Query 038082
Match_columns 149
No_of_seqs 214 out of 1103
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 07:23:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038082.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038082hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0216 PrfA Protein chain rel 100.0 8.4E-43 1.8E-47 298.8 7.4 132 3-143 208-360 (363)
2 TIGR00019 prfA peptide chain r 100.0 1.6E-34 3.5E-39 250.2 9.0 118 15-141 219-355 (360)
3 KOG2726 Mitochondrial polypept 100.0 1.8E-34 3.9E-39 250.6 8.5 111 16-135 247-376 (386)
4 PRK00591 prfA peptide chain re 100.0 4.6E-34 9.9E-39 247.3 9.1 119 14-141 218-355 (359)
5 PF00472 RF-1: RF-1 domain; I 100.0 3.6E-33 7.8E-38 207.0 7.9 101 5-118 4-104 (113)
6 TIGR03072 release_prfH putativ 100.0 2.9E-33 6.3E-38 226.1 6.7 101 4-118 97-197 (200)
7 PRK05589 peptide chain release 100.0 7.2E-33 1.6E-37 237.3 8.3 107 16-132 195-321 (325)
8 PRK08787 peptide chain release 100.0 1.1E-32 2.4E-37 234.9 9.3 112 16-137 175-305 (313)
9 PRK08179 prfH peptide chain re 100.0 1.9E-32 4.1E-37 221.3 7.2 100 4-117 98-197 (200)
10 PRK06746 peptide chain release 100.0 2.5E-32 5.5E-37 233.9 7.1 108 15-132 195-322 (326)
11 PRK07342 peptide chain release 100.0 5E-32 1.1E-36 233.1 8.8 109 16-134 198-326 (339)
12 PRK00578 prfB peptide chain re 100.0 6.1E-32 1.3E-36 234.7 7.6 113 16-138 234-366 (367)
13 TIGR00020 prfB peptide chain r 100.0 6.3E-32 1.4E-36 234.4 7.3 109 15-133 233-361 (364)
14 COG1186 PrfB Protein chain rel 99.9 7.6E-28 1.6E-32 198.7 3.5 63 16-78 109-171 (239)
15 PRK09256 hypothetical protein; 99.9 3.2E-26 6.9E-31 175.9 9.4 76 1-80 1-100 (138)
16 KOG3429 Predicted peptidyl-tRN 99.8 1.3E-19 2.7E-24 142.7 6.4 70 9-82 36-130 (172)
17 PF10213 MRP-S28: Mitochondria 78.5 17 0.00037 27.6 7.7 34 48-81 60-94 (127)
18 PF02954 HTH_8: Bacterial regu 55.7 4.8 0.0001 24.4 0.4 17 133-149 21-37 (42)
19 cd02394 vigilin_like_KH K homo 52.6 17 0.00036 23.0 2.7 39 27-70 15-60 (62)
20 PF11972 HTH_13: HTH DNA bindi 45.6 13 0.00028 24.6 1.3 22 125-146 2-29 (54)
21 KOG3933 Mitochondrial ribosoma 45.1 78 0.0017 27.6 6.3 31 48-78 202-233 (296)
22 PF12728 HTH_17: Helix-turn-he 44.8 7.7 0.00017 23.8 0.1 17 132-148 3-19 (51)
23 PF02815 MIR: MIR domain; Int 43.5 54 0.0012 25.4 4.8 39 21-59 121-159 (190)
24 PF02796 HTH_7: Helix-turn-hel 42.9 11 0.00023 23.1 0.6 17 133-149 24-40 (45)
25 COG3514 Uncharacterized protei 42.1 4.4 9.5E-05 29.6 -1.5 20 8-33 60-79 (93)
26 PF00126 HTH_1: Bacterial regu 40.4 11 0.00023 24.2 0.3 17 133-149 16-32 (60)
27 PF07638 Sigma70_ECF: ECF sigm 39.7 64 0.0014 24.9 4.7 34 116-149 118-170 (185)
28 PF05269 Phage_CII: Bacterioph 37.7 20 0.00044 25.9 1.4 25 125-149 15-42 (91)
29 TIGR01764 excise DNA binding d 35.5 14 0.0003 21.6 0.2 16 133-148 4-19 (49)
30 smart00322 KH K homology RNA-b 34.3 67 0.0015 19.3 3.3 45 28-75 19-68 (69)
31 PF04149 DUF397: Domain of unk 33.8 74 0.0016 20.6 3.5 18 39-56 16-33 (56)
32 PF01527 HTH_Tnp_1: Transposas 32.2 23 0.00049 23.0 0.9 35 114-148 5-41 (76)
33 PF01418 HTH_6: Helix-turn-hel 30.9 5.8 0.00013 26.9 -2.3 17 133-149 37-53 (77)
34 smart00497 IENR1 Intron encode 30.6 19 0.00041 21.9 0.3 17 133-149 20-36 (53)
35 PF00356 LacI: Bacterial regul 30.2 17 0.00037 22.8 0.0 17 133-149 2-18 (46)
36 cd04762 HTH_MerR-trunc Helix-T 28.9 20 0.00044 20.6 0.2 16 133-148 3-18 (49)
37 PF07292 NID: Nmi/IFP 35 domai 28.8 56 0.0012 23.4 2.5 26 4-31 60-85 (88)
38 PF13936 HTH_38: Helix-turn-he 28.8 16 0.00035 22.3 -0.3 17 133-149 23-39 (44)
39 cd00105 KH-I K homology RNA-bi 28.8 45 0.00097 20.6 1.8 42 27-71 15-63 (64)
40 smart00472 MIR Domain in ryano 28.4 66 0.0014 19.8 2.5 22 37-58 6-27 (57)
41 PF02042 RWP-RK: RWP-RK domain 27.6 29 0.00064 22.6 0.8 16 133-148 18-33 (52)
42 PF09048 Cro: Cro; InterPro: 27.3 27 0.00059 23.5 0.6 24 126-149 8-31 (59)
43 PF13384 HTH_23: Homeodomain-l 27.1 26 0.00057 21.1 0.4 23 126-148 13-35 (50)
44 PF00376 MerR: MerR family reg 26.9 30 0.00065 20.7 0.7 15 133-147 2-16 (38)
45 TIGR00637 ModE_repress ModE mo 26.1 41 0.00089 24.0 1.4 24 126-149 12-35 (99)
46 cd00552 RaiA RaiA ("ribosome-a 23.8 2.3E+02 0.0051 18.9 7.4 52 18-75 35-87 (93)
47 PF13412 HTH_24: Winged helix- 23.0 32 0.00069 20.7 0.3 16 133-148 20-35 (48)
48 PF13404 HTH_AsnC-type: AsnC-t 22.9 32 0.00069 21.0 0.3 16 133-148 20-35 (42)
49 COG2522 Predicted transcriptio 22.7 31 0.00067 26.1 0.2 16 133-148 25-40 (119)
50 PF04967 HTH_10: HTH DNA bindi 22.6 38 0.00083 22.0 0.6 16 133-148 26-41 (53)
51 PF13014 KH_3: KH domain 22.3 26 0.00057 20.8 -0.2 20 28-47 7-28 (43)
52 cd02395 SF1_like-KH Splicing f 21.8 1.2E+02 0.0027 22.5 3.3 25 50-76 70-94 (120)
53 PF13518 HTH_28: Helix-turn-he 21.7 47 0.001 19.8 0.9 22 127-148 9-30 (52)
54 PHA00437 tail assembly protein 21.6 60 0.0013 23.7 1.5 12 21-33 82-93 (94)
55 PRK11482 putative DNA-binding 21.0 63 0.0014 26.8 1.7 26 124-149 37-62 (317)
56 cd04761 HTH_MerR-SF Helix-Turn 20.9 48 0.001 19.5 0.8 15 133-147 3-17 (49)
57 PF07453 NUMOD1: NUMOD1 domain 20.5 47 0.001 19.1 0.7 16 133-148 19-34 (37)
58 PF11653 VirionAssem_T7: Bacte 20.1 68 0.0015 23.5 1.5 12 21-33 83-94 (95)
59 KOG3259 Peptidyl-prolyl cis-tr 20.1 2.8E+02 0.0061 22.2 5.0 46 24-76 41-94 (163)
No 1
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.4e-43 Score=298.76 Aligned_cols=132 Identities=30% Similarity=0.383 Sum_probs=112.8
Q ss_pred cCCCCCCC-ChhhhhccceEEEEeccCCCcCCCCccCceEEEEEcCCceEEEeccccCHHHHHHHHHHHHHHHHHHHHHh
Q 038082 3 VLPNYLEL-TDDELFRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLALKVRS 81 (149)
Q Consensus 3 ~~~~~~~i-~~~~l~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RSq~~Nr~~A~~~L~~~l~~~~~~ 81 (149)
+||..-.+ ..+.-++|++|++|||||+||||||+|+|||||||+||||+|+||++|||++||++||+.|+++|....++
T Consensus 208 VlPE~ee~~ei~I~~~DlrIDt~RsSGaGGQhVNtTdSAVRiTHlPTGIvV~cQderSQ~kNk~kAmkvL~ARl~~~~~~ 287 (363)
T COG0216 208 VLPEVEEVEEIEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQ 287 (363)
T ss_pred eccCCCcccccccChHHceeeeeecCCCCCCCcCccchhheeeecCCceEEEecchhhhhhhHHHHHHHHHHHHHHHHHH
Confidence 45554333 22333667799999999999999999999999999999999999999999999999999999988766555
Q ss_pred hcccCCCCCCccccccCCCCCccccCCCCCCCCCCCh------------------hhhh-h-HHHhhchhhHHHHHHHhC
Q 038082 82 SVNLDAYSPPPQLHQILPPKSTIRSSEVGPQIGPNNP------------------KFAL-V-LPYSLLLPFVINAAKIYG 141 (149)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~rksqir~~~r~~kIrtyn~------------------~f~~-g-L~~llD~L~~~~aA~~L~ 141 (149)
+.+. ..+..||+|+++||||++|||||| .||. | ||+++|+|+..++|++|.
