Query 030695
Match_columns 173
No_of_seqs 129 out of 300
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 03:11:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030695.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030695hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06200 tify: tify domain; I 99.7 4.4E-18 9.6E-23 108.2 5.1 34 92-125 2-36 (36)
2 PF09425 CCT_2: Divergent CCT 99.3 1.7E-12 3.8E-17 78.0 1.4 18 156-173 1-18 (27)
3 PF06203 CCT: CCT motif; Inte 91.4 0.088 1.9E-06 35.1 0.9 15 159-173 1-15 (45)
4 PF08114 PMP1_2: ATPase proteo 72.1 1.5 3.2E-05 29.1 0.4 10 157-166 34-43 (43)
5 PF08152 GUCT: GUCT (NUC152) d 71.3 3.1 6.7E-05 31.1 2.0 33 93-125 48-80 (97)
6 PRK00979 tetrahydromethanopter 52.9 14 0.00031 33.4 3.1 29 99-127 32-65 (308)
7 PF02007 MtrH: Tetrahydrometha 51.6 15 0.00032 33.2 3.0 29 99-127 27-60 (296)
8 PF13619 KTSC: KTSC domain 51.6 32 0.0007 23.1 4.1 30 92-121 12-43 (60)
9 PRK14047 putative methyltransf 51.1 14 0.0003 33.6 2.8 30 98-127 31-65 (310)
10 TIGR01114 mtrH N5-methyltetrah 49.6 19 0.00041 32.9 3.3 29 98-126 31-64 (314)
11 PF14268 YoaP: YoaP-like 48.6 20 0.00044 23.7 2.6 19 96-114 21-40 (44)
12 PF02582 DUF155: Uncharacteris 38.5 56 0.0012 26.1 4.3 28 98-125 2-29 (175)
13 COG1962 MtrH Tetrahydromethano 38.3 39 0.00085 30.6 3.5 34 98-131 34-72 (313)
14 PHA03071 late transcription fa 37.5 26 0.00057 30.6 2.3 24 97-120 54-78 (260)
15 PF03355 Pox_TAP: Viral Trans- 37.2 27 0.00059 30.6 2.3 24 97-120 54-78 (260)
16 PF12196 hNIFK_binding: FHA Ki 36.1 15 0.00033 24.2 0.5 7 165-171 14-20 (41)
17 cd06891 PX_Vps17p The phosphoi 34.1 27 0.00058 28.2 1.7 13 157-169 108-120 (140)
18 PF12860 PAS_7: PAS fold 33.7 34 0.00073 24.4 2.1 15 103-117 98-113 (115)
19 PF00352 TBP: Transcription fa 27.3 1.1E+02 0.0023 21.8 3.7 29 94-122 48-77 (86)
20 smart00320 WD40 WD40 repeats. 26.0 52 0.0011 16.2 1.5 15 96-110 26-40 (40)
21 PF11208 DUF2992: Protein of u 24.9 37 0.0008 27.1 1.0 9 98-106 1-9 (132)
22 PF14470 bPH_3: Bacterial PH d 24.5 1.9E+02 0.0041 19.9 4.5 28 96-123 66-94 (96)
23 PF02994 Transposase_22: L1 tr 24.3 71 0.0015 29.1 2.9 22 96-119 319-341 (370)
24 PF11344 DUF3146: Protein of u 24.2 45 0.00098 24.9 1.3 11 160-170 53-63 (80)
25 PF00400 WD40: WD domain, G-be 23.4 75 0.0016 18.0 2.0 15 96-110 25-39 (39)
26 cd07286 PX_SNX18 The phosphoin 23.2 55 0.0012 25.8 1.7 12 158-169 76-87 (127)
27 PF12322 T4_baseplate: T4 bact 21.9 1.2E+02 0.0026 25.6 3.6 25 99-123 137-162 (205)
28 PF02457 DisA_N: DisA bacteria 21.1 82 0.0018 24.5 2.3 16 92-107 107-122 (122)
29 cd07283 PX_SNX30 The phosphoin 20.7 66 0.0014 24.6 1.7 13 157-169 84-96 (116)
No 1
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=99.73 E-value=4.4e-18 Score=108.17 Aligned_cols=34 Identities=56% Similarity=0.797 Sum_probs=31.4
Q ss_pred CCCCCceeEEECcEEEEEe-CCHHHHHHHHHHHhc
Q 030695 92 VSETAPLTIFYNGTVAVFD-VHREKAEHILKLAVE 125 (173)
Q Consensus 92 ~~~t~qLTIFY~G~V~VfD-v~~~KA~~Im~lA~~ 125 (173)
.++++||||||+|+|+||| ||+|||++||.||++
T Consensus 2 ~~~~~qLTIfY~G~V~Vfd~v~~~Ka~~im~lA~r 36 (36)
T PF06200_consen 2 SPETAQLTIFYGGQVCVFDDVPPDKAQEIMLLASR 36 (36)
T ss_pred CCCCCcEEEEECCEEEEeCCCCHHHHHHHHHHhcC
Confidence 3578999999999999998 999999999999974
