Query 002489
Match_columns 916
No_of_seqs 257 out of 523
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 00:57:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002489.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002489hhsearch_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 99.6 1.2E-15 2.5E-20 134.3 10.5 99 367-468 1-100 (100)
2 PF07496 zf-CW: CW-type Zinc F 99.6 3.7E-16 7.9E-21 127.6 2.0 45 599-644 1-50 (50)
3 PF03754 DUF313: Domain of unk 97.8 4.1E-05 8.8E-10 73.1 6.4 79 361-440 18-114 (114)
4 PF09217 EcoRII-N: Restriction 97.7 8.6E-05 1.9E-09 74.2 6.8 89 364-452 7-110 (156)
5 smart00249 PHD PHD zinc finger 79.4 1.8 4E-05 32.8 2.7 30 597-626 10-45 (47)
6 PF10844 DUF2577: Protein of u 57.6 36 0.00078 32.0 6.7 78 364-463 18-97 (100)
7 smart00249 PHD PHD zinc finger 55.4 5.7 0.00012 30.1 0.9 25 77-101 10-34 (47)
8 PF04014 Antitoxin-MazE: Antid 50.0 26 0.00057 28.4 3.9 30 435-465 13-42 (47)
9 PF00628 PHD: PHD-finger; Int 40.4 20 0.00043 28.9 1.9 16 595-610 8-23 (51)
10 PF15396 FAM60A: Protein Famil 30.8 91 0.002 33.8 5.4 15 732-746 51-65 (213)
11 TIGR01439 lp_hng_hel_AbrB loop 27.2 1E+02 0.0022 23.8 3.8 28 435-463 13-40 (43)
12 PF02643 DUF192: Uncharacteriz 23.3 1.3E+02 0.0029 28.5 4.6 52 401-452 49-107 (108)
13 KOG4718 Non-SMC (structural ma 22.9 30 0.00065 37.5 0.2 19 82-100 195-213 (235)
14 COG2947 Uncharacterized conser 22.2 87 0.0019 32.4 3.2 30 435-466 36-65 (156)
15 COG2002 AbrB Regulators of sta 20.7 1.3E+02 0.0028 27.7 3.8 30 436-467 21-50 (89)
16 PHA02610 uvsY.-2 hypothetical 20.2 55 0.0012 28.6 1.2 21 712-732 3-30 (53)
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=99.64 E-value=1.2e-15 Score=134.34 Aligned_cols=99 Identities=23% Similarity=0.424 Sum_probs=70.1
Q ss_pred EEEecccccCCCCCcEEeehhhhhhcCCCCCCCCCceEEEEeCCCCeEEEEEEEcCCCCCccccccCchhhhhccCCCCC
Q 002489 367 FEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQLQAG 446 (916)
Q Consensus 367 FeKvLT~SDVgslGRLVIPK~~AEs~FPpLd~~eG~~L~v~D~~GK~WtFRfsyw~NN~SR~YVLeGWs~FVRsK~LqaG 446 (916)
|.|+|+++|+.+.++|+||++.++.|. +....++.|.++|..|+.|.+++.++. +..+.|+..||..||++++|++|
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~--~~~~~~~~v~l~~~~g~~W~v~~~~~~-~~~~~~l~~GW~~Fv~~n~L~~G 77 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHG--GNKRKSREVTLKDPDGRSWPVKLKYRK-NSGRYYLTGGWKKFVRDNGLKEG 77 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS----SS--CEEEEEETTTEEEEEEEEEEC-CTTEEEEETTHHHHHHHCT--TT
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhC--CCcCCCeEEEEEeCCCCEEEEEEEEEc-cCCeEEECCCHHHHHHHcCCCCC
Confidence 899999999998889999999999982 122357899999999999999999883 33443444699999999999999
Q ss_pred CEEEEEEec-CCCeEEEEEEeCC
Q 002489 447 DIVTFSRLE-PEGKLVMGFRKAS 468 (916)
Q Consensus 447 DtVVF~R~e-~~GkL~IGVRRas 468 (916)
|.|+|+... ...++.|.+.|++
T Consensus 78 D~~~F~~~~~~~~~~~v~i~~~~ 100 (100)
T PF02362_consen 78 DVCVFELIGNSNFTLKVHIFRKS 100 (100)
T ss_dssp -EEEEEE-SSSCE-EEEEEE---
T ss_pred CEEEEEEecCCCceEEEEEEECc
Confidence 999999975 3456799988863
No 2
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=99.59 E-value=3.7e-16 Score=127.57 Aligned_cols=45 Identities=42% Similarity=1.032 Sum_probs=30.3