T Consensus 288 ~~~~---------~~~~~RksqVGSGDRSErIRTYNfPQnRVTDHRI~lTl~kLd~vm~gG~LDeii~aLi~~~q~~~L~ 358 (363)
T COG0216 288 KAQA---------EEASERKSQVGSGDRSERIRTYNFPQNRVTDHRINLTLYKLDEVMEGGKLDEIIDALIAEDQAEQLA 358 (363)
T ss_pred HHHH---------HHHHHHHHhcCCCchhhhhhccCCCCCcccchhcccccccHHHHhccCcHHHHHHHHHHHHHHHHHH
Confidence 5432 245689999999999999999994 8999 5 999999999999999997
Q ss_pred CC
Q 038082 142 LK 143 (149)
Q Consensus 142 ~s 143 (149)
..
T Consensus 359 ~l 360 (363)
T COG0216 359 EL 360 (363)
T ss_pred Hh
Confidence 54
No 2
>TIGR00019 prfA peptide chain release factor 1. This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift.
Probab=100.00 E-value=1.6e-34 Score=250.19 Aligned_cols=118 Identities=30% Similarity=0.382 Sum_probs=103.0
Q ss_pred hhccceEEEEeccCCCcCCCCccCceEEEEEcCCceEEEeccccCHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCccc
Q 038082 15 LFRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLALKVRSSVNLDAYSPPPQL 94 (149)
Q Consensus 15 l~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RSq~~Nr~~A~~~L~~~l~~~~~~~~~~~~~~~~~~~ 94 (149)
-++||+|+|+|||||||||||||+|||||+|+||||+|.|+++|||++||+.||++|+++|.....++...+
T Consensus 219 ~~~dl~~~~~RssG~GGQ~VNkt~SaVrl~h~ptgi~V~~~~eRSQ~~Nk~~A~~~L~~~L~~~~~~~~~~~-------- 290 (360)
T TIGR00019 219 NPADLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMKVLRARLYEAEQEKQQAA-------- 290 (360)
T ss_pred CcccEEEEEEECCCCCCCCcCceeeeEEEEECCCcEEEEECCccCHHHHHHHHHHHHHHHHHHHHHHHHHHH--------
Confidence 356779999999999999999999999999999999999999999999999999999998876555432221
Q ss_pred cccCCCCCccccCCCCCCCCCCCh------------------hhhhh-HHHhhchhhHHHHHHHhC
Q 038082 95 HQILPPKSTIRSSEVGPQIGPNNP------------------KFALV-LPYSLLLPFVINAAKIYG 141 (149)
Q Consensus 95 ~~~~~rksqir~~~r~~kIrtyn~------------------~f~~g-L~~llD~L~~~~aA~~L~ 141 (149)
....|++++++++||++|||||+ .||+| |++++|.+..++..+.|.
T Consensus 291 -~~~~r~~~~~~~~Rs~~IRtY~~~~~rV~DhRtg~~~~~l~~vl~G~Ld~~I~~~l~~~~~~~l~ 355 (360)
T TIGR00019 291 -QASTRKSQVGSGDRSERIRTYNFPQNRVTDHRINLTLYKLDEVLEGDLDELIEALIAEDQAQQLA 355 (360)
T ss_pred -HHHHHhhhcceecccCCeEEEECCCCeeeeeccCCeEcChHHHhCCchHHHHHHHHHHHHHHHHH
Confidence 33467999999999999999994 89999 999999999888777764
No 3
>KOG2726 consensus Mitochondrial polypeptide chain release factor [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-34 Score=250.57 Aligned_cols=111 Identities=37% Similarity=0.512 Sum_probs=98.7
Q ss_pred hccceEEEEeccCCCcCCCCccCceEEEEEcCCceEEEeccccCHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCcccc
Q 038082 16 FRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLALKVRSSVNLDAYSPPPQLH 95 (149)
Q Consensus 16 ~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RSq~~Nr~~A~~~L~~~l~~~~~~~~~~~~~~~~~~~~ 95 (149)
++||+|+|+|+|||||||||||+|||+|+|+||||+|+|+++|||++||+.|+.+|+++|+...+++...+.
T Consensus 247 ~~dl~i~~~R~~G~GGQhvNktdsaVrl~HiPTGIvv~cq~eRSq~~Nr~~A~~~L~akL~~~~~~~~~~~~-------- 318 (386)
T KOG2726|consen 247 EKDLRIETFRASGPGGQHVNKTDSAVRLTHIPTGIVVECQEERSQHKNRALALKRLRAKLAVIYREEKSEEE-------- 318 (386)
T ss_pred chheeEEecccCCCCcccccccccceEEEeecCceEEEeecHHhHHhhHHHHHHHHHHHHHHHHHhhhhHHh--------
Confidence 777799999999999999999999999999999999999999999999999999999999887776655433
Q ss_pred ccCCCCCccccCCCCCCCCCCCh------------------hhhhh-HHHhhchhhHHH
Q 038082 96 QILPPKSTIRSSEVGPQIGPNNP------------------KFALV-LPYSLLLPFVIN 135 (149)
Q Consensus 96 ~~~~rksqir~~~r~~kIrtyn~------------------~f~~g-L~~llD~L~~~~ 135 (149)
...|+.++++++|+++|||||| .|+.| |+++|..+....
T Consensus 319 -~~~r~~qv~s~~rsekiRTy~~~q~rv~D~r~~~~~~d~~~~l~G~Ld~li~~~~~~~ 376 (386)
T KOG2726|consen 319 -KKKRKAQVGSLKRSEKIRTYNFKQDRVTDHRIGLESHDLESFLDGNLDELIEALLSLR 376 (386)
T ss_pred -hhhhHHhhcccCchhceeecccCccchhhhhhcccccchHHHHhccHHHHHHHHHHHh
Confidence 3468999999999999999995 78888 888888887333
No 4
>PRK00591 prfA peptide chain release factor 1; Validated
Probab=100.00 E-value=4.6e-34 Score=247.34 Aligned_cols=119 Identities=30% Similarity=0.403 Sum_probs=103.5
Q ss_pred hhhccceEEEEeccCCCcCCCCccCceEEEEEcCCceEEEeccccCHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCcc
Q 038082 14 ELFRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLALKVRSSVNLDAYSPPPQ 93 (149)
Q Consensus 14 ~l~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RSq~~Nr~~A~~~L~~~l~~~~~~~~~~~~~~~~~~ 93 (149)
.-++||+|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+++|+++|.....++...+
T Consensus 218 i~~~dl~~~~~RssG~GGQ~VNkt~saVrl~H~ptGi~v~~~~eRSQ~~Nk~~Al~~L~~~L~~~~~~~~~~~------- 290 (359)
T PRK00591 218 INPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAE------- 290 (359)
T ss_pred cCcccEEEEEEECCCCCCCCccceeeeEEEEECCCcEEEEECCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-------
Confidence 3356779999999999999999999999999999999999999999999999999999998876555554431
Q ss_pred ccccCCCCCccccCCCCCCCCCCCh------------------hhhhh-HHHhhchhhHHHHHHHhC
Q 038082 94 LHQILPPKSTIRSSEVGPQIGPNNP------------------KFALV-LPYSLLLPFVINAAKIYG 141 (149)
Q Consensus 94 ~~~~~~rksqir~~~r~~kIrtyn~------------------~f~~g-L~~llD~L~~~~aA~~L~ 141 (149)
....|++++.+++||++|||||| .||+| |+++|+.+..++..+.|.
T Consensus 291 --~~~~r~~~~~~~~Rse~IRtY~f~~~~V~DhRtg~~~~~l~~vl~G~Ld~fI~~~l~~~~~~~l~ 355 (359)
T PRK00591 291 --EAATRKSQVGSGDRSERIRTYNFPQGRVTDHRINLTLYKLDEVMEGDLDELIDALIAEDQAEKLA 355 (359)
T ss_pred --HHHHHHhhcccccccCCeeeEECCCCeeeeeccCCEEcChHHHhCCChHHHHHHHHHHHHHHHHH
Confidence 23367899999999999999994 89999 999999999777777664
No 5
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....
Probab=100.00 E-value=3.6e-33 Score=207.00 Aligned_cols=101 Identities=37% Similarity=0.525 Sum_probs=86.2
Q ss_pred CCCCCCChhhhhccceEEEEeccCCCcCCCCccCceEEEEEcCCceEEEeccccCHHHHHHHHHHHHHHHHHHHHHhhcc
Q 038082 5 PNYLELTDDELFRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLALKVRSSVN 84 (149)
Q Consensus 5 ~~~~~i~~~~l~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RSq~~Nr~~A~~~L~~~l~~~~~~~~~ 84 (149)
+..+.|++++| +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||+.|++.|+++|+++|.....++..
