Query 027518
Match_columns 222
No_of_seqs 180 out of 350
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 11:07:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027518.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027518hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1588 RNA-binding protein Sa 100.0 1.1E-45 2.5E-50 328.2 15.6 147 28-218 21-170 (259)
2 KOG0119 Splicing factor 1/bran 100.0 2.4E-34 5.3E-39 273.0 8.0 157 60-220 52-216 (554)
3 COG5176 MSL5 Splicing factor ( 100.0 1.4E-30 3.1E-35 227.2 4.1 152 67-221 70-227 (269)
4 cd02395 SF1_like-KH Splicing f 99.9 1.9E-26 4.2E-31 185.1 6.7 73 144-217 1-76 (120)
5 PF13014 KH_3: KH domain 98.1 2.9E-06 6.2E-11 56.0 3.1 28 159-186 1-28 (43)
6 cd02393 PNPase_KH Polynucleoti 98.0 6.9E-06 1.5E-10 58.4 4.5 39 144-188 3-41 (61)
7 cd00105 KH-I K homology RNA-bi 98.0 7.4E-06 1.6E-10 56.5 4.1 39 145-189 2-40 (64)
8 smart00322 KH K homology RNA-b 97.8 4.1E-05 9E-10 51.7 4.6 40 144-189 4-43 (69)
9 PF00013 KH_1: KH domain syndr 97.7 1.1E-05 2.4E-10 55.9 0.8 37 145-187 2-38 (60)
10 cd02396 PCBP_like_KH K homolog 97.6 4.6E-05 1E-09 54.2 3.3 36 145-186 2-37 (65)
11 cd02394 vigilin_like_KH K homo 97.6 3E-05 6.6E-10 54.0 2.2 38 145-188 2-39 (62)
12 KOG2193 IGF-II mRNA-binding pr 97.0 0.00012 2.7E-09 70.6 -0.6 62 147-208 278-357 (584)
13 PRK13763 putative RNA-processi 96.6 0.0015 3.2E-08 55.7 2.6 29 159-187 105-133 (180)
14 TIGR03665 arCOG04150 arCOG0415 96.4 0.0019 4.2E-08 54.6 2.1 28 159-186 99-126 (172)
15 COG1094 Predicted RNA-binding 96.1 0.0051 1.1E-07 53.8 3.2 29 159-187 112-140 (194)
16 TIGR03665 arCOG04150 arCOG0415 95.8 0.0041 8.9E-08 52.6 1.2 30 158-187 7-36 (172)
17 PRK13763 putative RNA-processi 95.6 0.0083 1.8E-07 51.1 2.4 40 145-190 5-45 (180)
18 TIGR03591 polynuc_phos polyrib 94.7 0.017 3.6E-07 58.5 2.1 43 143-191 551-593 (684)
19 KOG2874 rRNA processing protei 94.6 0.021 4.5E-07 53.0 2.2 27 161-187 161-187 (356)
20 KOG2191 RNA-binding protein NO 93.8 0.081 1.8E-06 50.1 4.4 37 143-185 39-75 (402)
21 KOG1960 Predicted RNA-binding 93.8 0.03 6.4E-07 54.2 1.5 51 141-192 208-258 (531)
22 TIGR02696 pppGpp_PNP guanosine 93.7 0.058 1.3E-06 55.2 3.4 44 142-191 577-620 (719)
23 KOG1676 K-homology type RNA bi 93.1 0.081 1.8E-06 53.0 3.4 59 140-204 136-195 (600)
24 KOG1676 K-homology type RNA bi 92.5 0.14 3E-06 51.4 4.0 28 158-185 239-266 (600)
25 KOG2814 Transcription coactiva 88.4 0.22 4.7E-06 47.0 1.3 34 158-191 66-99 (345)
26 KOG2190 PolyC-binding proteins 87.8 0.65 1.4E-05 45.7 4.2 39 143-187 138-176 (485)
27 PLN00207 polyribonucleotide nu 87.7 0.17 3.7E-06 53.0 0.1 43 143-191 685-728 (891)
28 KOG2193 IGF-II mRNA-binding pr 87.4 0.37 8.1E-06 47.2 2.2 31 157-187 207-237 (584)
29 cd02134 NusA_KH NusA_K homolog 87.3 1.3 2.8E-05 31.3 4.4 35 144-184 26-60 (61)
30 PRK04163 exosome complex RNA-b 86.9 0.28 6.1E-06 43.4 1.0 32 158-189 154-185 (235)
31 KOG2191 RNA-binding protein NO 85.8 0.85 1.8E-05 43.4 3.6 37 143-185 132-168 (402)
32 KOG2190 PolyC-binding proteins 84.7 0.93 2E-05 44.6 3.5 41 142-188 337-377 (485)
33 PRK11824 polynucleotide phosph 84.1 0.31 6.8E-06 49.5 -0.1 34 158-191 563-596 (693)
34 KOG0336 ATP-dependent RNA heli 79.3 0.99 2.1E-05 44.6 1.4 29 157-185 55-83 (629)
35 PF13184 KH_5: NusA-like KH do 74.0 1.5 3.3E-05 32.1 0.9 33 155-187 14-47 (69)
36 TIGR03319 YmdA_YtgF conserved 70.5 3.1 6.8E-05 41.1 2.4 36 145-185 206-241 (514)
37 cd02409 KH-II KH-II (K homolo 70.3 3.9 8.5E-05 27.5 2.3 23 160-182 36-58 (68)
38 PRK12704 phosphodiesterase; Pr 70.2 3.5 7.6E-05 40.8 2.7 36 145-185 212-247 (520)
39 COG1185 Pnp Polyribonucleotide 69.5 2.3 5E-05 43.6 1.3 44 144-193 553-596 (692)
40 PRK00106 hypothetical protein; 68.1 3.8 8.3E-05 40.9 2.5 37 144-185 226-262 (535)
41 COG1097 RRP4 RNA-binding prote 62.5 6.1 0.00013 35.8 2.5 32 158-189 155-186 (239)
42 PRK12705 hypothetical protein; 62.1 4.7 0.0001 40.1 1.8 31 155-185 205-235 (508)
43 cd02414 jag_KH jag_K homology 60.3 5.6 0.00012 29.1 1.5 20 160-179 35-54 (77)
44 PRK08406 transcription elongat 58.7 8.3 0.00018 31.8 2.4 29 158-186 41-69 (140)
45 COG1094 Predicted RNA-binding 49.1 14 0.0003 32.7 2.4 37 145-187 10-46 (194)
46 PF00126 HTH_1: Bacterial regu 46.4 16 0.00035 25.1 2.0 20 170-189 33-52 (60)
47 PF13083 KH_4: KH domain; PDB: 43.1 5.4 0.00012 28.6 -0.9 20 160-179 40-59 (73)
48 KOG2208 Vigilin [Lipid transpo 41.5 19 0.00041 37.5 2.4 37 143-185 709-745 (753)
49 PRK02821 hypothetical protein; 39.3 17 0.00038 27.3 1.3 20 158-177 40-59 (77)
50 PRK13348 chromosome replicatio 38.4 23 0.0005 30.6 2.2 21 169-189 35-55 (294)
51 PRK06418 transcription elongat 37.6 28 0.0006 29.9 2.4 27 161-187 72-98 (166)
52 KOG2113 Predicted RNA binding 37.6 18 0.0004 34.5 1.5 38 141-184 24-61 (394)
53 PRK12327 nusA transcription el 36.9 35 0.00077 32.5 3.3 39 146-185 234-273 (362)
54 PRK00468 hypothetical protein; 36.8 20 0.00043 26.8 1.3 17 160-176 41-57 (75)
55 TIGR00436 era GTP-binding prot 35.4 41 0.0009 29.6 3.3 40 141-185 219-266 (270)
56 COG0195 NusA Transcription elo 35.0 32 0.00069 30.0 2.5 34 155-188 82-115 (190)
57 TIGR01953 NusA transcription t 34.8 45 0.00098 31.5 3.6 39 146-185 232-271 (341)
58 TIGR01952 nusA_arch NusA famil 34.2 34 0.00073 28.5 2.4 29 158-186 42-70 (141)
59 PRK12329 nusA transcription el 33.3 62 0.0013 32.0 4.4 41 144-185 264-305 (449)
60 COG1837 Predicted RNA-binding 31.9 27 0.00059 26.4 1.3 17 160-176 41-57 (76)
61 TIGR03298 argP transcriptional 31.4 28 0.00061 30.0 1.6 21 170-190 35-55 (292)
62 PRK01064 hypothetical protein; 31.1 36 0.00078 25.6 1.9 20 160-179 41-60 (78)
63 COG1702 PhoH Phosphate starvat 30.5 40 0.00086 32.3 2.5 31 158-188 24-54 (348)
64 PRK00089 era GTPase Era; Revie 30.3 56 0.0012 28.8 3.3 40 141-185 224-271 (292)
65 KOG2113 Predicted RNA binding 29.8 27 0.0006 33.4 1.3 31 157-187 123-153 (394)
66 PRK03635 chromosome replicatio 29.3 41 0.00089 29.2 2.2 23 169-191 35-57 (294)
67 PRK05465 ethanolamine ammonia- 29.0 80 0.0017 29.1 4.1 49 7-55 190-240 (260)
68 PF08285 DPM3: Dolichol-phosph 28.9 65 0.0014 24.9 3.0 26 56-81 64-89 (91)
69 PRK09986 DNA-binding transcrip 28.4 47 0.001 28.4 2.4 23 169-191 40-62 (294)
70 PRK09791 putative DNA-binding 28.0 52 0.0011 28.6 2.7 22 170-191 39-60 (302)
71 TIGR01170 rplA_mito ribosomal 26.7 12 0.00026 31.1 -1.5 18 152-169 101-118 (141)
72 PRK12684 transcriptional regul 26.7 52 0.0011 29.1 2.5 20 170-189 36-56 (313)
73 PRK12683 transcriptional regul 26.0 55 0.0012 29.0 2.5 21 169-189 35-56 (309)
74 PRK15494 era GTPase Era; Provi 25.6 74 0.0016 29.4 3.3 40 141-185 271-318 (339)
75 PRK11013 DNA-binding transcrip 24.9 58 0.0012 28.6 2.4 23 170-192 38-60 (309)
76 PRK12682 transcriptional regul 24.9 62 0.0013 28.4 2.6 20 170-189 36-56 (309)
77 PRK11242 DNA-binding transcrip 23.9 62 0.0014 27.7 2.4 23 169-191 34-56 (296)
78 PRK10216 DNA-binding transcrip 22.9 74 0.0016 28.1 2.7 23 169-191 41-63 (319)
79 PRK09906 DNA-binding transcrip 22.7 69 0.0015 27.6 2.4 24 169-192 34-57 (296)
80 PRK12328 nusA transcription el 22.7 60 0.0013 31.3 2.2 38 146-184 240-278 (374)
81 TIGR02424 TF_pcaQ pca operon t 22.6 78 0.0017 27.3 2.7 24 170-193 37-60 (300)
82 PRK10094 DNA-binding transcrip 22.2 71 0.0015 28.2 2.4 22 170-191 36-57 (308)
83 PRK10837 putative DNA-binding 21.7 56 0.0012 27.9 1.6 22 170-191 37-58 (290)
84 PRK08406 transcription elongat 21.6 47 0.001 27.4 1.1 26 159-184 109-134 (140)
85 PRK11139 DNA-binding transcrip 21.5 62 0.0014 28.0 1.9 22 170-191 40-61 (297)
