHHHHH
Confidence 79999999999999986554
No 47
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=44.34 E-value=17 Score=30.81 Aligned_cols=20 Identities=35% Similarity=0.524 Sum_probs=18.0
Q ss_pred hhHHHHHHHhCCeEEEeccc
Q 029290 169 NSLKRVEASTECRVLIRGRG 188 (196)
Q Consensus 169 ~tlK~le~eTgckI~IrGkG 188 (196)
..+|+||++.|+++++|++|
T Consensus 35 ~~i~~LE~~lg~~Lf~R~r~ 54 (294)
T PRK13348 35 QRIKALEESLGQPLLVRGRP 54 (294)
T ss_pred HHHHHHHHHhCceeeecCCC
Confidence 45899999999999999975
No 48
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=39.94 E-value=30 Score=32.28 Aligned_cols=38 Identities=18% Similarity=0.466 Sum_probs=30.5
Q ss_pred EEecCCCCCCCCceeeeeecCCchhHHHHHHHh-CCeEEE
Q 029290 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEAST-ECRVLI 184 (196)
Q Consensus 146 kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eT-gckI~I 184 (196)
||-|=-. -|+++-||..+|++|..++.+..+. |=+|-|
T Consensus 234 KVAV~s~-~~~iDpvGa~iG~~G~rI~~i~~el~gekIdi 272 (362)
T PRK12327 234 KIAVRSN-NPNVDAKGACVGPKGQRVQNIVSELKGEKIDI 272 (362)
T ss_pred EEEEEcC-CCCCCchheeECCCChhHHHHHHHhCCCeEEE
Confidence 4544333 3899999999999999999999998 767654
No 49
>PRK02821 hypothetical protein; Provisional
Probab=39.64 E-value=17 Score=26.85 Aligned_cols=20 Identities=15% Similarity=0.444 Sum_probs=16.5
Q ss_pred ceeeeeecCCchhHHHHHHH
Q 029290 158 NFVGRLLGPRGNSLKRVEAS 177 (196)
Q Consensus 158 NfvG~ilGPrG~tlK~le~e 177 (196)
.=+|||||=+|.|++.|-.-
T Consensus 40 ~D~GrVIGk~Gr~i~AIRtl 59 (77)
T PRK02821 40 DDLGKVIGRGGRTATALRTV 59 (77)
T ss_pred hhCcceeCCCCchHHHHHHH
Confidence 44799999999999987543
No 50
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=38.84 E-value=26 Score=29.44 Aligned_cols=26 Identities=15% Similarity=0.129 Sum_probs=23.9
Q ss_pred eeeecCCchhHHHHHHHhCCeEEEec
Q 029290 161 GRLLGPRGNSLKRVEASTECRVLIRG 186 (196)
Q Consensus 161 G~ilGPrG~tlK~le~eTgckI~IrG 186 (196)
|..+|+.|.+.|+|++..|-+|.|=.
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEEE
Confidence 99999999999999999999987754
No 51
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=38.21 E-value=37 Score=29.22 Aligned_cols=40 Identities=18% Similarity=0.353 Sum_probs=30.3
Q ss_pred eeeEEEEecCCCCCCCCceeeeeecCCchhHHHH--------HHHhCCeEEEe
Q 029290 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRV--------EASTECRVLIR 185 (196)
Q Consensus 141 vk~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~l--------e~eTgckI~Ir 185 (196)
+.....|+|.-+.+ -|-|+|.+|.++|+| |+-.||+|.+.
