Query 030537
Match_columns 175
No_of_seqs 131 out of 418
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 15:14:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030537.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030537hhsearch_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 8.6E-51 1.9E-55 346.4 14.3 154 17-174 83-241 (259)
2 cd02395 SF1_like-KH Splicing f 100.0 2E-42 4.4E-47 266.7 13.2 116 27-146 1-120 (120)
3 KOG0119 Splicing factor 1/bran 100.0 6.8E-42 1.5E-46 311.2 11.6 143 15-164 128-278 (554)
4 COG5176 MSL5 Splicing factor ( 100.0 6.6E-31 1.4E-35 219.8 9.0 131 14-148 137-269 (269)
5 cd02393 PNPase_KH Polynucleoti 98.9 3.6E-09 7.7E-14 72.3 7.1 59 27-117 3-61 (61)
6 cd00105 KH-I K homology RNA-bi 98.7 5.7E-08 1.2E-12 64.7 7.1 62 28-116 2-63 (64)
7 PF00013 KH_1: KH domain syndr 98.7 7.1E-09 1.5E-13 69.3 2.5 60 27-116 1-60 (60)
8 cd02394 vigilin_like_KH K homo 98.5 1.2E-07 2.7E-12 63.7 4.4 60 28-116 2-61 (62)
9 smart00322 KH K homology RNA-b 98.5 5E-07 1.1E-11 59.1 7.1 66 26-120 3-68 (69)
10 KOG1960 Predicted RNA-binding 98.5 6E-08 1.3E-12 88.4 2.8 91 23-124 207-297 (531)
11 cd02396 PCBP_like_KH K homolog 98.5 5.5E-07 1.2E-11 61.6 6.1 63 28-116 2-64 (65)
12 PF13014 KH_3: KH domain 98.4 2.5E-07 5.4E-12 58.6 2.9 28 43-70 1-28 (43)
13 TIGR02696 pppGpp_PNP guanosine 98.2 5.4E-06 1.2E-10 80.3 7.8 71 20-122 572-642 (719)
14 PRK13763 putative RNA-processi 98.1 5.5E-06 1.2E-10 67.7 5.1 65 27-122 4-71 (180)
15 TIGR03665 arCOG04150 arCOG0415 98.0 6.3E-06 1.4E-10 66.8 4.5 53 43-122 99-151 (172)
16 TIGR03665 arCOG04150 arCOG0415 98.0 6.4E-06 1.4E-10 66.8 3.5 58 41-122 6-65 (172)
17 TIGR03591 polynuc_phos polyrib 97.9 1.4E-05 3E-10 77.1 6.0 70 21-122 546-615 (684)
18 PRK13763 putative RNA-processi 97.9 1.7E-05 3.7E-10 64.8 5.0 53 43-122 105-157 (180)
19 PLN00207 polyribonucleotide nu 97.6 3.8E-05 8.2E-10 76.0 3.6 71 21-123 680-751 (891)
20 KOG1676 K-homology type RNA bi 97.4 0.00032 7E-09 66.6 6.6 70 27-123 231-301 (600)
21 COG1094 Predicted RNA-binding 97.4 0.00034 7.5E-09 58.4 6.0 55 43-124 112-166 (194)
22 PRK04163 exosome complex RNA-b 97.3 0.00052 1.1E-08 58.2 5.7 58 41-123 153-210 (235)
23 KOG1676 K-homology type RNA bi 97.2 0.00083 1.8E-08 63.9 6.7 75 23-122 136-210 (600)
24 PRK11824 polynucleotide phosph 97.2 0.00029 6.3E-09 68.1 3.3 57 41-122 562-618 (693)
25 KOG2874 rRNA processing protei 96.8 0.0027 5.9E-08 56.2 5.9 68 45-139 161-228 (356)
26 KOG2193 IGF-II mRNA-binding pr 96.6 0.00065 1.4E-08 63.0 0.5 38 31-69 279-316 (584)
27 KOG2191 RNA-binding protein NO 96.5 0.0056 1.2E-07 55.3 5.6 57 26-100 39-95 (402)
28 KOG2191 RNA-binding protein NO 96.4 0.016 3.5E-07 52.4 8.2 37 26-69 132-168 (402)
29 KOG2193 IGF-II mRNA-binding pr 96.4 0.004 8.7E-08 57.9 4.4 63 41-122 207-269 (584)
30 KOG2190 PolyC-binding proteins 96.2 0.012 2.6E-07 55.1 6.7 71 25-121 137-207 (485)
31 COG1185 Pnp Polyribonucleotide 96.1 0.0074 1.6E-07 58.5 4.9 66 25-122 551-616 (692)
32 KOG2814 Transcription coactiva 95.6 0.014 2.9E-07 52.6 4.0 61 41-117 65-127 (345)
33 KOG1960 Predicted RNA-binding 94.8 0.01 2.2E-07 54.9 0.7 73 46-127 308-380 (531)
34 PRK00106 hypothetical protein; 94.7 0.054 1.2E-06 51.5 5.4 65 28-122 227-291 (535)
35 TIGR03319 YmdA_YtgF conserved 94.4 0.062 1.3E-06 50.6 4.9 64 28-121 206-269 (514)
36 PRK12704 phosphodiesterase; Pr 94.4 0.082 1.8E-06 49.9 5.7 51 28-103 212-262 (520)
37 cd02134 NusA_KH NusA_K homolog 94.1 0.11 2.4E-06 35.2 4.3 36 26-68 25-60 (61)
38 KOG0336 ATP-dependent RNA heli 93.0 0.2 4.3E-06 47.1 5.5 29 41-69 55-83 (629)
39 KOG2190 PolyC-binding proteins 92.8 0.14 3.1E-06 48.1 4.4 42 23-71 335-376 (485)
40 KOG1067 Predicted RNA-binding 89.3 0.63 1.4E-05 45.1 5.0 71 42-145 606-676 (760)
41 COG1097 RRP4 RNA-binding prote 89.3 1.2 2.6E-05 38.5 6.3 41 41-101 154-194 (239)
42 PF13184 KH_5: NusA-like KH do 87.5 0.3 6.5E-06 34.2 1.3 31 38-69 14-45 (69)
43 KOG2192 PolyC-binding hnRNP-K 87.0 3.8 8.2E-05 36.7 8.0 45 17-70 308-352 (390)
44 COG1094 Predicted RNA-binding 86.5 3.2 6.9E-05 34.9 7.0 66 27-123 9-78 (194)
45 KOG2113 Predicted RNA binding 86.5 0.6 1.3E-05 42.3 2.9 38 24-68 24-61 (394)
46 PRK12705 hypothetical protein; 85.5 0.74 1.6E-05 43.7 3.1 29 41-69 207-235 (508)
47 cd02409 KH-II KH-II (K homolo 85.4 0.79 1.7E-05 29.8 2.4 23 44-66 36-58 (68)
48 PRK08406 transcription elongat 79.6 1.4 2.9E-05 34.9 2.1 29 42-70 41-69 (140)
49 cd02414 jag_KH jag_K homology 78.9 1.3 2.8E-05 31.1 1.6 25 44-68 35-59 (77)
50 KOG0334 RNA helicase [RNA proc 71.9 3.1 6.8E-05 42.5 2.8 77 30-121 900-976 (997)
51 KOG2208 Vigilin [Lipid transpo 71.4 3.1 6.7E-05 41.3 2.6 39 24-69 707-745 (753)
52 KOG2192 PolyC-binding hnRNP-K 71.2 8.2 0.00018 34.6 4.9 41 44-101 59-99 (390)
53 PRK12329 nusA transcription el 71.0 5.6 0.00012 37.4 4.0 46 23-70 260-306 (449)
54 PRK12327 nusA transcription el 66.5 8.8 0.00019 34.9 4.3 41 28-70 233-274 (362)
55 TIGR01953 NusA transcription t 64.8 12 0.00025 33.8 4.7 41 28-70 231-272 (341)
56 PRK02821 hypothetical protein; 63.1 4.2 9.2E-05 29.2 1.3 23 42-64 40-62 (77)
57 TIGR01952 nusA_arch NusA famil 62.9 5.9 0.00013 31.5 2.2 29 42-70 42-70 (141)
58 PRK00468 hypothetical protein; 62.5 4.4 9.5E-05 28.9 1.3 19 44-62 41-59 (75)
59 PF13083 KH_4: KH domain; PDB: 61.8 1.2 2.6E-05 30.7 -1.8 20 44-63 40-59 (73)
60 COG1702 PhoH Phosphate starvat 60.2 18 0.00039 33.0 5.1 29 42-70 24-52 (348)
61 TIGR00436 era GTP-binding prot 59.6 23 0.00049 29.9 5.3 41 23-69 218-266 (270)
62 KOG4165 Gamma-glutamyl phospha 59.2 13 0.00029 34.2 4.0 62 42-122 190-260 (433)
63 PRK01064 hypothetical protein; 58.3 6.9 0.00015 28.2 1.7 20 44-63 41-60 (78)
64 PRK06418 transcription elongat 55.8 8.8 0.00019 31.4 2.1 27 45-71 72-98 (166)
65 COG1837 Predicted RNA-binding 53.4 7.8 0.00017 27.9 1.3 18 44-61 41-58 (76)
66 COG0195 NusA Transcription elo 53.2 10 0.00022 31.6 2.1 31 41-71 84-114 (190)
67 PRK00089 era GTPase Era; Revie 52.5 15 0.00032 31.1 3.1 41 23-69 223-271 (292)
68 PF15290 Syntaphilin: Golgi-lo 51.2 17 0.00037 32.5 3.3 67 95-162 105-195 (305)
69 PRK12328 nusA transcription el 51.0 15 0.00032 33.8 3.0 40 28-69 239-279 (374)
70 COG1855 ATPase (PilT family) [ 50.9 19 0.0004 34.7 3.7 42 28-76 488-529 (604)
71 PRK08406 transcription elongat 49.4 7.5 0.00016 30.7 0.7 26 43-68 109-134 (140)
72 KOG2113 Predicted RNA binding 49.1 8.9 0.00019 34.9 1.2 31 41-71 123-153 (394)
73 COG5082 AIR1 Arginine methyltr 48.9 5.9 0.00013 33.3 0.1 58 90-162 16-77 (190)
74 PRK15494 era GTPase Era; Provi 48.5 36 0.00078 30.1 5.0 41 23-69 270-318 (339)
75 PRK09202 nusA transcription el 47.2 21 0.00045 33.6 3.4 40 28-69 233-273 (470)
76 KOG3273 Predicted RNA-binding 44.6 13 0.00029 31.9 1.6 28 43-70 179-206 (252)
77 PTZ00225 60S ribosomal protein 42.9 65 0.0014 27.2 5.4 61 44-120 117-191 (214)
78 PRK05424 rplA 50S ribosomal pr 42.8 72 0.0016 27.1 5.8 64 41-120 123-199 (230)
79 PF00126 HTH_1: Bacterial regu 41.6 21 0.00045 23.4 1.9 19 54-72 33-51 (60)
80 TIGR01169 rplA_bact ribosomal 39.1 53 0.0012 27.8 4.4 12 41-52 122-133 (227)
81 PF14611 SLS: Mitochondrial in 38.7 88 0.0019 25.4 5.5 83 43-150 36-133 (210)
82 KOG2208 Vigilin [Lipid transpo 36.7 43 0.00093 33.4 3.9 31 43-73 357-387 (753)
83 PRK13764 ATPase; Provisional 36.2 27 0.00059 33.9 2.4 39 28-73 483-521 (602)
84 cd02410 archeal_CPSF_KH The ar 35.4 42 0.0009 27.1 3.0 26 44-69 87-112 (145)
85 PRK12328 nusA transcription el 35.4 53 0.0011 30.3 4.0 41 28-75 310-350 (374)
86 PRK13348 chromosome replicatio 34.4 28 0.00062 28.8 2.0 22 53-74 35-56 (294)
87 PRK09986 DNA-binding transcrip 34.0 54 0.0012 26.9 3.6 20 53-72 40-59 (294)
88 TIGR01170 rplA_mito ribosomal 33.3 7.9 0.00017 30.7 -1.4 18 35-53 101-118 (141)
89 KOG4797 Transcriptional regula 28.2 19 0.00041 28.0 -0.1 43 107-150 48-91 (123)
90 COG0484 DnaJ DnaJ-class molecu 28.0 80 0.0017 29.1 3.9 36 60-103 300-335 (371)
91 PF02559 CarD_CdnL_TRCF: CarD- 27.9 51 0.0011 23.6 2.2 26 29-59 43-68 (98)
92 PF07650 KH_2: KH domain syndr 27.8 8.7 0.00019 26.5 -1.8 25 42-66 34-58 (78)
93 KOG1423 Ras-like GTPase ERA [C 27.7 1.4E+02 0.003 27.6 5.2 41 23-69 325-373 (379)
94 TIGR03298 argP transcriptional 26.9 37 0.0008 28.1 1.4 22 54-75 35-56 (292)
95 cd02412 30S_S3_KH K homology R 26.8 32 0.00069 25.7 0.9 22 43-64 71-92 (109)
96 KOG2279 Kinase anchor protein 26.5 56 0.0012 31.8 2.7 41 25-72 67-107 (608)
97 PRK03635 chromosome replicatio 26.3 49 0.0011 27.5 2.1 21 54-74 36-56 (294)
98 PRK11074 putative DNA-binding 24.7 60 0.0013 27.1 2.4 18 53-70 35-52 (300)
99 PRK03601 transcriptional regul 24.6 58 0.0013 27.0 2.2 17 54-70 35-51 (275)
100 KOG2279 Kinase anchor protein 24.4 55 0.0012 31.9 2.2 42 27-70 292-333 (608)
101 COG1847 Jag Predicted RNA-bind 24.1 66 0.0014 27.4 2.5 60 44-121 102-162 (208)
102 COG3967 DltE Short-chain dehyd 24.0 84 0.0018 27.4 3.1 72 60-140 2-73 (245)
103 CHL00129 rpl1 ribosomal protei 23.8 26 0.00056 29.9 -0.0 10 44-53 126-135 (229)
104 PF07582 AP_endonuc_2_N: AP en 23.6 1.1E+02 0.0025 20.5 3.1 32 93-124 17-48 (55)
105 PRK12683 transcriptional regul 23.0 67 0.0014 27.2 2.3 19 54-72 36-55 (309)
106 PRK12684 transcriptional regul 22.8 69 0.0015 27.1 2.4 19 54-72 36-55 (313)
107 PF00381 PTS-HPr: PTS HPr comp 22.7 83 0.0018 21.9 2.4 58 55-121 22-82 (84)
108 PRK09791 putative DNA-binding 22.7 76 0.0017 26.4 2.6 21 54-74 39-59 (302)
109 PRK12682 transcriptional regul 22.1 74 0.0016 26.7 2.4 19 54-72 36-55 (309)
110 COG0080 RplK Ribosomal protein 21.2 2.4E+02 0.0052 22.7 5.0 98 25-142 5-111 (141)
111 COG0081 RplA Ribosomal protein 21.1 29 0.00062 30.0 -0.3 72 34-122 119-203 (228)
112 COG1159 Era GTPase [General fu 20.6 2E+02 0.0044 25.8 4.9 43 21-69 224-274 (298)
113 PRK10246 exonuclease subunit S 20.1 1.1E+02 0.0023 31.5 3.5 25 134-158 489-514 (1047)
No 1
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=100.00 E-value=8.6e-51 Score=346.39 Aligned_cols=154 Identities=52% Similarity=0.715 Sum_probs=141.0
Q ss_pred CCCCCCceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccC----CCCCCCCCCCc
Q 030537 17 GIPTAPVVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEG----KIRYEHLNEPL 92 (175)
Q Consensus 17 ~~~~~~~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~----~p~~e~~~epL 92 (175)
..+++..+|++.||+|||++||+ ||||||||||||+|+|+||++|||||+||||||+||..+|+ +|+|+|+++||
T Consensus 83 ~~~~~~~vk~~~Kv~vPv~~yP~-fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epL 161 (259)
T KOG1588|consen 83 DVYSGKPVKLTEKVLVPVKEYPK-FNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPL 161 (259)
T ss_pred cCccCCceeEEEEEEeccCCCCC-CccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCc
Confidence 58899999999999999999999 99999999999999999999999999999999999999987 89999999999
Q ss_pred EEEEEeeCchhhHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHhcCc-cCCCCCCCCCCCCCCCcccCccccccc
Q 030537 93 HVLGEAEFPEDIINSRLDHAVAILENLLKPVDESLDHYKKQQLREFATLNGT-LREESPSMSPSMSPSMWPFNSAGMKRA 171 (175)
Q Consensus 93 HV~Isa~~~~~~~~~~l~~A~e~Ie~lL~p~~e~~de~K~~QL~eLA~lNGt-~r~~~~~~~g~~~~~~~p~~~~~~~~~ 171 (175)
||+|++++++++|+.+|++|++.|++||+|++++.| |++||+|||++||| +++.+...+|.. -|+-||+..+++|.
