Query 037388
Match_columns 70
No_of_seqs 21 out of 23
Neff 2.0
Searched_HMMs 46136
Date Fri Mar 29 11:44:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037388.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037388hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07021 MetW: Methionine bios 90.7 0.096 2.1E-06 38.1 0.6 56 5-65 15-71 (193)
2 PF13489 Methyltransf_23: Meth 84.4 0.67 1.5E-05 28.1 1.5 33 4-37 23-55 (161)
3 PF03815 LCCL: LCCL domain; I 68.4 1.7 3.7E-05 27.7 0.1 28 24-53 31-58 (96)
4 smart00603 LCCL LCCL domain. 66.6 1.7 3.6E-05 27.6 -0.2 30 24-55 29-58 (85)
5 PF08241 Methyltransf_11: Meth 66.2 4.1 8.8E-05 22.3 1.3 30 8-37 1-30 (95)
6 cd02440 AdoMet_MTases S-adenos 63.8 7.1 0.00015 20.4 1.9 30 6-35 1-30 (107)
7 PF02887 PK_C: Pyruvate kinase 61.5 3.7 8.1E-05 25.6 0.7 14 28-41 57-70 (117)
8 smart00650 rADc Ribosomal RNA 59.2 7.8 0.00017 25.1 1.9 30 5-35 15-44 (169)
9 PF10007 DUF2250: Uncharacteri 58.2 7.4 0.00016 25.3 1.7 34 10-54 19-52 (92)
10 PF13465 zf-H2C2_2: Zinc-finge 52.5 16 0.00035 18.1 2.0 17 53-69 3-19 (26)
11 PF12847 Methyltransf_18: Meth 47.3 15 0.00033 21.2 1.6 31 5-35 3-34 (112)
12 PTZ00338 dimethyladenosine tra 45.9 15 0.00032 27.2 1.7 29 5-34 38-66 (294)
13 TIGR02081 metW methionine bios 45.9 18 0.0004 23.8 2.0 31 5-35 15-45 (194)
14 PHA02130 hypothetical protein 44.4 23 0.00049 23.5 2.3 31 26-56 41-78 (81)
15 PF08242 Methyltransf_12: Meth 43.2 9.7 0.00021 22.0 0.4 29 8-36 1-30 (99)
16 PF14545 DBB: Dof, BCAP, and B 42.7 20 0.00043 25.2 1.9 35 17-51 92-132 (142)
17 PF12317 IFT46_B_C: Intraflage 42.5 22 0.00047 26.7 2.2 28 36-64 107-134 (214)
18 cd04371 DEP DEP domain, named 41.8 15 0.00033 20.9 1.1 36 15-57 32-67 (81)
19 PF02677 DUF208: Uncharacteriz 41.2 20 0.00043 25.8 1.8 18 7-24 2-21 (176)
20 PF08003 Methyltransf_9: Prote 39.7 24 0.00053 27.7 2.2 39 3-41 115-153 (315)
21 PRK00274 ksgA 16S ribosomal RN 39.5 22 0.00047 25.3 1.8 30 5-35 44-73 (272)
22 TIGR00537 hemK_rel_arch HemK-r 39.1 35 0.00076 22.1 2.6 40 5-45 21-62 (179)
23 PRK14896 ksgA 16S ribosomal RN 38.4 22 0.00049 25.0 1.7 30 5-35 31-60 (258)
24 PF14078 DUF4259: Domain of un 38.3 14 0.00031 23.2 0.6 22 29-50 2-23 (128)
25 TIGR00755 ksgA dimethyladenosi 37.8 26 0.00056 24.4 1.9 30 5-35 31-60 (253)
