Query 038793
Match_columns 251
No_of_seqs 191 out of 495
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 03:21:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038793.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038793hhsearch_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 1.2E-17 2.5E-22 127.7 10.4 83 160-249 1-85 (100)
2 PF03754 DUF313: Domain of unk 97.7 8.6E-05 1.9E-09 60.9 6.7 79 156-235 20-114 (114)
3 PF09217 EcoRII-N: Restriction 97.6 0.00026 5.7E-09 60.9 7.8 89 156-247 6-110 (156)
4 KOG0644 Uncharacterized conser 81.6 0.99 2.1E-05 48.3 2.4 64 60-124 872-940 (1113)
5 PRK03760 hypothetical protein; 68.2 19 0.00041 29.4 6.2 48 199-249 61-117 (117)
6 PF03120 DNA_ligase_OB: NAD-de 39.9 23 0.00051 27.6 2.2 19 231-249 43-61 (82)
7 PF02643 DUF192: Uncharacteriz 34.9 81 0.0017 25.0 4.6 45 199-246 50-106 (108)
8 cd06919 Asp_decarbox Aspartate 30.3 3.2E+02 0.0069 22.7 8.2 70 162-247 12-87 (111)
9 PF12195 End_beta_barrel: Beta 28.9 31 0.00068 27.0 1.2 16 233-248 23-38 (83)
10 TIGR01643 YD_repeat_2x YD repe 28.2 79 0.0017 20.2 2.9 21 199-219 6-27 (42)
11 PF04014 Antitoxin-MazE: Antid 26.3 90 0.002 21.0 3.1 19 231-249 14-32 (47)
12 PRK11507 ribosome-associated p 25.6 46 0.00099 25.4 1.6 17 231-247 46-62 (70)
13 PF13275 S4_2: S4 domain; PDB: 24.6 33 0.00072 25.6 0.7 18 230-247 41-58 (65)
14 PF10367 Vps39_2: Vacuolar sor 24.4 56 0.0012 24.6 2.0 16 65-80 90-105 (109)
15 COG1430 Uncharacterized conser 24.4 2.5E+02 0.0054 23.6 5.9 77 154-248 27-121 (126)
16 PF02298 Cu_bind_like: Plastoc 21.5 48 0.001 25.4 1.0 16 232-247 13-28 (85)
17 PF14453 ThiS-like: ThiS-like 21.4 76 0.0016 23.2 2.0 16 234-249 41-56 (57)
18 PRK05449 aspartate alpha-decar 21.3 5.1E+02 0.011 21.9 8.2 70 162-247 13-88 (126)
19 PF01878 EVE: EVE domain; Int 21.2 61 0.0013 26.4 1.7 14 236-249 38-51 (143)
20 TIGR00223 panD L-aspartate-alp 21.0 5.2E+02 0.011 21.9 8.2 70 162-247 13-88 (126)
21 PF02261 Asp_decarbox: Asparta 20.8 5E+02 0.011 21.7 8.3 70 162-247 13-88 (116)
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=99.74 E-value=1.2e-17 Score=127.68 Aligned_cols=83 Identities=34% Similarity=0.483 Sum_probs=65.9
Q ss_pred EEEecccCCCCCCC-EEEehhhhhhhCCCCccccccCCCCeEEEEEeCCCCeEEEEE-EeCCCCceEEcccHHHHhhhcC
Q 038793 160 FYKKLRASDQSKKK-IVIRAKDAENVFPFLAHLDYKKQINYSVIAKDVHGVAWKFNF-VDGKSRRHYLTVGWKYFVRQKN 237 (251)
Q Consensus 160 F~K~LT~SDv~~~g-lsVPk~~Ae~~FP~l~~Ld~~~~~p~~L~~~D~~G~~W~Fr~-yr~~srrhlLTtGWs~FVr~K~ 237 (251)
|.|+|++||+.+.+ |.||+++++.+... . ..++.+.+.|..|+.|.+++ +++.+++++|++||..||++++
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~~-----~--~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~ 73 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHGGN-----K--RKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNG 73 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS-------S--S--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhCCC-----c--CCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcC
Confidence 89999999999877 99999999987311 1 11268999999999999999 8988888999999999999999
Q ss_pred CCCCCEEEEEec
Q 038793 238 LVPGDTVIFIRY 249 (251)
Q Consensus 238 L~aGD~VvF~R~ 249 (251)
|++||.|+|+..
