Query 007900
Match_columns 585
No_of_seqs 143 out of 405
Neff 3.4
Searched_HMMs 46136
Date Thu Mar 28 16:50:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007900.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007900hhsearch_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 1.9E-16 4E-21 133.0 10.5 98 359-460 1-100 (100)
2 PF03754 DUF313: Domain of unk 98.1 1.1E-05 2.5E-10 73.3 7.3 80 353-432 18-114 (114)
3 PF09217 EcoRII-N: Restriction 97.6 0.00014 2.9E-09 69.7 7.4 89 356-444 7-110 (156)
4 smart00249 PHD PHD zinc finger 67.7 2.7 5.8E-05 30.1 1.0 25 77-101 10-34 (47)
5 PF10844 DUF2577: Protein of u 67.6 24 0.00051 31.4 7.1 83 351-455 13-97 (100)
6 PF04014 Antitoxin-MazE: Antid 57.1 17 0.00036 27.9 3.7 31 427-458 13-43 (47)
7 KOG4718 Non-SMC (structural ma 34.2 15 0.00033 37.8 0.4 18 82-99 195-212 (235)
8 TIGR01439 lp_hng_hel_AbrB loop 32.5 76 0.0016 23.1 3.8 28 427-455 13-40 (43)
9 PF13248 zf-ribbon_3: zinc-rib 32.5 21 0.00046 24.7 0.8 15 77-91 12-26 (26)
10 PF02643 DUF192: Uncharacteriz 30.4 99 0.0021 27.7 4.8 52 393-444 49-107 (108)
11 COG1998 RPS31 Ribosomal protei 26.2 32 0.00069 28.3 0.9 6 89-94 36-41 (51)
12 PF03120 DNA_ligase_OB: NAD-de 25.3 51 0.0011 29.1 2.1 32 427-459 42-74 (82)
13 TIGR00375 conserved hypothetic 25.2 31 0.00067 37.8 0.8 43 54-106 238-281 (374)
14 COG2002 AbrB Regulators of sta 24.7 1E+02 0.0022 26.8 3.8 31 428-460 21-51 (89)
15 TIGR01643 YD_repeat_2x YD repe 24.6 1.1E+02 0.0024 22.2 3.4 21 392-412 4-24 (42)
16 PF09297 zf-NADH-PPase: NADH p 23.5 38 0.00082 24.3 0.8 24 58-90 5-30 (32)
17 PF09149 DUF1935: Domain of un 22.9 96 0.0021 28.3 3.4 68 385-458 13-80 (104)
18 COG2947 Uncharacterized conser 22.5 94 0.002 30.6 3.4 109 427-550 36-148 (156)
19 PF12760 Zn_Tnp_IS1595: Transp 22.0 49 0.0011 25.5 1.2 26 58-90 20-46 (46)
20 PRK03760 hypothetical protein; 21.7 1.6E+02 0.0035 27.2 4.7 27 419-445 90-116 (117)
21 COG5569 Uncharacterized conser 21.5 85 0.0018 29.2 2.7 27 429-455 78-104 (108)
22 PRK09838 periplasmic copper-bi 21.2 1.5E+02 0.0032 27.6 4.3 27 432-458 86-113 (115)
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=99.68 E-value=1.9e-16 Score=133.00 Aligned_cols=98 Identities=24% Similarity=0.437 Sum_probs=69.8
Q ss_pred EEEecccccCCCCCcEEeehhhhcccCCCCCCCCCceEEEEeCCCCeEEEEEEEcCCCCCcceec-cCchhhhhccCCCC
Q 007900 359 FEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVL-EGVTPCIQNMQLQA 437 (585)
Q Consensus 359 F~KvLT~SDVg~lgRLVIPKk~AE~~FP~L~~~eG~~L~v~D~~Gk~W~FRfrywpNn~SR~YVL-~GWs~FVRsK~Lqa 437 (585)
|.|+|+++|+.+.++|+||++.++.+. +....++.+.++|..|++|.+++.++. +..+ |++ .||.+||++++|++
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 FFKVLKPSDVSSSCRLIIPKEFAKKHG--GNKRKSREVTLKDPDGRSWPVKLKYRK-NSGR-YYLTGGWKKFVRDNGLKE 76 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS----SS--CEEEEEETTTEEEEEEEEEEC-CTTE-EEEETTHHHHHHHCT--T