26 cd04449 DEP_DEPDC5-like DEP (D 34.1 15 0.00033 22.5 0.2 30 36-65 48-81 (83)
27 KOG3147 6-phosphogluconolacton 33.0 15 0.00032 28.3 0.1 26 7-32 147-174 (252)
28 TIGR00452 methyltransferase, p 32.9 35 0.00076 25.7 2.0 33 5-37 123-155 (314)
29 TIGR02469 CbiT precorrin-6Y C5 32.7 38 0.00082 19.5 1.8 32 5-36 21-53 (124)
30 PRK00121 trmB tRNA (guanine-N( 31.6 62 0.0013 21.9 2.9 33 4-36 41-74 (202)
31 PRK00304 hypothetical protein; 31.0 53 0.0011 21.1 2.4 37 16-54 15-51 (75)
32 PF10959 DUF2761: Protein of u 28.0 22 0.00047 24.2 0.2 15 25-39 37-51 (95)
33 KOG0820 Ribosomal RNA adenine 28.0 43 0.00093 26.8 1.8 21 5-25 60-80 (315)
34 PF14217 DUF4327: Domain of un 27.8 26 0.00057 22.2 0.6 20 35-54 2-21 (68)
35 PF12140 DUF3588: Protein of u 26.5 35 0.00077 23.1 1.0 13 8-20 29-41 (118)
36 PRK07402 precorrin-6B methylas 26.0 96 0.0021 20.4 3.0 42 5-46 42-86 (196)
37 PF12129 Phtf-FEM1B_bdg: Male 25.3 57 0.0012 23.7 1.9 15 44-58 68-82 (159)
38 TIGR03587 Pse_Me-ase pseudamin 23.9 52 0.0011 22.6 1.5 32 5-36 45-77 (204)
39 smart00828 PKS_MT Methyltransf 23.6 1.5E+02 0.0032 19.5 3.6 30 5-34 1-31 (224)
40 PRK00312 pcm protein-L-isoaspa 23.3 1.4E+02 0.0029 19.9 3.3 30 5-35 80-109 (212)
41 PRK13942 protein-L-isoaspartat 23.2 63 0.0014 22.1 1.8 32 5-36 78-111 (212)
42 PRK15068 tRNA mo(5)U34 methylt 23.1 1.1E+02 0.0023 22.7 3.1 35 5-39 124-158 (322)
43 PRK05134 bifunctional 3-demeth 23.0 64 0.0014 21.5 1.7 29 5-34 50-78 (233)
44 COG2804 PulE Type II secretory 23.0 40 0.00087 28.0 0.9 22 13-40 363-384 (500)
45 PF01135 PCMT: Protein-L-isoas 22.8 96 0.0021 21.9 2.7 31 5-36 74-107 (209)
46 PF09079 Cdc6_C: CDC6, C termi 22.4 14 0.0003 21.9 -1.4 35 27-61 29-63 (85)
47 PF05402 PqqD: Coenzyme PQQ sy 22.1 71 0.0015 17.7 1.6 24 30-53 43-67 (68)
48 TIGR00417 speE spermidine synt 21.8 1.2E+02 0.0027 21.4 3.1 31 4-34 73-104 (270)
49 cd01986 Alpha_ANH_like Adenine 21.5 1.5E+02 0.0032 17.7 3.0 45 11-57 8-58 (103)
50 PRK11036 putative S-adenosyl-L 21.4 75 0.0016 21.9 1.9 31 5-36 46-76 (255)
51 PF15488 DUF4645: Domain of un 21.3 33 0.00072 27.2 0.1 16 18-34 37-52 (294)
52 COG0469 PykF Pyruvate kinase [ 21.3 35 0.00075 28.0 0.2 30 28-57 416-453 (477)
53 PRK03612 spermidine synthase; 21.3 72 0.0016 25.3 2.0 31 4-34 298-329 (521)