T Consensus 219 ~~i~~~i~v~~~s~-----k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l~ 266 (270)
T TIGR00436 219 LKIHALISVERESQ-----KKIIIGKNGSMIKAIGIAARKDILELFDCDVFLE 266 (270)
T ss_pred EEEEEEEEECcCCc-----eeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 44556677776543 588999999999976 77889998764
No 52
>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=37.32 E-value=39 Score=31.22 Aligned_cols=38 Identities=18% Similarity=0.434 Sum_probs=30.9
Q ss_pred EEecCCCCCCCCceeeeeecCCchhHHHHHHHh-CCeEEE
Q 029290 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEAST-ECRVLI 184 (196)
Q Consensus 146 kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eT-gckI~I 184 (196)
||-|=-. -|+++-||..+|++|..++.+..+. |=+|-|
T Consensus 232 KvAV~s~-~~~iDpvga~vG~~G~ri~~i~~el~ge~Idi 270 (341)
T TIGR01953 232 KIAVESN-DENIDPVGACVGPKGSRIQAISKELNGEKIDI 270 (341)
T ss_pred EEEEEcC-CCCCCcceeeECCCCchHHHHHHHhCCCeEEE
Confidence 5555433 4899999999999999999999998 666654
No 53
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=37.04 E-value=28 Score=29.73 Aligned_cols=30 Identities=23% Similarity=0.391 Sum_probs=26.4
Q ss_pred CCCceeeeeecCCchhHHHHHHHhCCeEEE
Q 029290 155 PNFNFVGRLLGPRGNSLKRVEASTECRVLI 184 (196)
Q Consensus 155 P~~NfvG~ilGPrG~tlK~le~eTgckI~I 184 (196)
++.+=+|..+|++|...|.|.++.|=+|-|
T Consensus 82 ~~~d~vG~~iG~~G~rvk~i~~eLgekIdV 111 (190)
T COG0195 82 VKIDPVGACIGKRGSRVKAVSEELGEKIDV 111 (190)
T ss_pred cCcCchhhhccCCChHHHHHHHHhCCceEE
Confidence 446789999999999999999999977765
No 54
>PRK00468 hypothetical protein; Provisional
Probab=36.85 E-value=20 Score=26.20 Aligned_cols=17 Identities=24% Similarity=0.659 Sum_probs=15.0
Q ss_pred eeeeecCCchhHHHHHH
Q 029290 160 VGRLLGPRGNSLKRVEA 176 (196)
Q Consensus 160 vG~ilGPrG~tlK~le~ 176 (196)
+||+||=+|.|++.|-.
T Consensus 41 ~GrVIGk~Gr~i~AIRt 57 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRT 57 (75)
T ss_pred CcceecCCChhHHHHHH
Confidence 69999999999998754
No 55
>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=36.52 E-value=30 Score=28.18 Aligned_cols=28 Identities=21% Similarity=0.340 Sum_probs=25.0
Q ss_pred ceeeeeecCCchhHHHHHHHhCCeEEEe
Q 029290 158 NFVGRLLGPRGNSLKRVEASTECRVLIR 185 (196)
Q Consensus 158 NfvG~ilGPrG~tlK~le~eTgckI~Ir 185 (196)
+-+|..+|++|...+.|++..|=+|-|=
T Consensus 42 g~vG~~IG~~G~rIk~i~el~gekIdVV 69 (141)
T TIGR01952 42 GEMGAAIGKGGENVKRLEELIGKSIELI 69 (141)
T ss_pred CCccccCCCCchHHHHHHHhcCCeeEEE
Confidence 5789999999999999999989888764
No 56
>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=36.29 E-value=21 Score=30.14 Aligned_cols=19 Identities=21% Similarity=0.307 Sum_probs=17.2
Q ss_pred hHHHHHHHhCCeEEEeccc
Q 029290 170 SLKRVEASTECRVLIRGRG 188 (196)
Q Consensus 170 tlK~le~eTgckI~IrGkG 188 (196)
-+|+||++.|+++++|++|
T Consensus 35 ~I~~LE~~lg~~Lf~R~r~ 53 (292)
T TIGR03298 35 RIKALEERLGQPLLVRTQP 53 (292)
T ss_pred HHHHHHHHhCchheecCCC
Confidence 4899999999999999865
No 57
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=35.69 E-value=29 Score=32.51 Aligned_cols=31 Identities=26% Similarity=0.441 Sum_probs=27.9
Q ss_pred ceeeeeecCCchhHHHHHHHhCCeEEEeccc
Q 029290 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRG 188 (196)
Q Consensus 158 NfvG~ilGPrG~tlK~le~eTgckI~IrGkG 188 (196)
|-+--|+||.+..++.||+.+|+.|.-||..