T Consensus 4 ~~~~~i~~~dl----~~~~~RssGpGGQ~VNk~~s~V~l~h~ptgi~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~~~~~~~ 79 (113)
T PF00472_consen 4 EKEIDIPEKDL----EISFSRSSGPGGQNVNKTNSKVRLRHIPTGIVVKCQESRSQHQNREDALEKLREKLDEAYREKRR 79 (113)
T ss_dssp SSSSCC-GGGE----EEEEEESSSSSSCHHHSSSEEEEEEETTTTEEEEEESSSSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccccCHHHe----EEEEEecCCCCCCcccccCCEEEEEEecccEEEEEcccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44567776666 99999999999999999999999999999999999999999999999999999999876644433
Q ss_pred cCCCCCCccccccCCCCCccccCCCCCCCCCCCh
Q 038082 85 LDAYSPPPQLHQILPPKSTIRSSEVGPQIGPNNP 118 (149)
Q Consensus 85 ~~~~~~~~~~~~~~~rksqir~~~r~~kIrtyn~ 118 (149)
.. ....++++.+..+++++||+||+
T Consensus 80 ~~---------~~~~~~~~~~~~~~~~~iR~y~~ 104 (113)
T PF00472_consen 80 EK---------TREIRKSQVKRLERKKKIRTYNF 104 (113)
T ss_dssp HH---------TTTTTTTSCCCSSTTSEEEEEET
T ss_pred HH---------HHHHHHHHHhHHhhhcceecccC
Confidence 21 23467888888899999999997
No 6
>TIGR03072 release_prfH putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon.
Probab=99.98 E-value=2.9e-33 Score=226.10 Aligned_cols=101 Identities=31% Similarity=0.362 Sum_probs=85.5
Q ss_pred CCCCCCCChhhhhccceEEEEeccCCCcCCCCccCceEEEEEcCCceEEEeccccCHHHHHHHHHHHHHHHHHHHHHhhc
Q 038082 4 LPNYLELTDDELFRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLALKVRSSV 83 (149)
Q Consensus 4 ~~~~~~i~~~~l~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RSq~~Nr~~A~~~L~~~l~~~~~~~~ 83 (149)
+|..+.|++ +||+|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+++|+++|.....++.
T Consensus 97 ~~~~~~i~~----~dl~~~~~RssGpGGQ~vNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~~l~~~~~~~~ 172 (200)
T TIGR03072 97 FSASEEATE----DEIRFETLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLATLLLAVRLADLQQEQA 172 (200)
T ss_pred ecCccccCh----hheEEEEEECCCCCcccccccceeEEEEECCCcEEEEECCccCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444544 4559999999999999999999999999999999999999999999999999999999876655554
Q ss_pred ccCCCCCCccccccCCCCCccccCCCCCCCCCCCh
Q 038082 84 NLDAYSPPPQLHQILPPKSTIRSSEVGPQIGPNNP 118 (149)
Q Consensus 84 ~~~~~~~~~~~~~~~~rksqir~~~r~~kIrtyn~ 118 (149)
+. ....++++..+.+||++|||||.
T Consensus 173 ~~----------~~~~~r~~~~~~~Rg~~iRty~~ 197 (200)
T TIGR03072 173 AA----------LRAERRTAHHQIERGNPVRVFKG 197 (200)
T ss_pred HH----------HHHHHHhccccccccCceEeeeC
Confidence 43 33467788888899999999993
No 7
>PRK05589 peptide chain release factor 2; Provisional
Probab=99.98 E-value=7.2e-33 Score=237.26 Aligned_cols=107 Identities=29% Similarity=0.411 Sum_probs=87.8
Q ss_pred hccceEEEEeccCCCcCCCCccCceEEEEEcCCceEEEeccccCHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCcccc
Q 038082 16 FRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLALKVRSSVNLDAYSPPPQLH 95 (149)
Q Consensus 16 ~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RSq~~Nr~~A~~~L~~~l~~~~~~~~~~~~~~~~~~~~ 95 (149)
++|++|+|+|||||||||||||+|||||+|+||||+|+|+++|||++||+.|+++|+++|.....++.+.
T Consensus 195 ~~dl~~~~~rssG~GGQ~VNkt~saVrl~H~ptgi~v~~q~eRSQ~~Nk~~A~~~L~~kL~~~~~~~~~~---------- 264 (325)
T PRK05589 195 SEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNKETAMKMLKSKLVELKERAHKE---------- 264 (325)
T ss_pred chheEEEEeeCCCCCCCcccceeeEEEEEECCCCEEEEECCccCHHHHHHHHHHHHHHHHHHHHHHHHHH----------
Confidence 4566999999999999999999999999999999999999999999999999999999887554333322
Q ss_pred ccCCCCCccccCCCCCCCCCCCh-------------------hhhhh-HHHhhchhh
Q 038082 96 QILPPKSTIRSSEVGPQIGPNNP-------------------KFALV-LPYSLLLPF 132 (149)
Q Consensus 96 ~~~~rksqir~~~r~~kIrtyn~-------------------~f~~g-L~~llD~L~ 132 (149)
+...++++.....||++|||||+ .||+| |+++||.+.
T Consensus 265 ~~~~~r~~~~~~~~g~~IRtY~~~p~~rVtDhR~g~~~~~l~~vl~G~Ld~~I~a~l 321 (325)
T PRK05589 265 KIEDLTGELKDMGWGSQIRSYVFHPYNLVKDHRTGVETSNVDSVMDGDIDNFITQYL 321 (325)
T ss_pred HHHHHhcccccccccCCceeeECCCCceeeeeccCceecChHHhhCCCHHHHHHHHH
Confidence 11123344445568889999995 78899 998888875
No 8
>PRK08787 peptide chain release factor 2; Provisional
Probab=99.98 E-value=1.1e-32 Score=234.89 Aligned_cols=112 Identities=34% Similarity=0.350 Sum_probs=90.4
Q ss_pred hccceEEEEeccCCCcCCCCccCceEEEEEcCCceEEEeccccCHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCcccc
Q 038082 16 FRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLALKVRSSVNLDAYSPPPQLH 95 (149)
Q Consensus 16 ~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RSq~~Nr~~A~~~L~~~l~~~~~~~~~~~~~~~~~~~~ 95 (149)
++||+|+|+|||||||||||||+|||+|+|+||||+|+|+++|||++||+.|+++|+++|.....++.+.+..
T Consensus 175 ~~dl~~~~~RssG~GGQ~VNkt~saVri~H~Ptgi~v~~q~eRSQ~~Nk~~A~~~L~~~L~~~~~e~~~~~~~------- 247 (313)
T PRK08787 175 PADLRTDVYRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAMKMLAAKLYELEVQKRNAEKD------- 247 (313)
T ss_pred hhHeEEEEEECCCCCCCCcCCEeeEEEEEECCCcEEEEECCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------
Confidence 4566999999999999999999999999999999999999999999999999999999886654444332110
Q ss_pred ccCCCCCccccCCCCCCCCCCCh------------------hhhhh-HHHhhchhhHHHHH
Q 038082 96 QILPPKSTIRSSEVGPQIGPNNP------------------KFALV-LPYSLLLPFVINAA 137 (149)
Q Consensus 96 ~~~~rksqir~~~r~~kIrtyn~------------------~f~~g-L~~llD~L~~~~aA 137 (149)
....+|++++ ||+||||||| .||+| |+++|+.+..+..|
T Consensus 248 ~~~~~k~~i~---~g~qIRtY~f~~~~V~DhRtg~~~~~l~~vldG~ld~fI~a~l~~~~~ 305 (313)
T PRK08787 248 ALEATKSDIG---WGSQIRNYVLDQSRIKDLRTGIERSDTQKVLDGDLDEFVEASLKAGLA 305 (313)
T ss_pred HHhhhhhhCc---ccccccceeCCCCcceeeccCceEcChhHhhCCChHHHHHHHHHHHHh
Confidence 1112355554 6679999994 89999 99999998855443
No 9
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=99.97 E-value=1.9e-32 Score=221.35 Aligned_cols=100 Identities=28% Similarity=0.325 Sum_probs=85.3
Q ss_pred CCCCCCCChhhhhccceEEEEeccCCCcCCCCccCceEEEEEcCCceEEEeccccCHHHHHHHHHHHHHHHHHHHHHhhc
Q 038082 4 LPNYLELTDDELFRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLALKVRSSV 83 (149)
Q Consensus 4 ~~~~~~i~~~~l~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RSq~~Nr~~A~~~L~~~l~~~~~~~~ 83 (149)
+|..+.|++++| +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+++|+++|.....++.
