Query 034135
Match_columns 103
No_of_seqs 10 out of 12
Neff 1.5
Searched_HMMs 46136
Date Fri Mar 29 10:09:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034135.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034135hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01436 NHL: NHL repeat; Int 65.4 7.5 0.00016 20.6 2.2 19 75-95 1-19 (28)
2 PF00595 PDZ: PDZ domain (Also 50.6 30 0.00066 20.6 3.4 25 76-100 9-36 (81)
3 KOG1004 Exosomal 3'-5' exoribo 47.7 14 0.00031 29.9 2.1 26 72-97 169-194 (230)
4 PRK05641 putative acetyl-CoA c 40.6 33 0.00071 25.0 2.9 29 64-93 6-35 (153)
5 KOG2358 NifU-like domain-conta 35.6 30 0.00065 27.7 2.2 44 6-49 32-79 (213)
6 PF13986 DUF4224: Domain of un 31.4 32 0.00069 20.8 1.3 15 79-93 27-41 (47)
7 PRK10858 nitrogen regulatory p 29.4 29 0.00062 24.0 1.0 13 85-97 85-97 (112)
8 PF10647 Gmad1: Lipoprotein Lp 29.4 60 0.0013 24.1 2.8 22 78-99 121-146 (253)
9 PF07646 Kelch_2: Kelch motif; 29.3 49 0.0011 18.4 1.8 12 84-95 7-18 (49)
10 cd00136 PDZ PDZ domain, also c 29.3 57 0.0012 18.4 2.1 24 77-100 1-24 (70)
11 PF13540 RCC1_2: Regulator of 29.0 51 0.0011 17.6 1.8 12 83-94 12-23 (30)
12 PF15614 WHIM3: WSTF, HB1, Itc 28.4 7.4 0.00016 24.4 -1.8 16 67-82 9-24 (46)
13 PF11805 DUF3326: Protein of u 28.4 13 0.00029 31.4 -0.9 52 39-91 78-134 (340)
14 KOG1784 Small Nuclear ribonucl 27.7 45 0.00097 24.1 1.8 13 85-97 16-28 (96)
15 PRK10665 nitrogen regulatory p 27.4 32 0.0007 23.7 1.0 13 85-97 85-97 (112)
16 PF06462 Hyd_WA: Propeller; I 26.3 50 0.0011 18.3 1.5 12 83-94 4-15 (32)
17 PF13186 SPASM: Iron-sulfur cl 26.2 59 0.0013 18.0 1.8 13 81-93 6-18 (64)
18 PF12900 Pyridox_ox_2: Pyridox 26.0 82 0.0018 20.9 2.7 19 81-100 30-48 (143)
19 PF04683 Proteasom_Rpn13: Prot 25.7 72 0.0016 21.1 2.4 26 64-89 1-27 (85)
20 KOG1520 Predicted alkaloid syn 25.0 33 0.00071 29.1 0.8 18 76-94 115-132 (376)
21 PF13964 Kelch_6: Kelch motif 25.0 67 0.0014 17.7 1.8 11 84-94 7-17 (50)
22 PF10781 DSRB: Dextransucrase 24.7 48 0.001 22.4 1.4 24 71-94 33-59 (62)
23 PRK11112 tRNA pseudouridine sy 24.4 34 0.00073 25.7 0.7 15 69-83 8-22 (257)
24 KOG1417 Homogentisate 1,2-diox 23.8 41 0.00089 29.3 1.2 21 67-90 178-198 (446)
25 cd02563 PseudoU_synth_TruC tRN 23.5 36 0.00078 24.7 0.7 14 69-82 7-20 (223)
26 PF01344 Kelch_1: Kelch motif; 23.1 80 0.0017 16.8 1.9 11 84-94 7-17 (47)
27 PF13313 DUF4082: Domain of un 22.9 60 0.0013 24.2 1.7 17 79-97 21-37 (149)
28 KOG1190 Polypyrimidine tract-b 22.7 26 0.00057 31.0 -0.2 14 65-78 302-315 (492)
29 PRK10158 23S rRNA/tRNA pseudou 22.3 39 0.00085 24.7 0.7 14 69-82 20-33 (219)
30 PF08068 DKCLD: DKCLD (NUC011) 22.3 37 0.00081 22.3 0.5 19 62-80 30-52 (59)
31 PF07995 GSDH: Glucose / Sorbo 22.2 61 0.0013 24.9 1.7 21 83-103 311-331 (331)
32 PF00543 P-II: Nitrogen regula 22.0 44 0.00096 21.6 0.8 12 86-97 83-94 (102)
33 PF09696 Ctf8: Ctf8; InterPro 21.8 47 0.001 23.2 0.9 11 71-81 71-81 (122)
34 KOG2509 Seryl-tRNA synthetase 21.8 35 0.00076 29.9 0.4 21 77-97 377-400 (455)
35 COG1097 RRP4 RNA-binding prote 21.3 67 0.0015 25.8 1.8 23 74-96 170-192 (239)
36 PF03725 RNase_PH_C: 3' exorib 21.0 1.2E+02 0.0027 17.7 2.6 17 78-95 3-19 (68)
37 TIGR01621 RluA-like pseudourid 20.4 45 0.00098 24.4 0.7 14 69-82 8-21 (217)
38 cd00992 PDZ_signaling PDZ doma 20.4 1.5E+02 0.0032 17.0 2.8 25 76-100 11-37 (82)
39 cd02557 PseudoU_synth_ScRIB2 P 20.3 46 0.00099 24.2 0.7 13 69-81 22-34 (213)
40 TIGR00005 rluA_subfam pseudour 20.3 45 0.00099 24.9 0.7 15 69-83 78-92 (299)
No 1
>PF01436 NHL: NHL repeat; InterPro: IPR001258 The NHL repeat, named after NCL-1, HT2A and Lin-41, is found largely in a large number of eukaryotic and prokaryotic proteins. For example, the repeat is found in a variety of enzymes of the copper type II, ascorbate-dependent monooxygenase family which catalyse the C terminus alpha-amidation of biological peptides []. In many it occurs in tandem arrays, for example in the ringfinger beta-box, coiled-coil (RBCC) eukaryotic growth regulators []. The 'Brain Tumor' protein (Brat) is one such growth regulator that contains a 6-bladed NHL-repeat beta-propeller [, ]. The NHL repeats are also found in serine/threonine protein kinase (STPK) in diverse range of pathogenic bacteria. These STPK are transmembrane receptors with a intracellular N-terminal kinase domain and extracellular C-terminal sensor domain. In the STPK, PknD, from Mycobacterium tuberculosis, the sensor domain forms a rigid, six-bladed b-propeller composed of NHL repeats with a flexible tether to the transmembrane domain.; GO: 0005515 protein binding; PDB: 3FVZ_A 3FW0_A 1RWL_A 1RWI_A 1Q7F_A.