No 2
>PF09425 CCT_2: Divergent CCT motif; InterPro: IPR018467 The short CCT (CO, COL, TOC1) motif is found in a number of plant proteins, including Constans (CO), Constans-like (COL) and TOC1. The CCT motif is about 45 amino acids long and contains a putative nuclear localisation signal within the second half of the CCT motif []. The CCT motif is found in the Arabidopsis circadian rhythm protein TOC1, an autoregulatory response regulator homologue the controls the photoperiodic flowering through its clock function []. ; GO: 0005515 protein binding; PDB: 3OGK_V 3OGL_S 3OGM_W.
Probab=99.26 E-value=1.7e-12 Score=78.02 Aligned_cols=18 Identities=83% Similarity=1.252 Sum_probs=10.0
Q ss_pred chHHHHHhHHHHHhhcCC
Q 030695 156 PIARRKSLQRFLEKRKER 173 (173)
Q Consensus 156 PiARKaSLqRFLEKRKeR 173 (173)
|||||+||||||||||||
T Consensus 1 P~aRK~SLqRFLeKRK~R 18 (27)
T PF09425_consen 1 PIARKASLQRFLEKRKDR 18 (27)
T ss_dssp -----HHHHHHHHHH---
T ss_pred CchHHHHHHHHHHHHHHh
Confidence 799999999999999998
No 3
>PF06203 CCT: CCT motif; InterPro: IPR010402 The CCT (CONSTANS, CO-like, and TOC1) domain is a highly conserved basic module of ~43 amino acids, which is found near the C terminus of plant proteins often involved in light signal transduction. The CCT domain is found in association with other domains, such as the B-box zinc finger, the GATA-type zinc finger, the ZIM motif or the response regulatory domain. The CCT domain contains a putative nuclear localisation signal within the second half of the CCT motif and has been shown to be involved in nuclear localization and probably also has a role in protein-protein interaction [].; GO: 0005515 protein binding
Probab=91.37 E-value=0.088 Score=35.12 Aligned_cols=15 Identities=60% Similarity=0.900 Sum_probs=13.5
Q ss_pred HHHHhHHHHHhhcCC
Q 030695 159 RRKSLQRFLEKRKER 173 (173)
Q Consensus 159 RKaSLqRFLEKRKeR 173 (173)
|.++|+||+|||+.|
T Consensus 1 R~~~l~Ry~~Kr~~R 15 (45)
T PF06203_consen 1 REEKLQRYREKRKRR 15 (45)
T ss_pred CHHHHHHHHHHHHhh
Confidence 678999999999976
No 4
>PF08114 PMP1_2: ATPase proteolipid family; InterPro: IPR012589 This family consists of small proteolipids associated with the plasma membrane H+ ATPase. Two proteolipids (PMP1 and PMP2) are associated with the ATPase and both genes are similarly expressed in the wild-type strain of yeast. No modification of the level of transcription of one PMP gene is detected in a strain deleted of the other. Though both proteolipids show similarity with other small proteolipids associated with other cation -transporting ATPases, their functions remain unclear [].
Probab=72.08 E-value=1.5 Score=29.12 Aligned_cols=10 Identities=60% Similarity=1.002 Sum_probs=9.1
Q ss_pred hHHHHHhHHH
Q 030695 157 IARRKSLQRF 166 (173)
Q Consensus 157 iARKaSLqRF 166 (173)
+|||++||||
T Consensus 34 ~aRkr~l~rf 43 (43)
T PF08114_consen 34 QARKRALQRF 43 (43)
T ss_pred HHHHHHHhcC
Confidence 5899999998
No 5
>PF08152 GUCT: GUCT (NUC152) domain; InterPro: IPR012562 This is the C-terminal domain found in the RNA helicase II / Gu protein family [].; GO: 0003723 RNA binding, 0004386 helicase activity, 0005524 ATP binding, 0005634 nucleus; PDB: 2E29_A.