Q ss_pred CceEecCCCccccccCCCC-----CCCCCcEeecCCCCCCCCCCCccccCC
Q 002489 599 IQWVQCEDCSKWRKVPANA-----RLPSKWTCSGNLWDPERSVCSVAQELR 644 (916)
Q Consensus 599 ~~WVQCD~C~KWRrLP~~~-----~lPdkW~CsmN~WDp~~~SCsaPEE~~ 644 (916)
+.|||||.|+|||+||.++ .+|+.|+|+||+ |+.+++|++|||.+
T Consensus 1 ~~WVQCd~C~KWR~lp~~~~~~~~~~~d~W~C~~n~-~~~~~sC~~pee~e 50 (50)
T PF07496_consen 1 DYWVQCDSCLKWRRLPEEVDPIREELPDPWYCSMNP-DPPFNSCDAPEEIE 50 (50)
T ss_dssp -EEEE-TTT--EEEE-CCHHCTSCCSSTT--GGGSS--CCC-STTS--SS-
T ss_pred CeEEECCCCCceeeCChhhCcccccCCCeEEcCCCC-CCCCCCCCCcccCC
Confidence 4799999999999999984 468999999999 89999999999963
No 3
>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=97.80 E-value=4.1e-05 Score=73.13 Aligned_cols=79 Identities=20% Similarity=0.368 Sum_probs=64.2
Q ss_pred CcccceEEEecccccCCC-CCcEEeehhhhhhcCCCCC---------------CCCCceEEEEeCCCCeEEEEEEEcCC-
Q 002489 361 SVITPLFEKMLSASDAGR-IGRLVLPKKCAEAYFPPIS---------------QPEGLPLKVQDSKGKEWIFQFRFWPN- 423 (916)
Q Consensus 361 s~~~~LFeKvLT~SDVgs-lGRLVIPK~~AEs~FPpLd---------------~~eG~~L~v~D~~GK~WtFRfsyw~N- 423 (916)
.....+|+|.|++|||.. ..||.||...... ..+|. ...|+.+.+.|..++.|..+++.|.-
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 EDPKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMG 96 (114)
T ss_pred CCCeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEeccc
Confidence 566899999999999995 6899999987643 23332 35789999999999999999999964
Q ss_pred CCCccccc-cCchhhhhc
Q 002489 424 NNSRMYVL-EGVTPCIQN 440 (916)
Q Consensus 424 N~SR~YVL-eGWs~FVRs 440 (916)
+..-.|+| .||.+.|.+
T Consensus 97 ~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 97 NGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CCceEEEEEcChHhhccC
Confidence 44668999 599998863
No 4
>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=97.68 E-value=8.6e-05 Score=74.22 Aligned_cols=89 Identities=21% Similarity=0.347 Sum_probs=58.5
Q ss_pred cceEEEecccccCCCC----CcEEeehhhhhhcCCCCCC----CCCceEEEEeCCC--CeEEEEEEEcCC----CCCccc
Q 002489 364 TPLFEKMLSASDAGRI----GRLVLPKKCAEAYFPPISQ----PEGLPLKVQDSKG--KEWIFQFRFWPN----NNSRMY 429 (916)
Q Consensus 364 ~~LFeKvLT~SDVgsl----GRLVIPK~~AEs~FPpLd~----~eG~~L~v~D~~G--K~WtFRfsyw~N----N~SR~Y 429 (916)
...|.|.||+.|++.+ .++.|||..++.+||.+.. .+.++|.+++..+ ..|+|||+|+-| ..+..|
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 4689999999999964 4899999999999998764 3558999999877 678899999932 236789
Q ss_pred cccCchhhhhccC-CCCCCEEEEE
Q 002489 430 VLEGVTPCIQNMQ-LQAGDIVTFS 452 (916)
Q Consensus 430 VLeGWs~FVRsK~-LqaGDtVVF~ 452 (916)
.+++|+.+..--+ =.+||.++|-
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 9999987766443 3689988876
No 5
>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=57.62 E-value=36 Score=31.99 Aligned_cols=78 Identities=14% Similarity=0.141 Sum_probs=44.6
Q ss_pred cceEEEecccccCC--CCCcEEeehhhhhhcCCCCCCCCCceEEEEeCCCCeEEEEEEEcCCCCCccccccCchhhhhcc
Q 002489 364 TPLFEKMLSASDAG--RIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNM 441 (916)
Q Consensus 364 ~~LFeKvLT~SDVg--slGRLVIPK~~AEs~FPpLd~~eG~~L~v~D~~GK~WtFRfsyw~NN~SR~YVLeGWs~FVRsK 441 (916)
...|-++++.+-+. -.++|+||++. -++|.+-......+.+....+. +- ..|.-..