T Consensus 98 ~~~~~~i~~~dl----~~~~~RssGpGGQ~VNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~~L~~~~~~~~ 173 (200)
T PRK08179 98 FSADEEEQSDEI----RFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLLIAWKLEQQQQEQS 173 (200)
T ss_pred eCCcCccCHHHe----EEEEEEccCCcccccccccceEEEEEcCCcEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455566665555 9999999999999999999999999999999999999999999999999999999876555554
Q ss_pred ccCCCCCCccccccCCCCCccccCCCCCCCCCCC
Q 038082 84 NLDAYSPPPQLHQILPPKSTIRSSEVGPQIGPNN 117 (149)
Q Consensus 84 ~~~~~~~~~~~~~~~~rksqir~~~r~~kIrtyn 117 (149)
+. ....++++..+.+||++||||-
T Consensus 174 ~~----------~~~~~~~~~~~~~Rg~~IRt~~ 197 (200)
T PRK08179 174 AA----------LKSQRRMFHHQIERGNPRRVFT 197 (200)
T ss_pred HH----------HHHHHHhccccccccCceEeee
Confidence 43 3345777788889999999984
No 10
>PRK06746 peptide chain release factor 2; Provisional
Probab=99.97 E-value=2.5e-32 Score=233.88 Aligned_cols=108 Identities=27% Similarity=0.283 Sum_probs=90.9
Q ss_pred hhccceEEEEeccCCCcCCCCccCceEEEEEcCCceEEEeccccCHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCccc
Q 038082 15 LFRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLALKVRSSVNLDAYSPPPQL 94 (149)
Q Consensus 15 l~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RSq~~Nr~~A~~~L~~~l~~~~~~~~~~~~~~~~~~~ 94 (149)
-++||+|+|+|||||||||||||+|||+|+|+||||+|+|+++|||++||+.|+++|+++|.....++...+
T Consensus 195 ~~~dl~~~~~rssG~GGQ~vNkt~saVrl~h~ptgi~v~~q~~RSQ~~Nk~~A~~~L~akL~~~~~~~~~~~-------- 266 (326)
T PRK06746 195 RTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAMKMLKAKLYQKKLEEQQAE-------- 266 (326)
T ss_pred ChHHeEEEEEeCCCCCCCCccceeeEEEEEEeCCeEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH--------
Confidence 355669999999999999999999999999999999999999999999999999999998866554443321
Q ss_pred cccCCCCCccccCCCCCCCCCCCh-------------------hhhhh-HHHhhchhh
Q 038082 95 HQILPPKSTIRSSEVGPQIGPNNP-------------------KFALV-LPYSLLLPF 132 (149)
Q Consensus 95 ~~~~~rksqir~~~r~~kIrtyn~-------------------~f~~g-L~~llD~L~ 132 (149)
....|++++.. .|+++|||||+ .||+| |+++|+.+.
T Consensus 267 -~~~~r~~~~~~-~rg~~IRtYnf~p~~rVtDhR~~~~~~~l~~vl~G~ld~~I~~~~ 322 (326)
T PRK06746 267 -LDEIRGEQKEI-GWGSQIRSYVFHPYSLVKDHRTNTEVGNVQAVMDGEIDPFIDAYL 322 (326)
T ss_pred -HHHHHhhhccC-ccCCCeEEEECCCCceeeeeecCceecChHHhhCCCHHHHHHHHH
Confidence 23457777766 47789999995 78888 888888775
No 11
>PRK07342 peptide chain release factor 2; Provisional
Probab=99.97 E-value=5e-32 Score=233.09 Aligned_cols=109 Identities=35% Similarity=0.413 Sum_probs=89.5
Q ss_pred hccceEEEEeccCCCcCCCCccCceEEEEEcCCceEEEeccccCHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCcccc
Q 038082 16 FRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLALKVRSSVNLDAYSPPPQLH 95 (149)
Q Consensus 16 ~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RSq~~Nr~~A~~~L~~~l~~~~~~~~~~~~~~~~~~~~ 95 (149)
++||+|+|+|||||||||||||+|||||+|+||||+|+|+++|||++||+.|+++|+++|.....++...+..
T Consensus 198 ~~dl~~~~~RssG~GGQ~VNkt~saVrl~H~ptgi~v~~~~eRSQ~~Nk~~A~~~L~~~L~~~~~~~~~~~~~------- 270 (339)
T PRK07342 198 ESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAWSMLRARLYEEELKKREEATN------- 270 (339)
T ss_pred cccEEEEEEECCCCCCCCccceeeeEEEEEcCCcEEEEECCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------
Confidence 5677999999999999999999999999999999999999999999999999999999887555444432111
Q ss_pred ccCCCCCccccCCCCCCCCCCCh-------------------hhhhh-HHHhhchhhHH
Q 038082 96 QILPPKSTIRSSEVGPQIGPNNP-------------------KFALV-LPYSLLLPFVI 134 (149)
Q Consensus 96 ~~~~rksqir~~~r~~kIrtyn~-------------------~f~~g-L~~llD~L~~~ 134 (149)
....++++++ ||++|||||+ .||+| |+++||.+..+
T Consensus 271 ~~~~~~~~i~---~g~~IRtY~~~p~~rVtDhRtg~~~~~l~~vl~G~Ld~~I~a~l~~ 326 (339)
T PRK07342 271 AAAASKTDIG---WGHQIRSYVLQPYQLVKDLRTGVESTNPQDVLDGDLNEFMEAALAH 326 (339)
T ss_pred HHHhhhhhcc---ccCCcCCccCCCCceeeeeccCceecChHHhhCCCHHHHHHHHHHH
Confidence 1123466665 5569999994 89999 99999988743
No 12
>PRK00578 prfB peptide chain release factor 2; Validated
Probab=99.97 E-value=6.1e-32 Score=234.67 Aligned_cols=113 Identities=31% Similarity=0.367 Sum_probs=93.4
Q ss_pred hccceEEEEeccCCCcCCCCccCceEEEEEcCCceEEEeccccCHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCcccc
Q 038082 16 FRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLALKVRSSVNLDAYSPPPQLH 95 (149)
Q Consensus 16 ~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RSq~~Nr~~A~~~L~~~l~~~~~~~~~~~~~~~~~~~~ 95 (149)
++||+|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+++|+++|.....++.+.+
T Consensus 234 ~~dl~~~~~rssGpGGQ~vNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~kL~~~~~~~~~~~--------- 304 (367)
T PRK00578 234 PKDLRIDTYRSSGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASAMKMLKAKLYELELEKRAAE--------- 304 (367)
T ss_pred hhhEEEEEeeCCCCCCCcccceeeEEEEEECCCcEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH---------
Confidence 45669999999999999999999999999999999999999999999999999999998876555554331
Q ss_pred ccCCCCCccccCCCCCCCCCCCh-------------------hhhhh-HHHhhchhhHHHHHH
Q 038082 96 QILPPKSTIRSSEVGPQIGPNNP-------------------KFALV-LPYSLLLPFVINAAK 138 (149)
Q Consensus 96 ~~~~rksqir~~~r~~kIrtyn~-------------------~f~~g-L~~llD~L~~~~aA~ 138 (149)
....|+.+ ...+||++|||||+ .||+| |++++|.+..+.+++
T Consensus 305 ~~~~r~~~-~~~~rg~~IRtYn~~p~~rVtDhR~g~~~~~l~~vl~G~ld~~I~~l~~~~~~~ 366 (367)
T PRK00578 305 KDALKGEK-KEIGWGSQIRSYVLHPYQMVKDLRTGYETGNTQAVLDGDLDGFIEAYLRWRASQ 366 (367)
T ss_pred HHHHHhhh-ccccccCCeEEEECCCCceeeeeccCceecCHHHhhCCChHHHHHHHHHHHhcc
Confidence 11233334 45568889999995 89999 999999998766553
No 13
>TIGR00020 prfB peptide chain release factor 2. In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a Pfam model called "RF-1" for the superfamily of RF-1, RF-2, mitochondrial, RF-H, etc.
Probab=99.97 E-value=6.3e-32 Score=234.41 Aligned_cols=109 Identities=30% Similarity=0.356 Sum_probs=89.2
Q ss_pred hhccceEEEEeccCCCcCCCCccCceEEEEEcCCceEEEeccccCHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCccc
Q 038082 15 LFRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLALKVRSSVNLDAYSPPPQL 94 (149)
Q Consensus 15 l~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RSq~~Nr~~A~~~L~~~l~~~~~~~~~~~~~~~~~~~ 94 (149)
.++|++|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+++|+++|.....++.+.+
T Consensus 233 ~~~d~~~~~~rssG~GGQ~VNkt~saVri~H~ptgi~v~~q~~RSQ~~Nk~~A~~~L~~kL~~~~~~~~~~~-------- 304 (364)
T TIGR00020 233 KPEDLRIDTYRASGAGGQHVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAMKVLKAKLYELEMEKEQAE-------- 304 (364)
T ss_pred ccccEEEEEeeCCCCCCccccccceEEEEEECCCcEEEEECCccCHHHHHHHHHHHHHHHHHHHHHHHHHHH--------
Confidence 356779999999999999999999999999999999999999999999999999999998876555444321
Q ss_pred cccCCCCCccccCCCCCCCCCCCh-------------------hhhhh-HHHhhchhhH
Q 038082 95 HQILPPKSTIRSSEVGPQIGPNNP-------------------KFALV-LPYSLLLPFV 133 (149)
Q Consensus 95 ~~~~~rksqir~~~r~~kIrtyn~-------------------~f~~g-L~~llD~L~~ 133 (149)
....|+++... +||++|||||+ .||+| |+++||.+..
T Consensus 305 -~~~~r~~~~~~-~rg~~IRtY~~~~~~rVtDhR~g~~~~~l~~vl~G~Ld~~I~a~~~ 361 (364)
T TIGR00020 305 -KDAKEGEKSEI-GWGSQIRSYVLHPYSMVKDLRTGYETGNVQAVLDGDIDQFIEAYLK 361 (364)
T ss_pred -HHHHHhhhhcc-CccCCeEEEECCCCCcccccccCCeecChHHHhCCChHHHHHHHHh
Confidence 11234333333 68889999995 78999 9998888763
No 14
>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=7.6e-28 Score=198.72 Aligned_cols=63 Identities=44% Similarity=0.670 Sum_probs=58.6
Q ss_pred hccceEEEEeccCCCcCCCCccCceEEEEEcCCceEEEeccccCHHHHHHHHHHHHHHHHHHH
Q 038082 16 FRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLALK 78 (149)
Q Consensus 16 ~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RSq~~Nr~~A~~~L~~~l~~~ 78 (149)
+.|++|+|+|||||||||||||+|||+|||+||||+|.|+.+|||++|++.|+..|+..|...
