Query 013565
Match_columns 440
No_of_seqs 162 out of 445
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 05:08:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013565.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013565hhsearch_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 99.8 9E-20 1.9E-24 147.9 11.9 100 136-241 1-100 (100)
2 PF03754 DUF313: Domain of unk 98.6 1.1E-07 2.4E-12 83.5 5.9 81 130-210 18-114 (114)
3 PF09217 EcoRII-N: Restriction 98.2 1.9E-05 4.1E-10 73.0 10.9 90 132-222 6-110 (156)
4 cd00018 AP2 DNA-binding domain 68.4 1.2 2.6E-05 34.3 -0.8 35 62-97 12-49 (61)
5 PF02261 Asp_decarbox: Asparta 65.3 71 0.0015 29.1 9.6 77 133-222 8-88 (116)
6 PF04014 Antitoxin-MazE: Antid 63.1 22 0.00049 26.2 5.2 41 192-239 3-43 (47)
7 cd06919 Asp_decarbox Aspartate 59.6 69 0.0015 28.9 8.4 76 134-223 8-88 (111)
8 PRK05449 aspartate alpha-decar 58.7 68 0.0015 29.5 8.4 76 134-223 9-89 (126)
9 TIGR00223 panD L-aspartate-alp 58.1 69 0.0015 29.5 8.3 76 134-223 9-89 (126)
10 PRK11347 antitoxin ChpS; Provi 55.8 35 0.00075 28.8 5.7 44 187-238 3-46 (83)
11 PF08922 DUF1905: Domain of un 54.5 71 0.0015 26.4 7.2 79 136-222 1-79 (80)
12 smart00380 AP2 DNA-binding dom 52.4 3.1 6.8E-05 32.5 -1.0 34 63-97 12-48 (64)
13 PRK06461 single-stranded DNA-b 46.0 67 0.0014 28.6 6.2 51 172-239 41-91 (129)
14 PF10844 DUF2577: Protein of u 44.1 67 0.0015 27.5 5.8 25 207-235 71-95 (100)
15 TIGR02609 doc_partner putative 43.6 52 0.0011 26.8 4.8 39 189-235 3-41 (74)
16 cd04491 SoSSB_OBF SoSSB_OBF: A 38.3 1.3E+02 0.0028 23.9 6.3 51 172-238 24-74 (82)
17 PRK09798 antitoxin MazE; Provi 38.1 98 0.0021 26.0 5.7 43 188-238 5-47 (82)
18 smart00536 AXH domain in Ataxi 34.9 22 0.00047 32.2 1.4 27 196-222 77-113 (116)
19 PRK03760 hypothetical protein; 34.8 88 0.0019 27.8 5.2 58 162-224 59-117 (117)
20 TIGR01439 lp_hng_hel_AbrB loop 31.5 78 0.0017 22.1 3.6 27 205-235 13-39 (43)
21 cd04451 S1_IF1 S1_IF1: Transla 30.7 2.6E+02 0.0055 21.7 6.8 14 211-224 39-52 (64)
22 PF03120 DNA_ligase_OB: NAD-de 30.7 31 0.00068 29.3 1.6 20 205-224 42-61 (82)
23 PF04617 Hox9_act: Hox9 activa 29.3 38 0.00082 32.8 2.1 43 25-77 60-102 (182)
24 PF02643 DUF192: Uncharacteriz 29.0 1.3E+02 0.0028 26.0 5.2 49 173-222 50-107 (108)
25 PF08517 AXH: Ataxin-1 and HBP 27.5 18 0.00038 32.6 -0.4 26 196-221 76-111 (115)
26 PLN03106 TCP2 Protein TCP2; Pr 25.0 1.9E+02 0.0042 31.2 6.5 81 279-362 274-355 (447)
27 PF01878 EVE: EVE domain; Int 24.8 93 0.002 27.4 3.6 27 211-240 38-64 (143)
28 KOG1924 RhoA GTPase effector D 23.5 4E+02 0.0087 31.8 8.9 18 350-367 601-618 (1102)
29 cd04485 DnaE_OBF DnaE_OBF: A s 23.4 2.1E+02 0.0045 21.4 4.9 52 173-238 21-72 (84)
30 PRK11507 ribosome-associated p 23.1 65 0.0014 26.9 2.1 25 198-222 38-62 (70)
31 PRK09570 rpoH DNA-directed RNA 23.0 1.1E+02 0.0023 26.1 3.5 21 205-225 44-64 (79)
32 TIGR01643 YD_repeat_2x YD repe 22.4 1.3E+02 0.0028 21.0 3.3 21 171-191 4-24 (42)
33 COG2336 MazE Growth regulator 21.0 1.2E+02 0.0027 26.1 3.4 47 188-241 4-50 (82)
34 PF05382 Amidase_5: Bacterioph 20.5 72 0.0015 29.6 2.1 27 198-224 59-87 (145)
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=99.82 E-value=9e-20 Score=147.92 Aligned_cols=100 Identities=35% Similarity=0.562 Sum_probs=76.3
Q ss_pred EEEecccCCCCCCCcEEeehhchhhhCCCCCCCCCCCeEEEEEeCCCCeEEEEEEEeCCCcceEEecChhhhhhccCCCC
Q 013565 136 FDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDA 215 (440)
Q Consensus 136 F~KvLT~SDV~k~gRLvIPKr~AEk~FPLd~s~~~~g~~L~veD~~GK~W~FRysywn~SrrYVLTkGWs~FVKdKkLka 215 (440)
|.|+|+++|+.+.++|.||+++++++.. ....++.|.++|..|+.|++++++++++.+++|++||.+||++++|++
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~----~~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~~ 76 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHGG----NKRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLKE 76 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--T
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhCC----CcCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCCC
Confidence 8999999999998999999999998821 123578999999999999999999988888999999999999999999
Q ss_pred CCEEEEEeccccCCCCeEEEEEEeCC
Q 013565 216 GDVVSFHRGVGDLAKGRLFIDWRRRS 241 (440)
Q Consensus 216 GDvVvF~R~~~e~~~grLfIgIRRa~ 241 (440)
||+|+|++.. ....++.|.|.|+.