86 PRK12328 nusA transcription el 20.8 1E+02 0.0022 29.8 3.3 45 145-195 310-354 (374)
87 PRK13764 ATPase; Provisional 20.6 78 0.0017 32.3 2.6 41 145-191 483-523 (602)
88 PRK12680 transcriptional regul 20.5 93 0.002 28.0 2.8 22 170-191 36-57 (327)
No 1
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=100.00 E-value=1.1e-45 Score=328.20 Aligned_cols=147 Identities=45% Similarity=0.669 Sum_probs=124.2
Q ss_pred cCCcccchhHHHHHHHHHHHHhhcCCCCCChhhHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCcCCCCCCcc
Q 027518 28 RSASSAILDQEKYLSELLAERHKLNPFLPVLPNAYRLLNQEIMRVTTLLGNASVLGQSGLEHASPLTSGGIFSNGGADTN 107 (222)
Q Consensus 28 r~~~~~~~~~~~YL~ELl~Ek~kL~pf~~v~ph~~rLL~qEI~RV~~~l~~~~~~~~d~~~~~SP~~s~g~~~N~~~d~~ 107 (222)
+.++......++||.||++|+++|++|+. |+||.|||++||.||...+++.+ ..+|
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 33444456789999999999999999987 88999999999999999877542 0000
Q ss_pred chhhhhHHHhhhhhhccccCCCCCCCCCCCCCceeeEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecc
Q 027518 108 GLASRFQSEISGLMQSSSAQNWLSSQGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (222)
Q Consensus 108 ~~~~~l~~Er~~li~~~~~~~~~~pp~~~~~p~vK~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGk 187 (222)
++. . -.+.++.+++|+++||+|||++||+||||||||||||||+||||++|||||+||||
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 000 0 00234456799999999999999999999999999999999999999999999999
Q ss_pred cCCCCchHHHHhhccCCccce---eeEEEEecCc
Q 027518 188 GSIKDPARVIVMLLLSLFVFI---VHILYVSGIS 218 (222)
Q Consensus 188 GS~kd~~kEe~lr~~~~~e~~---lHvli~~~~~ 218 (222)
|||||..|||+||++|+|||+ |||||++...
T Consensus 137 gSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p 170 (259)
T KOG1588|consen 137 GSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAP 170 (259)
T ss_pred CcccchHHHHHhhcCcchHHhCCCcEEEEEEeCC
Confidence 999999999999999999997 9999998654
No 2
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=100.00 E-value=2.4e-34 Score=272.97 Aligned_cols=157 Identities=25% Similarity=0.349 Sum_probs=126.0
Q ss_pred hHHHHHHHHHHHHHHHhhcCCCCCCC--CCCCCCCC---CCCCCcCCCCCCccchhhhhHHHhhhhhhccc--cCCCCCC
Q 027518 60 NAYRLLNQEIMRVTTLLGNASVLGQS--GLEHASPL---TSGGIFSNGGADTNGLASRFQSEISGLMQSSS--AQNWLSS 132 (222)
Q Consensus 60 h~~rLL~qEI~RV~~~l~~~~~~~~d--~~~~~SP~---~s~g~~~N~~~d~~~~~~~l~~Er~~li~~~~--~~~~~~p 132 (222)
.-.-+|+-+|++++.+|+.+++.... ..+++||. +..|.+.|||. .+++++|++||+++|++++ +++|++|
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 34567888999999999999994333 34677764 66788888875 3477899999999999986 4555554
Q ss_pred CCCCCCCceeeEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecccCCCCch-HHHHhhccCCccceeeE
Q 027518 133 QGSSSGLIVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPA-RVIVMLLLSLFVFIVHI 211 (222)
Q Consensus 133 p~~~~~p~vK~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkGS~kd~~-kEe~lr~~~~~e~~lHv 211 (222)
+||..+ .|++.|||||||+||+|||||+||||||+|+|+||+||||||.||||||+|+++ +-..+...++.++.||+
T Consensus 130 -~DYk~p-~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~ 207 (554)
T KOG0119|consen 130 -ADYKPP-AKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHC 207 (554)
T ss_pred -cccCcc-cccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeE
Confidence 455444 489999999999999999999999999999999999999999999999999987 11123345566678999
Q ss_pred EEEecCccc
Q 027518 212 LYVSGISNE 220 (222)
Q Consensus 212 li~~~~~~~ 220 (222)
||.||+-+-
T Consensus 208 ~Isadt~ek 216 (554)
T KOG0119|consen 208 LISADTQEK 216 (554)
T ss_pred EEecchHHH
Confidence 999998653
No 3
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.96 E-value=1.4e-30 Score=227.18 Aligned_cols=152 Identities=24% Similarity=0.307 Sum_probs=121.9
Q ss_pred HHHHHHHHHhhcCCCCCCCC-CCCCCCC---CCCCCcCCCCCCccchhhhhHHHhhhhhhcccc-CCCCCCCCCCCCCce
Q 027518 67 QEIMRVTTLLGNASVLGQSG-LEHASPL---TSGGIFSNGGADTNGLASRFQSEISGLMQSSSA-QNWLSSQGSSSGLIV 141 (222)
Q Consensus 67 qEI~RV~~~l~~~~~~~~d~-~~~~SP~---~s~g~~~N~~~d~~~~~~~l~~Er~~li~~~~~-~~~~~pp~~~~~p~v 141 (222)
-.+.++..+++..++++..+ ++++||+ +..|.+.||+. ..|+++|++||..|++.++. ..++-+|.++..| .
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 34678888899999988775 5899875 45588888874 35889999999999987753 2344455555444 7
Q ss_pred eeEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecccCCCCchHHHHh-hccCCccceeeEEEEecCccc
Q 027518 142 KRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARVIVM-LLLSLFVFIVHILYVSGISNE 220 (222)
Q Consensus 142 K~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkGS~kd~~kEe~l-r~~~~~e~~lHvli~~~~~~~ 220 (222)
|.+.||||||++||+.||||+||||||.|+|+||+.|+|||.|||+||+|++.-...+ ...-++|..||+||+||.-|-
T Consensus 147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedk 226 (269)
T COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDK 226 (269)
T ss_pred cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhh
Confidence 8899999999999999999999999999999999999999999999999987643332 234456678999999997665
Q ss_pred C
Q 027518 221 I 221 (222)
Q Consensus 221 ~ 221 (222)
|
T Consensus 227 i 227 (269)
T COG5176 227 I 227 (269)
T ss_pred H
Confidence 4
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=99.93 E-value=1.9e-26 Score=185.06 Aligned_cols=73 Identities=41% Similarity=0.757 Sum_probs=69.5
Q ss_pred EEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecccCCCCchHHHHhhccCCccce---eeEEEEecC
Q 027518 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPARVIVMLLLSLFVFI---VHILYVSGI 217 (222)
Q Consensus 144 ~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkGS~kd~~kEe~lr~~~~~e~~---lHvli~~~~ 217 (222)
++|||||+++||+|||||+||||+|+|+|+||++|||+|.|||+||+++.++|+++++ |.|+|+ +||+|.|++
T Consensus 1 ~~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~-~~~~~~~eplhV~I~a~~ 76 (120)
T cd02395 1 TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRG-PKYAHLNEPLHVLITAET 76 (120)
T ss_pred CCEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccC-cccccCCCCcEEEEEeCC
Confidence 4699999999999999999999999999999999999999999999999999999998 888874 999999987
No 5
>PF13014 KH_3: KH domain
Probab=98.09 E-value=2.9e-06 Score=55.97 Aligned_cols=28 Identities=32% Similarity=0.706 Sum_probs=26.8
Q ss_pred eeeeeecCCcchHHHHHHHhCCeEEEec
Q 027518 159 FVGRLLGPRGNSLKRVEASTECRVLIRG 186 (222)
Q Consensus 159 fvG~ilGPrG~tlk~le~etgckI~IrG 186 (222)
|+|.|+|++|.|+++|+++|||+|.|--
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=98.04 E-value=6.9e-06 Score=58.37 Aligned_cols=39 Identities=23% Similarity=0.509 Sum_probs=33.3
Q ss_pred EEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEeccc
Q 027518 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRG 188 (222)
Q Consensus 144 ~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkG 188 (222)
.+.+.||. .++|+|+|+.|.|+|+||++|||+|.|--.|
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 45677875 7899999999999999999999999986433
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=98.01 E-value=7.4e-06 Score=56.55 Aligned_cols=39 Identities=33% Similarity=0.651 Sum_probs=34.7
Q ss_pred EEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecccC
Q 027518 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGS 189 (222)
Q Consensus 145 ~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkGS 189 (222)
.++.||. +++|+|+||+|.++++|+++|||+|.|...++
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 89999999999999999999999999987654
No 8
>smart00322 KH K homology RNA-binding domain.