T Consensus 162 HVlIe~~~p~~ea~~rl~~AleeI~klL~P~~e~~d--k~~QL~ELa~lngt~~~~~~~~~~g~~-~~~~~~~~~~~~r~ 238 (259)
T KOG1588|consen 162 HVLIETEAPPAEAYARLAYALEEIKKLLVPDHEDED--KREQLRELAILNGTYLRSESRKPSGGN-GRGVPGNSAGGKRG 238 (259)
T ss_pred EEEEEEeCCHHHHHHHHHHHHHHHHHhcCCCCCCch--HHHHHHHHhhcCCccccccccccCCCC-CcCCCCCCCCcccc
Confidence 999999999999999999999999999999988777 99999999999999 555555555543 35568999999888
Q ss_pred ccc
Q 030537 172 KTR 174 (175)
Q Consensus 172 ~~~ 174 (175)
++.
T Consensus 239 ~~~ 241 (259)
T KOG1588|consen 239 KTG 241 (259)
T ss_pred cCC
Confidence 763
No 2
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=100.00 E-value=2e-42 Score=266.65 Aligned_cols=116 Identities=53% Similarity=0.805 Sum_probs=108.3
Q ss_pred EEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccC---CCCCCCCCCCcEEEEEeeCchh
Q 030537 27 VIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEG---KIRYEHLNEPLHVLGEAEFPED 103 (175)
Q Consensus 27 ~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~---~p~~e~~~epLHV~Isa~~~~~ 103 (175)
++|||||+++||+ |||+|+||||+|+|+|+||++|||+|.|||+||+++++++. .|.++|++|||||+|+++++
T Consensus 1 ~~ki~iP~~~~P~-~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~-- 77 (120)
T cd02395 1 TEKVYIPVKQYPK-YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETP-- 77 (120)
T ss_pred CCEEEcCcccCCC-CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCc--
Confidence 4799999999999 99999999999999999999999999999999999998876 37889999999999999995
Q ss_pred hHHHHHHHHHHHHHhccCCCCcc-hHHHHHHHHHHHHHhcCccC
Q 030537 104 IINSRLDHAVAILENLLKPVDES-LDHYKKQQLREFATLNGTLR 146 (175)
Q Consensus 104 ~~~~~l~~A~e~Ie~lL~p~~e~-~de~K~~QL~eLA~lNGt~r 146 (175)
+.+++++|+++|+.||.++.++ .|++|++||+|||++|||||
T Consensus 78 -~~e~~~~A~~~I~~ll~~~~~~~~~~~k~~ql~~la~~nGt~~ 120 (120)
T cd02395 78 -PEEALAKAVEAIEELLKPAIEGGNDELKREQLRELALLNGTYR 120 (120)
T ss_pred -HHHHHHHHHHHHHHHhccCCCccchHHHHHHHHHHHHhcccCC
Confidence 2358999999999999998777 99999999999999999996
No 3
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=100.00 E-value=6.8e-42 Score=311.22 Aligned_cols=143 Identities=38% Similarity=0.610 Sum_probs=128.7
Q ss_pred CCCCCCCCceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccC-CCCCC-CCCCCc
Q 030537 15 LPGIPTAPVVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEG-KIRYE-HLNEPL 92 (175)
Q Consensus 15 ~p~~~~~~~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~-~p~~e-~~~epL 92 (175)
.|+++..+. ++++||||||++||+ |||||+||||||+|+|+||++|||||.||||||+|+++... +.++. ..+|||
T Consensus 128 pP~DYk~p~-~~~~Kv~IPvke~Pd-~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epL 205 (554)
T KOG0119|consen 128 PPADYKPPA-KLHDKVYIPVKEFPD-INFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPL 205 (554)
T ss_pred CCcccCccc-ccccceecchhhcCC-cceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccce
Confidence 578888888 889999999999999 99999999999999999999999999999999999997222 34433 579999
Q ss_pred EEEEEeeCchhhHHHHHHHHHHHHHhccC---CCCcchHHHHHHHHHHHHHhcCccCCCC---CCCCCCCCCCCcccC
Q 030537 93 HVLGEAEFPEDIINSRLDHAVAILENLLK---PVDESLDHYKKQQLREFATLNGTLREES---PSMSPSMSPSMWPFN 164 (175)
Q Consensus 93 HV~Isa~~~~~~~~~~l~~A~e~Ie~lL~---p~~e~~de~K~~QL~eLA~lNGt~r~~~---~~~~g~~~~~~~p~~ 164 (175)
||+|+|++++ +|++|+++|+.||. .++|+++++|+.||+|||.+|||+|++. |.+||+++|+.|-|-
T Consensus 206 H~~Isadt~e-----ki~~Ai~vienli~~av~~~e~~n~l~~~Qlrela~lNgt~r~~d~~~c~~cg~~~H~q~~cp 278 (554)
T KOG0119|consen 206 HCLISADTQE-----KIKKAIAVIENLIQSAVSVPEGQNDLKRLQLRELARLNGTLRDDDNRACRNCGSTGHKQYDCP 278 (554)
T ss_pred eEEEecchHH-----HHHHHHHHHHHHHHhhccCccccccccHHHHHHHHHhCCCCCccccccccccCCCccccccCC
Confidence 9999999975 89999999999997 5789999999999999999999999887 589999999988754
No 4
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.97 E-value=6.6e-31 Score=219.79 Aligned_cols=131 Identities=33% Similarity=0.513 Sum_probs=104.1
Q ss_pred CCCCCCCCCceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCC--CCCCCCCCC
Q 030537 14 GLPGIPTAPVVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGK--IRYEHLNEP 91 (175)
Q Consensus 14 ~~p~~~~~~~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~--p~~e~~~ep 91 (175)
-.|.++..|. |.+.||||||++||+ .||||+||||||+|+|+||+.|+|||.|||+||+|+++-..+ ++.....++
T Consensus 137 v~p~dy~rps-k~q~KiYIPV~eyPe-~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~ 214 (269)
T COG5176 137 VLPNDYIRPS-KYQNKIYIPVQEYPE-SNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAV 214 (269)
T ss_pred cCCccccCcc-cccceEEeehhhCcc-cceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHh
Confidence 3456666664 568999999999999 999999999999999999999999999999999998865432 233357899
Q ss_pred cEEEEEeeCchhhHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHhcCccCCC
Q 030537 92 LHVLGEAEFPEDIINSRLDHAVAILENLLKPVDESLDHYKKQQLREFATLNGTLREE 148 (175)
Q Consensus 92 LHV~Isa~~~~~~~~~~l~~A~e~Ie~lL~p~~e~~de~K~~QL~eLA~lNGt~r~~ 148 (175)
||++|+++....++. .+......|.+... .+++++++|+.||++||.+|||+|++
T Consensus 215 lhcLI~adsedki~~-~ik~~~n~I~~a~~-~PeGqnDlkR~qlr~la~lngtlr~d 269 (269)
T COG5176 215 LHCLIEADSEDKICR-LIKSQLNAIREARR-NPEGQNDLKRFQLRWLAHLNGTLRAD 269 (269)
T ss_pred HHHHhhcchhhhHHH-HHHHHHHHHHHHhc-CCcccchHHHHHHHHHHHhcceecCC
Confidence 999999988653332 22333334444444 45889999999999999999999975
No 5
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.94 E-value=3.6e-09 Score=72.29 Aligned_cols=59 Identities=20% Similarity=0.356 Sum_probs=47.9
Q ss_pred EEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHH
Q 030537 27 VIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIIN 106 (175)
Q Consensus 27 ~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~ 106 (175)
.+.+.|| -+++|+|||++|+|+|+||++|||+|.|--.| .|.|++.+++
T Consensus 3 ~~~i~Ip-------~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g--------------------~v~I~G~~~~---- 51 (61)
T cd02393 3 IETMKIP-------PDKIRDVIGPGGKTIKKIIEETGVKIDIEDDG--------------------TVYIAASDKE---- 51 (61)
T ss_pred EEEEEeC-------hhheeeeECCCchHHHHHHHHHCCEEEeCCCC--------------------EEEEEeCCHH----
Confidence 4567777 47899999999999999999999999986311 5899997654
Q ss_pred HHHHHHHHHHH
Q 030537 107 SRLDHAVAILE 117 (175)
Q Consensus 107 ~~l~~A~e~Ie 117 (175)
.++.|.++|+
T Consensus 52 -~v~~A~~~I~ 61 (61)
T cd02393 52 -AAEKAKKMIE 61 (61)
T ss_pred -HHHHHHHHhC
Confidence 6888888874
No 6
>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=98.72 E-value=5.7e-08 Score=64.71 Aligned_cols=62 Identities=26% Similarity=0.339 Sum_probs=47.8
Q ss_pred EEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHH
Q 030537 28 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINS 107 (175)
Q Consensus 28 ~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~ 107 (175)
.+|.|| -+++|+||||+|+++++|+++|||+|.|...++ ...+-.|.|.+.. .
T Consensus 2 ~~i~ip-------~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~--------------~~~~~~v~i~G~~------~ 54 (64)
T cd00105 2 ERVLVP-------SSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS--------------GSEERIVTITGTP------E 54 (64)
T ss_pred EEEEEc-------hhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC--------------CCCceEEEEEcCH------H
Confidence 467887 488999999999999999999999999996442 1334467887762 2
Q ss_pred HHHHHHHHH
Q 030537 108 RLDHAVAIL 116 (175)
Q Consensus 108 ~l~~A~e~I 116 (175)
.+..|..+|
T Consensus 55 ~v~~a~~~i 63 (64)
T cd00105 55 AVEKAKELI 63 (64)
T ss_pred HHHHHHHHh
Confidence 577777765
No 7
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=98.72 E-value=7.1e-09 Score=69.33 Aligned_cols=60 Identities=30% Similarity=0.504 Sum_probs=48.0
Q ss_pred EEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHH
Q 030537 27 VIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIIN 106 (175)
Q Consensus 27 ~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~ 106 (175)
+.+|.|| ..++|+|||++|.++|+|+++|||+|.|...+ +.-.|.|++ +++
T Consensus 1 T~~i~vp-------~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~-----------------~~~~v~I~G-~~~---- 51 (60)
T PF00013_consen 1 TERIEVP-------SSLVGRIIGKKGSNIKEIEEETGVKIQIPDDD-----------------ERDIVTISG-SPE---- 51 (60)
T ss_dssp EEEEEEE-------HHHHHHHHTGGGHHHHHHHHHHTSEEEEESTT-----------------EEEEEEEEE-SHH----
T ss_pred CEEEEEC-------HHHcCEEECCCCCcHHHhhhhcCeEEEEcCCC-----------------CcEEEEEEe-CHH----
Confidence 4678888 68999999999999999999999999997431 233788888 543
Q ss_pred HHHHHHHHHH
Q 030537 107 SRLDHAVAIL 116 (175)
Q Consensus 107 ~~l~~A~e~I 116 (175)
.+++|.++|
T Consensus 52 -~v~~A~~~I 60 (60)
T PF00013_consen 52 -QVEKAKKMI 60 (60)
T ss_dssp -HHHHHHHHH
T ss_pred -HHHHHHhhC
Confidence 678888775
No 8
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.53 E-value=1.2e-07 Score=63.66 Aligned_cols=60 Identities=10% Similarity=0.213 Sum_probs=45.7
Q ss_pred EEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHH
Q 030537 28 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINS 107 (175)
Q Consensus 28 ~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~ 107 (175)
.+|.|| -.++|.|||++|+++++|+++|||+|.|-... +..=.|.|++.. +
T Consensus 2 ~~i~Vp-------~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~----------------~~~~~v~I~G~~------~ 52 (62)
T cd02394 2 EEVEIP-------KKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG----------------SKSDTITITGPK------E 52 (62)
T ss_pred eEEEeC-------HHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC----------------CCCCEEEEEcCH------H
Confidence 456676 36788999999999999999999999998544 112267888762 2
Q ss_pred HHHHHHHHH
Q 030537 108 RLDHAVAIL 116 (175)
Q Consensus 108 ~l~~A~e~I 116 (175)
.+..|+++|
T Consensus 53 ~v~~A~~~i 61 (62)
T cd02394 53 NVEKAKEEI 61 (62)
T ss_pred HHHHHHHHh
Confidence 677887776
No 9
>smart00322 KH K homology RNA-binding domain.
Probab=98.52 E-value=5e-07 Score=59.14 Aligned_cols=66 Identities=24% Similarity=0.332 Sum_probs=50.2
Q ss_pred EEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhH
Q 030537 26 RVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDII 105 (175)
Q Consensus 26 ~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~ 105 (175)
...+|.|| -+++|++||++|.+++.|++.|||+|.+...++ ..-.|.|.++.
T Consensus 3 ~~~~i~i~-------~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~----------------~~~~v~i~g~~----- 54 (69)
T smart00322 3 VTIEVLIP-------ADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS----------------EERVVEITGPP----- 54 (69)
T ss_pred eEEEEEEc-------chhcceeECCCchHHHHHHHHHCCEEEECCCCC----------------CccEEEEEcCH-----
Confidence 34667887 378899999999999999999999999986442 23367777662
Q ss_pred HHHHHHHHHHHHhcc
Q 030537 106 NSRLDHAVAILENLL 120 (175)
Q Consensus 106 ~~~l~~A~e~Ie~lL 120 (175)
..+..|.+.|.+.+
T Consensus 55 -~~v~~a~~~i~~~~ 68 (69)
T smart00322 55 -ENVEKAAELILEIL 68 (69)
T ss_pred -HHHHHHHHHHHHHh
Confidence 25677888777665
No 10
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=98.50 E-value=6e-08 Score=88.41 Aligned_cols=91 Identities=16% Similarity=-0.010 Sum_probs=78.8
Q ss_pred ceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCch
Q 030537 23 VVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPE 102 (175)
Q Consensus 23 ~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~ 102 (175)
-+++..|++|+++ .|. ||.-+..=||+..||..+|.+|+.++.||||+|+.- |...|.| ++|||+++|+..+.+
T Consensus 207 G~~Y~~k~~v~~~-~P~-~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~i---EP~~G~E-snEPMYI~i~h~~~~ 280 (531)
T KOG1960|consen 207 GRYYPNKALATDK-DPP-LYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRR---EPNEGNE-SNEPMYIFSTHGNGN 280 (531)
T ss_pred cccchhheecccC-Ccc-hhhhhhccCccchhhhhhhhhhhhhhhhcccccccc---Ccccccc-cCCceeEEeecCCch
Confidence 3467779999998 687 999999999999999999999999999999999764 3344544 899999999999876
Q ss_pred hhHHHHHHHHHHHHHhccCCCC
Q 030537 103 DIINSRLDHAVAILENLLKPVD 124 (175)
Q Consensus 103 ~~~~~~l~~A~e~Ie~lL~p~~ 124 (175)
.+.+|+.++..|+..+.
T Consensus 281 -----g~~~A~r~~~nl~~~v~ 297 (531)
T KOG1960|consen 281 -----GENGAPRRKWNLEEKVY 297 (531)
T ss_pred -----hhccchhHHHhHHHHHH
Confidence 57899999999998764
No 11
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=98.45 E-value=5.5e-07 Score=61.59 Aligned_cols=63 Identities=22% Similarity=0.290 Sum_probs=45.5
Q ss_pred EEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHH
Q 030537 28 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINS 107 (175)
Q Consensus 28 ~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~ 107 (175)
.++.|| -+.+|+|||.+|.++++|+++|||+|.|.-... + ..++- -|.|++.. .