T Consensus 77 GD~~~F~~~~--~~~~~~~v~i~~~~ 100 (100)
T PF02362_consen 77 GDVCVFELIG--NSNFTLKVHIFRKS 100 (100)
T ss_dssp T-EEEEEE-S--SSCE-EEEEEE---
T ss_pred CCEEEEEEec--CCCceEEEEEEECc
Confidence 9999999973 36677799999863
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=98.55 E-value=1.1e-07 Score=83.51 Aligned_cols=81 Identities=23% Similarity=0.555 Sum_probs=65.8
Q ss_pred cccceeEEEecccCCCC-CCCcEEeehhchhh--hC-CC---------CCCCCCCCeEEEEEeCCCCeEEEEEEEeCC--
Q 013565 130 LEKEHMFDKVVTPSDVG-KLNRLVIPKQHAEK--YF-PL---------DSSSNEKGLLLNFEDRNGKPWRFRYSYWNS-- 194 (440)
Q Consensus 130 ~eke~lF~KvLT~SDV~-k~gRLvIPKr~AEk--~F-PL---------d~s~~~~g~~L~veD~~GK~W~FRysywn~-- 194 (440)
.....+|+|+|+.|||. ..+||.||...... +| |. .......|+.+.+.|..++.|.++++.|+.
T Consensus 18 ~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~ 97 (114)
T PF03754_consen 18 EDPKLIIEKTLFKTDVDPHQSRLSMPFNQIIDNDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGN 97 (114)
T ss_pred CCCeEEEeeeecccCCCCCCceeeccHHHhcccccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccC
Confidence 45578999999999999 57899999987743 23 21 112356889999999999999999999965
Q ss_pred -CcceEEecChhhhhhc
Q 013565 195 -SQSYVMTKGWSRFVKD 210 (440)
Q Consensus 195 -SrrYVLTkGWs~FVKd 210 (440)
.-.|+|..||..+|++
T Consensus 98 ~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 98 GTSNYVLNSGWNKVVED 114 (114)
T ss_pred CceEEEEEcChHhhccC
Confidence 4689999999999974
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=98.16 E-value=1.9e-05 Score=73.04 Aligned_cols=90 Identities=20% Similarity=0.381 Sum_probs=58.4
Q ss_pred cceeEEEecccCCCCC----CCcEEeehhchhhhCC-CCC-CCCCCCeEEEEEeCCC--CeEEEEEEEeCC------Ccc
Q 013565 132 KEHMFDKVVTPSDVGK----LNRLVIPKQHAEKYFP-LDS-SSNEKGLLLNFEDRNG--KPWRFRYSYWNS------SQS 197 (440)
Q Consensus 132 ke~lF~KvLT~SDV~k----~gRLvIPKr~AEk~FP-Ld~-s~~~~g~~L~veD~~G--K~W~FRysywn~------Srr 197 (440)
....|+|.|++.|++. ..++.|||..++.+|| +.. ...++.+.|.+++..+ ..|+||++|.|+ ++.
T Consensus 6 ~~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE 85 (156)
T PF09217_consen 6 SWAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNE 85 (156)
T ss_dssp SEEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--E
T ss_pred ceEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCc
Confidence 3457999999999994 3599999999999997 332 3566789999998877 569999999977 577
Q ss_pred eEEecChhhhhhccC-CCCCCEEEEE
Q 013565 198 YVMTKGWSRFVKDKK-LDAGDVVSFH 222 (440)
Q Consensus 198 YVLTkGWs~FVKdKk-LkaGDvVvF~ 222 (440)
|.||. |.....--+ =.+||.++|.
T Consensus 86 ~RIT~-~G~~~~~~~~~~tGaL~vla 110 (156)
T PF09217_consen 86 YRITR-FGRGFPLQNPENTGALLVLA 110 (156)
T ss_dssp EEEE----TTSGGG-GGGTT-EEEEE
T ss_pred eEEee-ecCCCccCCccccccEEEEE
Confidence 99987 876655333 3679999887
No 4
>cd00018 AP2 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.
Probab=68.39 E-value=1.2 Score=34.27 Aligned_cols=35 Identities=17% Similarity=0.097 Sum_probs=27.6
Q ss_pred cccccccccc---cccceeeccCCccccccccccccccc
Q 013565 62 QNYNKQQQPQ---MGSWLLGKTTTTTTAAELEDVSNEEE 97 (440)
Q Consensus 62 ~~~~~q~~~h---~~~w~~~~~~~~~~Aa~~~~v~~~~~ 97 (440)
.+|.++|... -..||+...+++ +||.+||.+..+.
T Consensus 12 gkw~A~I~~~~~gk~~~lG~f~t~e-eAa~Ayd~a~~~~ 49 (61)
T cd00018 12 GKWVAEIRDPSGGRRIWLGTFDTAE-EAARAYDRAALKL 49 (61)
T ss_pred CcEEEEEEeCCCCceEccCCCCCHH-HHHHHHHHHHHHh
Confidence 3899998764 468999998888 8999998765554
No 5
>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=65.30 E-value=71 Score=29.05 Aligned_cols=77 Identities=14% Similarity=0.201 Sum_probs=48.5
Q ss_pred ceeEEEecccCCCCCCCcEEeehhchhh--hCCCCCCCCCCCeEEEEEeC-CCCeEEEEEEEeCC-CcceEEecChhhhh
Q 013565 133 EHMFDKVVTPSDVGKLNRLVIPKQHAEK--YFPLDSSSNEKGLLLNFEDR-NGKPWRFRYSYWNS-SQSYVMTKGWSRFV 208 (440)
Q Consensus 133 e~lF~KvLT~SDV~k~gRLvIPKr~AEk--~FPLd~s~~~~g~~L~veD~-~GK~W~FRysywn~-SrrYVLTkGWs~FV 208 (440)
..+-+-++|..|+...|-+.|..+.+++ ++|.. .|.+.+. +|..|.---+.-.. +..-.|.+ .
