Query 041864
Match_columns 300
No_of_seqs 128 out of 335
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 11:29:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041864.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041864hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02362 B3: B3 DNA binding do 99.7 2E-17 4.3E-22 128.4 12.3 97 111-212 1-99 (100)
2 PF03754 DUF313: Domain of unk 98.5 6E-07 1.3E-11 75.3 8.2 80 105-185 18-114 (114)
3 PF09217 EcoRII-N: Restriction 98.0 2.5E-05 5.5E-10 69.0 7.7 90 108-197 7-110 (156)
4 PF10844 DUF2577: Protein of u 75.2 16 0.00034 29.7 7.1 79 109-210 19-99 (100)
5 cd06919 Asp_decarbox Aspartate 63.4 67 0.0015 27.5 8.7 77 111-198 10-88 (111)
6 PRK05449 aspartate alpha-decar 60.9 74 0.0016 27.8 8.7 77 111-198 11-89 (126)
7 TIGR00223 panD L-aspartate-alp 59.5 82 0.0018 27.6 8.7 77 111-198 11-89 (126)
8 PF04014 Antitoxin-MazE: Antid 50.8 27 0.00059 24.3 3.7 29 180-209 13-41 (47)
9 PF02261 Asp_decarbox: Asparta 41.0 2.4E+02 0.0052 24.4 9.4 78 110-198 10-89 (116)
10 PF03120 DNA_ligase_OB: NAD-de 38.1 47 0.001 26.7 3.7 22 180-201 42-63 (82)
11 PF01878 EVE: EVE domain; Int 36.0 43 0.00093 28.0 3.3 23 186-208 38-60 (143)
12 COG2002 AbrB Regulators of sta 35.6 58 0.0013 25.8 3.8 28 180-207 20-47 (89)
13 COG0853 PanD Aspartate 1-decar 33.9 2.5E+02 0.0054 24.7 7.6 78 110-198 9-88 (126)
14 COG1430 Uncharacterized conser 32.5 1.1E+02 0.0025 26.4 5.4 54 146-199 64-122 (126)
15 COG5569 Uncharacterized conser 31.7 51 0.0011 28.0 3.0 25 184-208 80-104 (108)
16 PF12690 BsuPI: Intracellular 31.3 65 0.0014 25.4 3.4 53 144-208 24-81 (82)
17 TIGR02609 doc_partner putative 28.9 1.5E+02 0.0032 22.8 5.0 39 164-208 4-42 (74)
18 PF02643 DUF192: Uncharacteriz 27.8 1.2E+02 0.0027 24.7 4.7 53 144-196 48-106 (108)
19 PF02431 Chalcone: Chalcone-fl 27.2 32 0.00069 30.6 1.2 58 179-237 120-185 (199)
20 PRK09838 periplasmic copper-bi 26.7 1.1E+02 0.0023 26.0 4.2 28 185-212 86-114 (115)
21 TIGR01439 lp_hng_hel_AbrB loop 26.0 1.5E+02 0.0032 19.5 4.0 28 180-208 13-40 (43)
22 PLN02311 chalcone isomerase 25.1 70 0.0015 31.0 3.1 61 177-238 191-256 (271)
23 PRK09570 rpoH DNA-directed RNA 23.1 1.2E+02 0.0026 24.4 3.7 25 180-204 44-69 (79)
24 PRK03760 hypothetical protein; 22.3 2.7E+02 0.0059 23.4 5.8 29 170-198 88-116 (117)
25 cd06555 ASCH_PF0470_like ASC-1 22.3 1.3E+02 0.0028 25.4 3.8 24 186-209 30-53 (109)
26 PF14250 AbrB-like: AbrB-like 22.2 1.9E+02 0.0042 23.1 4.5 40 152-197 23-62 (71)
27 cd05829 Sortase_E Sortase E (S 22.0 1.5E+02 0.0032 25.4 4.2 43 171-213 49-99 (144)
28 PF01568 Molydop_binding: Moly 21.8 1.4E+02 0.0031 23.1 3.8 29 181-211 37-65 (110)
29 TIGR01643 YD_repeat_2x YD repe 20.8 1.5E+02 0.0032 19.5 3.2 22 144-166 4-25 (42)
30 PF07076 DUF1344: Protein of u 20.6 1.2E+02 0.0026 23.4 3.1 23 185-207 35-57 (61)
31 PF01191 RNA_pol_Rpb5_C: RNA p 20.3 1.5E+02 0.0034 23.4 3.7 25 180-204 41-66 (74)
32 cd04459 Rho_CSD Rho_CSD: Rho p 20.1 71 0.0015 24.8 1.7 18 180-197 33-50 (68)
No 1
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=99.75 E-value=2e-17 Score=128.43 Aligned_cols=97 Identities=32% Similarity=0.447 Sum_probs=69.5
Q ss_pred EEEecccCCCCCCCceEeehhhhhhcCCCCCCCCceEEEEEeCCCCeEEEEEEEEcCCCCCcceeec-ChhhHHhhcCCC
Q 041864 111 FQKELKNSDVSSLRRMILPKKAAEAHLPVLESKEGIFISMEDLDGLHVWTFKYRFWPNNNSRMYVLE-NTGDFVNAHGLQ 189 (300)
Q Consensus 111 F~KvLT~SDVgslgRLVIPK~~AE~~LP~Ld~~eGi~L~V~D~~G~k~W~FRf~yw~NnkSR~YVLt-GW~~FVr~K~Lk 189 (300)
|.|+|+++|+....+|.||++.++++. +....++.+.+.|..| ++|.++++++. .+..|+|+ ||.+||++++|+
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~--~~~~~~~~v~l~~~~g-~~W~v~~~~~~--~~~~~~l~~GW~~Fv~~n~L~ 75 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHG--GNKRKSREVTLKDPDG-RSWPVKLKYRK--NSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS----SS--CEEEEEETTT-EEEEEEEEEEC--CTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhC--CCcCCCeEEEEEeCCC-CEEEEEEEEEc--cCCeEEECCCHHHHHHHcCCC
Confidence 899999999999899999999999982 1223467888899999 59999999883 44447776 899999999999
Q ss_pred CCCEEEEEEcC-CCCeEEEEEEEc
Q 041864 190 LGDFIIVYKDD-QNQNYVIQAKKA 212 (300)
Q Consensus 190 aGD~IvF~rd~-~~G~L~IgiRRa 212 (300)
+||.|+|+..+ ...++.|.+.|+
T Consensus 76 ~GD~~~F~~~~~~~~~~~v~i~~~ 99 (100)
T PF02362_consen 76 EGDVCVFELIGNSNFTLKVHIFRK 99 (100)
T ss_dssp TT-EEEEEE-SSSCE-EEEEEE--
T ss_pred CCCEEEEEEecCCCceEEEEEEEC
Confidence 99999999875 345678988775
No 2
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=98.48 E-value=6e-07 Score=75.32 Aligned_cols=80 Identities=23% Similarity=0.406 Sum_probs=64.0
Q ss_pred CCceEeEEEecccCCCCC-CCceEeehhhhhh--cCCC-----C-------CCCCceEEEEEeCCCCeEEEEEEEEcCC-
Q 041864 105 GRLRFLFQKELKNSDVSS-LRRMILPKKAAEA--HLPV-----L-------ESKEGIFISMEDLDGLHVWTFKYRFWPN- 168 (300)
Q Consensus 105 ~~~~~LF~KvLT~SDVgs-lgRLVIPK~~AE~--~LP~-----L-------d~~eGi~L~V~D~~G~k~W~FRf~yw~N- 168 (300)
.+...+++|.|++|||.. ++||.||...... +|-. + +...|+.+.+.|..+. .|..+++.|..