T Consensus 24 ~~~~~l~G~~~~~l~l~e~~~gv~i~~rG~~ 54 (348)
T COG1702 24 NELVALFGPTDTNLSLLEIALGVSIVARGEA 54 (348)
T ss_pred hhhhhhcCCCCccHHHHHHHhCcEEEeCCce
Confidence 6667799999999999999999999999863
No 58
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=34.90 E-value=35 Score=29.05 Aligned_cols=21 Identities=14% Similarity=0.384 Sum_probs=18.6
Q ss_pred hHHHHHHHhCCeEEEecccCC
Q 029290 170 SLKRVEASTECRVLIRGRGSI 190 (196)
Q Consensus 170 tlK~le~eTgckI~IrGkGS~ 190 (196)
.+|+||++.||++++|.++.+
T Consensus 39 ~i~~LE~~lG~~LF~R~~r~~ 59 (302)
T PRK09791 39 SIQELEEGLAAQLFFRRSKGV 59 (302)
T ss_pred HHHHHHHHhCCeEEEEcCCCc
Confidence 489999999999999987665
No 59
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=34.32 E-value=31 Score=29.41 Aligned_cols=20 Identities=20% Similarity=0.307 Sum_probs=17.8
Q ss_pred hhHHHHHHHhCCeEEEeccc
Q 029290 169 NSLKRVEASTECRVLIRGRG 188 (196)
Q Consensus 169 ~tlK~le~eTgckI~IrGkG 188 (196)
..+|+||++.||+++.|++|
T Consensus 35 ~~I~~LE~~lg~~LF~R~~~ 54 (294)
T PRK03635 35 QRIKALEERVGQVLLVRTQP 54 (294)
T ss_pred HHHHHHHHHhCceeeecCCC
Confidence 35899999999999999875
No 60
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=33.23 E-value=36 Score=28.57 Aligned_cols=22 Identities=23% Similarity=0.311 Sum_probs=18.6
Q ss_pred hhHHHHHHHhCCeEEEecccCC
Q 029290 169 NSLKRVEASTECRVLIRGRGSI 190 (196)
Q Consensus 169 ~tlK~le~eTgckI~IrGkGS~ 190 (196)
..+|+||++.||++++|..+.+
T Consensus 40 ~~i~~LE~~lg~~Lf~R~~r~~ 61 (294)
T PRK09986 40 IHIKELEDQLGTPLFIRHSRSV 61 (294)
T ss_pred HHHHHHHHHhCCeeEeeCCCce
Confidence 4689999999999999986543
No 61
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=32.49 E-value=37 Score=29.40 Aligned_cols=19 Identities=11% Similarity=0.270 Sum_probs=16.7
Q ss_pred hHHHHHHHhCCeEEEec-cc
Q 029290 170 SLKRVEASTECRVLIRG-RG 188 (196)
Q Consensus 170 tlK~le~eTgckI~IrG-kG 188 (196)
.+|+||++.||++++|. +|
T Consensus 36 ~ik~LE~~lg~~Lf~R~~r~ 55 (313)
T PRK12684 36 AIIELEDELGVEIFTRHGKR 55 (313)
T ss_pred HHHHHHHHhCCeeEEEcCCc
Confidence 48999999999999994 55
No 62
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=32.12 E-value=67 Score=31.16 Aligned_cols=40 Identities=15% Similarity=0.301 Sum_probs=31.9
Q ss_pred EEEEecCCCCCCCCceeeeeecCCchhHHHHHHHh-CCeEEE
Q 029290 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEAST-ECRVLI 184 (196)
Q Consensus 144 ~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eT-gckI~I 184 (196)
..||-|=-. -|+++-||..+|++|..++.|..+. |=+|-|
T Consensus 264 RtKVAV~S~-d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDV 304 (449)
T PRK12329 264 RTKIAVDTL-ERDVDPVGACIGARGSRIQAVVNELRGEKIDV 304 (449)
T ss_pred eeEEEEEcC-CCCCChhhccCCCCcchHHHHHHHhCCCeEEE
Confidence 445655433 3899999999999999999999998 766654
No 63
>PRK00089 era GTPase Era; Reviewed
Probab=32.05 E-value=53 Score=28.29 Aligned_cols=40 Identities=20% Similarity=0.360 Sum_probs=30.7
Q ss_pred eeeEEEEecCCCCCCCCceeeeeecCCchhHHHH--------HHHhCCeEEEe
Q 029290 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRV--------EASTECRVLIR 185 (196)
Q Consensus 141 vk~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~l--------e~eTgckI~Ir 185 (196)
++....|+|.-+.+ .+-|+|-+|.++|+| |+-+||+|.+.
T Consensus 224 ~~i~~~i~v~~~~~-----k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 224 VRIEATIYVERDSQ-----KGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEEEccCCc-----eeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 44556677776544 689999999999876 78889998764
No 64
>PRK01064 hypothetical protein; Provisional
Probab=32.02 E-value=35 Score=25.22 Aligned_cols=19 Identities=21% Similarity=0.683 Sum_probs=16.7
Q ss_pred eeeeecCCchhHHHHHHHh
Q 029290 160 VGRLLGPRGNSLKRVEAST 178 (196)
Q Consensus 160 vG~ilGPrG~tlK~le~eT 178 (196)
+|++||=+|.|++.|..-.
T Consensus 41 ~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred ceEEECCCCccHHHHHHHH
Confidence 6999999999999987643
No 65
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=31.27 E-value=29 Score=25.75 Aligned_cols=17 Identities=18% Similarity=0.769 Sum_probs=15.1
Q ss_pred eeeeecCCchhHHHHHH
Q 029290 160 VGRLLGPRGNSLKRVEA 176 (196)
Q Consensus 160 vG~ilGPrG~tlK~le~ 176 (196)
+|++||=+|.|++.|-.
