Query 039634
Match_columns 127
No_of_seqs 109 out of 334
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 11:37:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039634.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039634hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1588 RNA-binding protein Sa 100.0 2.6E-36 5.7E-41 244.6 10.9 117 2-126 120-241 (259)
2 cd02395 SF1_like-KH Splicing f 99.9 2.3E-27 5.1E-32 173.5 9.7 88 2-98 28-120 (120)
3 KOG0119 Splicing factor 1/bran 99.9 1.1E-24 2.3E-29 189.3 7.6 91 2-103 166-262 (554)
4 COG5176 MSL5 Splicing factor ( 99.7 2.1E-17 4.5E-22 132.4 5.4 91 2-100 176-269 (269)
5 KOG1960 Predicted RNA-binding 95.7 0.0057 1.2E-07 53.8 1.9 61 2-76 237-297 (531)
6 cd02393 PNPase_KH Polynucleoti 95.3 0.035 7.6E-07 35.6 4.2 38 2-69 24-61 (61)
7 PF00013 KH_1: KH domain syndr 95.3 0.036 7.9E-07 34.6 4.0 39 2-68 22-60 (60)
8 cd00105 KH-I K homology RNA-bi 93.3 0.26 5.7E-06 30.4 4.8 42 2-68 22-63 (64)
9 smart00322 KH K homology RNA-b 93.1 0.32 6.9E-06 29.3 4.9 44 2-72 25-68 (69)
10 KOG1676 K-homology type RNA bi 92.3 0.24 5.1E-06 45.2 4.8 50 1-74 251-300 (600)
11 cd02394 vigilin_like_KH K homo 91.6 0.41 8.9E-06 29.9 4.1 40 2-68 22-61 (62)
12 cd02396 PCBP_like_KH K homolog 91.1 0.64 1.4E-05 29.7 4.7 43 2-68 22-64 (65)
13 TIGR03665 arCOG04150 arCOG0415 90.1 0.47 1E-05 36.3 4.0 41 2-74 111-151 (172)
14 PRK13763 putative RNA-processi 88.7 0.91 2E-05 35.0 4.7 44 2-74 25-71 (180)
15 PF13014 KH_3: KH domain 87.9 0.31 6.8E-06 28.7 1.3 16 2-17 13-28 (43)
16 PRK13763 putative RNA-processi 86.9 1.1 2.3E-05 34.6 4.2 41 2-74 117-157 (180)
17 TIGR02696 pppGpp_PNP guanosine 84.8 1.9 4.1E-05 40.3 5.3 43 2-74 600-642 (719)
18 KOG1960 Predicted RNA-binding 81.4 0.78 1.7E-05 40.7 1.3 64 2-79 317-380 (531)
19 TIGR03665 arCOG04150 arCOG0415 80.1 3.9 8.5E-05 31.2 4.7 43 2-74 20-65 (172)
20 TIGR03591 polynuc_phos polyrib 76.0 4.7 0.0001 37.2 4.8 44 1-74 572-615 (684)
21 PRK13348 chromosome replicatio 67.5 3.6 7.7E-05 32.2 1.7 21 2-22 37-57 (294)
22 PRK04163 exosome complex RNA-b 67.1 12 0.00026 29.9 4.7 26 44-74 184-209 (235)
23 COG1094 Predicted RNA-binding 64.2 31 0.00068 27.5 6.5 44 2-77 124-167 (194)
24 PLN00207 polyribonucleotide nu 59.7 10 0.00023 36.4 3.6 30 40-74 721-750 (891)
25 KOG0334 RNA helicase [RNA proc 58.9 6.9 0.00015 38.0 2.2 56 2-73 921-976 (997)
26 TIGR03298 argP transcriptional 55.6 6.2 0.00013 30.8 1.2 20 2-21 36-55 (292)
27 PRK11824 polynucleotide phosph 55.1 15 0.00033 34.0 3.7 28 42-74 591-618 (693)
28 PF00126 HTH_1: Bacterial regu 55.0 6.1 0.00013 24.6 0.8 18 2-19 34-51 (60)
29 PRK03635 chromosome replicatio 54.9 8.5 0.00018 30.3 1.9 21 2-22 37-57 (294)
30 PRK15421 DNA-binding transcrip 53.9 8.3 0.00018 31.1 1.7 20 2-21 37-57 (317)
31 PRK10094 DNA-binding transcrip 53.6 8.4 0.00018 30.8 1.6 19 2-20 37-56 (308)
32 PRK11139 DNA-binding transcrip 52.6 6.5 0.00014 30.8 0.9 19 2-20 41-60 (297)
33 PRK03601 transcriptional regul 51.5 8.2 0.00018 30.2 1.2 19 2-20 36-55 (275)
34 TIGR03339 phn_lysR aminoethylp 51.1 7 0.00015 29.8 0.8 18 2-19 32-50 (279)
35 KOG2814 Transcription coactiva 47.4 36 0.00078 29.5 4.5 46 2-73 79-124 (345)
36 PRK11074 putative DNA-binding 46.6 12 0.00027 29.4 1.6 18 2-19 37-55 (300)
37 PRK10216 DNA-binding transcrip 46.3 14 0.0003 29.5 1.9 21 2-22 43-64 (319)
38 KOG1676 K-homology type RNA bi 46.0 29 0.00064 32.0 4.0 50 2-74 161-210 (600)
39 TIGR00637 ModE_repress ModE mo 45.1 10 0.00022 26.4 0.8 18 2-19 37-54 (99)
40 PRK12684 transcriptional regul 42.8 16 0.00035 29.1 1.8 18 2-19 37-55 (313)
41 PRK12683 transcriptional regul 42.4 16 0.00035 29.2 1.7 19 2-20 37-56 (309)
42 KOG2190 PolyC-binding proteins 41.0 43 0.00093 30.0 4.2 49 1-73 159-207 (485)
43 PRK12682 transcriptional regul 40.4 19 0.00041 28.5 1.8 18 2-19 37-55 (309)
44 PRK09986 DNA-binding transcrip 37.1 22 0.00047 27.5 1.6 18 2-19 42-59 (294)
45 PRK09791 putative DNA-binding 35.5 25 0.00055 27.5 1.8 18 2-19 40-57 (302)
46 PRK10082 cell density-dependen 34.8 30 0.00065 27.3 2.1 19 2-20 46-65 (303)
47 PRK11013 DNA-binding transcrip 34.3 24 0.00053 27.9 1.5 18 2-19 39-56 (309)
48 PRK15243 transcriptional regul 33.5 22 0.00047 29.0 1.1 20 2-21 39-59 (297)
49 PF07582 AP_endonuc_2_N: AP en 33.4 55 0.0012 20.9 2.8 32 46-77 18-49 (55)
50 PRK10837 putative DNA-binding 32.4 26 0.00055 27.1 1.3 18 2-19 38-56 (290)
51 PRK11242 DNA-binding transcrip 31.3 31 0.00067 26.7 1.6 20 2-21 36-56 (296)
52 KOG2193 IGF-II mRNA-binding pr 30.9 24 0.00053 31.8 1.1 15 2-16 302-316 (584)
53 PRK15092 DNA-binding transcrip 30.1 31 0.00067 27.8 1.5 18 2-19 46-63 (310)
54 PRK12681 cysB transcriptional 29.7 36 0.00077 27.6 1.8 19 2-20 37-56 (324)
55 COG0484 DnaJ DnaJ-class molecu 29.2 90 0.002 27.2 4.2 35 8-55 301-335 (371)
56 TIGR02424 TF_pcaQ pca operon t 28.7 38 0.00083 26.4 1.8 18 2-19 38-55 (300)
57 PF06689 zf-C4_ClpX: ClpX C4-t 27.8 40 0.00086 20.0 1.3 27 44-70 14-40 (41)
58 PF01565 FAD_binding_4: FAD bi 26.6 1.8E+02 0.0038 20.2 4.8 47 7-53 21-73 (139)
59 KOG2874 rRNA processing protei 26.3 1.6E+02 0.0035 25.3 5.1 18 2-19 171-188 (356)
60 PRK09906 DNA-binding transcrip 25.9 46 0.00099 25.9 1.7 18 2-19 36-53 (296)
61 PF13189 Cytidylate_kin2: Cyti 25.5 50 0.0011 24.8 1.8 21 42-67 114-134 (179)
62 PRK14295 chaperone protein Dna 25.0 1.2E+02 0.0027 25.9 4.3 15 41-55 343-357 (389)
63 PRK12680 transcriptional regul 24.6 51 0.0011 26.8 1.8 18 2-19 37-54 (327)
64 PRK14997 LysR family transcrip 23.8 49 0.0011 25.9 1.5 18 2-19 37-54 (301)
65 PF13046 DUF3906: Protein of u 23.8 1.7E+02 0.0037 19.5 3.9 35 40-78 11-45 (64)
66 PRK11716 DNA-binding transcrip 23.2 56 0.0012 24.6 1.7 18 2-19 12-29 (269)
67 PRK11062 nhaR transcriptional 22.5 49 0.0011 26.0 1.4 18 2-19 39-56 (296)
68 PRK12679 cbl transcriptional r 22.5 59 0.0013 25.9 1.8 17 2-18 37-53 (316)
69 PRK09801 transcriptional activ 22.3 55 0.0012 26.2 1.6 18 2-19 41-58 (310)
70 CHL00180 rbcR LysR transcripti 21.1 66 0.0014 25.3 1.8 18 2-19 40-57 (305)
71 PF00639 Rotamase: PPIC-type P 20.6 1.4E+02 0.003 19.8 3.1 29 45-73 1-29 (95)
72 PHA00731 hypothetical protein 20.3 2.3E+02 0.005 20.3 4.2 51 43-93 30-91 (96)