T Consensus 18 ~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~-~~~m~lkkW~mg 96 (114)
T PF03754_consen 18 EDPKLIIEKTLFKTDVDPHQSRLSMPFNQIIDNDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLR-KWTMRLKKWNMG 96 (114)
T ss_pred CCCeEEEeeeecccCCCCCCceeeccHHHhcccccCCHHHHHHHHHhhccCcccCCceEEEECCcCc-EEEEEEEEeccc
Confidence 566899999999999995 8999999987743 2321 1 1246899999999995 99999999977
Q ss_pred CCCcceeec-ChhhHHhh
Q 041864 169 NNSRMYVLE-NTGDFVNA 185 (300)
Q Consensus 169 nkSR~YVLt-GW~~FVr~ 185 (300)
+.+-.|+|. ||.++|++
T Consensus 97 ~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 97 NGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CCceEEEEEcChHhhccC
Confidence 446679997 79998863
No 3
>PF09217 EcoRII-N: Restriction endonuclease EcoRII, N-terminal; InterPro: IPR023372 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the N-terminal effector-binding domain of the type II restriction endonuclease EcoRII, which has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not []. The domain represented by this entry is only found in bacterial proteins.; PDB: 3HQF_A 1NA6_A.
Probab=97.98 E-value=2.5e-05 Score=68.96 Aligned_cols=90 Identities=16% Similarity=0.292 Sum_probs=56.7
Q ss_pred eEeEEEecccCCCCC----CCceEeehhhhhhcCCCCCC----CCceEEEEEeCCCC-eEEEEEEEEcCC----CCCcce
Q 041864 108 RFLFQKELKNSDVSS----LRRMILPKKAAEAHLPVLES----KEGIFISMEDLDGL-HVWTFKYRFWPN----NNSRMY 174 (300)
Q Consensus 108 ~~LF~KvLT~SDVgs----lgRLVIPK~~AE~~LP~Ld~----~eGi~L~V~D~~G~-k~W~FRf~yw~N----nkSR~Y 174 (300)
...|.|.|++.|++. ..++.|||..++.+||.+.. .+.+.|.+.+..+. ..|++|++|+.| +.+..|
T Consensus 7 ~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE~ 86 (156)
T PF09217_consen 7 WAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNEY 86 (156)
T ss_dssp EEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--EE
T ss_pred eEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCce
Confidence 568999999999994 57999999999999988754 35588888887763 368899999944 346789
Q ss_pred eecChhhHHhhcC-CCCCCEEEEE
Q 041864 175 VLENTGDFVNAHG-LQLGDFIIVY 197 (300)
Q Consensus 175 VLtGW~~FVr~K~-LkaGD~IvF~ 197 (300)
.||.|.....--+ =.+||.++|-
T Consensus 87 RIT~~G~~~~~~~~~~tGaL~vla 110 (156)
T PF09217_consen 87 RITRFGRGFPLQNPENTGALLVLA 110 (156)
T ss_dssp EEE---TTSGGG-GGGTT-EEEEE
T ss_pred EEeeecCCCccCCccccccEEEEE
Confidence 9999966555333 3568888775
No 4
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=75.20 E-value=16 Score=29.74 Aligned_cols=79 Identities=18% Similarity=0.277 Sum_probs=46.0
Q ss_pred EeEEEecccCCCC--CCCceEeehhhhhhcCCCCCCCCceEEEEEeCCCCeEEEEEEEEcCCCCCcceeecChhhHHhhc
Q 041864 109 FLFQKELKNSDVS--SLRRMILPKKAAEAHLPVLESKEGIFISMEDLDGLHVWTFKYRFWPNNNSRMYVLENTGDFVNAH 186 (300)
Q Consensus 109 ~LF~KvLT~SDVg--slgRLVIPK~~AE~~LP~Ld~~eGi~L~V~D~~G~k~W~FRf~yw~NnkSR~YVLtGW~~FVr~K 186 (300)
..|-++++.+-+. -.++++||++.. ++|.+-......+.+....... ... |.-..