Probab=65.37 E-value=7.5 Score=20.57 Aligned_cols=19 Identities=32% Similarity=0.665 Sum_probs=14.4
Q ss_pred eccceeeEEEEeeCCeEEeee
Q 034135 75 LEKPLGIRFALTVDGKIFVHA 95 (103)
Q Consensus 75 leKPLGIRFALtvdGKVfVHa 95 (103)
+..|.||-.. .+|.|||--
T Consensus 1 f~~P~gvav~--~~g~i~VaD 19 (28)
T PF01436_consen 1 FNYPHGVAVD--SDGNIYVAD 19 (28)
T ss_dssp BSSEEEEEEE--TTSEEEEEE
T ss_pred CcCCcEEEEe--CCCCEEEEE
Confidence 4578888554 999999954
No 2
>PF00595 PDZ: PDZ domain (Also known as DHR or GLGF) Coordinates are not yet available; InterPro: IPR001478 PDZ domains are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates [, ]. PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. They bind either the carboxyl-terminal sequences of proteins or internal peptide sequences []. In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. Direct interaction between PIP2 and a subset of class II PDZ domains (syntenin, CASK, Tiam-1) has been demonstrated. PDZ domains consist of 80 to 90 amino acids comprising six beta-strands (beta-A to beta-F) and two alpha-helices, A and B, compactly arranged in a globular structure. Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel beta-strand interacts with the beta-B strand and the B helix. The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the beta-A and beta-B strands.; GO: 0005515 protein binding; PDB: 3AXA_A 1WF8_A 1QAV_B 1QAU_A 1B8Q_A 1MC7_A 2KAW_A 1I16_A 1VB7_A 1WI4_A ....
Probab=50.61 E-value=30 Score=20.60 Aligned_cols=25 Identities=28% Similarity=0.493 Sum_probs=20.7
Q ss_pred ccceeeEEEEeeCC---eEEeeeecccc
Q 034135 76 EKPLGIRFALTVDG---KIFVHALRKGV 100 (103)
Q Consensus 76 eKPLGIRFALtvdG---KVfVHaLkKG~ 100 (103)
+.|+|+.+.-..+. -+||..+.+|+
T Consensus 9 ~~~lG~~l~~~~~~~~~~~~V~~v~~~~ 36 (81)
T PF00595_consen 9 NGPLGFTLRGGSDNDEKGVFVSSVVPGS 36 (81)
T ss_dssp TSBSSEEEEEESTSSSEEEEEEEECTTS
T ss_pred CCCcCEEEEecCCCCcCCEEEEEEeCCC
Confidence 45899999988885 89999888774
No 3
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=47.65 E-value=14 Score=29.86 Aligned_cols=26 Identities=27% Similarity=0.460 Sum_probs=20.4
Q ss_pred eeeeccceeeEEEEeeCCeEEeeeec
Q 034135 72 MVTLEKPLGIRFALTVDGKIFVHALR 97 (103)
Q Consensus 72 MVtleKPLGIRFALtvdGKVfVHaLk 97 (103)
+-+|-|=+-.+.|+..+|||||||=+
T Consensus 169 Lq~vGk~~~FEia~GlNGriWV~ae~ 194 (230)
T KOG1004|consen 169 LQTVGKKYPFEIAFGLNGRIWVKAET 194 (230)
T ss_pred HHHhhcccceEEEEecCceEEEeccC
Confidence 33566666788899999999999843
No 4
>PRK05641 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=40.60 E-value=33 Score=24.99 Aligned_cols=29 Identities=31% Similarity=0.554 Sum_probs=20.9
Q ss_pred cccccceeeeeeccceeeE-EEEeeCCeEEe
Q 034135 64 LKMNLNEYMVTLEKPLGIR-FALTVDGKIFV 93 (103)
Q Consensus 64 fKMNLNEYMVtleKPLGIR-FALtvdGKVfV 93 (103)
+.||=+||=|.++. |+.| |-.|+||+.|.
T Consensus 6 ~~~~g~~~~v~v~~-~~~~~~~itvnG~~y~ 35 (153)
T PRK05641 6 VIVDGVEYEVEVEE-LGPGKFRVSFEGKTYE 35 (153)
T ss_pred EEECCEEEEEEEEe-ecCccEEEEECCEEEE
Confidence 45677788888765 3354 88888888883
No 5
>KOG2358 consensus NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones]
Probab=35.57 E-value=30 Score=27.69 Aligned_cols=44 Identities=30% Similarity=0.280 Sum_probs=35.0
Q ss_pred cccccccccCC----ChhhhhhccccccCcccccccccceEEEEeehh
Q 034135 6 LSSRRTTSFPS----SSSFLEKNLFSINGVPKQLSFGRDRVKVRFSKK 49 (103)
Q Consensus 6 lssrrttsfps----sssfleknlfsingvpkqlsfgrdrv~~~~sk~ 49 (103)
++.|.+.+||. .+++|-+.+|.++|-++..-||-|-|.+.=++.