T Consensus 2 ~r~~ip-------~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~---------~---~~~~r-~v~I~G~~------~ 55 (65)
T cd02396 2 LRLLVP-------SSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL---------P---GSTER-VVTISGKP------S 55 (65)
T ss_pred EEEEEC-------HHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC---------C---CCCce-EEEEEeCH------H
Confidence 467888 588999999999999999999999999963221 0 11222 36666552 2
Q ss_pred HHHHHHHHH
Q 030537 108 RLDHAVAIL 116 (175)
Q Consensus 108 ~l~~A~e~I 116 (175)
.+.+|.++|
T Consensus 56 ~v~~A~~~I 64 (65)
T cd02396 56 AVQKALLLI 64 (65)
T ss_pred HHHHHHHhh
Confidence 577888776
No 12
>PF13014 KH_3: KH domain
Probab=98.39 E-value=2.5e-07 Score=58.61 Aligned_cols=28 Identities=36% Similarity=0.652 Sum_probs=26.8
Q ss_pred eeEEEeCCCCchHHHHHhhhCceEEEec
Q 030537 43 FVGRILGPRGNSLKRVEAMTECTVFIRG 70 (175)
Q Consensus 43 fvGrIiGPrG~TlK~ie~eTgckI~IRG 70 (175)
|+|+|||++|+|+++|+++|||+|.|--
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 6899999999999999999999999985
No 13
>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=98.16 E-value=5.4e-06 Score=80.33 Aligned_cols=71 Identities=21% Similarity=0.459 Sum_probs=61.1
Q ss_pred CCCceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEee
Q 030537 20 TAPVVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAE 99 (175)
Q Consensus 20 ~~~~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~ 99 (175)
-++.......+.|| .+.+|.||||+|.|+|.|+++|||+|.|--.| +|.|.+.
T Consensus 572 ~s~~aP~~~~~~I~-------~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G--------------------~V~I~a~ 624 (719)
T TIGR02696 572 MSPYAPRIITVKIP-------VDKIGEVIGPKGKMINQIQDETGAEISIEDDG--------------------TVYIGAA 624 (719)
T ss_pred cccCCCeeEEEEeC-------hHHhhheeCCCcHhHHHHHHHHCCEEEEecCc--------------------EEEEEeC
Confidence 45555667888998 46799999999999999999999999998654 8899998
Q ss_pred CchhhHHHHHHHHHHHHHhccCC
Q 030537 100 FPEDIINSRLDHAVAILENLLKP 122 (175)
Q Consensus 100 ~~~~~~~~~l~~A~e~Ie~lL~p 122 (175)
+.+ ++++|+++|+.++.+
T Consensus 625 d~~-----~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 625 DGP-----SAEAARAMINAIANP 642 (719)
T ss_pred CHH-----HHHHHHHHHHHhhCc
Confidence 864 799999999999984
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.07 E-value=5.5e-06 Score=67.70 Aligned_cols=65 Identities=22% Similarity=0.310 Sum_probs=52.7
Q ss_pred EEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEE---eeCchh
Q 030537 27 VIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGE---AEFPED 103 (175)
Q Consensus 27 ~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Is---a~~~~~ 103 (175)
...+.|| -+-+|.||||+|.|+|.|+++|||+|.|.-.. =.|.|. +.++.
T Consensus 4 ~~~i~IP-------~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~-------------------g~V~I~~~~~~d~~- 56 (180)
T PRK13763 4 MEYVKIP-------KDRIGVLIGKKGETKKEIEERTGVKLEIDSET-------------------GEVIIEPTDGEDPL- 56 (180)
T ss_pred eEEEEcC-------HHHhhhHhccchhHHHHHHHHHCcEEEEECCC-------------------CeEEEEeCCCCCHH-
Confidence 3456776 47899999999999999999999999998530 166776 55654
Q ss_pred hHHHHHHHHHHHHHhccCC
Q 030537 104 IINSRLDHAVAILENLLKP 122 (175)
Q Consensus 104 ~~~~~l~~A~e~Ie~lL~p 122 (175)
.+.+|+++|+.|+..
T Consensus 57 ----~i~kA~~~I~ai~~g 71 (180)
T PRK13763 57 ----AVLKARDIVKAIGRG 71 (180)
T ss_pred ----HHHHHHHHHHHHhcC
Confidence 799999999999884
No 15
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.02 E-value=6.3e-06 Score=66.80 Aligned_cols=53 Identities=26% Similarity=0.374 Sum_probs=45.6
Q ss_pred eeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHHHHHHHHHHHHhccCC
Q 030537 43 FVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINSRLDHAVAILENLLKP 122 (175)
Q Consensus 43 fvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~~l~~A~e~Ie~lL~p 122 (175)
.+|||||++|.|++.||..|||+|.|-| . .|.|.+ +++ .++.|.+.|+.|+.-
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~-------~--------------~v~i~G-~~~-----~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYG-------K--------------TVGIIG-DPE-----QVQIAREAIEMLIEG 151 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcC-------C--------------EEEEEC-CHH-----HHHHHHHHHHHHHcC
Confidence 6999999999999999999999999974 0 578887 443 789999999999964
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=97.96 E-value=6.4e-06 Score=66.78 Aligned_cols=58 Identities=21% Similarity=0.226 Sum_probs=47.3
Q ss_pred cceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEE--EeeCchhhHHHHHHHHHHHHHh
Q 030537 41 FNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLG--EAEFPEDIINSRLDHAVAILEN 118 (175)
Q Consensus 41 ~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~I--sa~~~~~~~~~~l~~A~e~Ie~ 118 (175)
-+.+|.||||+|.|+|.||++|||+|.|--. .=.|.| .+.++. .+.+|.++|+.
T Consensus 6 ~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-------------------~g~V~I~~~t~d~~-----~i~kA~~~I~~ 61 (172)
T TIGR03665 6 KDRIGVLIGKGGETKKEIEERTGVKLDIDSE-------------------TGEVKIEEEDEDPL-----AVMKAREVVKA 61 (172)
T ss_pred HHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-------------------CceEEEecCCCCHH-----HHHHHHHHHHH
Confidence 3889999999999999999999999999842 014677 344543 78999999999
Q ss_pred ccCC
Q 030537 119 LLKP 122 (175)
Q Consensus 119 lL~p 122 (175)
|...
T Consensus 62 i~~g 65 (172)
T TIGR03665 62 IGRG 65 (172)
T ss_pred HHcC
Confidence 8884
No 17
>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=97.94 E-value=1.4e-05 Score=77.06 Aligned_cols=70 Identities=17% Similarity=0.312 Sum_probs=57.4
Q ss_pred CCceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeC
Q 030537 21 APVVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEF 100 (175)
Q Consensus 21 ~~~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~ 100 (175)
++.......+.|| -..+|.||||+|.|+|.|+++|||+|.|--.| +|.|.+.+
T Consensus 546 ~~~~p~~~~~~I~-------~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG--------------------~V~i~~~~ 598 (684)
T TIGR03591 546 SPYAPRIETIKIN-------PDKIRDVIGPGGKVIREITEETGAKIDIEDDG--------------------TVKIAASD 598 (684)
T ss_pred cccCCeEEEEecC-------HHHHHhhcCCCcHHHHHHHHHHCCEEEEecCe--------------------EEEEEECc
Confidence 3444556778887 46789999999999999999999999997544 78888887
Q ss_pred chhhHHHHHHHHHHHHHhccCC
Q 030537 101 PEDIINSRLDHAVAILENLLKP 122 (175)
Q Consensus 101 ~~~~~~~~l~~A~e~Ie~lL~p 122 (175)
.+ .+++|.+.|+.+...
T Consensus 599 ~~-----~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 599 GE-----AAEAAIKMIEGITAE 615 (684)
T ss_pred HH-----HHHHHHHHHHhhhcc
Confidence 54 789999999988653
No 18
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.90 E-value=1.7e-05 Score=64.80 Aligned_cols=53 Identities=26% Similarity=0.418 Sum_probs=44.3
Q ss_pred eeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHHHHHHHHHHHHhccCC
Q 030537 43 FVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINSRLDHAVAILENLLKP 122 (175)
Q Consensus 43 fvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~~l~~A~e~Ie~lL~p 122 (175)
.+|||||++|.|+|.||..|||+|.|-++ .|.|.+ +++ .++.|.+.|+.|+.-
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~---------------------~v~i~G-~~~-----~~~~A~~~I~~li~g 157 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGK---------------------TVAIIG-DPE-----QVEIAREAIEMLIEG 157 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCC---------------------EEEEEe-CHH-----HHHHHHHHHHHHHcC
Confidence 69999999999999999999999999630 266766 443 789999999999964
No 19
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.64 E-value=3.8e-05 Score=76.05 Aligned_cols=71 Identities=18% Similarity=0.148 Sum_probs=59.4
Q ss_pred CCceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCce-EEEeccCCCCCccccCCCCCCCCCCCcEEEEEee
Q 030537 21 APVVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECT-VFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAE 99 (175)
Q Consensus 21 ~~~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgck-I~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~ 99 (175)
++...+...+.|| -+.||.||||+|.|+|.|+++||++ |.|+-.| +|.|.+.
T Consensus 680 s~~aP~i~~~~i~-------~~ki~~vIG~GGktIk~I~eetg~~~Idi~ddg--------------------~V~I~a~ 732 (891)
T PLN00207 680 SKYAPLIHIMKVK-------PEKVNMIIGSGGKKVKSIIEETGVEAIDTQDDG--------------------TVKITAK 732 (891)
T ss_pred cccCCeeEEEEcC-------HHHHHHHhcCCchhHHHHHHHHCCCccCcCCCe--------------------eEEEEeC
Confidence 4455566778887 5789999999999999999999999 8888543 8899998
Q ss_pred CchhhHHHHHHHHHHHHHhccCCC
Q 030537 100 FPEDIINSRLDHAVAILENLLKPV 123 (175)
Q Consensus 100 ~~~~~~~~~l~~A~e~Ie~lL~p~ 123 (175)
+.+ ++++|+++|+.|...+
T Consensus 733 d~~-----~i~~A~~~I~~l~~~~ 751 (891)
T PLN00207 733 DLS-----SLEKSKAIISSLTMVP 751 (891)
T ss_pred CHH-----HHHHHHHHHHHHhcCc
Confidence 865 8999999999998743
No 20
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=97.42 E-value=0.00032 Score=66.61 Aligned_cols=70 Identities=19% Similarity=0.343 Sum_probs=50.2
Q ss_pred EEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEE-EEEeeCchhhH
Q 030537 27 VIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHV-LGEAEFPEDII 105 (175)
Q Consensus 27 ~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV-~Isa~~~~~~~ 105 (175)
+..|.|| -+-||.|||=+|.|+|+|+.+||+||.++= |. +| .-++.. .|.+. .
T Consensus 231 ~~~V~VP-------r~~VG~IIGkgGE~IKklq~etG~KIQfkp-----Dd----~p-----~speR~~~IiG~-~---- 284 (600)
T KOG1676|consen 231 TREVKVP-------RSKVGIIIGKGGEMIKKLQNETGAKIQFKP-----DD----DP-----SSPERPAQIIGT-V---- 284 (600)
T ss_pred eeEEecc-------ccceeeEEecCchHHHHHhhccCceeEeec-----CC----CC-----CCccceeeeecC-H----
Confidence 4456665 378999999999999999999999999983 11 11 223333 33332 2
Q ss_pred HHHHHHHHHHHHhccCCC
Q 030537 106 NSRLDHAVAILENLLKPV 123 (175)
Q Consensus 106 ~~~l~~A~e~Ie~lL~p~ 123 (175)
.++.+|.++|.+||.-.
T Consensus 285 -d~ie~Aa~lI~eii~~~ 301 (600)
T KOG1676|consen 285 -DQIEHAAELINEIIAEA 301 (600)
T ss_pred -HHHHHHHHHHHHHHHHH
Confidence 27899999999999753
No 21
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.42 E-value=0.00034 Score=58.42 Aligned_cols=55 Identities=22% Similarity=0.329 Sum_probs=46.1
Q ss_pred eeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHHHHHHHHHHHHhccCC
Q 030537 43 FVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINSRLDHAVAILENLLKP 122 (175)
Q Consensus 43 fvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~~l~~A~e~Ie~lL~p 122 (175)
..|||||+.|.|.+.||..|||.|+|.|+ +|.|.+. + ..++.|.+.|+.|+.-
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~---------------------tVaiiG~-~-----~~v~iAr~AVemli~G 164 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK---------------------TVAIIGG-F-----EQVEIAREAVEMLING 164 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc---------------------EEEEecC-h-----hhhHHHHHHHHHHHcC
Confidence 57999999999999999999999999972 5666654 2 2688999999999976
Q ss_pred CC
Q 030537 123 VD 124 (175)
Q Consensus 123 ~~ 124 (175)
.+
T Consensus 165 ~~ 166 (194)
T COG1094 165 AP 166 (194)
T ss_pred CC
Confidence 43
No 22
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.28 E-value=0.00052 Score=58.20 Aligned_cols=58 Identities=14% Similarity=0.276 Sum_probs=49.2
Q ss_pred cceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHHHHHHHHHHHHhcc
Q 030537 41 FNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINSRLDHAVAILENLL 120 (175)
Q Consensus 41 ~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~~l~~A~e~Ie~lL 120 (175)
.+++++||||+|.+++.|.++|+|+|.|--.| .|+|.+.+.+ .+.+|++.|+.+-
T Consensus 153 ~~~i~~lig~~g~~i~~l~~~~~~~I~ig~NG--------------------~VwI~~~~~~-----~~~~a~~~I~~~e 207 (235)
T PRK04163 153 PVKVPRVIGKKGSMINMLKEETGCDIIVGQNG--------------------RIWIKGPDEE-----DEEIAIEAIKKIE 207 (235)
T ss_pred HHHHHhhcCCCChhHhhhhhhhCcEEEEcCCc--------------------EEEEeeCCHH-----HHHHHHHHHHHHH
Confidence 47899999999999999999999999995333 8999999865 6788899988887
Q ss_pred CCC
Q 030537 121 KPV 123 (175)
Q Consensus 121 ~p~ 123 (175)
.-.
T Consensus 208 ~~~ 210 (235)
T PRK04163 208 REA 210 (235)
T ss_pred hhh
Confidence 643
No 23
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=97.20 E-value=0.00083 Score=63.91 Aligned_cols=75 Identities=17% Similarity=0.407 Sum_probs=58.9
Q ss_pred ceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCch
Q 030537 23 VVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPE 102 (175)
Q Consensus 23 ~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~ 102 (175)
.++.+..|.|| =|-+|+|||-+|.|+|+|++.||||+.+-=.|+..++ .+-||. |+++. .
T Consensus 136 ~~~ttqeI~IP-------a~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~----------~~Kplr--itGdp-~ 195 (600)
T KOG1676|consen 136 SVETTQEILIP-------ANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG----------ADKPLR--ITGDP-D 195 (600)
T ss_pred ccceeeeeccC-------ccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC----------CCCcee--ecCCH-H
Confidence 34567889998 4789999999999999999999999998877765432 344554 44443 2
Q ss_pred hhHHHHHHHHHHHHHhccCC
Q 030537 103 DIINSRLDHAVAILENLLKP 122 (175)
Q Consensus 103 ~~~~~~l~~A~e~Ie~lL~p 122 (175)
+++.|.++|.++|..
T Consensus 196 -----~ve~a~~lV~dil~e 210 (600)
T KOG1676|consen 196 -----KVEQAKQLVADILRE 210 (600)
T ss_pred -----HHHHHHHHHHHHHHh
Confidence 799999999999984
No 24
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.16 E-value=0.00029 Score=68.14 Aligned_cols=57 Identities=18% Similarity=0.239 Sum_probs=48.9
Q ss_pred cceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHHHHHHHHHHHHhcc
Q 030537 41 FNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINSRLDHAVAILENLL 120 (175)
Q Consensus 41 ~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~~l~~A~e~Ie~lL 120 (175)
.+.++.+|||+|.|+|.|+++||++|.|+-.| .|.|.+.+.+ .+++|.+.|+.+.
T Consensus 562 ~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~G--------------------~v~i~~~~~~-----~~~~a~~~I~~~~ 616 (693)
T PRK11824 562 PDKIRDVIGPGGKTIREITEETGAKIDIEDDG--------------------TVKIAATDGE-----AAEAAKERIEGIT 616 (693)
T ss_pred HHHHHHHhcCCchhHHHHHHHHCCccccCCCc--------------------eEEEEcccHH-----HHHHHHHHHHHhc
Confidence 46789999999999999999999999987544 6788887754 7899999999988
Q ss_pred CC
Q 030537 121 KP 122 (175)
Q Consensus 121 ~p 122 (175)
..