T Consensus 19 i~~G~V~s~~PL~I~i~~~liL~~~~L--~i~~~l~~~~~~~~~~~~~~~~--~~~-------------------i~~~~ 75 (100)
T PF10844_consen 19 IVIGTVVSVPPLKIKIDQKLILDKDFL--IIPELLKDYTRDITIEHNSETD--NIT-------------------ITFTD 75 (100)
T ss_pred eEEEEEEecccEEEEECCeEEEchHHE--EeehhccceEEEEEEecccccc--cee-------------------EEEec
Confidence 4688888888744 234599988643 4444222233444443332210 000 44556
Q ss_pred CCCCCCEEEEEEcCCCCeEEEEEE
Q 041864 187 GLQLGDFIIVYKDDQNQNYVIQAK 210 (300)
Q Consensus 187 ~LkaGD~IvF~rd~~~G~L~IgiR 210 (300)
+|++||.|.+.+...+.+|+|-.|
T Consensus 76 ~Lk~GD~V~ll~~~~gQ~yiVlDk 99 (100)
T PF10844_consen 76 GLKVGDKVLLLRVQGGQKYIVLDK 99 (100)
T ss_pred CCcCCCEEEEEEecCCCEEEEEEe
Confidence 899999999999654445666443
No 5
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=63.40 E-value=67 Score=27.52 Aligned_cols=77 Identities=17% Similarity=0.159 Sum_probs=56.0
Q ss_pred EEEecccCCCCCCCceEeehhhhhh--cCCCCCCCCceEEEEEeCCCCeEEEEEEEEcCCCCCcceeecChhhHHhhcCC
Q 041864 111 FQKELKNSDVSSLRRMILPKKAAEA--HLPVLESKEGIFISMEDLDGLHVWTFKYRFWPNNNSRMYVLENTGDFVNAHGL 188 (300)
Q Consensus 111 F~KvLT~SDVgslgRLVIPK~~AE~--~LP~Ld~~eGi~L~V~D~~G~k~W~FRf~yw~NnkSR~YVLtGW~~FVr~K~L 188 (300)
=.-+.|..|+..-|.+.|..+..++ ++| .-.+.+++......| =.|.+.....|+.-.|.| .-++..
T Consensus 10 HratVT~a~L~YeGSitID~~Ll~aagi~~------~E~V~I~Nv~NG~Rf-~TYvI~g~~gSg~I~lNG----AAAr~~ 78 (111)
T cd06919 10 HRATVTEADLNYEGSITIDEDLLEAAGILP------YEKVLVVNVNNGARF-ETYVIPGERGSGVICLNG----AAARLG 78 (111)
T ss_pred cceEEeccccccceeEEECHHHHHhcCCCC------CCEEEEEECCCCcEE-EEEEEEcCCCCCEEEeCC----HHHhcC
Confidence 3457899999999999999998765 455 345777888754223 356676444567777777 457888
Q ss_pred CCCCEEEEEE
Q 041864 189 QLGDFIIVYK 198 (300)
Q Consensus 189 kaGD~IvF~r 198 (300)
++||.|+++-
T Consensus 79 ~~GD~vII~s 88 (111)
T cd06919 79 QPGDRVIIMA 88 (111)
T ss_pred CCCCEEEEEE
Confidence 9999999974
No 6
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=60.93 E-value=74 Score=27.79 Aligned_cols=77 Identities=14% Similarity=0.206 Sum_probs=55.7
Q ss_pred EEEecccCCCCCCCceEeehhhhhh--cCCCCCCCCceEEEEEeCCCCeEEEEEEEEcCCCCCcceeecChhhHHhhcCC
Q 041864 111 FQKELKNSDVSSLRRMILPKKAAEA--HLPVLESKEGIFISMEDLDGLHVWTFKYRFWPNNNSRMYVLENTGDFVNAHGL 188 (300)
Q Consensus 111 F~KvLT~SDVgslgRLVIPK~~AE~--~LP~Ld~~eGi~L~V~D~~G~k~W~FRf~yw~NnkSR~YVLtGW~~FVr~K~L 188 (300)
=.-+.|..|+..-|.+.|..+..++ ++|. -.+.+++......| =.|.+.....|+.-.|.| .-++..
T Consensus 11 HratVT~a~L~Y~GSitID~~Ll~aagi~p~------E~V~V~Nv~NG~Rf-~TYvI~g~~GSg~I~lNG----AAAr~~ 79 (126)
T PRK05449 11 HRATVTEADLNYEGSITIDEDLLDAAGILEN------EKVQIVNVNNGARF-ETYVIAGERGSGVICLNG----AAARLV 79 (126)
T ss_pred cceEEeccccccceeEEECHHHHHhcCCCCC------CEEEEEECCCCcEE-EEEEEEcCCCCCEEEeCC----HHHhcC
Confidence 3457899999999999999998775 5663 44677887754233 356666444467777777 457888
Q ss_pred CCCCEEEEEE
Q 041864 189 QLGDFIIVYK 198 (300)
Q Consensus 189 kaGD~IvF~r 198 (300)
++||.|++.-
T Consensus 80 ~~GD~vII~a 89 (126)
T PRK05449 80 QVGDLVIIAA 89 (126)
T ss_pred CCCCEEEEEE
Confidence 9999999974
No 7
>TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group.
Probab=59.48 E-value=82 Score=27.55 Aligned_cols=77 Identities=12% Similarity=0.249 Sum_probs=55.8
Q ss_pred EEEecccCCCCCCCceEeehhhhhh--cCCCCCCCCceEEEEEeCCCCeEEEEEEEEcCCCCCcceeecChhhHHhhcCC
Q 041864 111 FQKELKNSDVSSLRRMILPKKAAEA--HLPVLESKEGIFISMEDLDGLHVWTFKYRFWPNNNSRMYVLENTGDFVNAHGL 188 (300)
Q Consensus 111 F~KvLT~SDVgslgRLVIPK~~AE~--~LP~Ld~~eGi~L~V~D~~G~k~W~FRf~yw~NnkSR~YVLtGW~~FVr~K~L 188 (300)
=.-+.|..|+..-|.+.|..+..++ ++|. -.+.+.|.+....|. .|.+.....|+.-.|.| .-++..