T Consensus 109 ~~dl~idt~RASGaGGQhVNKt~SAVrlth~ptgivv~cq~eRSq~~n~~~a~~~l~~kL~~~ 171 (239)
T COG1186 109 DDDLRIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALARKMLKGKLYIL 171 (239)
T ss_pred ccceEEEEEEcCCCCCCccccccccEEEEEcCCCCEecCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455599999999999999999999999999999999999999999999999999999976543
No 15
>PRK09256 hypothetical protein; Provisional
Probab=99.93 E-value=3.2e-26 Score=175.85 Aligned_cols=76 Identities=39% Similarity=0.600 Sum_probs=70.0
Q ss_pred CccCCCCCCCChhhhhccceEEEEeccCCCcCCCCccCceEEEEE------cC-----------------Cc-eEEEecc
Q 038082 1 MNVLPNYLELTDDELFRECEMDAYKSSGPGGQHRNKRESAVRLKH------AP-----------------TG-VIAQAAE 56 (149)
Q Consensus 1 ~~~~~~~~~i~~~~l~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h------~p-----------------tG-i~v~~~~ 56 (149)
|+.|++.+.||.+++ +|+|+|||||||||||||+|+|+|+| +| +| |+|+|++
T Consensus 1 ~~~~~~~~~i~~~~l----~~~~~RSSGPGGQ~VNKt~SkV~l~~~~~~~~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~ 76 (138)
T PRK09256 1 MLRITRRLVIPENEL----EWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQE 76 (138)
T ss_pred CcccCccCccCHHHe----EEEEEEcCCCCcccccccceeeEEEechhhccCCHHHHHHHHHHhcCcccCCCcEEEEECC
Confidence 677888899998888 99999999999999999999999996 77 46 9999999
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHH
Q 038082 57 DRSQHKNRASALSRLRTLLALKVR 80 (149)
Q Consensus 57 ~RSq~~Nr~~A~~~L~~~l~~~~~ 80 (149)
+|||++|++.|+++|.++|.....
T Consensus 77 ~RSQ~~Nr~~al~kL~~~i~~~~~ 100 (138)
T PRK09256 77 FRSQERNREDALERLVALIREALK 100 (138)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999999999987665
No 16
>KOG3429 consensus Predicted peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=99.79 E-value=1.3e-19 Score=142.71 Aligned_cols=70 Identities=36% Similarity=0.603 Sum_probs=61.4
Q ss_pred CCChhhhhccceEEEEeccCCCcCCCCccCceEEEEE-------cC-----------------Cc-eEEEeccccCHHHH
Q 038082 9 ELTDDELFRECEMDAYKSSGPGGQHRNKRESAVRLKH-------AP-----------------TG-VIAQAAEDRSQHKN 63 (149)
Q Consensus 9 ~i~~~~l~~d~~i~~~RssGpGGQ~vNk~~s~V~l~h-------~p-----------------tG-i~v~~~~~RSq~~N 63 (149)
.||.+.+ ++.|.||||||||||||++|+|.|++ || .| |+|.++.+|||+.|
T Consensus 36 ~ipld~~----~i~y~RSSGPGGQNVNKvNTKv~vrf~vs~a~Wipe~~R~~~~~~~~~rink~gelvI~Sd~TRsq~~N 111 (172)
T KOG3429|consen 36 KIPLDQL----EISYSRSSGPGGQNVNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRSQHKN 111 (172)
T ss_pred CCchhhe----EEEEeecCCCCCcccccccceEEEEEecchhhhccHHHHHHHHHHHHHhhccCccEEEecchhHHhhcc
Confidence 4666666 99999999999999999999999995 45 35 99999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhh
Q 038082 64 RASALSRLRTLLALKVRSS 82 (149)
Q Consensus 64 r~~A~~~L~~~l~~~~~~~ 82 (149)
.++||++|+.+|.......
T Consensus 112 iaDcleKlr~~I~~~~~~~ 130 (172)
T KOG3429|consen 112 IADCLEKLRDIIRAAEQTP 130 (172)
T ss_pred HHHHHHHHHHHHHHHhcCC
Confidence 9999999999997655433
No 17
>PF10213 MRP-S28: Mitochondrial ribosomal subunit protein ; InterPro: IPR019349 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a conserved region of approx. 125 residues of one of the proteins that makes up the small subunit of the mitochondrial ribosome. In Saccharomyces cerevisiae (Baker's yeast) it is mitochondrial ribosomal protein S24 whereas in humans it is S35.
Probab=78.52 E-value=17 Score=27.58 Aligned_cols=34 Identities=12% Similarity=0.029 Sum_probs=30.8
Q ss_pred Cc-eEEEeccccCHHHHHHHHHHHHHHHHHHHHHh
Q 038082 48 TG-VIAQAAEDRSQHKNRASALSRLRTLLALKVRS 81 (149)
Q Consensus 48 tG-i~v~~~~~RSq~~Nr~~A~~~L~~~l~~~~~~ 81 (149)
+| |.++|+..-++.+|+.-|...|..++.++.+.
T Consensus 60 ~d~l~i~sdr~~~~~qN~~~l~~~l~~L~~EA~~~ 94 (127)
T PF10213_consen 60 TDILKISSDRFPTRAQNKKYLSDLLTRLIHEAKDL 94 (127)
T ss_pred CCEEEEecccCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 67 99999999999999999999999999877663
No 18
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=55.66 E-value=4.8 Score=24.36 Aligned_cols=17 Identities=24% Similarity=0.440 Sum_probs=14.1
Q ss_pred HHHHHHHhCCCcccccC
Q 038082 133 VINAAKIYGLKSGEIQE 149 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l~~ 149 (149)
+..+|+.||.|.++|.|
T Consensus 21 ~~~aA~~Lgisr~tL~~ 37 (42)
T PF02954_consen 21 VSKAARLLGISRRTLYR 37 (42)
T ss_dssp HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHCCCHHHHHH
Confidence 89999999999998763
No 19
>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=52.58 E-value=17 Score=23.03 Aligned_cols=39 Identities=18% Similarity=0.326 Sum_probs=24.2
Q ss_pred cCCCcCCCCc--cCceEEEEEcC----Cc-eEEEeccccCHHHHHHHHHHH
Q 038082 27 SGPGGQHRNK--RESAVRLKHAP----TG-VIAQAAEDRSQHKNRASALSR 70 (149)
Q Consensus 27 sGpGGQ~vNk--~~s~V~l~h~p----tG-i~v~~~~~RSq~~Nr~~A~~~ 70 (149)
=|+||.++++ .++.|.|..-+ .+ +.+... ..+-..|...
T Consensus 15 IG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-----~~~v~~A~~~ 60 (62)
T cd02394 15 IGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP-----KENVEKAKEE 60 (62)
T ss_pred cCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC-----HHHHHHHHHH
Confidence 3899999995 45677777655 45 555554 2344455443
No 20
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=45.62 E-value=13 Score=24.58 Aligned_cols=22 Identities=23% Similarity=0.190 Sum_probs=16.6
Q ss_pred HHhhchhh------HHHHHHHhCCCccc
Q 038082 125 PYSLLLPF------VINAAKIYGLKSGE 146 (149)
Q Consensus 125 ~~llD~L~------~~~aA~~L~~s~~~ 146 (149)
.+++|.++ +..+|+.|++|+.+
T Consensus 2 p~Lidll~~~P~Vsa~mva~~L~vT~~~ 29 (54)
T PF11972_consen 2 PRLIDLLLSRPLVSAPMVAKELGVTPQA 29 (54)
T ss_pred HHHHHHHHhCccccHHHHHHHhCCCHHH
Confidence 35566665 88999999999754
No 21
>KOG3933 consensus Mitochondrial ribosomal protein S28 [Translation, ribosomal structure and biogenesis]
Probab=45.11 E-value=78 Score=27.61 Aligned_cols=31 Identities=19% Similarity=0.122 Sum_probs=28.0
Q ss_pred Cc-eEEEeccccCHHHHHHHHHHHHHHHHHHH
Q 038082 48 TG-VIAQAAEDRSQHKNRASALSRLRTLLALK 78 (149)
Q Consensus 48 tG-i~v~~~~~RSq~~Nr~~A~~~L~~~l~~~ 78 (149)
|+ +.|.|+..-+..+|+..|+..|..++.+.
T Consensus 202 tD~~tissDR~~~r~QN~~y~~~lLt~L~~ES 233 (296)
T KOG3933|consen 202 TDLLTISSDRCEHREQNYDYALYLLTVLYHES 233 (296)
T ss_pred CCeEEEeccccchhhHhHHHHHHHHHHHHHHh
Confidence 56 89999999999999999999999999765
No 22
>PF12728 HTH_17: Helix-turn-helix domain
Probab=44.79 E-value=7.7 Score=23.75 Aligned_cols=17 Identities=24% Similarity=0.389 Sum_probs=14.4
Q ss_pred hHHHHHHHhCCCccccc
Q 038082 132 FVINAAKIYGLKSGEIQ 148 (149)
Q Consensus 132 ~~~~aA~~L~~s~~~l~ 148 (149)
-++++|+.||+|.+++.