Probab=97.78 E-value=4.1e-05 Score=51.74 Aligned_cols=40 Identities=38% Similarity=0.619 Sum_probs=35.1
Q ss_pred EEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecccC
Q 027518 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGS 189 (222)
Q Consensus 144 ~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkGS 189 (222)
..+|.||. +++|.++|++|.+++.|++.|||+|.+...++
T Consensus 4 ~~~i~i~~------~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~ 43 (69)
T smart00322 4 TIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS 43 (69)
T ss_pred EEEEEEcc------hhcceeECCCchHHHHHHHHHCCEEEECCCCC
Confidence 45678876 88999999999999999999999999987654
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=97.71 E-value=1.1e-05 Score=55.95 Aligned_cols=37 Identities=30% Similarity=0.720 Sum_probs=32.8
Q ss_pred EEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecc
Q 027518 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (222)
Q Consensus 145 ~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGk 187 (222)
.+|.||. .++|+|+|++|.++|+||++|||+|.|...
T Consensus 2 ~~i~vp~------~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~ 38 (60)
T PF00013_consen 2 ERIEVPS------SLVGRIIGKKGSNIKEIEEETGVKIQIPDD 38 (60)
T ss_dssp EEEEEEH------HHHHHHHTGGGHHHHHHHHHHTSEEEEEST
T ss_pred EEEEECH------HHcCEEECCCCCcHHHhhhhcCeEEEEcCC
Confidence 4677774 789999999999999999999999999654
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=97.65 E-value=4.6e-05 Score=54.19 Aligned_cols=36 Identities=19% Similarity=0.529 Sum_probs=32.4
Q ss_pred EEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEec
Q 027518 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRG 186 (222)
Q Consensus 145 ~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrG 186 (222)
.++.||. +.+|+|+|.+|.++++|+++|||+|.|.-
T Consensus 2 ~r~~ip~------~~vg~iIG~~G~~i~~i~~~tga~I~i~~ 37 (65)
T cd02396 2 LRLLVPS------SQAGSIIGKGGSTIKEIREETGAKIRVSK 37 (65)
T ss_pred EEEEECH------HHcCeeECCCcHHHHHHHHHHCCEEEEcC
Confidence 4688886 78999999999999999999999999953
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=97.64 E-value=3e-05 Score=54.04 Aligned_cols=38 Identities=18% Similarity=0.472 Sum_probs=32.7
Q ss_pred EEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEeccc
Q 027518 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRG 188 (222)
Q Consensus 145 ~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkG 188 (222)
+++.||. .++|.|+|++|.++++|+++|||+|.|-..+
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 3566765 6789999999999999999999999998755
No 12
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.03 E-value=0.00012 Score=70.57 Aligned_cols=62 Identities=29% Similarity=0.439 Sum_probs=52.5
Q ss_pred EecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEe---------------cccCCCCchHHHHh---hccCCccce
Q 027518 147 VDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR---------------GRGSIKDPARVIVM---LLLSLFVFI 208 (222)
Q Consensus 147 i~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~Ir---------------GkGS~kd~~kEe~l---r~~~~~e~~ 208 (222)
-.||++-...-||+|||||-.|.++|.||.+||+||.|- -|||+..+.+.|.+ +-+.-||.+
T Consensus 278 ~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnD 357 (584)
T KOG2193|consen 278 EEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYEND 357 (584)
T ss_pred hhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhh
Confidence 368888888899999999999999999999999999864 67899999886654 466778754
No 13
>PRK13763 putative RNA-processing protein; Provisional
Probab=96.58 E-value=0.0015 Score=55.71 Aligned_cols=29 Identities=24% Similarity=0.528 Sum_probs=26.8
Q ss_pred eeeeeecCCcchHHHHHHHhCCeEEEecc
Q 027518 159 FVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (222)
Q Consensus 159 fvG~ilGPrG~tlk~le~etgckI~IrGk 187 (222)
.+|+|+|+.|.|.|.||..|||+|.|-++
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~ 133 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGK 133 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCC
Confidence 68999999999999999999999998653
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=96.38 E-value=0.0019 Score=54.57 Aligned_cols=28 Identities=25% Similarity=0.516 Sum_probs=26.4
Q ss_pred eeeeeecCCcchHHHHHHHhCCeEEEec
Q 027518 159 FVGRLLGPRGNSLKRVEASTECRVLIRG 186 (222)
Q Consensus 159 fvG~ilGPrG~tlk~le~etgckI~IrG 186 (222)
.+|||+|+.|.|.+.||..|||+|.|-|
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~ 126 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYG 126 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcC
Confidence 5899999999999999999999999875
No 15
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.07 E-value=0.0051 Score=53.80 Aligned_cols=29 Identities=24% Similarity=0.543 Sum_probs=27.4
Q ss_pred eeeeeecCCcchHHHHHHHhCCeEEEecc
Q 027518 159 FVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (222)
Q Consensus 159 fvG~ilGPrG~tlk~le~etgckI~IrGk 187 (222)
..|||+|+.|.|.+.||.-|||.|.|.|+
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~ 140 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK 140 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc
Confidence 45999999999999999999999999986
No 16
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=95.76 E-value=0.0041 Score=52.57 Aligned_cols=30 Identities=27% Similarity=0.470 Sum_probs=28.2
Q ss_pred ceeeeeecCCcchHHHHHHHhCCeEEEecc
Q 027518 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (222)
Q Consensus 158 NfvG~ilGPrG~tlk~le~etgckI~IrGk 187 (222)
+.+|.|+||.|.|.|+||++|||+|.|--.
T Consensus 7 ~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~ 36 (172)
T TIGR03665 7 DRIGVLIGKGGETKKEIEERTGVKLDIDSE 36 (172)
T ss_pred HHhhhHhCCchhHHHHHHHHhCcEEEEEcC
Confidence 789999999999999999999999999865
No 17
>PRK13763 putative RNA-processing protein; Provisional
Probab=95.57 E-value=0.0083 Score=51.13 Aligned_cols=40 Identities=30% Similarity=0.553 Sum_probs=34.5
Q ss_pred EEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecc-cCC
Q 027518 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGR-GSI 190 (222)
Q Consensus 145 ~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGk-GS~ 190 (222)
..+.||. +-+|.|+||.|.|.|.|+++|||+|.|--. |.+
T Consensus 5 ~~i~IP~------~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V 45 (180)
T PRK13763 5 EYVKIPK------DRIGVLIGKKGETKKEIEERTGVKLEIDSETGEV 45 (180)
T ss_pred EEEEcCH------HHhhhHhccchhHHHHHHHHHCcEEEEECCCCeE
Confidence 4566775 678999999999999999999999999987 554
No 18
>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=94.73 E-value=0.017 Score=58.52 Aligned_cols=43 Identities=21% Similarity=0.487 Sum_probs=36.3
Q ss_pred eEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecccCCC
Q 027518 143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIK 191 (222)
Q Consensus 143 ~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkGS~k 191 (222)
+...+.||. ..||.||||+|.|+|.|+++|||+|.|--.|.++
T Consensus 551 ~~~~~~I~~------~kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG~V~ 593 (684)
T TIGR03591 551 RIETIKINP------DKIRDVIGPGGKVIREITEETGAKIDIEDDGTVK 593 (684)
T ss_pred eEEEEecCH------HHHHhhcCCCcHHHHHHHHHHCCEEEEecCeEEE
Confidence 355677875 6789999999999999999999999998666555
No 19
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=94.60 E-value=0.021 Score=53.04 Aligned_cols=27 Identities=44% Similarity=0.918 Sum_probs=25.7
Q ss_pred eeeecCCcchHHHHHHHhCCeEEEecc
Q 027518 161 GRLLGPRGNSLKRVEASTECRVLIRGR 187 (222)
Q Consensus 161 G~ilGPrG~tlk~le~etgckI~IrGk 187 (222)
-||+||.|+|||.||--|.|-|.|.|.