T Consensus 11 HratVT~a~L~Y~GSItID~~Lm~aagi~p~------E~V~V~Nv~NG~Rf~-TYvI~G~~GSg~I~lNG----AAArl~ 79 (126)
T TIGR00223 11 HRATVTHANLNYEGSITIDEDLLDAAGILEN------EKVDIVNVNNGKRFS-TYAIAGKRGSRIICVNG----AAARCV 79 (126)
T ss_pred cceEEeccccccceeEEECHHHHHhcCCCCC------CEEEEEECCCCcEEE-EEEEEcCCCCCEEEeCC----HHHhcC
Confidence 3457899999989999999987765 5663 446778877443333 56666444467777777 457888
Q ss_pred CCCCEEEEEE
Q 041864 189 QLGDFIIVYK 198 (300)
Q Consensus 189 kaGD~IvF~r 198 (300)
++||.|+++-
T Consensus 80 ~~GD~VII~s 89 (126)
T TIGR00223 80 SVGDIVIIAS 89 (126)
T ss_pred CCCCEEEEEE
Confidence 9999999974
No 8
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=50.84 E-value=27 Score=24.32 Aligned_cols=29 Identities=21% Similarity=0.318 Sum_probs=22.6
Q ss_pred hhHHhhcCCCCCCEEEEEEcCCCCeEEEEE
Q 041864 180 GDFVNAHGLQLGDFIIVYKDDQNQNYVIQA 209 (300)
Q Consensus 180 ~~FVr~K~LkaGD~IvF~rd~~~G~L~Igi 209 (300)
.+|.+..+|++||.|.|.-++. |++.|.-
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~~-g~i~i~p 41 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEGD-GKIVIRP 41 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEETT-SEEEEEE
T ss_pred HHHHHHcCCCCCCEEEEEEeCC-CEEEEEE
Confidence 5678888999999999998743 4666654
No 9
>PF02261 Asp_decarbox: Aspartate decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process; PDB: 1PYU_C 1AW8_A 1PYQ_B 3TM7_C 1PT1_A 1PQH_A 1PPY_B 1PT0_B 1PQF_A 1PQE_A ....
Probab=40.96 E-value=2.4e+02 Score=24.40 Aligned_cols=78 Identities=15% Similarity=0.257 Sum_probs=47.9
Q ss_pred eEEEecccCCCCCCCceEeehhhhhh--cCCCCCCCCceEEEEEeCCCCeEEEEEEEEcCCCCCcceeecChhhHHhhcC
Q 041864 110 LFQKELKNSDVSSLRRMILPKKAAEA--HLPVLESKEGIFISMEDLDGLHVWTFKYRFWPNNNSRMYVLENTGDFVNAHG 187 (300)
Q Consensus 110 LF~KvLT~SDVgslgRLVIPK~~AE~--~LP~Ld~~eGi~L~V~D~~G~k~W~FRf~yw~NnkSR~YVLtGW~~FVr~K~ 187 (300)
+=.-+.|..|+..-|.+.|..+..++ ++|. -.+.+.+...+..|. .|.+-....|+.-.|.| .-++.
T Consensus 10 iHratVT~a~L~Y~GSitID~~Ll~aagi~p~------E~V~V~Nv~nG~Rf~-TYvI~g~~GSg~I~lNG----aAArl 78 (116)
T PF02261_consen 10 IHRATVTEADLNYEGSITIDEDLLDAAGILPY------EQVQVVNVNNGERFE-TYVIPGERGSGVICLNG----AAARL 78 (116)
T ss_dssp EEEEE--EEETTSTSCEEEEHHHHHHCT--TT------BEEEEEETTT--EEE-EEEEEESTTTT-EEEEG----GGGGC
T ss_pred hcceEEeccccccceeeEECHHHHHHcCCCcC------CEEEEEECCCCcEEE-EEEEEccCCCcEEEECC----HHHhc
Confidence 34457899999999999999997765 5663 456778887543333 45555333355666666 45788
Q ss_pred CCCCCEEEEEE
Q 041864 188 LQLGDFIIVYK 198 (300)
Q Consensus 188 LkaGD~IvF~r 198 (300)
.++||.|+++-
T Consensus 79 ~~~GD~vII~s 89 (116)
T PF02261_consen 79 VQVGDRVIIMS 89 (116)
T ss_dssp S-TT-EEEEEE
T ss_pred cCCCCEEEEEE
Confidence 99999999863
No 10
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=38.12 E-value=47 Score=26.72 Aligned_cols=22 Identities=18% Similarity=0.530 Sum_probs=17.8
Q ss_pred hhHHhhcCCCCCCEEEEEEcCC
Q 041864 180 GDFVNAHGLQLGDFIIVYKDDQ 201 (300)
Q Consensus 180 ~~FVr~K~LkaGD~IvF~rd~~ 201 (300)
.+|+++++|..||.|.++|.+.
T Consensus 42 ~~~i~~~~i~~Gd~V~V~raGd 63 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRAGD 63 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEETT
T ss_pred HHHHHHcCCCCCCEEEEEECCC
Confidence 7899999999999999999743
No 11
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=35.95 E-value=43 Score=27.98 Aligned_cols=23 Identities=17% Similarity=0.410 Sum_probs=13.3
Q ss_pred cCCCCCCEEEEEEcCCCCeEEEE
Q 041864 186 HGLQLGDFIIVYKDDQNQNYVIQ 208 (300)
Q Consensus 186 K~LkaGD~IvF~rd~~~G~L~Ig 208 (300)
+++++||.|+||..+..++-+++
T Consensus 38 ~~mk~GD~vifY~s~~~~~~iva 60 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVA 60 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEE
Confidence 49999999999997632344443
No 12
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=35.58 E-value=58 Score=25.77 Aligned_cols=28 Identities=21% Similarity=0.396 Sum_probs=21.6
Q ss_pred hhHHhhcCCCCCCEEEEEEcCCCCeEEE
Q 041864 180 GDFVNAHGLQLGDFIIVYKDDQNQNYVI 207 (300)
Q Consensus 180 ~~FVr~K~LkaGD~IvF~rd~~~G~L~I 207 (300)
.+.-+..+|++||.+.|+.++..|++.|
T Consensus 20 keiR~~lgi~~Gd~lei~~~~~~~~ivl 47 (89)
T COG2002 20 KEIREALGIKEGDVLEIIVDGDGGRIVL 47 (89)
T ss_pred HHHHHHhCCCCCCEEEEEEeCCCCEEEE
Confidence 3455678999999999999877677443
No 13
>COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism]
Probab=33.92 E-value=2.5e+02 Score=24.68 Aligned_cols=78 Identities=14% Similarity=0.232 Sum_probs=53.0
Q ss_pred eEEEecccCCCCCCCceEeehhhhhh--cCCCCCCCCceEEEEEeCCCCeEEEEEEEEcCCCCCcceeecChhhHHhhcC
Q 041864 110 LFQKELKNSDVSSLRRMILPKKAAEA--HLPVLESKEGIFISMEDLDGLHVWTFKYRFWPNNNSRMYVLENTGDFVNAHG 187 (300)
Q Consensus 110 LF~KvLT~SDVgslgRLVIPK~~AE~--~LP~Ld~~eGi~L~V~D~~G~k~W~FRf~yw~NnkSR~YVLtGW~~FVr~K~ 187 (300)
+=.-+.|+.|+...|.+.|-.+..++ ++|. -.+.+++.... .--=.|.+-....|+.-.|.| .-++.