T Consensus 617 ~~ 618 (693)
T PRK11824 617 AE 618 (693)
T ss_pred cc
Confidence 64
No 25
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=96.80 E-value=0.0027 Score=56.21 Aligned_cols=68 Identities=28% Similarity=0.455 Sum_probs=48.4
Q ss_pred EEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHHHHHHHHHHHHhccCCCC
Q 030537 45 GRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINSRLDHAVAILENLLKPVD 124 (175)
Q Consensus 45 GrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~~l~~A~e~Ie~lL~p~~ 124 (175)
.|||||.|+|||.||=.|.|-|.+.|. -|++-.+ +..|..+..+|++.+..++
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~-----------------------TVsaiGp----fkGlkevr~IV~DcM~NiH 213 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN-----------------------TVSAIGP----FKGLKEVRKIVEDCMKNIH 213 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc-----------------------EEEeecC----cchHHHHHHHHHHHHhccc
Confidence 589999999999999999999999983 2344444 2368888888888887776
Q ss_pred cchHHHHHHHHHHHH
Q 030537 125 ESLDHYKKQQLREFA 139 (175)
Q Consensus 125 e~~de~K~~QL~eLA 139 (175)
.-++.--.+--+||+
T Consensus 214 PiY~IK~LmiKRel~ 228 (356)
T KOG2874|consen 214 PIYNIKTLMIKRELA 228 (356)
T ss_pred hHHHHHHHHHHHHhh
Confidence 544432233334444
No 26
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.59 E-value=0.00065 Score=62.97 Aligned_cols=38 Identities=32% Similarity=0.629 Sum_probs=32.8
Q ss_pred EccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEe
Q 030537 31 DVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIR 69 (175)
Q Consensus 31 ~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IR 69 (175)
.||.+-..- -||+|||||-.|.++|.||++||+||.|-
T Consensus 279 e~pLk~lAH-N~lvGRLIGKeGrnlKkIeq~TgTkITis 316 (584)
T KOG2193|consen 279 EIPLKILAH-NNLVGRLIGKEGRNLKKIEQDTGTKITIS 316 (584)
T ss_pred hcchhhhhh-cchhhhhhhhccccHHHHHhhcCCceeee
Confidence 455555444 69999999999999999999999999996
No 27
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.46 E-value=0.0056 Score=55.27 Aligned_cols=57 Identities=14% Similarity=0.172 Sum_probs=43.6
Q ss_pred EEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeC
Q 030537 26 RVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEF 100 (175)
Q Consensus 26 ~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~ 100 (175)
+..||+|| -+-.|-|||-+|.|+.+||++|||+|.+- ..++-.|+- -+=-|+|++..
T Consensus 39 y~ikvLip-------s~AaGsIIGKGG~ti~~lqk~tgariklS-------ks~dfyPGT----TeRvcli~Gt~ 95 (402)
T KOG2191|consen 39 YFLKVLIP-------SYAAGSIIGKGGQTIVQLQKETGARIKLS-------KSKDFYPGT----TERVCLIQGTV 95 (402)
T ss_pred eEEEEEee-------cccccceeccchHHHHHHHhccCcEEEec-------cccccCCCc----cceEEEEeccH
Confidence 67899998 47789999999999999999999999997 122224542 23357777654
No 28
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.41 E-value=0.016 Score=52.37 Aligned_cols=37 Identities=24% Similarity=0.461 Sum_probs=32.5
Q ss_pred EEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEe
Q 030537 26 RVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIR 69 (175)
Q Consensus 26 ~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IR 69 (175)
++.||.+|- .-.|.|||++|.|+|.+.+++||-|+|-
T Consensus 132 kqikivvPN-------stag~iigkggAtiK~~~Eqsga~iqis 168 (402)
T KOG2191|consen 132 KQIKIVVPN-------STAGMIIGKGGATIKAIQEQSGAWIQIS 168 (402)
T ss_pred ceeEEeccC-------CcccceecCCcchHHHHHHhhCcceEec
Confidence 457788883 4579999999999999999999999997
No 29
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.41 E-value=0.004 Score=57.87 Aligned_cols=63 Identities=16% Similarity=0.335 Sum_probs=44.6
Q ss_pred cceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHHHHHHHHHHHHhcc
Q 030537 41 FNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINSRLDHAVAILENLL 120 (175)
Q Consensus 41 ~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~~l~~A~e~Ie~lL 120 (175)
--|+|.||||.|+|+|.|-+.|.|+|-+.-+- +.|. .+-.+-|+=+.+ .-.+||++|-+++
T Consensus 207 tqyvgaIIGkeG~TIknItkqTqsriD~hrke---------n~Ga--aek~itvh~tpE--------g~s~Ac~~ILeim 267 (584)
T KOG2193|consen 207 TQYVGAIIGKEGATIKNITKQTQSRIDVHRKE---------NAGA--AEKIITVHSTPE--------GTSKACKMILEIM 267 (584)
T ss_pred cceeEEEecCCCccccCcchhhhheeeeeecc---------cCCc--ccCceEEecCcc--------chHHHHHHHHHHH
Confidence 58999999999999999999999999998532 1121 234454544332 2357777777777
Q ss_pred CC
Q 030537 121 KP 122 (175)
Q Consensus 121 ~p 122 (175)
..
T Consensus 268 qk 269 (584)
T KOG2193|consen 268 QK 269 (584)
T ss_pred HH
Confidence 53
No 30
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.24 E-value=0.012 Score=55.14 Aligned_cols=71 Identities=21% Similarity=0.247 Sum_probs=54.2
Q ss_pred eEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhh
Q 030537 25 KRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDI 104 (175)
Q Consensus 25 k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~ 104 (175)
..+.++.|| -+-+|-|||=+|+.+|.|.++|||+|.|.+. + .|. ..|.. |.|+++-.
T Consensus 137 ~v~~RLlVp-------~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~--~-------lP~---ster~-V~IsG~~~--- 193 (485)
T KOG2190|consen 137 EVTCRLLVP-------SSQVGSLIGKGGSLIKEIREETGAKIRVSSD--M-------LPN---STERA-VTISGEPD--- 193 (485)
T ss_pred ceEEEEEec-------hhheeeeeccCcHHHHHHHHhcCceEEecCC--C-------CCc---cccee-EEEcCchH---
Confidence 567899999 6889999999999999999999999999975 1 132 23444 77776542
Q ss_pred HHHHHHHHHHHHHhccC
Q 030537 105 INSRLDHAVAILENLLK 121 (175)
Q Consensus 105 ~~~~l~~A~e~Ie~lL~ 121 (175)
.+.+|+..|-.+|.
T Consensus 194 ---av~~al~~Is~~L~ 207 (485)
T KOG2190|consen 194 ---AVKKALVQISSRLL 207 (485)
T ss_pred ---HHHHHHHHHHHHHH
Confidence 56777777766654
No 31
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.15 E-value=0.0074 Score=58.55 Aligned_cols=66 Identities=21% Similarity=0.328 Sum_probs=51.9
Q ss_pred eEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhh
Q 030537 25 KRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDI 104 (175)
Q Consensus 25 k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~ 104 (175)
...+.+-|+++. ++-+|||+|.|++.|.++|||+|.|--.|+ |.|.+.+.+
T Consensus 551 Pri~t~~i~~dK-------I~dvIG~gGk~I~~I~eetg~~IdieddGt--------------------v~i~~s~~~-- 601 (692)
T COG1185 551 PRIETIKIDPDK-------IRDVIGPGGKTIKAITEETGVKIDIEDDGT--------------------VKIAASDGE-- 601 (692)
T ss_pred CceEEEccCHHH-------HhhccCCcccchhhhhhhhCcEEEecCCCc--------------------EEEEecchH--
Confidence 344556677655 455999999999999999999999997774 567776643
Q ss_pred HHHHHHHHHHHHHhccCC
Q 030537 105 INSRLDHAVAILENLLKP 122 (175)
Q Consensus 105 ~~~~l~~A~e~Ie~lL~p 122 (175)
++.+|++.|+.++.-
T Consensus 602 ---~~~~ak~~I~~i~~e 616 (692)
T COG1185 602 ---SAKKAKERIEAITRE 616 (692)
T ss_pred ---HHHHHHHHHHHHHhh
Confidence 788999999998843
No 32
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.61 E-value=0.014 Score=52.55 Aligned_cols=61 Identities=16% Similarity=0.233 Sum_probs=43.5
Q ss_pred cceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchh--hHHHHHHHHHHHHH
Q 030537 41 FNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPED--IINSRLDHAVAILE 117 (175)
Q Consensus 41 ~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~--~~~~~l~~A~e~Ie 117 (175)
--|+|-|+|-+|.|.|.||+||+|+|.+=-.+..+ =|+-|++-.-.+ .|..||+.++.-..
T Consensus 65 s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~----------------~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 65 SSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNK----------------EEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred HHHhhhhhcccchHHHHHHHhhccceEccCCCCCc----------------ceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 36899999999999999999999999997444222 278888765443 23345555555444
No 33
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=94.80 E-value=0.01 Score=54.89 Aligned_cols=73 Identities=29% Similarity=0.436 Sum_probs=60.6
Q ss_pred EEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHHHHHHHHHHHHhccCCCCc
Q 030537 46 RILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINSRLDHAVAILENLLKPVDE 125 (175)
Q Consensus 46 rIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~~l~~A~e~Ie~lL~p~~e 125 (175)
.|.||.|.+.|.++.+|-+.+.|.|-||..- +..+..+ .++|.||.|.+.++- .|+.|.-+++.++-+++.
T Consensus 308 ~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i---~p~~~~~-~~~p~~~~~~~~~~~-----~~~~~~~~~~~~i~~v~~ 378 (531)
T KOG1960|consen 308 AIVGPQGAYVKHIQQETRTRVQIKGQGSAFI---EPSTNRE-SDEPIHLCIMSHDPN-----AIQRAKVLCEDLIASVHQ 378 (531)
T ss_pred ccccCCcccccccCCCCCcceeccCccceee---cCCCCCC-CCCCcccccccCChh-----hhhhhhhcccccCCcccc
Confidence 4789999999999999999999999999863 3344444 899999999988864 577788889999999874
Q ss_pred ch
Q 030537 126 SL 127 (175)
Q Consensus 126 ~~ 127 (175)
.+
T Consensus 379 qy 380 (531)
T KOG1960|consen 379 QY 380 (531)
T ss_pred cC
Confidence 43
No 34
>PRK00106 hypothetical protein; Provisional
Probab=94.74 E-value=0.054 Score=51.47 Aligned_cols=65 Identities=32% Similarity=0.485 Sum_probs=51.9
Q ss_pred EEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHH
Q 030537 28 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINS 107 (175)
Q Consensus 28 ~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~ 107 (175)
--|.+|-+ .+-|||||.-|-+++.+|..||+.|.|= +.|=-|.||++||.
T Consensus 227 s~v~lp~d------emkGriIGreGrNir~~E~~tGvdliid-------------------dtp~~v~lS~fdpv----- 276 (535)
T PRK00106 227 TTVHLPDD------NMKGRIIGREGRNIRTLESLTGIDVIID-------------------DTPEVVVLSGFDPI----- 276 (535)
T ss_pred eeEEcCCh------HhhcceeCCCcchHHHHHHHhCceEEEc-------------------CCCCeEEEeCCChH-----
Confidence 34666644 5679999999999999999999999985 34558999999996
Q ss_pred HHHHHHHHHHhccCC
Q 030537 108 RLDHAVAILENLLKP 122 (175)
Q Consensus 108 ~l~~A~e~Ie~lL~p 122 (175)
|-.-|..-+++|+..
T Consensus 277 RReiAr~~le~Li~d 291 (535)
T PRK00106 277 RREIARMTLESLIKD 291 (535)
T ss_pred HHHHHHHHHHHHHHc
Confidence 556777777887763
No 35
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.39 E-value=0.062 Score=50.63 Aligned_cols=64 Identities=28% Similarity=0.476 Sum_probs=49.6
Q ss_pred EEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHH
Q 030537 28 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINS 107 (175)
Q Consensus 28 ~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~ 107 (175)
.-|.+|-+ .+-|||||--|-++|.+|..||+.|.|= |.|=-|.||++||.
T Consensus 206 ~~v~lp~d------~~kgriigreGrnir~~e~~tgvd~iid-------------------dtp~~v~ls~fdp~----- 255 (514)
T TIGR03319 206 SVVNLPND------EMKGRIIGREGRNIRALETLTGVDLIID-------------------DTPEAVILSGFDPV----- 255 (514)
T ss_pred eeEEcCCh------hhhccccCCCcchHHHHHHHhCceEEEc-------------------CCCCeEEecCCchH-----
Confidence 34666644 5679999999999999999999999995 23447899999985
Q ss_pred HHHHHHHHHHhccC
Q 030537 108 RLDHAVAILENLLK 121 (175)
Q Consensus 108 ~l~~A~e~Ie~lL~ 121 (175)
+=.-|..-+++|+.
T Consensus 256 rreia~~~l~~li~ 269 (514)
T TIGR03319 256 RREIARMALEKLIQ 269 (514)
T ss_pred HHHHHHHHHHHHHH
Confidence 44566666666664
No 36
>PRK12704 phosphodiesterase; Provisional
Probab=94.37 E-value=0.082 Score=49.89 Aligned_cols=51 Identities=25% Similarity=0.469 Sum_probs=41.4
Q ss_pred EEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchh
Q 030537 28 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPED 103 (175)
Q Consensus 28 ~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~ 103 (175)
--|.+|-+ .+-|||||--|-++|.+|..||+.|.|= +.|=-|+||+.||..
T Consensus 212 ~~v~lp~d------~mkgriigreGrnir~~e~~tgvd~iid-------------------dtp~~v~ls~~~~~r 262 (520)
T PRK12704 212 SVVNLPND------EMKGRIIGREGRNIRALETLTGVDLIID-------------------DTPEAVILSGFDPIR 262 (520)
T ss_pred eeeecCCc------hhhcceeCCCcchHHHHHHHhCCeEEEc-------------------CCCCeEEEecCChhh
Confidence 34566644 5679999999999999999999999995 335589999999863
No 37
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=94.05 E-value=0.11 Score=35.21 Aligned_cols=36 Identities=19% Similarity=0.327 Sum_probs=29.8
Q ss_pred EEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEE
Q 030537 26 RVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFI 68 (175)
Q Consensus 26 ~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~I 68 (175)
...+|++|. .-+|+.||.+|.+++.++..+|.+|.|
T Consensus 25 ~~~~v~V~~-------~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPD-------DQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECc-------ccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 345677774 347899999999999999999988876
No 38
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=93.01 E-value=0.2 Score=47.15 Aligned_cols=29 Identities=28% Similarity=0.548 Sum_probs=27.7
Q ss_pred cceeEEEeCCCCchHHHHHhhhCceEEEe
Q 030537 41 FNFVGRILGPRGNSLKRVEAMTECTVFIR 69 (175)
Q Consensus 41 ~NfvGrIiGPrG~TlK~ie~eTgckI~IR 69 (175)
-+|||.+||-+|+.+|+||..|+++|.|-
T Consensus 55 s~mvg~vigrggskik~iq~~tnt~iqii 83 (629)
T KOG0336|consen 55 SEMVGKVIGRGGSKIKRIQNDTNTRIQII 83 (629)
T ss_pred hhhhheeeccCcchhhhhhcccceeEEEe
Confidence 48999999999999999999999999986
No 39
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=92.83 E-value=0.14 Score=48.09 Aligned_cols=42 Identities=24% Similarity=0.399 Sum_probs=37.3
Q ss_pred ceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEecc
Q 030537 23 VVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQ 71 (175)
Q Consensus 23 ~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGk 71 (175)
....+.++.|| .+++|.|||..|+.+-.|++.|||.|.|-++
T Consensus 335 ~~~v~~~l~vp-------s~~igciiGk~G~~iseir~~tgA~I~I~~~ 376 (485)
T KOG2190|consen 335 TQTVTQRLLVP-------SDLIGCIIGKGGAKISEIRQRTGASISILNK 376 (485)
T ss_pred cceeeeeeccC-------ccccceeecccccchHHHHHhcCCceEEccc
Confidence 44566788888 6999999999999999999999999999964
No 40
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=89.33 E-value=0.63 Score=45.10 Aligned_cols=71 Identities=17% Similarity=0.157 Sum_probs=50.6
Q ss_pred ceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHHHHHHHHHHHHhccC
Q 030537 42 NFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINSRLDHAVAILENLLK 121 (175)
Q Consensus 42 NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~~l~~A~e~Ie~lL~ 121 (175)
.-+..+|||.|..+|+|+.|||+.-++- +=|+-|-|.++. .+++|.+.|..+..
T Consensus 606 sk~~~lIGp~G~~~kki~~EtGai~~vD---------------------e~t~~i~A~~~~-----am~~Ak~~I~~i~~ 659 (760)
T KOG1067|consen 606 SKRATLIGPGGVLKKKIEVETGAISQVD---------------------EGTFSIFAPTQA-----AMEEAKEFIDGIIK 659 (760)
T ss_pred hhhheeecCccceeeeEeeeccceeeec---------------------CceEEEEecCHH-----HHHHHHHHHHHHhc
Confidence 3456799999999999999999433321 228888888864 79999999999987
Q ss_pred CCCcchHHHHHHHHHHHHHhcCcc
Q 030537 122 PVDESLDHYKKQQLREFATLNGTL 145 (175)
Q Consensus 122 p~~e~~de~K~~QL~eLA~lNGt~ 145 (175)
.+.. +||.-=+++++|.