T Consensus 3 t~~e~a~~l~is~~tv~ 19 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVY 19 (51)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 37899999999998764
No 23
>PF02815 MIR: MIR domain; InterPro: IPR003608 The MIR domain is named after three of the proteins in which it occurs: protein Mannosyltransferase (2.4.1.109 from EC), Inositol 1,4,5-trisphosphate receptor (IP3R) and Ryanodine receptor (RyR). MIR domains have also been found in eukaryotic stromal cell-derived factor 2 (SDF-2) and in Chlamydia trachomatis protein CT153. The MIR domain may have a ligand transferase function. This domain has a closed beta-barrel structure with a hairpin triplet, and has an internal pseudo-threefold symmetry. The MIR motifs that make up the MIR domain consist of ~50 residues and are often found in multiple copies. Inositol 1,4,5-trisphosphate (InsP3) is an intracellular second messenger that transduces growth factor and neurotransmitter signals. InsP3 mediates the release of Ca2+ from intracellular stores by binding to specific Ca2+ channel-coupled receptors. Ryanodine receptors are involved in communication between transverse-tubules and the sarcoplamic reticulum of cardiac and skeletal muscle. The proteins function as a Ca2+-release channels following depolarisation of transverse-tubules []. The function is modulated by Ca2+, Mg2+, ATP and calmodulin. Deficiency in the ryanodine receptor may be the cause of malignant hyperthermia (MH) and of central core disease of muscle (CCD) []. protein O-mannosyltransferases transfer mannose from DOL-P-mannose to ser or thr residues on proteins.; GO: 0016020 membrane; PDB: 1T9F_A 3UJ4_B 3UJ0_B 3T8S_B 3MAL_B 2XOA_A 1N4K_A.
Probab=43.55 E-value=54 Score=25.43 Aligned_cols=39 Identities=23% Similarity=0.362 Sum_probs=29.6
Q ss_pred EEEEeccCCCcCCCCccCceEEEEEcCCceEEEeccccC
Q 038082 21 MDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRS 59 (149)
Q Consensus 21 i~~~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RS 59 (149)
++..-..|.++..+-..+|.|+|+|..||..+.++..+.
T Consensus 121 ~~~~~~~~~~~~~~~~~~s~frL~H~~t~~~L~~~~~~l 159 (190)
T PF02815_consen 121 FEEKSSTGMGEDEIKTLDSYFRLRHVATGCWLHSHDVKL 159 (190)
T ss_dssp EEEEESSSCSSSSBBBTTSEEEEEETTTTEEEEEEEEES
T ss_pred EEecccCCccCCcEEecccEEEEEECCcCEEEecCCccc
Confidence 344445677788888889999999999997777766543
No 24
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=42.87 E-value=11 Score=23.07 Aligned_cols=17 Identities=18% Similarity=0.425 Sum_probs=14.3
Q ss_pred HHHHHHHhCCCcccccC
Q 038082 133 VINAAKIYGLKSGEIQE 149 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l~~ 149 (149)
+...|+.+|+|.+.+.|
T Consensus 24 i~~IA~~~gvsr~TvyR 40 (45)
T PF02796_consen 24 IAEIAKQFGVSRSTVYR 40 (45)
T ss_dssp HHHHHHHTTS-HHHHHH
T ss_pred HHHHHHHHCcCHHHHHH
Confidence 99999999999988764
No 25
>COG3514 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.10 E-value=4.4 Score=29.62 Aligned_cols=20 Identities=30% Similarity=0.605 Sum_probs=14.8
Q ss_pred CCCChhhhhccceEEEEeccCCCcCC
Q 038082 8 LELTDDELFRECEMDAYKSSGPGGQH 33 (149)
Q Consensus 8 ~~i~~~~l~~d~~i~~~RssGpGGQ~ 33 (149)
|.|+.+.| +.||.+|+|.|-
T Consensus 60 lRiDaDVl------e~fra~GkGwQt 79 (93)
T COG3514 60 LRIDADVL------EKFRAGGKGWQT 79 (93)
T ss_pred eEecHHHH------HHHHcCCccHHH
Confidence 45555555 569999999984
No 26
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=40.39 E-value=11 Score=24.15 Aligned_cols=17 Identities=18% Similarity=0.356 Sum_probs=15.4
Q ss_pred HHHHHHHhCCCcccccC
Q 038082 133 VINAAKIYGLKSGEIQE 149 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l~~ 149 (149)
...+|+.|+.|.+++|+
T Consensus 16 ~~~AA~~l~is~~~vs~ 32 (60)
T PF00126_consen 16 ISAAAEELGISQSAVSR 32 (60)
T ss_dssp HHHHHHHCTSSHHHHHH
T ss_pred HHHHHHHhhccchHHHH
Confidence 89999999999998874
No 27
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=39.75 E-value=64 Score=24.93 Aligned_cols=34 Identities=21% Similarity=0.217 Sum_probs=24.2
Q ss_pred CChhhhhhHHHhhchhh-------------------HHHHHHHhCCCcccccC
Q 038082 116 NNPKFALVLPYSLLLPF-------------------VINAAKIYGLKSGEIQE 149 (149)
Q Consensus 116 yn~~f~~gL~~llD~L~-------------------~~~aA~~L~~s~~~l~~ 149 (149)
..++...-|++.++.|. .+++|+.||+|+.++.|
T Consensus 118 ~~~~~~~~l~e~l~~L~~l~~~~~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r 170 (185)
T PF07638_consen 118 PSPEELLELEEALERLLALDPRQRRVVELRFFEGLSVEEIAERLGISERTVRR 170 (185)
T ss_pred CCHHHHHHHHHHHHHHHccCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHH
Confidence 44555545666666552 89999999999987653
No 28
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=37.66 E-value=20 Score=25.89 Aligned_cols=25 Identities=16% Similarity=0.056 Sum_probs=20.2
Q ss_pred HHhhchhh---HHHHHHHhCCCcccccC
Q 038082 125 PYSLLLPF---VINAAKIYGLKSGEIQE 149 (149)
Q Consensus 125 ~~llD~L~---~~~aA~~L~~s~~~l~~ 149 (149)
..+|..|. ....|+..|++.|++||
T Consensus 15 s~iL~rlA~~gq~~vA~~~Gv~eStISR 42 (91)
T PF05269_consen 15 SEILNRLASVGQKKVAEAMGVDESTISR 42 (91)
T ss_dssp HHHHHHHHHHHHHHHHHHHTSSTTTHHH
T ss_pred HHHHHHHHHHhhHHHHHHhCCCHHHHHH
Confidence 34555555 88899999999999987
No 29
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=35.52 E-value=14 Score=21.59 Aligned_cols=16 Identities=25% Similarity=0.353 Sum_probs=13.5
Q ss_pred HHHHHHHhCCCccccc
Q 038082 133 VINAAKIYGLKSGEIQ 148 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l~ 148 (149)
++++|+.||+|.+.+.
T Consensus 4 ~~e~a~~lgis~~ti~ 19 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVY 19 (49)
T ss_pred HHHHHHHHCCCHHHHH
Confidence 6789999999988764
No 30
>smart00322 KH K homology RNA-binding domain.
Probab=34.29 E-value=67 Score=19.28 Aligned_cols=45 Identities=22% Similarity=0.372 Sum_probs=26.4
Q ss_pred CCCcCCCCc--cCceEEEEEcCCc---eEEEeccccCHHHHHHHHHHHHHHHH
Q 038082 28 GPGGQHRNK--RESAVRLKHAPTG---VIAQAAEDRSQHKNRASALSRLRTLL 75 (149)
Q Consensus 28 GpGGQ~vNk--~~s~V~l~h~ptG---i~v~~~~~RSq~~Nr~~A~~~L~~~l 75 (149)
|++|.++.. ..+.+.+...+.+ -.+..... ..|...|...|...+
T Consensus 19 G~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~---~~~v~~a~~~i~~~~ 68 (69)
T smart00322 19 GKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGP---PENVEKAAELILEIL 68 (69)
T ss_pred CCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcC---HHHHHHHHHHHHHHh
Confidence 888988874 3445555544421 33333333 577778877776654
No 31
>PF04149 DUF397: Domain of unknown function (DUF397); InterPro: IPR007278 The function of this family is unknown. It has been suggested that some members of this family are regulators of transcription.
Probab=33.80 E-value=74 Score=20.61 Aligned_cols=18 Identities=22% Similarity=0.469 Sum_probs=11.7
Q ss_pred ceEEEEEcCCceEEEecc
Q 038082 39 SAVRLKHAPTGVIAQAAE 56 (149)
Q Consensus 39 s~V~l~h~ptGi~v~~~~ 56 (149)
++|++...|.|+-|..+.