T Consensus 32 ~~~~~~~~~~~~~s~~~s~La~s~~~~~~gvv~~~~g~dfvtv~k~~e 79 (213)
T KOG2358|consen 32 LSERGLGDFATPCSAFFSPLAKSILFRDGGVVKVFFGPDFVTVTKLTE 79 (213)
T ss_pred cccccccccccccchhhcHHHHHHHhhcCCcEEEEecCCeEEEeccch
Confidence 34677777776 467899999999998899999999887765544
No 6
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=31.38 E-value=32 Score=20.76 Aligned_cols=15 Identities=40% Similarity=0.696 Sum_probs=13.6
Q ss_pred eeeEEEEeeCCeEEe
Q 034135 79 LGIRFALTVDGKIFV 93 (103)
Q Consensus 79 LGIRFALtvdGKVfV 93 (103)
.||+|-...||+..|
T Consensus 27 ~Gi~~~~~~~G~p~V 41 (47)
T PF13986_consen 27 NGIPFVVRADGRPIV 41 (47)
T ss_pred CCCeeEECCCCCEEe
Confidence 499999999999887
No 7
>PRK10858 nitrogen regulatory protein P-II 1; Provisional
Probab=29.41 E-value=29 Score=23.97 Aligned_cols=13 Identities=46% Similarity=0.608 Sum_probs=9.3
Q ss_pred EeeCCeEEeeeec
Q 034135 85 LTVDGKIFVHALR 97 (103)
Q Consensus 85 LtvdGKVfVHaLk 97 (103)
..=||||||--+.
T Consensus 85 ~~GDGkIfV~pV~ 97 (112)
T PRK10858 85 KIGDGKIFVFDVA 97 (112)
T ss_pred CCCCcEEEEEEhh
Confidence 4459999996543
No 8
>PF10647 Gmad1: Lipoprotein LpqB beta-propeller domain; InterPro: IPR018910 The Gmad1 domain is found associated with IPR019606 from INTERPRO, in bacterial spore formation. It is predicted to have a beta-propeller fold and to have a passive binding role rather than a catalytic function owing to the low number of conserved hydrophilic residues.
Probab=29.35 E-value=60 Score=24.09 Aligned_cols=22 Identities=32% Similarity=0.687 Sum_probs=18.7
Q ss_pred ceeeEEEEee----CCeEEeeeeccc
Q 034135 78 PLGIRFALTV----DGKIFVHALRKG 99 (103)
Q Consensus 78 PLGIRFALtv----dGKVfVHaLkKG 99 (103)
|=|.|.|+-+ +|+|+|-.+.++
T Consensus 121 pDG~RvA~v~~~~~~~~v~va~V~r~ 146 (253)
T PF10647_consen 121 PDGTRVAVVVEDGGGGRVYVAGVVRD 146 (253)
T ss_pred CCCcEEEEEEecCCCCeEEEEEEEeC
Confidence 6699999999 999999887643
No 9
>PF07646 Kelch_2: Kelch motif; InterPro: IPR011498 Kelch is a 50-residue motif, named after the Drosophila mutant in which it was first identified []. This sequence motif represents one beta-sheet blade, and several of these repeats can associate to form a beta-propeller. For instance, the motif appears 6 times in Drosophila egg-chamber regulatory protein, creating a 6-bladed beta-propeller. The motif is also found in mouse protein MIPP [] and in a number of poxviruses. In addition, kelch repeats have been recognised in alpha- and beta-scruin [, ], and in galactose oxidase from the fungus Dactylium dendroides [, ]. The structure of galactose oxidase reveals that the repeated sequence corresponds to a 4-stranded anti-parallel beta-sheet motif that forms the repeat unit in a super-barrel structural fold []. The known functions of kelch-containing proteins are diverse: scruin is an actin cross-linking protein; galactose oxidase catalyses the oxidation of the hydroxyl group at the C6 position in D-galactose; neuraminidase hydrolyses sialic acid residues from glycoproteins; and kelch may have a cytoskeletal function, as it is localised to the actin-rich ring canals that connect the 15 nurse cells to the developing oocyte in Drosophila []. Nevertheless, based on the location of the kelch pattern in the catalytic unit in galactose oxidase, functionally important residues have been predicted in glyoxal oxidase []. This entry represents a type of kelch sequence motif that comprises one beta-sheet blade.; GO: 0005515 protein binding
Probab=29.33 E-value=49 Score=18.44 Aligned_cols=12 Identities=50% Similarity=0.927 Sum_probs=9.4
Q ss_pred EEeeCCeEEeee
Q 034135 84 ALTVDGKIFVHA 95 (103)
Q Consensus 84 ALtvdGKVfVHa 95 (103)
+..+||||||-.
