Query 008961
Match_columns 547
No_of_seqs 246 out of 499
Neff 3.7
Searched_HMMs 46136
Date Thu Mar 28 18:42:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008961.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008961hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07496 zf-CW: CW-type Zinc F 99.6 6.2E-17 1.4E-21 125.4 1.8 45 230-275 1-50 (50)
2 PF02362 B3: B3 DNA binding do 99.6 3.1E-15 6.8E-20 125.5 9.8 96 1-99 4-100 (100)
3 PF09217 EcoRII-N: Restriction 97.8 4.2E-05 9.1E-10 72.6 6.2 82 1-83 13-110 (156)
4 PF03754 DUF313: Domain of unk 97.1 0.0012 2.6E-08 60.0 6.2 69 1-70 27-113 (114)
5 smart00249 PHD PHD zinc finger 80.2 1.8 3.8E-05 30.9 2.7 30 228-257 10-45 (47)
6 PF04014 Antitoxin-MazE: Antid 62.0 14 0.00031 28.1 4.0 29 66-95 13-41 (47)
7 PF00628 PHD: PHD-finger; Int 45.0 16 0.00034 27.6 1.8 32 226-257 8-46 (51)
8 TIGR01439 lp_hng_hel_AbrB loop 37.8 60 0.0013 23.4 3.9 27 66-93 13-39 (43)
9 PHA02610 uvsY.-2 hypothetical 37.0 19 0.0004 29.4 1.2 21 343-363 3-30 (53)
10 PF10844 DUF2577: Protein of u 34.6 59 0.0013 28.7 4.1 27 68-94 71-97 (100)
11 PF03120 DNA_ligase_OB: NAD-de 31.1 39 0.00085 29.5 2.3 36 66-101 42-77 (82)
12 PF02643 DUF192: Uncharacteriz 30.4 1.1E+02 0.0023 27.3 5.1 51 33-83 50-107 (108)
13 COG5132 BUD31 Cell cycle contr 30.3 17 0.00037 34.3 0.0 20 344-366 102-121 (146)
14 COG2002 AbrB Regulators of sta 26.8 82 0.0018 27.2 3.6 24 70-93 24-47 (89)
15 PF01878 EVE: EVE domain; Int 25.9 65 0.0014 29.4 3.0 27 72-98 38-64 (143)
16 KOG3794 CBF1-interacting corep 24.3 40 0.00087 37.3 1.5 23 225-247 117-139 (453)
17 TIGR01643 YD_repeat_2x YD repe 23.7 1.1E+02 0.0025 22.0 3.3 22 31-52 4-25 (42)
18 TIGR00223 panD L-aspartate-alp 23.6 4E+02 0.0087 25.4 7.6 72 2-84 15-89 (126)
19 PRK03760 hypothetical protein; 22.4 1.6E+02 0.0035 27.0 4.8 49 30-84 68-116 (117)
20 COG4384 Mu-like prophage prote 22.4 1.2E+02 0.0026 30.7 4.2 30 70-99 92-127 (203)
21 PRK09838 periplasmic copper-bi 20.9 1.5E+02 0.0032 27.4 4.2 29 70-98 85-114 (115)
22 PF10886 DUF2685: Protein of u 20.8 50 0.0011 27.1 1.1 20 343-362 3-29 (54)
23 TIGR02609 doc_partner putative 20.6 1.5E+02 0.0031 25.0 3.8 33 60-94 10-42 (74)
No 1
>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=99.63 E-value=6.2e-17 Score=125.43 Aligned_cols=45 Identities=42% Similarity=1.032 Sum_probs=30.4
Q ss_pred CceEecCCcccccccCCCC-----CCCCCcEeecCCCCCCCCCCCcccccC
Q 008961 230 IQWVQCEDCSKWRKVPANA-----RLPSKWTCSGNLWDPERSVCSVAQELR 275 (547)
Q Consensus 230 ~~WVQCD~C~KWRrLP~~~-----~lP~~W~CsmN~WDp~~~sCsaPEE~~ 275 (547)
+.|||||.|+|||+||.++ .+|+.|+|+||+ |+.+++|++|||.+