54 PF00610 DEP: Domain found in 21.0 33 0.00071 19.5 0.0 22 35-56 36-57 (74)
55 cd04448 DEP_PIKfyve DEP (Dishe 20.7 55 0.0012 20.2 1.0 34 16-56 33-66 (81)
56 PF01281 Ribosomal_L9_N: Ribos 20.3 47 0.001 19.3 0.6 17 48-64 21-37 (48)
57 TIGR00438 rrmJ cell division p 20.2 85 0.0018 20.5 1.9 33 5-37 34-68 (188)
58 smart00049 DEP Domain found in 20.2 34 0.00074 19.6 0.0 34 17-57 26-59 (77)
No 1
>PF07021 MetW: Methionine biosynthesis protein MetW; InterPro: IPR010743 This family consists of several bacterial and one archaeal methionine biosynthesis MetW proteins. Biosynthesis of methionine from homoserine in Pseudomonas putida takes place in three steps. The first step is the acylation of homoserine to yield an acyl-L-homoserine. This reaction is catalysed by the products of the metXW genes and is equivalent to the first step in enterobacteria, Gram-positive bacteria and fungi, except that in these microorganisms the reaction is catalysed by a single polypeptide (the product of the metA gene in Escherichia coli and the met5 gene product in Neurospora crassa). In P. putida, as in Gram-positive bacteria and certain fungi, the second and third steps are a direct sulphydrylation that converts the O-acyl-L-homoserine into homocysteine and further methylation to yield methionine. The latter reaction can be mediated by either of the two methionine synthetases present in the cells [].
Probab=90.70 E-value=0.096 Score=38.13 Aligned_cols=56 Identities=9% Similarity=0.106 Sum_probs=43.7
Q ss_pred eeeeeeCCCchhHhHhhhcccccccccccccchhhHHHHHHHHHHHHH-HHHhHhhcCccee
Q 037388 5 CTKFEVSPDTYPVVSRFLNEEETKAWGLEPYDTEVAENLCIKALYAWL-ISNFLFHTGQHFF 65 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkEeeTeAWGVEPYd~edad~~CksLvrkgl-vr~~~~h~g~~~~ 65 (70)
.+||.+|-+.-...+.|.++-..++.|||-. +.+-.+.++||+ |--.|.-.|+..|
T Consensus 15 srVLDLGCGdG~LL~~L~~~k~v~g~GvEid-----~~~v~~cv~rGv~Viq~Dld~gL~~f 71 (193)
T PF07021_consen 15 SRVLDLGCGDGELLAYLKDEKQVDGYGVEID-----PDNVAACVARGVSVIQGDLDEGLADF 71 (193)
T ss_pred CEEEecCCCchHHHHHHHHhcCCeEEEEecC-----HHHHHHHHHcCCCEEECCHHHhHhhC
Confidence 5899999999999999999999999999843 344667788887 5555655666544
No 2
>PF13489 Methyltransf_23: Methyltransferase domain; PDB: 3JWJ_A 3JWH_B 2AOV_B 2AOT_A 1JQD_B 2AOX_A 1JQE_A 2AOU_B 2AOW_A 3DLI_C ....