T Consensus 8 sKiHratVT~a~L~Y~GSitID~~Ll~aagi~p~E--------~V~V~Nv~nG~Rf~TYvI~g~~GSg~I~lNG-----a 74 (116)
T PF02261_consen 8 SKIHRATVTEADLNYEGSITIDEDLLDAAGILPYE--------QVQVVNVNNGERFETYVIPGERGSGVICLNG-----A 74 (116)
T ss_dssp EEEEEEE--EEETTSTSCEEEEHHHHHHCT--TTB--------EEEEEETTT--EEEEEEEEESTTTT-EEEEG-----G
T ss_pred hhhcceEEeccccccceeeEECHHHHHHcCCCcCC--------EEEEEECCCCcEEEEEEEEccCCCcEEEECC-----H
Confidence 3455678999999999999999999886 56654 6777775 88888754443322 45556644 4
Q ss_pred hccCCCCCCEEEEE
Q 013565 209 KDKKLDAGDVVSFH 222 (440)
Q Consensus 209 KdKkLkaGDvVvF~ 222 (440)
-++..++||.|++.
T Consensus 75 AArl~~~GD~vII~ 88 (116)
T PF02261_consen 75 AARLVQVGDRVIIM 88 (116)
T ss_dssp GGGCS-TT-EEEEE
T ss_pred HHhccCCCCEEEEE
Confidence 56778999999984
No 6
>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=63.09 E-value=22 Score=26.17 Aligned_cols=41 Identities=20% Similarity=0.259 Sum_probs=28.3
Q ss_pred eCCCcceEEecChhhhhhccCCCCCCEEEEEeccccCCCCeEEEEEEe
Q 013565 192 WNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRR 239 (440)
Q Consensus 192 wn~SrrYVLTkGWs~FVKdKkLkaGDvVvF~R~~~e~~~grLfIgIRR 239 (440)
++++..-.|-+ +|.++.+|++||.|.|.-. .+|++.|.-.+
T Consensus 3 vg~s~~v~iPk---~~~~~l~l~~Gd~v~i~~~----~~g~i~i~p~~ 43 (47)
T PF04014_consen 3 VGNSGQVTIPK---EIREKLGLKPGDEVEIEVE----GDGKIVIRPVK 43 (47)
T ss_dssp ETTCSEEEE-H---HHHHHTTSSTTTEEEEEEE----TTSEEEEEEST
T ss_pred ECCCceEECCH---HHHHHcCCCCCCEEEEEEe----CCCEEEEEECC
Confidence 34455555544 7888899999999999986 44567764433
No 7
>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=59.62 E-value=69 Score=28.94 Aligned_cols=76 Identities=16% Similarity=0.166 Sum_probs=54.8
Q ss_pred eeEEEecccCCCCCCCcEEeehhchhh--hCCCCCCCCCCCeEEEEEeC-CCCeEEEEEEEeCC--CcceEEecChhhhh
Q 013565 134 HMFDKVVTPSDVGKLNRLVIPKQHAEK--YFPLDSSSNEKGLLLNFEDR-NGKPWRFRYSYWNS--SQSYVMTKGWSRFV 208 (440)
Q Consensus 134 ~lF~KvLT~SDV~k~gRLvIPKr~AEk--~FPLd~s~~~~g~~L~veD~-~GK~W~FRysywn~--SrrYVLTkGWs~FV 208 (440)
.+-+-++|..|+..-|-+.|..+.+++ ++|.. .|.+.|. +|..|.-- .+.+. |..-.|.+ .
T Consensus 8 KiHratVT~a~L~YeGSitID~~Ll~aagi~~~E--------~V~I~Nv~NG~Rf~TY-vI~g~~gSg~I~lNG-----A 73 (111)
T cd06919 8 KIHRATVTEADLNYEGSITIDEDLLEAAGILPYE--------KVLVVNVNNGARFETY-VIPGERGSGVICLNG-----A 73 (111)
T ss_pred cccceEEeccccccceeEEECHHHHHhcCCCCCC--------EEEEEECCCCcEEEEE-EEEcCCCCCEEEeCC-----H
Confidence 445668899999988999999998886 45553 6777775 78877643 34432 45566644 4
Q ss_pred hccCCCCCCEEEEEe
Q 013565 209 KDKKLDAGDVVSFHR 223 (440)
Q Consensus 209 KdKkLkaGDvVvF~R 223 (440)
.++..++||.|++.-
T Consensus 74 AAr~~~~GD~vII~s 88 (111)
T cd06919 74 AARLGQPGDRVIIMA 88 (111)
T ss_pred HHhcCCCCCEEEEEE
Confidence 667789999999854
No 8
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=58.68 E-value=68 Score=29.54 Aligned_cols=76 Identities=13% Similarity=0.185 Sum_probs=54.7
Q ss_pred eeEEEecccCCCCCCCcEEeehhchhh--hCCCCCCCCCCCeEEEEEeC-CCCeEEEEEEEeCC--CcceEEecChhhhh
Q 013565 134 HMFDKVVTPSDVGKLNRLVIPKQHAEK--YFPLDSSSNEKGLLLNFEDR-NGKPWRFRYSYWNS--SQSYVMTKGWSRFV 208 (440)
Q Consensus 134 ~lF~KvLT~SDV~k~gRLvIPKr~AEk--~FPLd~s~~~~g~~L~veD~-~GK~W~FRysywn~--SrrYVLTkGWs~FV 208 (440)
.+-+-++|..|+..-|-+.|-.+.+++ ++|.. .|.+.|. +|..|.-- .+.+. |..-.|.+ .