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 4799999999999999987 468999999999 99999999999863
No 2
>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=99.61 E-value=3.1e-15 Score=125.53 Aligned_cols=96 Identities=22% Similarity=0.415 Sum_probs=67.3
Q ss_pred CCCcCcCCCCCcEEeehhhhhhcCCCCCCCCCceEEEEeCCCCeEEEEEEEcCCCCCcceeecCchhHhhhcCCCCCCEE
Q 008961 1 MLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQLQAGDIV 80 (547)
Q Consensus 1 vLT~SDVg~lgRLVIPK~~AE~~FP~Ld~~~G~~L~v~D~~Gk~W~FR~~yw~Nn~SR~YLLtGWs~FVRsK~LqaGDtV 80 (547)
+|+++|+...++|.||++.++.|. +....++.|.+.|..|+.|.+++.++. +..+.|+..||..||++++|++||.|
T Consensus 4 ~l~~s~~~~~~~l~iP~~f~~~~~--~~~~~~~~v~l~~~~g~~W~v~~~~~~-~~~~~~l~~GW~~Fv~~n~L~~GD~~ 80 (100)
T PF02362_consen 4 VLKPSDVSSSCRLIIPKEFAKKHG--GNKRKSREVTLKDPDGRSWPVKLKYRK-NSGRYYLTGGWKKFVRDNGLKEGDVC 80 (100)
T ss_dssp E--TTCCCCTT-EEE-HHHHTTTS----SS--CEEEEEETTTEEEEEEEEEEC-CTTEEEEETTHHHHHHHCT--TT-EE
T ss_pred EEEccCcCCCCEEEeCHHHHHHhC--CCcCCCeEEEEEeCCCCEEEEEEEEEc-cCCeEEECCCHHHHHHHcCCCCCCEE
Confidence 478999998889999999999982 222357899999999999999999883 44454555699999999999999999
Q ss_pred EEEEec-CCCeEEEEEEecC
Q 008961 81 TFSRLE-PEGKLVMGFRKAS 99 (547)
Q Consensus 81 vF~R~e-~~GkL~IGvRRa~ 99 (547)
+|+... ...++.|.+.|++
T Consensus 81 ~F~~~~~~~~~~~v~i~~~~ 100 (100)
T PF02362_consen 81 VFELIGNSNFTLKVHIFRKS 100 (100)
T ss_dssp EEEE-SSSCE-EEEEEE---
T ss_pred EEEEecCCCceEEEEEEECc
Confidence 999875 3456799988763
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=97.79 E-value=4.2e-05 Score=72.58 Aligned_cols=82 Identities=24% Similarity=0.398 Sum_probs=53.2
Q ss_pred CCCcCcCCCCC----cEEeehhhhhhcCCCCCC----CCCceEEEEeCCC--CeEEEEEEEcCCC-----CCcceeecCc
Q 008961 1 MLSASDAGRIG----RLVLPKKCAEAYFPPISQ----PEGLPLKVQDSKG--KEWIFQFRFWPNN-----NSRMYVLEGV 65 (547)
Q Consensus 1 vLT~SDVg~lg----RLVIPK~~AE~~FP~Ld~----~~G~~L~v~D~~G--k~W~FR~~yw~Nn-----~SR~YLLtGW 65 (547)
.||+.|+|.+| ++.|||..++.+||.+.. .+...|.+++..+ ..|.|||+|+ || .+..|.+++|
T Consensus 13 ~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYY-nn~~~~gTRNE~RIT~~ 91 (156)
T PF09217_consen 13 RLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYY-NNRLFGGTRNEYRITRF 91 (156)
T ss_dssp E--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE--CCCTTSS--EEEEE--
T ss_pred EccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEE-cccccCCCcCceEEeee
Confidence 48999999764 899999999999998764 4568899999877 6789999999 44 3678999999
Q ss_pred hhHhhhcC-CCCCCEEEEE
Q 008961 66 TPCIQNMQ-LQAGDIVTFS 83 (547)
Q Consensus 66 s~FVRsK~-LqaGDtVvF~ 83 (547)
+.+..--+ =.+||.++|.