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhC--CCcCCCeEEEEEeCCCCEEEEEEEEEc-cCCe-EEECCCHHHHHHHcCCCC
Confidence 899999999998889999999999982 112357899999999999999999873 3334 555 59999999999999
Q ss_pred CCEEEEEEec-CCCeEEEEEEeCC
Q 007900 438 GDIVTFSRLE-PEGKLVMGFRKAS 460 (585)
Q Consensus 438 GDtVvF~R~e-p~GkL~IGVRRa~ 460 (585)
||.|+|+... ...++.|.+.|++
T Consensus 77 GD~~~F~~~~~~~~~~~v~i~~~~ 100 (100)
T PF02362_consen 77 GDVCVFELIGNSNFTLKVHIFRKS 100 (100)
T ss_dssp T-EEEEEE-SSSCE-EEEEEE---
T ss_pred CCEEEEEEecCCCceEEEEEEECc
Confidence 9999999975 3346799998863
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=98.06 E-value=1.1e-05 Score=73.32 Aligned_cols=80 Identities=21% Similarity=0.427 Sum_probs=63.7
Q ss_pred CcccceEEEecccccCCC-CCcEEeehhhhcc--cCCC-----C-------CCCCCceEEEEeCCCCeEEEEEEEcCC-C
Q 007900 353 SVITPLFEKMLSASDAGR-IGRLVLPKKCAEA--YFPP-----I-------SQPEGLPLKVQDSKGKEWIFQFRFWPN-N 416 (585)
Q Consensus 353 s~~~~LF~KvLT~SDVg~-lgRLVIPKk~AE~--~FP~-----L-------~~~eG~~L~v~D~~Gk~W~FRfrywpN-n 416 (585)
..+..+|+|.|++|||.. .+||.||-..... +|=+ | ....|+.+.+.|..++.|..+++.|.- +
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 556789999999999995 7999999876533 2321 2 235789999999999999999999964 5
Q ss_pred CCcceecc-Cchhhhhc
Q 007900 417 NSRMYVLE-GVTPCIQN 432 (585)
Q Consensus 417 ~SR~YVL~-GWs~FVRs 432 (585)
.+-.|+|. ||.+.|++
T Consensus 98 ~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 98 GTSNYVLNSGWNKVVED 114 (114)
T ss_pred CceEEEEEcChHhhccC
Confidence 56689995 99999863
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=97.65 E-value=0.00014 Score=69.66 Aligned_cols=89 Identities=21% Similarity=0.347 Sum_probs=57.7
Q ss_pred cceEEEecccccCCCC----CcEEeehhhhcccCCCCCC----CCCceEEEEeCCC--CeEEEEEEEcCC----CCCcce
Q 007900 356 TPLFEKMLSASDAGRI----GRLVLPKKCAEAYFPPISQ----PEGLPLKVQDSKG--KEWIFQFRFWPN----NNSRMY 421 (585)
Q Consensus 356 ~~LF~KvLT~SDVg~l----gRLVIPKk~AE~~FP~L~~----~eG~~L~v~D~~G--k~W~FRfrywpN----n~SR~Y 421 (585)
...|.|.||+.|++.. .++.|||..++.+||.+.. .+.+.|.+++..+ ..|+||++|+-| ..+..|
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 4689999999999963 5899999988999988764 3458899999877 679999999933 246789
Q ss_pred eccCchhhhhccC-CCCCCEEEEE
Q 007900 422 VLEGVTPCIQNMQ-LQAGDIVTFS 444 (585)
Q Consensus 422 VL~GWs~FVRsK~-LqaGDtVvF~ 444 (585)
-++.|+....--+ =.+||.++|-
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 9999986665333 3689988876
No 4
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=67.56 E-value=24 Score=31.45 Aligned_cols=83 Identities=13% Similarity=0.175 Sum_probs=47.7
Q ss_pred CCCcccceEEEecccccCC--CCCcEEeehhhhcccCCCCCCCCCceEEEEeCCCCeEEEEEEEcCCCCCcceeccCchh
Q 007900 351 SNSVITPLFEKMLSASDAG--RIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTP 428 (585)
Q Consensus 351 ~ns~~~~LF~KvLT~SDVg--~lgRLVIPKk~AE~~FP~L~~~eG~~L~v~D~~Gk~W~FRfrywpNn~SR~YVL~GWs~ 428 (585)
.+.+....|-++++.+-+. -.++++|+++. -++|..-......+.+....+. ... .