T Consensus 9 KiHratVT~a~L~Y~GSitID~~Ll~aagi~p~E--------~V~V~Nv~NG~Rf~TY-vI~g~~GSg~I~lNG-----A 74 (126)
T PRK05449 9 KIHRATVTEADLNYEGSITIDEDLLDAAGILENE--------KVQIVNVNNGARFETY-VIAGERGSGVICLNG-----A 74 (126)
T ss_pred cccceEEeccccccceeEEECHHHHHhcCCCCCC--------EEEEEECCCCcEEEEE-EEEcCCCCCEEEeCC-----H
Confidence 345667899999988999999999887 56654 6677775 88877643 34432 45556644 4
Q ss_pred hccCCCCCCEEEEEe
Q 013565 209 KDKKLDAGDVVSFHR 223 (440)
Q Consensus 209 KdKkLkaGDvVvF~R 223 (440)
.++..++||.|++.-
T Consensus 75 AAr~~~~GD~vII~a 89 (126)
T PRK05449 75 AARLVQVGDLVIIAA 89 (126)
T ss_pred HHhcCCCCCEEEEEE
Confidence 677789999999853
No 9
>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=58.08 E-value=69 Score=29.53 Aligned_cols=76 Identities=13% Similarity=0.206 Sum_probs=54.8
Q ss_pred eeEEEecccCCCCCCCcEEeehhchhh--hCCCCCCCCCCCeEEEEEeC-CCCeEEEEEEEeCC--CcceEEecChhhhh
Q 013565 134 HMFDKVVTPSDVGKLNRLVIPKQHAEK--YFPLDSSSNEKGLLLNFEDR-NGKPWRFRYSYWNS--SQSYVMTKGWSRFV 208 (440)
Q Consensus 134 ~lF~KvLT~SDV~k~gRLvIPKr~AEk--~FPLd~s~~~~g~~L~veD~-~GK~W~FRysywn~--SrrYVLTkGWs~FV 208 (440)
.+-+-++|..|+..-|-+.|-.+.+++ ++|.. .|.+.|. +|..|.-- .+.+. |..-.|.+ .
T Consensus 9 KIHratVT~a~L~Y~GSItID~~Lm~aagi~p~E--------~V~V~Nv~NG~Rf~TY-vI~G~~GSg~I~lNG-----A 74 (126)
T TIGR00223 9 KLHRATVTHANLNYEGSITIDEDLLDAAGILENE--------KVDIVNVNNGKRFSTY-AIAGKRGSRIICVNG-----A 74 (126)
T ss_pred hhcceEEeccccccceeEEECHHHHHhcCCCCCC--------EEEEEECCCCcEEEEE-EEEcCCCCCEEEeCC-----H
Confidence 445668899999988999999998886 56654 6777775 88887753 44432 45556644 4
Q ss_pred hccCCCCCCEEEEEe
Q 013565 209 KDKKLDAGDVVSFHR 223 (440)
Q Consensus 209 KdKkLkaGDvVvF~R 223 (440)
.++..++||.|++.-
T Consensus 75 AArl~~~GD~VII~s 89 (126)
T TIGR00223 75 AARCVSVGDIVIIAS 89 (126)
T ss_pred HHhcCCCCCEEEEEE
Confidence 567789999999853
No 10
>PRK11347 antitoxin ChpS; Provisional
Probab=55.84 E-value=35 Score=28.77 Aligned_cols=44 Identities=18% Similarity=0.323 Sum_probs=35.3
Q ss_pred EEEEEeCCCcceEEecChhhhhhccCCCCCCEEEEEeccccCCCCeEEEEEE
Q 013565 187 FRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWR 238 (440)
Q Consensus 187 FRysywn~SrrYVLTkGWs~FVKdKkLkaGDvVvF~R~~~e~~~grLfIgIR 238 (440)
.+.+.|++|.--.|-+ .|.++-+|.+||.|.+... ++.+.|.-.
T Consensus 3 ~~v~kwGNS~~vriPk---~il~~l~l~~G~~v~i~v~-----~~~iii~p~ 46 (83)
T PRK11347 3 ITIKRWGNSAGMVIPN---IVMKELNLQPGQSVEAQVS-----NNQLILTPI 46 (83)
T ss_pred EEEEEEcCceeEEeCH---HHHHHcCCCCCCEEEEEEE-----CCEEEEEEC
Confidence 4667888888888876 9999999999999999875 355666443
No 11
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=54.47 E-value=71 Score=26.37 Aligned_cols=79 Identities=19% Similarity=0.198 Sum_probs=41.0
Q ss_pred EEEecccCCCCCCCcEEeehhchhhhCCCCCCCCCCCeEEEEEeCCCCeEEEEEEEeCCCcceEEecChhhhhhccCCCC
Q 013565 136 FDKVVTPSDVGKLNRLVIPKQHAEKYFPLDSSSNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDA 215 (440)
Q Consensus 136 F~KvLT~SDV~k~gRLvIPKr~AEk~FPLd~s~~~~g~~L~veD~~GK~W~FRysywn~SrrYVLTkGWs~FVKdKkLka 215 (440)
|+-+|-+.+-+. --+.||.+.++.+-.. +.+.+.|.++ .+|..|+-...- .....|+|-= =....++-++.+
T Consensus 1 F~a~l~~~~~~~-~fv~vP~~v~~~l~~~----~~g~v~V~~t-I~g~~~~~sl~p-~g~G~~~Lpv-~~~vRk~~g~~~ 72 (80)
T PF08922_consen 1 FTATLWKGEGGW-TFVEVPFDVAEELGEG----GWGRVPVRGT-IDGHPWRTSLFP-MGNGGYILPV-KAAVRKAIGKEA 72 (80)
T ss_dssp EEEE-EE-TTS--EEEE--S-HHHHH--S------S-EEEEEE-ETTEEEEEEEEE-SSTT-EEEEE--HHHHHHHT--T
T ss_pred CeEEEEecCCce-EEEEeCHHHHHHhccc----cCCceEEEEE-ECCEEEEEEEEE-CCCCCEEEEE-cHHHHHHcCCCC
Confidence 444455444332 2467898888877432 1245677666 677777764443 2335576622 147888999999
Q ss_pred CCEEEEE
Q 013565 216 GDVVSFH 222 (440)
Q Consensus 216 GDvVvF~ 222 (440)
||.|.+.