T Consensus 41 ~GkvIGk~GRti~AIRT 57 (76)
T COG1837 41 MGKVIGKQGRTIQAIRT 57 (76)
T ss_pred ccceecCCChhHHHHHH
Confidence 79999999999998843
No 66
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=30.88 E-value=40 Score=29.15 Aligned_cols=20 Identities=25% Similarity=0.541 Sum_probs=17.1
Q ss_pred hhHHHHHHHhCCeEEEe-ccc
Q 029290 169 NSLKRVEASTECRVLIR-GRG 188 (196)
Q Consensus 169 ~tlK~le~eTgckI~Ir-GkG 188 (196)
..+|+||++.|+++++| |+|
T Consensus 35 ~~I~~LE~~lg~~Lf~R~~r~ 55 (309)
T PRK12683 35 KQIKDLEDELGVEIFIRRGKR 55 (309)
T ss_pred HHHHHHHHHhCCeeEeeCCCC
Confidence 35899999999999999 455
No 67
>PRK05465 ethanolamine ammonia-lyase small subunit; Provisional
Probab=30.70 E-value=73 Score=28.79 Aligned_cols=48 Identities=10% Similarity=0.269 Sum_probs=34.7
Q ss_pred CccccccCCCCCCCCC--CCCCCcCCcccchhHHHHHHHHHHHHhhcCCC
Q 029290 7 GRFMAYSLSPSAPHSP--HLPSLRSASSAILDQEKYLSELLAERHKLNPF 54 (196)
Q Consensus 7 ~~~~~~~~~~~~~~sp--~~~~~r~~~~~~~~~~~YL~ELl~Ek~kL~pf 54 (196)
|-|+.|.|....+-+- =|+|+|..--...+...+|.+|++|..++...
T Consensus 190 g~YlT~~p~~G~~Da~RncISNI~~~Gl~~~~Aa~~l~~Li~~~~~~~~S 239 (260)
T PRK05465 190 GAYLTYAPRVGTTDADRNCISNIHPGGLPYAEAAAKIAYLIKEALRLKAS 239 (260)
T ss_pred eEEEEecCCCCCCccccceeccCCCCCCCHHHHHHHHHHHHHHHHHhCCC
Confidence 6799999886532211 27788864334667789999999999888764
No 68
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=30.58 E-value=26 Score=32.92 Aligned_cols=30 Identities=27% Similarity=0.547 Sum_probs=26.5
Q ss_pred CceeeeeecCCchhHHHHHHHhCCeEEEec
Q 029290 157 FNFVGRLLGPRGNSLKRVEASTECRVLIRG 186 (196)
Q Consensus 157 ~NfvG~ilGPrG~tlK~le~eTgckI~IrG 186 (196)
+-.||.+.||.|+|+|++|+.|..-|.--+
T Consensus 123 ~rvvglvv~~~~~ti~~iqq~tnt~I~T~v 152 (394)
T KOG2113|consen 123 LRVVGLVVGPKGATIKRIQQFTNTYIATPV 152 (394)
T ss_pred ceeeeeccccccCccchheecccceEeeec
Confidence 688999999999999999999998876443
No 69
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=30.52 E-value=42 Score=28.80 Aligned_cols=19 Identities=16% Similarity=0.336 Sum_probs=16.7
Q ss_pred hHHHHHHHhCCeEEEec-cc
Q 029290 170 SLKRVEASTECRVLIRG-RG 188 (196)
Q Consensus 170 tlK~le~eTgckI~IrG-kG 188 (196)
.+|+||++.||++++|. +|
T Consensus 36 ~I~~LE~~lg~~LF~R~~~~ 55 (309)
T PRK12682 36 AIIELEEELGIEIFIRHGKR 55 (309)
T ss_pred HHHHHHHHhCCeeEEECCCC
Confidence 58999999999999995 44
No 70
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=29.28 E-value=44 Score=28.75 Aligned_cols=21 Identities=29% Similarity=0.430 Sum_probs=18.4
Q ss_pred hHHHHHHHhCCeEEEecccCC
Q 029290 170 SLKRVEASTECRVLIRGRGSI 190 (196)
Q Consensus 170 tlK~le~eTgckI~IrGkGS~ 190 (196)
-+|+||++.|+++++|..+-+
T Consensus 38 ~Ik~LE~~lg~~Lf~R~~~~v 58 (309)
T PRK11013 38 ELARFEKVIGLKLFERVRGRL 58 (309)
T ss_pred HHHHHHHHhCceeeeecCCCc
Confidence 489999999999999987654
No 71
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=28.79 E-value=47 Score=27.85 Aligned_cols=20 Identities=15% Similarity=0.302 Sum_probs=17.4
Q ss_pred hhHHHHHHHhCCeEEEeccc
Q 029290 169 NSLKRVEASTECRVLIRGRG 188 (196)
Q Consensus 169 ~tlK~le~eTgckI~IrGkG 188 (196)
..+|+||++.|+++++|...