T Consensus 660 ~~~~-------~~l~~g~vy~~tI 676 (760)
T KOG1067|consen 660 DDQV-------QDLEFGGVYTATI 676 (760)
T ss_pred Cccc-------cceEeeeEEEEEE
Confidence 5422 2333336666664
No 41
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=89.32 E-value=1.2 Score=38.50 Aligned_cols=41 Identities=20% Similarity=0.392 Sum_probs=35.7
Q ss_pred cceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCc
Q 030537 41 FNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFP 101 (175)
Q Consensus 41 ~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~ 101 (175)
..++-|+||++|+-++.|.+.|+|.|.|==.| .|+|.+++.
T Consensus 154 p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG--------------------~IWV~~~~~ 194 (239)
T COG1097 154 PSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG--------------------RIWVDGENE 194 (239)
T ss_pred hhhcceEecCCCcHHHHhhhhcCeEEEEecCC--------------------EEEecCCCc
Confidence 57888999999999999999999999997544 778888776
No 42
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=87.54 E-value=0.3 Score=34.24 Aligned_cols=31 Identities=23% Similarity=0.424 Sum_probs=24.3
Q ss_pred CCCcceeEEEeCCCCchHHHHHhhh-CceEEEe
Q 030537 38 PNQFNFVGRILGPRGNSLKRVEAMT-ECTVFIR 69 (175)
Q Consensus 38 P~~~NfvGrIiGPrG~TlK~ie~eT-gckI~IR 69 (175)
|+ ++-+|..+|++|..+|.|+++. |-+|.|=
T Consensus 14 ~~-~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 14 PN-IDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp TT-S-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred CC-cCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 66 9999999999999999999999 6555544
No 43
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=87.00 E-value=3.8 Score=36.68 Aligned_cols=45 Identities=20% Similarity=0.428 Sum_probs=37.2
Q ss_pred CCCCCCceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEec
Q 030537 17 GIPTAPVVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRG 70 (175)
Q Consensus 17 ~~~~~~~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRG 70 (175)
.+-.+|+.+.+ |.|| -.+-|-|||-+|.-+|+|-.|+|+.|.|--
T Consensus 308 GdlGGPitTaQ--vtip-------~dlggsiigkggqri~~ir~esGA~Ikide 352 (390)
T KOG2192|consen 308 GDLGGPITTAQ--VTIP-------KDLGGSIIGKGGQRIKQIRHESGASIKIDE 352 (390)
T ss_pred CCCCCceeeee--Eecc-------cccCcceecccchhhhhhhhccCceEEecC
Confidence 44457877654 7777 478899999999999999999999999873
No 44
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=86.52 E-value=3.2 Score=34.93 Aligned_cols=66 Identities=18% Similarity=0.248 Sum_probs=46.6
Q ss_pred EEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEee----Cch
Q 030537 27 VIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAE----FPE 102 (175)
Q Consensus 27 ~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~----~~~ 102 (175)
.+.+.||- -=+|-|+|+.|.+.+.||+.++|+|.|-.+.. -|-|... ||
T Consensus 9 ~~~v~iPk-------~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~-------------------~V~i~~~~~t~Dp- 61 (194)
T COG1094 9 SEAVKIPK-------DRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTG-------------------SVTIRTTRKTEDP- 61 (194)
T ss_pred eeeeecCc-------hhheeeecccccchHHHHhhcCeEEEEECCCC-------------------eEEEEecCCCCCh-
Confidence 44566663 34789999999999999999999999987521 2333333 33
Q ss_pred hhHHHHHHHHHHHHHhccCCC
Q 030537 103 DIINSRLDHAVAILENLLKPV 123 (175)
Q Consensus 103 ~~~~~~l~~A~e~Ie~lL~p~ 123 (175)
..+.+|.++|+.+=.-.
T Consensus 62 ----~~~~ka~d~VkAIgrGF 78 (194)
T COG1094 62 ----LALLKARDVVKAIGRGF 78 (194)
T ss_pred ----HHHHHHHHHHHHHhcCC
Confidence 26778888888766543
No 45
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=86.50 E-value=0.6 Score=42.26 Aligned_cols=38 Identities=24% Similarity=0.350 Sum_probs=30.8
Q ss_pred eeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEE
Q 030537 24 VKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFI 68 (175)
Q Consensus 24 ~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~I 68 (175)
..+++.+-+| +-|++.|.|++|.++|.|+.+|.+.|.-
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 4455556666 4689999999999999999999998763
No 46
>PRK12705 hypothetical protein; Provisional
Probab=85.52 E-value=0.74 Score=43.65 Aligned_cols=29 Identities=28% Similarity=0.543 Sum_probs=26.7
Q ss_pred cceeEEEeCCCCchHHHHHhhhCceEEEe
Q 030537 41 FNFVGRILGPRGNSLKRVEAMTECTVFIR 69 (175)
Q Consensus 41 ~NfvGrIiGPrG~TlK~ie~eTgckI~IR 69 (175)
=.+-|||||--|.+++.+|..||+-|.|-
T Consensus 207 demkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 207 DAMKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred hHhhccccCccchhHHHHHHhhCCceEec
Confidence 46779999999999999999999999886
No 47
>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=85.36 E-value=0.79 Score=29.82 Aligned_cols=23 Identities=13% Similarity=0.498 Sum_probs=20.6
Q ss_pred eEEEeCCCCchHHHHHhhhCceE
Q 030537 44 VGRILGPRGNSLKRVEAMTECTV 66 (175)
Q Consensus 44 vGrIiGPrG~TlK~ie~eTgckI 66 (175)
.|++||.+|.+++.|+..++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 58999999999999999998554
No 48
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=79.65 E-value=1.4 Score=34.87 Aligned_cols=29 Identities=21% Similarity=0.292 Sum_probs=26.9
Q ss_pred ceeEEEeCCCCchHHHHHhhhCceEEEec
Q 030537 42 NFVGRILGPRGNSLKRVEAMTECTVFIRG 70 (175)
Q Consensus 42 NfvGrIiGPrG~TlK~ie~eTgckI~IRG 70 (175)
+.+|..+|++|+.+|.|++..|-+|-|=.
T Consensus 41 ~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 41 GDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 67899999999999999999999998875
No 49
>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=78.86 E-value=1.3 Score=31.06 Aligned_cols=25 Identities=20% Similarity=0.494 Sum_probs=21.0
Q ss_pred eEEEeCCCCchHHHHHhhhCceEEE
Q 030537 44 VGRILGPRGNSLKRVEAMTECTVFI 68 (175)
Q Consensus 44 vGrIiGPrG~TlK~ie~eTgckI~I 68 (175)
.|+|||.+|.|+..||--+..-+.-
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred CCeEECCCCccHHHHHHHHHHHHhh
Confidence 5999999999999999998744443
No 50
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=71.91 E-value=3.1 Score=42.46 Aligned_cols=77 Identities=22% Similarity=0.254 Sum_probs=57.6
Q ss_pred EEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHHHH
Q 030537 30 LDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINSRL 109 (175)
Q Consensus 30 i~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~~l 109 (175)
.-.++++||- |..+++.+-.- |.+|...|+|.|.+||+== ...+ .| ...++.||.+|++.+. ..+
T Consensus 900 ~~~~inD~Pq--~~r~~vt~~~~--L~~i~e~~~~~it~rg~f~--~~gk--~p--~~gErklyl~ve~~~e-----~~v 964 (997)
T KOG0334|consen 900 AELEINDFPQ--NARWRVTYKEA--LLRISEPTAAGITTRGKFN--PPGK--EP--KPGERKLYLLVEGPDE-----LSV 964 (997)
T ss_pred eeccccccch--hcceeeechhh--hhhccCccccceeeccccC--CCCC--CC--CCcchhhhhhhhcchh-----HHH
Confidence 3466789996 89999988654 9999999999999999641 1111 12 2357889999997764 368
Q ss_pred HHHHHHHHhccC
Q 030537 110 DHAVAILENLLK 121 (175)
Q Consensus 110 ~~A~e~Ie~lL~ 121 (175)
.+|++.++.+|.
T Consensus 965 qra~~e~~r~l~ 976 (997)
T KOG0334|consen 965 QRAIEELERLLE 976 (997)
T ss_pred HHHHHHHHHHHH
Confidence 899999888664
No 51
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=71.43 E-value=3.1 Score=41.25 Aligned_cols=39 Identities=15% Similarity=0.427 Sum_probs=31.6
Q ss_pred eeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEe
Q 030537 24 VKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIR 69 (175)
Q Consensus 24 ~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IR 69 (175)
...+..++|| +-|-+-||||+|+++++++.+++|.|.+-
T Consensus 707 ~~~~~~~~~p-------~~~~~~~ig~~g~~~r~~~~~~~~~~~~~ 745 (753)
T KOG2208|consen 707 NLVTKEIEIP-------RSLHRYLIGPKGSNLRQLEKEFNVNIVVP 745 (753)
T ss_pred cceeeEEecc-------HHHhhhccCCCCccHHHHHHHhccceecC
Confidence 3455567777 55666799999999999999999998775
No 52
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=71.19 E-value=8.2 Score=34.58 Aligned_cols=41 Identities=17% Similarity=0.287 Sum_probs=32.9
Q ss_pred eEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCc
Q 030537 44 VGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFP 101 (175)
Q Consensus 44 vGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~ 101 (175)
.|.|||-+|.++|+|..+.++.|++-. ++.|-||+-...|.
T Consensus 59 agavigkgg~nik~lr~d~na~v~vpd-----------------s~~peri~tisad~ 99 (390)
T KOG2192|consen 59 AGAVIGKGGKNIKALRTDYNASVSVPD-----------------SSGPERILTISADI 99 (390)
T ss_pred ccceeccccccHHHHhhhccceeeccC-----------------CCCCceeEEEeccH
Confidence 689999999999999999999998862 45566777554443
No 53
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=70.97 E-value=5.6 Score=37.39 Aligned_cols=46 Identities=17% Similarity=0.196 Sum_probs=35.6
Q ss_pred ceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhh-CceEEEec
Q 030537 23 VVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMT-ECTVFIRG 70 (175)
Q Consensus 23 ~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eT-gckI~IRG 70 (175)
+.=...||-|=. .-|+ ++-+|..||++|+.++.|.++. |=+|-|=-
T Consensus 260 ipG~RtKVAV~S-~d~~-VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~ 306 (449)
T PRK12329 260 YVGPRTKIAVDT-LERD-VDPVGACIGARGSRIQAVVNELRGEKIDVIR 306 (449)
T ss_pred CCcceeEEEEEc-CCCC-CChhhccCCCCcchHHHHHHHhCCCeEEEEE
Confidence 333346676643 3477 9999999999999999999998 88887753
No 54
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=66.47 E-value=8.8 Score=34.93 Aligned_cols=41 Identities=20% Similarity=0.368 Sum_probs=32.8
Q ss_pred EEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhh-CceEEEec
Q 030537 28 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMT-ECTVFIRG 70 (175)
Q Consensus 28 ~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eT-gckI~IRG 70 (175)
.||-|=- .-|+ ++-+|..+|++|+.++.|.++. |=+|-|=-
T Consensus 233 tKVAV~s-~~~~-iDpvGa~iG~~G~rI~~i~~el~gekIdiv~ 274 (362)
T PRK12327 233 TKIAVRS-NNPN-VDAKGACVGPKGQRVQNIVSELKGEKIDIID 274 (362)
T ss_pred eEEEEEc-CCCC-CCchheeECCCChhHHHHHHHhCCCeEEEEE
Confidence 3555532 3477 9999999999999999999998 88887763
No 55
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=64.79 E-value=12 Score=33.81 Aligned_cols=41 Identities=20% Similarity=0.342 Sum_probs=32.6
Q ss_pred EEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhh-CceEEEec
Q 030537 28 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMT-ECTVFIRG 70 (175)
Q Consensus 28 ~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eT-gckI~IRG 70 (175)
.||-|=-. -|+ ++-+|..+|++|+.++.|.++. |=+|-|=-
T Consensus 231 tKvAV~s~-~~~-iDpvga~vG~~G~ri~~i~~el~ge~Idiv~ 272 (341)
T TIGR01953 231 TKIAVESN-DEN-IDPVGACVGPKGSRIQAISKELNGEKIDIIE 272 (341)
T ss_pred eEEEEEcC-CCC-CCcceeeECCCCchHHHHHHHhCCCeEEEEE
Confidence 35555333 477 9999999999999999999998 77776653
No 56
>PRK02821 hypothetical protein; Provisional
Probab=63.13 E-value=4.2 Score=29.23 Aligned_cols=23 Identities=13% Similarity=0.450 Sum_probs=18.8
Q ss_pred ceeEEEeCCCCchHHHHHhhhCc
Q 030537 42 NFVGRILGPRGNSLKRVEAMTEC 64 (175)
Q Consensus 42 NfvGrIiGPrG~TlK~ie~eTgc 64 (175)
.=+|||||-+|.|++.|-.--.+
T Consensus 40 ~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 40 DDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred hhCcceeCCCCchHHHHHHHHHH
Confidence 34899999999999999776543
No 57
>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=62.86 E-value=5.9 Score=31.49 Aligned_cols=29 Identities=21% Similarity=0.386 Sum_probs=26.7
Q ss_pred ceeEEEeCCCCchHHHHHhhhCceEEEec
Q 030537 42 NFVGRILGPRGNSLKRVEAMTECTVFIRG 70 (175)
Q Consensus 42 NfvGrIiGPrG~TlK~ie~eTgckI~IRG 70 (175)
+-+|..+|++|+.+|.|++..|=+|-|=.
T Consensus 42 g~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 42 GEMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred CCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 67899999999999999999999998876
No 58
>PRK00468 hypothetical protein; Provisional
Probab=62.49 E-value=4.4 Score=28.92 Aligned_cols=19 Identities=21% Similarity=0.641 Sum_probs=16.6
Q ss_pred eEEEeCCCCchHHHHHhhh
Q 030537 44 VGRILGPRGNSLKRVEAMT 62 (175)
Q Consensus 44 vGrIiGPrG~TlK~ie~eT 62 (175)
+|||||=+|.|++.|..--
T Consensus 41 ~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CcceecCCChhHHHHHHHH
Confidence 6999999999999987644
No 59
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=61.83 E-value=1.2 Score=30.71 Aligned_cols=20 Identities=25% Similarity=0.695 Sum_probs=18.3
Q ss_pred eEEEeCCCCchHHHHHhhhC
Q 030537 44 VGRILGPRGNSLKRVEAMTE 63 (175)
Q Consensus 44 vGrIiGPrG~TlK~ie~eTg 63 (175)
.|+|||-+|.|++.||--++
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 79999999999999998765
No 60
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=60.25 E-value=18 Score=32.99 Aligned_cols=29 Identities=24% Similarity=0.426 Sum_probs=26.8
Q ss_pred ceeEEEeCCCCchHHHHHhhhCceEEEec
Q 030537 42 NFVGRILGPRGNSLKRVEAMTECTVFIRG 70 (175)
Q Consensus 42 NfvGrIiGPrG~TlK~ie~eTgckI~IRG 70 (175)
|-+-.|+||.|..++.||+..|+.|.-||
T Consensus 24 ~~~~~l~G~~~~~l~l~e~~~gv~i~~rG 52 (348)
T COG1702 24 NELVALFGPTDTNLSLLEIALGVSIVARG 52 (348)
T ss_pred hhhhhhcCCCCccHHHHHHHhCcEEEeCC
Confidence 66777999999999999999999999997
No 61
>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=59.62 E-value=23 Score=29.92 Aligned_cols=41 Identities=22% Similarity=0.430 Sum_probs=31.1
Q ss_pred ceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHH--------HhhhCceEEEe
Q 030537 23 VVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRV--------EAMTECTVFIR 69 (175)
Q Consensus 23 ~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~i--------e~eTgckI~IR 69 (175)
.+.....|++.-+.+ -|-|||.+|.++|+| |+..||+|.+.