T Consensus 73 Gd~V~v~ 79 (80)
T PF08922_consen 73 GDTVEVT 79 (80)
T ss_dssp TSEEEEE
T ss_pred CCEEEEE
Confidence 9999875
No 12
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=52.36 E-value=3.1 Score=32.48 Aligned_cols=34 Identities=18% Similarity=0.091 Sum_probs=26.8
Q ss_pred cccccccc---ccccceeeccCCccccccccccccccc
Q 013565 63 NYNKQQQP---QMGSWLLGKTTTTTTAAELEDVSNEEE 97 (440)
Q Consensus 63 ~~~~q~~~---h~~~w~~~~~~~~~~Aa~~~~v~~~~~ 97 (440)
+|.++|.. .-..|||....++ +||.+||.++.+.
T Consensus 12 kw~A~I~~~~~~k~~~lG~f~t~e-eAa~Ayd~a~~~~ 48 (64)
T smart00380 12 KWVAEIRDPSKGKRVWLGTFDTAE-EAARAYDRAAFKF 48 (64)
T ss_pred eEEEEEEecCCCcEEecCCCCCHH-HHHHHHHHHHHHh
Confidence 89999874 3358999999888 8999998766554
No 13
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=45.95 E-value=67 Score=28.58 Aligned_cols=51 Identities=18% Similarity=0.375 Sum_probs=33.5
Q ss_pred CeEEEEEeCCCCeEEEEEEEeCCCcceEEecChhhhhhccCCCCCCEEEEEeccccCCCCeEEEEEEe
Q 013565 172 GLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRR 239 (440)
Q Consensus 172 g~~L~veD~~GK~W~FRysywn~SrrYVLTkGWs~FVKdKkLkaGDvVvF~R~~~e~~~grLfIgIRR 239 (440)
-..+.+.|..|. +++..|+. ....|++||+|.+.-..-..-.|++-+.+-+
T Consensus 41 v~~~~l~D~TG~---I~~tlW~~--------------~a~~l~~GdvV~I~na~v~~f~G~lqL~i~~ 91 (129)
T PRK06461 41 ISEAVVGDETGR---VKLTLWGE--------------QAGSLKEGEVVEIENAWTTLYRGKVQLNVGK 91 (129)
T ss_pred EEEEEEECCCCE---EEEEEeCC--------------ccccCCCCCEEEEECcEEeeeCCEEEEEECC
Confidence 357888999996 77888864 1346899999999833212245655554443
No 14
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=44.11 E-value=67 Score=27.52 Aligned_cols=25 Identities=28% Similarity=0.373 Sum_probs=19.0
Q ss_pred hhhccCCCCCCEEEEEeccccCCCCeEEE
Q 013565 207 FVKDKKLDAGDVVSFHRGVGDLAKGRLFI 235 (440)
Q Consensus 207 FVKdKkLkaGDvVvF~R~~~e~~~grLfI 235 (440)
|.-...|++||.|.+.+. .+|+.||
T Consensus 71 i~~~~~Lk~GD~V~ll~~----~~gQ~yi 95 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRV----QGGQKYI 95 (100)
T ss_pred EEEecCCcCCCEEEEEEe----cCCCEEE
Confidence 666778999999999996 4454444
No 15
>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=43.61 E-value=52 Score=26.76 Aligned_cols=39 Identities=18% Similarity=0.234 Sum_probs=29.2
Q ss_pred EEEeCCCcceEEecChhhhhhccCCCCCCEEEEEeccccCCCCeEEE
Q 013565 189 YSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFI 235 (440)
Q Consensus 189 ysywn~SrrYVLTkGWs~FVKdKkLkaGDvVvF~R~~~e~~~grLfI 235 (440)
...|++|..-.|-+ .++.+-+|..||.|.|... ++.+.|
T Consensus 3 i~k~GNS~~vtIPk---~i~~~lgl~~Gd~v~v~~~-----~~~iii 41 (74)
T TIGR02609 3 IRKVGNSLVVTLPK---EVLESLGLKEGDTLYVDEE-----EGGLKL 41 (74)
T ss_pred EEEECCeeEEEECH---HHHHHcCcCCCCEEEEEEE-----CCEEEE
Confidence 34677776666655 8899999999999988764 355666
No 16
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=38.34 E-value=1.3e+02 Score=23.95 Aligned_cols=51 Identities=24% Similarity=0.365 Sum_probs=32.9
Q ss_pred CeEEEEEeCCCCeEEEEEEEeCCCcceEEecChhhhhhccCCCCCCEEEEEeccccCCCCeEEEEEE
Q 013565 172 GLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWR 238 (440)
Q Consensus 172 g~~L~veD~~GK~W~FRysywn~SrrYVLTkGWs~FVKdKkLkaGDvVvF~R~~~e~~~grLfIgIR 238 (440)
-+.+.+.|..| ..++.+|+..- ...|++||+|.+....-..-.+.+-+.+.
T Consensus 24 ~~~~~l~D~TG---~i~~~~W~~~~-------------~~~~~~G~vv~i~~~~v~~~~g~~ql~i~ 74 (82)
T cd04491 24 VQSGLVGDETG---TIRFTLWDEKA-------------ADDLEPGDVVRIENAYVREFNGRLELSVG 74 (82)
T ss_pred EEEEEEECCCC---EEEEEEECchh-------------cccCCCCCEEEEEeEEEEecCCcEEEEeC
Confidence 36888999998 48888986421 45589999998873221223444444443
No 17
>PRK09798 antitoxin MazE; Provisional
Probab=38.11 E-value=98 Score=26.05 Aligned_cols=43 Identities=19% Similarity=0.313 Sum_probs=34.4
Q ss_pred EEEEeCCCcceEEecChhhhhhccCCCCCCEEEEEeccccCCCCeEEEEEE
Q 013565 188 RYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWR 238 (440)
Q Consensus 188 Rysywn~SrrYVLTkGWs~FVKdKkLkaGDvVvF~R~~~e~~~grLfIgIR 238 (440)
+...|++|..-.|-+ .|.++-+|..||.|.+... ++++.|.-.