T Consensus 34 ~~i~~LE~~lg~~Lf~R~~~ 53 (296)
T PRK11242 34 QQIRQLEESLGVQLFDRSGR 53 (296)
T ss_pred HHHHHHHHHhCCeeEeEcCC
Confidence 46899999999999999643
No 72
>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=28.24 E-value=10 Score=30.77 Aligned_cols=18 Identities=39% Similarity=0.761 Sum_probs=14.2
Q ss_pred CCCCCCceeeeeecCCch
Q 029290 152 EKYPNFNFVGRLLGPRGN 169 (196)
Q Consensus 152 ~~~P~~NfvG~ilGPrG~ 169 (196)
+-.|.+..+|++|||||.
T Consensus 101 ~~m~~l~~Lg~iLGprGl 118 (141)
T TIGR01170 101 DIVPELAQLRRLLGPKGL 118 (141)
T ss_pred HHHHHHHHhhcccccCcC
Confidence 335667889999999974
No 73
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=27.94 E-value=49 Score=27.90 Aligned_cols=22 Identities=18% Similarity=0.436 Sum_probs=18.8
Q ss_pred hhHHHHHHHhCCeEEEecccCC
Q 029290 169 NSLKRVEASTECRVLIRGRGSI 190 (196)
Q Consensus 169 ~tlK~le~eTgckI~IrGkGS~ 190 (196)
..+|+||++.||++++|-.+.+
T Consensus 34 r~i~~LE~~lg~~Lf~R~~~~~ 55 (296)
T PRK09906 34 QQIKDLENCVGVPLLVRDKRKV 55 (296)
T ss_pred HHHHHHHHHhCCeeeeeCCCcc
Confidence 4589999999999999976654
No 74
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=27.59 E-value=45 Score=27.90 Aligned_cols=20 Identities=15% Similarity=0.160 Sum_probs=17.2
Q ss_pred hHHHHHHHhCCeEEEecccC
Q 029290 170 SLKRVEASTECRVLIRGRGS 189 (196)
Q Consensus 170 tlK~le~eTgckI~IrGkGS 189 (196)
.+|+||++.||++++|+..-
T Consensus 37 ~I~~LE~~lg~~Lf~R~~r~ 56 (290)
T PRK10837 37 ALTDLEGQLGVQLFDRVGKR 56 (290)
T ss_pred HHHHHHHHhCCccEeecCCe
Confidence 48999999999999997543
No 75
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=27.06 E-value=57 Score=28.19 Aligned_cols=22 Identities=14% Similarity=0.168 Sum_probs=18.5
Q ss_pred hhHHHHHHHhCCeEEEecccCC
Q 029290 169 NSLKRVEASTECRVLIRGRGSI 190 (196)
Q Consensus 169 ~tlK~le~eTgckI~IrGkGS~ 190 (196)
..+|+||++.|+++++|....+
T Consensus 41 ~~I~~LE~~lg~~LF~R~~r~~ 62 (319)
T PRK10216 41 KSLAKLRAWFDDPLFVNTPLGL 62 (319)
T ss_pred HHHHHHHHHhCCceEEecCCCc
Confidence 3589999999999999965544
No 76
>PRK15494 era GTPase Era; Provisional
Probab=27.03 E-value=71 Score=28.88 Aligned_cols=40 Identities=23% Similarity=0.276 Sum_probs=31.3
Q ss_pred eeeEEEEecCCCCCCCCceeeeeecCCchhHHHH--------HHHhCCeEEEe
Q 029290 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRV--------EASTECRVLIR 185 (196)
Q Consensus 141 vk~~~kv~IPv~~~P~~NfvG~ilGPrG~tlK~l--------e~eTgckI~Ir 185 (196)
++....|||.-+. --|-|||-+|..+|+| |+-.||+|...
T Consensus 271 ~~i~~~i~v~~~s-----qk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 271 VKINQVIVVSRES-----YKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred EEEEEEEEECCCC-----ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 4556677777654 4689999999999976 88899998764
No 77
>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=27.00 E-value=59 Score=27.48 Aligned_cols=22 Identities=23% Similarity=0.386 Sum_probs=19.0
Q ss_pred hHHHHHHHhCCeEEEecccCCC
Q 029290 170 SLKRVEASTECRVLIRGRGSIK 191 (196)
Q Consensus 170 tlK~le~eTgckI~IrGkGS~k 191 (196)
.+|+||++.||++++|..+-+.