T Consensus 74 L~~GD~~~F~~~ 85 (100)
T PF02362_consen 74 LKEGDVCVFELI 85 (100)
T ss_dssp --TT-EEEEEE-
T ss_pred CCCCCEEEEEEe
Confidence 999999999853
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=97.75 E-value=8.6e-05 Score=60.86 Aligned_cols=79 Identities=18% Similarity=0.254 Sum_probs=57.7
Q ss_pred CCCeEEEecccCCCCCCC--EEEehhhhhhhCCCCcc-----c----cc-cCCCCeEEEEEeCCCCeEEEEE-EeCC---
Q 038793 156 TPPLFYKKLRASDQSKKK--IVIRAKDAENVFPFLAH-----L----DY-KKQINYSVIAKDVHGVAWKFNF-VDGK--- 219 (251)
Q Consensus 156 ~~~~F~K~LT~SDv~~~g--lsVPk~~Ae~~FP~l~~-----L----d~-~~~~p~~L~~~D~~G~~W~Fr~-yr~~--- 219 (251)
....|.|+|++||+..+- |+||-..-.. ..+|.. + .. .....+.+.+.|..++.|..++ .|..
T Consensus 20 ~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~ 98 (114)
T PF03754_consen 20 PKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNG 98 (114)
T ss_pred CeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCC
Confidence 457899999999998764 9999875532 233110 1 00 1122288999999999999999 8866
Q ss_pred CCceEEcccHHHHhhh
Q 038793 220 SRRHYLTVGWKYFVRQ 235 (251)
Q Consensus 220 srrhlLTtGWs~FVr~ 235 (251)
...|+|.+||..+|.+
T Consensus 99 ~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 99 TSNYVLNSGWNKVVED 114 (114)
T ss_pred ceEEEEEcChHhhccC
Confidence 4579999999999863
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=97.60 E-value=0.00026 Score=60.91 Aligned_cols=89 Identities=18% Similarity=0.173 Sum_probs=52.7
Q ss_pred CCCeEEEecccCCCCCCC-----EEEehhhhhhhCCCCccccccCCCC-eEEEEEeCCC--CeEEEEE-EeCC------C
Q 038793 156 TPPLFYKKLRASDQSKKK-----IVIRAKDAENVFPFLAHLDYKKQIN-YSVIAKDVHG--VAWKFNF-VDGK------S 220 (251)
Q Consensus 156 ~~~~F~K~LT~SDv~~~g-----lsVPk~~Ae~~FP~l~~Ld~~~~~p-~~L~~~D~~G--~~W~Fr~-yr~~------s 220 (251)
....|+|.|++.|++..| +.||+..++..||.+. ..+..+| ..|.+++..| ..|+||+ |.|+ .
T Consensus 6 ~~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~--~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTR 83 (156)
T PF09217_consen 6 SWAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSIN--HTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTR 83 (156)
T ss_dssp SEEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG---SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS-
T ss_pred ceEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCC--cccccCCceeEEEEECCCCccceeEEEEEEcccccCCCc
Confidence 345799999999996643 9999999999999843 2355677 9999999988 5687888 6655 2
Q ss_pred CceEEcccHHHHhh-hcCCCCCCEEEEE
Q 038793 221 RRHYLTVGWKYFVR-QKNLVPGDTVIFI 247 (251)
Q Consensus 221 rrhlLTtGWs~FVr-~K~L~aGD~VvF~ 247 (251)
+-+-|| +|...-. .+-=..||-+||.