73 PF00408 PGM_PMM_IV: Phosphogl 20.2 1.8E+02 0.0039 18.5 3.5 11 44-54 49-59 (73)
No 1
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=100.00 E-value=2.6e-36 Score=244.63 Aligned_cols=117 Identities=38% Similarity=0.525 Sum_probs=104.9
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccc-----cCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCC
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVE-----IKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVD 76 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~-----~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~ 76 (127)
+||||++|||||+||||| |+||. .+++|+|+|+++||||+|++++++.+|+.+|++|++.|++||+|.+
T Consensus 120 lkrLe~eTgCki~IrGrg------SmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~P~~ 193 (259)
T KOG1588|consen 120 LKRLEEETGCKIMIRGRG------SMRDKAKEEELRGDPGYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLVPDH 193 (259)
T ss_pred HHHHHHHHCCeEEEecCC------cccchHHHHHhhcCcchHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcCCCC
Confidence 799999999999999999 99988 6789999999999999999999999999999999999999999999
Q ss_pred cchhHHHHHHHHHHHHHhCcccCCCCCCCCCCCCCCCCCCcccccccccC
Q 039634 77 ESLDHYKKQQLRELAILNGTLREESPSMSPSMSPSMSPFNNAGMKCAETG 126 (127)
Q Consensus 77 e~~delK~~QL~eLA~lNGt~r~~~~~~~~~~~~~~~p~~~~~~~~~~~~ 126 (127)
++.| |++||+|||++||||..+....++...++++||+..+++|++++
T Consensus 194 e~~d--k~~QL~ELa~lngt~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~ 241 (259)
T KOG1588|consen 194 EDED--KREQLRELAILNGTYLRSESRKPSGGNGRGVPGNSAGGKRGKTG 241 (259)
T ss_pred CCch--HHHHHHHHhhcCCccccccccccCCCCCcCCCCCCCCcccccCC
Confidence 8877 99999999999999654444333333368999999999999875
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=99.95 E-value=2.3e-27 Score=173.52 Aligned_cols=88 Identities=48% Similarity=0.670 Sum_probs=78.3
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCC----CCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCCc
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKD----KPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDE 77 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~----~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~e 77 (127)
+|+||++|||+|.|||+| |+|++... .+.|+|++|||||+|+|+++ |.+++++|+++|+.||.++.+
T Consensus 28 iK~i~~eTg~kI~Irg~g------s~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~---~~e~~~~A~~~I~~ll~~~~~ 98 (120)
T cd02395 28 LKQLEKETGAKISIRGKG------SMKDGKKEEELRGPKYAHLNEPLHVLITAETP---PEEALAKAVEAIEELLKPAIE 98 (120)
T ss_pred HHHHHHHHCCEEEEecCc------ccccccccccccCcccccCCCCcEEEEEeCCc---HHHHHHHHHHHHHHHhccCCC
Confidence 699999999999999999 88877211 27899999999999999996 346799999999999999877
Q ss_pred c-hhHHHHHHHHHHHHHhCccc
Q 039634 78 S-LDHYKKQQLRELAILNGTLR 98 (127)
Q Consensus 78 ~-~delK~~QL~eLA~lNGt~r 98 (127)
+ .|++|++||+|||++|||||
T Consensus 99 ~~~~~~k~~ql~~la~~nGt~~ 120 (120)
T cd02395 99 GGNDELKREQLRELALLNGTYR 120 (120)
T ss_pred ccchHHHHHHHHHHHHhcccCC
Confidence 6 99999999999999999996
No 3
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=99.91 E-value=1.1e-24 Score=189.28 Aligned_cols=91 Identities=38% Similarity=0.552 Sum_probs=80.6
Q ss_pred chhhhhhcCcEEEEecCCCCCCcccccccc--CCCCCCC-CCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC---CC
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEI--KDKPGYE-HLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK---PV 75 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~--~~~~~~e-h~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~---p~ 75 (127)
||+||+||||||+||||| |+|||+ .++..|. ..+|||||+|+|+++++ |++|+++|+.||. .+
T Consensus 166 qK~lE~etgAKI~IRGkg------SvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek-----i~~Ai~vienli~~av~~ 234 (554)
T KOG0119|consen 166 QKRLERETGAKIAIRGKG------SVKEGKGRSDDLSYIPKENEPLHCLISADTQEK-----IKKAIAVIENLIQSAVSV 234 (554)
T ss_pred HHHHHHHhCCeEEEeccc------cccccccCCcccccccccccceeEEEecchHHH-----HHHHHHHHHHHHHhhccC
Confidence 799999999999999999 999995 2234442 47899999999999765 9999999999998 58
Q ss_pred CcchhHHHHHHHHHHHHHhCcccCCCCC
Q 039634 76 DESLDHYKKQQLRELAILNGTLREESPS 103 (127)
Q Consensus 76 ~e~~delK~~QL~eLA~lNGt~r~~~~~ 103 (127)
+|+++++|+.||+|||.+|||+|++++.
T Consensus 235 ~e~~n~l~~~Qlrela~lNgt~r~~d~~ 262 (554)
T KOG0119|consen 235 PEGQNDLKRLQLRELARLNGTLRDDDNR 262 (554)
T ss_pred ccccccccHHHHHHHHHhCCCCCccccc
Confidence 9999999999999999999999998843
No 4
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.69 E-value=2.1e-17 Score=132.41 Aligned_cols=91 Identities=26% Similarity=0.367 Sum_probs=71.9
Q ss_pred chhhhhhcCcEEEEecCCCCCCcccccccc-CC--CCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCCcc
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEI-KD--KPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDES 78 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~-~~--~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~e~ 78 (127)
||+||+.|+|||.|||+| |+|++. +. .++.....++||+||+++....+|.. +.-....|.+.-. +|+|
T Consensus 176 lk~le~~s~akIaIRG~g------svKegk~ssd~p~~~~N~e~~lhcLI~adsedki~~~-ik~~~n~I~~a~~-~PeG 247 (269)
T COG5176 176 LKQLERISRAKIAIRGSG------SVKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRL-IKSQLNAIREARR-NPEG 247 (269)
T ss_pred HHHHHHHhCCeEEEeccc------ccccCcccccCchhhhhhHHhHHHHhhcchhhhHHHH-HHHHHHHHHHHhc-CCcc
Confidence 799999999999999999 999982 22 23344578999999999997765433 2334444555555 6899
Q ss_pred hhHHHHHHHHHHHHHhCcccCC
Q 039634 79 LDHYKKQQLRELAILNGTLREE 100 (127)
Q Consensus 79 ~delK~~QL~eLA~lNGt~r~~ 100 (127)
++++|+-||++||.+|||+|++
T Consensus 248 qnDlkR~qlr~la~lngtlr~d 269 (269)
T COG5176 248 QNDLKRFQLRWLAHLNGTLRAD 269 (269)
T ss_pred cchHHHHHHHHHHHhcceecCC
Confidence 9999999999999999999864
No 5
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=95.70 E-value=0.0057 Score=53.77 Aligned_cols=61 Identities=18% Similarity=0.032 Sum_probs=47.6
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCC
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVD 76 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~ 76 (127)
|..+|.||+.++.||||||+ -.|... +.| .+|||.++|+....+. +.+|+.++.+|+.-+.
