Query 005563
Match_columns 691
No_of_seqs 255 out of 548
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 01:26:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005563.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005563hhsearch_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 6.7E-16 1.5E-20 132.6 10.0 98 142-243 1-100 (100)
2 PF07496 zf-CW: CW-type Zinc F 99.6 1.9E-16 4.1E-21 125.8 2.0 45 374-419 1-50 (50)
3 PF03754 DUF313: Domain of unk 98.1 3.7E-06 8E-11 78.0 6.1 80 136-215 18-114 (114)
4 PF09217 EcoRII-N: Restriction 97.6 0.00012 2.5E-09 71.4 6.1 89 139-227 7-110 (156)
5 smart00249 PHD PHD zinc finger 76.1 2.6 5.6E-05 30.9 2.6 30 372-401 10-45 (47)
6 PF10844 DUF2577: Protein of u 56.1 41 0.0009 30.6 6.7 79 138-238 17-97 (100)
7 PF04014 Antitoxin-MazE: Antid 48.3 29 0.00062 27.3 3.8 29 211-240 14-42 (47)
8 PF00628 PHD: PHD-finger; Int 38.4 22 0.00048 27.7 1.8 31 371-401 9-46 (51)
9 PF02643 DUF192: Uncharacteriz 33.8 86 0.0019 28.8 5.1 52 176-227 49-107 (108)
10 PHA02610 uvsY.-2 hypothetical 29.9 28 0.00061 29.3 1.2 21 487-507 3-30 (53)
11 COG5132 BUD31 Cell cycle contr 25.8 22 0.00049 34.5 -0.0 20 488-510 102-121 (146)
12 TIGR01439 lp_hng_hel_AbrB loop 25.1 1.1E+02 0.0025 22.7 3.7 28 210-238 13-40 (43)
13 PF15396 FAM60A: Protein Famil 22.5 1.5E+02 0.0032 31.3 5.0 15 507-521 51-65 (213)
14 PF03120 DNA_ligase_OB: NAD-de 21.6 64 0.0014 29.1 2.0 32 210-242 42-74 (82)
15 PF09149 DUF1935: Domain of un 20.9 1.1E+02 0.0024 28.5 3.4 64 168-237 13-76 (104)
16 PRK03760 hypothetical protein; 20.2 1.6E+02 0.0034 27.9 4.3 27 202-228 90-116 (117)
17 COG2002 AbrB Regulators of sta 20.1 1.3E+02 0.0029 26.7 3.7 31 211-243 21-51 (89)
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=99.65 E-value=6.7e-16 Score=132.59 Aligned_cols=98 Identities=24% Similarity=0.437 Sum_probs=70.0
Q ss_pred EEEecccccCCCCCcEEeehhcccccCCCCCCCCCceEEEEeCCCCeEEEEEEEeCCCCCccccc-cCchhhhhccCCCC
Q 005563 142 FEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVL-EGVTPCIQNMQLQA 220 (691)
Q Consensus 142 F~KvLT~SDVgklgRLVIPK~~AE~~FPpL~~~~G~~L~v~D~~GK~W~FRfsyw~nn~SR~YVL-~GWs~FVrsK~Lqa 220 (691)
|.|+|+++|+....+|+||++.++.|. +....++.|.++|..|+.|.+++.++. +..+ |+| .||..||++++|++
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 112357899999999999999999883 3333 566 69999999999999
Q ss_pred CCEEEEEEec-CCCeEEEEEEecC
Q 005563 221 GDIVTFSRLE-PEGKLVMGFRKAS 243 (691)
Q Consensus 221 GDtVvF~R~e-~~GkL~IGVRRa~ 243 (691)
||+|+|+... ...++.|.+.|++
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 3446799998863
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=99.60 E-value=1.9e-16 Score=125.81 Aligned_cols=45 Identities=42% Similarity=1.032 Sum_probs=30.3
Q ss_pred CceEeccccccccccCCCC-----CCCCCcEeecCCCCCCCCCCCccccCC
Q 005563 374 IQWVQCEDCSKWRKVPANA-----RLPSKWTCSGNLWDPERSVCSVAQELR 419 (691)
Q Consensus 374 ~~WVQCD~C~KWRrLP~~~-----~lP~~W~CsmN~WDp~~~sCsaPEE~~ 419 (691)
+.|||||.|+|||+||..+ .+|+.|||+||+ |+.+++|++|||.+
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 4799999999999999885 478999999999 89999999999964
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=98.15 E-value=3.7e-06 Score=77.98 Aligned_cols=80 Identities=21% Similarity=0.424 Sum_probs=64.4