T Consensus 16 ~CVEva~~~~~v~vRDSk 33 (56)
T PF04149_consen 16 NCVEVARLPGGVAVRDSK 33 (56)
T ss_pred CcEEEEeecceEEEecCC
Confidence 477777777775555444
No 32
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=32.24 E-value=23 Score=23.05 Aligned_cols=35 Identities=20% Similarity=0.224 Sum_probs=22.3
Q ss_pred CCCChhhhhh-HHHh-hchhhHHHHHHHhCCCccccc
Q 038082 114 GPNNPKFALV-LPYS-LLLPFVINAAKIYGLKSGEIQ 148 (149)
Q Consensus 114 rtyn~~f~~g-L~~l-lD~L~~~~aA~~L~~s~~~l~ 148 (149)
+.|.++|=.- +.+. .+..-+...|..+|+++++|+
T Consensus 5 ~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~ 41 (76)
T PF01527_consen 5 RRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLY 41 (76)
T ss_dssp ----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHH
T ss_pred CCCCHHHHHHHHHHHHHCCCceEeeeccccccccccc
Confidence 4577777666 5555 334449999999999998875
No 33
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=30.90 E-value=5.8 Score=26.88 Aligned_cols=17 Identities=18% Similarity=0.245 Sum_probs=14.3
Q ss_pred HHHHHHHhCCCcccccC
Q 038082 133 VINAAKIYGLKSGEIQE 149 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l~~ 149 (149)
+.+.|+..+.|++.++|
T Consensus 37 i~elA~~~~vS~sti~R 53 (77)
T PF01418_consen 37 ISELAEKAGVSPSTIVR 53 (77)
T ss_dssp HHHHHHHCTS-HHHHHH
T ss_pred HHHHHHHcCCCHHHHHH
Confidence 89999999999998875
No 34
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=30.60 E-value=19 Score=21.88 Aligned_cols=17 Identities=29% Similarity=0.475 Sum_probs=14.4
Q ss_pred HHHHHHHhCCCcccccC
Q 038082 133 VINAAKIYGLKSGEIQE 149 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l~~ 149 (149)
..+||+.||++.+.+++
T Consensus 20 ~~eAa~~lg~~~~~I~~ 36 (53)
T smart00497 20 IREAAKYLGISHSSISK 36 (53)
T ss_pred HHHHHHHhCCCHHHHHH
Confidence 78999999999887653
No 35
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 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 groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=30.23 E-value=17 Score=22.76 Aligned_cols=17 Identities=12% Similarity=0.300 Sum_probs=14.1
Q ss_pred HHHHHHHhCCCcccccC
Q 038082 133 VINAAKIYGLKSGEIQE 149 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l~~ 149 (149)
.++.|+.+|+|.+.+||
T Consensus 2 i~dIA~~agvS~~TVSr 18 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSR 18 (46)
T ss_dssp HHHHHHHHTSSHHHHHH
T ss_pred HHHHHHHHCcCHHHHHH
Confidence 36789999999998875
No 36
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=28.94 E-value=20 Score=20.62 Aligned_cols=16 Identities=19% Similarity=0.441 Sum_probs=12.8
Q ss_pred HHHHHHHhCCCccccc
Q 038082 133 VINAAKIYGLKSGEIQ 148 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l~ 148 (149)
..++|+.||+|.+.|.
T Consensus 3 ~~e~a~~lgvs~~tl~ 18 (49)
T cd04762 3 TKEAAELLGVSPSTLR 18 (49)
T ss_pred HHHHHHHHCcCHHHHH
Confidence 4688999999987764
No 37
>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi). This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].
Probab=28.82 E-value=56 Score=23.40 Aligned_cols=26 Identities=35% Similarity=0.567 Sum_probs=20.7
Q ss_pred CCCCCCCChhhhhccceEEEEeccCCCc
Q 038082 4 LPNYLELTDDELFRECEMDAYKSSGPGG 31 (149)
Q Consensus 4 ~~~~~~i~~~~l~~d~~i~~~RssGpGG 31 (149)
||+ .++++++..-++|.|.|++--||
T Consensus 60 ip~--~l~ee~l~D~LeIhFqK~snGGG 85 (88)
T PF07292_consen 60 IPD--VLDEEELRDKLEIHFQKPSNGGG 85 (88)
T ss_pred CCC--CCChhhheeeEEEEEecCCCCCc
Confidence 454 68888888889999999887555
No 38
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=28.77 E-value=16 Score=22.26 Aligned_cols=17 Identities=18% Similarity=0.243 Sum_probs=13.0
Q ss_pred HHHHHHHhCCCcccccC
Q 038082 133 VINAAKIYGLKSGEIQE 149 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l~~ 149 (149)
..+.|+.||.|.+.++|
T Consensus 23 ~~~IA~~lg~s~sTV~r 39 (44)
T PF13936_consen 23 IREIAKRLGRSRSTVSR 39 (44)
T ss_dssp HHHHHHHTT--HHHHHH
T ss_pred HHHHHHHHCcCcHHHHH
Confidence 88999999999988764
No 39
>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=28.77 E-value=45 Score=20.64 Aligned_cols=42 Identities=14% Similarity=0.192 Sum_probs=24.3
Q ss_pred cCCCcCCCCccC--ceEEEEEcCC-----ceEEEeccccCHHHHHHHHHHHH
Q 038082 27 SGPGGQHRNKRE--SAVRLKHAPT-----GVIAQAAEDRSQHKNRASALSRL 71 (149)
Q Consensus 27 sGpGGQ~vNk~~--s~V~l~h~pt-----Gi~v~~~~~RSq~~Nr~~A~~~L 71 (149)
=||||.+++... |.|.|...+. .-.|..... ..|...|...|
T Consensus 15 IG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~---~~~v~~a~~~i 63 (64)
T cd00105 15 IGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT---PEAVEKAKELI 63 (64)
T ss_pred ECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcC---HHHHHHHHHHh
Confidence 488999999643 5577776552 233333332 45666665543
No 40
>smart00472 MIR Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.
Probab=28.39 E-value=66 Score=19.82 Aligned_cols=22 Identities=32% Similarity=0.522 Sum_probs=17.1
Q ss_pred cCceEEEEEcCCceEEEecccc
Q 038082 37 RESAVRLKHAPTGVIAQAAEDR 58 (149)
Q Consensus 37 ~~s~V~l~h~ptGi~v~~~~~R 58 (149)
..+.|||+|.-||--+.+++.+
T Consensus 6 ~g~~vrL~H~~tg~yL~s~~~~ 27 (57)
T smart00472 6 WGDVVRLRHVTTGRYLHSHENK 27 (57)
T ss_pred cCCEEEEEEhhhCcEeecCCCC
Confidence 3589999999999666666655
No 41
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=27.56 E-value=29 Score=22.58 Aligned_cols=16 Identities=25% Similarity=0.372 Sum_probs=13.9
Q ss_pred HHHHHHHhCCCccccc
Q 038082 133 VINAAKIYGLKSGEIQ 148 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l~ 148 (149)
..+||+.||.|.+.|-
T Consensus 18 ~~eAA~~Lgv~~T~LK 33 (52)
T PF02042_consen 18 IKEAAKELGVSVTTLK 33 (52)
T ss_pred HHHHHHHhCCCHHHHH
Confidence 7899999999998764
No 42
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=27.31 E-value=27 Score=23.52 Aligned_cols=24 Identities=17% Similarity=0.081 Sum_probs=16.5
Q ss_pred HhhchhhHHHHHHHhCCCcccccC
Q 038082 126 YSLLLPFVINAAKIYGLKSGEIQE 149 (149)
Q Consensus 126 ~llD~L~~~~aA~~L~~s~~~l~~ 149 (149)
+.+.-.=...+|+.||++.+++|+
T Consensus 8 eyv~~~GQ~kaA~~lGV~Q~AIsK 31 (59)
T PF09048_consen 8 EYVKEHGQAKAARALGVTQSAISK 31 (59)
T ss_dssp HHHHHHHHHHHHHHHTS-HHHHHH
T ss_pred HHHHHhChHHHHHHcCCcHHHHHH
Confidence 333333378899999999998873
No 43
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=27.07 E-value=26 Score=21.10 Aligned_cols=23 Identities=13% Similarity=-0.074 Sum_probs=15.4
Q ss_pred HhhchhhHHHHHHHhCCCccccc
Q 038082 126 YSLLLPFVINAAKIYGLKSGEIQ 148 (149)
Q Consensus 126 ~llD~L~~~~aA~~L~~s~~~l~ 148 (149)
.+.+..-..++|+.||+|.+.++
T Consensus 13 l~~~G~s~~~ia~~lgvs~~Tv~ 35 (50)
T PF13384_consen 13 LLREGWSIREIAKRLGVSRSTVY 35 (50)
T ss_dssp HHHHT--HHHHHHHHTS-HHHHH
T ss_pred HHHCCCCHHHHHHHHCcCHHHHH
Confidence 33344558999999999988765
No 44
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=26.90 E-value=30 Score=20.66 Aligned_cols=15 Identities=20% Similarity=0.415 Sum_probs=11.6
Q ss_pred HHHHHHHhCCCcccc
Q 038082 133 VINAAKIYGLKSGEI 147 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l 147 (149)
+.++|+++|+|+.+|
T Consensus 2 i~e~A~~~gvs~~tl 16 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTL 16 (38)
T ss_dssp HHHHHHHHTS-HHHH
T ss_pred HHHHHHHHCCCHHHH
Confidence 467899999998876
No 45
>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=26.11 E-value=41 Score=24.04 Aligned_cols=24 Identities=17% Similarity=0.015 Sum_probs=18.1
Q ss_pred HhhchhhHHHHHHHhCCCcccccC
Q 038082 126 YSLLLPFVINAAKIYGLKSGEIQE 149 (149)
Q Consensus 126 ~llD~L~~~~aA~~L~~s~~~l~~ 149 (149)
.+.+.--...||+.|+.|.+++|+
T Consensus 12 av~~~gSis~AA~~L~iS~stvs~ 35 (99)
T TIGR00637 12 AIARMGSISQAAKDAGISYKSAWD 35 (99)
T ss_pred HHHHhCCHHHHHHHHCCCHHHHHH
Confidence 333333399999999999998874
No 46
>cd00552 RaiA RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).