T Consensus 7 ~~~~~~kiyv~G 18 (49)
T PF07646_consen 7 AVVLDGKIYVFG 18 (49)
T ss_pred EEEECCEEEEEC
Confidence 567899999853
No 10
>cd00136 PDZ PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(pos
Probab=29.30 E-value=57 Score=18.44 Aligned_cols=24 Identities=21% Similarity=0.346 Sum_probs=16.7
Q ss_pred cceeeEEEEeeCCeEEeeeecccc
Q 034135 77 KPLGIRFALTVDGKIFVHALRKGV 100 (103)
Q Consensus 77 KPLGIRFALtvdGKVfVHaLkKG~ 100 (103)
.|+|+++.-.-++.++|..+.+|+
T Consensus 1 ~~~G~~~~~~~~~~~~V~~v~~~s 24 (70)
T cd00136 1 GGLGFSIRGGTEGGVVVLSVEPGS 24 (70)
T ss_pred CCccEEEecCCCCCEEEEEeCCCC
Confidence 367888777666578887776654
No 11
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=29.00 E-value=51 Score=17.61 Aligned_cols=12 Identities=42% Similarity=0.750 Sum_probs=8.5
Q ss_pred EEEeeCCeEEee
Q 034135 83 FALTVDGKIFVH 94 (103)
Q Consensus 83 FALtvdGKVfVH 94 (103)
.||+-||+||.-
T Consensus 12 ~al~~~g~v~~w 23 (30)
T PF13540_consen 12 CALTSDGEVYCW 23 (30)
T ss_dssp EEEE-TTEEEEE
T ss_pred EEEEcCCCEEEE
Confidence 578889998854
No 12
>PF15614 WHIM3: WSTF, HB1, Itc1p, MBD9 motif 3
Probab=28.43 E-value=7.4 Score=24.40 Aligned_cols=16 Identities=44% Similarity=0.737 Sum_probs=13.3
Q ss_pred ccceeeeeeccceeeE
Q 034135 67 NLNEYMVTLEKPLGIR 82 (103)
Q Consensus 67 NLNEYMVtleKPLGIR 82 (103)
+|||-+.+|+-|.|+|
T Consensus 9 ~ld~L~~aL~~prG~R 24 (46)
T PF15614_consen 9 ELDELLKALENPRGKR 24 (46)
T ss_pred HHHHHHHHHcCcccHh
Confidence 5778888888899998
No 13
>PF11805 DUF3326: Protein of unknown function (DUF3326); InterPro: IPR021763 This family of functionally uncharacterised proteins is found in plants and bacteria.
Probab=28.38 E-value=13 Score=31.38 Aligned_cols=52 Identities=21% Similarity=0.408 Sum_probs=38.7
Q ss_pred cceEEEEeehh-----heeeeeeeecCccccccccceeeeeeccceeeEEEEeeCCeE
Q 034135 39 RDRVKVRFSKK-----IVRVHALSSNSNSYLKMNLNEYMVTLEKPLGIRFALTVDGKI 91 (103)
Q Consensus 39 rdrv~~~~sk~-----~~R~l~~s~~~~s~fKMNLNEYMVtleKPLGIRFALtvdGKV 91 (103)
+.||-+-|.+- .+|-+-++.++-.++-.|+-+|++| |+|||++.-.+.+|.=
T Consensus 78 ~nrVGlilD~gie~el~~rhlq~ada~RAtlGl~i~~~v~T-d~pl~v~~~~~~sG~s 134 (340)
T PF11805_consen 78 QNRVGLILDAGIEPELRLRHLQVADAARATLGLNITPVVVT-DAPLGVELRYSPSGAS 134 (340)
T ss_pred cceEEEEEecCCCHHHHHHHHHHHHHHHHhcCCCCcceEEc-CCCcEEEEEEcCCCcc
Confidence 35555555443 4555556666668899999999887 9999999998888853
No 14
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=27.68 E-value=45 Score=24.08 Aligned_cols=13 Identities=38% Similarity=0.795 Sum_probs=11.8
Q ss_pred EeeCCeEEeeeec
Q 034135 85 LTVDGKIFVHALR 97 (103)
Q Consensus 85 LtvdGKVfVHaLk 97 (103)
.|.||+++|-+||
T Consensus 16 It~DGr~ivgsLk 28 (96)
T KOG1784|consen 16 ITNDGRVIVGSLK 28 (96)
T ss_pred EecCCeEEEEEec
Confidence 6999999999986
No 15
>PRK10665 nitrogen regulatory protein P-II 2; Provisional
Probab=27.43 E-value=32 Score=23.69 Aligned_cols=13 Identities=54% Similarity=0.708 Sum_probs=9.3
Q ss_pred EeeCCeEEeeeec
Q 034135 85 LTVDGKIFVHALR 97 (103)
Q Consensus 85 LtvdGKVfVHaLk 97 (103)
..=||||||--+.
T Consensus 85 ~~GDGkIfV~pV~ 97 (112)
T PRK10665 85 KIGDGKIFVAELQ 97 (112)
T ss_pred CCCCcEEEEEEhh
Confidence 4569999996543
No 16
>PF06462 Hyd_WA: Propeller; InterPro: IPR006624 Tectonins I and II are two dominant proteins in the nuclei and nuclear matrix from plasmodia of Physarum polycephalum (Slime mold) which encode 217 and 353 amino acids, respectively. Tectonin I is homologous to the C-terminal two-thirds of tectonin II. Both proteins contain six tandem repeats that are each 33-37 amino acids in length and define a new consensus sequence. Homologous repeats are found in L-6, a bacterial lipopolysaccharide-binding lectin from horseshoe crab hemocytes. The repetitive sequences of the tectonins and L-6 are reminiscent of the WD repeats of the beta-subunit of G proteins, suggesting that they form beta-propeller domains. The tectonins may be lectins that function as part of a transmembrane signalling complex during phagocytosis [].
Probab=26.27 E-value=50 Score=18.34 Aligned_cols=12 Identities=33% Similarity=0.822 Sum_probs=10.4
Q ss_pred EEEeeCCeEEee
Q 034135 83 FALTVDGKIFVH 94 (103)
Q Consensus 83 FALtvdGKVfVH 94 (103)
+|++-||+||.-
T Consensus 4 Wav~~~G~v~~R 15 (32)
T PF06462_consen 4 WAVTSDGSVYFR 15 (32)
T ss_pred EEEcCCCCEEEE
Confidence 789999999974
No 17
>PF13186 SPASM: Iron-sulfur cluster-binding domain
Probab=26.19 E-value=59 Score=17.97 Aligned_cols=13 Identities=15% Similarity=0.411 Sum_probs=10.7
Q ss_pred eEEEEeeCCeEEe
Q 034135 81 IRFALTVDGKIFV 93 (103)
Q Consensus 81 IRFALtvdGKVfV 93 (103)
-.++++.||.|+.