T Consensus 9 iHratVT~A~L~Y~GSitID~dlldaagile~------EkV~I~N~nNG-aRf~TYvI~g~rGSg~I~lNG----AAArl 77 (126)
T COG0853 9 IHRATVTEADLNYVGSITIDEDLLDAAGILEN------EKVDIVNVNNG-ARFSTYVIAGERGSGVICLNG----AAARL 77 (126)
T ss_pred eeeeEEeecccceEEeEEECHHHHhhcCCCCC------ceEEEEECCCC-cEEEEEEEEccCCCcEEEech----HHHhh
Confidence 34567899999999999999887764 5553 34566887643 222345555444456666666 45678
Q ss_pred CCCCCEEEEEE
Q 041864 188 LQLGDFIIVYK 198 (300)
Q Consensus 188 LkaGD~IvF~r 198 (300)
.++||.|+++-
T Consensus 78 ~~~GD~VII~s 88 (126)
T COG0853 78 VQVGDLVIIMS 88 (126)
T ss_pred CCCCCEEEEEE
Confidence 89999999975
No 14
>COG1430 Uncharacterized conserved protein [Function unknown]
Probab=32.53 E-value=1.1e+02 Score=26.39 Aligned_cols=54 Identities=24% Similarity=0.284 Sum_probs=34.2
Q ss_pred eEEEEEeCCCCeEEEEEEEEcC---CCC--CcceeecChhhHHhhcCCCCCCEEEEEEc
Q 041864 146 IFISMEDLDGLHVWTFKYRFWP---NNN--SRMYVLENTGDFVNAHGLQLGDFIIVYKD 199 (300)
Q Consensus 146 i~L~V~D~~G~k~W~FRf~yw~---Nnk--SR~YVLtGW~~FVr~K~LkaGD~IvF~rd 199 (300)
+.+.+.|.+|.-+|.-...=|. ..+ +..|+|+-=...++..+++.||.|.|...
T Consensus 64 LDiiFid~dg~i~~i~~~~P~~~~~~~~~~~~~yvLEl~~G~~~~~~i~vGd~v~~~~~ 122 (126)
T COG1430 64 LDIIFIDSDGRVVDIVELVPWSTYPCKSYGPVRYVLELPAGWAARLGIKVGDRVEFRPL 122 (126)
T ss_pred eEEEEEcCCCCEEEEEeccccccCCCCCCCCccEEEEecCCchhhcCCccCCEEEeccc
Confidence 4556666666555555422221 122 23599994455578999999999998764
No 15
>COG5569 Uncharacterized conserved protein [Function unknown]
Probab=31.70 E-value=51 Score=28.03 Aligned_cols=25 Identities=24% Similarity=0.309 Sum_probs=20.2
Q ss_pred hhcCCCCCCEEEEEEcCCCCeEEEE
Q 041864 184 NAHGLQLGDFIIVYKDDQNQNYVIQ 208 (300)
Q Consensus 184 r~K~LkaGD~IvF~rd~~~G~L~Ig 208 (300)
+-.+|++||.|.|--+..+|++.+.
T Consensus 80 ~lsglKeGdkV~fvferv~gk~tv~ 104 (108)
T COG5569 80 KLSGLKEGDKVEFVFERVNGKLTVQ 104 (108)
T ss_pred HhhccccCCcEEEEEEeeCCEEEEE
Confidence 3467999999999887788887754
No 16
>PF12690 BsuPI: Intracellular proteinase inhibitor; InterPro: IPR020481 BsuPI is a intracellular proteinase inhibitor that directly regulates the major intracellular proteinase (ISP-1) activity in vivo. It inhibits ISP-1 in the early stages of sporulation and then may be inactivated by a membrane-bound proteinase [].; PDB: 3ISY_A.
Probab=31.30 E-value=65 Score=25.39 Aligned_cols=53 Identities=19% Similarity=0.458 Sum_probs=26.3
Q ss_pred CceEEEEEeCCCCeEEEEEEEEcCCCCCcceeecChhhHHhhcCCCCCCEEEEE--EcC-C--CCeEEEE
Q 041864 144 EGIFISMEDLDGLHVWTFKYRFWPNNNSRMYVLENTGDFVNAHGLQLGDFIIVY--KDD-Q--NQNYVIQ 208 (300)
Q Consensus 144 eGi~L~V~D~~G~k~W~FRf~yw~NnkSR~YVLtGW~~FVr~K~LkaGD~IvF~--rd~-~--~G~L~Ig 208 (300)
...++.+.|.+|+.+|+ | +..++| ..-+....|.+|+.++|- ++. . .|.|.+.