T Consensus 218 ~~~i~~~i~v~~~s~------k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l~ 266 (270)
T TIGR00436 218 LLKIHALISVERESQ------KKIIIGKNGSMIKAIGIAARKDILELFDCDVFLE 266 (270)
T ss_pred eEEEEEEEEECcCCc------eeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 356667778775443 578999999999986 66778888774
No 62
>KOG4165 consensus Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism]
Probab=59.19 E-value=13 Score=34.17 Aligned_cols=62 Identities=23% Similarity=0.400 Sum_probs=40.2
Q ss_pred ceeEEEeCCCCch--HHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHH-------HHHHH
Q 030537 42 NFVGRILGPRGNS--LKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINS-------RLDHA 112 (175)
Q Consensus 42 NfvGrIiGPrG~T--lK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~-------~l~~A 112 (175)
++|.+|| |||++ +++|+..|. |-+.| |.+.--||+|--+.....|.. -.-.|
T Consensus 190 ~~IDLvI-PRGSs~LVr~Ik~~tk--IPVLG----------------HA~GichvYvd~dad~~kA~riv~DaK~dYPAa 250 (433)
T KOG4165|consen 190 DYIDLVI-PRGSSDLVRSIKDTTK--IPVLG----------------HAEGICHVYVDKDADLDKAKRIVRDAKCDYPAA 250 (433)
T ss_pred hheeEEe-cCCcHHHHHHHhhccc--Ccccc----------------cccceeEEEeccccCHHHHHHHHhcccCCCchh
Confidence 5666666 99987 578887765 88887 667788999965544322211 01246
Q ss_pred HHHHHhccCC
Q 030537 113 VAILENLLKP 122 (175)
Q Consensus 113 ~e~Ie~lL~p 122 (175)
|..+|-||..
T Consensus 251 CNAmETLLIh 260 (433)
T KOG4165|consen 251 CNAMETLLIH 260 (433)
T ss_pred hhhHHHHhcc
Confidence 6666777764
No 63
>PRK01064 hypothetical protein; Provisional
Probab=58.33 E-value=6.9 Score=28.18 Aligned_cols=20 Identities=25% Similarity=0.718 Sum_probs=17.8
Q ss_pred eEEEeCCCCchHHHHHhhhC
Q 030537 44 VGRILGPRGNSLKRVEAMTE 63 (175)
Q Consensus 44 vGrIiGPrG~TlK~ie~eTg 63 (175)
+|++||-+|.|++.|..-..
T Consensus 41 ~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred ceEEECCCCccHHHHHHHHH
Confidence 69999999999999988654
No 64
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=55.85 E-value=8.8 Score=31.44 Aligned_cols=27 Identities=15% Similarity=0.076 Sum_probs=25.3
Q ss_pred EEEeCCCCchHHHHHhhhCceEEEecc
Q 030537 45 GRILGPRGNSLKRVEAMTECTVFIRGQ 71 (175)
Q Consensus 45 GrIiGPrG~TlK~ie~eTgckI~IRGk 71 (175)
|.-||++|.++|+|++..|=+|.|=.-
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEEEc
Confidence 999999999999999999999998873
No 65
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=53.36 E-value=7.8 Score=27.93 Aligned_cols=18 Identities=17% Similarity=0.802 Sum_probs=16.0
Q ss_pred eEEEeCCCCchHHHHHhh
Q 030537 44 VGRILGPRGNSLKRVEAM 61 (175)
Q Consensus 44 vGrIiGPrG~TlK~ie~e 61 (175)
+|++||=+|.|++.|-.-
T Consensus 41 ~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 41 MGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred ccceecCCChhHHHHHHH
Confidence 799999999999998653
No 66
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=53.21 E-value=10 Score=31.64 Aligned_cols=31 Identities=23% Similarity=0.278 Sum_probs=27.8
Q ss_pred cceeEEEeCCCCchHHHHHhhhCceEEEecc
Q 030537 41 FNFVGRILGPRGNSLKRVEAMTECTVFIRGQ 71 (175)
Q Consensus 41 ~NfvGrIiGPrG~TlK~ie~eTgckI~IRGk 71 (175)
.+=+|..+|++|+.+|.|.++.|=+|-|=.-
T Consensus 84 ~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~ 114 (190)
T COG0195 84 IDPVGACIGKRGSRVKAVSEELGEKIDVVEW 114 (190)
T ss_pred cCchhhhccCCChHHHHHHHHhCCceEEEEe
Confidence 7789999999999999999999988877653
No 67
>PRK00089 era GTPase Era; Reviewed
Probab=52.55 E-value=15 Score=31.08 Aligned_cols=41 Identities=29% Similarity=0.430 Sum_probs=30.8
Q ss_pred ceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHH--------HhhhCceEEEe
Q 030537 23 VVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRV--------EAMTECTVFIR 69 (175)
Q Consensus 23 ~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~i--------e~eTgckI~IR 69 (175)
.++....|++.-+. -.+-|||-+|.++|+| |+..||+|.+.
T Consensus 223 ~~~i~~~i~v~~~~------~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 223 LVRIEATIYVERDS------QKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred eEEEEEEEEEccCC------ceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 35566677776444 3578999999999986 66778888876
No 68
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=51.24 E-value=17 Score=32.47 Aligned_cols=67 Identities=22% Similarity=0.132 Sum_probs=40.5
Q ss_pred EEEeeCchhhHHHHHHHHHHHHHhccCCCCcchH-------------------HHH---HHHHHHHHHhcCccCCCCC--
Q 030537 95 LGEAEFPEDIINSRLDHAVAILENLLKPVDESLD-------------------HYK---KQQLREFATLNGTLREESP-- 150 (175)
Q Consensus 95 ~Isa~~~~~~~~~~l~~A~e~Ie~lL~p~~e~~d-------------------e~K---~~QL~eLA~lNGt~r~~~~-- 150 (175)
+|+-+...=.|..+|+.|..+|+.|=+.++...+ ..| .-|-||||. ||++|++.+
T Consensus 105 WIEEECHRVEAQLALKEARkEIkQLkQvieTmrssL~ekDkGiQKYFvDINiQN~KLEsLLqsMElAq-~g~~rde~~l~ 183 (305)
T PF15290_consen 105 WIEEECHRVEAQLALKEARKEIKQLKQVIETMRSSLAEKDKGIQKYFVDINIQNKKLESLLQSMELAQ-SGSLRDEGCLD 183 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchhhhhHHHHHhhhhhhHhHHHHHHHHHHHHH-hccccccCCcC
Confidence 3433333334566788888888877554321111 111 246678886 677999877
Q ss_pred CCCCCCCCCCcc
Q 030537 151 SMSPSMSPSMWP 162 (175)
Q Consensus 151 ~~~g~~~~~~~p 162 (175)
+.|+|.+++.-+
T Consensus 184 ~~c~SP~~sLt~ 195 (305)
T PF15290_consen 184 FSCDSPAKSLTR 195 (305)
T ss_pred CccCCccccccc
Confidence 778888765554
No 69
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=50.99 E-value=15 Score=33.83 Aligned_cols=40 Identities=15% Similarity=0.242 Sum_probs=31.9
Q ss_pred EEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhh-CceEEEe
Q 030537 28 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMT-ECTVFIR 69 (175)
Q Consensus 28 ~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eT-gckI~IR 69 (175)
.||-|= ..-|+ ++-+|..+|++|+.++.|.++. |=+|-|=
T Consensus 239 tKVAV~-S~d~~-iDPvGacIG~~G~rI~~I~~eL~gEkIDvI 279 (374)
T PRK12328 239 AKVALF-SNNPN-IDPIGATVGVKGVRINAVSKELNGENIDCI 279 (374)
T ss_pred eEEEEE-cCCCC-CChHHhhcCCCcchHHHHHHHhCCCeEEEE
Confidence 355553 34577 9999999999999999999998 7777665
No 70
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=50.95 E-value=19 Score=34.70 Aligned_cols=42 Identities=14% Similarity=0.387 Sum_probs=34.0
Q ss_pred EEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCC
Q 030537 28 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKD 76 (175)
Q Consensus 28 ~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~ 76 (175)
.-|+||- -+++++||-+|..+++||+..|-+|.++-.+.-..
T Consensus 488 avv~vpe-------~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~~~~ 529 (604)
T COG1855 488 AVVKVPE-------KYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEEE 529 (604)
T ss_pred EEEEeCH-------HHhhHHhhcccchHHHHHHHhCCceEEEEcccccc
Confidence 3466663 56778999999999999999999999998765433
No 71
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=49.39 E-value=7.5 Score=30.65 Aligned_cols=26 Identities=19% Similarity=0.335 Sum_probs=22.6
Q ss_pred eeEEEeCCCCchHHHHHhhhCceEEE
Q 030537 43 FVGRILGPRGNSLKRVEAMTECTVFI 68 (175)
Q Consensus 43 fvGrIiGPrG~TlK~ie~eTgckI~I 68 (175)
-.|+.||.+|.|++.++.-+|-.+-|
T Consensus 109 d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 109 DKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred ccchhhCCCCHHHHHHHHHhCCccCC
Confidence 36899999999999999999877654
No 72
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=49.13 E-value=8.9 Score=34.94 Aligned_cols=31 Identities=26% Similarity=0.594 Sum_probs=27.8
Q ss_pred cceeEEEeCCCCchHHHHHhhhCceEEEecc
Q 030537 41 FNFVGRILGPRGNSLKRVEAMTECTVFIRGQ 71 (175)
Q Consensus 41 ~NfvGrIiGPrG~TlK~ie~eTgckI~IRGk 71 (175)
+-++|++.||.|.|+|++|+.|..-|.--++
T Consensus 123 ~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 123 LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred ceeeeeccccccCccchheecccceEeeecc
Confidence 6889999999999999999999998876654
No 73
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=48.93 E-value=5.9 Score=33.26 Aligned_cols=58 Identities=17% Similarity=0.146 Sum_probs=32.0
Q ss_pred CCcEEEEEeeCchhhHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHHHhcCccCCCCC--CCCCCCCC--CCcc
Q 030537 90 EPLHVLGEAEFPEDIINSRLDHAVAILENLLKPVDESLDHYKKQQLREFATLNGTLREESP--SMSPSMSP--SMWP 162 (175)
Q Consensus 90 epLHV~Isa~~~~~~~~~~l~~A~e~Ie~lL~p~~e~~de~K~~QL~eLA~lNGt~r~~~~--~~~g~~~~--~~~p 162 (175)
+|+|.+++..+++......+......+..+-.+..++.+ ++++++. ++||..+| +-+|
T Consensus 16 ~~~~~~~~~s~ee~~~~~~~~~~~~~~~~~~~~~~~d~~---------------~~~~~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 16 LPIDKLSANSIEESSSNPNELRSLRSSGRYEDRSVEDVS---------------AIREENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred cChhhhcccchhhhhcCccceeeccceeeeecccccccc---------------cccccccccchhcccCcccccCC
Confidence 788888887776644333333333333333333222222 4554544 89999999 4555
No 74
>PRK15494 era GTPase Era; Provisional
Probab=48.52 E-value=36 Score=30.07 Aligned_cols=41 Identities=24% Similarity=0.300 Sum_probs=32.1
Q ss_pred ceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHH--------HhhhCceEEEe
Q 030537 23 VVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRV--------EAMTECTVFIR 69 (175)
Q Consensus 23 ~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~i--------e~eTgckI~IR 69 (175)
.++....||+.-+. --+-|||-+|..+|+| |+..||+|.+.
T Consensus 270 ~~~i~~~i~v~~~s------qk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 270 SVKINQVIVVSRES------YKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred eEEEEEEEEECCCC------ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 35667778887544 4579999999999986 77789998876
No 75
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=47.23 E-value=21 Score=33.65 Aligned_cols=40 Identities=20% Similarity=0.328 Sum_probs=32.6
Q ss_pred EEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhh-CceEEEe
Q 030537 28 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMT-ECTVFIR 69 (175)
Q Consensus 28 ~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eT-gckI~IR 69 (175)
.||-|- ..-|+ ++-+|..+|++|+.++.|.++. |=+|-|=
T Consensus 233 aKvAV~-s~d~~-iDpvga~vG~~G~ri~~i~~el~ge~Idiv 273 (470)
T PRK09202 233 AKIAVK-SNDPR-IDPVGACVGMRGSRIQAISNELGGEKIDII 273 (470)
T ss_pred eEEEEE-cCCCC-CChhHccCCCCCchHHHHHHHhCCCeEEEE
Confidence 355553 45577 9999999999999999999998 7777765
No 76
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=44.61 E-value=13 Score=31.90 Aligned_cols=28 Identities=25% Similarity=0.459 Sum_probs=26.2
Q ss_pred eeEEEeCCCCchHHHHHhhhCceEEEec
Q 030537 43 FVGRILGPRGNSLKRVEAMTECTVFIRG 70 (175)
Q Consensus 43 fvGrIiGPrG~TlK~ie~eTgckI~IRG 70 (175)
-||||.|-+|.|--.||..|.++|.|-+
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVlad 206 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIENVTRTRIVLAD 206 (252)
T ss_pred HHHHhhcCCCcceeeeeccceeEEEecC
Confidence 4899999999999999999999999974
No 77
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=42.89 E-value=65 Score=27.16 Aligned_cols=61 Identities=23% Similarity=0.172 Sum_probs=35.3
Q ss_pred eEEEeCCC-------------CchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCc-hhhHHHHH
Q 030537 44 VGRILGPR-------------GNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFP-EDIINSRL 109 (175)
Q Consensus 44 vGrIiGPr-------------G~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~-~~~~~~~l 109 (175)
+|++|||+ ...+...-+++.+++.+|=+- .--+|+.|--.+. .+...+-+
T Consensus 117 lgk~LGp~~~p~gK~P~~~~~~~dl~~~i~~~k~~v~~r~~k----------------~~~~~~~VGk~~m~~e~i~eNi 180 (214)
T PTZ00225 117 VPRLVGPHMHRMGKFPTVCSPSESLPDKVVELRSTVKFQLKK----------------VLCLGTCVGHVEMTEEQLRQNV 180 (214)
T ss_pred hhhhcCCCCCcCCCCCcccCCccCHHHHHHHHhheeEEEecC----------------ccEEEeEEccCCCCHHHHHHHH
Confidence 49999998 334555555666666666211 2245888765543 33333455
Q ss_pred HHHHHHHHhcc
Q 030537 110 DHAVAILENLL 120 (175)
Q Consensus 110 ~~A~e~Ie~lL 120 (175)
..+++.|...|
T Consensus 181 ~a~l~~l~~~~ 191 (214)
T PTZ00225 181 VMAINFLVSLL 191 (214)
T ss_pred HHHHHHHHHhC
Confidence 55566665555
No 78
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=42.78 E-value=72 Score=27.11 Aligned_cols=64 Identities=19% Similarity=0.229 Sum_probs=33.9
Q ss_pred cceeEEEeCCCCc-----------hHHHHHhhhCc-eEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCc-hhhHHH
Q 030537 41 FNFVGRILGPRGN-----------SLKRVEAMTEC-TVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFP-EDIINS 107 (175)
Q Consensus 41 ~NfvGrIiGPrG~-----------TlK~ie~eTgc-kI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~-~~~~~~ 107 (175)
..-+|+||||||. .+..+-++.-. +|.+|-+ ...-+|+-|--.+. .+...+
T Consensus 123 l~~Lg~iLGPrGlMP~pk~gTv~~di~~~I~~~k~g~v~~r~~----------------k~g~i~~~IG~~~m~~e~i~e 186 (230)
T PRK05424 123 VGKLGRILGPRGLMPNPKTGTVTMDVAKAVKEAKAGKVEFRVD----------------KAGIIHAPIGKVSFDAEKLKE 186 (230)
T ss_pred HHHhccccccccCCCCCCCCCcchhHHHHHHHHhcCcEEEEec----------------CCCEEEEEEeCCCCCHHHHHH
Confidence 3347999999982 23333333322 4666632 13356777765443 333444
Q ss_pred HHHHHHHHHHhcc
Q 030537 108 RLDHAVAILENLL 120 (175)
Q Consensus 108 ~l~~A~e~Ie~lL 120 (175)
-+...++.|.+.+
T Consensus 187 Ni~a~l~~i~~~~ 199 (230)
T PRK05424 187 NLKALIDAIKKAK 199 (230)
T ss_pred HHHHHHHHHHHhC
Confidence 5555555555544
No 79
>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=41.61 E-value=21 Score=23.42 Aligned_cols=19 Identities=21% Similarity=0.336 Sum_probs=15.6
Q ss_pred hHHHHHhhhCceEEEeccC
Q 030537 54 SLKRVEAMTECTVFIRGQS 72 (175)
Q Consensus 54 TlK~ie~eTgckI~IRGkG 72 (175)
.+++||++.|+++.+|..+
T Consensus 33 ~i~~LE~~lg~~Lf~r~~~ 51 (60)
T PF00126_consen 33 QIKQLEEELGVPLFERSGR 51 (60)
T ss_dssp HHHHHHHHHTS-SEEECSS
T ss_pred HHHHHHHHhCCeEEEECCC
Confidence 5799999999999999654
No 80
>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=39.06 E-value=53 Score=27.85 Aligned_cols=12 Identities=67% Similarity=1.215 Sum_probs=9.5
Q ss_pred cceeEEEeCCCC
Q 030537 41 FNFVGRILGPRG 52 (175)
Q Consensus 41 ~NfvGrIiGPrG 52 (175)
...+|+||||||
T Consensus 122 l~~Lg~iLGPrG 133 (227)
T TIGR01169 122 VGKLGRILGPRG 133 (227)
T ss_pred HHHhcccccccc
Confidence 344599999996
No 81
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=38.70 E-value=88 Score=25.38 Aligned_cols=83 Identities=13% Similarity=0.150 Sum_probs=51.7
Q ss_pred eeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHHHHHHHHHHHHhccCC
Q 030537 43 FVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINSRLDHAVAILENLLKP 122 (175)
Q Consensus 43 fvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~~l~~A~e~Ie~lL~p 122 (175)
.+-+|+.++|..++.|-...||+|.+.- +.-.+.|+|.-. .++.+.+.|.++|..