T Consensus 6 ~~~~I~~dG~v~p 18 (64)
T PF13186_consen 6 NSLYIDPDGDVYP 18 (64)
T ss_pred eEEEEeeCccEEe
Confidence 3678999999986
No 18
>PF12900 Pyridox_ox_2: Pyridoxamine 5'-phosphate oxidase; InterPro: IPR024747 Pyridoxamine 5'-phosphate oxidase is a FMN flavoprotein that catalyses the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This entry contains several uncharacterised proteins, some annotated as pyridoxamine 5'-phosphate oxidase-related.; PDB: 3U5W_A 3U0I_A 2X1K_A 1W3Q_A 1W3P_A 1W3O_A 2VPA_A 2X1J_A 1W3R_A 3FKH_A ....
Probab=26.04 E-value=82 Score=20.93 Aligned_cols=19 Identities=26% Similarity=0.686 Sum_probs=14.9
Q ss_pred eEEEEeeCCeEEeeeecccc
Q 034135 81 IRFALTVDGKIFVHALRKGV 100 (103)
Q Consensus 81 IRFALtvdGKVfVHaLkKG~ 100 (103)
+.|+.. ||+||+|.-+.|.
T Consensus 30 ~~f~~~-~~~ly~h~~~~g~ 48 (143)
T PF12900_consen 30 VNFVYD-GGSLYFHGARGGK 48 (143)
T ss_dssp EEEEEE-TTEEEEEECSHSH
T ss_pred EEEEEE-CCEEEEEECCcch
Confidence 356766 8899999988764
No 19
>PF04683 Proteasom_Rpn13: Proteasome complex subunit Rpn13 ubiquitin receptor; InterPro: IPR006773 This family was thought originally to be involved in cell-adhesion [, ], but the members are now known to be proteasome subunit Rpn13, a novel ubiquitin receptor. The 26S proteasome is a huge macromolecular protein-degradation machine consisting of a proteolytically active 20S core, in the form of four disc-like proteins, and one or two 19S regulatory particles. The regulatory particle(s) sit on the top and or bottom of the core, de-ubiquitinate the substrate peptides, unfold them and guide them into the narrow channel through the centre of the core. Rpn13 and its homologues dock onto the regulatory particle through the N-terminal region which binds Rpn2. The C-terminal part of the domain binds de-ubiquitinating enzyme Uch37/UCHL5 and enhances its isopeptidase activity. Rpn13 binds ubiquitin via a conserved amino-terminal region called the pleckstrin-like receptor for ubiquitin, termed Pru, domain []. The domain forms two contiguous anti-parallel beta-sheets with a configuration similar to the pleckstrin-homology domain (PHD) fold []. Rpn13's ability to bind ubiquitin and the proteasome subunit Rpn2/S1 simultaneously supports evidence of its role as a ubiquitin receptor. Finally, when complexed to di-ubiquitin, via the Pru, and Uch37 via the C-terminal part, it frees up the distal ubiquitin for de-ubiquitination by the Uch37 []. ; GO: 0005634 nucleus, 0005737 cytoplasm; PDB: 2Z4D_A 2KR0_A 2Z59_A 2R2Y_A.
Probab=25.69 E-value=72 Score=21.05 Aligned_cols=26 Identities=31% Similarity=0.386 Sum_probs=16.2
Q ss_pred cccccceeeeeecccee-eEEEEeeCC
Q 034135 64 LKMNLNEYMVTLEKPLG-IRFALTVDG 89 (103)
Q Consensus 64 fKMNLNEYMVtleKPLG-IRFALtvdG 89 (103)
+||++++++|+-|.=.| |++..+-||
T Consensus 1 Gk~~~~~~~V~pd~~KG~l~l~~~~d~ 27 (85)
T PF04683_consen 1 GKMDLDGKIVTPDPRKGLLYLYKSEDG 27 (85)
T ss_dssp EEEEEETTEEEE-SS-EEEEEEETTTS
T ss_pred CcEEEeCCEEeECCCCEEEEEEECCCC
Confidence 47889998888877666 344444444
No 20
>KOG1520 consensus Predicted alkaloid synthase/Surface mucin Hemomucin [General function prediction only]
Probab=25.02 E-value=33 Score=29.14 Aligned_cols=18 Identities=44% Similarity=0.914 Sum_probs=13.2
Q ss_pred ccceeeEEEEeeCCeEEee
Q 034135 76 EKPLGIRFALTVDGKIFVH 94 (103)
Q Consensus 76 eKPLGIRFALtvdGKVfVH 94 (103)
-|||||||-- ..|.+||-
T Consensus 115 GRPLGl~f~~-~ggdL~Va 132 (376)
T KOG1520|consen 115 GRPLGIRFDK-KGGDLYVA 132 (376)
T ss_pred CCcceEEecc-CCCeEEEE
Confidence 6999999964 34477764
No 21
>PF13964 Kelch_6: Kelch motif
Probab=24.99 E-value=67 Score=17.73 Aligned_cols=11 Identities=55% Similarity=0.905 Sum_probs=8.1
Q ss_pred EEeeCCeEEee
Q 034135 84 ALTVDGKIFVH 94 (103)
Q Consensus 84 ALtvdGKVfVH 94 (103)
+.+++|+|||=
T Consensus 7 ~v~~~~~iyv~ 17 (50)
T PF13964_consen 7 AVVVGGKIYVF 17 (50)
T ss_pred EEEECCEEEEE
Confidence 45688999874
No 22
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=24.66 E-value=48 Score=22.36 Aligned_cols=24 Identities=46% Similarity=0.696 Sum_probs=17.3
Q ss_pred eeeeec-cceeeEEEEeeCCe--EEee
Q 034135 71 YMVTLE-KPLGIRFALTVDGK--IFVH 94 (103)
Q Consensus 71 YMVtle-KPLGIRFALtvdGK--VfVH 94 (103)
|+|+|| -|.||=|=--.|++ +||.