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~ 187 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN 187 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc
Confidence 589999999999999999999999986
No 20
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=93.82 E-value=0.081 Score=50.14 Aligned_cols=37 Identities=22% Similarity=0.452 Sum_probs=33.2
Q ss_pred eEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEe
Q 027518 143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (222)
Q Consensus 143 ~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~Ir 185 (222)
...||+||- +-.|-|||-.|.|+.+||++|||+|..-
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 467899995 6789999999999999999999999875
No 21
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=93.79 E-value=0.03 Score=54.21 Aligned_cols=51 Identities=16% Similarity=-0.007 Sum_probs=45.7
Q ss_pred eeeEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecccCCCC
Q 027518 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKD 192 (222)
Q Consensus 141 vK~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkGS~kd 192 (222)
++...|.+|+++ -|.+|.-+..=|++..+|..+|.+|+.+++||||||..-
T Consensus 208 ~~Y~~k~~v~~~-~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~i 258 (531)
T KOG1960|consen 208 RYYPNKALATDK-DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRR 258 (531)
T ss_pred ccchhheecccC-CcchhhhhhccCccchhhhhhhhhhhhhhhhcccccccc
Confidence 344458999998 799999999999999999999999999999999999863
No 22
>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=93.67 E-value=0.058 Score=55.23 Aligned_cols=44 Identities=30% Similarity=0.678 Sum_probs=38.2
Q ss_pred eeEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecccCCC
Q 027518 142 KRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIK 191 (222)
Q Consensus 142 K~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkGS~k 191 (222)
-+...+.||. .-+|.||||.|.|+|.|+++|||+|-|--.|.++
T Consensus 577 P~~~~~~I~~------~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G~V~ 620 (719)
T TIGR02696 577 PRIITVKIPV------DKIGEVIGPKGKMINQIQDETGAEISIEDDGTVY 620 (719)
T ss_pred CeeEEEEeCh------HHhhheeCCCcHhHHHHHHHHCCEEEEecCcEEE
Confidence 3456788875 5699999999999999999999999999888765
No 23
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=93.13 E-value=0.081 Score=52.96 Aligned_cols=59 Identities=20% Similarity=0.344 Sum_probs=46.6
Q ss_pred ceeeEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecccCCCC-chHHHHhhccCC
Q 027518 140 IVKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKD-PARVIVMLLLSL 204 (222)
Q Consensus 140 ~vK~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkGS~kd-~~kEe~lr~~~~ 204 (222)
.++.+.+|.||. |=+|+|||-.|.|.|+|++++|||+.+-=.|+..+ ..|+-++-+.|.
T Consensus 136 ~~~ttqeI~IPa------~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~ 195 (600)
T KOG1676|consen 136 SVETTQEILIPA------NKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPD 195 (600)
T ss_pred ccceeeeeccCc------cceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHH
Confidence 366788899996 66899999999999999999999999888888666 444444444443
No 24
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=92.47 E-value=0.14 Score=51.37 Aligned_cols=28 Identities=21% Similarity=0.526 Sum_probs=26.6
Q ss_pred ceeeeeecCCcchHHHHHHHhCCeEEEe
Q 027518 158 NFVGRLLGPRGNSLKRVEASTECRVLIR 185 (222)
Q Consensus 158 NfvG~ilGPrG~tlk~le~etgckI~Ir 185 (222)
+=||.|||-.|.|+|+|+.+||+||.++
T Consensus 239 ~~VG~IIGkgGE~IKklq~etG~KIQfk 266 (600)
T KOG1676|consen 239 SKVGIIIGKGGEMIKKLQNETGAKIQFK 266 (600)
T ss_pred cceeeEEecCchHHHHHhhccCceeEee
Confidence 5699999999999999999999999986
No 25
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=88.43 E-value=0.22 Score=47.02 Aligned_cols=34 Identities=26% Similarity=0.588 Sum_probs=29.4
Q ss_pred ceeeeeecCCcchHHHHHHHhCCeEEEecccCCC
Q 027518 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIK 191 (222)
Q Consensus 158 NfvG~ilGPrG~tlk~le~etgckI~IrGkGS~k 191 (222)
-|+|.|+|-+|.|.|+||+||+|+|.+=-.+.-+
T Consensus 66 ~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~ 99 (345)
T KOG2814|consen 66 SFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNK 99 (345)
T ss_pred HHhhhhhcccchHHHHHHHhhccceEccCCCCCc
Confidence 6889999999999999999999999986555333
No 26
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=87.77 E-value=0.65 Score=45.66 Aligned_cols=39 Identities=26% Similarity=0.478 Sum_probs=35.7
Q ss_pred eEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecc
Q 027518 143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (222)
Q Consensus 143 ~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGk 187 (222)
...++.||- +-+|-|||-+|..+|.|.++|||+|.|.+.
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 357899996 679999999999999999999999999987
No 27
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=87.67 E-value=0.17 Score=53.03 Aligned_cols=43 Identities=16% Similarity=0.280 Sum_probs=37.5
Q ss_pred eEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCe-EEEecccCCC
Q 027518 143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECR-VLIRGRGSIK 191 (222)
Q Consensus 143 ~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgck-I~IrGkGS~k 191 (222)
+...+.||. +-||.||||.|.|+|.|+++||++ |-|+-.|.++
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 456677874 679999999999999999999999 9999888776
No 28
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=87.43 E-value=0.37 Score=47.18 Aligned_cols=31 Identities=23% Similarity=0.596 Sum_probs=28.2
Q ss_pred CceeeeeecCCcchHHHHHHHhCCeEEEecc
Q 027518 157 FNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (222)
Q Consensus 157 ~NfvG~ilGPrG~tlk~le~etgckI~IrGk 187 (222)
.-|+|-||||.|.|+|-|-+.|.|||-|.-+
T Consensus 207 tqyvgaIIGkeG~TIknItkqTqsriD~hrk 237 (584)
T KOG2193|consen 207 TQYVGAIIGKEGATIKNITKQTQSRIDVHRK 237 (584)
T ss_pred cceeEEEecCCCccccCcchhhhheeeeeec
Confidence 4799999999999999999999999988643
No 29
>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=87.26 E-value=1.3 Score=31.30 Aligned_cols=35 Identities=20% Similarity=0.320 Sum_probs=29.9
Q ss_pred EEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEE
Q 027518 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLI 184 (222)
Q Consensus 144 ~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~I 184 (222)
..+|.||. .-+|+.||.+|.+++.++..+|.+|-|
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 457899999999999999999998876
No 30
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=86.91 E-value=0.28 Score=43.41 Aligned_cols=32 Identities=22% Similarity=0.543 Sum_probs=28.1
Q ss_pred ceeeeeecCCcchHHHHHHHhCCeEEEecccC
Q 027518 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRGS 189 (222)
Q Consensus 158 NfvG~ilGPrG~tlk~le~etgckI~IrGkGS 189 (222)
+.+++++||+|.+++.|.++|+|+|.|-=.|-
T Consensus 154 ~~i~~lig~~g~~i~~l~~~~~~~I~ig~NG~ 185 (235)
T PRK04163 154 VKVPRVIGKKGSMINMLKEETGCDIIVGQNGR 185 (235)
T ss_pred HHHHhhcCCCChhHhhhhhhhCcEEEEcCCcE
Confidence 77999999999999999999999999854443
No 31
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=85.80 E-value=0.85 Score=43.44 Aligned_cols=37 Identities=19% Similarity=0.495 Sum_probs=32.5
Q ss_pred eEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEe
Q 027518 143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (222)
Q Consensus 143 ~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~Ir 185 (222)
++.||.+|.- --|.|||+.|.|+|.+.+++||-|.|.