T Consensus 13 ~~~p~~i~~G~V~s~~PL~I~i~~~liL~~~~--L~i~~~l~~~~~~~~~~~~~~~------------~~~--------~ 70 (100)
T PF10844_consen 13 ASNPVDIVIGTVVSVPPLKIKIDQKLILDKDF--LIIPELLKDYTRDITIEHNSET------------DNI--------T 70 (100)
T ss_pred cCCCceeEEEEEEecccEEEEECCeEEEchHH--EEeehhccceEEEEEEeccccc------------cce--------e
Confidence 3344445899999999743 23459998852 3455421222233333322110 000 0
Q ss_pred hhhccCCCCCCEEEEEEecCCCeEEEE
Q 007900 429 CIQNMQLQAGDIVTFSRLEPEGKLVMG 455 (585)
Q Consensus 429 FVRsK~LqaGDtVvF~R~ep~GkL~IG 455 (585)
|.-...|++||.|...|.+.+.+|+|=
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 556678999999999997644466664
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=57.13 E-value=17 Score=27.93 Aligned_cols=31 Identities=26% Similarity=0.329 Sum_probs=24.1
Q ss_pred hhhhhccCCCCCCEEEEEEecCCCeEEEEEEe
Q 007900 427 TPCIQNMQLQAGDIVTFSRLEPEGKLVMGFRK 458 (585)
Q Consensus 427 s~FVRsK~LqaGDtVvF~R~ep~GkL~IGVRR 458 (585)
.++.+..+|++||.|.|.-. .+|++.|.-.+
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~-~~g~i~i~p~~ 43 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVE-GDGKIVIRPVK 43 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEE-TTSEEEEEEST
T ss_pred HHHHHHcCCCCCCEEEEEEe-CCCEEEEEECC
Confidence 36788889999999999986 36677765443
No 7
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=34.21 E-value=15 Score=37.77 Aligned_cols=18 Identities=39% Similarity=0.829 Sum_probs=15.4
Q ss_pred cccccCCCcceechhhhh
Q 007900 82 RCCESCGKRVHCGCITSV 99 (585)
Q Consensus 82 R~C~~C~KrlHCGCIaS~ 99 (585)
+.|.+||-|.|||||.--
T Consensus 195 ~rCg~c~i~~h~~c~qty 212 (235)
T KOG4718|consen 195 IRCGSCNIQYHRGCIQTY 212 (235)
T ss_pred eccCcccchhhhHHHHHH
Confidence 468899999999999753
No 8
>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=32.53 E-value=76 Score=23.05 Aligned_cols=28 Identities=21% Similarity=0.514 Sum_probs=22.7
Q ss_pred hhhhhccCCCCCCEEEEEEecCCCeEEEE
Q 007900 427 TPCIQNMQLQAGDIVTFSRLEPEGKLVMG 455 (585)
Q Consensus 427 s~FVRsK~LqaGDtVvF~R~ep~GkL~IG 455 (585)
.+|.+..++..||.|.+.... +|.+.|-
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~-~~~l~l~ 40 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVE-DGEIILR 40 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeC-CCEEEEE
Confidence 478999999999999999763 6766653
No 9
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=32.51 E-value=21 Score=24.69 Aligned_cols=15 Identities=20% Similarity=0.662 Sum_probs=12.4
Q ss_pred CCCCccccccCCCcc
Q 007900 77 NASGWRCCESCGKRV 91 (585)
Q Consensus 77 ~~sGWR~C~~C~Krl 91 (585)
.+.++|-|..||.+|
T Consensus 12 ~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 12 IDPDAKFCPNCGAKL 26 (26)
T ss_pred CCcccccChhhCCCC
Confidence 467899999999875
No 10
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=30.35 E-value=99 Score=27.75 Aligned_cols=52 Identities=23% Similarity=0.273 Sum_probs=29.4
Q ss_pred CceEEEEeCCCCeEEEEEEEcCCC-------CCcceeccCchhhhhccCCCCCCEEEEE
Q 007900 393 GLPLKVQDSKGKEWIFQFRFWPNN-------NSRMYVLEGVTPCIQNMQLQAGDIVTFS 444 (585)
Q Consensus 393 G~~L~v~D~~Gk~W~FRfrywpNn-------~SR~YVL~GWs~FVRsK~LqaGDtVvF~ 444 (585)
.+.|.+.|..|++=....-..|.. ..-.|+|+-=..++.+.++++||.|.|-
T Consensus 49 pLDi~fld~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~~aG~~~~~~i~~Gd~v~~~ 107 (108)