T Consensus 92 G~~~~~~~~~~tGaL~vla 110 (156)
T PF09217_consen 92 GRGFPLQNPENTGALLVLA 110 (156)
T ss_dssp -TTSGGG-GGGTT-EEEEE
T ss_pred cCCCccCCccccccEEEEE
Confidence 86665333 3678888776
No 4
>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=97.07 E-value=0.0012 Score=59.97 Aligned_cols=69 Identities=20% Similarity=0.406 Sum_probs=55.0
Q ss_pred CCCcCcCC-CCCcEEeehhhhhhcCCCCC---------------CCCCceEEEEeCCCCeEEEEEEEcCC-CCCcceeec
Q 008961 1 MLSASDAG-RIGRLVLPKKCAEAYFPPIS---------------QPEGLPLKVQDSKGKEWIFQFRFWPN-NNSRMYVLE 63 (547)
Q Consensus 1 vLT~SDVg-~lgRLVIPK~~AE~~FP~Ld---------------~~~G~~L~v~D~~Gk~W~FR~~yw~N-n~SR~YLLt 63 (547)
.|++|||. ..+||.||...... ..+|. ...|+.+.+.|..++.|..+++.|.- +..-.|+|.
T Consensus 27 ~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~~~~YvL~ 105 (114)
T PF03754_consen 27 TLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNGTSNYVLN 105 (114)
T ss_pred eecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCCceEEEEE
Confidence 48999998 56899999877643 23332 35789999999999999999999964 445679996
Q ss_pred -CchhHhh
Q 008961 64 -GVTPCIQ 70 (547)
Q Consensus 64 -GWs~FVR 70 (547)
||..+|.
T Consensus 106 ~gWn~VV~ 113 (114)
T PF03754_consen 106 SGWNKVVE 113 (114)
T ss_pred cChHhhcc
Confidence 9999886
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 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=61.96 E-value=14 Score=28.08 Aligned_cols=29 Identities=24% Similarity=0.347 Sum_probs=23.4
Q ss_pred hhHhhhcCCCCCCEEEEEEecCCCeEEEEE
Q 008961 66 TPCIQNMQLQAGDIVTFSRLEPEGKLVMGF 95 (547)
Q Consensus 66 s~FVRsK~LqaGDtVvF~R~e~~GkL~IGv 95 (547)
.+|.+..+|++||.|.|.-.+ +|++.|--
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~-~g~i~i~p 41 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEG-DGKIVIRP 41 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEET-TSEEEEEE
T ss_pred HHHHHHcCCCCCCEEEEEEeC-CCEEEEEE
Confidence 367888899999999999864 66787754
No 7
>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=44.98 E-value=16 Score=27.65 Aligned_cols=32 Identities=19% Similarity=0.674 Sum_probs=21.5
Q ss_pred CCCcCceEecCCcccccccCC---CC----CCCCCcEee
Q 008961 226 VGEKIQWVQCEDCSKWRKVPA---NA----RLPSKWTCS 257 (547)
Q Consensus 226 ~~e~~~WVQCD~C~KWRrLP~---~~----~lP~~W~Cs 257 (547)
......||+||.|..|--+.= .. .....|+|.
T Consensus 8 ~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~ 46 (51)
T PF00628_consen 8 SDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCP 46 (51)
T ss_dssp SCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSH
T ss_pred cCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECc
Confidence 356789999999999965322 11 223488885
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=37.84 E-value=60 Score=23.44 Aligned_cols=27 Identities=22% Similarity=0.545 Sum_probs=22.4
Q ss_pred hhHhhhcCCCCCCEEEEEEecCCCeEEE
Q 008961 66 TPCIQNMQLQAGDIVTFSRLEPEGKLVM 93 (547)
Q Consensus 66 s~FVRsK~LqaGDtVvF~R~e~~GkL~I 93 (547)
..|.+..++..||.|.|.... +|.|.|
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~-~~~l~l 39 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVE-DGEIIL 39 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeC-CCEEEE
Confidence 478899999999999999764 677765
No 9
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=36.98 E-value=19 Score=29.44 Aligned_cols=21 Identities=48% Similarity=0.991 Sum_probs=17.2
Q ss_pred ceeeecCCCC-------CCCCCCCCccc
Q 008961 343 SCIVCIQPPS-------GKGPKHKQTCT 363 (547)
Q Consensus 343 ~civciqpps-------gkgpkhk~~c~ 363 (547)
-|+||-||=- .+||-|-.-|-
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 58999998874
No 10
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=34.63 E-value=59 Score=28.73 Aligned_cols=27 Identities=22% Similarity=0.215 Sum_probs=20.8
Q ss_pred HhhhcCCCCCCEEEEEEecCCCeEEEE
Q 008961 68 CIQNMQLQAGDIVTFSRLEPEGKLVMG 94 (547)
Q Consensus 68 FVRsK~LqaGDtVvF~R~e~~GkL~IG 94 (547)
|.-...|++||.|...+...+.+|+|=
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 566678999999999998644466653
No 11
>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=31.14 E-value=39 Score=29.54 Aligned_cols=36 Identities=19% Similarity=0.288 Sum_probs=21.8
Q ss_pred hhHhhhcCCCCCCEEEEEEecCCCeEEEEEEecCCC
Q 008961 66 TPCIQNMQLQAGDIVTFSRLEPEGKLVMGFRKASSA 101 (547)
Q Consensus 66 s~FVRsK~LqaGDtVvF~R~e~~GkL~IGvRRa~~~ 101 (547)
.+|+++++|..||.|.++|...-=-.++++-...+.