T Consensus 237 La~~~ie~~i~~l~~Gr~SG-----~iEP~~---G~E-snEPMYI~i~h~~~~g-----~~~A~r~~~nl~~~v~ 297 (531)
T KOG1960|consen 237 LALQEIESWINPLIDGRRSG-----RREPNE---GNE-SNEPMYIFSTHGNGNG-----ENGAPRRKWNLEEKVY 297 (531)
T ss_pred hhhhhhhhhhhhhhcccccc-----ccCccc---ccc-cCCceeEEeecCCchh-----hccchhHHHhHHHHHH
Confidence 34578899999999999943 234432 333 7999999999999765 8899999999998653
No 6
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=95.33 E-value=0.035 Score=35.64 Aligned_cols=38 Identities=16% Similarity=0.142 Sum_probs=28.9
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHH
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILE 69 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie 69 (127)
+|+||++|||+|.|--.| .|.|+|.+++. ++.|.++|+
T Consensus 24 ik~I~~~tg~~I~i~~~g-------------------------~v~I~G~~~~~-----v~~A~~~I~ 61 (61)
T cd02393 24 IKKIIEETGVKIDIEDDG-------------------------TVYIAASDKEA-----AEKAKKMIE 61 (61)
T ss_pred HHHHHHHHCCEEEeCCCC-------------------------EEEEEeCCHHH-----HHHHHHHhC
Confidence 689999999999874322 38899987544 788888774
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=95.27 E-value=0.036 Score=34.58 Aligned_cols=39 Identities=18% Similarity=0.233 Sum_probs=29.1
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHH
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAIL 68 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~I 68 (127)
+|+||++|||+|.|... ++.-.|.|+| +++ .+++|.++|
T Consensus 22 i~~I~~~t~~~I~i~~~----------------------~~~~~v~I~G-~~~-----~v~~A~~~I 60 (60)
T PF00013_consen 22 IKEIEEETGVKIQIPDD----------------------DERDIVTISG-SPE-----QVEKAKKMI 60 (60)
T ss_dssp HHHHHHHHTSEEEEEST----------------------TEEEEEEEEE-SHH-----HHHHHHHHH
T ss_pred HHHhhhhcCeEEEEcCC----------------------CCcEEEEEEe-CHH-----HHHHHHhhC
Confidence 68999999999999552 1335788999 543 478888765
No 8
>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=93.30 E-value=0.26 Score=30.40 Aligned_cols=42 Identities=14% Similarity=0.106 Sum_probs=30.6
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHH
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAIL 68 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~I 68 (127)
+++|+++|||+|.|...+ + ...+-.|.|.|.. ..+..|..+|
T Consensus 22 i~~I~~~s~~~I~i~~~~------~-------------~~~~~~v~i~G~~------~~v~~a~~~i 63 (64)
T cd00105 22 IKEIREETGAKIKIPDSG------S-------------GSEERIVTITGTP------EAVEKAKELI 63 (64)
T ss_pred HHHHHHHHCCEEEEcCCC------C-------------CCCceEEEEEcCH------HHHHHHHHHh
Confidence 688999999999998755 1 2244668888883 3477777765
No 9
>smart00322 KH K homology RNA-binding domain.
Probab=93.07 E-value=0.32 Score=29.33 Aligned_cols=44 Identities=14% Similarity=0.142 Sum_probs=32.1
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhc
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLL 72 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL 72 (127)
++.|++.|||+|.|.+.+ + ..-.|.|.|+. ..+..|...|.+.+
T Consensus 25 i~~i~~~~~~~i~~~~~~------~---------------~~~~v~i~g~~------~~v~~a~~~i~~~~ 68 (69)
T smart00322 25 IKKIEEETGVKIDIPEDG------S---------------EERVVEITGPP------ENVEKAAELILEIL 68 (69)
T ss_pred HHHHHHHHCCEEEECCCC------C---------------CccEEEEEcCH------HHHHHHHHHHHHHh
Confidence 578999999999998755 1 23568888873 23677887777665
No 10
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=92.26 E-value=0.24 Score=45.20 Aligned_cols=50 Identities=12% Similarity=0.253 Sum_probs=34.7
Q ss_pred CchhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634 1 MTPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP 74 (127)
Q Consensus 1 ~~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p 74 (127)
|+|+|+.|||+||+|+=-- +|. ..+-+ +.|.|.. .++.+|.++|.+||.-
T Consensus 251 ~IKklq~etG~KIQfkpDd--------------~p~--speR~--~~IiG~~------d~ie~Aa~lI~eii~~ 300 (600)
T KOG1676|consen 251 MIKKLQNETGAKIQFKPDD--------------DPS--SPERP--AQIIGTV------DQIEHAAELINEIIAE 300 (600)
T ss_pred HHHHHhhccCceeEeecCC--------------CCC--Cccce--eeeecCH------HHHHHHHHHHHHHHHH
Confidence 7899999999999997632 121 01122 3345543 4689999999999874
No 11
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=91.56 E-value=0.41 Score=29.89 Aligned_cols=40 Identities=5% Similarity=-0.017 Sum_probs=28.6
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHH
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAIL 68 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~I 68 (127)
+++|+++|||+|.|-..+ +.+=.|.|.|+. +.+..|.++|
T Consensus 22 i~~i~~~~g~~I~i~~~~---------------------~~~~~v~I~G~~------~~v~~A~~~i 61 (62)
T cd02394 22 IRKIMEETGVKIRFPDPG---------------------SKSDTITITGPK------ENVEKAKEEI 61 (62)
T ss_pred HHHHHHHhCCEEEcCCCC---------------------CCCCEEEEEcCH------HHHHHHHHHh
Confidence 688999999999987543 122358899883 3477887765
No 12
>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=91.06 E-value=0.64 Score=29.67 Aligned_cols=43 Identities=14% Similarity=0.174 Sum_probs=28.5
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHH
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAIL 68 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~I 68 (127)
+++|+++|||+|.|.-.. . + ..++. -|.|+|.. ..+..|..+|
T Consensus 22 i~~i~~~tga~I~i~~~~------~--------~---~~~~r-~v~I~G~~------~~v~~A~~~I 64 (65)
T cd02396 22 IKEIREETGAKIRVSKSV------L--------P---GSTER-VVTISGKP------SAVQKALLLI 64 (65)
T ss_pred HHHHHHHHCCEEEEcCCC------C--------C---CCCce-EEEEEeCH------HHHHHHHHhh
Confidence 689999999999995433 1 1 12233 47777774 3467887776
No 13
>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=90.05 E-value=0.47 Score=36.27 Aligned_cols=41 Identities=17% Similarity=0.180 Sum_probs=32.6
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP 74 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p 74 (127)
.+.||..|||+|.|-|+ .|.|.| ++ .+++.|.+.|+.||.-
T Consensus 111 ~~~ie~~t~~~i~i~~~--------------------------~v~i~G-~~-----~~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 111 RRIIEELTGVSISVYGK--------------------------TVGIIG-DP-----EQVQIAREAIEMLIEG 151 (172)
T ss_pred HHHHHHHHCCeEEEcCC--------------------------EEEEEC-CH-----HHHHHHHHHHHHHHcC
Confidence 57899999999998641 377888 54 3489999999999964
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=88.73 E-value=0.91 Score=35.00 Aligned_cols=44 Identities=18% Similarity=0.210 Sum_probs=34.3
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEE---ecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVE---AEFPEVIINSCLDHAVAILENLLKP 74 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~---a~~~~~~~~~~l~~A~~~Ie~lL~p 74 (127)
.|.|+++|||+|.|.-.. =.|.|. +.++.. +.+|+++|+.++..
T Consensus 25 Ik~I~e~tg~~I~i~~~~------------------------g~V~I~~~~~~d~~~-----i~kA~~~I~ai~~g 71 (180)
T PRK13763 25 KKEIEERTGVKLEIDSET------------------------GEVIIEPTDGEDPLA-----VLKARDIVKAIGRG 71 (180)
T ss_pred HHHHHHHHCcEEEEECCC------------------------CeEEEEeCCCCCHHH-----HHHHHHHHHHHhcC
Confidence 588999999999997641 145566 566544 89999999999985
No 15
>PF13014 KH_3: KH domain
Probab=87.94 E-value=0.31 Score=28.75 Aligned_cols=16 Identities=19% Similarity=0.077 Sum_probs=14.6
Q ss_pred chhhhhhcCcEEEEec
Q 039634 2 TPEVDLLIKFKVSING 17 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRG 17 (127)
+++|+++|||+|.|--
T Consensus 13 I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 13 IKEIREETGAKIQIPP 28 (43)
T ss_pred HHHHHHHhCcEEEECC
Confidence 6899999999999976
No 16
>PRK13763 putative RNA-processing protein; Provisional
Probab=86.93 E-value=1.1 Score=34.59 Aligned_cols=41 Identities=17% Similarity=0.224 Sum_probs=31.3
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP 74 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p 74 (127)
.|.||..|||+|.|-|+ .|.|.| ++ .+++.|.+.|+.|+.-
T Consensus 117 ~k~ie~~t~~~i~i~~~--------------------------~v~i~G-~~-----~~~~~A~~~I~~li~g 157 (180)
T PRK13763 117 RRIIEELTGVDISVYGK--------------------------TVAIIG-DP-----EQVEIAREAIEMLIEG 157 (180)
T ss_pred HHHHHHHHCcEEEEcCC--------------------------EEEEEe-CH-----HHHHHHHHHHHHHHcC
Confidence 57899999999998541 166777 43 3489999999999964
No 17
>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=84.83 E-value=1.9 Score=40.34 Aligned_cols=43 Identities=14% Similarity=0.149 Sum_probs=36.3
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP 74 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p 74 (127)
.|.|+++|||+|.|--.| +|.|.|.+.+ .+++|+++|+.+..+
T Consensus 600 I~~i~~~tg~~Idi~d~G-------------------------~V~I~a~d~~-----~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 600 INQIQDETGAEISIEDDG-------------------------TVYIGAADGP-----SAEAARAMINAIANP 642 (719)
T ss_pred HHHHHHHHCCEEEEecCc-------------------------EEEEEeCCHH-----HHHHHHHHHHHhhCc
Confidence 588999999999886655 6889999864 489999999999995
No 18
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=81.41 E-value=0.78 Score=40.74 Aligned_cols=64 Identities=20% Similarity=0.385 Sum_probs=50.1
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCCcch
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDESL 79 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~e~~ 79 (127)
+|.++.++-+++.|.|-||+| + +. -+..+ .++|.||-|...++.. |+.|.-++++++-||+...