T PF02643_consen 49 PLDIAFLDSDGRVVKIERMVPPWRTYPCPSYKPARYVLELPAGWFEKLGIKVGDRVRIE 107 (108)
T ss_dssp -EEEEEE-TTSBEEEEEEEE-TT--S-EEECCEECEEEEEETTHHHHHT--TT-EEE--
T ss_pred eEEEEEECCCCeEEEEEccCCCCccCCCCCCCccCEEEEcCCCchhhcCCCCCCEEEec
Confidence 367777777776555554432221 1236888855667889999999999873
No 11
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=26.18 E-value=32 Score=28.27 Aligned_cols=6 Identities=50% Similarity=1.104 Sum_probs=4.5
Q ss_pred Ccceec
Q 007900 89 KRVHCG 94 (585)
Q Consensus 89 KrlHCG 94 (585)
+|+|||
T Consensus 36 dR~~CG 41 (51)
T COG1998 36 DRWACG 41 (51)
T ss_pred ceeEec
Confidence 488887
No 12
>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=25.27 E-value=51 Score=29.07 Aligned_cols=32 Identities=22% Similarity=0.377 Sum_probs=21.7
Q ss_pred hhhhhccCCCCCCEEEEEEecCCC-eEEEEEEeC
Q 007900 427 TPCIQNMQLQAGDIVTFSRLEPEG-KLVMGFRKA 459 (585)
Q Consensus 427 s~FVRsK~LqaGDtVvF~R~ep~G-kL~IGVRRa 459 (585)
.+|+++++|..||.|.++|. .+. -.++++-+.
T Consensus 42 ~~~i~~~~i~~Gd~V~V~ra-GdVIP~I~~vv~~ 74 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRA-GDVIPKIVGVVKE 74 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEE-TTTEEEEEEE-GG
T ss_pred HHHHHHcCCCCCCEEEEEEC-CCccceEeEeehh
Confidence 58999999999999999995 233 355555443
No 13
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=25.22 E-value=31 Score=37.76 Aligned_cols=43 Identities=23% Similarity=0.339 Sum_probs=28.9
Q ss_pred HHHHhh-ccccccccccccccccCCCCCccccccCCCcceechhhhhhhhhhhh
Q 007900 54 LTLILC-VYRSIYEEGRFCDTFHVNASGWRCCESCGKRVHCGCITSVHAFTLLD 106 (585)
Q Consensus 54 ~~a~LC-~CgsayE~~~FCe~FH~~~sGWR~C~~C~KrlHCGCIaS~~~~~lLD 106 (585)
|+-+-| +|+.-|+.. + ..+-||+ |. |||+|-=| |.--..+|=|
T Consensus 238 Yh~~~c~~C~~~~~~~---~---~~~~~~~-Cp-CG~~i~~G--V~~Rv~eLad 281 (374)
T TIGR00375 238 YHQTACEACGEPAVSE---D---AETACAN-CP-CGGRIKKG--VSDRLRELSD 281 (374)
T ss_pred cchhhhcccCCcCCch---h---hhhcCCC-CC-CCCcceec--hHHHHHHHhc
Confidence 778889 998877643 1 1233788 88 99998766 4445556656
No 14
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=24.73 E-value=1e+02 Score=26.82 Aligned_cols=31 Identities=13% Similarity=0.268 Sum_probs=23.2
Q ss_pred hhhhccCCCCCCEEEEEEecCCCeEEEEEEeCC
Q 007900 428 PCIQNMQLQAGDIVTFSRLEPEGKLVMGFRKAS 460 (585)
Q Consensus 428 ~FVRsK~LqaGDtVvF~R~ep~GkL~IGVRRa~ 460 (585)
..-+..++++||.|.|+.....|+ |-++|..
T Consensus 21 eiR~~lgi~~Gd~lei~~~~~~~~--ivl~k~~ 51 (89)
T COG2002 21 EIREALGIKEGDVLEIIVDGDGGR--IVLKKYK 51 (89)
T ss_pred HHHHHhCCCCCCEEEEEEeCCCCE--EEEEECC
Confidence 556788999999999999865576 4445544
No 15
>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=24.62 E-value=1.1e+02 Score=22.24 Aligned_cols=21 Identities=14% Similarity=0.213 Sum_probs=17.9
Q ss_pred CCceEEEEeCCCCeEEEEEEE
Q 007900 392 EGLPLKVQDSKGKEWIFQFRF 412 (585)
Q Consensus 392 eG~~L~v~D~~Gk~W~FRfry 412 (585)
.|..+.+.|..|..|+|.|--
T Consensus 4 ~g~l~~~~~p~G~~~~~~YD~ 24 (42)
T TIGR01643 4 AGRLTGSTDADGTTTRYTYDA 24 (42)
T ss_pred CCCEEEEECCCCCEEEEEECC
Confidence 578889999999999999754
No 16
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=23.50 E-value=38 Score=24.30 Aligned_cols=24 Identities=33% Similarity=0.861 Sum_probs=12.8
Q ss_pred hh-ccccccccccccccccCCCCCc-cccccCCCc
Q 007900 58 LC-VYRSIYEEGRFCDTFHVNASGW-RCCESCGKR 90 (585)
Q Consensus 58 LC-~CgsayE~~~FCe~FH~~~sGW-R~C~~C~Kr 90 (585)
-| +||+.-+ ..+.|| |-|..||..