Probab=84.42 E-value=0.67 Score=28.06 Aligned_cols=33 Identities=6% Similarity=0.053 Sum_probs=26.2
Q ss_pred eeeeeeeCCCchhHhHhhhcccccccccccccch
Q 037388 4 ACTKFEVSPDTYPVVSRFLNEEETKAWGLEPYDT 37 (70)
Q Consensus 4 ~~kvLHVGPdTC~VVSkLLkEeeTeAWGVEPYd~ 37 (70)
-.+||.+|+++-.....| ++...+..|++|++-
T Consensus 23 ~~~vLDiGcG~G~~~~~l-~~~~~~~~g~D~~~~ 55 (161)
T PF13489_consen 23 GKRVLDIGCGTGSFLRAL-AKRGFEVTGVDISPQ 55 (161)
T ss_dssp TSEEEEESSTTSHHHHHH-HHTTSEEEEEESSHH
T ss_pred CCEEEEEcCCCCHHHHHH-HHhCCEEEEEECCHH
Confidence 368999999999665555 677779999999853
No 3
>PF03815 LCCL: LCCL domain; InterPro: IPR004043 The LCCL domain has been named after the best characterised proteins that were found to contain it, namely Limulus factor C, Coch-5b2 and Lgl1. It is an about 100 amino acids domain whose C-terminal part contains a highly conserved histidine in a conserved motif YxxxSxxCxAAVHxGVI. The LCCL module is thought to be an autonomously folding domain that has been used for the construction of various modular proteins through exon-shuffling. It has been found in various metazoan proteins in association with complement B-type domains, C-type lectin domains, von Willebrand type A domains, CUB domains, discoidin lectin domains or CAP domains. It has been proposed that the LCCL domain could be involved in lipopolysaccharide (LPS) binding [, ]. Secondary structure prediction suggests that the LCCL domain contains six beta strands and two alpha helices []. Some proteins known to contain a LCCL domain include Limulus factor C, a LPS endotoxin-sensitive trypsin type serine protease which serves to protect the organism from bacterial infection; vertebrate cochlear protein cochlin or coch-5b2 (Cochlin is probably a secreted protein, mutations affecting the LCCL domain of coch-5b2 cause the deafness disorder DFNA9 in humans); and mammalian late gestation lung protein Lgl1, contains two tandem copies of the LCCL domain [].; PDB: 1JBI_A.
Probab=68.41 E-value=1.7 Score=27.67 Aligned_cols=28 Identities=21% Similarity=0.503 Sum_probs=22.1
Q ss_pred ccccccccccccchhhHHHHHHHHHHHHHH
Q 037388 24 EEETKAWGLEPYDTEVAENLCIKALYAWLI 53 (70)
Q Consensus 24 EeeTeAWGVEPYd~edad~~CksLvrkglv 53 (70)
++....||-.+|.. -++-|++.|..|+|
T Consensus 31 ~~~~~v~Gt~~Y~~--~SsIC~AAIHaGvi 58 (96)
T PF03815_consen 31 DSKGTVYGTDVYSA--DSSICKAAIHAGVI 58 (96)
T ss_dssp SSS--EESSSSEET--TSBHHHHHHHHTSS
T ss_pred CCCCeEECCccccC--CCHHHHHHHhCCEE
Confidence 34489999999984 46899999999998
No 4
>smart00603 LCCL LCCL domain.
Probab=66.64 E-value=1.7 Score=27.61 Aligned_cols=30 Identities=33% Similarity=0.478 Sum_probs=25.0
Q ss_pred ccccccccccccchhhHHHHHHHHHHHHHHHH
Q 037388 24 EEETKAWGLEPYDTEVAENLCIKALYAWLISN 55 (70)
Q Consensus 24 EeeTeAWGVEPYd~edad~~CksLvrkglvr~ 55 (70)
++..+.||-..|+. -++-|++.|..|+|++
T Consensus 29 ~~~~~V~Gt~~Y~~--dS~iC~AAiHaGvi~~ 58 (85)
T smart00603 29 LEKAKVFGTIVYAS--LSSICRAAVHAGVISN 58 (85)
T ss_pred cCCCeEEeccccCC--CCHHHHHhhhCCEEcC
Confidence 34489999999986 4678999999999975
No 5
>PF08241 Methyltransf_11: Methyltransferase domain; InterPro: IPR013216 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to: Arsenite methyltransferase (2.1.1.137 from EC) which converts arsenical compounds to their methylated forms [] Biotin synthesis protein bioC, which is involved in the early stages of biotin biosyntheis [] Arginine N-methyltransferase 1, an arginine-methylating enzyme which acts on residues present in a glycine and argine-rich domain and can methylate histones [] Hexaprenyldihydroxybenzoate methyltransferase (2.1.1.114 from EC), a mitochodrial enzyme involved in ubiquinone biosynthesis [] A probable cobalt-precorrin-6Y C(15)-methyltransferase thought to be involved in adenosylcobalamin biosynthesis [] Sterol 24-C-methyltransferase (2.1.1.41 from EC), shown to participate in ergosterol biosynthesis [] 3-demethylubiquinone-9 3-methyltransferase (2.1.1.64 from EC) involved in ubiquinone biosynthesis [] Structural studies show that this domain forms the Rossman-like alpha-beta fold typical of SAM-dependent methyltransferases [, , ]. ; GO: 0008168 methyltransferase activity, 0008152 metabolic process; PDB: 3CGG_B 3CCF_B 3BKW_B 2PXX_A 3I9F_A 2YQZ_B 2YR0_A 3BUS_A 3EGE_A 3G5L_B ....