Probab=71.32 E-value=3.1 Score=31.12 Aligned_cols=33 Identities=30% Similarity=0.326 Sum_probs=25.8
Q ss_pred CCCCceeEEECcEEEEEeCCHHHHHHHHHHHhc
Q 030695 93 SETAPLTIFYNGTVAVFDVHREKAEHILKLAVE 125 (173)
Q Consensus 93 ~~t~qLTIFY~G~V~VfDv~~~KA~~Im~lA~~ 125 (173)
..-..||+.=++.=+|||||.+.++.|+.....
T Consensus 48 ~~v~~m~l~~d~~GavFDvP~~~~~~~~~~~~~ 80 (97)
T PF08152_consen 48 DKVKGMTLLKDKMGAVFDVPSEIAEEFLAKWED 80 (97)
T ss_dssp TT-EEEEE-TTSSEEEEEEEHHHHHHHHHH--S
T ss_pred HhhCcEEEecCCCEEEEEChHHHHHHHHHhCcc
Confidence 355789999999999999999999999987644
No 6
>PRK00979 tetrahydromethanopterin S-methyltransferase subunit H; Provisional
Probab=52.87 E-value=14 Score=33.36 Aligned_cols=29 Identities=38% Similarity=0.535 Sum_probs=24.3
Q ss_pred eEEECcEEEEEe-----CCHHHHHHHHHHHhcCC
Q 030695 99 TIFYNGTVAVFD-----VHREKAEHILKLAVEGN 127 (173)
Q Consensus 99 TIFY~G~V~VfD-----v~~~KA~~Im~lA~~~~ 127 (173)
||||+|.=.|-| |-.+||++++..-..-.
T Consensus 32 siFY~~h~iV~D~~~G~FDk~~Ae~Li~~~~els 65 (308)
T PRK00979 32 SIFYAGHKIVSDEKKGIFDKEKAEALINRQEELS 65 (308)
T ss_pred EeeecCceeeeccccCccCHHHHHHHHHHHHHHH
Confidence 899999999987 56999999998765543
No 7
>PF02007 MtrH: Tetrahydromethanopterin S-methyltransferase MtrH subunit; InterPro: IPR023467 In archaea the enzyme tetrahydromethanopterin S-methyltransferase is composed of eight subunits, MtrA-H. The enzyme is a membrane- associated enzyme complex which catalyzes an energy-conserving, sodium-ion-translocating step in methanogenesis from hydrogen and carbon dioxide []. Subunit MtrH catalyzes the methylation reaction and was shown to exhibit methyltetrahydromethanopterin:cob(I)alamin methyltransferase activity []. CH3-H4MPT + cob(I)alamin --> H4MPT + CH3-cob(III)alamin (H4MPT = tetrahydromethanopterin); GO: 0008168 methyltransferase activity, 0006730 one-carbon metabolic process
Probab=51.63 E-value=15 Score=33.24 Aligned_cols=29 Identities=38% Similarity=0.528 Sum_probs=24.2
Q ss_pred eEEECcEEEEEe-----CCHHHHHHHHHHHhcCC
Q 030695 99 TIFYNGTVAVFD-----VHREKAEHILKLAVEGN 127 (173)
Q Consensus 99 TIFY~G~V~VfD-----v~~~KA~~Im~lA~~~~ 127 (173)
||||+|.=.|-| |-.++|++++..-..-.
T Consensus 27 SIFY~gHkIV~D~~~G~FDk~~Ae~Li~~q~els 60 (296)
T PF02007_consen 27 SIFYNGHKIVEDEKKGIFDKEAAEALINRQEELS 60 (296)
T ss_pred eeeecCceeeeccCCCccCHHHHHHHHHHHHHHH
Confidence 899999999987 56999999998765443
No 8
>PF13619 KTSC: KTSC domain
Probab=51.59 E-value=32 Score=23.12 Aligned_cols=30 Identities=30% Similarity=0.352 Sum_probs=24.7
Q ss_pred CCCCCceeEEE-CcEEEEEe-CCHHHHHHHHH
Q 030695 92 VSETAPLTIFY-NGTVAVFD-VHREKAEHILK 121 (173)
Q Consensus 92 ~~~t~qLTIFY-~G~V~VfD-v~~~KA~~Im~ 121 (173)
.+++..|.|.| +|.++.|. ||++-.+++|.