T Consensus 5 fC~~CG~~t~---------~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTK---------PAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEE---------E-SSSS-EEESSSS-E
T ss_pred ccCcCCcccc---------CCCCcCEeECCCCcCE
Confidence 36 7776543 345677 679999865
No 17
>PF09149 DUF1935: Domain of unknown function (DUF1935); InterPro: IPR015232 This entry represents a conserved region found in various bacterial and eukaryotic hypothetical proteins, as well as in the cysteine protease calpain. Its function has not, as yet, been defined. ; PDB: 1R75_A 2FE0_A.
Probab=22.89 E-value=96 Score=28.25 Aligned_cols=68 Identities=21% Similarity=0.358 Sum_probs=39.7
Q ss_pred CCCCCCCCCceEEEEeCCCCeEEEEEEEcCCCCCcceeccCchhhhhccCCCCCCEEEEEEecCCCeEEEEEEe
Q 007900 385 FPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQLQAGDIVTFSRLEPEGKLVMGFRK 458 (585)
Q Consensus 385 FP~L~~~eG~~L~v~D~~Gk~W~FRfrywpNn~SR~YVL~GWs~FVRsK~LqaGDtVvF~R~ep~GkL~IGVRR 458 (585)
.|-++..+|+..++.|...+.|-|- |+++.|.+.=--.|-..-.+++.+.....+.+++|.+.+.+--
T Consensus 13 ~~cF~~~~GlLfRiv~~~~~~WaFY------NDT~~y~m~V~v~F~~~S~v~~lg~t~~~~~~~~g~~~~~v~V 80 (104)
T PF09149_consen 13 YPCFKERNGLLFRIVDEKEGRWAFY------NDTKDYEMHVTVTFGPDSSVKPLGNTTVEREEEDGETVAEVVV 80 (104)
T ss_dssp EESSTTTT-SEEEEEETTTTEEEEE------E--SSEEEEEEEEEETT-EEEE-TT-EEEEE-TTSEEEEEEEE
T ss_pred EEeecCCCcEEEEEEECCCCEEEEE------eCCCcEEEEEEEEECCCCcEEECCCcEEEEecCCCcEEEEEEE
Confidence 3333344499999999888899873 6777777764445555555677665566644567766555443
No 18
>COG2947 Uncharacterized conserved protein [Function unknown]
Probab=22.53 E-value=94 Score=30.61 Aligned_cols=109 Identities=17% Similarity=0.199 Sum_probs=52.2
Q ss_pred hhhhhccCCCCCCEEEEEEecCCCeEEEEEEeCC--CCcCccchhhccccCCCCCCCCCCCCCCCCCccccccccchhcc
Q 007900 427 TPCIQNMQLQAGDIVTFSRLEPEGKLVMGFRKAS--SASASDQDNEANKAGTGIPANGHAELADPSSWSKVDKSGYIATE 504 (585)
Q Consensus 427 s~FVRsK~LqaGDtVvF~R~ep~GkL~IGVRRa~--~~~~s~q~~~~~~~~~g~~~~~~~~~~~~~~~~k~~~~~~~~~~ 504 (585)
..|+|+ .+.||.+.||-..-.+-=++|+-+-. ..+.+.|.... +..-.-.+..++--|.-||-.-.+.-.