Probab=66.19 E-value=4.1 Score=22.25 Aligned_cols=30 Identities=7% Similarity=0.129 Sum_probs=23.8
Q ss_pred eeeCCCchhHhHhhhcccccccccccccch
Q 037388 8 FEVSPDTYPVVSRFLNEEETKAWGLEPYDT 37 (70)
Q Consensus 8 LHVGPdTC~VVSkLLkEeeTeAWGVEPYd~ 37 (70)
|.+|..+-.....|.+....+.+|++|..-
T Consensus 1 LdiG~G~G~~~~~l~~~~~~~v~~~D~~~~ 30 (95)
T PF08241_consen 1 LDIGCGTGRFAAALAKRGGASVTGIDISEE 30 (95)
T ss_dssp EEET-TTSHHHHHHHHTTTCEEEEEES-HH
T ss_pred CEecCcCCHHHHHHHhccCCEEEEEeCCHH
Confidence 678888988888888887899999998753
No 6
>cd02440 AdoMet_MTases S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
Probab=63.83 E-value=7.1 Score=20.36 Aligned_cols=30 Identities=7% Similarity=0.070 Sum_probs=23.0
Q ss_pred eeeeeCCCchhHhHhhhccccccccccccc
Q 037388 6 TKFEVSPDTYPVVSRFLNEEETKAWGLEPY 35 (70)
Q Consensus 6 kvLHVGPdTC~VVSkLLkEeeTeAWGVEPY 35 (70)
+++++|+.+-.....+++....+.+|+|+-
T Consensus 1 ~ildig~G~G~~~~~~~~~~~~~~~~~d~~ 30 (107)
T cd02440 1 RVLDLGCGTGALALALASGPGARVTGVDIS 30 (107)
T ss_pred CeEEEcCCccHHHHHHhcCCCCEEEEEeCC
Confidence 578999999777777776567788888763
No 7
>PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP: ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C ....
Probab=61.50 E-value=3.7 Score=25.60 Aligned_cols=14 Identities=29% Similarity=0.468 Sum_probs=10.3
Q ss_pred ccccccccchhhHH
Q 037388 28 KAWGLEPYDTEVAE 41 (70)
Q Consensus 28 eAWGVEPYd~edad 41 (70)
=.|||.|+-+++.+
T Consensus 57 l~~GV~p~~~~~~~ 70 (117)
T PF02887_consen 57 LYWGVYPVLIEEFD 70 (117)
T ss_dssp GSTTEEEEECSSHS
T ss_pred cccceEEEEecccc
Confidence 47999997665554
No 8
>smart00650 rADc Ribosomal RNA adenine dimethylases.