T Consensus 84 NE~RIT-~~G~~~~~~~~~~tGaL~vla 110 (156)
T PF09217_consen 84 NEYRIT-RFGRGFPLQNPENTGALLVLA 110 (156)
T ss_dssp -EEEEE----TTSGGG-GGGTT-EEEEE
T ss_pred CceEEe-eecCCCccCCccccccEEEEE
Confidence 335665 3332222 2222478888886
No 4
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=81.60 E-value=0.99 Score=48.35 Aligned_cols=64 Identities=28% Similarity=0.472 Sum_probs=43.8
Q ss_pred CCCCCCCeEEEecCCccccccCCCCCCCCCCC-----CCCCcceEEEEEEEEeecCCcCceeEEEEEeec
Q 038793 60 SLPKKGDLVVYFPQGHLEYSAPASVSKAPPTF-----DLKPEIICRVADVRYLVSKKTDKVYTKMTLLPL 124 (251)
Q Consensus 60 ~lP~~gs~V~YFPqGH~Eq~~~s~~~~~~p~~-----~lp~~i~C~V~~V~l~Ad~~TDEVyA~i~L~P~ 124 (251)
-||..|+.|.||-|||-|.+.+..-. .++.- ++-..=.|.|..+..--=+-...---+|.|.=.
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n-~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~i 940 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLN-NIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVI 940 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhc-cccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeee
Confidence 68999999999999999999986421 12211 232334688888877666666666666666544
No 5
>PRK03760 hypothetical protein; Provisional
Probab=68.15 E-value=19 Score=29.44 Aligned_cols=48 Identities=25% Similarity=0.264 Sum_probs=31.6
Q ss_pred eEEEEEeCCCCeEEEEE---Ee----CCCCceEE--cccHHHHhhhcCCCCCCEEEEEec
Q 038793 199 YSVIAKDVHGVAWKFNF---VD----GKSRRHYL--TVGWKYFVRQKNLVPGDTVIFIRY 249 (251)
Q Consensus 199 ~~L~~~D~~G~~W~Fr~---yr----~~srrhlL--TtGWs~FVr~K~L~aGD~VvF~R~ 249 (251)
..+.+.|.+|++=.... ++ ..+-+|+| ..|| +.+.++++||.|.|.|+
T Consensus 61 LDiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~---~~~~gi~~Gd~v~~~~~ 117 (117)
T PRK03760 61 IDVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGK---IRVLKVEVGDEIEWIDE 117 (117)
T ss_pred eEEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCCh---HHHcCCCCCCEEEEeeC
Confidence 45666676666444322 11 22345777 6775 67899999999999874
No 6
>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=39.92 E-value=23 Score=27.55 Aligned_cols=19 Identities=26% Similarity=0.529 Sum_probs=15.7
Q ss_pred HHhhhcCCCCCCEEEEEec
Q 038793 231 YFVRQKNLVPGDTVIFIRY 249 (251)
Q Consensus 231 ~FVr~K~L~aGD~VvF~R~ 249 (251)
.|+++++|..||.|.++|.