T Consensus 5 ~v~KwGNS~~vRIPk---~~l~~l~l~~g~~vei~v~-----~~~iiI~p~ 47 (82)
T PRK09798 5 SVKRWGNSPAVRIPA---TLMQALNLNIDDEVKIDLV-----DGKLIIEPV 47 (82)
T ss_pred EEEEEcCcceEEcCH---HHHHHcCCCCCCEEEEEEE-----CCEEEEEEC
Confidence 456788887777765 9999999999999999884 577777443
No 18
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=34.91 E-value=22 Score=32.24 Aligned_cols=27 Identities=33% Similarity=0.428 Sum_probs=21.8
Q ss_pred cceEEecChhhhh----------hccCCCCCCEEEEE
Q 013565 196 QSYVMTKGWSRFV----------KDKKLDAGDVVSFH 222 (440)
Q Consensus 196 rrYVLTkGWs~FV----------KdKkLkaGDvVvF~ 222 (440)
.-||..+||+.|- .-..|++||+|+-.
T Consensus 77 PfFV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl~l 113 (116)
T smart00536 77 PFFVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLSL 113 (116)
T ss_pred CeEEcCccccccChhhhhhhcCCcceecccCCEEecc
Confidence 6788999999885 44678999999754
No 19
>PRK03760 hypothetical protein; Provisional
Probab=34.82 E-value=88 Score=27.80 Aligned_cols=58 Identities=17% Similarity=0.360 Sum_probs=32.4
Q ss_pred CCCCCC-CCCCCeEEEEEeCCCCeEEEEEEEeCCCcceEEecChhhhhhccCCCCCCEEEEEec
Q 013565 162 FPLDSS-SNEKGLLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRG 224 (440)
Q Consensus 162 FPLd~s-~~~~g~~L~veD~~GK~W~FRysywn~SrrYVLTkGWs~FVKdKkLkaGDvVvF~R~ 224 (440)
||+|.. -+..+..+.+.+ -+.|+.-.. ...-+|+|+- =..++.+.++++||.|.|.++
T Consensus 59 ~pLDiiFld~~g~Vv~i~~--~~P~~~~~~--~~~a~~VLEl-~aG~~~~~gi~~Gd~v~~~~~ 117 (117)
T PRK03760 59 SSIDVIFLDSNRRVVDFKT--LKPWRIYVP--KKPARYIIEG-PVGKIRVLKVEVGDEIEWIDE 117 (117)
T ss_pred CeeEEEEECCCCeEEEEEe--CCCccccCC--CccceEEEEe-CCChHHHcCCCCCCEEEEeeC
Confidence 465431 133344444433 256653111 2345688842 123478999999999999763
No 20
>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=31.49 E-value=78 Score=22.07 Aligned_cols=27 Identities=19% Similarity=0.337 Sum_probs=21.3
Q ss_pred hhhhhccCCCCCCEEEEEeccccCCCCeEEE
Q 013565 205 SRFVKDKKLDAGDVVSFHRGVGDLAKGRLFI 235 (440)
Q Consensus 205 s~FVKdKkLkaGDvVvF~R~~~e~~~grLfI 235 (440)
..|.+..+++.||.|.+... .++++.|
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~----~~~~l~l 39 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRV----EDGEIIL 39 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEe----CCCEEEE
Confidence 38899999999999999975 3455555
No 21
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=30.75 E-value=2.6e+02 Score=21.70 Aligned_cols=14 Identities=21% Similarity=0.268 Sum_probs=11.4
Q ss_pred cCCCCCCEEEEEec
Q 013565 211 KKLDAGDVVSFHRG 224 (440)
Q Consensus 211 KkLkaGDvVvF~R~ 224 (440)
..+.+||.|.|...
T Consensus 39 ~~~~vGD~V~~~~~ 52 (64)
T cd04451 39 IRILPGDRVKVELS 52 (64)
T ss_pred cccCCCCEEEEEEe
Confidence 34899999999864
No 22
>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=30.71 E-value=31 Score=29.27 Aligned_cols=20 Identities=25% Similarity=0.494 Sum_probs=16.8
Q ss_pred hhhhhccCCCCCCEEEEEec
Q 013565 205 SRFVKDKKLDAGDVVSFHRG 224 (440)
Q Consensus 205 s~FVKdKkLkaGDvVvF~R~ 224 (440)
.+|+++++|..||.|.++|.
T Consensus 42 ~~~i~~~~i~~Gd~V~V~ra 61 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRA 61 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEE
T ss_pred HHHHHHcCCCCCCEEEEEEC
Confidence 58999999999999999996
No 23
>PF04617 Hox9_act: Hox9 activation region ; InterPro: IPR006711 This domain constitutes the N-terminal of the paralogous homeobox proteins HoxA9, HoxB9, HoxC9 and HoxD9. The N-terminal region is thought to act as a transcription activation region. Activation may be by interaction with proteins such as Btg proteins, which are thought to recruit a multi-protein Ccr4-like complex [].; GO: 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=29.31 E-value=38 Score=32.82 Aligned_cols=43 Identities=30% Similarity=0.539 Sum_probs=26.5
Q ss_pred eeeeeccCCCCCCCCCCCcccCccccceeeeccccccccccccccccccccee
Q 013565 25 FSTTYASNSSSSPSSASSHHHHYTTQTQQLLPLTTHHQNYNKQQQPQMGSWLL 77 (440)
Q Consensus 25 ~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~p~~~~~~~~~~q~~~h~~~w~~ 77 (440)
|..|++.-...++...+.-||.|.-+.+.| |-..+ || +|+||.
T Consensus 60 Fs~SWspv~p~~s~~~s~vYHPY~h~q~~~-~~~d~--rY-------vRSWle 102 (182)
T PF04617_consen 60 FSASWSPVHPQSSGAVSSVYHPYVHPQPHL-PASDG--RY-------VRSWLE 102 (182)
T ss_pred ccCCCCCcCCCcCCCCcccccCCccCCCCC-CCCCC--ce-------eeeccc
Confidence 445555554455556678899998433333 66555 77 489964
No 24
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=28.98 E-value=1.3e+02 Score=25.96 Aligned_cols=49 Identities=20% Similarity=0.392 Sum_probs=26.9
Q ss_pred eEEEEEeCCCCeEEEEEEE--e-------CCCcceEEecChhhhhhccCCCCCCEEEEE
Q 013565 173 LLLNFEDRNGKPWRFRYSY--W-------NSSQSYVMTKGWSRFVKDKKLDAGDVVSFH 222 (440)
Q Consensus 173 ~~L~veD~~GK~W~FRysy--w-------n~SrrYVLTkGWs~FVKdKkLkaGDvVvF~ 222 (440)
+.|.+.|.+|++-...... | ..+-+|+|+- =..++..++|++||.|.|.