T Consensus 18 ~i~~G~V~s~~PL~I~i~~~liL~~~~--L~i~~~l~~~~~~~~~~~~~~~----------------~~----~~i~~~~ 75 (100)
T PF10844_consen 18 DIVIGTVVSVPPLKIKIDQKLILDKDF--LIIPELLKDYTRDITIEHNSET----------------DN----ITITFTD 75 (100)
T ss_pred eeEEEEEEecccEEEEECCeEEEchHH--EEeehhccceEEEEEEeccccc----------------cc----eeEEEec
Confidence 44799999999733 23458888764 2344321112222222222110 00 0055667
Q ss_pred CCCCCCEEEEEEecCCCeEEEE
Q 002489 442 QLQAGDIVTFSRLEPEGKLVMG 463 (916)
Q Consensus 442 ~LqaGDtVVF~R~e~~GkL~IG 463 (916)
.|++||.|...+.+.+.+|+|=
T Consensus 76 ~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 76 GLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred CCcCCCEEEEEEecCCCEEEEE
Confidence 8999999999998644466653
No 7
>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 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=49.98 E-value=26 Score=28.44 Aligned_cols=30 Identities=23% Similarity=0.314 Sum_probs=23.6
Q ss_pred hhhhhccCCCCCCEEEEEEecCCCeEEEEEE
Q 002489 435 TPCIQNMQLQAGDIVTFSRLEPEGKLVMGFR 465 (916)
Q Consensus 435 s~FVRsK~LqaGDtVVF~R~e~~GkL~IGVR 465 (916)
.+|.+..+|++||.|.|.-.+ +|++.|--.
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~-~g~i~i~p~ 42 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEG-DGKIVIRPV 42 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEET-TSEEEEEES
T ss_pred HHHHHHcCCCCCCEEEEEEeC-CCEEEEEEC
Confidence 367888899999999999864 667776543
No 9
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=40.41 E-value=20 Score=28.89 Aligned_cols=16 Identities=25% Similarity=0.989 Sum_probs=0.0
Q ss_pred CCCcCceEecCCCccc
Q 002489 595 VGEKIQWVQCEDCSKW 610 (916)
Q Consensus 595 ~ge~~~WVQCD~C~KW 610 (916)
......|||||.|..|
T Consensus 8 ~~~~~~~i~C~~C~~~ 23 (51)
T PF00628_consen 8 SDDDGDMIQCDSCNRW 23 (51)
T ss_dssp SCTTSSEEEBSTTSCE
T ss_pred cCCCCCeEEcCCCChh
No 10
>PF15396 FAM60A: Protein Family FAM60A
Probab=30.84 E-value=91 Score=33.80 Aligned_cols=15 Identities=33% Similarity=0.946 Sum_probs=11.2
Q ss_pred ccchhhhhhhhhhhh
Q 002489 732 TCNVCLTVKRRFHTL 746 (916)
Q Consensus 732 tcnvc~tvkrrfktl 746 (916)
.||.|.-.=.|||.|
T Consensus 51 ICNACVLLVKRwKKL 65 (213)
T PF15396_consen 51 ICNACVLLVKRWKKL 65 (213)
T ss_pred hhHHHHHHHHHHhhC
Confidence 699998776777654
No 11
>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=27.15 E-value=1e+02 Score=23.83 Aligned_cols=28 Identities=21% Similarity=0.514 Sum_probs=22.8
Q ss_pred hhhhhccCCCCCCEEEEEEecCCCeEEEE
Q 002489 435 TPCIQNMQLQAGDIVTFSRLEPEGKLVMG 463 (916)
Q Consensus 435 s~FVRsK~LqaGDtVVF~R~e~~GkL~IG 463 (916)
.+|.+..++..||.|.|.... +|.+.|-
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~-~~~l~l~ 40 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVE-DGEIILR 40 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeC-CCEEEEE