T Consensus 317 ~~~~~~~~~~~~~~~g~~s~~----i-~p---~~~~~-~~~p~~~~~~~~~~~~-----~~~~~~~~~~~i~~v~~qy 380 (531)
T KOG1960|consen 317 VKHIQQETRTRVQIKGQGSAF----I-EP---STNRE-SDEPIHLCIMSHDPNA-----IQRAKVLCEDLIASVHQQY 380 (531)
T ss_pred ccccCCCCCcceeccCcccee----e-cC---CCCCC-CCCCcccccccCChhh-----hhhhhhcccccCCcccccC
Confidence 467889999999999999664 2 22 13333 7899999999999766 7788999999999987543
No 19
>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=80.14 E-value=3.9 Score=31.19 Aligned_cols=43 Identities=16% Similarity=0.200 Sum_probs=32.8
Q ss_pred chhhhhhcCcEEEEecC-CCCCCccccccccCCCCCCCCCCCCceEEE--EecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634 2 TPEVDLLIKFKVSINGC-PYTYTSLSIKVEIKDKPGYEHLNEPLHMLV--EAEFPEVIINSCLDHAVAILENLLKP 74 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGk-G~~~~~~S~Kd~~~~~~~~eh~~epLHVlI--~a~~~~~~~~~~l~~A~~~Ie~lL~p 74 (127)
.|+||++|||+|.|--. | .|.| .+.++. .+.+|.++|+.+...
T Consensus 20 Ik~I~~~tgv~I~Id~~~g-------------------------~V~I~~~t~d~~-----~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 20 KKEIEERTGVKLDIDSETG-------------------------EVKIEEEDEDPL-----AVMKAREVVKAIGRG 65 (172)
T ss_pred HHHHHHHhCcEEEEEcCCc-------------------------eEEEecCCCCHH-----HHHHHHHHHHHHHcC
Confidence 58899999999998753 2 3556 445554 489999999998885
No 20
>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=76.02 E-value=4.7 Score=37.18 Aligned_cols=44 Identities=16% Similarity=0.175 Sum_probs=34.9
Q ss_pred CchhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634 1 MTPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP 74 (127)
Q Consensus 1 ~~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p 74 (127)
++|.|+++|||+|.|-=.| +|.|.+.+.. .+++|.+.|+.+...
T Consensus 572 ~Ik~I~~~tg~~I~i~ddG-------------------------~V~i~~~~~~-----~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 572 VIREITEETGAKIDIEDDG-------------------------TVKIAASDGE-----AAEAAIKMIEGITAE 615 (684)
T ss_pred HHHHHHHHHCCEEEEecCe-------------------------EEEEEECcHH-----HHHHHHHHHHhhhcc
Confidence 3689999999999986545 5778888854 489999999988653
No 21
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=67.48 E-value=3.6 Score=32.21 Aligned_cols=21 Identities=10% Similarity=0.132 Sum_probs=18.4
Q ss_pred chhhhhhcCcEEEEecCCCCC
Q 039634 2 TPEVDLLIKFKVSINGCPYTY 22 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~ 22 (127)
+|+||++.|+++.+||+|...
T Consensus 37 i~~LE~~lg~~Lf~R~r~i~l 57 (294)
T PRK13348 37 IKALEESLGQPLLVRGRPCRP 57 (294)
T ss_pred HHHHHHHhCceeeecCCCCcc
Confidence 689999999999999988554
No 22
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=67.09 E-value=12 Score=29.94 Aligned_cols=26 Identities=8% Similarity=0.097 Sum_probs=20.4
Q ss_pred ceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634 44 LHMLVEAEFPEVIINSCLDHAVAILENLLKP 74 (127)
Q Consensus 44 LHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p 74 (127)
=.|+|.|.+.+. +..|.+.|+.+-.-
T Consensus 184 G~VwI~~~~~~~-----~~~a~~~I~~~e~~ 209 (235)
T PRK04163 184 GRIWIKGPDEED-----EEIAIEAIKKIERE 209 (235)
T ss_pred cEEEEeeCCHHH-----HHHHHHHHHHHHhh
Confidence 369999999655 78888888887663
No 23
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=64.17 E-value=31 Score=27.53 Aligned_cols=44 Identities=16% Similarity=0.224 Sum_probs=33.0
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCCc
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDE 77 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~e 77 (127)
.+.||.-|||.|+|-|+- |.|.|+- ..++-|.+.|+.|+.-.+-
T Consensus 124 r~~IE~lt~~~I~V~g~t--------------------------VaiiG~~------~~v~iAr~AVemli~G~~h 167 (194)
T COG1094 124 RRAIEELTGVYISVYGKT--------------------------VAIIGGF------EQVEIAREAVEMLINGAPH 167 (194)
T ss_pred HHHHHHHhCCeEEEeCcE--------------------------EEEecCh------hhhHHHHHHHHHHHcCCCc
Confidence 357899999999999833 4555554 3478899999999986543
No 24
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=59.75 E-value=10 Score=36.36 Aligned_cols=30 Identities=17% Similarity=0.144 Sum_probs=24.1
Q ss_pred CCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634 40 LNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP 74 (127)
Q Consensus 40 ~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p 74 (127)
.+|+-+|.|.+.+.+ .+++|+++|+.+..-
T Consensus 721 i~ddg~V~I~a~d~~-----~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 721 TQDDGTVKITAKDLS-----SLEKSKAIISSLTMV 750 (891)
T ss_pred cCCCeeEEEEeCCHH-----HHHHHHHHHHHHhcC
Confidence 344578999999965 489999999999874
No 25
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=58.85 E-value=6.9 Score=37.99 Aligned_cols=56 Identities=20% Similarity=0.141 Sum_probs=41.4
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK 73 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~ 73 (127)
|.+|...++|.|.+||+= ..++.- | ...+.-||.+|++.+.. -+++|++.++.+|.
T Consensus 921 L~~i~e~~~~~it~rg~f-------~~~gk~--p--~~gErklyl~ve~~~e~-----~vqra~~e~~r~l~ 976 (997)
T KOG0334|consen 921 LLRISEPTAAGITTRGKF-------NPPGKE--P--KPGERKLYLLVEGPDEL-----SVQRAIEELERLLE 976 (997)
T ss_pred hhhccCccccceeecccc-------CCCCCC--C--CCcchhhhhhhhcchhH-----HHHHHHHHHHHHHH
Confidence 567889999999999976 332211 2 12567799999988854 48999999888665
No 26
>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=55.57 E-value=6.2 Score=30.80 Aligned_cols=20 Identities=5% Similarity=0.057 Sum_probs=17.8
Q ss_pred chhhhhhcCcEEEEecCCCC
Q 039634 2 TPEVDLLIKFKVSINGCPYT 21 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~ 21 (127)
+|+||++.|+++.+|+||..
T Consensus 36 I~~LE~~lg~~Lf~R~r~~~ 55 (292)
T TIGR03298 36 IKALEERLGQPLLVRTQPCR 55 (292)
T ss_pred HHHHHHHhCchheecCCCCc
Confidence 68999999999999998844
No 27
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=55.15 E-value=15 Score=33.96 Aligned_cols=28 Identities=14% Similarity=0.076 Sum_probs=21.7
Q ss_pred CCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634 42 EPLHMLVEAEFPEVIINSCLDHAVAILENLLKP 74 (127)
Q Consensus 42 epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p 74 (127)
|+-.|.|.+.+... +++|.++|+.+...