T Consensus 12 d~~~~~L~V~F~~G~~Y~Y~~Vp~~~~~~l~~ 43 (60)
T PF13619_consen 12 DPETRTLEVEFKSGSVYRYFGVPPEVYEALLN 43 (60)
T ss_pred CCCCCEEEEEEcCCCEEEECCCCHHHHHHHHc
Confidence 45678999865 78999995 99999998875
No 9
>PRK14047 putative methyltransferase; Provisional
Probab=51.10 E-value=14 Score=33.61 Aligned_cols=30 Identities=43% Similarity=0.513 Sum_probs=24.8
Q ss_pred eeEEECcEEEEEe-----CCHHHHHHHHHHHhcCC
Q 030695 98 LTIFYNGTVAVFD-----VHREKAEHILKLAVEGN 127 (173)
Q Consensus 98 LTIFY~G~V~VfD-----v~~~KA~~Im~lA~~~~ 127 (173)
=||||+|.=.|-| |-.++|++++.....-.
T Consensus 31 GsIFY~~HkIV~D~~~GiFDk~~Ae~Lin~q~els 65 (310)
T PRK14047 31 GTIFYNRHKIVTDEDKGLFDREAAEKLVNLQEEMS 65 (310)
T ss_pred EEEeecCceeeeccccCccCHHHHHHHHHHHHHHH
Confidence 3899999999996 56999999998775543
No 10
>TIGR01114 mtrH N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit H. coenzyme M methyltransferase subunit H in methanogenic archaea. This methyltranfersae is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.
Probab=49.57 E-value=19 Score=32.86 Aligned_cols=29 Identities=34% Similarity=0.347 Sum_probs=24.2
Q ss_pred eeEEECcEEEEEe-----CCHHHHHHHHHHHhcC
Q 030695 98 LTIFYNGTVAVFD-----VHREKAEHILKLAVEG 126 (173)
Q Consensus 98 LTIFY~G~V~VfD-----v~~~KA~~Im~lA~~~ 126 (173)
=||||+|.=.|-| |-.++|++++.....-
T Consensus 31 GSIFY~~HkIV~D~~~GiFDk~~Ae~Lin~q~el 64 (314)
T TIGR01114 31 GTIFYARHKIVEDEDKGIFDKAAAETLIKTQEEL 64 (314)
T ss_pred EEEeecCceeeeccccCccCHHHHHHHHHHHHHH
Confidence 3899999999997 5699999999876543
No 11
>PF14268 YoaP: YoaP-like
Probab=48.62 E-value=20 Score=23.67 Aligned_cols=19 Identities=21% Similarity=0.553 Sum_probs=14.3
Q ss_pred CceeEEECcEEEEEe-CCHH
Q 030695 96 APLTIFYNGTVAVFD-VHRE 114 (173)
Q Consensus 96 ~qLTIFY~G~V~VfD-v~~~ 114 (173)
....|||+|+..--+ ++..
T Consensus 21 t~yalFYnGkfiT~eils~~ 40 (44)
T PF14268_consen 21 TTYALFYNGKFITNEILSEK 40 (44)
T ss_pred eEEEEEECCEEEEeeccChh
Confidence 456799999998888 4443
No 12
>PF02582 DUF155: Uncharacterised ACR, YagE family COG1723; InterPro: IPR003734 This entry describes proteins of unknown function.
Probab=38.47 E-value=56 Score=26.13 Aligned_cols=28 Identities=21% Similarity=0.394 Sum_probs=24.6
Q ss_pred eeEEECcEEEEEeCCHHHHHHHHHHHhc
Q 030695 98 LTIFYNGTVAVFDVHREKAEHILKLAVE 125 (173)
Q Consensus 98 LTIFY~G~V~VfDv~~~KA~~Im~lA~~ 125 (173)
+-||-.|.|+.|++++++...+|.....