Probab=59.20 E-value=7.8 Score=25.09 Aligned_cols=30 Identities=17% Similarity=0.245 Sum_probs=25.3
Q ss_pred eeeeeeCCCchhHhHhhhccccccccccccc
Q 037388 5 CTKFEVSPDTYPVVSRFLNEEETKAWGLEPY 35 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkEeeTeAWGVEPY 35 (70)
.++|.+||++-.+...|++. ..+++|||.-
T Consensus 15 ~~vLEiG~G~G~lt~~l~~~-~~~v~~vE~~ 44 (169)
T smart00650 15 DTVLEIGPGKGALTEELLER-AARVTAIEID 44 (169)
T ss_pred CEEEEECCCccHHHHHHHhc-CCeEEEEECC
Confidence 47999999998888888876 6788998875
No 9
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=58.24 E-value=7.4 Score=25.32 Aligned_cols=34 Identities=21% Similarity=0.100 Sum_probs=29.3
Q ss_pred eCCCchhHhHhhhcccccccccccccchhhHHHHHHHHHHHHHHH
Q 037388 10 VSPDTYPVVSRFLNEEETKAWGLEPYDTEVAENLCIKALYAWLIS 54 (70)
Q Consensus 10 VGPdTC~VVSkLLkEeeTeAWGVEPYd~edad~~CksLvrkglvr 54 (70)
.|||.=..+++.+ -.+++++...|+.|.+.|||.
T Consensus 19 ~~~Dy~k~ia~~l-----------~~~~~~v~~~l~~Le~~GLle 52 (92)
T PF10007_consen 19 AGPDYAKSIARRL-----------KIPLEEVREALEKLEEMGLLE 52 (92)
T ss_pred HCCCcHHHHHHHH-----------CCCHHHHHHHHHHHHHCCCeE
Confidence 5899888888876 367899999999999999984
No 10
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=52.51 E-value=16 Score=18.09 Aligned_cols=17 Identities=24% Similarity=0.544 Sum_probs=12.9
Q ss_pred HHHhHhhcCcceeeeec
Q 037388 53 ISNFLFHTGQHFFCCKF 69 (70)
Q Consensus 53 vr~~~~h~g~~~~~~~~ 69 (70)
-|=...|+|+.+|-|+.
T Consensus 3 ~~H~~~H~~~k~~~C~~ 19 (26)
T PF13465_consen 3 RRHMRTHTGEKPYKCPY 19 (26)
T ss_dssp HHHHHHHSSSSSEEESS
T ss_pred HHHhhhcCCCCCCCCCC
Confidence 34455799999999974
No 11
>PF12847 Methyltransf_18: Methyltransferase domain; PDB: 3G2Q_A 3G2O_A 3G2M_B 3G2P_B 3D2L_B 1IM8_B 3NJR_A 3E05_H 3EVZ_A 3HM2_A ....
Probab=47.31 E-value=15 Score=21.19 Aligned_cols=31 Identities=6% Similarity=-0.005 Sum_probs=25.8
Q ss_pred eeeeeeCCCchhHhHhhhc-cccccccccccc
Q 037388 5 CTKFEVSPDTYPVVSRFLN-EEETKAWGLEPY 35 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLk-EeeTeAWGVEPY 35 (70)
.+||.+|-.|=...-.|++ ....+..|||+.
T Consensus 3 ~~vLDlGcG~G~~~~~l~~~~~~~~v~gvD~s 34 (112)
T PF12847_consen 3 GRVLDLGCGTGRLSIALARLFPGARVVGVDIS 34 (112)
T ss_dssp CEEEEETTTTSHHHHHHHHHHTTSEEEEEESS
T ss_pred CEEEEEcCcCCHHHHHHHhcCCCCEEEEEeCC
Confidence 4799999999888888887 478889999884
No 12
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=45.91 E-value=15 Score=27.23 Aligned_cols=29 Identities=24% Similarity=0.306 Sum_probs=23.2
Q ss_pred eeeeeeCCCchhHhHhhhcccccccccccc
Q 037388 5 CTKFEVSPDTYPVVSRFLNEEETKAWGLEP 34 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkEeeTeAWGVEP 34 (70)
.+||.|||++..+-..|++. ..+.+|||.