T Consensus 42 ~~~i~~~~i~~Gd~V~V~raGdVIP~I~~vv~~~r~ 77 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRAGDVIPKIVGVVKEKRT 77 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEETTTEEEEEEE-GGG--
T ss_pred HHHHHHcCCCCCCEEEEEECCCccceEeEeehhcCC
Confidence 589999999999999999952111345555544433
No 12
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=30.42 E-value=1.1e+02 Score=27.34 Aligned_cols=51 Identities=24% Similarity=0.289 Sum_probs=28.3
Q ss_pred ceEEEEeCCCCeEEEEEEEcCCC-------CCcceeecCchhHhhhcCCCCCCEEEEE
Q 008961 33 LPLKVQDSKGKEWIFQFRFWPNN-------NSRMYVLEGVTPCIQNMQLQAGDIVTFS 83 (547)
Q Consensus 33 ~~L~v~D~~Gk~W~FR~~yw~Nn-------~SR~YLLtGWs~FVRsK~LqaGDtVvF~ 83 (547)
..|.+.|..|+.=....-..|.. ..-.|+|+==..++..++|++||.|.|-
T Consensus 50 LDi~fld~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~~aG~~~~~~i~~Gd~v~~~ 107 (108)
T PF02643_consen 50 LDIAFLDSDGRVVKIERMVPPWRTYPCPSYKPARYVLELPAGWFEKLGIKVGDRVRIE 107 (108)
T ss_dssp EEEEEE-TTSBEEEEEEEE-TT--S-EEECCEECEEEEEETTHHHHHT--TT-EEE--
T ss_pred EEEEEECCCCeEEEEEccCCCCccCCCCCCCccCEEEEcCCCchhhcCCCCCCEEEec
Confidence 45666677776544444332211 1236899866677899999999999873
No 13
>COG5132 BUD31 Cell cycle control protein, G10 family [Transcription / Cell division and chromosome partitioning]
Probab=30.27 E-value=17 Score=34.32 Aligned_cols=20 Identities=55% Similarity=1.215 Sum_probs=17.0
Q ss_pred eeeecCCCCCCCCCCCCccccch
Q 008961 344 CIVCIQPPSGKGPKHKQTCTCNV 366 (547)
Q Consensus 344 civciqppsgkgpkhk~~c~c~v 366 (547)
|.-||||-.. ||-.||.|-|
T Consensus 102 CLRCIQ~~es---k~GstCICRV 121 (146)
T COG5132 102 CLRCIQPIES---KHGSTCICRV 121 (146)
T ss_pred hHhhcCcccc---cCCCEEEEeC
Confidence 9999999654 6889999976
No 14
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=26.75 E-value=82 Score=27.18 Aligned_cols=24 Identities=17% Similarity=0.457 Sum_probs=19.2
Q ss_pred hhcCCCCCCEEEEEEecCCCeEEE
Q 008961 70 QNMQLQAGDIVTFSRLEPEGKLVM 93 (547)
Q Consensus 70 RsK~LqaGDtVvF~R~e~~GkL~I 93 (547)
+..+|++||.|.|+.....|+++|
T Consensus 24 ~~lgi~~Gd~lei~~~~~~~~ivl 47 (89)
T COG2002 24 EALGIKEGDVLEIIVDGDGGRIVL 47 (89)
T ss_pred HHhCCCCCCEEEEEEeCCCCEEEE
Confidence 567999999999999865677554
No 15
>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=25.90 E-value=65 Score=29.39 Aligned_cols=27 Identities=15% Similarity=0.268 Sum_probs=16.5
Q ss_pred cCCCCCCEEEEEEecCCCeEEEEEEec
Q 008961 72 MQLQAGDIVTFSRLEPEGKLVMGFRKA 98 (547)
Q Consensus 72 K~LqaGDtVvF~R~e~~GkL~IGvRRa 98 (547)
++++.||.|+||.....++-+||+=+-