Confidence 478999999999999999764 6777653
No 12
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=23.25 E-value=1.3e+02 Score=28.47 Aligned_cols=52 Identities=23% Similarity=0.273 Sum_probs=29.9
Q ss_pred CceEEEEeCCCCeEEEEEEEcCCC-------CCccccccCchhhhhccCCCCCCEEEEE
Q 002489 401 GLPLKVQDSKGKEWIFQFRFWPNN-------NSRMYVLEGVTPCIQNMQLQAGDIVTFS 452 (916)
Q Consensus 401 G~~L~v~D~~GK~WtFRfsyw~NN-------~SR~YVLeGWs~FVRsK~LqaGDtVVF~ 452 (916)
-+.|.+.|..|++=....-..|.. ..-.|||+-=..++..++|++||.|.|-
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 367777777777655554432211 1236899866777899999999999873
No 13
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=22.88 E-value=30 Score=37.51 Aligned_cols=19 Identities=37% Similarity=0.752 Sum_probs=15.9
Q ss_pred ccccccCCceeechhhhhh
Q 002489 82 RCCESCGKRVHCGCITSVH 100 (916)
Q Consensus 82 R~C~~CgKrlHCGCI~S~~ 100 (916)
+.|.+||-|.|||||.--.
T Consensus 195 ~rCg~c~i~~h~~c~qty~ 213 (235)
T KOG4718|consen 195 IRCGSCNIQYHRGCIQTYL 213 (235)
T ss_pred eccCcccchhhhHHHHHHh
Confidence 4688999999999998543
No 14
>COG2947 Uncharacterized conserved protein [Function unknown]
Probab=22.19 E-value=87 Score=32.45 Aligned_cols=30 Identities=13% Similarity=0.294 Sum_probs=21.6
Q ss_pred hhhhhccCCCCCCEEEEEEecCCCeEEEEEEe
Q 002489 435 TPCIQNMQLQAGDIVTFSRLEPEGKLVMGFRK 466 (916)
Q Consensus 435 s~FVRsK~LqaGDtVVF~R~e~~GkL~IGVRR 466 (916)
..|+|+ .+.||.+.||-..-.+-=++|+-+
T Consensus 36 RNfmR~--M~iGD~~fFYHSNc~~pgIvGl~~ 65 (156)
T COG2947 36 RNFMRD--MKIGDLGFFYHSNCKPPGIVGLAE 65 (156)
T ss_pred HHHHHh--cccCceEEEEecCCCCCCceehhh
Confidence 368888 789999999997545544555544
No 15
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=20.66 E-value=1.3e+02 Score=27.71 Aligned_cols=30 Identities=13% Similarity=0.279 Sum_probs=22.6
Q ss_pred hhhhccCCCCCCEEEEEEecCCCeEEEEEEeC
Q 002489 436 PCIQNMQLQAGDIVTFSRLEPEGKLVMGFRKA 467 (916)
Q Consensus 436 ~FVRsK~LqaGDtVVF~R~e~~GkL~IGVRRa 467 (916)
..-+..+|++||.|.|+.....|++ -++|.
T Consensus 21 eiR~~lgi~~Gd~lei~~~~~~~~i--vl~k~ 50 (89)
T COG2002 21 EIREALGIKEGDVLEIIVDGDGGRI--VLKKY 50 (89)
T ss_pred HHHHHhCCCCCCEEEEEEeCCCCEE--EEEEC
Confidence 4567789999999999998756773 34444
No 16
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=20.24 E-value=55 Score=28.64 Aligned_cols=21 Identities=48% Similarity=0.991 Sum_probs=17.2
Q ss_pred ceeeecCCCC-------CCCCCCCCccc
Q 002489 712 SCIVCIQPPS-------GKGPKHKQTCT 732 (916)
Q Consensus 712 scivCiqPps-------Gkgpkhk~tct 732 (916)
-|+||-||=. .+||-|-.-|-
T Consensus 3 iCvvCK~Pi~~al~v~T~~Gpvh~g~C~ 30 (53)
T PHA02610 3 ICVVCKQPIEKALVVETEKGPVHPGPCY 30 (53)
T ss_pred eeeeeCCchhhceEEecCCCCCCChhHH
Confidence 4999999954 68999998874
Done!