T Consensus 24 q~~D~~v~d~~g~~vwr-----w--S~~~~F-----tQal~~~~l~pGe~~~~~~~~~~~~~~~G~Y~~~ 81 (82)
T PF12690_consen 24 QRYDFVVKDKEGKEVWR-----W--SDGKMF-----TQALQEETLEPGESLTYEETWDLKDLSPGEYTLE 81 (82)
T ss_dssp --EEEEEE-TT--EEEE-----T--TTT------------EEEEE-TT-EEEEEEEESS----SEEEEEE
T ss_pred CEEEEEEECCCCCEEEE-----e--cCCchh-----hheeeEEEECCCCEEEEEEEECCCCCCCceEEEe
Confidence 34678889999987776 3 344443 344567889999999984 332 2 4666654
No 17
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=28.87 E-value=1.5e+02 Score=22.81 Aligned_cols=39 Identities=23% Similarity=0.334 Sum_probs=27.8
Q ss_pred EEcCCCCCcceeecChhhHHhhcCCCCCCEEEEEEcCCCCeEEEE
Q 041864 164 RFWPNNNSRMYVLENTGDFVNAHGLQLGDFIIVYKDDQNQNYVIQ 208 (300)
Q Consensus 164 ~yw~NnkSR~YVLtGW~~FVr~K~LkaGD~IvF~rd~~~G~L~Ig 208 (300)
+.| ++| +.++==.+++..-+|.+||.|.+... +|.+.|.
T Consensus 4 ~k~--GNS--~~vtIPk~i~~~lgl~~Gd~v~v~~~--~~~iii~ 42 (74)
T TIGR02609 4 RKV--GNS--LVVTLPKEVLESLGLKEGDTLYVDEE--EGGLKLK 42 (74)
T ss_pred EEE--CCe--eEEEECHHHHHHcCcCCCCEEEEEEE--CCEEEEE
Confidence 567 445 45553468899999999999988765 3566664
No 18
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=27.81 E-value=1.2e+02 Score=24.69 Aligned_cols=53 Identities=25% Similarity=0.336 Sum_probs=27.8
Q ss_pred CceEEEEEeCCCCeEEEEEEE-EcCC-----CCCcceeecChhhHHhhcCCCCCCEEEE
Q 041864 144 EGIFISMEDLDGLHVWTFKYR-FWPN-----NNSRMYVLENTGDFVNAHGLQLGDFIIV 196 (300)
Q Consensus 144 eGi~L~V~D~~G~k~W~FRf~-yw~N-----nkSR~YVLtGW~~FVr~K~LkaGD~IvF 196 (300)
-.+.+.+.|.+|.-....+.. -|.. ..+-.|+|+==..++.++++++||.|.|
T Consensus 48 ~pLDi~fld~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~~aG~~~~~~i~~Gd~v~~ 106 (108)
T PF02643_consen 48 FPLDIAFLDSDGRVVKIERMVPPWRTYPCPSYKPARYVLELPAGWFEKLGIKVGDRVRI 106 (108)
T ss_dssp S-EEEEEE-TTSBEEEEEEEE-TT--S-EEECCEECEEEEEETTHHHHHT--TT-EEE-
T ss_pred eeEEEEEECCCCeEEEEEccCCCCccCCCCCCCccCEEEEcCCCchhhcCCCCCCEEEe
Confidence 345666666666533333333 2211 1234799984466788999999999976
No 19
>PF02431 Chalcone: Chalcone-flavanone isomerase; InterPro: IPR003466 Chalcone isomerase (5.5.1.6 from EC) also known as chalcone-flavanone isomerase, is a plant enzyme responsible for the isomerisation of chalcone to naringenin a key step in the biosynthesis of flavonoids. The Petunia hybrida (Petunia) genome contains two genes coding for very similar enzymes, ChiA and ChiB, but only the first seems to encode a functional chalcone isomerase. Chalcone isomerase has a core 2-layer alpha/beta structure consisting of beta(3)-alpha(2)-beta-alpha(2)-beta(3) []. This entry represents a subgroup of Chalcone isomerase.; GO: 0016872 intramolecular lyase activity, 0042398 cellular modified amino acid biosynthetic process; PDB: 1JX0_B 1JEP_A 1EYP_B 1JX1_B 1EYQ_B 1FM8_A 1FM7_A 4DOL_A 4DOI_A 4DOK_B ....
Probab=27.23 E-value=32 Score=30.56 Aligned_cols=58 Identities=14% Similarity=0.144 Sum_probs=34.7
Q ss_pred hhhHHhhc-CCCCCCEEEEEEcCCCCeEEEEEEEcCC----CCccCc--ccccccccccc-cCcccc
Q 041864 179 TGDFVNAH-GLQLGDFIIVYKDDQNQNYVIQAKKASD----QDVYTN--LTSDSVNDILL-NDYEVN 237 (300)
Q Consensus 179 W~~FVr~K-~LkaGD~IvF~rd~~~G~L~IgiRRa~~----q~~~~~--~~~~~v~~~~~-~~~~~~ 237 (300)
-.++...+ .+++||.|.|.|.+ +|.+.+.+..... ....++ .+..|+.+++| -+..++
T Consensus 120 f~~~F~~~g~~~kG~~i~l~~~~-~g~l~v~~~~~~~~~~~~~g~I~~~~~~~al~~~yL~G~~pvs 185 (199)
T PF02431_consen 120 FKSLFKSKGSVPKGDVITLTWSP-DGSLTVSYNGQGKIPGKELGTIKSPRFARALFDIYLSGDKPVS 185 (199)
T ss_dssp HHHHHTTB-EE-TT-EEEEEEET-TTEEEEEEESSSS--SSECEEEE-HHHHHHHHHHHH-STT-S-
T ss_pred HHHHhcccccccCCCEEEEEECC-CCcEEEEEecCCCCCccceeEEcCHHHHHHHHHHHcCCCCCCC
Confidence 35566666 89999999999975 4678787774332 222222 33367777777 555544
No 20
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=26.66 E-value=1.1e+02 Score=26.01 Aligned_cols=28 Identities=14% Similarity=0.182 Sum_probs=19.3
Q ss_pred hcCCCCCCEEEEE-EcCCCCeEEEEEEEc
Q 041864 185 AHGLQLGDFIIVY-KDDQNQNYVIQAKKA 212 (300)
Q Consensus 185 ~K~LkaGD~IvF~-rd~~~G~L~IgiRRa 212 (300)
-.+|++||.|.|- ....++...+.+|+.