Q ss_pred CcccceEEEecccccCCC-CCcEEeehhccc--ccCCC-----C-------CCCCCceEEEEeCCCCeEEEEEEEeCC-C
Q 005563 136 SVITPLFEKMLSASDAGR-IGRLVLPKKCAE--AYFPP-----I-------SQPEGLPLKVQDSKGKEWIFQFRFWPN-N 199 (691)
Q Consensus 136 s~~~~LF~KvLT~SDVgk-lgRLVIPK~~AE--~~FPp-----L-------~~~~G~~L~v~D~~GK~W~FRfsyw~n-n 199 (691)
..+..+|+|.|++|||.. .+||.||..... .||-+ + ....|+.+.+.|..++.|..+++.|.- +
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 667899999999999995 789999987653 33322 2 235689999999999999999999964 4
Q ss_pred CCccccc-cCchhhhhc
Q 005563 200 NSRMYVL-EGVTPCIQN 215 (691)
Q Consensus 200 ~SR~YVL-~GWs~FVrs 215 (691)
.+-.|+| .||..+|.+
T Consensus 98 ~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 98 GTSNYVLNSGWNKVVED 114 (114)
T ss_pred CceEEEEEcChHhhccC
Confidence 5667999 599999863
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=97.59 E-value=0.00012 Score=71.36 Aligned_cols=89 Identities=21% Similarity=0.347 Sum_probs=57.4
Q ss_pred cceEEEecccccCCCC----CcEEeehhcccccCCCCCC----CCCceEEEEeCCC--CeEEEEEEEeCC----CCCccc
Q 005563 139 TPLFEKMLSASDAGRI----GRLVLPKKCAEAYFPPISQ----PEGLPLKVQDSKG--KEWIFQFRFWPN----NNSRMY 204 (691)
Q Consensus 139 ~~LF~KvLT~SDVgkl----gRLVIPK~~AE~~FPpL~~----~~G~~L~v~D~~G--K~W~FRfsyw~n----n~SR~Y 204 (691)
..+|.|.|++.|++.+ .+++|||..++.+||.+.. .+.+.|.+++..+ ..|+|||+|+-| ..+..|
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 5689999999999964 5899999988999987653 3458999999877 678899999922 245678
Q ss_pred cccCchhhhhccC-CCCCCEEEEE
Q 005563 205 VLEGVTPCIQNMQ-LQAGDIVTFS 227 (691)
Q Consensus 205 VL~GWs~FVrsK~-LqaGDtVvF~ 227 (691)
-++.|..+..--+ =.+||.++|.
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 8999997766433 3689977766
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=56.12 E-value=41 Score=30.60 Aligned_cols=79 Identities=14% Similarity=0.164 Sum_probs=45.0
Q ss_pred ccceEEEecccccCC--CCCcEEeehhcccccCCCCCCCCCceEEEEeCCCCeEEEEEEEeCCCCCccccccCchhhhhc
Q 005563 138 ITPLFEKMLSASDAG--RIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQN 215 (691)
Q Consensus 138 ~~~LF~KvLT~SDVg--klgRLVIPK~~AE~~FPpL~~~~G~~L~v~D~~GK~W~FRfsyw~nn~SR~YVL~GWs~FVrs 215 (691)
...+|-++++.+-+. -.++|+|+++. -++|..-......+.+..... .+-. .|.-.
T Consensus 17 ~~i~~G~V~s~~PL~I~i~~~liL~~~~--L~i~~~l~~~~~~~~~~~~~~----------------~~~~----~i~~~ 74 (100)
T PF10844_consen 17 VDIVIGTVVSVPPLKIKIDQKLILDKDF--LIIPELLKDYTRDITIEHNSE----------------TDNI----TITFT 74 (100)
T ss_pred ceeEEEEEEecccEEEEECCeEEEchHH--EEeehhccceEEEEEEecccc----------------ccce----eEEEe
Confidence 344799999999744 23458888753 334432111222222222111 0000 06666
Q ss_pred cCCCCCCEEEEEEecCCCeEEEE
Q 005563 216 MQLQAGDIVTFSRLEPEGKLVMG 238 (691)
Q Consensus 216 K~LqaGDtVvF~R~e~~GkL~IG 238 (691)
..|++||.|...+...+.+|+|=
T Consensus 75 ~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 75 DGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred cCCcCCCEEEEEEecCCCEEEEE
Confidence 78999999999998644466653
No 7
>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=48.27 E-value=29 Score=27.25 Aligned_cols=29 Identities=24% Similarity=0.323 Sum_probs=23.1
Q ss_pred hhhhccCCCCCCEEEEEEecCCCeEEEEEE
Q 005563 211 PCIQNMQLQAGDIVTFSRLEPEGKLVMGFR 240 (691)
Q Consensus 211 ~FVrsK~LqaGDtVvF~R~e~~GkL~IGVR 240 (691)
+|.+..+|++||.|.|.-.+ +|++.|--.