T Consensus 33 YLvaL~dYP~GiWFFNE~~~~dG~FVe 59 (62)
T PF10781_consen 33 YLVALEDYPAGIWFFNEKDSPDGTFVE 59 (62)
T ss_pred EEEEcCcCCcceEEEecCCCCCcEEee
Confidence 889985 69999996555443 5664
No 23
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=24.43 E-value=34 Score=25.72 Aligned_cols=15 Identities=33% Similarity=0.705 Sum_probs=12.9
Q ss_pred ceeeeeeccceeeEE
Q 034135 69 NEYMVTLEKPLGIRF 83 (103)
Q Consensus 69 NEYMVtleKPLGIRF 83 (103)
+|+++.+|||-|+--
T Consensus 8 d~~~lvvnKPaGl~~ 22 (257)
T PRK11112 8 DEWLVAVNKPAGWLV 22 (257)
T ss_pred cCCEEEEECCCCCee
Confidence 688999999999954
No 24
>KOG1417 consensus Homogentisate 1,2-dioxygenase [Amino acid transport and metabolism]
Probab=23.81 E-value=41 Score=29.33 Aligned_cols=21 Identities=48% Similarity=0.736 Sum_probs=15.9
Q ss_pred ccceeeeeeccceeeEEEEeeCCe
Q 034135 67 NLNEYMVTLEKPLGIRFALTVDGK 90 (103)
Q Consensus 67 NLNEYMVtleKPLGIRFALtvdGK 90 (103)
+-||--| -|-||||++.|+|+
T Consensus 178 ~P~EI~V---IpqG~RFsi~v~~~ 198 (446)
T KOG1417|consen 178 TPNEIAV---IPQGIRFSIDVPGP 198 (446)
T ss_pred cccceEE---eecccEEEEecCCC
Confidence 3455544 38999999999985
No 25
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.
Probab=23.54 E-value=36 Score=24.71 Aligned_cols=14 Identities=36% Similarity=0.714 Sum_probs=12.1
Q ss_pred ceeeeeeccceeeE
Q 034135 69 NEYMVTLEKPLGIR 82 (103)
Q Consensus 69 NEYMVtleKPLGIR 82 (103)
||+.+.+|||-|+=
T Consensus 7 d~~~lvvnKP~G~~ 20 (223)
T cd02563 7 DEHLVAINKPSGLL 20 (223)
T ss_pred cCCEEEEECCCCCe
Confidence 67888999999983
No 26
>PF01344 Kelch_1: Kelch motif; InterPro: IPR006652 Kelch is a 50-residue motif, named after the Drosophila mutant in which it was first identified []. This sequence motif represents one beta-sheet blade, and several of these repeats can associate to form a beta-propeller. For instance, the motif appears 6 times in Drosophila egg-chamber regulatory protein, creating a 6-bladed beta-propeller. The motif is also found in mouse protein MIPP [] and in a number of poxviruses. In addition, kelch repeats have been recognised in alpha- and beta-scruin [, ], and in galactose oxidase from the fungus Dactylium dendroides [, ]. The structure of galactose oxidase reveals that the repeated sequence corresponds to a 4-stranded anti-parallel beta-sheet motif that forms the repeat unit in a super-barrel structural fold []. The known functions of kelch-containing proteins are diverse: scruin is an actin cross-linking protein; galactose oxidase catalyses the oxidation of the hydroxyl group at the C6 position in D-galactose; neuraminidase hydrolyses sialic acid residues from glycoproteins; and kelch may have a cytoskeletal function, as it is localised to the actin-rich ring canals that connect the 15 nurse cells to the developing oocyte in Drosophila []. Nevertheless, based on the location of the kelch pattern in the catalytic unit in galactose oxidase, functionally important residues have been predicted in glyoxal oxidase []. This entry represents a type of kelch sequence motif that comprises one beta-sheet blade.; GO: 0005515 protein binding; PDB: 2XN4_A 2WOZ_A 3II7_A 4ASC_A 1U6D_X 1ZGK_A 2FLU_X 2VPJ_A 2DYH_A 1X2R_A ....
Probab=23.08 E-value=80 Score=16.80 Aligned_cols=11 Identities=45% Similarity=0.655 Sum_probs=8.5
Q ss_pred EEeeCCeEEee
Q 034135 84 ALTVDGKIFVH 94 (103)
Q Consensus 84 ALtvdGKVfVH 94 (103)
+.+++|+|||-
T Consensus 7 ~~~~~~~iyv~ 17 (47)
T PF01344_consen 7 AVVVGNKIYVI 17 (47)
T ss_dssp EEEETTEEEEE
T ss_pred EEEECCEEEEE
Confidence 45788999985
No 27
>PF13313 DUF4082: Domain of unknown function (DUF4082)
Probab=22.93 E-value=60 Score=24.24 Aligned_cols=17 Identities=35% Similarity=0.847 Sum_probs=13.9
Q ss_pred eeeEEEEeeCCeEEeeeec
Q 034135 79 LGIRFALTVDGKIFVHALR 97 (103)
Q Consensus 79 LGIRFALtvdGKVfVHaLk 97 (103)
||+||--+++|.| .+|+
T Consensus 21 LG~kF~~~~~G~v--tgvr 37 (149)
T PF13313_consen 21 LGVKFRSSVAGQV--TGVR 37 (149)
T ss_pred EEeEEEecCCcEE--EEEE
Confidence 8999999999976 4554
No 28
>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]
Probab=22.75 E-value=26 Score=31.05 Aligned_cols=14 Identities=43% Similarity=0.264 Sum_probs=11.8
Q ss_pred ccccceeeeeeccc
Q 034135 65 KMNLNEYMVTLEKP 78 (103)
Q Consensus 65 KMNLNEYMVtleKP 78 (103)
-.||||||||.|.=
T Consensus 302 vsnln~~~VT~d~L 315 (492)
T KOG1190|consen 302 VSNLNEEAVTPDVL 315 (492)
T ss_pred EecCchhccchhHH
Confidence 35899999999974
No 29
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=22.34 E-value=39 Score=24.70 Aligned_cols=14 Identities=29% Similarity=0.627 Sum_probs=11.6