T Consensus 86 l~~lk~G~~V~F~~~~~~~~~~i~~i~~~ 114 (115)
T PRK09838 86 MSEIKTGDKVAFNFVQQGNLSLLQDIKVS 114 (115)
T ss_pred hccCCCCCEEEEEEEEcCCcEEEEEEeeC
Confidence 4589999999994 444445555667763
No 21
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=26.01 E-value=1.5e+02 Score=19.46 Aligned_cols=28 Identities=18% Similarity=0.367 Sum_probs=22.1
Q ss_pred hhHHhhcCCCCCCEEEEEEcCCCCeEEEE
Q 041864 180 GDFVNAHGLQLGDFIIVYKDDQNQNYVIQ 208 (300)
Q Consensus 180 ~~FVr~K~LkaGD~IvF~rd~~~G~L~Ig 208 (300)
.+|.+.-+++.||.|.+.... +|++.|.
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~-~~~l~l~ 40 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVE-DGEIILR 40 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeC-CCEEEEE
Confidence 678899999999999999753 4566654
No 22
>PLN02311 chalcone isomerase
Probab=25.10 E-value=70 Score=30.96 Aligned_cols=61 Identities=11% Similarity=0.149 Sum_probs=39.6
Q ss_pred cChhhHHhhcCCCCCCEEEEEEcCCCCeEEEEEEEcCC---CCccCc--ccccccccccccCccccc
Q 041864 177 ENTGDFVNAHGLQLGDFIIVYKDDQNQNYVIQAKKASD---QDVYTN--LTSDSVNDILLNDYEVNR 238 (300)
Q Consensus 177 tGW~~FVr~K~LkaGD~IvF~rd~~~G~L~IgiRRa~~---q~~~~~--~~~~~v~~~~~~~~~~~~ 238 (300)
+....+.+...|++||.|.|.|.+. +.+.|.+..... .+..++ ...+|+-++++-+.-++.
T Consensus 191 ekF~~~F~~~~l~kGd~I~~~~~p~-~~~~v~~s~~g~~~~~~g~Ies~~f~~ALf~i~LGd~PVs~ 256 (271)
T PLN02311 191 STFRSIFQNRSLNKGTVIFLTWINP-SKMLVCISSEGLPSSVDATIESGNVTSALFDVFFGDSPVSP 256 (271)
T ss_pred HHHHHHhcCCCCCCCCEEEEEEeCC-CceEEEEecCCcccceeEEECCHHHHHHHHHHhcCCCCCCH
Confidence 3456667778999999999999753 566665543221 122233 334788888887776654
No 23
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=23.11 E-value=1.2e+02 Score=24.38 Aligned_cols=25 Identities=24% Similarity=0.371 Sum_probs=19.4
Q ss_pred hhHHhhcCCCCCCEEEEEEcCCC-Ce
Q 041864 180 GDFVNAHGLQLGDFIIVYKDDQN-QN 204 (300)
Q Consensus 180 ~~FVr~K~LkaGD~IvF~rd~~~-G~ 204 (300)
-..++.-+|+.||.|-+.|.+.. |+
T Consensus 44 DPv~r~~g~k~GdVvkI~R~S~taG~ 69 (79)
T PRK09570 44 DPVVKAIGAKPGDVIKIVRKSPTAGE 69 (79)
T ss_pred ChhhhhcCCCCCCEEEEEECCCCCCc
Confidence 45667779999999999998543 54
No 24
>PRK03760 hypothetical protein; Provisional
Probab=22.34 E-value=2.7e+02 Score=23.40 Aligned_cols=29 Identities=17% Similarity=0.253 Sum_probs=22.0
Q ss_pred CCcceeecChhhHHhhcCCCCCCEEEEEE
Q 041864 170 NSRMYVLENTGDFVNAHGLQLGDFIIVYK 198 (300)
Q Consensus 170 kSR~YVLtGW~~FVr~K~LkaGD~IvF~r 198 (300)
.+-.|+|+==..++.++++++||.|.|-+
T Consensus 88 ~~a~~VLEl~aG~~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 88 KPARYIIEGPVGKIRVLKVEVGDEIEWID 116 (117)
T ss_pred ccceEEEEeCCChHHHcCCCCCCEEEEee
Confidence 34569998334457899999999998765
No 25
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=22.30 E-value=1.3e+02 Score=25.38 Aligned_cols=24 Identities=21% Similarity=0.436 Sum_probs=16.1
Q ss_pred cCCCCCCEEEEEEcCCCCeEEEEE
Q 041864 186 HGLQLGDFIIVYKDDQNQNYVIQA 209 (300)
Q Consensus 186 K~LkaGD~IvF~rd~~~G~L~Igi 209 (300)
+++++||.|+|..-..+-++.+.+
T Consensus 30 ~~ikvGD~I~f~~~~~~~~l~v~V 53 (109)
T cd06555 30 QQIKVGDKILFNDLDTGQQLLVKV 53 (109)
T ss_pred hcCCCCCEEEEEEcCCCcEEEEEE
Confidence 579999999998653323454443
No 26
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=22.25 E-value=1.9e+02 Score=23.09 Aligned_cols=40 Identities=20% Similarity=0.300 Sum_probs=28.7
Q ss_pred eCCCCeEEEEEEEEcCCCCCcceeecChhhHHhhcCCCCCCEEEEE
Q 041864 152 DLDGLHVWTFKYRFWPNNNSRMYVLENTGDFVNAHGLQLGDFIIVY 197 (300)
Q Consensus 152 D~~G~k~W~FRf~yw~NnkSR~YVLtGW~~FVr~K~LkaGD~IvF~ 197 (300)
+..| +.=+||-+-..|++ +|-| ..|-+..+|++||++.+-
T Consensus 23 ~~~G-R~~syr~~Vq~NGn----LLIG-~AYT~~m~L~PGdEFeI~ 62 (71)
T PF14250_consen 23 GRRG-RKASYRVSVQGNGN----LLIG-SAYTKQMGLKPGDEFEIK 62 (71)
T ss_pred CCCC-cCceEEEEEecCCC----EEEc-HHHHHHhCCCCCCEEEEE
Confidence 3445 36677777765543 5556 788999999999998764
No 27
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=22.00 E-value=1.5e+02 Score=25.35 Aligned_cols=43 Identities=21% Similarity=0.293 Sum_probs=28.9
Q ss_pred CcceeecC--hhh-----HHhhcCCCCCCEEEEEE-cCCCCeEEEEEEEcC
Q 041864 171 SRMYVLEN--TGD-----FVNAHGLQLGDFIIVYK-DDQNQNYVIQAKKAS 213 (300)
Q Consensus 171 SR~YVLtG--W~~-----FVr~K~LkaGD~IvF~r-d~~~G~L~IgiRRa~ 213 (300)
...++|.| |.. |-+=++|++||.|.+.. ++..=.|.|.-.+..