T Consensus 43 ~~i~~~~i~~Gd~V~V~ra 61 (82)
T PF03120_consen 43 DYIKELDIRIGDTVLVTRA 61 (82)
T ss_dssp HHHHHTT-BBT-EEEEEEE
T ss_pred HHHHHcCCCCCCEEEEEEC
Confidence 7899999999999999985
No 7
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=34.95 E-value=81 Score=25.04 Aligned_cols=45 Identities=24% Similarity=0.298 Sum_probs=27.7
Q ss_pred eEEEEEeCCCCeEEEEE-E---eC------CCCceEE--cccHHHHhhhcCCCCCCEEEE
Q 038793 199 YSVIAKDVHGVAWKFNF-V---DG------KSRRHYL--TVGWKYFVRQKNLVPGDTVIF 246 (251)
Q Consensus 199 ~~L~~~D~~G~~W~Fr~-y---r~------~srrhlL--TtGWs~FVr~K~L~aGD~VvF 246 (251)
..+.+.|..|++=.... . +. ++-+|+| ..| ++.+.+|++||.|.|
T Consensus 50 LDi~fld~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~~aG---~~~~~~i~~Gd~v~~ 106 (108)
T PF02643_consen 50 LDIAFLDSDGRVVKIERMVPPWRTYPCPSYKPARYVLELPAG---WFEKLGIKVGDRVRI 106 (108)
T ss_dssp EEEEEE-TTSBEEEEEEEE-TT--S-EEECCEECEEEEEETT---HHHHHT--TT-EEE-
T ss_pred EEEEEECCCCeEEEEEccCCCCccCCCCCCCccCEEEEcCCC---chhhcCCCCCCEEEe
Confidence 67888898888666655 3 11 1236787 455 578999999999987
No 8
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=30.30 E-value=3.2e+02 Score=22.69 Aligned_cols=70 Identities=23% Similarity=0.365 Sum_probs=49.3
Q ss_pred EecccCCCCCCC-EEEehhhhh--hhCCCCccccccCCCCeEEEEEeC-CCCeEEEEEEeCC--CCceEEcccHHHHhhh
Q 038793 162 KKLRASDQSKKK-IVIRAKDAE--NVFPFLAHLDYKKQINYSVIAKDV-HGVAWKFNFVDGK--SRRHYLTVGWKYFVRQ 235 (251)
Q Consensus 162 K~LT~SDv~~~g-lsVPk~~Ae--~~FP~l~~Ld~~~~~p~~L~~~D~-~G~~W~Fr~yr~~--srrhlLTtGWs~FVr~ 235 (251)
-+.|..|..-.| +.|...-.+ .++|. ..+.+.|. +|..|.=--..+. |+.-.|.+. -+
T Consensus 12 atVT~a~L~YeGSitID~~Ll~aagi~~~-----------E~V~I~Nv~NG~Rf~TYvI~g~~gSg~I~lNGA-----AA 75 (111)
T cd06919 12 ATVTEADLNYEGSITIDEDLLEAAGILPY-----------EKVLVVNVNNGARFETYVIPGERGSGVICLNGA-----AA 75 (111)
T ss_pred eEEeccccccceeEEECHHHHHhcCCCCC-----------CEEEEEECCCCcEEEEEEEEcCCCCCEEEeCCH-----HH
Confidence 468899998889 999887544 34444 45777787 6887764336655 344566554 57
Q ss_pred cCCCCCCEEEEE
Q 038793 236 KNLVPGDTVIFI 247 (251)
Q Consensus 236 K~L~aGD~VvF~ 247 (251)
+.-..||.||++
T Consensus 76 r~~~~GD~vII~ 87 (111)
T cd06919 76 RLGQPGDRVIIM 87 (111)
T ss_pred hcCCCCCEEEEE
Confidence 788999999986
No 9
>PF12195 End_beta_barrel: Beta barrel domain of bacteriophage endosialidase; InterPro: IPR024427 This entry represents the beta barrel domain of endosialidases which is nested in a beta propeller domain. This beta barrel domain is approximately 80 amino acids in length and represents one of the two sialic acid binding sites of the enzyme [].; PDB: 1V0E_B 1V0F_E 3JU4_A 3GVL_A 3GVK_B 3GVJ_A.