T Consensus 2 vf~F~~G~vVfw~~~~~~~~~~l~~l~~ 29 (175)
T PF02582_consen 2 VFLFRYGVVVFWGVSEEEEKQFLDYLKP 29 (175)
T ss_pred EEEecCcEEEEEeCCHHHHHHHHHHHHH
Confidence 4589999999999999999999988754
No 13
>COG1962 MtrH Tetrahydromethanopterin S-methyltransferase, subunit H [Coenzyme metabolism]
Probab=38.26 E-value=39 Score=30.57 Aligned_cols=34 Identities=35% Similarity=0.331 Sum_probs=25.7
Q ss_pred eeEEECcEEEEEe-----CCHHHHHHHHHHHhcCCCCCC
Q 030695 98 LTIFYNGTVAVFD-----VHREKAEHILKLAVEGNSKSF 131 (173)
Q Consensus 98 LTIFY~G~V~VfD-----v~~~KA~~Im~lA~~~~~~s~ 131 (173)
=||||+|.=.|=| +-.+.|++++.+-......+.
T Consensus 34 gTIFY~~HkIVeDe~kGiFDr~aAE~Li~~qe~lsD~TG 72 (313)
T COG1962 34 GTIFYAKHKIVEDEKKGIFDREAAEALINTQEELSDKTG 72 (313)
T ss_pred eeeeeccceeeeccccccccHHHHHHHHHHHHHhccccC
Confidence 4999999999886 568899999987655443333
No 14
>PHA03071 late transcription factor VLTF-1; Provisional
Probab=37.52 E-value=26 Score=30.61 Aligned_cols=24 Identities=29% Similarity=0.603 Sum_probs=20.5
Q ss_pred ceeEEECcEE-EEEeCCHHHHHHHH
Q 030695 97 PLTIFYNGTV-AVFDVHREKAEHIL 120 (173)
Q Consensus 97 qLTIFY~G~V-~VfDv~~~KA~~Im 120 (173)
+-.+||+|.+ .||++|..|++.-+
T Consensus 54 ~a~vfydG~~n~VFNlPV~KvK~CL 78 (260)
T PHA03071 54 SASVFYDGDENIVFNLPVSKVKSCL 78 (260)
T ss_pred cceEEEcCCCCeEEeeehHHhhhhh
Confidence 3468999999 89999999998765
No 15
>PF03355 Pox_TAP: Viral Trans-Activator Protein ; InterPro: IPR005022 This family of proteins function as a trans-activator of viral late genes.; GO: 0006355 regulation of transcription, DNA-dependent
Probab=37.18 E-value=27 Score=30.62 Aligned_cols=24 Identities=29% Similarity=0.567 Sum_probs=20.5
Q ss_pred ceeEEECcEE-EEEeCCHHHHHHHH
Q 030695 97 PLTIFYNGTV-AVFDVHREKAEHIL 120 (173)
Q Consensus 97 qLTIFY~G~V-~VfDv~~~KA~~Im 120 (173)
+-.|||+|.+ .||++|..|++.-+
T Consensus 54 sasvfydG~~n~VFNlPV~KvKsCL 78 (260)
T PF03355_consen 54 SASVFYDGDENKVFNLPVLKVKSCL 78 (260)
T ss_pred cceEEEcCCCCeEEeeehHHhhhhh
Confidence 3469999999 89999999998765
No 16
>PF12196 hNIFK_binding: FHA Ki67 binding domain of hNIFK; InterPro: IPR021043 This entry represents eukaryotic proteins that contain a domain of approximately 40 amino acids in length. These proteins are found in association with PF00076 from PFAM. There are two conserved sequence motifs: TPVCTP and LERRKS. This domain is found on the human nucleolar protein hNIFK. It binds to the fork-head-associated domain of human Ki67. High-affinity binding requires sequential phosphorylation by two kinases, CDK1 and GSK3, yielding pThr238, pThr234 and pSer230. This interaction is involved in cell cycle regulation []. ; PDB: 2AFF_B.