T Consensus 38 ~~VLEIG~G~G~LT~~Ll~~-~~~V~avEi 66 (294)
T PTZ00338 38 DTVLEIGPGTGNLTEKLLQL-AKKVIAIEI 66 (294)
T ss_pred CEEEEecCchHHHHHHHHHh-CCcEEEEEC
Confidence 46999999999998888865 456777764
No 13
>TIGR02081 metW methionine biosynthesis protein MetW. This protein is found alongside MetX, of the enzyme that acylates homoserine as a first step toward methionine biosynthesis, in many species. It appears to act in methionine biosynthesis but is not fully characterized.
Probab=45.90 E-value=18 Score=23.80 Aligned_cols=31 Identities=10% Similarity=0.254 Sum_probs=24.3
Q ss_pred eeeeeeCCCchhHhHhhhccccccccccccc
Q 037388 5 CTKFEVSPDTYPVVSRFLNEEETKAWGLEPY 35 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkEeeTeAWGVEPY 35 (70)
.++|.+|.++-.+...|.+.-...++|||+-
T Consensus 15 ~~iLDiGcG~G~~~~~l~~~~~~~~~giD~s 45 (194)
T TIGR02081 15 SRVLDLGCGDGELLALLRDEKQVRGYGIEID 45 (194)
T ss_pred CEEEEeCCCCCHHHHHHHhccCCcEEEEeCC
Confidence 4799999999888776665556677999875
No 14
>PHA02130 hypothetical protein
Probab=44.41 E-value=23 Score=23.48 Aligned_cols=31 Identities=29% Similarity=0.242 Sum_probs=25.2
Q ss_pred ccccccccccchhh-------HHHHHHHHHHHHHHHHh
Q 037388 26 ETKAWGLEPYDTEV-------AENLCIKALYAWLISNF 56 (70)
Q Consensus 26 eTeAWGVEPYd~ed-------ad~~CksLvrkglvr~~ 56 (70)
+|--||+=||+-+- +=+-||.|+.|-|-++|
T Consensus 41 stv~w~lcp~~qdi~ngke~fvwn~~k~llekeles~a 78 (81)
T PHA02130 41 STVYWDLCPYAQDIHNGKENFVWNTDKDLLEKELESIA 78 (81)
T ss_pred ceeeeccCcchhhhhcCcceeehhhhHHHHHHHHHHHh
Confidence 57789999998653 45789999999987765
No 15
>PF08242 Methyltransf_12: Methyltransferase domain; InterPro: IPR013217 Methyl transfer from the ubiquitous donor S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to: Hexaprenyldihydroxybenzoate methyltransferase (2.1.1.114 from EC), a mitochodrial enzyme involved in ubiquinone biosynthesis [] Fatty acid synthase (2.3.1.85 from EC), a biosynthetic enzyme catalysing the formation of long-chain fatty acids Glycine N-methyltransferase (2.1.1.20 from EC) which catalyses the SAM-dependent methylation of glycine to form sarcosine and may play a role in regulating the methylation potential of the cell [] Enniatin synthetase, involved in non-ribosomal biosynthesis of cyclohexadepsipeptidase, enniatin [] Histamine N-methyltransferase (2.1.1.8 from EC), a SAM-dependent histamine-inactivating enzyme [] A probable cobalt-precorrin-6Y C(15)-methyltransferase thought to be involved in adenosylcobalamin biosynthesis [] Structural studies show that this domain forms the Rossman-like alpha-beta fold typical of SAM-dependent methyltransferases [, , ].; PDB: 2VZ8_A 2VZ9_A.
Probab=43.22 E-value=9.7 Score=21.95 Aligned_cols=29 Identities=14% Similarity=0.252 Sum_probs=21.4
Q ss_pred eeeCCCchhHhHhhhcc-cccccccccccc
Q 037388 8 FEVSPDTYPVVSRFLNE-EETKAWGLEPYD 36 (70)
Q Consensus 8 LHVGPdTC~VVSkLLkE-eeTeAWGVEPYd 36 (70)
|.||+.|-.....|+++ ...+..|+++..