T Consensus 36 ~~~LLl~~~~~~L~~l~~~~~~~I~~~~-------------------~~~~i~I~g~k~------~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 36 EFFLLLTGNGRILENLAARNGAKIEVSR-------------------SENRIRITGTKS------TAEYIEASINEILSN 90 (210)
T ss_pred heeeeecCCchHHHHHHHhcCceEEEec-------------------CCcEEEEEccHH------HHHHHHHHHHHHHhh
Confidence 4567999999999999888899999973 112677877543 234444445555432
Q ss_pred C-------Cc--------chHHHHHHHHHHHHHhcCccCCCCC
Q 030537 123 V-------DE--------SLDHYKKQQLREFATLNGTLREESP 150 (175)
Q Consensus 123 ~-------~e--------~~de~K~~QL~eLA~lNGt~r~~~~ 150 (175)
+ +. +...+...=|.+++-+-+||-+...
T Consensus 91 i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~ 133 (210)
T PF14611_consen 91 IRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNP 133 (210)
T ss_pred cEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECC
Confidence 2 11 1112345557788888888754433
No 82
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=36.71 E-value=43 Score=33.38 Aligned_cols=31 Identities=13% Similarity=0.341 Sum_probs=27.5
Q ss_pred eeEEEeCCCCchHHHHHhhhCceEEEeccCC
Q 030537 43 FVGRILGPRGNSLKRVEAMTECTVFIRGQSS 73 (175)
Q Consensus 43 fvGrIiGPrG~TlK~ie~eTgckI~IRGkGS 73 (175)
|..-++|..|..+..|++++.|+|.++=.||
T Consensus 357 ~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~ 387 (753)
T KOG2208|consen 357 ELKFVIGKKGANIEKIREESQVKIDLPKQGS 387 (753)
T ss_pred hhhhhcCCCCccHHHHHHhhhhceecccccC
Confidence 5667899999999999999999999996564
No 83
>PRK13764 ATPase; Provisional
Probab=36.20 E-value=27 Score=33.93 Aligned_cols=39 Identities=21% Similarity=0.414 Sum_probs=32.7
Q ss_pred EEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCC
Q 030537 28 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSS 73 (175)
Q Consensus 28 ~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS 73 (175)
..||||-+..| .+||-+|.++++||+..|-.|.||-...
T Consensus 483 ~~v~~~~~~~~-------~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 483 AVVYVPEKDIP-------KVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred EEEEEChhhhh-------HHhccCcchHHHHHHHhCCceEEEEccc
Confidence 45788865554 5899999999999999999999997654
No 84
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=35.40 E-value=42 Score=27.07 Aligned_cols=26 Identities=19% Similarity=0.351 Sum_probs=23.5
Q ss_pred eEEEeCCCCchHHHHHhhhCceEEEe
Q 030537 44 VGRILGPRGNSLKRVEAMTECTVFIR 69 (175)
Q Consensus 44 vGrIiGPrG~TlK~ie~eTgckI~IR 69 (175)
-|+++|-+|.|++.|-++||=+..|.
T Consensus 87 PG~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 87 PGLVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred CeEEEecCchhHHHHHHHhCCeeEEE
Confidence 38999999999999999999877775
No 85
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=35.36 E-value=53 Score=30.27 Aligned_cols=41 Identities=12% Similarity=0.215 Sum_probs=34.0
Q ss_pred EEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCC
Q 030537 28 IRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVK 75 (175)
Q Consensus 28 ~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k 75 (175)
..++||.++ .++.||-+|.+++.--+.||.+|-|+.-+|.-
T Consensus 310 ~~V~V~~~q-------lslAIGk~GqNvrLA~~LtGwkIDI~s~~~~~ 350 (374)
T PRK12328 310 AIVTLLSDQ-------KSKAIGKNGINIRLASMLTGYEIELNEIGSKE 350 (374)
T ss_pred EEEEEChHH-------hhhhhcCCChhHHHHHHHhCCEEEEEECCCCc
Confidence 456666444 36899999999999999999999999888743
No 86
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=34.38 E-value=28 Score=28.80 Aligned_cols=22 Identities=18% Similarity=0.360 Sum_probs=18.7
Q ss_pred chHHHHHhhhCceEEEeccCCC
Q 030537 53 NSLKRVEAMTECTVFIRGQSSV 74 (175)
Q Consensus 53 ~TlK~ie~eTgckI~IRGkGS~ 74 (175)
..+|+||++.|+++..|++|..
T Consensus 35 ~~i~~LE~~lg~~Lf~R~r~i~ 56 (294)
T PRK13348 35 QRIKALEESLGQPLLVRGRPCR 56 (294)
T ss_pred HHHHHHHHHhCceeeecCCCCc
Confidence 3589999999999999997643
No 87
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=34.04 E-value=54 Score=26.91 Aligned_cols=20 Identities=25% Similarity=0.353 Sum_probs=17.5
Q ss_pred chHHHHHhhhCceEEEeccC
Q 030537 53 NSLKRVEAMTECTVFIRGQS 72 (175)
Q Consensus 53 ~TlK~ie~eTgckI~IRGkG 72 (175)
..+|+||++.|+++.+|...
T Consensus 40 ~~i~~LE~~lg~~Lf~R~~r 59 (294)
T PRK09986 40 IHIKELEDQLGTPLFIRHSR 59 (294)
T ss_pred HHHHHHHHHhCCeeEeeCCC
Confidence 46899999999999999754
No 88
>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=33.30 E-value=7.9 Score=30.70 Aligned_cols=18 Identities=39% Similarity=0.776 Sum_probs=14.4
Q ss_pred CCCCCCcceeEEEeCCCCc
Q 030537 35 DKYPNQFNFVGRILGPRGN 53 (175)
Q Consensus 35 ~~yP~~~NfvGrIiGPrG~ 53 (175)
+-.|. ...+|+||||||.
T Consensus 101 ~~m~~-l~~Lg~iLGprGl 118 (141)
T TIGR01170 101 DIVPE-LAQLRRLLGPKGL 118 (141)
T ss_pred HHHHH-HHHhhcccccCcC
Confidence 33565 7889999999985
No 89
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=28.20 E-value=19 Score=28.02 Aligned_cols=43 Identities=26% Similarity=0.431 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhccC-CCCcchHHHHHHHHHHHHHhcCccCCCCC
Q 030537 107 SRLDHAVAILENLLK-PVDESLDHYKKQQLREFATLNGTLREESP 150 (175)
Q Consensus 107 ~~l~~A~e~Ie~lL~-p~~e~~de~K~~QL~eLA~lNGt~r~~~~ 150 (175)
.+|..|+.+|+.-|. .+.|+ -|.=+.|.+||...|..++..+.
T Consensus 48 NKIeQAMDLVKtHLmfAVREE-Ve~Lk~qI~eL~er~~~Le~EN~ 91 (123)
T KOG4797|consen 48 NKIEQAMDLVKTHLMFAVREE-VEVLKEQIRELEERNSALERENS 91 (123)
T ss_pred hHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 389999999998664 34443 34556889999888877765543
No 90
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=27.98 E-value=80 Score=29.09 Aligned_cols=36 Identities=22% Similarity=0.128 Sum_probs=26.4
Q ss_pred hhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchh
Q 030537 60 AMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPED 103 (175)
Q Consensus 60 ~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~ 103 (175)
..+|+.+.|||+|--+-. .+-..+|+|.|....|.+
T Consensus 300 tq~G~~~rl~gkG~p~~~--------~~~~GDl~v~v~v~~P~~ 335 (371)
T COG0484 300 TQTGEVFRLRGKGMPKLR--------SGGRGDLYVRVKVETPKN 335 (371)
T ss_pred CccCcEEEEcCCCccccC--------CCCcCCEEEEEEEEcCCC
Confidence 356999999999953321 123479999999999865
No 91
>PF02559 CarD_CdnL_TRCF: CarD-like/TRCF domain; InterPro: IPR003711 The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. A single gene, carD, is required for the activation of both light- and starvation-inducible genes []. The predicted protein contains four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3MLQ_H 2EYQ_A.
Probab=27.90 E-value=51 Score=23.62 Aligned_cols=26 Identities=31% Similarity=0.595 Sum_probs=15.8
Q ss_pred EEEccCCCCCCCcceeEEEeCCCCchHHHHH
Q 030537 29 RLDVPVDKYPNQFNFVGRILGPRGNSLKRVE 59 (175)
Q Consensus 29 Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie 59 (175)
+||||+++ .+-++|-+++.+.. ..|.
T Consensus 43 ~i~vPv~~----~~~i~R~v~~~~~~-~~l~ 68 (98)
T PF02559_consen 43 TIYVPVDN----ADKIGRYVGSREEA-PLLD 68 (98)
T ss_dssp EEEEECCC----GGGEEE--SS-SSS-----
T ss_pred EEEEEcCC----hhhccCCcCCccch-hHHH
Confidence 79999998 56677999988766 4443
No 92
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=27.78 E-value=8.7 Score=26.47 Aligned_cols=25 Identities=16% Similarity=0.426 Sum_probs=20.0
Q ss_pred ceeEEEeCCCCchHHHHHhhhCceE
Q 030537 42 NFVGRILGPRGNSLKRVEAMTECTV 66 (175)
Q Consensus 42 NfvGrIiGPrG~TlK~ie~eTgckI 66 (175)
...|.+||-+|++++.|....+-.+
T Consensus 34 ~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 34 SQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CCccHhHHhhhHHHHHHHHHHHHHH
Confidence 4457899999999999988776444
No 93
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=27.74 E-value=1.4e+02 Score=27.59 Aligned_cols=41 Identities=17% Similarity=0.290 Sum_probs=28.6
Q ss_pred ceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhh--------hCceEEEe
Q 030537 23 VVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAM--------TECTVFIR 69 (175)
Q Consensus 23 ~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~e--------TgckI~IR 69 (175)
.+.++.+|..|- -...-+|||++|.-+++|-.+ .+|++.+|
T Consensus 325 ~l~I~~~v~~pK------~s~~klliGkgG~ki~qI~~~a~~dL~~if~r~V~l~ 373 (379)
T KOG1423|consen 325 VLFIQVEVVCPK------NSQKKLLIGKGGKKISQIGTRANEDLEDIFQRKVFLR 373 (379)
T ss_pred EEEEEEEEEcCC------CcceeEEEcCCCccHHHHHHHHHHHHHHHhhceeeEE
Confidence 345555666663 455668999999999998554 46776665
No 94
>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=26.94 E-value=37 Score=28.11 Aligned_cols=22 Identities=18% Similarity=0.241 Sum_probs=18.4
Q ss_pred hHHHHHhhhCceEEEeccCCCC
Q 030537 54 SLKRVEAMTECTVFIRGQSSVK 75 (175)
Q Consensus 54 TlK~ie~eTgckI~IRGkGS~k 75 (175)
.+|+||++.|+++..|++|-.-
T Consensus 35 ~I~~LE~~lg~~Lf~R~r~~~l 56 (292)
T TIGR03298 35 RIKALEERLGQPLLVRTQPCRA 56 (292)
T ss_pred HHHHHHHHhCchheecCCCCcC
Confidence 4799999999999999876433
No 95
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=26.82 E-value=32 Score=25.70 Aligned_cols=22 Identities=18% Similarity=0.388 Sum_probs=18.4
Q ss_pred eeEEEeCCCCchHHHHHhhhCc
Q 030537 43 FVGRILGPRGNSLKRVEAMTEC 64 (175)
Q Consensus 43 fvGrIiGPrG~TlK~ie~eTgc 64 (175)
+-|.|||-+|.+++.|+.....
T Consensus 71 rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 71 RPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred CCCcccCCchHHHHHHHHHHHH
Confidence 4579999999999999887653
No 96
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=26.47 E-value=56 Score=31.85 Aligned_cols=41 Identities=22% Similarity=0.349 Sum_probs=33.4
Q ss_pred eEEEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccC
Q 030537 25 KRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQS 72 (175)
Q Consensus 25 k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkG 72 (175)
+...++.+| .-||-+|+|-.|+..|.|+..|++||.++-+-
T Consensus 67 ~v~~e~Vv~-------~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed 107 (608)
T KOG2279|consen 67 DIEIEMVVP-------QEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED 107 (608)
T ss_pred heeeeEeec-------ccceeeeeccccCCcchhhcccccceecCccc
Confidence 444555665 46788999999999999999999999999543
No 97
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=26.35 E-value=49 Score=27.55 Aligned_cols=21 Identities=19% Similarity=0.278 Sum_probs=18.3
Q ss_pred hHHHHHhhhCceEEEeccCCC
Q 030537 54 SLKRVEAMTECTVFIRGQSSV 74 (175)
Q Consensus 54 TlK~ie~eTgckI~IRGkGS~ 74 (175)
.+|+||++.|+++..|++|-.
T Consensus 36 ~I~~LE~~lg~~LF~R~~~~~ 56 (294)
T PRK03635 36 RIKALEERVGQVLLVRTQPCR 56 (294)
T ss_pred HHHHHHHHhCceeeecCCCCc
Confidence 589999999999999987644
No 98
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=24.75 E-value=60 Score=27.12 Aligned_cols=18 Identities=17% Similarity=0.355 Sum_probs=16.1
Q ss_pred chHHHHHhhhCceEEEec
Q 030537 53 NSLKRVEAMTECTVFIRG 70 (175)
Q Consensus 53 ~TlK~ie~eTgckI~IRG 70 (175)
..+|+||++.|+.+.+|.
T Consensus 35 ~~I~~LE~~lg~~LF~R~ 52 (300)
T PRK11074 35 YTVRQLEEWLAVPLFERR 52 (300)
T ss_pred HHHHHHHHHhCCeeEEeC
Confidence 358999999999999994
No 99
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=24.58 E-value=58 Score=26.96 Aligned_cols=17 Identities=18% Similarity=0.409 Sum_probs=15.6
Q ss_pred hHHHHHhhhCceEEEec
Q 030537 54 SLKRVEAMTECTVFIRG 70 (175)
Q Consensus 54 TlK~ie~eTgckI~IRG 70 (175)
.+|+||++.|+++..|.
T Consensus 35 ~I~~LE~~lG~~LF~R~ 51 (275)
T PRK03601 35 RIRQLENQLGVNLFTRH 51 (275)
T ss_pred HHHHHHHHhCCceEEEC
Confidence 58999999999999994
No 100
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=24.35 E-value=55 Score=31.87 Aligned_cols=42 Identities=19% Similarity=0.296 Sum_probs=34.1
Q ss_pred EEEEEccCCCCCCCcceeEEEeCCCCchHHHHHhhhCceEEEec
Q 030537 27 VIRLDVPVDKYPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRG 70 (175)
Q Consensus 27 ~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRG 70 (175)
.+-+.||-=+.|+ -.+|+|||-.|.|++-+-..++.++.|+=
T Consensus 292 ~~~l~i~e~e~p~--~lsg~lig~~gey~s~yssasn~~~hi~t 333 (608)
T KOG2279|consen 292 SEALAIPEMEMPE--ILSGDLIGHAGEYLSVYSSASNHPNHIWT 333 (608)
T ss_pred ccccccceeecCc--ccccchhhhhhhhhhhhhhccCccceEEe
Confidence 3444555445665 78999999999999999999999999984
No 101
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=24.14 E-value=66 Score=27.41 Aligned_cols=60 Identities=17% Similarity=0.190 Sum_probs=39.0
Q ss_pred eEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchh-hHHHHHHHHHHHHHhccC
Q 030537 44 VGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPED-IINSRLDHAVAILENLLK 121 (175)
Q Consensus 44 vGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~-~~~~~l~~A~e~Ie~lL~ 121 (175)
.|+|||-+|.||..||-.+..-+..++ +. -..|.+.+.++.. +.+.-+..|..+-++.+.