T Consensus 38 ~~mk~GD~vifY~s~~~~~~ivai~~V 64 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVAIGEV 64 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEEEEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEEEEEE
Confidence 499999999999965335677775544
No 16
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=24.28 E-value=40 Score=37.29 Aligned_cols=23 Identities=26% Similarity=0.768 Sum_probs=18.0
Q ss_pred CCCCcCceEecCCcccccccCCC
Q 008961 225 NVGEKIQWVQCEDCSKWRKVPAN 247 (547)
Q Consensus 225 ~~~e~~~WVQCD~C~KWRrLP~~ 247 (547)
+-|.+..=|+|-.|.||=-+..+
T Consensus 117 PFGiqVRNVrC~kChkwGH~n~D 139 (453)
T KOG3794|consen 117 PFGIQVRNVRCLKCHKWGHINTD 139 (453)
T ss_pred ccceEeeeeeEEeecccccccCC
Confidence 45677888999999999766544
No 17
>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=23.69 E-value=1.1e+02 Score=21.98 Aligned_cols=22 Identities=14% Similarity=0.149 Sum_probs=18.4
Q ss_pred CCceEEEEeCCCCeEEEEEEEc
Q 008961 31 EGLPLKVQDSKGKEWIFQFRFW 52 (547)
Q Consensus 31 ~G~~L~v~D~~Gk~W~FR~~yw 52 (547)
.|..+.+.|..|..|.|.|--.
T Consensus 4 ~g~l~~~~~p~G~~~~~~YD~~ 25 (42)
T TIGR01643 4 AGRLTGSTDADGTTTRYTYDAA 25 (42)
T ss_pred CCCEEEEECCCCCEEEEEECCC
Confidence 5788899999999999997544
No 18
>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=23.62 E-value=4e+02 Score=25.40 Aligned_cols=72 Identities=15% Similarity=0.311 Sum_probs=50.5
Q ss_pred CCcCcCCCCCcEEeehhhhhh--cCCCCCCCCCceEEEEeC-CCCeEEEEEEEcCCCCCcceeecCchhHhhhcCCCCCC
Q 008961 2 LSASDAGRIGRLVLPKKCAEA--YFPPISQPEGLPLKVQDS-KGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQLQAGD 78 (547)
Q Consensus 2 LT~SDVg~lgRLVIPK~~AE~--~FP~Ld~~~G~~L~v~D~-~Gk~W~FR~~yw~Nn~SR~YLLtGWs~FVRsK~LqaGD 78 (547)
+|..|+.--|.+.|..+..++ ++| +..+.+.|. .|.+|.= |.+....-|+..-|.|= -++..+.||
T Consensus 15 VT~a~L~Y~GSItID~~Lm~aagi~p------~E~V~V~Nv~NG~Rf~T-YvI~G~~GSg~I~lNGA----AArl~~~GD 83 (126)
T TIGR00223 15 VTHANLNYEGSITIDEDLLDAAGILE------NEKVDIVNVNNGKRFST-YAIAGKRGSRIICVNGA----AARCVSVGD 83 (126)
T ss_pred EeccccccceeEEECHHHHHhcCCCC------CCEEEEEECCCCcEEEE-EEEEcCCCCCEEEeCCH----HHhcCCCCC
Confidence 567777777999999887664 344 478899998 6887764 44442223555566663 567889999
Q ss_pred EEEEEE
Q 008961 79 IVTFSR 84 (547)
Q Consensus 79 tVvF~R 84 (547)
.|+++-
T Consensus 84 ~VII~s 89 (126)
T TIGR00223 84 IVIIAS 89 (126)
T ss_pred EEEEEE
Confidence 998864
No 19
>PRK03760 hypothetical protein; Provisional
Probab=22.41 E-value=1.6e+02 Score=26.96 Aligned_cols=49 Identities=18% Similarity=0.430 Sum_probs=30.6
Q ss_pred CCCceEEEEeCCCCeEEEEEEEcCCCCCcceeecCchhHhhhcCCCCCCEEEEEE
Q 008961 30 PEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQLQAGDIVTFSR 84 (547)
Q Consensus 30 ~~G~~L~v~D~~Gk~W~FR~~yw~Nn~SR~YLLtGWs~FVRsK~LqaGDtVvF~R 84 (547)