T Consensus 132 kqikivvPNs------tag~iigkggAtiK~~~Eqsga~iqis 168 (402)
T KOG2191|consen 132 KQIKIVVPNS------TAGMIIGKGGATIKAIQEQSGAWIQIS 168 (402)
T ss_pred ceeEEeccCC------cccceecCCcchHHHHHHhhCcceEec
Confidence 4678999853 358999999999999999999999997
No 32
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=84.71 E-value=0.93 Score=44.59 Aligned_cols=41 Identities=20% Similarity=0.433 Sum_probs=36.4
Q ss_pred eeEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEeccc
Q 027518 142 KRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRG 188 (222)
Q Consensus 142 K~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkG 188 (222)
-.+.++.||. +++|.|+|..|+.+-.|++.|||.|.|.++-
T Consensus 337 ~v~~~l~vps------~~igciiGk~G~~iseir~~tgA~I~I~~~~ 377 (485)
T KOG2190|consen 337 TVTQRLLVPS------DLIGCIIGKGGAKISEIRQRTGASISILNKE 377 (485)
T ss_pred eeeeeeccCc------cccceeecccccchHHHHHhcCCceEEcccc
Confidence 3467888885 8999999999999999999999999998765
No 33
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=84.11 E-value=0.31 Score=49.53 Aligned_cols=34 Identities=21% Similarity=0.580 Sum_probs=31.5
Q ss_pred ceeeeeecCCcchHHHHHHHhCCeEEEecccCCC
Q 027518 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIK 191 (222)
Q Consensus 158 NfvG~ilGPrG~tlk~le~etgckI~IrGkGS~k 191 (222)
.-+|.+|||.|.|+|.|+++||++|-|+-.|.++
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 6689999999999999999999999999888776
No 34
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=79.29 E-value=0.99 Score=44.56 Aligned_cols=29 Identities=31% Similarity=0.641 Sum_probs=26.5
Q ss_pred CceeeeeecCCcchHHHHHHHhCCeEEEe
Q 027518 157 FNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (222)
Q Consensus 157 ~NfvG~ilGPrG~tlk~le~etgckI~Ir 185 (222)
-||||.+||=.|+.+|+||..|+++|.|-
T Consensus 55 s~mvg~vigrggskik~iq~~tnt~iqii 83 (629)
T KOG0336|consen 55 SEMVGKVIGRGGSKIKRIQNDTNTRIQII 83 (629)
T ss_pred hhhhheeeccCcchhhhhhcccceeEEEe
Confidence 48999999999999999999999988764
No 35
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=74.00 E-value=1.5 Score=32.10 Aligned_cols=33 Identities=21% Similarity=0.421 Sum_probs=26.8
Q ss_pred CCCceeeeeecCCcchHHHHHHHh-CCeEEEecc
Q 027518 155 PNFNFVGRLLGPRGNSLKRVEAST-ECRVLIRGR 187 (222)
Q Consensus 155 P~~NfvG~ilGPrG~tlk~le~et-gckI~IrGk 187 (222)
++++-+|..+|.+|...|.|+++. |-+|-|=.-
T Consensus 14 ~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 14 PNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp TTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred CCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 889999999999999999999999 888877543
No 36
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=70.48 E-value=3.1 Score=41.07 Aligned_cols=36 Identities=25% Similarity=0.582 Sum_probs=30.8
Q ss_pred EEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEe
Q 027518 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (222)
Q Consensus 145 ~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~Ir 185 (222)
.-|.+|-+ .+-|||||-.|-+.|.+|+-||+-|.|=
T Consensus 206 ~~v~lp~d-----~~kgriigreGrnir~~e~~tgvd~iid 241 (514)
T TIGR03319 206 SVVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIID 241 (514)
T ss_pred eeEEcCCh-----hhhccccCCCcchHHHHHHHhCceEEEc
Confidence 34667665 5679999999999999999999999885
No 37
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=70.32 E-value=3.9 Score=27.54 Aligned_cols=23 Identities=13% Similarity=0.395 Sum_probs=20.4
Q ss_pred eeeeecCCcchHHHHHHHhCCeE
Q 027518 160 VGRLLGPRGNSLKRVEASTECRV 182 (222)
Q Consensus 160 vG~ilGPrG~tlk~le~etgckI 182 (222)
.|+++|.+|.+++.|+..++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 69999999999999999998443
No 38
>PRK12704 phosphodiesterase; Provisional
Probab=70.23 E-value=3.5 Score=40.79 Aligned_cols=36 Identities=25% Similarity=0.582 Sum_probs=30.5
Q ss_pred EEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEe
Q 027518 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (222)
Q Consensus 145 ~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~Ir 185 (222)
.-|.+|-+ .+-|||||-.|-+.|.+|+-||+-|.|=
T Consensus 212 ~~v~lp~d-----~mkgriigreGrnir~~e~~tgvd~iid 247 (520)
T PRK12704 212 SVVNLPND-----EMKGRIIGREGRNIRALETLTGVDLIID 247 (520)
T ss_pred eeeecCCc-----hhhcceeCCCcchHHHHHHHhCCeEEEc
Confidence 34666665 5679999999999999999999999885
No 39
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=69.54 E-value=2.3 Score=43.64 Aligned_cols=44 Identities=23% Similarity=0.480 Sum_probs=36.6
Q ss_pred EEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecccCCCCc
Q 027518 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDP 193 (222)
Q Consensus 144 ~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkGS~kd~ 193 (222)
.+.+-|+.+. ++-++||.|.|.+.|.++|||+|-|--.|+++-.
T Consensus 553 i~t~~i~~dK------I~dvIG~gGk~I~~I~eetg~~IdieddGtv~i~ 596 (692)
T COG1185 553 IETIKIDPDK------IRDVIGPGGKTIKAITEETGVKIDIEDDGTVKIA 596 (692)
T ss_pred eEEEccCHHH------HhhccCCcccchhhhhhhhCcEEEecCCCcEEEE
Confidence 3455677665 4578999999999999999999999999998743
No 40
>PRK00106 hypothetical protein; Provisional
Probab=68.07 E-value=3.8 Score=40.90 Aligned_cols=37 Identities=30% Similarity=0.604 Sum_probs=31.1
Q ss_pred EEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEe
Q 027518 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (222)
Q Consensus 144 ~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~Ir 185 (222)
+.-|.+|-+ .+-|||||-.|.+.+.+|+-||+-|.|=
T Consensus 226 vs~v~lp~d-----emkGriIGreGrNir~~E~~tGvdliid 262 (535)
T PRK00106 226 ITTVHLPDD-----NMKGRIIGREGRNIRTLESLTGIDVIID 262 (535)
T ss_pred eeeEEcCCh-----HhhcceeCCCcchHHHHHHHhCceEEEc
Confidence 335667665 5679999999999999999999999884
No 41
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=62.51 E-value=6.1 Score=35.84 Aligned_cols=32 Identities=25% Similarity=0.594 Sum_probs=28.3
Q ss_pred ceeeeeecCCcchHHHHHHHhCCeEEEecccC
Q 027518 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRGS 189 (222)
Q Consensus 158 NfvG~ilGPrG~tlk~le~etgckI~IrGkGS 189 (222)
++|-|++|.+|+-++.|.+.|+|.|.|==.|-
T Consensus 155 ~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG~ 186 (239)
T COG1097 155 SKVPRVIGKKGSMLNMLKEKTGCEIIVGQNGR 186 (239)
T ss_pred hhcceEecCCCcHHHHhhhhcCeEEEEecCCE
Confidence 77889999999999999999999999865553
No 42
>PRK12705 hypothetical protein; Provisional
Probab=62.10 E-value=4.7 Score=40.07 Aligned_cols=31 Identities=26% Similarity=0.550 Sum_probs=27.4
Q ss_pred CCCceeeeeecCCcchHHHHHHHhCCeEEEe
Q 027518 155 PNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (222)
Q Consensus 155 P~~NfvG~ilGPrG~tlk~le~etgckI~Ir 185 (222)
|+-..-|||||-.|...+.+|..||+-|.|=
T Consensus 205 p~demkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 205 PSDAMKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred CChHhhccccCccchhHHHHHHhhCCceEec
Confidence 3446779999999999999999999999885
No 43
>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=60.30 E-value=5.6 Score=29.07 Aligned_cols=20 Identities=30% Similarity=0.642 Sum_probs=17.9
Q ss_pred eeeeecCCcchHHHHHHHhC
Q 027518 160 VGRLLGPRGNSLKRVEASTE 179 (222)
Q Consensus 160 vG~ilGPrG~tlk~le~etg 179 (222)
.|++||-+|.|+..||--+.
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~ 54 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLAN 54 (77)
T ss_pred CCeEECCCCccHHHHHHHHH
Confidence 49999999999999997665
No 44
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=58.65 E-value=8.3 Score=31.81 Aligned_cols=29 Identities=21% Similarity=0.314 Sum_probs=26.6
Q ss_pred ceeeeeecCCcchHHHHHHHhCCeEEEec
Q 027518 158 NFVGRLLGPRGNSLKRVEASTECRVLIRG 186 (222)
Q Consensus 158 NfvG~ilGPrG~tlk~le~etgckI~IrG 186 (222)
+.+|..+|++|...+.|++..|-+|-|=.
T Consensus 41 ~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 41 GDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 57899999999999999999999998865
No 45
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=49.12 E-value=14 Score=32.65 Aligned_cols=37 Identities=30% Similarity=0.483 Sum_probs=30.6
Q ss_pred EEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecc
Q 027518 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (222)
Q Consensus 145 ~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGk 187 (222)
+.|.||-+ =+|-++|+.|.+.|.||+.++|++.|=.+
T Consensus 10 ~~v~iPk~------R~~~lig~~g~v~k~ie~~~~~~~~iD~~ 46 (194)
T COG1094 10 EAVKIPKD------RIGVLIGKWGEVKKAIEEKTGVKLRIDSK 46 (194)
T ss_pred eeeecCch------hheeeecccccchHHHHhhcCeEEEEECC
Confidence 44556643 37899999999999999999999988776
No 46
>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=46.38 E-value=16 Score=25.11 Aligned_cols=20 Identities=15% Similarity=0.250 Sum_probs=16.1
Q ss_pred hHHHHHHHhCCeEEEecccC
Q 027518 170 SLKRVEASTECRVLIRGRGS 189 (222)
Q Consensus 170 tlk~le~etgckI~IrGkGS 189 (222)
.+++||++.|+++.+|..+.
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 47
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=43.13 E-value=5.4 Score=28.60 Aligned_cols=20 Identities=30% Similarity=0.634 Sum_probs=17.7
Q ss_pred eeeeecCCcchHHHHHHHhC
Q 027518 160 VGRLLGPRGNSLKRVEASTE 179 (222)
Q Consensus 160 vG~ilGPrG~tlk~le~etg 179 (222)
.|++||-+|.|++.||--++
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 48
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=41.46 E-value=19 Score=37.46 Aligned_cols=37 Identities=24% Similarity=0.576 Sum_probs=30.0
Q ss_pred eEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEe
Q 027518 143 RTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIR 185 (222)
Q Consensus 143 ~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~Ir 185 (222)
.+..+.||. -|-+-|+||.|.++++++++++|.|.+-
T Consensus 709 ~~~~~~~p~------~~~~~~ig~~g~~~r~~~~~~~~~~~~~ 745 (753)
T KOG2208|consen 709 VTKEIEIPR------SLHRYLIGPKGSNLRQLEKEFNVNIVVP 745 (753)
T ss_pred eeeEEeccH------HHhhhccCCCCccHHHHHHHhccceecC
Confidence 345677775 4556899999999999999999998764
No 49
>PRK02821 hypothetical protein; Provisional
Probab=39.28 E-value=17 Score=27.33 Aligned_cols=20 Identities=15% Similarity=0.444 Sum_probs=16.6
Q ss_pred ceeeeeecCCcchHHHHHHH
Q 027518 158 NFVGRLLGPRGNSLKRVEAS 177 (222)
Q Consensus 158 NfvG~ilGPrG~tlk~le~e 177 (222)
.=+||+||-+|.|++.|-.-
T Consensus 40 ~D~GrVIGk~Gr~i~AIRtl 59 (77)
T PRK02821 40 DDLGKVIGRGGRTATALRTV 59 (77)
T ss_pred hhCcceeCCCCchHHHHHHH
Confidence 44899999999999987543
No 50
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=38.40 E-value=23 Score=30.58 Aligned_cols=21 Identities=33% Similarity=0.501 Sum_probs=18.4
Q ss_pred chHHHHHHHhCCeEEEecccC
Q 027518 169 NSLKRVEASTECRVLIRGRGS 189 (222)
Q Consensus 169 ~tlk~le~etgckI~IrGkGS 189 (222)
..+|+||++.|+++.+|++|.