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~-~g~i~i~p~ 42 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEG-DGKIVIRPV 42 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEET-TSEEEEEES
T ss_pred HHHHHcCCCCCCEEEEEEeC-CCEEEEEEC
Confidence 67788899999999999874 667776543
No 8
>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=38.40 E-value=22 Score=27.65 Aligned_cols=31 Identities=19% Similarity=0.707 Sum_probs=21.1
Q ss_pred CCCCceEeccccccccccCC---CC----CCCCCcEee
Q 005563 371 GEKIQWVQCEDCSKWRKVPA---NA----RLPSKWTCS 401 (691)
Q Consensus 371 ge~~~WVQCD~C~KWRrLP~---~~----~lP~~W~Cs 401 (691)
.....||+||.|..|--+.= .. .....|+|.
T Consensus 9 ~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~ 46 (51)
T PF00628_consen 9 DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCP 46 (51)
T ss_dssp CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSH
T ss_pred CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECc
Confidence 45788999999999965441 11 223488885
No 9
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=33.80 E-value=86 Score=28.80 Aligned_cols=52 Identities=23% Similarity=0.273 Sum_probs=30.2
Q ss_pred CceEEEEeCCCCeEEEEEEEeCCC-------CCccccccCchhhhhccCCCCCCEEEEE
Q 005563 176 GLPLKVQDSKGKEWIFQFRFWPNN-------NSRMYVLEGVTPCIQNMQLQAGDIVTFS 227 (691)
Q Consensus 176 G~~L~v~D~~GK~W~FRfsyw~nn-------~SR~YVL~GWs~FVrsK~LqaGDtVvF~ 227 (691)
.+.|.+.|..|++=....-..|.. ..-.|||+-=..++..++|++||.|.|-
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 477788888887655554432211 1236899866677899999999999874
No 10
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=29.94 E-value=28 Score=29.31 Aligned_cols=21 Identities=48% Similarity=0.991 Sum_probs=17.3
Q ss_pred ceeeeccCCC-------CCCCCCCCccc
Q 005563 487 SCIVCIQPPS-------GKGPKHKQTCT 507 (691)
Q Consensus 487 ~civciqpps-------gkgpkhk~tct 507 (691)
-|+||-||=. .+||-|-.-|-
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 58999998884
No 11
>COG5132 BUD31 Cell cycle control protein, G10 family [Transcription / Cell division and chromosome partitioning]
Probab=25.85 E-value=22 Score=34.51 Aligned_cols=20 Identities=55% Similarity=1.215 Sum_probs=17.0
Q ss_pred eeeeccCCCCCCCCCCCccccch
Q 005563 488 CIVCIQPPSGKGPKHKQTCTCNV 510 (691)
Q Consensus 488 civciqppsgkgpkhk~tctcnv 510 (691)
|.-||||-.. ||-.||.|-|
T Consensus 102 CLRCIQ~~es---k~GstCICRV 121 (146)
T COG5132 102 CLRCIQPIES---KHGSTCICRV 121 (146)
T ss_pred hHhhcCcccc---cCCCEEEEeC
Confidence 8999999654 6889999976
No 12
>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=25.13 E-value=1.1e+02 Score=22.68 Aligned_cols=28 Identities=21% Similarity=0.514 Sum_probs=22.5
Q ss_pred hhhhhccCCCCCCEEEEEEecCCCeEEEE
Q 005563 210 TPCIQNMQLQAGDIVTFSRLEPEGKLVMG 238 (691)
Q Consensus 210 s~FVrsK~LqaGDtVvF~R~e~~GkL~IG 238 (691)
..|.+..++..||.|.|.... +|.+.|-
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~-~~~l~l~ 40 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVE-DGEIILR 40 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeC-CCEEEEE
Confidence 478899999999999999764 6666653
No 13
>PF15396 FAM60A: Protein Family FAM60A
Probab=22.50 E-value=1.5e+02 Score=31.34 Aligned_cols=15 Identities=33% Similarity=0.946 Sum_probs=11.6
Q ss_pred ccchhhhhhhhhhHh
Q 005563 507 TCNVCLTVKRRFHTL 521 (691)
Q Consensus 507 tcnvc~tvkrrfktl 521 (691)
.||.|.-.=.|||.|
T Consensus 51 ICNACVLLVKRwKKL 65 (213)
T PF15396_consen 51 ICNACVLLVKRWKKL 65 (213)
T ss_pred hhHHHHHHHHHHhhC
Confidence 699998877777655
No 14
>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=21.61 E-value=64 Score=29.11 Aligned_cols=32 Identities=22% Similarity=0.386 Sum_probs=21.4
Q ss_pred hhhhhccCCCCCCEEEEEEecCCC-eEEEEEEec
Q 005563 210 TPCIQNMQLQAGDIVTFSRLEPEG-KLVMGFRKA 242 (691)
Q Consensus 210 s~FVrsK~LqaGDtVvF~R~e~~G-kL~IGVRRa 242 (691)
.+|+++++|..||.|.++|.. +. -..+++-..