T Consensus 37 ~I~~LE~~lg~~LF~R~~~~~~ 58 (300)
T TIGR02424 37 TLRELEEILGTPLFERDRRGIR 58 (300)
T ss_pred HHHHHHHHhCCeEEEEcCCCcc
Confidence 5899999999999999876553
No 78
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=26.76 E-value=52 Score=28.44 Aligned_cols=22 Identities=23% Similarity=0.336 Sum_probs=18.2
Q ss_pred hhHHHHHHHhCCeEEEecccCC
Q 029290 169 NSLKRVEASTECRVLIRGRGSI 190 (196)
Q Consensus 169 ~tlK~le~eTgckI~IrGkGS~ 190 (196)
..+|+||++.||++++|....+
T Consensus 35 ~~I~~LE~~lg~~Lf~R~~r~~ 56 (308)
T PRK10094 35 YRIKLLEENTGVALFFRTTRSV 56 (308)
T ss_pred HHHHHHHHHhCCEEEeeCCCce
Confidence 3589999999999999965443
No 79
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=26.06 E-value=94 Score=29.39 Aligned_cols=42 Identities=14% Similarity=0.241 Sum_probs=35.4
Q ss_pred EEEecCCCCCCCCceeeeeecCCchhHHHHHHHhCCeEEEecccCCCC
Q 029290 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKD 192 (196)
Q Consensus 145 ~kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eTgckI~IrGkGS~kd 192 (196)
..|+||-+++ ++.||=+|.+++.--.-||++|-|+.-+|.-+
T Consensus 310 ~~V~V~~~ql------slAIGk~GqNvrLA~~LtGwkIDI~s~~~~~~ 351 (374)
T PRK12328 310 AIVTLLSDQK------SKAIGKNGINIRLASMLTGYEIELNEIGSKEN 351 (374)
T ss_pred EEEEEChHHh------hhhhcCCChhHHHHHHHhCCEEEEEECCCCcc
Confidence 4566666554 78999999999999999999999999988654
No 80
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=25.50 E-value=47 Score=28.15 Aligned_cols=22 Identities=18% Similarity=0.268 Sum_probs=18.1
Q ss_pred hhHHHHHHHhCCeEEEecccCC
Q 029290 169 NSLKRVEASTECRVLIRGRGSI 190 (196)
Q Consensus 169 ~tlK~le~eTgckI~IrGkGS~ 190 (196)
..+|+||++.||++++|...-+
T Consensus 39 ~~i~~LE~~lg~~Lf~R~~r~l 60 (297)
T PRK11139 39 HQIKALEDFLGLKLFRRRNRSL 60 (297)
T ss_pred HHHHHHHHHhCchheEecCCce
Confidence 3589999999999999975433
No 81
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=24.83 E-value=68 Score=28.22 Aligned_cols=23 Identities=22% Similarity=0.358 Sum_probs=19.5
Q ss_pred hhHHHHHHHhCCeEEEecccCCC
Q 029290 169 NSLKRVEASTECRVLIRGRGSIK 191 (196)
Q Consensus 169 ~tlK~le~eTgckI~IrGkGS~k 191 (196)
..+|+||++.||++++|..+.++
T Consensus 35 ~~I~~LE~~lG~~LF~R~~r~v~ 57 (327)
T PRK12680 35 KQLKQLEDELGFLLFVRKGRSLE 57 (327)
T ss_pred HHHHHHHHHhCCeEEEECCCcCC
Confidence 34899999999999999877663
No 82
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=24.30 E-value=52 Score=31.11 Aligned_cols=38 Identities=18% Similarity=0.308 Sum_probs=30.3
Q ss_pred EEecCCCCCCCCceeeeeecCCchhHHHHHHHh-CCeEEE
Q 029290 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEAST-ECRVLI 184 (196)
Q Consensus 146 kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eT-gckI~I 184 (196)
||-|=- .-|+++-||-.+|++|..++.|.++. |=+|-|
T Consensus 240 KVAV~S-~d~~iDPvGacIG~~G~rI~~I~~eL~gEkIDv 278 (374)
T PRK12328 240 KVALFS-NNPNIDPIGATVGVKGVRINAVSKELNGENIDC 278 (374)
T ss_pred EEEEEc-CCCCCChHHhhcCCCcchHHHHHHHhCCCeEEE
Confidence 454433 34899999999999999999999998 666654
No 83
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=24.12 E-value=78 Score=24.00 Aligned_cols=26 Identities=27% Similarity=0.259 Sum_probs=22.7
Q ss_pred CChhhHHHHHHHHHHHHHHhhcCCcc
Q 029290 56 PVLPNAYRLLNQEIMRVTTLLGNASV 81 (196)
Q Consensus 56 ~vlph~~rLLnqEI~RV~~~l~~~~~ 81 (196)
+-+|.+...|.+||......++..|+
T Consensus 64 nDcpeA~~eL~~eI~eAK~dLr~kGv 89 (91)
T PF08285_consen 64 NDCPEAAKELQKEIKEAKADLRKKGV 89 (91)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 34699999999999999999988776
No 84
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=23.96 E-value=59 Score=28.39 Aligned_cols=20 Identities=15% Similarity=0.237 Sum_probs=17.4
Q ss_pred hhHHHHHHHhCCeEEEeccc
Q 029290 169 NSLKRVEASTECRVLIRGRG 188 (196)
Q Consensus 169 ~tlK~le~eTgckI~IrGkG 188 (196)
..+|+||++.||++++|...