Probab=28.86 E-value=31 Score=27.04 Aligned_cols=16 Identities=31% Similarity=0.439 Sum_probs=8.4
Q ss_pred hhhcCCCCCCEEEEEe
Q 038793 233 VRQKNLVPGDTVIFIR 248 (251)
Q Consensus 233 Vr~K~L~aGD~VvF~R 248 (251)
+-+++|.+||.|.|.-
T Consensus 23 l~~HGl~vGD~VnFsn 38 (83)
T PF12195_consen 23 LTDHGLFVGDFVNFSN 38 (83)
T ss_dssp -TT----TT-EEEEES
T ss_pred EccCceeecceEEEec
Confidence 4579999999999964
No 10
>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=28.16 E-value=79 Score=20.16 Aligned_cols=21 Identities=14% Similarity=0.385 Sum_probs=17.1
Q ss_pred eEEEEEeCCCCeEEEEE-EeCC
Q 038793 199 YSVIAKDVHGVAWKFNF-VDGK 219 (251)
Q Consensus 199 ~~L~~~D~~G~~W~Fr~-yr~~ 219 (251)
+.+.+.|..|..|+|.| -.|+
T Consensus 6 ~l~~~~~p~G~~~~~~YD~~Gr 27 (42)
T TIGR01643 6 RLTGSTDADGTTTRYTYDAAGR 27 (42)
T ss_pred CEEEEECCCCCEEEEEECCCCC
Confidence 56788899999999999 5543
No 11
>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=26.28 E-value=90 Score=20.96 Aligned_cols=19 Identities=26% Similarity=0.211 Sum_probs=15.7
Q ss_pred HHhhhcCCCCCCEEEEEec
Q 038793 231 YFVRQKNLVPGDTVIFIRY 249 (251)
Q Consensus 231 ~FVr~K~L~aGD~VvF~R~ 249 (251)
.|.++.+|.+||.|.|.-.
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~ 32 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVE 32 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEE
T ss_pred HHHHHcCCCCCCEEEEEEe
Confidence 5678889999999998643
No 12
>PRK11507 ribosome-associated protein; Provisional
Probab=25.60 E-value=46 Score=25.37 Aligned_cols=17 Identities=29% Similarity=0.386 Sum_probs=14.1
Q ss_pred HHhhhcCCCCCCEEEEE
Q 038793 231 YFVRQKNLVPGDTVIFI 247 (251)
Q Consensus 231 ~FVr~K~L~aGD~VvF~ 247 (251)
..-|.|+|+.||.|.|-
T Consensus 46 e~rRgkKl~~GD~V~~~ 62 (70)
T PRK11507 46 ETRKRCKIVAGQTVSFA 62 (70)
T ss_pred ecccCCCCCCCCEEEEC
Confidence 45577999999999984
No 13
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=24.63 E-value=33 Score=25.60 Aligned_cols=18 Identities=39% Similarity=0.333 Sum_probs=8.6
Q ss_pred HHHhhhcCCCCCCEEEEE
Q 038793 230 KYFVRQKNLVPGDTVIFI 247 (251)
Q Consensus 230 s~FVr~K~L~aGD~VvF~ 247 (251)
...-|.++|++||.|.|-
T Consensus 41 ~e~rrg~Kl~~GD~V~~~ 58 (65)
T PF13275_consen 41 VETRRGKKLRPGDVVEID 58 (65)
T ss_dssp ----SS----SSEEEEET
T ss_pred EccccCCcCCCCCEEEEC
Confidence 455678999999999983
No 14
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=24.45 E-value=56 Score=24.60 Aligned_cols=16 Identities=31% Similarity=0.559 Sum_probs=13.2
Q ss_pred CCeEEEecCCcccccc
Q 038793 65 GDLVVYFPQGHLEYSA 80 (251)
Q Consensus 65 gs~V~YFPqGH~Eq~~ 80 (251)
++.+++||.||+-|..