T Consensus 591 d~G~v~i~~~~~~~-----~~~a~~~I~~~~~~ 618 (693)
T PRK11824 591 DDGTVKIAATDGEA-----AEAAKERIEGITAE 618 (693)
T ss_pred CCceEEEEcccHHH-----HHHHHHHHHHhccc
Confidence 33568888888644 89999999998864
No 28
>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=55.03 E-value=6.1 Score=24.63 Aligned_cols=18 Identities=0% Similarity=-0.095 Sum_probs=15.0
Q ss_pred chhhhhhcCcEEEEecCC
Q 039634 2 TPEVDLLIKFKVSINGCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG 19 (127)
+++||++.|+++.+|..+
T Consensus 34 i~~LE~~lg~~Lf~r~~~ 51 (60)
T PF00126_consen 34 IKQLEEELGVPLFERSGR 51 (60)
T ss_dssp HHHHHHHHTS-SEEECSS
T ss_pred HHHHHHHhCCeEEEECCC
Confidence 689999999999999655
No 29
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=54.89 E-value=8.5 Score=30.27 Aligned_cols=21 Identities=5% Similarity=-0.007 Sum_probs=18.5
Q ss_pred chhhhhhcCcEEEEecCCCCC
Q 039634 2 TPEVDLLIKFKVSINGCPYTY 22 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~ 22 (127)
+|+||++.|+++..|++|...
T Consensus 37 I~~LE~~lg~~LF~R~~~~~l 57 (294)
T PRK03635 37 IKALEERVGQVLLVRTQPCRP 57 (294)
T ss_pred HHHHHHHhCceeeecCCCCcc
Confidence 689999999999999988554
No 30
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=53.85 E-value=8.3 Score=31.07 Aligned_cols=20 Identities=10% Similarity=0.348 Sum_probs=16.9
Q ss_pred chhhhhhcCcEEEEe-cCCCC
Q 039634 2 TPEVDLLIKFKVSIN-GCPYT 21 (127)
Q Consensus 2 ~K~LE~eTgcKI~IR-GkG~~ 21 (127)
+|+||++.|+++.+| |||..
T Consensus 37 Ik~LE~~lg~~LF~R~~r~v~ 57 (317)
T PRK15421 37 FSDLEQRLGFRLFVRKSQPLR 57 (317)
T ss_pred HHHHHHHhCCEEEEecCCCce
Confidence 689999999999999 56644
No 31
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=53.57 E-value=8.4 Score=30.80 Aligned_cols=19 Identities=0% Similarity=-0.190 Sum_probs=16.3
Q ss_pred chhhhhhcCcEEEEec-CCC
Q 039634 2 TPEVDLLIKFKVSING-CPY 20 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRG-kG~ 20 (127)
+|+||++.||++.+|. ||.
T Consensus 37 I~~LE~~lg~~Lf~R~~r~~ 56 (308)
T PRK10094 37 IKLLEENTGVALFFRTTRSV 56 (308)
T ss_pred HHHHHHHhCCEEEeeCCCce
Confidence 6899999999999994 553
No 32
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=52.58 E-value=6.5 Score=30.82 Aligned_cols=19 Identities=5% Similarity=0.043 Sum_probs=16.4
Q ss_pred chhhhhhcCcEEEEec-CCC
Q 039634 2 TPEVDLLIKFKVSING-CPY 20 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRG-kG~ 20 (127)
+|+||++.||++.+|. +|.
T Consensus 41 i~~LE~~lg~~Lf~R~~r~l 60 (297)
T PRK11139 41 IKALEDFLGLKLFRRRNRSL 60 (297)
T ss_pred HHHHHHHhCchheEecCCce
Confidence 6899999999999995 553
No 33
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=51.45 E-value=8.2 Score=30.21 Aligned_cols=19 Identities=0% Similarity=-0.050 Sum_probs=16.5
Q ss_pred chhhhhhcCcEEEEe-cCCC
Q 039634 2 TPEVDLLIKFKVSIN-GCPY 20 (127)
Q Consensus 2 ~K~LE~eTgcKI~IR-GkG~ 20 (127)
+|+||++.|+++.+| |+|.
T Consensus 36 I~~LE~~lG~~LF~R~~r~~ 55 (275)
T PRK03601 36 IRQLENQLGVNLFTRHRNNI 55 (275)
T ss_pred HHHHHHHhCCceEEECCCce
Confidence 689999999999998 6663
No 34
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=51.08 E-value=7 Score=29.82 Aligned_cols=18 Identities=0% Similarity=-0.114 Sum_probs=15.8
Q ss_pred chhhhhhcCcEEEEec-CC
Q 039634 2 TPEVDLLIKFKVSING-CP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRG-kG 19 (127)
+|+||++.|+.+.+|. ||
T Consensus 32 i~~LE~~lg~~Lf~R~~~~ 50 (279)
T TIGR03339 32 VRKLEERYGVELFHRNGRR 50 (279)
T ss_pred HHHHHHHhCCccEEEcCCe
Confidence 6899999999999994 55
No 35
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=47.35 E-value=36 Score=29.47 Aligned_cols=46 Identities=4% Similarity=0.015 Sum_probs=28.9
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK 73 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~ 73 (127)
.|+||+||+|+|.+=-.+ . ..=|+-|++-.... |.+|.+.|..++.
T Consensus 79 rkkle~Etq~~i~lp~p~---------------~------n~~~i~i~~~~~~~-----V~~a~~Ri~~~id 124 (345)
T KOG2814|consen 79 RKKLEEETQTNIFLPRPN---------------T------NKEEIKIIGISRNC-----VIQALERIAKLID 124 (345)
T ss_pred HHHHHHhhccceEccCCC---------------C------CcceEEEeehhHHH-----HHHHHHHHHHHHH
Confidence 578999999999874433 1 11367788877543 4455555555444
No 36
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=46.56 E-value=12 Score=29.44 Aligned_cols=18 Identities=0% Similarity=-0.071 Sum_probs=16.1
Q ss_pred chhhhhhcCcEEEEe-cCC
Q 039634 2 TPEVDLLIKFKVSIN-GCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IR-GkG 19 (127)
+|+||++.|+.+.+| |+|
T Consensus 37 I~~LE~~lg~~LF~R~~r~ 55 (300)
T PRK11074 37 VRQLEEWLAVPLFERRHRD 55 (300)
T ss_pred HHHHHHHhCCeeEEeCCCC
Confidence 689999999999999 565
No 37
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=46.34 E-value=14 Score=29.47 Aligned_cols=21 Identities=5% Similarity=-0.064 Sum_probs=17.2
Q ss_pred chhhhhhcCcEEEEe-cCCCCC
Q 039634 2 TPEVDLLIKFKVSIN-GCPYTY 22 (127)
Q Consensus 2 ~K~LE~eTgcKI~IR-GkG~~~ 22 (127)
+++||++.|+++.+| |||..+
T Consensus 43 I~~LE~~lg~~LF~R~~r~~~l 64 (319)
T PRK10216 43 LAKLRAWFDDPLFVNTPLGLSP 64 (319)
T ss_pred HHHHHHHhCCceEEecCCCccc
Confidence 689999999999999 555443
No 38
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=46.03 E-value=29 Score=32.04 Aligned_cols=50 Identities=16% Similarity=0.286 Sum_probs=35.3
Q ss_pred chhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCC
Q 039634 2 TPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKP 74 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p 74 (127)
.|+|++.||||+.+-=-| +.-+ + .+.||. |+|+. .+++.|.++|.++|.-
T Consensus 161 ikqlqe~sg~k~i~iqd~------~~~~------~---~~Kplr--itGdp------~~ve~a~~lV~dil~e 210 (600)
T KOG1676|consen 161 IKQLQEQSGVKMILVQDG------SIAT------G---ADKPLR--ITGDP------DKVEQAKQLVADILRE 210 (600)
T ss_pred HHHHHhhcCCceEEEecC------CcCC------C---CCCcee--ecCCH------HHHHHHHHHHHHHHHh
Confidence 489999999998876656 3321 1 334454 56655 3589999999999984
No 39
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=45.06 E-value=10 Score=26.44 Aligned_cols=18 Identities=6% Similarity=-0.132 Sum_probs=15.9
Q ss_pred chhhhhhcCcEEEEecCC
Q 039634 2 TPEVDLLIKFKVSINGCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG 19 (127)
+++||++.|+++..|..|
T Consensus 37 I~~LE~~lg~~Lf~R~~~ 54 (99)
T TIGR00637 37 IRAMNNLSGEPLVERATG 54 (99)
T ss_pred HHHHHHHhCCCeEEecCC
Confidence 689999999999999653
No 40
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=42.83 E-value=16 Score=29.13 Aligned_cols=18 Identities=11% Similarity=0.076 Sum_probs=16.3
Q ss_pred chhhhhhcCcEEEEe-cCC
Q 039634 2 TPEVDLLIKFKVSIN-GCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IR-GkG 19 (127)
+|+||++.||++.+| |||
T Consensus 37 ik~LE~~lg~~Lf~R~~r~ 55 (313)
T PRK12684 37 IIELEDELGVEIFTRHGKR 55 (313)
T ss_pred HHHHHHHhCCeeEEEcCCc
Confidence 689999999999999 567
No 41
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=42.37 E-value=16 Score=29.15 Aligned_cols=19 Identities=11% Similarity=0.172 Sum_probs=16.8
Q ss_pred chhhhhhcCcEEEEe-cCCC
Q 039634 2 TPEVDLLIKFKVSIN-GCPY 20 (127)
Q Consensus 2 ~K~LE~eTgcKI~IR-GkG~ 20 (127)
+|+||++.|+++.+| |||.