T Consensus 44 ~~I~~LE~~lG~~LF~R~~~ 63 (310)
T PRK15092 44 QQMQRLEQLVGKELFARHGR 63 (310)
T ss_pred HHHHHHHHHhCcceEEECCC
Confidence 35899999999999999764
No 85
>PRK09801 transcriptional activator TtdR; Provisional
Probab=22.89 E-value=76 Score=27.51 Aligned_cols=22 Identities=14% Similarity=0.261 Sum_probs=18.9
Q ss_pred hhHHHHHHHhCCeEEEecccCC
Q 029290 169 NSLKRVEASTECRVLIRGRGSI 190 (196)
Q Consensus 169 ~tlK~le~eTgckI~IrGkGS~ 190 (196)
..+|+||++.|++++.|.+..+
T Consensus 39 ~~I~~LE~~LG~~Lf~R~~r~~ 60 (310)
T PRK09801 39 KRIQILENTLATTLLNRSARGV 60 (310)
T ss_pred HHHHHHHHHhCCEeeeecCCCC
Confidence 4589999999999999986654
No 86
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=22.86 E-value=72 Score=24.04 Aligned_cols=18 Identities=6% Similarity=0.110 Sum_probs=16.1
Q ss_pred hHHHHHHHhCCeEEEecc
Q 029290 170 SLKRVEASTECRVLIRGR 187 (196)
Q Consensus 170 tlK~le~eTgckI~IrGk 187 (196)
.+++||...|++++.|.+
T Consensus 36 ~I~~LE~~lg~~Lf~R~~ 53 (99)
T TIGR00637 36 YIRAMNNLSGEPLVERAT 53 (99)
T ss_pred HHHHHHHHhCCCeEEecC
Confidence 479999999999999964
No 87
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=22.70 E-value=44 Score=26.96 Aligned_cols=25 Identities=20% Similarity=0.356 Sum_probs=21.8
Q ss_pred eeeeecCCchhHHHHHHHhCCeEEE
Q 029290 160 VGRLLGPRGNSLKRVEASTECRVLI 184 (196)
Q Consensus 160 vG~ilGPrG~tlK~le~eTgckI~I 184 (196)
.|+.||.+|.+++.++.-+|-.+-|
T Consensus 110 ~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 110 KGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred cchhhCCCCHHHHHHHHHhCCccCC
Confidence 6999999999999999999876544
No 88
>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=22.19 E-value=69 Score=27.48 Aligned_cols=21 Identities=10% Similarity=0.376 Sum_probs=18.3
Q ss_pred hHHHHHHHhCCeEEEecccCC
Q 029290 170 SLKRVEASTECRVLIRGRGSI 190 (196)
Q Consensus 170 tlK~le~eTgckI~IrGkGS~ 190 (196)
.+++||++.|+++++|..+.+
T Consensus 42 ~I~~LE~~lg~~Lf~R~~r~~ 62 (302)
T TIGR02036 42 RINQLEEELGIQLFVRSHRKV 62 (302)
T ss_pred HHHHHHHHhCCceEEECCCce
Confidence 489999999999999987654
No 89
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=21.65 E-value=79 Score=27.73 Aligned_cols=20 Identities=10% Similarity=0.247 Sum_probs=17.1
Q ss_pred hhHHHHHHHhCCeEEEeccc
Q 029290 169 NSLKRVEASTECRVLIRGRG 188 (196)
Q Consensus 169 ~tlK~le~eTgckI~IrGkG 188 (196)
..+|+||++.|+++++|...