Q ss_pred ceeeeeeccceeeE
Q 034135 69 NEYMVTLEKPLGIR 82 (103)
Q Consensus 69 NEYMVtleKPLGIR 82 (103)
+|.++.+|||-|+-
T Consensus 20 d~~~lvvnKPaGl~ 33 (219)
T PRK10158 20 DEHIMVVNKPSGLL 33 (219)
T ss_pred CCCEEEEECCCCCc
Confidence 56777899999994
No 30
>PF08068 DKCLD: DKCLD (NUC011) domain; InterPro: IPR012960 This is an N-terminal domain of dyskerin-like proteins, which is often associated with the TruB N-terminal(IPR002501 from INTERPRO) and PUA(IPR002478 from INTERPRO) domains [].; PDB: 3ZV0_D 3UAI_A 3U28_A 2AUS_C 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=22.30 E-value=37 Score=22.33 Aligned_cols=19 Identities=47% Similarity=0.807 Sum_probs=12.1
Q ss_pred ccccccccee----eeeecccee
Q 034135 62 SYLKMNLNEY----MVTLEKPLG 80 (103)
Q Consensus 62 s~fKMNLNEY----MVtleKPLG 80 (103)
+..+-.+.|| +|.||||-|
T Consensus 30 ~P~~R~i~~~i~~GvinlDKP~g 52 (59)
T PF08068_consen 30 SPLKRPIEEYIKYGVINLDKPSG 52 (59)
T ss_dssp -GGGS-HHHHHHTEEEEEEE-SS
T ss_pred CcccCCHHHHHhCCcEEeeCCCC
Confidence 5556666676 599999987
No 31
>PF07995 GSDH: Glucose / Sorbosone dehydrogenase; InterPro: IPR012938 Proteins containing this domain are thought to be glucose/sorbosone dehydrogenases. The best characterised of these proteins is soluble glucose dehydrogenase (P13650 from SWISSPROT) from Acinetobacter calcoaceticus, which oxidises glucose to gluconolactone. The enzyme is a calcium-dependent homodimer which uses PQQ as a cofactor [].; GO: 0016901 oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor, 0048038 quinone binding, 0005975 carbohydrate metabolic process; PDB: 2ISM_A 2WG3_D 3HO5_A 3HO4_A 3HO3_A 2WFT_A 2WG4_B 2WFX_B 1CRU_A 1CQ1_B ....
Probab=22.22 E-value=61 Score=24.92 Aligned_cols=21 Identities=33% Similarity=0.436 Sum_probs=17.1
Q ss_pred EEEeeCCeEEeeeeccccccC
Q 034135 83 FALTVDGKIFVHALRKGVIHR 103 (103)
Q Consensus 83 FALtvdGKVfVHaLkKG~ihr 103 (103)
+|++.||.+||-....|.|.|
T Consensus 311 v~~~pDG~Lyv~~d~~G~iyR 331 (331)
T PF07995_consen 311 VAQGPDGALYVSDDSDGKIYR 331 (331)
T ss_dssp EEEETTSEEEEEE-TTTTEEE
T ss_pred EEEcCCCeEEEEECCCCeEeC
Confidence 577789999999989898865
No 32
>PF00543 P-II: Nitrogen regulatory protein P-II members of this family.; InterPro: IPR002187 In Gram-negative bacteria, the activity and concentration of glutamine synthetase (GS) is regulated in response to nitrogen source availability. PII, a tetrameric protein encoded by the glnB gene, is a component of the adenylation cascade involved in the regulation of GS activity []. In nitrogen-limiting conditions, when the ratio of glutamine to 2-ketoglutarate decreases, P-II is uridylylated on a tyrosine residue to form P-II-UMP. P-II-UMP allows the deadenylation of GS, thus activating the enzyme. Conversely, in nitrogen excess, P-II-UMP is deuridylated and then promotes the adenylation of GS. P-II also indirectly controls the transcription of the GS gene (glnA) by preventing NR-II (ntrB) to phosphorylate NR-I (ntrC) which is the transcriptional activator of glnA. Once P-II is uridylylated, these events are reversed. P-II is a protein of about 110 amino acid residues extremely well conserved. The tyrosine which is uridylated is located in the central part of the protein. In cyanobacteria, P-II seems to be phosphorylated on a serine residue rather than being uridylated. In methanogenic archaebacteria, the nitrogenase iron protein gene (nifH) is followed by two open reading frames highly similar to the eubacterial P-II protein []. These proteins could be involved in the regulation of nitrogen fixation. In the red alga, Porphyra purpurea, there is a glnB homologue encoded in the chloroplast genome. Other proteins highly similar to glnB are: Bacillus subtilis protein nrgB []. Escherichia coli hypothetical protein ybaI []. ; GO: 0030234 enzyme regulator activity, 0006808 regulation of nitrogen utilization; PDB: 1V3S_B 1V3R_C 2XZW_A 2XUL_A 2V5H_J 2XG8_C 2JJ4_F 1QY7_C 4AFF_A 2XBP_A ....
Probab=21.98 E-value=44 Score=21.61 Aligned_cols=12 Identities=50% Similarity=0.778 Sum_probs=8.2
Q ss_pred eeCCeEEeeeec
Q 034135 86 TVDGKIFVHALR 97 (103)
Q Consensus 86 tvdGKVfVHaLk 97 (103)
.=||||||--+.
T Consensus 83 ~GdGkIfV~~V~ 94 (102)
T PF00543_consen 83 PGDGKIFVSPVE 94 (102)
T ss_dssp TTSEEEEEEEES
T ss_pred CCCEEEEEEEhh
Confidence 348999986543
No 33
>PF09696 Ctf8: Ctf8; InterPro: IPR018607 Ctf8 (chromosome transmissions fidelity 8) is a component of the Ctf18 RFC-like complex which is a DNA clamp loader involved in sister chromatid cohesion.