.+|..+.+.+ -+.|++ |.+.. .-.|+|+==..++...++++||.|.|.+
T Consensus 68 ~~g~Vv~i~~--~~P~~~---~~~~~-~a~~VLEl~aG~~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 68 SNRRVVDFKT--LKPWRI---YVPKK-PARYIIEGPVGKIRVLKVEVGDEIEWID 116 (117)
T ss_pred CCCeEEEEEe--CCCccc---cCCCc-cceEEEEeCCChHHHcCCCCCCEEEEee
Confidence 4555555443 255652 33222 3348987444457899999999999876
No 20
>COG4384 Mu-like prophage protein gp45 [Function unknown]
Probab=22.38 E-value=1.2e+02 Score=30.71 Aligned_cols=30 Identities=20% Similarity=0.337 Sum_probs=21.4
Q ss_pred hhcCCCCCCEEEEE------EecCCCeEEEEEEecC
Q 008961 70 QNMQLQAGDIVTFS------RLEPEGKLVMGFRKAS 99 (547)
Q Consensus 70 RsK~LqaGDtVvF~------R~e~~GkL~IGvRRa~ 99 (547)
|-++|.+||+++|. |...++.+.+.+..-.
T Consensus 92 R~~GL~aGeT~iY~~eG~~i~Lteg~~Ie~~ck~~~ 127 (203)
T COG4384 92 RITGLKAGETVIYNHEGAKIVLTEGGIIEADCKTLT 127 (203)
T ss_pred ccccccCCceEEEeccCcEEEEccCcEEEEeccEEE
Confidence 45789999999984 3345666777776654
No 21
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=20.91 E-value=1.5e+02 Score=27.37 Aligned_cols=29 Identities=17% Similarity=0.308 Sum_probs=20.6
Q ss_pred hhcCCCCCCEEEEE-EecCCCeEEEEEEec
Q 008961 70 QNMQLQAGDIVTFS-RLEPEGKLVMGFRKA 98 (547)
Q Consensus 70 RsK~LqaGDtVvF~-R~e~~GkL~IGvRRa 98 (547)
.-.+|++||.|.|. ....++.+++.+++.
T Consensus 85 ~l~~lk~G~~V~F~~~~~~~~~~i~~i~~~ 114 (115)
T PRK09838 85 KMSEIKTGDKVAFNFVQQGNLSLLQDIKVS 114 (115)
T ss_pred hhccCCCCCEEEEEEEEcCCcEEEEEEeeC
Confidence 34689999999995 444566666777663
No 22
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=20.78 E-value=50 Score=27.13 Aligned_cols=20 Identities=45% Similarity=1.024 Sum_probs=15.0
Q ss_pred ceeeecCCCC-------CCCCCCCCcc
Q 008961 343 SCIVCIQPPS-------GKGPKHKQTC 362 (547)
Q Consensus 343 ~civciqpps-------gkgpkhk~~c 362 (547)
-|+||-||=- ..||-|..-|
T Consensus 3 ~CvVCKqpi~~a~~v~T~~G~VH~g~C 29 (54)
T PF10886_consen 3 ICVVCKQPIDDALVVETESGPVHPGVC 29 (54)
T ss_pred eeeeeCCccCcceEEEcCCCccCcHHH
Confidence 5999999932 4678887765
No 23
>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=20.57 E-value=1.5e+02 Score=24.96 Aligned_cols=33 Identities=21% Similarity=0.336 Sum_probs=24.1
Q ss_pred eeecCchhHhhhcCCCCCCEEEEEEecCCCeEEEE
Q 008961 60 YVLEGVTPCIQNMQLQAGDIVTFSRLEPEGKLVMG 94 (547)
Q Consensus 60 YLLtGWs~FVRsK~LqaGDtVvF~R~e~~GkL~IG 94 (547)
|.++==..++...+|..||.|.|... +|.++|-
T Consensus 10 ~~vtIPk~i~~~lgl~~Gd~v~v~~~--~~~iii~ 42 (74)
T TIGR02609 10 LVVTLPKEVLESLGLKEGDTLYVDEE--EGGLKLK 42 (74)
T ss_pred eEEEECHHHHHHcCcCCCCEEEEEEE--CCEEEEE
Confidence 33333357899999999999988764 5667764
Done!