T Consensus 90 ~~~f~~~p~~~v~H~~ 105 (109)
T PF10367_consen 90 NSVFVVFPCGHVVHYS 105 (109)
T ss_pred CceEEEeCCCeEEecc
Confidence 4789999999998754
No 15
>COG1430 Uncharacterized conserved protein [Function unknown]
Probab=24.38 E-value=2.5e+02 Score=23.58 Aligned_cols=77 Identities=18% Similarity=0.230 Sum_probs=47.5
Q ss_pred CCCCCeEEEecccCCCCCCC--EEEehhhhh-----hhCCCCccccccCCCCeEEEEEeCCCC-eEEEEE--Ee----CC
Q 038793 154 NSTPPLFYKKLRASDQSKKK--IVIRAKDAE-----NVFPFLAHLDYKKQINYSVIAKDVHGV-AWKFNF--VD----GK 219 (251)
Q Consensus 154 ~~~~~~F~K~LT~SDv~~~g--lsVPk~~Ae-----~~FP~l~~Ld~~~~~p~~L~~~D~~G~-~W~Fr~--yr----~~ 219 (251)
+..-.+|.+.| ...+| |..|+ -.. +.++. |.+|.+.|..|+ +|.-.- ++ .+
T Consensus 27 r~~GLMfR~sl----~~d~GMLFv~~~-~~~~~~wMknt~l----------pLDiiFid~dg~i~~i~~~~P~~~~~~~~ 91 (126)
T COG1430 27 RARGLMFRTSL----PDDHGMLFVFPE-TRRVAFWMKNTML----------PLDIIFIDSDGRVVDIVELVPWSTYPCKS 91 (126)
T ss_pred HhccccccccC----CCCceEEEecCC-CceeEEeeecCCc----------ceEEEEEcCCCCEEEEEeccccccCCCCC
Confidence 55667888887 33457 66662 211 22232 257888888887 344332 22 11
Q ss_pred --CCceEE--cccHHHHhhhcCCCCCCEEEEEe
Q 038793 220 --SRRHYL--TVGWKYFVRQKNLVPGDTVIFIR 248 (251)
Q Consensus 220 --srrhlL--TtGWs~FVr~K~L~aGD~VvF~R 248 (251)
+.+|+| ..|| ++.+++++||.|.|..
T Consensus 92 ~~~~~yvLEl~~G~---~~~~~i~vGd~v~~~~ 121 (126)
T COG1430 92 YGPVRYVLELPAGW---AARLGIKVGDRVEFRP 121 (126)
T ss_pred CCCccEEEEecCCc---hhhcCCccCCEEEecc
Confidence 224777 5776 6789999999999864
No 16
>PF02298 Cu_bind_like: Plastocyanin-like domain; InterPro: IPR003245 Blue (type 1) copper proteins are small proteins which bind a single copper atom and which are characterised by an intense electronic absorption band near 600 nm [, ]. The most well known members of this class of proteins are the plant chloroplastic plastocyanins, which exchange electrons with cytochrome c6, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. This family of proteins also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus (Thiobacillus versutus) that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus []; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings []; cusacyanin (basic blue protein; plantacyanin, CBP) from cucumber; halocyanin from Natronomonas pharaonis (Natronobacterium pharaonis) [], a membrane associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans []; stellacyanin from Rhus vernicifera (Japanese lacquer tree); umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved. This domain is found in a variety of plant cyanins and pollern allergen. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Amb a 3.; GO: 0005507 copper ion binding, 0009055 electron carrier activity; PDB: 1JER_A 1WS7_A 1WS8_D 1F56_B 1X9R_B 1X9U_A 2CBP_A.
Probab=21.50 E-value=48 Score=25.37 Aligned_cols=16 Identities=31% Similarity=0.569 Sum_probs=12.7
Q ss_pred HhhhcCCCCCCEEEEE
Q 038793 232 FVRQKNLVPGDTVIFI 247 (251)
Q Consensus 232 FVr~K~L~aGD~VvF~ 247 (251)
-...|.+++||+++|.
T Consensus 13 Wa~~~~F~vGD~LvF~ 28 (85)
T PF02298_consen 13 WASGKTFRVGDTLVFN 28 (85)
T ss_dssp HHCTS-BETTEEEEEE
T ss_pred hhcCCcEeCCCEEEEE
Confidence 3578999999999994
No 17
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=21.38 E-value=76 Score=23.24 Aligned_cols=16 Identities=31% Similarity=0.503 Sum_probs=13.7
Q ss_pred hhcCCCCCCEEEEEec
Q 038793 234 RQKNLVPGDTVIFIRY 249 (251)
Q Consensus 234 r~K~L~aGD~VvF~R~ 249 (251)
.+..|+.||.|+|.|.