T Consensus 35 ~~I~~LE~~lG~~LF~R~~r 54 (324)
T PRK12681 35 KQVRMLEDELGIQIFARSGK 54 (324)
T ss_pred HHHHHHHHHhCCEeEEECCC
Confidence 35899999999999999643
No 90
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=20.90 E-value=25 Score=35.45 Aligned_cols=24 Identities=29% Similarity=0.398 Sum_probs=20.2
Q ss_pred eeeeecCCchhHHHHHHHhCCeEE
Q 029290 160 VGRLLGPRGNSLKRVEASTECRVL 183 (196)
Q Consensus 160 vG~ilGPrG~tlK~le~eTgckI~ 183 (196)
+..+|||.|-.+|+||.|||+.-+
T Consensus 608 ~~~lIGp~G~~~kki~~EtGai~~ 631 (760)
T KOG1067|consen 608 RATLIGPGGVLKKKIEVETGAISQ 631 (760)
T ss_pred hheeecCccceeeeEeeeccceee
Confidence 457899999999999999995433
No 91
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=20.69 E-value=89 Score=26.69 Aligned_cols=22 Identities=9% Similarity=0.231 Sum_probs=18.2
Q ss_pred hhHHHHHHHhCCeEEEecccCC
Q 029290 169 NSLKRVEASTECRVLIRGRGSI 190 (196)
Q Consensus 169 ~tlK~le~eTgckI~IrGkGS~ 190 (196)
..+|+||++.||+++.|....+
T Consensus 44 ~~I~~LE~~lG~~Lf~R~~r~~ 65 (303)
T PRK10082 44 RRIRALEQAIGVELFNRQVTPL 65 (303)
T ss_pred HHHHHHHHHcCCEEEEecCCCC
Confidence 3589999999999999985543
No 92
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=20.68 E-value=77 Score=26.83 Aligned_cols=20 Identities=15% Similarity=0.282 Sum_probs=17.5
Q ss_pred hHHHHHHHhCCeEEEecccC
Q 029290 170 SLKRVEASTECRVLIRGRGS 189 (196)
Q Consensus 170 tlK~le~eTgckI~IrGkGS 189 (196)
.+|+||++.|++++.|...-
T Consensus 36 ~I~~LE~~lG~~LF~R~~r~ 55 (301)
T PRK14997 36 RIAQLEERLGVRLIQRTTRQ 55 (301)
T ss_pred HHHHHHHHhCCEeeeeccCc
Confidence 58999999999999998643
No 93
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=20.56 E-value=70 Score=27.30 Aligned_cols=21 Identities=14% Similarity=0.294 Sum_probs=17.9
Q ss_pred hHHHHHHHhCCeEEEecccCC
Q 029290 170 SLKRVEASTECRVLIRGRGSI 190 (196)
Q Consensus 170 tlK~le~eTgckI~IrGkGS~ 190 (196)
-+|+||++.|+++++|....+
T Consensus 38 ~I~~LE~~lg~~Lf~R~~r~~ 58 (296)
T PRK11062 38 QIKALEERLQGKLFKRKGRGL 58 (296)
T ss_pred HHHHHHHHcCccceeecCCce
Confidence 489999999999999976544
No 94
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=20.32 E-value=80 Score=30.51 Aligned_cols=38 Identities=18% Similarity=0.413 Sum_probs=30.5
Q ss_pred EEecCCCCCCCCceeeeeecCCchhHHHHHHHh-CCeEEE
Q 029290 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEAST-ECRVLI 184 (196)
Q Consensus 146 kv~IPv~~~P~~NfvG~ilGPrG~tlK~le~eT-gckI~I 184 (196)
||-|= ..-|++.-||..+|++|+.++.+..+. |=+|-|
T Consensus 234 KvAV~-s~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idi 272 (470)
T PRK09202 234 KIAVK-SNDPRIDPVGACVGMRGSRIQAISNELGGEKIDI 272 (470)
T ss_pred EEEEE-cCCCCCChhHccCCCCCchHHHHHHHhCCCeEEE
Confidence 44444 334889999999999999999999998 666654
No 95
>TIGR01169 rplA_bact ribosomal protein L1, bacterial/chloroplast. This model describes bacterial (and chloroplast) ribosomal protein L1. The apparent mitochondrial L1 is sufficiently diverged to be the subject of a separate model.
Probab=20.04 E-value=20 Score=31.12 Aligned_cols=14 Identities=50% Similarity=0.940 Sum_probs=10.6
Q ss_pred CCCceeeeeecCCc
Q 029290 155 PNFNFVGRLLGPRG 168 (196)
Q Consensus 155 P~~NfvG~ilGPrG 168 (196)
|.+..+|++|||||
T Consensus 120 ~~l~~Lg~iLGPrG 133 (227)
T TIGR01169 120 RVVGKLGRILGPRG 133 (227)
T ss_pred HHHHHhcccccccc
Confidence 33455699999996
Done!