Probab=21.84 E-value=47 Score=23.17 Aligned_cols=11 Identities=45% Similarity=0.806 Sum_probs=9.3
Q ss_pred eeeeeccceee
Q 034135 71 YMVTLEKPLGI 81 (103)
Q Consensus 71 YMVtleKPLGI 81 (103)
=++.|+|||+|
T Consensus 71 kv~kL~kPLaV 81 (122)
T PF09696_consen 71 KVVKLKKPLAV 81 (122)
T ss_pred EEeccCCCEEE
Confidence 36899999997
No 34
>KOG2509 consensus Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=21.79 E-value=35 Score=29.93 Aligned_cols=21 Identities=52% Similarity=0.907 Sum_probs=18.1
Q ss_pred cceeeEEEE--eeCC-eEEeeeec
Q 034135 77 KPLGIRFAL--TVDG-KIFVHALR 97 (103)
Q Consensus 77 KPLGIRFAL--tvdG-KVfVHaLk 97 (103)
|=|||||.. +-|| +-|||-|-
T Consensus 377 RRL~IRy~~~k~~~~~~~yvHtLN 400 (455)
T KOG2509|consen 377 RRLGIRYGQKKTNDGEKKYVHTLN 400 (455)
T ss_pred hhhhhhcccccccCCccceeeecc
Confidence 679999999 8888 78999873
No 35
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=21.26 E-value=67 Score=25.82 Aligned_cols=23 Identities=22% Similarity=0.433 Sum_probs=18.7
Q ss_pred eeccceeeEEEEeeCCeEEeeee
Q 034135 74 TLEKPLGIRFALTVDGKIFVHAL 96 (103)
Q Consensus 74 tleKPLGIRFALtvdGKVfVHaL 96 (103)
+|.+=++++.++..+|+|||.+=
T Consensus 170 ~l~~~~~~~I~VG~NG~IWV~~~ 192 (239)
T COG1097 170 MLKEKTGCEIIVGQNGRIWVDGE 192 (239)
T ss_pred HhhhhcCeEEEEecCCEEEecCC
Confidence 34555799999999999999753
No 36
>PF03725 RNase_PH_C: 3' exoribonuclease family, domain 2 This Prosite family only includes Ribonuclease PH; InterPro: IPR015847 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 2, which has a core 3-layer alpha/beta/alpha structure. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 2NN6_E 2WNR_A 3U1K_B 2BA0_H 2BA1_H 3M85_G 3M7N_H 3H1C_K ....
Probab=20.98 E-value=1.2e+02 Score=17.72 Aligned_cols=17 Identities=24% Similarity=0.688 Sum_probs=12.3
Q ss_pred ceeeEEEEeeCCeEEeee
Q 034135 78 PLGIRFALTVDGKIFVHA 95 (103)
Q Consensus 78 PLGIRFALtvdGKVfVHa 95 (103)
|.++++|+- ||+++|+-
T Consensus 3 ~~avt~~~i-~~~~v~Dp 19 (68)
T PF03725_consen 3 PVAVTVGII-DGELVVDP 19 (68)
T ss_dssp EEEEEEEEE-TTEEEES-
T ss_pred eEEEEEEEE-CCEEEECC
Confidence 778888886 77777753
No 37
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621. This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.
Probab=20.43 E-value=45 Score=24.42 Aligned_cols=14 Identities=21% Similarity=0.332 Sum_probs=12.1
Q ss_pred ceeeeeeccceeeE
Q 034135 69 NEYMVTLEKPLGIR 82 (103)
Q Consensus 69 NEYMVtleKPLGIR 82 (103)
+|+.+.++||-|+-
T Consensus 8 d~~~lvvnKP~Gl~ 21 (217)
T TIGR01621 8 HPDFLLINKHPGIS 21 (217)
T ss_pred CCCEEEEECCCCCe
Confidence 67889999999983
No 38
>cd00992 PDZ_signaling PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
Probab=20.42 E-value=1.5e+02 Score=16.96 Aligned_cols=25 Identities=32% Similarity=0.412 Sum_probs=15.6
Q ss_pred ccceeeEEEEeeC--CeEEeeeecccc
Q 034135 76 EKPLGIRFALTVD--GKIFVHALRKGV 100 (103)
Q Consensus 76 eKPLGIRFALtvd--GKVfVHaLkKG~ 100 (103)
.+|+|+++.-..+ +-++|..+..|+
T Consensus 11 ~~~~G~~~~~~~~~~~~~~V~~v~~~s 37 (82)
T cd00992 11 GGGLGFSLRGGKDSGGGIFVSRVEPGG 37 (82)
T ss_pred CCCcCEEEeCcccCCCCeEEEEECCCC
Confidence 3568877654432 347888777664
No 39
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.
Probab=20.28 E-value=46 Score=24.16 Aligned_cols=13 Identities=31% Similarity=0.782 Sum_probs=11.2
Q ss_pred ceeeeeeccceee
Q 034135 69 NEYMVTLEKPLGI 81 (103)
Q Consensus 69 NEYMVtleKPLGI 81 (103)
+|.++.+|||-|+
T Consensus 22 d~~~ivvnKP~Gl 34 (213)
T cd02557 22 DDDLLVVDKPSGI 34 (213)
T ss_pred CCCEEEEECCCCC
Confidence 6778889999997
No 40
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=20.27 E-value=45 Score=24.86 Aligned_cols=15 Identities=27% Similarity=0.634 Sum_probs=12.5
Q ss_pred ceeeeeeccceeeEE
Q 034135 69 NEYMVTLEKPLGIRF 83 (103)
Q Consensus 69 NEYMVtleKPLGIRF 83 (103)
+++++.+|||-|+=-
T Consensus 78 d~~~lvvnKP~g~~~ 92 (299)
T TIGR00005 78 DEDIIVINKPSGLVV 92 (299)
T ss_pred CCCEEEEECCCCCeE
Confidence 478899999999844
Done!