T Consensus 36 RNfmR~--M~iGD~~fFYHSNc~~pgIvGl~~V~~~a~pD~tq~d~~------spYyDPka~~e~pRW~~Vdv~~v~~~~ 107 (156)
T COG2947 36 RNFMRD--MKIGDLGFFYHSNCKPPGIVGLAEVCALAHPDPTQFDPA------SPYYDPKATPEDPRWYCVDVRFVRKLP 107 (156)
T ss_pred HHHHHh--cccCceEEEEecCCCCCCceehhhhhhccCCCccccCCC------CcccCcccccCCCCeeEEeeHHHhhcC
Confidence 368888 78999999999754444445554432 22222222211 111122333445567776654333222
Q ss_pred ccCCCcccccccccccCC--CccceeeecchhhhhhhhcHHHHhcccC
Q 007900 505 ALGAKSSISRKRKNTTLG--SKSKRLKIENEDVIELKLTWEEAQGLLR 550 (585)
Q Consensus 505 ~~~~~~~~~~kk~~~~iG--~k~krl~~~~~d~~eLKlTweeaq~llr 550 (585)
-+..-.-+....+.-.++ .|+-||-|- .+|=||+|.+|+
T Consensus 108 ~~vtL~~lK~~~~~~~~~~l~~g~RLSV~-------PVt~~ew~~i~~ 148 (156)
T COG2947 108 RPVTLKELKANPELAEMSLLVKGNRLSVQ-------PVTPEEWKEILR 148 (156)
T ss_pred CCccHHHHhcCcchhhhhhhhccCeeeee-------eCCHHHHHHHHH
Confidence 221111121223333333 467788774 345555555543
No 19
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=22.00 E-value=49 Score=25.46 Aligned_cols=26 Identities=23% Similarity=0.645 Sum_probs=17.9
Q ss_pred hh-ccccccccccccccccCCCCCccccccCCCc
Q 007900 58 LC-VYRSIYEEGRFCDTFHVNASGWRCCESCGKR 90 (585)
Q Consensus 58 LC-~CgsayE~~~FCe~FH~~~sGWR~C~~C~Kr 90 (585)
-| +||+. +.+.....+-..|..|+++
T Consensus 20 ~CP~Cg~~-------~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 20 VCPHCGST-------KHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCe-------eeEEeCCCCeEECCCCCCc
Confidence 38 99985 2233344788899999875
No 20
>PRK03760 hypothetical protein; Provisional
Probab=21.71 E-value=1.6e+02 Score=27.16 Aligned_cols=27 Identities=22% Similarity=0.491 Sum_probs=20.7
Q ss_pred cceeccCchhhhhccCCCCCCEEEEEE
Q 007900 419 RMYVLEGVTPCIQNMQLQAGDIVTFSR 445 (585)
Q Consensus 419 R~YVL~GWs~FVRsK~LqaGDtVvF~R 445 (585)
-.|+|+==..++.+.++++||.|.|.+
T Consensus 90 a~~VLEl~aG~~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 90 ARYIIEGPVGKIRVLKVEVGDEIEWID 116 (117)
T ss_pred ceEEEEeCCChHHHcCCCCCCEEEEee
Confidence 348887334456789999999999876
No 21
>COG5569 Uncharacterized conserved protein [Function unknown]
Probab=21.50 E-value=85 Score=29.21 Aligned_cols=27 Identities=30% Similarity=0.308 Sum_probs=21.2
Q ss_pred hhhccCCCCCCEEEEEEecCCCeEEEE
Q 007900 429 CIQNMQLQAGDIVTFSRLEPEGKLVMG 455 (585)
Q Consensus 429 FVRsK~LqaGDtVvF~R~ep~GkL~IG 455 (585)
=..=.+|++||.|.|--...+|++.+.
T Consensus 78 ~a~lsglKeGdkV~fvferv~gk~tv~ 104 (108)
T COG5569 78 QAKLSGLKEGDKVEFVFERVNGKLTVQ 104 (108)
T ss_pred HHHhhccccCCcEEEEEEeeCCEEEEE
Confidence 344578999999998877789987664
No 22
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=21.19 E-value=1.5e+02 Score=27.59 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=19.6
Q ss_pred ccCCCCCCEEEEEE-ecCCCeEEEEEEe
Q 007900 432 NMQLQAGDIVTFSR-LEPEGKLVMGFRK 458 (585)
Q Consensus 432 sK~LqaGDtVvF~R-~ep~GkL~IGVRR 458 (585)
-.+|++||.|.|.- .+.++.+++.+|+
T Consensus 86 l~~lk~G~~V~F~~~~~~~~~~i~~i~~ 113 (115)
T PRK09838 86 MSEIKTGDKVAFNFVQQGNLSLLQDIKV 113 (115)
T ss_pred hccCCCCCEEEEEEEEcCCcEEEEEEee
Confidence 45899999999954 3455566677765
Done!