Probab=36.12 E-value=15 Score=24.19 Aligned_cols=7 Identities=71% Similarity=1.189 Sum_probs=6.0
Q ss_pred HHHHhhc
Q 030695 165 RFLEKRK 171 (173)
Q Consensus 165 RFLEKRK 171 (173)
-||||||
T Consensus 14 tfLErRK 20 (41)
T PF12196_consen 14 TFLERRK 20 (41)
T ss_dssp HHHHHHH
T ss_pred HHHHHhh
Confidence 4999998
No 17
>cd06891 PX_Vps17p The phosphoinositide binding Phox Homology domain of yeast sorting nexin Vps17p. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Vsp17p forms a dimer with Vps5p, the yeast counterpart of human SNX1, and is part of the retromer complex that mediates the transport of the carboxypeptidase Y receptor Vps10p from endosomes to Golgi. Similar to Vps5p and SNX1, Vps17p harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvatur
Probab=34.06 E-value=27 Score=28.16 Aligned_cols=13 Identities=23% Similarity=0.483 Sum_probs=11.1
Q ss_pred hHHHHHhHHHHHh
Q 030695 157 IARRKSLQRFLEK 169 (173)
Q Consensus 157 iARKaSLqRFLEK 169 (173)
..|+++|||||++
T Consensus 108 ~~rr~~LqrfL~R 120 (140)
T cd06891 108 RKLKANLQRWFNR 120 (140)
T ss_pred HHHHHHHHHHHHH
Confidence 4689999999985
No 18
>PF12860 PAS_7: PAS fold
Probab=33.69 E-value=34 Score=24.40 Aligned_cols=15 Identities=33% Similarity=0.550 Sum_probs=12.5
Q ss_pred CcEEEEE-eCCHHHHH
Q 030695 103 NGTVAVF-DVHREKAE 117 (173)
Q Consensus 103 ~G~V~Vf-Dv~~~KA~ 117 (173)
+|.|.+| |||..+..
T Consensus 98 Gg~v~~~~DVT~~~~~ 113 (115)
T PF12860_consen 98 GGFVLTFTDVTERRRA 113 (115)
T ss_pred CCEEEEEEeCCHHHHh
Confidence 7999999 79988754
No 19
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=27.29 E-value=1.1e+02 Score=21.83 Aligned_cols=29 Identities=21% Similarity=0.370 Sum_probs=22.9
Q ss_pred CCCceeEEECcEEEEEe-CCHHHHHHHHHH
Q 030695 94 ETAPLTIFYNGTVAVFD-VHREKAEHILKL 122 (173)
Q Consensus 94 ~t~qLTIFY~G~V~VfD-v~~~KA~~Im~l 122 (173)
...-+.||..|+|.+.- =+.+.++..+..
T Consensus 48 p~~t~~IF~sGki~itGaks~~~~~~a~~~ 77 (86)
T PF00352_consen 48 PKATVLIFSSGKIVITGAKSEEEAKKAIEK 77 (86)
T ss_dssp TTEEEEEETTSEEEEEEESSHHHHHHHHHH
T ss_pred CcEEEEEEcCCEEEEEecCCHHHHHHHHHH
Confidence 35789999999999998 578877665543
No 20
>smart00320 WD40 WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
Probab=26.02 E-value=52 Score=16.21 Aligned_cols=15 Identities=20% Similarity=0.302 Sum_probs=10.8
Q ss_pred CceeEEECcEEEEEe
Q 030695 96 APLTIFYNGTVAVFD 110 (173)
Q Consensus 96 ~qLTIFY~G~V~VfD 110 (173)
--++..++|.|.+||
T Consensus 26 ~~~~~~~d~~~~~~~ 40 (40)
T smart00320 26 YLASASDDGTIKLWD 40 (40)
T ss_pred EEEEecCCCeEEEcC
Confidence 345666788888886
No 21
>PF11208 DUF2992: Protein of unknown function (DUF2992); InterPro: IPR016787 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=24.95 E-value=37 Score=27.10 Aligned_cols=9 Identities=33% Similarity=1.065 Sum_probs=7.0
Q ss_pred eeEEECcEE
Q 030695 98 LTIFYNGTV 106 (173)
Q Consensus 98 LTIFY~G~V 106 (173)
|||||+|.-
T Consensus 1 LTV~Fdg~F 9 (132)
T PF11208_consen 1 LTVYFDGPF 9 (132)
T ss_pred CeEEecCCc
Confidence 789988763
No 22
>PF14470 bPH_3: Bacterial PH domain
Probab=24.52 E-value=1.9e+02 Score=19.87 Aligned_cols=28 Identities=18% Similarity=0.299 Sum_probs=25.4
Q ss_pred CceeEEECcEEEEEe-CCHHHHHHHHHHH
Q 030695 96 APLTIFYNGTVAVFD-VHREKAEHILKLA 123 (173)
Q Consensus 96 ~qLTIFY~G~V~VfD-v~~~KA~~Im~lA 123 (173)
..++|-++|..+.++ ++...++.++...