T Consensus 102 ~~~LIG~~Gk~LdALQ~L~n~~l~~~~--g~----------------~~~v~ldv~~yRerR~e~L~~LA~~~A~rV~~ 162 (208)
T COG1847 102 AGRLIGKHGKTLDALQYLANLYLNKIG--GK----------------FKRVTLDVGDYRERRKETLIKLAERAAERVLE 162 (208)
T ss_pred hhhhhccCCcchHHHHHHHHHHhhhhc--Cc----------------ceEEEEEhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 899999999999999999987665532 21 2356666667633 333334445555555543
No 102
>COG3967 DltE Short-chain dehydrogenase involved in D-alanine esterification of lipoteichoic acid and wall teichoic acid (D-alanine transfer protein) [Cell envelope biogenesis, outer membrane]
Probab=23.96 E-value=84 Score=27.36 Aligned_cols=72 Identities=24% Similarity=0.180 Sum_probs=49.4
Q ss_pred hhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchhhHHHHHHHHHHHHHhccCCCCcchHHHHHHHHHHHH
Q 030537 60 AMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPEDIINSRLDHAVAILENLLKPVDESLDHYKKQQLREFA 139 (175)
Q Consensus 60 ~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~~~~~~l~~A~e~Ie~lL~p~~e~~de~K~~QL~eLA 139 (175)
+.||-.|.|-|-+|+=.-..-. .+ ...-=-|.|.+++.+ +|+.|.+..-.+..-+-|-.|...+.+|.|..
T Consensus 2 k~tgnTiLITGG~sGIGl~lak--~f--~elgN~VIi~gR~e~-----~L~e~~~~~p~~~t~v~Dv~d~~~~~~lvewL 72 (245)
T COG3967 2 KTTGNTILITGGASGIGLALAK--RF--LELGNTVIICGRNEE-----RLAEAKAENPEIHTEVCDVADRDSRRELVEWL 72 (245)
T ss_pred cccCcEEEEeCCcchhhHHHHH--HH--HHhCCEEEEecCcHH-----HHHHHHhcCcchheeeecccchhhHHHHHHHH
Confidence 4688999999988753221100 00 011126899998864 89999999999988877777777777777765
Q ss_pred H
Q 030537 140 T 140 (175)
Q Consensus 140 ~ 140 (175)
.
T Consensus 73 k 73 (245)
T COG3967 73 K 73 (245)
T ss_pred H
Confidence 4
No 103
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=23.78 E-value=26 Score=29.87 Aligned_cols=10 Identities=70% Similarity=1.421 Sum_probs=8.3
Q ss_pred eEEEeCCCCc
Q 030537 44 VGRILGPRGN 53 (175)
Q Consensus 44 vGrIiGPrG~ 53 (175)
+|+||||||.
T Consensus 126 LgriLGprGl 135 (229)
T CHL00129 126 LGRVLGPRGL 135 (229)
T ss_pred hcCcccccCC
Confidence 5999999963
No 104
>PF07582 AP_endonuc_2_N: AP endonuclease family 2 C terminus; InterPro: IPR011418 DNA damaging agents such as the anti-tumour drugs bleomycin and neocarzinostatin or those that generate oxygen radicals produce a variety of lesions in DNA. Amongst these is base-loss which forms apurinic/apyrimidinic (AP) sites or strand breaks with atypical 3' termini. DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3' terminus of DNA strand breaks. AP endonucleases can be classified into two families based on sequence similarity []. This entry represents a highly-conserved sequence found at the C terminus of several apurinic/apyrimidinic (AP) endonucleases in a range of Gram-positive and Gram-negative bacteria. ; PDB: 3LMZ_A 2ZDS_D.
Probab=23.56 E-value=1.1e+02 Score=20.50 Aligned_cols=32 Identities=22% Similarity=-0.030 Sum_probs=17.9
Q ss_pred EEEEEeeCchhhHHHHHHHHHHHHHhccCCCC
Q 030537 93 HVLGEAEFPEDIINSRLDHAVAILENLLKPVD 124 (175)
Q Consensus 93 HV~Isa~~~~~~~~~~l~~A~e~Ie~lL~p~~ 124 (175)
-|-|+.++..-.....+.+|++.++++|..++
T Consensus 17 ~~siE~ED~~~~~~~G~~~a~~~lr~~l~~~~ 48 (55)
T PF07582_consen 17 WLSIEHEDALMDPEEGAREAAAFLRKLLIREP 48 (55)
T ss_dssp EEEE---STTTSHHHHHHHHHHHHHTT-----
T ss_pred eEEEEeecCCCCHHHHHHHHHHHHHHhcCCCC
Confidence 34566665444456799999999999987654
No 105
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=23.00 E-value=67 Score=27.21 Aligned_cols=19 Identities=32% Similarity=0.588 Sum_probs=16.8
Q ss_pred hHHHHHhhhCceEEEe-ccC
Q 030537 54 SLKRVEAMTECTVFIR-GQS 72 (175)
Q Consensus 54 TlK~ie~eTgckI~IR-GkG 72 (175)
.+|+||++.|+++.+| |+|
T Consensus 36 ~I~~LE~~lg~~Lf~R~~r~ 55 (309)
T PRK12683 36 QIKDLEDELGVEIFIRRGKR 55 (309)
T ss_pred HHHHHHHHhCCeeEeeCCCC
Confidence 5899999999999999 455
No 106
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=22.84 E-value=69 Score=27.11 Aligned_cols=19 Identities=16% Similarity=0.303 Sum_probs=16.6
Q ss_pred hHHHHHhhhCceEEEec-cC
Q 030537 54 SLKRVEAMTECTVFIRG-QS 72 (175)
Q Consensus 54 TlK~ie~eTgckI~IRG-kG 72 (175)
.+|+||++.|+++.+|. +|
T Consensus 36 ~ik~LE~~lg~~Lf~R~~r~ 55 (313)
T PRK12684 36 AIIELEDELGVEIFTRHGKR 55 (313)
T ss_pred HHHHHHHHhCCeeEEEcCCc
Confidence 58999999999999994 55
No 107
>PF00381 PTS-HPr: PTS HPr component phosphorylation site; InterPro: IPR005698 The histidine-containing phosphocarrier protein (HPr) is a central component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), which transfers metabolic carbohydrates across the cell membrane in many bacterial species [, ]. PTS catalyses the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is as follows: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to Enzyme I (EI) of the PTS, which in turn transfers it to the phosphoryl carrier protein (HPr) [, ]. Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease complex (enzymes EII/EIII). HPr [, ] is a small cytoplasmic protein of 70 to 90 amino acid residues. In some bacteria, HPr is a domain in a larger protein that includes a EIII(Fru) (IIA) domain and in some cases also the EI domain. A conserved histidine in the N-terminal section of HPr serves as an acceptor for the phosphoryl group of EI. In the central part of HPr, there is a conserved serine which (in Gram-positive bacteria only) is phosphorylated by an ATP-dependent protein kinase; a process which probably play a regulatory role in sugar transport. The overall architecture of the HPr domain has been described as an open faced beta-sandwich in which a beta-sheet is packed against three alpha-helices. Regulatory phosphorylation at the conserved Ser residue does not appear to induce large structural changes to the HPr domain, in particular in the region of the active site [, ].; GO: 0005351 sugar:hydrogen symporter activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TXE_A 1QR5_A 1RZR_S 2NZU_L 2OEN_L 2NZV_L 1Y51_B 1Y4Y_A 1Y50_A 2HPR_A ....
Probab=22.73 E-value=83 Score=21.92 Aligned_cols=58 Identities=14% Similarity=0.204 Sum_probs=32.2
Q ss_pred HHHHHhhhCceEEEeccCCCCCccccC---CCCCCCCCCCcEEEEEeeCchhhHHHHHHHHHHHHHhccC
Q 030537 55 LKRVEAMTECTVFIRGQSSVKDSLKEG---KIRYEHLNEPLHVLGEAEFPEDIINSRLDHAVAILENLLK 121 (175)
Q Consensus 55 lK~ie~eTgckI~IRGkGS~k~~~~e~---~p~~e~~~epLHV~Isa~~~~~~~~~~l~~A~e~Ie~lL~ 121 (175)
+-++-+..+|.|.|+-.+..-|.++-- .-+. .-.+.++|.+++++. +.|++.|.++|.
T Consensus 22 lv~~a~~~~~~i~i~~~~~~vdakSil~l~~L~~-~~G~~i~i~~~G~de--------~~a~~~i~~~~~ 82 (84)
T PF00381_consen 22 LVQIASKFDSDITIRKGGKTVDAKSILGLMSLGA-KKGDEIEIEAEGEDE--------EEALEAIAEFLE 82 (84)
T ss_dssp HHHHHHTSSSEEEEEETTEEEETTSHHHHHHHTB-STTEEEEEEEESTTH--------HHHHHHHHHHHH
T ss_pred HHHHHhhCCCEEEEEeCceeEecCCHHHHhhhhc-CCCCEEEEEEECcCH--------HHHHHHHHHHHh
Confidence 345566779999999655332221100 0011 135667777777664 356666666653
No 108
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=22.67 E-value=76 Score=26.40 Aligned_cols=21 Identities=24% Similarity=0.407 Sum_probs=18.1
Q ss_pred hHHHHHhhhCceEEEeccCCC
Q 030537 54 SLKRVEAMTECTVFIRGQSSV 74 (175)
Q Consensus 54 TlK~ie~eTgckI~IRGkGS~ 74 (175)
.+|+||++.|+++..|.++.+
T Consensus 39 ~i~~LE~~lG~~LF~R~~r~~ 59 (302)
T PRK09791 39 SIQELEEGLAAQLFFRRSKGV 59 (302)
T ss_pred HHHHHHHHhCCeEEEEcCCCc
Confidence 589999999999999976644
No 109
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=22.09 E-value=74 Score=26.71 Aligned_cols=19 Identities=21% Similarity=0.370 Sum_probs=16.6
Q ss_pred hHHHHHhhhCceEEEec-cC
Q 030537 54 SLKRVEAMTECTVFIRG-QS 72 (175)
Q Consensus 54 TlK~ie~eTgckI~IRG-kG 72 (175)
.+|+||++.|+++.+|. +|
T Consensus 36 ~I~~LE~~lg~~LF~R~~~~ 55 (309)
T PRK12682 36 AIIELEEELGIEIFIRHGKR 55 (309)
T ss_pred HHHHHHHHhCCeeEEECCCC
Confidence 58999999999999995 45
No 110
>COG0080 RplK Ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=21.22 E-value=2.4e+02 Score=22.67 Aligned_cols=98 Identities=20% Similarity=0.203 Sum_probs=56.3
Q ss_pred eEEEEEEccCCC-CCCCcceeEEEeCCCCchHHHHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCchh
Q 030537 25 KRVIRLDVPVDK-YPNQFNFVGRILGPRGNSLKRVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFPED 103 (175)
Q Consensus 25 k~~~Ki~IPv~~-yP~~~NfvGrIiGPrG~TlK~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~~~ 103 (175)
....|+.||-=+ -|. -=+|--|||.|-++...-++.+.+-.= . ...++.|.|++.....
T Consensus 5 ~~~ikl~v~aGkA~p~--PpvGPALG~~Gvni~~f~k~fN~~T~~-~-----------------~G~~vPV~Itv~~drs 64 (141)
T COG0080 5 VKIIKLQVPAGKANPS--PPVGPALGQLGVNIMEFCKEFNAATKD-E-----------------KGLPVPVVITVYEDRS 64 (141)
T ss_pred ceEEEEEecccccCCC--CCCCccccccCCCHHHHHHHHHHHhhc-c-----------------CCCeeeEEEEEEcCCc
Confidence 445667777544 343 568999999999999988888754322 1 2457778887762110
Q ss_pred -hHHHHHHHHHHHHHhccCCCC-------cchHHHHHHHHHHHHHhc
Q 030537 104 -IINSRLDHAVAILENLLKPVD-------ESLDHYKKQQLREFATLN 142 (175)
Q Consensus 104 -~~~~~l~~A~e~Ie~lL~p~~-------e~~de~K~~QL~eLA~lN 142 (175)
...-+.==|-.+|.+.+.-.. +-.-.+-+.|++|.|.+-
T Consensus 65 ftf~~ktPPas~LlkKa~g~~~Gs~~p~k~~vG~lt~~qv~eIA~~K 111 (141)
T COG0080 65 FTFIVKTPPASALLKKAAGIEKGSGKPNKNKVGKLTLAQVREIAKTK 111 (141)
T ss_pred EEEEECCCCHHHHHHHHhCCCCCCCCCCcceeeeeeHHHHHHHHHHh
Confidence 000011224455555553221 112245578888888654
No 111
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=21.09 E-value=29 Score=29.96 Aligned_cols=72 Identities=21% Similarity=0.293 Sum_probs=41.7
Q ss_pred CCCCCCCcceeEEEeCCCCch-----------HH-HHHhhhCceEEEeccCCCCCccccCCCCCCCCCCCcEEEEEeeCc
Q 030537 34 VDKYPNQFNFVGRILGPRGNS-----------LK-RVEAMTECTVFIRGQSSVKDSLKEGKIRYEHLNEPLHVLGEAEFP 101 (175)
Q Consensus 34 v~~yP~~~NfvGrIiGPrG~T-----------lK-~ie~eTgckI~IRGkGS~k~~~~e~~p~~e~~~epLHV~Isa~~~ 101 (175)
.+-.|. +-.+|++|||||.. +. .+++.-+-+|..|=+. ..-+|+.|-..+.
T Consensus 119 pdmM~~-v~~LG~vLGPRGlMP~Pk~gTvt~Dv~~av~~~K~g~v~~R~dk----------------~g~ih~~iGk~sf 181 (228)
T COG0081 119 PDMMPL-VGKLGKVLGPRGLMPNPKTGTVTDDVAKAVEELKKGTVEFRADK----------------AGVIHVPIGKVSF 181 (228)
T ss_pred chHHHH-HHHHhhhcCCCCCCCCCCCCCCCcCHHHHHHHHhcCcEEEEECC----------------CceEEEEecCCCC
Confidence 344555 67799999999963 22 3333333367777322 3357998876554
Q ss_pred h-hhHHHHHHHHHHHHHhccCC
Q 030537 102 E-DIINSRLDHAVAILENLLKP 122 (175)
Q Consensus 102 ~-~~~~~~l~~A~e~Ie~lL~p 122 (175)
. +...+-+...++.|...+..
T Consensus 182 ~~e~L~eNi~a~l~~i~~~~p~ 203 (228)
T COG0081 182 DDEKLAENIEALLNAIVKAKPA 203 (228)
T ss_pred CHHHHHHHHHHHHHHHHHhCcC
Confidence 2 23344556666666665543
No 112
>COG1159 Era GTPase [General function prediction only]
Probab=20.56 E-value=2e+02 Score=25.76 Aligned_cols=43 Identities=23% Similarity=0.473 Sum_probs=31.1
Q ss_pred CCceeEEEEEEccCCCCCCCcceeEEEeCCCCchHHHH--------HhhhCceEEEe
Q 030537 21 APVVKRVIRLDVPVDKYPNQFNFVGRILGPRGNSLKRV--------EAMTECTVFIR 69 (175)
Q Consensus 21 ~~~~k~~~Ki~IPv~~yP~~~NfvGrIiGPrG~TlK~i--------e~eTgckI~IR 69 (175)
.-.++...-|+|+-+.+ -|-|||-+|..+|+| |+-.+|+|.+-
T Consensus 224 ~~~~~I~a~I~Ver~sQ------K~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L~ 274 (298)
T COG1159 224 KGLLKIHATIYVERESQ------KGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYLE 274 (298)
T ss_pred CCeEEEEEEEEEecCCc------cceEECCCcHHHHHHHHHHHHHHHHHhCCceEEE
Confidence 34556666788875544 478999999999976 56667777654
No 113
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=20.13 E-value=1.1e+02 Score=31.51 Aligned_cols=25 Identities=16% Similarity=0.380 Sum_probs=19.5
Q ss_pred HHHHHHHhcCccCCCCC-CCCCCCCC
Q 030537 134 QLREFATLNGTLREESP-SMSPSMSP 158 (175)
Q Consensus 134 QL~eLA~lNGt~r~~~~-~~~g~~~~ 158 (175)
.+.+++.|...+.+..+ ++|||++|
T Consensus 489 ~~~~~~~Lr~~L~~GePCPVCGS~~H 514 (1047)
T PRK10246 489 RIKDLEAQRAQLQAGQPCPLCGSTSH 514 (1047)
T ss_pred HHHHHHHHHHhCCCCCCcCCCCcccC
Confidence 34457778888886665 99999999
Done!