T Consensus 42 ~~~i~~~~i~~Gd~V~V~raG-dVIP~I~~vv~~ 74 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRAG-DVIPKIVGVVKE 74 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEET-TTEEEEEEE-GG
T ss_pred HHHHHHcCCCCCCEEEEEECC-CccceEeEeehh
Confidence 589999999999999999952 33 344555443
No 15
>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=20.94 E-value=1.1e+02 Score=28.48 Aligned_cols=64 Identities=22% Similarity=0.403 Sum_probs=33.4
Q ss_pred CCCCCCCCCceEEEEeCCCCeEEEEEEEeCCCCCccccccCchhhhhccCCCCCCEEEEEEecCCCeEEE
Q 005563 168 FPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQLQAGDIVTFSRLEPEGKLVM 237 (691)
Q Consensus 168 FPpL~~~~G~~L~v~D~~GK~W~FRfsyw~nn~SR~YVL~GWs~FVrsK~LqaGDtVvF~R~e~~GkL~I 237 (691)
+|-++..+|+-+++.|...+.|.|- |+++.|.+.=--.|-..-.+++.......+..++|.+.+
T Consensus 13 ~~cF~~~~GlLfRiv~~~~~~WaFY------NDT~~y~m~V~v~F~~~S~v~~lg~t~~~~~~~~g~~~~ 76 (104)
T PF09149_consen 13 YPCFKERNGLLFRIVDEKEGRWAFY------NDTKDYEMHVTVTFGPDSSVKPLGNTTVEREEEDGETVA 76 (104)
T ss_dssp EESSTTTT-SEEEEEETTTTEEEEE------E--SSEEEEEEEEEETT-EEEE-TT-EEEEE-TTSEEEE
T ss_pred EEeecCCCcEEEEEEECCCCEEEEE------eCCCcEEEEEEEEECCCCcEEECCCcEEEEecCCCcEEE
Confidence 3434343489999999888899873 566666654334444444455555444443334554443
No 16
>PRK03760 hypothetical protein; Provisional
Probab=20.17 E-value=1.6e+02 Score=27.91 Aligned_cols=27 Identities=22% Similarity=0.491 Sum_probs=21.1
Q ss_pred ccccccCchhhhhccCCCCCCEEEEEE
Q 005563 202 RMYVLEGVTPCIQNMQLQAGDIVTFSR 228 (691)
Q Consensus 202 R~YVL~GWs~FVrsK~LqaGDtVvF~R 228 (691)
-.|+|+==..++...++++||.|.|.+
T Consensus 90 a~~VLEl~aG~~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 90 ARYIIEGPVGKIRVLKVEVGDEIEWID 116 (117)
T ss_pred ceEEEEeCCChHHHcCCCCCCEEEEee
Confidence 348887444557889999999999876
No 17
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=20.14 E-value=1.3e+02 Score=26.70 Aligned_cols=31 Identities=16% Similarity=0.343 Sum_probs=22.6
Q ss_pred hhhhccCCCCCCEEEEEEecCCCeEEEEEEecC
Q 005563 211 PCIQNMQLQAGDIVTFSRLEPEGKLVMGFRKAS 243 (691)
Q Consensus 211 ~FVrsK~LqaGDtVvF~R~e~~GkL~IGVRRa~ 243 (691)
.+-+..+|++||.|.|+.....|+++ ++|..
T Consensus 21 eiR~~lgi~~Gd~lei~~~~~~~~iv--l~k~~ 51 (89)
T COG2002 21 EIREALGIKEGDVLEIIVDGDGGRIV--LKKYK 51 (89)
T ss_pred HHHHHhCCCCCCEEEEEEeCCCCEEE--EEECC
Confidence 44567899999999999987667743 44443
Done!