T Consensus 66 ~~i~i~~~~~~~~i~~i~k~~~~~~~~~i 94 (96)
T PF14470_consen 66 GKITIETNGEKIKIDNIQKGDVKEFYEYI 94 (96)
T ss_pred cEEEEEECCEEEEEEEcCHHHHHHHHHHH
Confidence 579999999999999 9999999998765
No 23
>PF02994 Transposase_22: L1 transposable element; InterPro: IPR004244 Many human L1 elements are capable of retrotransposition. Some of these have been shown to exhibit reverse transcriptase (RT) activity [] although the function of many are, as yet, unknown. More information about these proteins can be found at Protein of the Month: Transposase [].; PDB: 2LDY_A 3SOO_A 2YKQ_A 2YKO_C 2YKP_B 2W7A_B 2JRB_A.
Probab=24.32 E-value=71 Score=29.07 Aligned_cols=22 Identities=45% Similarity=0.681 Sum_probs=17.0
Q ss_pred CceeEEECcEEEEE-eCCHHHHHHH
Q 030695 96 APLTIFYNGTVAVF-DVHREKAEHI 119 (173)
Q Consensus 96 ~qLTIFY~G~V~Vf-Dv~~~KA~~I 119 (173)
+-|.|+|+|.+..| | +++|++-
T Consensus 319 akL~i~~~G~~~~F~~--~~~~~~f 341 (370)
T PF02994_consen 319 AKLRITYNGKTKSFTD--PEEAKEF 341 (370)
T ss_dssp TEEEEESSSSEEEESS--HHHHHHH
T ss_pred chhcceeCCceecCCC--HHHHHHH
Confidence 78999999999999 5 3444443
No 24
>PF11344 DUF3146: Protein of unknown function (DUF3146); InterPro: IPR021492 This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=24.24 E-value=45 Score=24.87 Aligned_cols=11 Identities=55% Similarity=0.839 Sum_probs=9.5
Q ss_pred HHHhHHHHHhh
Q 030695 160 RKSLQRFLEKR 170 (173)
Q Consensus 160 KaSLqRFLEKR 170 (173)
+..|.|||||-
T Consensus 53 ~d~L~RFL~k~ 63 (80)
T PF11344_consen 53 QDPLGRFLEKS 63 (80)
T ss_pred HhHHHHHHhhc
Confidence 78899999983
No 25
>PF00400 WD40: WD domain, G-beta repeat; InterPro: IPR019781 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events.; PDB: 2ZKQ_a 3CFV_B 3CFS_B 1PEV_A 1NR0_A 1VYH_T 3RFH_A 3O2Z_T 3FRX_C 3U5G_g ....
Probab=23.40 E-value=75 Score=18.05 Aligned_cols=15 Identities=27% Similarity=0.268 Sum_probs=11.9
Q ss_pred CceeEEECcEEEEEe
Q 030695 96 APLTIFYNGTVAVFD 110 (173)
Q Consensus 96 ~qLTIFY~G~V~VfD 110 (173)
.=+|--++|.|.|||
T Consensus 25 ~~~s~~~D~~i~vwd 39 (39)
T PF00400_consen 25 FLASGSSDGTIRVWD 39 (39)
T ss_dssp EEEEEETTSEEEEEE
T ss_pred cceeeCCCCEEEEEC
Confidence 346777889999997
No 26
>cd07286 PX_SNX18 The phosphoinositide binding Phox Homology domain of Sorting Nexin 18. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX18, like SNX9, contains an N-terminal Src Homology 3 (SH3) domain, a PX domain, and a C-terminal Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature. The PX-BAR structural unit helps determine specific membrane localization. SNX18 is localized to peripheral endosomal structures, and acts in a trafficki
Probab=23.16 E-value=55 Score=25.81 Aligned_cols=12 Identities=33% Similarity=0.634 Sum_probs=10.8
Q ss_pred HHHHHhHHHHHh
Q 030695 158 ARRKSLQRFLEK 169 (173)
Q Consensus 158 ARKaSLqRFLEK 169 (173)
-|++.||+||++
T Consensus 76 ~Rr~~Lq~FL~r 87 (127)
T cd07286 76 KRRKGLIWWMDH 87 (127)
T ss_pred HHHHHHHHHHHH
Confidence 699999999986
No 27
>PF12322 T4_baseplate: T4 bacteriophage base plate protein; InterPro: IPR024364 Proteins in this family are found in T4-like viruses. They have a single completely conserved residue S that may be functionally important. The family includes the two base plate proteins from bacteriophage T4: Gp51 and Gp26, encoded by late genes []. Gp26 is a structural component of central hub of the baseplate. It associates with Gp25 (tail lysozyme) in the assembly process. Gp51 is essential for the formation of the central hub of the phage baseplate, playing a catalytic role for the central hub formation. It may be also a structural component of the hub.