T Consensus 49 ~Gn~viaGH~~~~g~~~~F~~L~~l~~GD~I~v~~~~g~~~~Y~V~~~~~v 99 (144)
T cd05829 49 KGTAVLAGHVDSRGGPAVFFRLGDLRKGDKVEVTRADGQTATFRVDRVEVY 99 (144)
T ss_pred CCCEEEEEecCCCCCChhhcchhcCCCCCEEEEEECCCCEEEEEEeEEEEE
Confidence 35677774 433 99999999999999987 322234666544333
No 28
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=21.76 E-value=1.4e+02 Score=23.11 Aligned_cols=29 Identities=17% Similarity=0.260 Sum_probs=19.4
Q ss_pred hHHhhcCCCCCCEEEEEEcCCCCeEEEEEEE
Q 041864 181 DFVNAHGLQLGDFIIVYKDDQNQNYVIQAKK 211 (300)
Q Consensus 181 ~FVr~K~LkaGD~IvF~rd~~~G~L~IgiRR 211 (300)
+=.++.+|+.||.|.++-. .|++.+.++-
T Consensus 37 ~dA~~~Gi~~Gd~V~v~s~--~G~v~~~v~~ 65 (110)
T PF01568_consen 37 EDAAKLGIKDGDWVRVSSP--RGSVEVRVKV 65 (110)
T ss_dssp HHHHHCT--TTCEEEEEET--TEEEEEEEEE
T ss_pred HHHHHhcCcCCCEEEEEec--cceEeeeeEE
Confidence 4467889999999999974 5666655543
No 29
>TIGR01643 YD_repeat_2x YD repeat (two copies). This model describes two tandem copies of a 21-residue extracellular repeat found in Gram-negative, Gram-positive, and animal proteins. The repeat is named for a YD dipeptide, the most strongly conserved motif of the repeat. These repeats appear in general to be involved in binding carbohydrate; the chicken teneurin-1 YD-repeat region has been shown to bind heparin.
Probab=20.79 E-value=1.5e+02 Score=19.48 Aligned_cols=22 Identities=23% Similarity=0.321 Sum_probs=17.0
Q ss_pred CceEEEEEeCCCCeEEEEEEEEc
Q 041864 144 EGIFISMEDLDGLHVWTFKYRFW 166 (300)
Q Consensus 144 eGi~L~V~D~~G~k~W~FRf~yw 166 (300)
.|..+.+.|..|. .|+|.|--.
T Consensus 4 ~g~l~~~~~p~G~-~~~~~YD~~ 25 (42)
T TIGR01643 4 AGRLTGSTDADGT-TTRYTYDAA 25 (42)
T ss_pred CCCEEEEECCCCC-EEEEEECCC
Confidence 4667888999995 899977543
No 30
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=20.60 E-value=1.2e+02 Score=23.44 Aligned_cols=23 Identities=30% Similarity=0.498 Sum_probs=19.3
Q ss_pred hcCCCCCCEEEEEEcCCCCeEEE
Q 041864 185 AHGLQLGDFIIVYKDDQNQNYVI 207 (300)
Q Consensus 185 ~K~LkaGD~IvF~rd~~~G~L~I 207 (300)
--+|++|..|+++.+..+|+-+|
T Consensus 35 ~~~L~~G~kV~V~yd~~~gk~vi 57 (61)
T PF07076_consen 35 FDGLKPGMKVVVFYDEVDGKRVI 57 (61)
T ss_pred ccccCCCCEEEEEEEccCCcEEe
Confidence 46799999999999888887665
No 31
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=20.27 E-value=1.5e+02 Score=23.42 Aligned_cols=25 Identities=12% Similarity=0.282 Sum_probs=17.9
Q ss_pred hhHHhhcCCCCCCEEEEEEcCCC-Ce
Q 041864 180 GDFVNAHGLQLGDFIIVYKDDQN-QN 204 (300)
Q Consensus 180 ~~FVr~K~LkaGD~IvF~rd~~~-G~ 204 (300)
-..++.-+++.||.|-+.|.+.. |+
T Consensus 41 DPv~r~~g~k~GdVvkI~R~S~taG~ 66 (74)
T PF01191_consen 41 DPVARYLGAKPGDVVKIIRKSETAGE 66 (74)
T ss_dssp SHHHHHTT--TTSEEEEEEEETTTSE
T ss_pred ChhhhhcCCCCCCEEEEEecCCCCCC
Confidence 56677889999999999997543 54
No 32
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=20.09 E-value=71 Score=24.78 Aligned_cols=18 Identities=17% Similarity=0.259 Sum_probs=15.3
Q ss_pred hhHHhhcCCCCCCEEEEE
Q 041864 180 GDFVNAHGLQLGDFIIVY 197 (300)
Q Consensus 180 ~~FVr~K~LkaGD~IvF~ 197 (300)
..-+|..+|+.||.|.=.
T Consensus 33 ~~~Irr~~LR~GD~V~G~ 50 (68)
T cd04459 33 PSQIRRFNLRTGDTVVGQ 50 (68)
T ss_pred HHHHHHhCCCCCCEEEEE
Confidence 668999999999999743
Done!