T Consensus 35 ~~i~~LE~~lg~~Lf~R~r~i 55 (294)
T PRK13348 35 QRIKALEESLGQPLLVRGRPC 55 (294)
T ss_pred HHHHHHHHHhCceeeecCCCC
Confidence 458999999999999999763
No 51
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=37.64 E-value=28 Score=29.91 Aligned_cols=27 Identities=15% Similarity=0.158 Sum_probs=25.2
Q ss_pred eeeecCCcchHHHHHHHhCCeEEEecc
Q 027518 161 GRLLGPRGNSLKRVEASTECRVLIRGR 187 (222)
Q Consensus 161 G~ilGPrG~tlk~le~etgckI~IrGk 187 (222)
|..+|+.|.+.|+|++..|-+|.|=.-
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEEEc
Confidence 999999999999999999999988773
No 52
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=37.56 E-value=18 Score=34.50 Aligned_cols=38 Identities=24% Similarity=0.397 Sum_probs=30.4
Q ss_pred eeeEEEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEE
Q 027518 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLI 184 (222)
Q Consensus 141 vK~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~I 184 (222)
..+.+-|-+| +-||+.|.|++|.+.|.|+++|.+.|.-
T Consensus 24 ~nvt~sv~vp------s~~v~~ivg~qg~kikalr~KTqtyi~t 61 (394)
T KOG2113|consen 24 QNVTESVEVP------SEHVAEIVGRQGCKIKALRAKTQTYIKT 61 (394)
T ss_pred CccceeeecC------cccceeecccCccccchhhhhhcceecc
Confidence 3345555565 4589999999999999999999998863
No 53
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=36.93 E-value=35 Score=32.49 Aligned_cols=39 Identities=18% Similarity=0.433 Sum_probs=31.5
Q ss_pred EEecCCCCCCCCceeeeeecCCcchHHHHHHHh-CCeEEEe
Q 027518 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEAST-ECRVLIR 185 (222)
Q Consensus 146 ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~et-gckI~Ir 185 (222)
||-|=- .-|+++-+|..+|++|..++.+.++. |=+|-|=
T Consensus 234 KVAV~s-~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv 273 (362)
T PRK12327 234 KIAVRS-NNPNVDAKGACVGPKGQRVQNIVSELKGEKIDII 273 (362)
T ss_pred EEEEEc-CCCCCCchheeECCCChhHHHHHHHhCCCeEEEE
Confidence 555432 34999999999999999999999999 7777653
No 54
>PRK00468 hypothetical protein; Provisional
Probab=36.85 E-value=20 Score=26.76 Aligned_cols=17 Identities=24% Similarity=0.659 Sum_probs=15.1
Q ss_pred eeeeecCCcchHHHHHH
Q 027518 160 VGRLLGPRGNSLKRVEA 176 (222)
Q Consensus 160 vG~ilGPrG~tlk~le~ 176 (222)
+||+||=+|.|++.|-.
T Consensus 41 ~GrVIGk~Gr~i~AIRt 57 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRT 57 (75)
T ss_pred CcceecCCChhHHHHHH
Confidence 69999999999998754
No 55
>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=35.41 E-value=41 Score=29.56 Aligned_cols=40 Identities=18% Similarity=0.346 Sum_probs=29.2
Q ss_pred eeeEEEEecCCCCCCCCceeeeeecCCcchHHHH--------HHHhCCeEEEe
Q 027518 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRV--------EASTECRVLIR 185 (222)
Q Consensus 141 vK~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~l--------e~etgckI~Ir 185 (222)
+.....|+|.-+. --|-|+|.+|.++|+| |+-.||+|.+.
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 4455567776543 4488999999999986 77788888753
No 56
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=34.96 E-value=32 Score=30.02 Aligned_cols=34 Identities=21% Similarity=0.306 Sum_probs=28.7
Q ss_pred CCCceeeeeecCCcchHHHHHHHhCCeEEEeccc
Q 027518 155 PNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRG 188 (222)
Q Consensus 155 P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkG 188 (222)
++.+=+|..+|++|...|.+.++.|=+|-|=--.
T Consensus 82 ~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s 115 (190)
T COG0195 82 VKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS 115 (190)
T ss_pred cCcCchhhhccCCChHHHHHHHHhCCceEEEEeC
Confidence 4567799999999999999999999888765443
No 57
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=34.78 E-value=45 Score=31.48 Aligned_cols=39 Identities=18% Similarity=0.402 Sum_probs=32.0
Q ss_pred EEecCCCCCCCCceeeeeecCCcchHHHHHHHh-CCeEEEe
Q 027518 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEAST-ECRVLIR 185 (222)
Q Consensus 146 ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~et-gckI~Ir 185 (222)
||-|=-. -|+++-+|..+|++|..++.+.++. |=+|-|=
T Consensus 232 KvAV~s~-~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv 271 (341)
T TIGR01953 232 KIAVESN-DENIDPVGACVGPKGSRIQAISKELNGEKIDII 271 (341)
T ss_pred EEEEEcC-CCCCCcceeeECCCCchHHHHHHHhCCCeEEEE
Confidence 5555333 5999999999999999999999999 7777664
No 58
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=34.17 E-value=34 Score=28.46 Aligned_cols=29 Identities=21% Similarity=0.319 Sum_probs=26.5
Q ss_pred ceeeeeecCCcchHHHHHHHhCCeEEEec
Q 027518 158 NFVGRLLGPRGNSLKRVEASTECRVLIRG 186 (222)
Q Consensus 158 NfvG~ilGPrG~tlk~le~etgckI~IrG 186 (222)
+-+|..+|++|...+.+++..|=+|-|=.
T Consensus 42 g~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 42 GEMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred CCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 57999999999999999999999998876
No 59
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=33.34 E-value=62 Score=32.00 Aligned_cols=41 Identities=15% Similarity=0.274 Sum_probs=33.0
Q ss_pred EEEEecCCCCCCCCceeeeeecCCcchHHHHHHHh-CCeEEEe
Q 027518 144 TIRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEAST-ECRVLIR 185 (222)
Q Consensus 144 ~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~et-gckI~Ir 185 (222)
..||-|=-. -|+++-||..+|++|..++.+.++. |=||-|=
T Consensus 264 RtKVAV~S~-d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDVI 305 (449)
T PRK12329 264 RTKIAVDTL-ERDVDPVGACIGARGSRIQAVVNELRGEKIDVI 305 (449)
T ss_pred eeEEEEEcC-CCCCChhhccCCCCcchHHHHHHHhCCCeEEEE
Confidence 456665433 4899999999999999999999999 7777653
No 60
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=31.95 E-value=27 Score=26.38 Aligned_cols=17 Identities=18% Similarity=0.769 Sum_probs=15.1
Q ss_pred eeeeecCCcchHHHHHH
Q 027518 160 VGRLLGPRGNSLKRVEA 176 (222)
Q Consensus 160 vG~ilGPrG~tlk~le~ 176 (222)
+|++||-+|.|++.|-.
T Consensus 41 ~GkvIGk~GRti~AIRT 57 (76)
T COG1837 41 MGKVIGKQGRTIQAIRT 57 (76)
T ss_pred ccceecCCChhHHHHHH
Confidence 79999999999998843
No 61
>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=31.38 E-value=28 Score=30.01 Aligned_cols=21 Identities=19% Similarity=0.241 Sum_probs=18.0
Q ss_pred hHHHHHHHhCCeEEEecccCC
Q 027518 170 SLKRVEASTECRVLIRGRGSI 190 (222)
Q Consensus 170 tlk~le~etgckI~IrGkGS~ 190 (222)
.+|+||++.|+++.+|++|-.
T Consensus 35 ~I~~LE~~lg~~Lf~R~r~~~ 55 (292)
T TIGR03298 35 RIKALEERLGQPLLVRTQPCR 55 (292)
T ss_pred HHHHHHHHhCchheecCCCCc
Confidence 479999999999999997543
No 62
>PRK01064 hypothetical protein; Provisional
Probab=31.11 E-value=36 Score=25.64 Aligned_cols=20 Identities=20% Similarity=0.617 Sum_probs=17.1
Q ss_pred eeeeecCCcchHHHHHHHhC
Q 027518 160 VGRLLGPRGNSLKRVEASTE 179 (222)
Q Consensus 160 vG~ilGPrG~tlk~le~etg 179 (222)
+|++||-+|.|++.|..-..
T Consensus 41 ~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred ceEEECCCCccHHHHHHHHH
Confidence 69999999999999876443
No 63
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=30.53 E-value=40 Score=32.26 Aligned_cols=31 Identities=26% Similarity=0.441 Sum_probs=28.1
Q ss_pred ceeeeeecCCcchHHHHHHHhCCeEEEeccc
Q 027518 158 NFVGRLLGPRGNSLKRVEASTECRVLIRGRG 188 (222)
Q Consensus 158 NfvG~ilGPrG~tlk~le~etgckI~IrGkG 188 (222)
|-+--++||.+..++.||+.+|+.|.-||..