Probab=23.77 E-value=2.3e+02 Score=18.95 Aligned_cols=52 Identities=19% Similarity=0.246 Sum_probs=26.0
Q ss_pred cceEEEEeccCCCcCCCCccCceEEEE-EcCCceEEEeccccCHHHHHHHHHHHHHHHH
Q 038082 18 ECEMDAYKSSGPGGQHRNKRESAVRLK-HAPTGVIAQAAEDRSQHKNRASALSRLRTLL 75 (149)
Q Consensus 18 d~~i~~~RssGpGGQ~vNk~~s~V~l~-h~ptGi~v~~~~~RSq~~Nr~~A~~~L~~~l 75 (149)
.|++.+..-.+||+. -.|+++ |+|.+.++...+.-+-+.=-..|+++|...|
T Consensus 35 ~~~V~l~~~~~~~~~------~~v~i~v~~~g~~~~a~~~~~d~~~Aid~a~~kl~rqL 87 (93)
T cd00552 35 SVDVVLSVEKNHGKR------FKVEITIHLPGGVLRAEASAEDLYAAIDLAVDKLERQL 87 (93)
T ss_pred eEEEEEEEecCCCCc------eEEEEEEEeCCCEEEEEEccCCHHHHHHHHHHHHHHHH
Confidence 356666665555222 255555 6673333333333455555555555555444
No 47
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=22.96 E-value=32 Score=20.68 Aligned_cols=16 Identities=13% Similarity=0.231 Sum_probs=13.0
Q ss_pred HHHHHHHhCCCccccc
Q 038082 133 VINAAKIYGLKSGEIQ 148 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l~ 148 (149)
..+.|+.+|+|.++++
T Consensus 20 ~~ela~~~~is~~tv~ 35 (48)
T PF13412_consen 20 QKELAEKLGISRSTVN 35 (48)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHhCCCHHHHH
Confidence 8999999999988764
No 48
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=22.94 E-value=32 Score=20.97 Aligned_cols=16 Identities=19% Similarity=0.304 Sum_probs=12.7
Q ss_pred HHHHHHHhCCCccccc
Q 038082 133 VINAAKIYGLKSGEIQ 148 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l~ 148 (149)
..+.|+.+|+|.+++.
T Consensus 20 ~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 20 YAELAEELGLSESTVR 35 (42)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCcCHHHHH
Confidence 7889999999988753
No 49
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=22.68 E-value=31 Score=26.13 Aligned_cols=16 Identities=25% Similarity=0.426 Sum_probs=13.7
Q ss_pred HHHHHHHhCCCccccc
Q 038082 133 VINAAKIYGLKSGEIQ 148 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l~ 148 (149)
....|++||+|++|.|
T Consensus 25 q~~iA~LLGltqaAVS 40 (119)
T COG2522 25 QYRIAKLLGLTQAAVS 40 (119)
T ss_pred HHHHHHHhCCCHHHHH
Confidence 5678999999999887
No 50
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=22.63 E-value=38 Score=21.95 Aligned_cols=16 Identities=13% Similarity=0.270 Sum_probs=13.6
Q ss_pred HHHHHHHhCCCccccc
Q 038082 133 VINAAKIYGLKSGEIQ 148 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l~ 148 (149)
..+.|+.||+|.++++
T Consensus 26 l~elA~~lgis~st~~ 41 (53)
T PF04967_consen 26 LEELAEELGISKSTVS 41 (53)
T ss_pred HHHHHHHhCCCHHHHH
Confidence 6788999999998876
No 51
>PF13014 KH_3: KH domain
Probab=22.28 E-value=26 Score=20.82 Aligned_cols=20 Identities=25% Similarity=0.625 Sum_probs=15.2
Q ss_pred CCCcCCCCc--cCceEEEEEcC
Q 038082 28 GPGGQHRNK--RESAVRLKHAP 47 (149)
Q Consensus 28 GpGGQ~vNk--~~s~V~l~h~p 47 (149)
|+||.++|+ .+|.|+|...+
T Consensus 7 G~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 7 GKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred CCCChHHHHHHHHhCcEEEECC
Confidence 888999984 66777777655
No 52
>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=21.84 E-value=1.2e+02 Score=22.55 Aligned_cols=25 Identities=24% Similarity=0.307 Sum_probs=13.9
Q ss_pred eEEEeccccCHHHHHHHHHHHHHHHHH
Q 038082 50 VIAQAAEDRSQHKNRASALSRLRTLLA 76 (149)
Q Consensus 50 i~v~~~~~RSq~~Nr~~A~~~L~~~l~ 76 (149)
+.|++... ....-+.|.+.+..++.
T Consensus 70 V~I~a~~~--~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 70 VLITAETP--PEEALAKAVEAIEELLK 94 (120)
T ss_pred EEEEeCCc--HHHHHHHHHHHHHHHhc
Confidence 66666653 23455566665555554
No 53
>PF13518 HTH_28: Helix-turn-helix domain
Probab=21.72 E-value=47 Score=19.81 Aligned_cols=22 Identities=18% Similarity=0.172 Sum_probs=16.6
Q ss_pred hhchhhHHHHHHHhCCCccccc
Q 038082 127 SLLLPFVINAAKIYGLKSGEIQ 148 (149)
Q Consensus 127 llD~L~~~~aA~~L~~s~~~l~ 148 (149)
+++---+.++|+.+|+|.+++.
T Consensus 9 ~~~g~s~~~~a~~~gis~~tv~ 30 (52)
T PF13518_consen 9 YLEGESVREIAREFGISRSTVY 30 (52)
T ss_pred HHcCCCHHHHHHHHCCCHhHHH
Confidence 3344348899999999998875
No 54
>PHA00437 tail assembly protein
Probab=21.61 E-value=60 Score=23.70 Aligned_cols=12 Identities=42% Similarity=0.761 Sum_probs=8.8
Q ss_pred EEEEeccCCCcCC
Q 038082 21 MDAYKSSGPGGQH 33 (149)
Q Consensus 21 i~~~RssGpGGQ~ 33 (149)
.+..|||| ||-|
T Consensus 82 LSVaRSSG-gGiN 93 (94)
T PHA00437 82 LSVARSSG-GGIN 93 (94)
T ss_pred eeEeeccC-CCcC
Confidence 56788888 7755
No 55
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=20.96 E-value=63 Score=26.77 Aligned_cols=26 Identities=27% Similarity=0.330 Sum_probs=20.0
Q ss_pred HHHhhchhhHHHHHHHhCCCcccccC
Q 038082 124 LPYSLLLPFVINAAKIYGLKSGEIQE 149 (149)
Q Consensus 124 L~~llD~L~~~~aA~~L~~s~~~l~~ 149 (149)
+..+.+.--.+.||+.|+.|.+++||
T Consensus 37 f~av~e~gs~s~AA~~L~isQpavS~ 62 (317)
T PRK11482 37 FEAVYVHKGIVNAAKILNLTPSAISQ 62 (317)
T ss_pred HHHHHHcCCHHHHHHHhCCChHHHHH
Confidence 44444444499999999999999985
No 56
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.92 E-value=48 Score=19.51 Aligned_cols=15 Identities=20% Similarity=0.375 Sum_probs=12.5
Q ss_pred HHHHHHHhCCCcccc
Q 038082 133 VINAAKIYGLKSGEI 147 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l 147 (149)
++++|+.||+|.+.|
T Consensus 3 ~~e~a~~~gv~~~tl 17 (49)
T cd04761 3 IGELAKLTGVSPSTL 17 (49)
T ss_pred HHHHHHHHCcCHHHH
Confidence 578899999998765
No 57
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=20.50 E-value=47 Score=19.14 Aligned_cols=16 Identities=25% Similarity=0.463 Sum_probs=13.7
Q ss_pred HHHHHHHhCCCccccc
Q 038082 133 VINAAKIYGLKSGEIQ 148 (149)
Q Consensus 133 ~~~aA~~L~~s~~~l~ 148 (149)
..+||+.|+.+.+.++
T Consensus 19 i~eAa~~l~i~~~~I~ 34 (37)
T PF07453_consen 19 IREAARYLGISHSTIS 34 (37)
T ss_pred HHHHHHHhCCCHHHHH
Confidence 7899999999988765
No 58
>PF11653 VirionAssem_T7: Bacteriophage T7 virion assembly protein; InterPro: IPR024281 This family of proteins represents the gene product 7.3 from T7 bacteriophage and T7-like phages. The protein is localised to the tail and is thought to be important in virion assembly. Particles assembled in the absence of the protein fail to adsorb to cells [].
Probab=20.15 E-value=68 Score=23.52 Aligned_cols=12 Identities=42% Similarity=0.761 Sum_probs=8.6
Q ss_pred EEEEeccCCCcCC
Q 038082 21 MDAYKSSGPGGQH 33 (149)
Q Consensus 21 i~~~RssGpGGQ~ 33 (149)
.++.|||| ||-|
T Consensus 83 LSVaRSSG-~GiN 94 (95)
T PF11653_consen 83 LSVARSSG-GGIN 94 (95)
T ss_pred eeEEeccC-CCcC
Confidence 56789998 5654
No 59
>KOG3259 consensus Peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=20.07 E-value=2.8e+02 Score=22.17 Aligned_cols=46 Identities=26% Similarity=0.316 Sum_probs=27.5
Q ss_pred EeccCCCcCCCCccCceEEEEEcCCceEEEeccccC--------HHHHHHHHHHHHHHHHH
Q 038082 24 YKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRS--------QHKNRASALSRLRTLLA 76 (149)
Q Consensus 24 ~RssGpGGQ~vNk~~s~V~l~h~ptGi~v~~~~~RS--------q~~Nr~~A~~~L~~~l~ 76 (149)
..++|++||.-+. .|+..|| .|+-+.+|- -..-|++|+..|+....
T Consensus 41 ~~~~~~~~~~~p~---~Vr~sHl----LVKH~~SRrpsSwr~~~it~skeeA~~llk~~~~ 94 (163)
T KOG3259|consen 41 SKSGGKIGQGEPA---RVRCSHL----LVKHKGSRRPSSWRSENITRSKEEALDLLKGYHE 94 (163)
T ss_pred ccccccccCCCcc---ceeEEEE----EEccccCCCCcccccccchhhHHHHHHHHHHhHH
Confidence 3455566666444 7887785 344444433 34568899888876543
Done!