T Consensus 37 I~~LE~~lg~~Lf~R~~r~~ 56 (309)
T PRK12683 37 IKDLEDELGVEIFIRRGKRL 56 (309)
T ss_pred HHHHHHHhCCeeEeeCCCCc
Confidence 689999999999999 6773
No 42
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=40.96 E-value=43 Score=30.01 Aligned_cols=49 Identities=14% Similarity=0.150 Sum_probs=32.8
Q ss_pred CchhhhhhcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634 1 MTPEVDLLIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEVIINSCLDHAVAILENLLK 73 (127)
Q Consensus 1 ~~K~LE~eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~ 73 (127)
++|+|.++|||+|.|-+.- .|. -.|.. |-|+|+-. .+.+|...|-.+|.
T Consensus 159 ~Ik~Ire~TgA~I~v~~~~--------------lP~---ster~-V~IsG~~~------av~~al~~Is~~L~ 207 (485)
T KOG2190|consen 159 LIKEIREETGAKIRVSSDM--------------LPN---STERA-VTISGEPD------AVKKALVQISSRLL 207 (485)
T ss_pred HHHHHHHhcCceEEecCCC--------------CCc---cccee-EEEcCchH------HHHHHHHHHHHHHH
Confidence 3689999999999998842 233 23444 88887763 35666666666555
No 43
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=40.40 E-value=19 Score=28.49 Aligned_cols=18 Identities=17% Similarity=0.200 Sum_probs=16.1
Q ss_pred chhhhhhcCcEEEEe-cCC
Q 039634 2 TPEVDLLIKFKVSIN-GCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IR-GkG 19 (127)
+|+||++.||++.+| |+|
T Consensus 37 I~~LE~~lg~~LF~R~~~~ 55 (309)
T PRK12682 37 IIELEEELGIEIFIRHGKR 55 (309)
T ss_pred HHHHHHHhCCeeEEECCCC
Confidence 689999999999999 466
No 44
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=37.13 E-value=22 Score=27.53 Aligned_cols=18 Identities=11% Similarity=0.026 Sum_probs=16.1
Q ss_pred chhhhhhcCcEEEEecCC
Q 039634 2 TPEVDLLIKFKVSINGCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG 19 (127)
+|+||++.|+++.+|...
T Consensus 42 i~~LE~~lg~~Lf~R~~r 59 (294)
T PRK09986 42 IKELEDQLGTPLFIRHSR 59 (294)
T ss_pred HHHHHHHhCCeeEeeCCC
Confidence 689999999999999854
No 45
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=35.50 E-value=25 Score=27.53 Aligned_cols=18 Identities=6% Similarity=0.012 Sum_probs=16.5
Q ss_pred chhhhhhcCcEEEEecCC
Q 039634 2 TPEVDLLIKFKVSINGCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG 19 (127)
+|+||++.|+++.+|.++
T Consensus 40 i~~LE~~lG~~LF~R~~r 57 (302)
T PRK09791 40 IQELEEGLAAQLFFRRSK 57 (302)
T ss_pred HHHHHHHhCCeEEEEcCC
Confidence 689999999999999776
No 46
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=34.84 E-value=30 Score=27.26 Aligned_cols=19 Identities=11% Similarity=0.125 Sum_probs=16.4
Q ss_pred chhhhhhcCcEEEEec-CCC
Q 039634 2 TPEVDLLIKFKVSING-CPY 20 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRG-kG~ 20 (127)
+|+||++.|+++..|. ||.
T Consensus 46 I~~LE~~lG~~Lf~R~~r~~ 65 (303)
T PRK10082 46 IRALEQAIGVELFNRQVTPL 65 (303)
T ss_pred HHHHHHHcCCEEEEecCCCC
Confidence 6899999999999987 553
No 47
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=34.33 E-value=24 Score=27.94 Aligned_cols=18 Identities=11% Similarity=-0.007 Sum_probs=16.5
Q ss_pred chhhhhhcCcEEEEecCC
Q 039634 2 TPEVDLLIKFKVSINGCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG 19 (127)
+|+||++.|+++.+|..+
T Consensus 39 Ik~LE~~lg~~Lf~R~~~ 56 (309)
T PRK11013 39 LARFEKVIGLKLFERVRG 56 (309)
T ss_pred HHHHHHHhCceeeeecCC
Confidence 689999999999999875
No 48
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=33.53 E-value=22 Score=29.05 Aligned_cols=20 Identities=10% Similarity=0.157 Sum_probs=17.0
Q ss_pred chhhhhhcCcEEEEe-cCCCC
Q 039634 2 TPEVDLLIKFKVSIN-GCPYT 21 (127)
Q Consensus 2 ~K~LE~eTgcKI~IR-GkG~~ 21 (127)
+|+||++.|+++..| |||..
T Consensus 39 Ik~LE~eLG~~LF~R~~r~~~ 59 (297)
T PRK15243 39 ISDLERELKQRLFIRKNGTLI 59 (297)
T ss_pred HHHHHHHhCCccEEeCCCCee
Confidence 689999999999999 66644
No 49
>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=33.41 E-value=55 Score=20.92 Aligned_cols=32 Identities=22% Similarity=0.100 Sum_probs=17.6
Q ss_pred EEEEecCcHHHHHHHHHHHHHHHHhhcCCCCc
Q 039634 46 MLVEAEFPEVIINSCLDHAVAILENLLKPVDE 77 (127)
Q Consensus 46 VlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~e 77 (127)
|-||-++.......-+.+|++.++++|.+++.
T Consensus 18 ~siE~ED~~~~~~~G~~~a~~~lr~~l~~~~~ 49 (55)
T PF07582_consen 18 LSIEHEDALMDPEEGAREAAAFLRKLLIREPP 49 (55)
T ss_dssp EEE---STTTSHHHHHHHHHHHHHTT------
T ss_pred EEEEeecCCCCHHHHHHHHHHHHHHhcCCCCc
Confidence 44555555444567899999999999987653
No 50
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=32.41 E-value=26 Score=27.07 Aligned_cols=18 Identities=0% Similarity=-0.149 Sum_probs=15.9
Q ss_pred chhhhhhcCcEEEEec-CC
Q 039634 2 TPEVDLLIKFKVSING-CP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRG-kG 19 (127)
+|+||++.||++.+|+ +|
T Consensus 38 I~~LE~~lg~~Lf~R~~r~ 56 (290)
T PRK10837 38 LTDLEGQLGVQLFDRVGKR 56 (290)
T ss_pred HHHHHHHhCCccEeecCCe
Confidence 5899999999999995 55
No 51
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=31.30 E-value=31 Score=26.71 Aligned_cols=20 Identities=0% Similarity=-0.071 Sum_probs=16.7
Q ss_pred chhhhhhcCcEEEEec-CCCC
Q 039634 2 TPEVDLLIKFKVSING-CPYT 21 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRG-kG~~ 21 (127)
+|+||++.|+++.+|+ +|..
T Consensus 36 i~~LE~~lg~~Lf~R~~~~~~ 56 (296)
T PRK11242 36 IRQLEESLGVQLFDRSGRTVR 56 (296)
T ss_pred HHHHHHHhCCeeEeEcCCcee
Confidence 6899999999999995 5533
No 52
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=30.87 E-value=24 Score=31.84 Aligned_cols=15 Identities=13% Similarity=0.186 Sum_probs=13.8
Q ss_pred chhhhhhcCcEEEEe
Q 039634 2 TPEVDLLIKFKVSIN 16 (127)
Q Consensus 2 ~K~LE~eTgcKI~IR 16 (127)
+|++|++||+||.|-
T Consensus 302 lKkIeq~TgTkITis 316 (584)
T KOG2193|consen 302 LKKIEQDTGTKITIS 316 (584)
T ss_pred HHHHHhhcCCceeee
Confidence 799999999999994
No 53
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=30.15 E-value=31 Score=27.78 Aligned_cols=18 Identities=6% Similarity=0.014 Sum_probs=16.1
Q ss_pred chhhhhhcCcEEEEecCC
Q 039634 2 TPEVDLLIKFKVSINGCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG 19 (127)
+|+||++.||++.+|...