T Consensus 24 ~~~~~l~G~~~~~l~l~e~~~gv~i~~rG~~ 54 (348)
T COG1702 24 NELVALFGPTDTNLSLLEIALGVSIVARGEA 54 (348)
T ss_pred hhhhhhcCCCCccHHHHHHHhCcEEEeCCce
Confidence 6677799999999999999999999999864
No 64
>PRK00089 era GTPase Era; Reviewed
Probab=30.32 E-value=56 Score=28.77 Aligned_cols=40 Identities=20% Similarity=0.353 Sum_probs=30.2
Q ss_pred eeeEEEEecCCCCCCCCceeeeeecCCcchHHHH--------HHHhCCeEEEe
Q 027518 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRV--------EASTECRVLIR 185 (222)
Q Consensus 141 vK~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~l--------e~etgckI~Ir 185 (222)
++....|+|.-+. -.+-|+|-+|.++|+| |+-+||+|.+.
T Consensus 224 ~~i~~~i~v~~~~-----~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 224 VRIEATIYVERDS-----QKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEEEccCC-----ceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 4455667776543 3689999999999876 78889998765
No 65
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=29.83 E-value=27 Score=33.36 Aligned_cols=31 Identities=29% Similarity=0.580 Sum_probs=27.2
Q ss_pred CceeeeeecCCcchHHHHHHHhCCeEEEecc
Q 027518 157 FNFVGRLLGPRGNSLKRVEASTECRVLIRGR 187 (222)
Q Consensus 157 ~NfvG~ilGPrG~tlk~le~etgckI~IrGk 187 (222)
+-.||.+.||.|+|+|++|+.|..-|.--++
T Consensus 123 ~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 123 LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred ceeeeeccccccCccchheecccceEeeecc
Confidence 6789999999999999999999988865543
No 66
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=29.32 E-value=41 Score=29.24 Aligned_cols=23 Identities=17% Similarity=0.225 Sum_probs=19.2
Q ss_pred chHHHHHHHhCCeEEEecccCCC
Q 027518 169 NSLKRVEASTECRVLIRGRGSIK 191 (222)
Q Consensus 169 ~tlk~le~etgckI~IrGkGS~k 191 (222)
..+|+||++.||++..|++|-.-
T Consensus 35 ~~I~~LE~~lg~~LF~R~~~~~l 57 (294)
T PRK03635 35 QRIKALEERVGQVLLVRTQPCRP 57 (294)
T ss_pred HHHHHHHHHhCceeeecCCCCcc
Confidence 35899999999999999975443
No 67
>PRK05465 ethanolamine ammonia-lyase small subunit; Provisional
Probab=28.99 E-value=80 Score=29.13 Aligned_cols=49 Identities=10% Similarity=0.247 Sum_probs=35.3
Q ss_pred CccccccCCCCCCCCCC--CCCCcCCcccchhHHHHHHHHHHHHhhcCCCC
Q 027518 7 GRFMAYSLSPSAPHSPH--LPSLRSASSAILDQEKYLSELLAERHKLNPFL 55 (222)
Q Consensus 7 ~~~~~~~~~~~~~~~p~--~~~~r~~~~~~~~~~~YL~ELl~Ek~kL~pf~ 55 (222)
|-|+.|.|.+..+-+-+ |+|+|..--...+...+|.+|++|..++.-+-
T Consensus 190 g~YlT~~p~~G~~Da~RncISNI~~~Gl~~~~Aa~~l~~Li~~~~~~~~SG 240 (260)
T PRK05465 190 GAYLTYAPRVGTTDADRNCISNIHPGGLPYAEAAAKIAYLIKEALRLKASG 240 (260)
T ss_pred eEEEEecCCCCCCccccceeccCCCCCCCHHHHHHHHHHHHHHHHHhCCCC
Confidence 67999998865332222 77888643346678899999999998887653
No 68
>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=28.92 E-value=65 Score=24.93 Aligned_cols=26 Identities=27% Similarity=0.259 Sum_probs=23.3
Q ss_pred CChhhHHHHHHHHHHHHHHHhhcCCC
Q 027518 56 PVLPNAYRLLNQEIMRVTTLLGNASV 81 (222)
Q Consensus 56 ~v~ph~~rLL~qEI~RV~~~l~~~~~ 81 (222)
+.+|.+...|.+||......|+..|+
T Consensus 64 nDcpeA~~eL~~eI~eAK~dLr~kGv 89 (91)
T PF08285_consen 64 NDCPEAAKELQKEIKEAKADLRKKGV 89 (91)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 56899999999999999999988776
No 69
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=28.36 E-value=47 Score=28.42 Aligned_cols=23 Identities=22% Similarity=0.273 Sum_probs=19.4
Q ss_pred chHHHHHHHhCCeEEEecccCCC
Q 027518 169 NSLKRVEASTECRVLIRGRGSIK 191 (222)
Q Consensus 169 ~tlk~le~etgckI~IrGkGS~k 191 (222)
..+|+||++.||++.+|..+.+.
T Consensus 40 ~~i~~LE~~lg~~Lf~R~~r~~~ 62 (294)
T PRK09986 40 IHIKELEDQLGTPLFIRHSRSVV 62 (294)
T ss_pred HHHHHHHHHhCCeeEeeCCCcee
Confidence 46899999999999999865554
No 70
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=28.02 E-value=52 Score=28.57 Aligned_cols=22 Identities=14% Similarity=0.368 Sum_probs=19.6
Q ss_pred hHHHHHHHhCCeEEEecccCCC
Q 027518 170 SLKRVEASTECRVLIRGRGSIK 191 (222)
Q Consensus 170 tlk~le~etgckI~IrGkGS~k 191 (222)
.+|+||++.||++..|.++.+.
T Consensus 39 ~i~~LE~~lG~~LF~R~~r~~~ 60 (302)
T PRK09791 39 SIQELEEGLAAQLFFRRSKGVT 60 (302)
T ss_pred HHHHHHHHhCCeEEEEcCCCce
Confidence 4899999999999999887765
No 71
>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=26.69 E-value=12 Score=31.05 Aligned_cols=18 Identities=39% Similarity=0.761 Sum_probs=14.2
Q ss_pred CCCCCCceeeeeecCCcc
Q 027518 152 EKYPNFNFVGRLLGPRGN 169 (222)
Q Consensus 152 ~~~P~~NfvG~ilGPrG~ 169 (222)
+-.|.+..+|++|||||.
T Consensus 101 ~~m~~l~~Lg~iLGprGl 118 (141)
T TIGR01170 101 DIVPELAQLRRLLGPKGL 118 (141)
T ss_pred HHHHHHHHhhcccccCcC
Confidence 335667789999999974
No 72
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=26.66 E-value=52 Score=29.06 Aligned_cols=20 Identities=15% Similarity=0.355 Sum_probs=17.2
Q ss_pred hHHHHHHHhCCeEEEe-cccC
Q 027518 170 SLKRVEASTECRVLIR-GRGS 189 (222)
Q Consensus 170 tlk~le~etgckI~Ir-GkGS 189 (222)
.+|+||++.||++.+| |+|-
T Consensus 36 ~ik~LE~~lg~~Lf~R~~r~~ 56 (313)
T PRK12684 36 AIIELEDELGVEIFTRHGKRL 56 (313)
T ss_pred HHHHHHHHhCCeeEEEcCCcc
Confidence 4899999999999999 4554
No 73
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=25.96 E-value=55 Score=28.95 Aligned_cols=21 Identities=24% Similarity=0.482 Sum_probs=17.7
Q ss_pred chHHHHHHHhCCeEEEe-cccC
Q 027518 169 NSLKRVEASTECRVLIR-GRGS 189 (222)
Q Consensus 169 ~tlk~le~etgckI~Ir-GkGS 189 (222)
..+|+||++.|+++.+| |+|-
T Consensus 35 ~~I~~LE~~lg~~Lf~R~~r~~ 56 (309)
T PRK12683 35 KQIKDLEDELGVEIFIRRGKRL 56 (309)
T ss_pred HHHHHHHHHhCCeeEeeCCCCc
Confidence 35899999999999999 5554
No 74
>PRK15494 era GTPase Era; Provisional
Probab=25.61 E-value=74 Score=29.38 Aligned_cols=40 Identities=23% Similarity=0.282 Sum_probs=30.9
Q ss_pred eeeEEEEecCCCCCCCCceeeeeecCCcchHHHH--------HHHhCCeEEEe
Q 027518 141 VKRTIRVDIPVEKYPNFNFVGRLLGPRGNSLKRV--------EASTECRVLIR 185 (222)
Q Consensus 141 vK~~~ki~IPv~~~P~~NfvG~ilGPrG~tlk~l--------e~etgckI~Ir 185 (222)
++....|||.-+ .--|-|||-+|.++|+| |+-+||||...