T Consensus 41 ~d~~L~e~D~v~~Ikk 56 (57)
T PF14453_consen 41 EDIELKEGDEVFLIKK 56 (57)
T ss_pred CccccCCCCEEEEEeC
Confidence 4678999999999875
No 18
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=21.29 E-value=5.1e+02 Score=21.94 Aligned_cols=70 Identities=19% Similarity=0.223 Sum_probs=49.1
Q ss_pred EecccCCCCCCC-EEEehhhhh--hhCCCCccccccCCCCeEEEEEeC-CCCeEEEEEEeCC--CCceEEcccHHHHhhh
Q 038793 162 KKLRASDQSKKK-IVIRAKDAE--NVFPFLAHLDYKKQINYSVIAKDV-HGVAWKFNFVDGK--SRRHYLTVGWKYFVRQ 235 (251)
Q Consensus 162 K~LT~SDv~~~g-lsVPk~~Ae--~~FP~l~~Ld~~~~~p~~L~~~D~-~G~~W~Fr~yr~~--srrhlLTtGWs~FVr~ 235 (251)
-+.|..|..-.| +.|-..-.+ .++|. ..+.+.|. +|..|.=--..+. |+.-.|++. -+
T Consensus 13 atVT~a~L~Y~GSitID~~Ll~aagi~p~-----------E~V~V~Nv~NG~Rf~TYvI~g~~GSg~I~lNGA-----AA 76 (126)
T PRK05449 13 ATVTEADLNYEGSITIDEDLLDAAGILEN-----------EKVQIVNVNNGARFETYVIAGERGSGVICLNGA-----AA 76 (126)
T ss_pred eEEeccccccceeEEECHHHHHhcCCCCC-----------CEEEEEECCCCcEEEEEEEEcCCCCCEEEeCCH-----HH
Confidence 468899998889 999887544 45554 35777786 6887764335655 344556554 57
Q ss_pred cCCCCCCEEEEE
Q 038793 236 KNLVPGDTVIFI 247 (251)
Q Consensus 236 K~L~aGD~VvF~ 247 (251)
+.-..||.||++
T Consensus 77 r~~~~GD~vII~ 88 (126)
T PRK05449 77 RLVQVGDLVIIA 88 (126)
T ss_pred hcCCCCCEEEEE
Confidence 788999999986
No 19
>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=21.22 E-value=61 Score=26.38 Aligned_cols=14 Identities=50% Similarity=0.857 Sum_probs=9.6
Q ss_pred cCCCCCCEEEEEec
Q 038793 236 KNLVPGDTVIFIRY 249 (251)
Q Consensus 236 K~L~aGD~VvF~R~ 249 (251)
++++.||.|+||..