T Consensus 46 I~~LE~~lG~~LF~R~~~ 63 (310)
T PRK15092 46 MQRLEQLVGKELFARHGR 63 (310)
T ss_pred HHHHHHHhCcceEEECCC
Confidence 689999999999999654
No 54
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=29.67 E-value=36 Score=27.56 Aligned_cols=19 Identities=0% Similarity=-0.080 Sum_probs=16.5
Q ss_pred chhhhhhcCcEEEEec-CCC
Q 039634 2 TPEVDLLIKFKVSING-CPY 20 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRG-kG~ 20 (127)
+|+||++.|+++..|. +|.
T Consensus 37 I~~LE~~lG~~LF~R~~r~~ 56 (324)
T PRK12681 37 VRMLEDELGIQIFARSGKHL 56 (324)
T ss_pred HHHHHHHhCCEeEEECCCCC
Confidence 6899999999999995 663
No 55
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=29.16 E-value=90 Score=27.20 Aligned_cols=35 Identities=14% Similarity=0.038 Sum_probs=24.3
Q ss_pred hcCcEEEEecCCCCCCccccccccCCCCCCCCCCCCceEEEEecCcHH
Q 039634 8 LIKFKVSINGCPYTYTSLSIKVEIKDKPGYEHLNEPLHMLVEAEFPEV 55 (127)
Q Consensus 8 eTgcKI~IRGkG~~~~~~S~Kd~~~~~~~~eh~~epLHVlI~a~~~~~ 55 (127)
.+|+.+.|||+| ++-- + . +-.-+|+|.|..+.|.+
T Consensus 301 q~G~~~rl~gkG-------~p~~-~--~---~~~GDl~v~v~v~~P~~ 335 (371)
T COG0484 301 QTGEVFRLRGKG-------MPKL-R--S---GGRGDLYVRVKVETPKN 335 (371)
T ss_pred ccCcEEEEcCCC-------cccc-C--C---CCcCCEEEEEEEEcCCC
Confidence 579999999999 3211 0 1 12256999999998865
No 56
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=28.68 E-value=38 Score=26.36 Aligned_cols=18 Identities=6% Similarity=-0.027 Sum_probs=16.4
Q ss_pred chhhhhhcCcEEEEecCC
Q 039634 2 TPEVDLLIKFKVSINGCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG 19 (127)
+|+||++.|+++.+|..+
T Consensus 38 I~~LE~~lg~~LF~R~~~ 55 (300)
T TIGR02424 38 LRELEEILGTPLFERDRR 55 (300)
T ss_pred HHHHHHHhCCeEEEEcCC
Confidence 689999999999999766
No 57
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=27.76 E-value=40 Score=19.98 Aligned_cols=27 Identities=22% Similarity=0.422 Sum_probs=20.9
Q ss_pred ceEEEEecCcHHHHHHHHHHHHHHHHh
Q 039634 44 LHMLVEAEFPEVIINSCLDHAVAILEN 70 (127)
Q Consensus 44 LHVlI~a~~~~~~~~~~l~~A~~~Ie~ 70 (127)
.-.+|+|++...+++..|+.|.++|.+
T Consensus 14 v~~li~g~~~~~IC~~Cv~~~~~il~~ 40 (41)
T PF06689_consen 14 VGRLISGPNGAYICDECVEQAYEILKE 40 (41)
T ss_dssp SSSEEEES-SEEEEHHHHHHHHHHHHT
T ss_pred HhceecCCCCcEECHHHHHHHHHHHhc
Confidence 344678886688999999999998864
No 58
>PF01565 FAD_binding_4: FAD binding domain This is only a subset of the Pfam family; InterPro: IPR006094 Various enzymes use FAD as a co-factor, most of these enzymes are oxygen-dependent oxidoreductases, containing a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage. One of the enzymes Vanillyl-alcohol oxidase (VAO, 1.1.3.38 from EC) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 []. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging from aromatic amines to 4-alkylphenols. ; GO: 0008762 UDP-N-acetylmuramate dehydrogenase activity, 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 1ZR6_A 3HSU_A 2AXR_A 3D2J_A 3D2H_A 3FW9_A 3FW8_A 3FW7_A 3GSY_A 3FWA_A ....
Probab=26.57 E-value=1.8e+02 Score=20.19 Aligned_cols=47 Identities=17% Similarity=-0.009 Sum_probs=26.5
Q ss_pred hhcCcEEEEecCCCCCCcccc-ccc----cCCCCC-CCCCCCCceEEEEecCc
Q 039634 7 LLIKFKVSINGCPYTYTSLSI-KVE----IKDKPG-YEHLNEPLHMLVEAEFP 53 (127)
Q Consensus 7 ~eTgcKI~IRGkG~~~~~~S~-Kd~----~~~~~~-~eh~~epLHVlI~a~~~ 53 (127)
.+.+.++.|||-|+++.-.+. .++ ...-.+ .+-+.+...|.|++=..
T Consensus 21 ~~~~~~v~~~g~G~~~~~~~~~~~~ivi~~~~l~~i~~id~~~~~v~v~aG~~ 73 (139)
T PF01565_consen 21 NENGVPVRVRGGGHSWTGQSSDEGGIVIDMSRLNKIIEIDPENGTVTVGAGVT 73 (139)
T ss_dssp HHTTSEEEEESSSTTSSSTTSSTTEEEEECTTCGCEEEEETTTTEEEEETTSB
T ss_pred HHcCCcEEEEcCCCCcccccccCCcEEEeeccccccccccccceeEEEecccc
Confidence 467999999999977764444 222 111111 11223456666666554
No 59
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=26.32 E-value=1.6e+02 Score=25.32 Aligned_cols=18 Identities=17% Similarity=0.327 Sum_probs=13.4
Q ss_pred chhhhhhcCcEEEEecCC
Q 039634 2 TPEVDLLIKFKVSINGCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG 19 (127)
||-||--|+|-|.+.|.-
T Consensus 171 LKAlelLT~CYilVqG~T 188 (356)
T KOG2874|consen 171 LKALELLTNCYILVQGNT 188 (356)
T ss_pred HHHHHHHhhcEEEeeCcE
Confidence 577788888888888743
No 60
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=25.88 E-value=46 Score=25.87 Aligned_cols=18 Identities=0% Similarity=0.049 Sum_probs=15.9
Q ss_pred chhhhhhcCcEEEEecCC
Q 039634 2 TPEVDLLIKFKVSINGCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG 19 (127)
+|+||++.||++.+|-.+
T Consensus 36 i~~LE~~lg~~Lf~R~~~ 53 (296)
T PRK09906 36 IKDLENCVGVPLLVRDKR 53 (296)
T ss_pred HHHHHHHhCCeeeeeCCC
Confidence 689999999999998654
No 61
>PF13189 Cytidylate_kin2: Cytidylate kinase-like family; PDB: 3FDI_A.
Probab=25.45 E-value=50 Score=24.75 Aligned_cols=21 Identities=14% Similarity=0.240 Sum_probs=14.0
Q ss_pred CCceEEEEecCcHHHHHHHHHHHHHH
Q 039634 42 EPLHMLVEAEFPEVIINSCLDHAVAI 67 (127)
Q Consensus 42 epLHVlI~a~~~~~~~~~~l~~A~~~ 67 (127)
.-|||+|.|+.. .|++++++.
T Consensus 114 ~~l~V~i~A~~~-----~Rv~ri~~~ 134 (179)
T PF13189_consen 114 NVLHVFIYAPLE-----FRVERIMER 134 (179)
T ss_dssp TEEEEEEEE-HH-----HHHHHHHHH
T ss_pred CeEEEEEECCHH-----HHHHHHHHH
Confidence 459999999873 456665554
No 62
>PRK14295 chaperone protein DnaJ; Provisional
Probab=24.96 E-value=1.2e+02 Score=25.90 Aligned_cols=15 Identities=27% Similarity=0.319 Sum_probs=11.6
Q ss_pred CCCceEEEEecCcHH
Q 039634 41 NEPLHMLVEAEFPEV 55 (127)
Q Consensus 41 ~epLHVlI~a~~~~~ 55 (127)
.-+|+|.|...-|..