Probab=21.92 E-value=1.2e+02 Score=25.62 Aligned_cols=25 Identities=12% Similarity=0.260 Sum_probs=20.5
Q ss_pred eEEECcEEEEEe-CCHHHHHHHHHHH
Q 030695 99 TIFYNGTVAVFD-VHREKAEHILKLA 123 (173)
Q Consensus 99 TIFY~G~V~VfD-v~~~KA~~Im~lA 123 (173)
+|.++|+|+.|| ++.+.-.+++..-
T Consensus 137 ~I~~~~~~~~~~dl~e~e~~~~~d~i 162 (205)
T PF12322_consen 137 YIYDGEQVYNWEDLSEEEKDEFFDSI 162 (205)
T ss_pred eEEECCEEEECCCCCHHHHHHHHHHc
Confidence 899999999996 9988767766543
No 28
>PF02457 DisA_N: DisA bacterial checkpoint controller nucleotide-binding; InterPro: IPR003390 The DisA protein is a bacterial checkpoint protein that dimerises into an octameric complex. The protein consists of three distinct domains. This domain is the first and is a globular, nucleotide-binding region; the next 146-289 residues constitute the DisA-linker family, IPR018906 from INTERPRO that consists of an elongated bundle of three alpha helices (alpha-6, alpha-10, and alpha-11), one side of which carries an additional three helices (alpha7-9), which thus forms a spine like-linker between domains 1 and 3. The C-terminal residues, of domain 3, are represented by family HHH, IPR000445 from INTERPRO the specific DNA-binding domain. The octameric complex thus has structurally linked nucleotide-binding and DNA-binding HhH domains and the nucleotide-binding domains are bound to a cyclic di-adenosine phosphate such that DisA is a specific di-adenylate cyclase. The di-adenylate cyclase activity is strongly suppressed by binding to branched DNA, but not to duplex or single-stranded DNA, suggesting a role for DisA as a monitor of the presence of stalled replication forks or recombination intermediates via DNA structure-modulated c-di-AMP synthesis.; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 2FB5_A.
Probab=21.07 E-value=82 Score=24.45 Aligned_cols=16 Identities=25% Similarity=0.526 Sum_probs=11.5
Q ss_pred CCCCCceeEEECcEEE
Q 030695 92 VSETAPLTIFYNGTVA 107 (173)
Q Consensus 92 ~~~t~qLTIFY~G~V~ 107 (173)
..++..++|||+|++|
T Consensus 107 SEe~G~Is~~~~G~~y 122 (122)
T PF02457_consen 107 SEETGTISLAYGGKLY 122 (122)
T ss_dssp -TTTS-EEEEETTEE-
T ss_pred EccCCcEEEEECCEEC
Confidence 3567899999999986
No 29
>cd07283 PX_SNX30 The phosphoinositide binding Phox Homology domain of Sorting Nexin 30. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX30 harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to the sorting nexins SNX1-2, SNX4-8, and SNX32
Probab=20.72 E-value=66 Score=24.55 Aligned_cols=13 Identities=46% Similarity=0.874 Sum_probs=10.9
Q ss_pred hHHHHHhHHHHHh
Q 030695 157 IARRKSLQRFLEK 169 (173)
Q Consensus 157 iARKaSLqRFLEK 169 (173)
--|+..|++||.+
T Consensus 84 e~Rr~~Le~FL~~ 96 (116)
T cd07283 84 ETRRKALDKFLKR 96 (116)
T ss_pred HHHHHHHHHHHHH
Confidence 3589999999975
Done!