T Consensus 271 ~~i~~~i~v~~~-----sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 271 VKINQVIVVSRE-----SYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred EEEEEEEEECCC-----CceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 445567777654 34589999999999976 88889998875
No 75
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=24.93 E-value=58 Score=28.62 Aligned_cols=23 Identities=26% Similarity=0.391 Sum_probs=19.9
Q ss_pred hHHHHHHHhCCeEEEecccCCCC
Q 027518 170 SLKRVEASTECRVLIRGRGSIKD 192 (222)
Q Consensus 170 tlk~le~etgckI~IrGkGS~kd 192 (222)
.+|+||++.|+++.+|..+-+.=
T Consensus 38 ~Ik~LE~~lg~~Lf~R~~~~v~L 60 (309)
T PRK11013 38 ELARFEKVIGLKLFERVRGRLHP 60 (309)
T ss_pred HHHHHHHHhCceeeeecCCCccc
Confidence 48999999999999998776663
No 76
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=24.87 E-value=62 Score=28.35 Aligned_cols=20 Identities=15% Similarity=0.285 Sum_probs=17.2
Q ss_pred hHHHHHHHhCCeEEEec-ccC
Q 027518 170 SLKRVEASTECRVLIRG-RGS 189 (222)
Q Consensus 170 tlk~le~etgckI~IrG-kGS 189 (222)
.+|+||++.||++.+|. +|-
T Consensus 36 ~I~~LE~~lg~~LF~R~~~~~ 56 (309)
T PRK12682 36 AIIELEEELGIEIFIRHGKRL 56 (309)
T ss_pred HHHHHHHHhCCeeEEECCCCc
Confidence 58999999999999995 554
No 77
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=23.89 E-value=62 Score=27.71 Aligned_cols=23 Identities=13% Similarity=0.368 Sum_probs=18.5
Q ss_pred chHHHHHHHhCCeEEEecccCCC
Q 027518 169 NSLKRVEASTECRVLIRGRGSIK 191 (222)
Q Consensus 169 ~tlk~le~etgckI~IrGkGS~k 191 (222)
..+|+||++.|+++.+|...-+.
T Consensus 34 ~~i~~LE~~lg~~Lf~R~~~~~~ 56 (296)
T PRK11242 34 QQIRQLEESLGVQLFDRSGRTVR 56 (296)
T ss_pred HHHHHHHHHhCCeeEeEcCCcee
Confidence 46899999999999999644333
No 78
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=22.92 E-value=74 Score=28.06 Aligned_cols=23 Identities=13% Similarity=0.163 Sum_probs=19.1
Q ss_pred chHHHHHHHhCCeEEEecccCCC
Q 027518 169 NSLKRVEASTECRVLIRGRGSIK 191 (222)
Q Consensus 169 ~tlk~le~etgckI~IrGkGS~k 191 (222)
..+++||++.||++.+|....+.
T Consensus 41 ~~I~~LE~~lg~~LF~R~~r~~~ 63 (319)
T PRK10216 41 KSLAKLRAWFDDPLFVNTPLGLS 63 (319)
T ss_pred HHHHHHHHHhCCceEEecCCCcc
Confidence 35899999999999999655555
No 79
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=22.73 E-value=69 Score=27.58 Aligned_cols=24 Identities=17% Similarity=0.339 Sum_probs=20.0
Q ss_pred chHHHHHHHhCCeEEEecccCCCC
Q 027518 169 NSLKRVEASTECRVLIRGRGSIKD 192 (222)
Q Consensus 169 ~tlk~le~etgckI~IrGkGS~kd 192 (222)
..+|+||++.||++.+|-.+.+.=
T Consensus 34 r~i~~LE~~lg~~Lf~R~~~~~~l 57 (296)
T PRK09906 34 QQIKDLENCVGVPLLVRDKRKVAL 57 (296)
T ss_pred HHHHHHHHHhCCeeeeeCCCcceE
Confidence 458999999999999997766653
No 80
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=22.69 E-value=60 Score=31.32 Aligned_cols=38 Identities=18% Similarity=0.308 Sum_probs=31.1
Q ss_pred EEecCCCCCCCCceeeeeecCCcchHHHHHHHh-CCeEEE
Q 027518 146 RVDIPVEKYPNFNFVGRLLGPRGNSLKRVEAST-ECRVLI 184 (222)
Q Consensus 146 ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~et-gckI~I 184 (222)
||-|=- .-|+++-||-.+|++|..++.+.++. |=+|-|
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 555532 44899999999999999999999999 777765
No 81
>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=22.57 E-value=78 Score=27.30 Aligned_cols=24 Identities=21% Similarity=0.300 Sum_probs=20.5
Q ss_pred hHHHHHHHhCCeEEEecccCCCCc
Q 027518 170 SLKRVEASTECRVLIRGRGSIKDP 193 (222)
Q Consensus 170 tlk~le~etgckI~IrGkGS~kd~ 193 (222)
.+|+||++.||++.+|..+-++=.
T Consensus 37 ~I~~LE~~lg~~LF~R~~~~~~lT 60 (300)
T TIGR02424 37 TLRELEEILGTPLFERDRRGIRLT 60 (300)
T ss_pred HHHHHHHHhCCeEEEEcCCCcccc
Confidence 489999999999999987777643
No 82
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=22.22 E-value=71 Score=28.22 Aligned_cols=22 Identities=23% Similarity=0.359 Sum_probs=18.6
Q ss_pred hHHHHHHHhCCeEEEecccCCC
Q 027518 170 SLKRVEASTECRVLIRGRGSIK 191 (222)
Q Consensus 170 tlk~le~etgckI~IrGkGS~k 191 (222)
.+|+||++.||++.+|.+..+.
T Consensus 36 ~I~~LE~~lg~~Lf~R~~r~~~ 57 (308)
T PRK10094 36 RIKLLEENTGVALFFRTTRSVT 57 (308)
T ss_pred HHHHHHHHhCCEEEeeCCCcee
Confidence 5899999999999999655554
No 83
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=21.70 E-value=56 Score=27.91 Aligned_cols=22 Identities=14% Similarity=0.163 Sum_probs=18.6
Q ss_pred hHHHHHHHhCCeEEEecccCCC
Q 027518 170 SLKRVEASTECRVLIRGRGSIK 191 (222)
Q Consensus 170 tlk~le~etgckI~IrGkGS~k 191 (222)
.+|+||++.||++.+|+..-+.
T Consensus 37 ~I~~LE~~lg~~Lf~R~~r~~~ 58 (290)
T PRK10837 37 ALTDLEGQLGVQLFDRVGKRLV 58 (290)
T ss_pred HHHHHHHHhCCccEeecCCeEE
Confidence 4899999999999999755555
No 84
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=21.62 E-value=47 Score=27.37 Aligned_cols=26 Identities=19% Similarity=0.285 Sum_probs=22.2
Q ss_pred eeeeeecCCcchHHHHHHHhCCeEEE
Q 027518 159 FVGRLLGPRGNSLKRVEASTECRVLI 184 (222)
Q Consensus 159 fvG~ilGPrG~tlk~le~etgckI~I 184 (222)
-.|+.+|.+|.+++.++.-+|-.+-|
T Consensus 109 d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 109 DKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred ccchhhCCCCHHHHHHHHHhCCccCC
Confidence 36899999999999999999876644
No 85
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=21.46 E-value=62 Score=28.01 Aligned_cols=22 Identities=18% Similarity=0.218 Sum_probs=18.5
Q ss_pred hHHHHHHHhCCeEEEecccCCC
Q 027518 170 SLKRVEASTECRVLIRGRGSIK 191 (222)
Q Consensus 170 tlk~le~etgckI~IrGkGS~k 191 (222)
.+|+||++.||++.+|.+.-++
T Consensus 40 ~i~~LE~~lg~~Lf~R~~r~l~ 61 (297)
T PRK11139 40 QIKALEDFLGLKLFRRRNRSLL 61 (297)
T ss_pred HHHHHHHHhCchheEecCCcee
Confidence 5899999999999999655554
No 86
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=20.83 E-value=1e+02 Score=29.80 Aligned_cols=45 Identities=13% Similarity=0.241 Sum_probs=36.8
Q ss_pred EEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecccCCCCchH
Q 027518 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIKDPAR 195 (222)
Q Consensus 145 ~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkGS~kd~~k 195 (222)
..|+||-++ .++.||-+|.+++.--.-||++|-|+.-+|..+..-
T Consensus 310 ~~V~V~~~q------lslAIGk~GqNvrLA~~LtGwkIDI~s~~~~~~~~~ 354 (374)
T PRK12328 310 AIVTLLSDQ------KSKAIGKNGINIRLASMLTGYEIELNEIGSKENASN 354 (374)
T ss_pred EEEEEChHH------hhhhhcCCChhHHHHHHHhCCEEEEEECCCCccccc
Confidence 456666554 368999999999999999999999999998765443
No 87
>PRK13764 ATPase; Provisional
Probab=20.65 E-value=78 Score=32.25 Aligned_cols=41 Identities=17% Similarity=0.304 Sum_probs=33.8
Q ss_pred EEEecCCCCCCCCceeeeeecCCcchHHHHHHHhCCeEEEecccCCC
Q 027518 145 IRVDIPVEKYPNFNFVGRLLGPRGNSLKRVEASTECRVLIRGRGSIK 191 (222)
Q Consensus 145 ~ki~IPv~~~P~~NfvG~ilGPrG~tlk~le~etgckI~IrGkGS~k 191 (222)
..|+||-+.. +.++|-+|..+++||...|-+|-||-...-.
T Consensus 483 ~~v~~~~~~~------~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 483 AVVYVPEKDI------PKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred EEEEEChhhh------hHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 4688887654 5788999999999999999999999765543
No 88
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=20.46 E-value=93 Score=27.98 Aligned_cols=22 Identities=23% Similarity=0.362 Sum_probs=19.5
Q ss_pred hHHHHHHHhCCeEEEecccCCC
Q 027518 170 SLKRVEASTECRVLIRGRGSIK 191 (222)
Q Consensus 170 tlk~le~etgckI~IrGkGS~k 191 (222)
.+|+||++.||++.+|..+.++
T Consensus 36 ~I~~LE~~lG~~LF~R~~r~v~ 57 (327)
T PRK12680 36 QLKQLEDELGFLLFVRKGRSLE 57 (327)
T ss_pred HHHHHHHHhCCeEEEECCCcCC
Confidence 4899999999999999877774
Done!