T Consensus 38 ~~mk~GD~vifY~s 51 (143)
T PF01878_consen 38 KRMKPGDKVIFYHS 51 (143)
T ss_dssp HC--TT-EEEEEET
T ss_pred hcCCCCCEEEEEEc
Confidence 39999999999975
No 20
>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=20.97 E-value=5.2e+02 Score=21.92 Aligned_cols=70 Identities=19% Similarity=0.209 Sum_probs=48.9
Q ss_pred EecccCCCCCCC-EEEehhhhh--hhCCCCccccccCCCCeEEEEEeC-CCCeEEEEEEeCC--CCceEEcccHHHHhhh
Q 038793 162 KKLRASDQSKKK-IVIRAKDAE--NVFPFLAHLDYKKQINYSVIAKDV-HGVAWKFNFVDGK--SRRHYLTVGWKYFVRQ 235 (251)
Q Consensus 162 K~LT~SDv~~~g-lsVPk~~Ae--~~FP~l~~Ld~~~~~p~~L~~~D~-~G~~W~Fr~yr~~--srrhlLTtGWs~FVr~ 235 (251)
-+.|..|..-.| +.|-..-.+ .++|. ..+.+.|. +|..|+=--..|. |+.-.|.+. -+
T Consensus 13 atVT~a~L~Y~GSItID~~Lm~aagi~p~-----------E~V~V~Nv~NG~Rf~TYvI~G~~GSg~I~lNGA-----AA 76 (126)
T TIGR00223 13 ATVTHANLNYEGSITIDEDLLDAAGILEN-----------EKVDIVNVNNGKRFSTYAIAGKRGSRIICVNGA-----AA 76 (126)
T ss_pred eEEeccccccceeEEECHHHHHhcCCCCC-----------CEEEEEECCCCcEEEEEEEEcCCCCCEEEeCCH-----HH
Confidence 467889998889 999887544 34554 35777786 6888764335655 344556554 57
Q ss_pred cCCCCCCEEEEE
Q 038793 236 KNLVPGDTVIFI 247 (251)
Q Consensus 236 K~L~aGD~VvF~ 247 (251)
+.-..||.||++
T Consensus 77 rl~~~GD~VII~ 88 (126)
T TIGR00223 77 RCVSVGDIVIIA 88 (126)
T ss_pred hcCCCCCEEEEE
Confidence 788999999986
No 21
>PF02261 Asp_decarbox: Aspartate decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process; PDB: 1PYU_C 1AW8_A 1PYQ_B 3TM7_C 1PT1_A 1PQH_A 1PPY_B 1PT0_B 1PQF_A 1PQE_A ....
Probab=20.82 E-value=5e+02 Score=21.69 Aligned_cols=70 Identities=20% Similarity=0.314 Sum_probs=42.6
Q ss_pred EecccCCCCCCC-EEEehhhhh--hhCCCCccccccCCCCeEEEEEeC-CCCeEEEEEEeCC--CCceEEcccHHHHhhh
Q 038793 162 KKLRASDQSKKK-IVIRAKDAE--NVFPFLAHLDYKKQINYSVIAKDV-HGVAWKFNFVDGK--SRRHYLTVGWKYFVRQ 235 (251)
Q Consensus 162 K~LT~SDv~~~g-lsVPk~~Ae--~~FP~l~~Ld~~~~~p~~L~~~D~-~G~~W~Fr~yr~~--srrhlLTtGWs~FVr~ 235 (251)
-+.|..|..-.| +.|...-.+ .++|. -.+.+.+. +|..|.=--..+. |+.--|.+. -+
T Consensus 13 atVT~a~L~Y~GSitID~~Ll~aagi~p~-----------E~V~V~Nv~nG~Rf~TYvI~g~~GSg~I~lNGa-----AA 76 (116)
T PF02261_consen 13 ATVTEADLNYEGSITIDEDLLDAAGILPY-----------EQVQVVNVNNGERFETYVIPGERGSGVICLNGA-----AA 76 (116)
T ss_dssp EE--EEETTSTSCEEEEHHHHHHCT--TT-----------BEEEEEETTT--EEEEEEEEESTTTT-EEEEGG-----GG
T ss_pred eEEeccccccceeeEECHHHHHHcCCCcC-----------CEEEEEECCCCcEEEEEEEEccCCCcEEEECCH-----HH
Confidence 367889998889 999987544 45554 35777786 6888874335544 344566554 67
Q ss_pred cCCCCCCEEEEE
Q 038793 236 KNLVPGDTVIFI 247 (251)
Q Consensus 236 K~L~aGD~VvF~ 247 (251)
+.-++||.||++
T Consensus 77 rl~~~GD~vII~ 88 (116)
T PF02261_consen 77 RLVQVGDRVIIM 88 (116)
T ss_dssp GCS-TT-EEEEE
T ss_pred hccCCCCEEEEE
Confidence 788999999986
Done!