T Consensus 50 LDi~fld~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~-~aG~~~~~~i~~Gd~v~~~ 107 (108)
T PF02643_consen 50 LDIAFLDSDGRVVKIERMVPPWRTYPCPSYKPARYVLEL-PAGWFEKLGIKVGDRVRIE 107 (108)
T ss_dssp EEEEEE-TTSBEEEEEEEE-TT--S-EEECCEECEEEEE-ETTHHHHHT--TT-EEE--
T ss_pred EEEEEECCCCeEEEEEccCCCCccCCCCCCCccCEEEEc-CCCchhhcCCCCCCEEEec
Confidence 5666667666654444333 1 1234688854 2466889999999999874
No 25
>PF08517 AXH: Ataxin-1 and HBP1 module (AXH); InterPro: IPR013723 AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1)[]. ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans. The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression []. ; GO: 0005488 binding; PDB: 1OA8_C 3QVE_C 1V06_A.
Probab=27.51 E-value=18 Score=32.60 Aligned_cols=26 Identities=35% Similarity=0.529 Sum_probs=16.9
Q ss_pred cceEEecChhhhh----------hccCCCCCCEEEE
Q 013565 196 QSYVMTKGWSRFV----------KDKKLDAGDVVSF 221 (440)
Q Consensus 196 rrYVLTkGWs~FV----------KdKkLkaGDvVvF 221 (440)
.-||..+||+.|- .-+.|++||+|+-
T Consensus 76 PFFV~gkGWsS~~P~~T~~~ygL~C~~L~vGDvCl~ 111 (115)
T PF08517_consen 76 PFFVKGKGWSSCNPSLTVQLYGLPCRQLQVGDVCLS 111 (115)
T ss_dssp EEEETTTEEEESSHHHHHHHHTS--EE--TT-EEEE
T ss_pred ceEEeCCcccccCcchhceecCCcccccccCCEEec
Confidence 5688889998774 4568899999974
No 26
>PLN03106 TCP2 Protein TCP2; Provisional
Probab=24.99 E-value=1.9e+02 Score=31.19 Aligned_cols=81 Identities=21% Similarity=0.270 Sum_probs=47.1
Q ss_pred cccccccccccccCccccCCCCCCCCcccCCCcceEEEeccCCCCCCCCCCCCCCCCCCCcccccccccCcceeeec-cc
Q 013565 279 YSQSQINNNFYNRNSISLGGTGNNNNVLSTRTLGSILYLRSQLPAAPATQQPPPPPPPPHTEIGMTKWQQHPIVFDS-VP 357 (440)
Q Consensus 279 ~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~v~dS-vp 357 (440)
+.++...++-|+..++ +|+.++--. ....+.+++ +++-.+|.+|.|--+|--..-+||+.-.++.++.+.|-|- ||
T Consensus 274 ~r~~~tspmdyf~~Gl-lg~sss~t~-h~s~g~~~~-~lGNsi~q~m~m~~~pfn~~gd~hh~~~~~~Q~f~f~~dhlip 350 (447)
T PLN03106 274 AARQWPSPMDYFGSGL-LGGSSSRTH-HSSGFPGQI-QLGNSIPQPISTNSHPFSSIGDHHHHHHHQHQHFSFVPDHLIP 350 (447)
T ss_pred cccCCCChHHhhcccc-ccccccccc-cccCCCccc-ccCCCCCCccccCCCcccccccccccccccccccCCcCCcccc
Confidence 4444446777875544 555553321 223444555 8999888887775444445556665544455566666654 78
Q ss_pred ccCCC
Q 013565 358 VVQGK 362 (440)
Q Consensus 358 v~~~~ 362 (440)
|....
T Consensus 351 va~s~ 355 (447)
T PLN03106 351 VATSN 355 (447)
T ss_pred ccccC
Confidence 87544
No 27
>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=24.79 E-value=93 Score=27.42 Aligned_cols=27 Identities=26% Similarity=0.320 Sum_probs=16.0
Q ss_pred cCCCCCCEEEEEeccccCCCCeEEEEEEeC
Q 013565 211 KKLDAGDVVSFHRGVGDLAKGRLFIDWRRR 240 (440)
Q Consensus 211 KkLkaGDvVvF~R~~~e~~~grLfIgIRRa 240 (440)
+++++||.|+||... ...+-++++-+=
T Consensus 38 ~~mk~GD~vifY~s~---~~~~~ivai~~V 64 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSG---CKERGIVAIGEV 64 (143)
T ss_dssp HC--TT-EEEEEETS---SSS-EEEEEEEE
T ss_pred hcCCCCCEEEEEEcC---CCCCEEEEEEEE
Confidence 489999999999963 234666666554
No 28
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=23.49 E-value=4e+02 Score=31.78 Aligned_cols=18 Identities=28% Similarity=0.392 Sum_probs=8.9
Q ss_pred ceeeecccccCCCcccce
Q 013565 350 PIVFDSVPVVQGKATAKR 367 (440)
Q Consensus 350 ~~v~dSvpv~~~~~~~kr 367 (440)
|+..--+||.+--..-|+
T Consensus 601 ~gm~pmaPvlP~gLkpKK 618 (1102)
T KOG1924|consen 601 PGMFPMAPVLPFGLKPKK 618 (1102)
T ss_pred CCcccccccCCCCCCccc
Confidence 344446677764333333
No 29
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=23.40 E-value=2.1e+02 Score=21.45 Aligned_cols=52 Identities=13% Similarity=0.240 Sum_probs=33.5
Q ss_pred eEEEEEeCCCCeEEEEEEEeCCCcceEEecChhhhhhccCCCCCCEEEEEeccccCCCCeEEEEEE