T Consensus 343 ~GDL~i~~~v~~P~~ 357 (389)
T PRK14295 343 RGDLLVTVEVAVPKD 357 (389)
T ss_pred CCCEEEEEEEECCCC
Confidence 467999998888754
No 63
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=24.60 E-value=51 Score=26.76 Aligned_cols=18 Identities=6% Similarity=0.049 Sum_probs=16.0
Q ss_pred chhhhhhcCcEEEEecCC
Q 039634 2 TPEVDLLIKFKVSINGCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG 19 (127)
+|+||++.||++.+|..+
T Consensus 37 I~~LE~~lG~~LF~R~~r 54 (327)
T PRK12680 37 LKQLEDELGFLLFVRKGR 54 (327)
T ss_pred HHHHHHHhCCeEEEECCC
Confidence 689999999999999655
No 64
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=23.80 E-value=49 Score=25.85 Aligned_cols=18 Identities=0% Similarity=0.027 Sum_probs=16.0
Q ss_pred chhhhhhcCcEEEEecCC
Q 039634 2 TPEVDLLIKFKVSINGCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG 19 (127)
+++||++.|+++.+|+..
T Consensus 37 I~~LE~~lG~~LF~R~~r 54 (301)
T PRK14997 37 IAQLEERLGVRLIQRTTR 54 (301)
T ss_pred HHHHHHHhCCEeeeeccC
Confidence 689999999999999864
No 65
>PF13046 DUF3906: Protein of unknown function (DUF3906)
Probab=23.79 E-value=1.7e+02 Score=19.49 Aligned_cols=35 Identities=26% Similarity=0.306 Sum_probs=24.0
Q ss_pred CCCCceEEEEecCcHHHHHHHHHHHHHHHHhhcCCCCcc
Q 039634 40 LNEPLHMLVEAEFPEVIINSCLDHAVAILENLLKPVDES 78 (127)
Q Consensus 40 ~~epLHVlI~a~~~~~~~~~~l~~A~~~Ie~lL~p~~e~ 78 (127)
.+++++|.|.|++.+. .-+.+-..+++-.-|.|+-
T Consensus 11 ~~~~~~viv~Ae~ee~----AF~~~e~eler~fl~~P~v 45 (64)
T PF13046_consen 11 EEGPIPVIVAAENEEQ----AFRLVEVELERHFLPLPEV 45 (64)
T ss_pred cCCcEEEEEEecCHHH----HHHHHHHHhhhhccCCCCc
Confidence 4578999999999753 3556666666666555543
No 66
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=23.16 E-value=56 Score=24.58 Aligned_cols=18 Identities=0% Similarity=-0.056 Sum_probs=15.2
Q ss_pred chhhhhhcCcEEEEecCC
Q 039634 2 TPEVDLLIKFKVSINGCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG 19 (127)
+|+||++.|+++.+|...
T Consensus 12 I~~LE~~lg~~Lf~R~~r 29 (269)
T PRK11716 12 IQRLEEELGQPLFVRDNR 29 (269)
T ss_pred HHHHHHHhCCeeEEecCC
Confidence 688999999999998633
No 67
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=22.53 E-value=49 Score=26.00 Aligned_cols=18 Identities=6% Similarity=-0.112 Sum_probs=15.9
Q ss_pred chhhhhhcCcEEEEecCC
Q 039634 2 TPEVDLLIKFKVSINGCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG 19 (127)
+|+||++.|+++.+|...
T Consensus 39 I~~LE~~lg~~Lf~R~~r 56 (296)
T PRK11062 39 IKALEERLQGKLFKRKGR 56 (296)
T ss_pred HHHHHHHcCccceeecCC
Confidence 689999999999998654
No 68
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=22.47 E-value=59 Score=25.93 Aligned_cols=17 Identities=12% Similarity=0.106 Sum_probs=15.6
Q ss_pred chhhhhhcCcEEEEecC
Q 039634 2 TPEVDLLIKFKVSINGC 18 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGk 18 (127)
+|+||++.|+++.+|..
T Consensus 37 I~~LE~~lg~~LF~R~~ 53 (316)
T PRK12679 37 IRELEDELGIEIFIRRG 53 (316)
T ss_pred HHHHHHHhCCEEEEECC
Confidence 68999999999999974
No 69
>PRK09801 transcriptional activator TtdR; Provisional
Probab=22.29 E-value=55 Score=26.15 Aligned_cols=18 Identities=0% Similarity=-0.105 Sum_probs=16.1
Q ss_pred chhhhhhcCcEEEEecCC
Q 039634 2 TPEVDLLIKFKVSINGCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG 19 (127)
+|+||++.|+++..|++.
T Consensus 41 I~~LE~~LG~~Lf~R~~r 58 (310)
T PRK09801 41 IQILENTLATTLLNRSAR 58 (310)
T ss_pred HHHHHHHhCCEeeeecCC
Confidence 689999999999999854
No 70
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=21.07 E-value=66 Score=25.34 Aligned_cols=18 Identities=0% Similarity=-0.058 Sum_probs=15.9
Q ss_pred chhhhhhcCcEEEEecCC
Q 039634 2 TPEVDLLIKFKVSINGCP 19 (127)
Q Consensus 2 ~K~LE~eTgcKI~IRGkG 19 (127)
+++||++-||++.+|...
T Consensus 40 i~~LE~~lg~~Lf~R~~r 57 (305)
T CHL00180 40 IKNLEKQLNIPLFDRSKN 57 (305)
T ss_pred HHHHHHHhCCEEEEecCC
Confidence 689999999999999754
No 71
>PF00639 Rotamase: PPIC-type PPIASE domain; InterPro: IPR000297 Peptidylprolyl isomerase (5.2.1.8 from EC) is an enzyme that accelerates protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides []. It has been reported in bacteria and eukayotes. Synonyms for proteins with this domain are: Peptidylprolyl isomerase, Peptidyl-prolyl cis-trans isomerase, PPIase, rotamase, cyclophilin, FKBP65.; GO: 0016853 isomerase activity; PDB: 2JZV_A 2PV3_B 1M5Y_A 2PV2_B 2PV1_A 1JNS_A 1JNT_A 3KAB_A 2ZR6_A 2XPB_A ....
Probab=20.63 E-value=1.4e+02 Score=19.82 Aligned_cols=29 Identities=28% Similarity=0.303 Sum_probs=17.5
Q ss_pred eEEEEecCcHHHHHHHHHHHHHHHHhhcC
Q 039634 45 HMLVEAEFPEVIINSCLDHAVAILENLLK 73 (127)
Q Consensus 45 HVlI~a~~~~~~~~~~l~~A~~~Ie~lL~ 73 (127)
|+||..+......++.-+.|.++.+.|..
T Consensus 1 HIl~~~~~~~~~~~~~~~~a~~i~~~l~~ 29 (95)
T PF00639_consen 1 HILVKPPPSDEEKDAAKKKAEEIYEQLKK 29 (95)
T ss_dssp EEEEESTTSCCHHHHHHHHHHHHHHHHHT
T ss_pred CEEEECCCchhhHHHHHHHHHHHHHHHHh
Confidence 89998876444334445555555555555
No 72
>PHA00731 hypothetical protein
Probab=20.27 E-value=2.3e+02 Score=20.25 Aligned_cols=51 Identities=29% Similarity=0.376 Sum_probs=30.6
Q ss_pred CceEEEEecCcHHHHHH-------HHHHHHHHHHhhcC----CCCcchhHHHHHHHHHHHHH
Q 039634 43 PLHMLVEAEFPEVIINS-------CLDHAVAILENLLK----PVDESLDHYKKQQLRELAIL 93 (127)
Q Consensus 43 pLHVlI~a~~~~~~~~~-------~l~~A~~~Ie~lL~----p~~e~~delK~~QL~eLA~l 93 (127)
-||+-|+-+..+.+..+ .++....-++.|-. ..++.|..+++.=|.+.|-|
T Consensus 30 ylhlkIE~nedekI~k~~~~~e~i~~e~vl~klkrLYevy~d~~~etQeaIrKE~lleIAKl 91 (96)
T PHA00731 30 YLHLKIEINEDEKIEKKFFFTEKIALEEVLLKLKRLYEVYEDSEDETQEAIRKEVLLEIAKL 91 (96)
T ss_pred eEEEEEEeCchhhhhhheeecccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 39999998886665433 22333333333322 13467888888888888754
No 73
>PF00408 PGM_PMM_IV: Phosphoglucomutase/phosphomannomutase, C-terminal domain; InterPro: IPR005843 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1KFQ_B 1KFI_A 3PDK_B 2F7L_A 1TUO_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=20.24 E-value=1.8e+02 Score=18.48 Aligned_cols=11 Identities=36% Similarity=0.380 Sum_probs=9.1
Q ss_pred ceEEEEecCcH
Q 039634 44 LHMLVEAEFPE 54 (127)
Q Consensus 44 LHVlI~a~~~~ 54 (127)
+-|+++|.+.+
T Consensus 49 iRv~~Ea~~~~ 59 (73)
T PF00408_consen 49 IRVYVEAPDEE 59 (73)
T ss_dssp EEEEEEESSHH
T ss_pred EEEEEEeCCHH
Confidence 88999999754
Done!