Q 013565 173 LLLNFEDRNGKPWRFRYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWR 238 (440)
Q Consensus 173 ~~L~veD~~GK~W~FRysywn~SrrYVLTkGWs~FVKdKkLkaGDvVvF~R~~~e~~~grLfIgIR 238 (440)
..+.+.|.+|. +.+.+|+. .|..+ ...|++|..|.+.-.... ..+.+.+.++
T Consensus 21 ~~~~l~D~tg~---~~~~~f~~--------~~~~~--~~~l~~g~~v~v~G~v~~-~~~~~~l~~~ 72 (84)
T cd04485 21 AFVTLEDLTGS---IEVVVFPE--------TYEKY--RDLLKEDALLLVEGKVER-RDGGLRLIAE 72 (84)
T ss_pred EEEEEEeCCCe---EEEEECHH--------HHHHH--HHHhcCCCEEEEEEEEEe-cCCceEEEee
Confidence 67888999888 78888842 24344 456888999988765322 2344444443
No 30
>PRK11507 ribosome-associated protein; Provisional
Probab=23.11 E-value=65 Score=26.86 Aligned_cols=25 Identities=36% Similarity=0.320 Sum_probs=20.2
Q ss_pred eEEecChhhhhhccCCCCCCEEEEE
Q 013565 198 YVMTKGWSRFVKDKKLDAGDVVSFH 222 (440)
Q Consensus 198 YVLTkGWs~FVKdKkLkaGDvVvF~ 222 (440)
.++-+|=-+..|.++|+.||+|.|-
T Consensus 38 ~V~VNGeve~rRgkKl~~GD~V~~~ 62 (70)
T PRK11507 38 QVKVDGAVETRKRCKIVAGQTVSFA 62 (70)
T ss_pred ceEECCEEecccCCCCCCCCEEEEC
Confidence 4555666788899999999999984
No 31
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=23.03 E-value=1.1e+02 Score=26.11 Aligned_cols=21 Identities=29% Similarity=0.349 Sum_probs=18.4
Q ss_pred hhhhhccCCCCCCEEEEEecc
Q 013565 205 SRFVKDKKLDAGDVVSFHRGV 225 (440)
Q Consensus 205 s~FVKdKkLkaGDvVvF~R~~ 225 (440)
-..++..+|+.||+|.+.|..
T Consensus 44 DPv~r~~g~k~GdVvkI~R~S 64 (79)
T PRK09570 44 DPVVKAIGAKPGDVIKIVRKS 64 (79)
T ss_pred ChhhhhcCCCCCCEEEEEECC
Confidence 377888899999999999974
No 32
>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=22.37 E-value=1.3e+02 Score=21.00 Aligned_cols=21 Identities=29% Similarity=0.469 Sum_probs=16.9
Q ss_pred CCeEEEEEeCCCCeEEEEEEE
Q 013565 171 KGLLLNFEDRNGKPWRFRYSY 191 (440)
Q Consensus 171 ~g~~L~veD~~GK~W~FRysy 191 (440)
.+..+.+.|..|..|+|.|--
T Consensus 4 ~g~l~~~~~p~G~~~~~~YD~ 24 (42)
T TIGR01643 4 AGRLTGSTDADGTTTRYTYDA 24 (42)
T ss_pred CCCEEEEECCCCCEEEEEECC
Confidence 456788889999999998653
No 33
>COG2336 MazE Growth regulator [Signal transduction mechanisms]
Probab=20.98 E-value=1.2e+02 Score=26.10 Aligned_cols=47 Identities=23% Similarity=0.369 Sum_probs=32.9
Q ss_pred EEEEeCCCcceEEecChhhhhhccCCCCCCEEEEEeccccCCCCeEEEEEEeCC
Q 013565 188 RYSYWNSSQSYVMTKGWSRFVKDKKLDAGDVVSFHRGVGDLAKGRLFIDWRRRS 241 (440)
Q Consensus 188 Rysywn~SrrYVLTkGWs~FVKdKkLkaGDvVvF~R~~~e~~~grLfIgIRRa~ 241 (440)
+.+.|++|.-..|=. ..+++-+|..||.|.+... .++.+.|...|+.
T Consensus 4 ~I~KWGNS~avrIP~---~l~kql~l~~g~~v~v~v~----n~~~i~~~p~rr~ 50 (82)
T COG2336 4 TIKKWGNSAAVRIPA---ALLKQLNLTIGDEVEVEVG----NDQSILIRPVRRR 50 (82)
T ss_pred ehhhhCCcceeeccH---HHHHHhCCCcCceEEEEEc----CCcEEEecccccc
Confidence 345677776566644 8999999999999999985 3445666544433
No 34
>PF05382 Amidase_5: Bacteriophage peptidoglycan hydrolase ; InterPro: IPR008044 This entry is represented by Bacteriophage SFi21, lysin (Cell wall hydrolase; 3.5.1.28 from EC). At least one of proteins in this entry, the Pal protein from the pneumococcal bacteriophage Dp-1 (O03979 from SWISSPROT) has been shown to be an N-acetylmuramoyl-L-alanine amidase []. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside within this domain while a C-terminal domain binds to the choline residues of the cell wall teichoic acids [, ].
Probab=20.54 E-value=72 Score=29.65 Aligned_cols=27 Identities=19% Similarity=0.519 Sum_probs=18.5
Q ss_pred eEEecChhhhhhc--cCCCCCCEEEEEec
Q 013565 198 YVMTKGWSRFVKD--KKLDAGDVVSFHRG 224 (440)
Q Consensus 198 YVLTkGWs~FVKd--KkLkaGDvVvF~R~ 224 (440)
.++..||...-+. ++|+.||+|++-+.
T Consensus 59 ~L~~~G~~~I~~~~~~~~q~GDI~I~g~~ 87 (145)
T PF05382_consen 59 WLKKNGFKKISENVDWNLQRGDIFIWGRR 87 (145)
T ss_pred HHhhCCcEEeccCCcccccCCCEEEEcCC
Confidence 3445666555544 58999999997554
Done!