T Consensus 1 LdiGcG~G~~~~~l~~~~~~~~~~~~D~s~ 30 (99)
T PF08242_consen 1 LDIGCGTGRLLRALLEELPDARYTGVDISP 30 (99)
T ss_dssp -EESTTTS-TTTTHHHHC-EEEEEEEESSS
T ss_pred CEeCccChHHHHHHHHhCCCCEEEEEECCH
Confidence 68999999998888876 577788887764
No 16
>PF14545 DBB: Dof, BCAP, and BANK (DBB) motif,
Probab=42.72 E-value=20 Score=25.18 Aligned_cols=35 Identities=23% Similarity=0.415 Sum_probs=25.2
Q ss_pred HhHhhhcccc------cccccccccchhhHHHHHHHHHHHH
Q 037388 17 VVSRFLNEEE------TKAWGLEPYDTEVAENLCIKALYAW 51 (70)
Q Consensus 17 VVSkLLkEee------TeAWGVEPYd~edad~~CksLvrkg 51 (70)
-+++||+... =+|.|++|||+|..|+.=-+..+|.
T Consensus 92 el~~lL~~~~~PvefmCQa~~i~p~~~E~LD~~Lt~sfk~n 132 (142)
T PF14545_consen 92 ELEQLLRKAANPVEFMCQAFGISPNDREELDNLLTESFKKN 132 (142)
T ss_pred HHHHHHHhcCChhhhhhhhcCCCCCCHHHHHHHHHHHHHhc
Confidence 4567776433 3799999999999998655555553
No 17
>PF12317 IFT46_B_C: Intraflagellar transport complex B protein 46 C terminal; InterPro: IPR022088 This entry represents proteins is found in eukaryotes. Proteins are typically between 298 and 416 amino acids in length. It is thought to be a flagellar protein of complex B and like all IFT proteins, it is required for transport of IFT particles into the flagella [].
Probab=42.48 E-value=22 Score=26.74 Aligned_cols=28 Identities=25% Similarity=0.205 Sum_probs=24.0
Q ss_pred chhhHHHHHHHHHHHHHHHHhHhhcCcce
Q 037388 36 DTEVAENLCIKALYAWLISNFLFHTGQHF 64 (70)
Q Consensus 36 d~edad~~CksLvrkglvr~~~~h~g~~~ 64 (70)
.+|+|++| .+.+.+||=.+..+||.+|.
T Consensus 107 sie~ae~n-~k~Id~WI~~i~elHr~kp~ 134 (214)
T PF12317_consen 107 SIENAEKN-PKEIDKWIESIEELHRSKPP 134 (214)
T ss_pred chhchhhC-HHHHHHHHHHHHHHHhcCCC
Confidence 36788876 77899999999999998875
No 18
>cd04371 DEP DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction.
Probab=41.76 E-value=15 Score=20.93 Aligned_cols=36 Identities=25% Similarity=0.159 Sum_probs=27.4
Q ss_pred hhHhHhhhcccccccccccccchhhHHHHHHHHHHHHHHHHhH
Q 037388 15 YPVVSRFLNEEETKAWGLEPYDTEVAENLCIKALYAWLISNFL 57 (70)
Q Consensus 15 C~VVSkLLkEeeTeAWGVEPYd~edad~~CksLvrkglvr~~~ 57 (70)
+.+|+-|++.-+. .+-++|..-|+.|++.|+|+-..
T Consensus 32 ~e~v~WL~~~~~~-------~~r~ea~~~~~~ll~~g~i~~v~ 67 (81)
T cd04371 32 SELVDWLLDNLEA-------ITREEAVELGQALLKHGLIHHVS 67 (81)
T ss_pred HHHHHHHHHhCCC-------CCHHHHHHHHHHHHHCCCEEEeC
Confidence 3466666655433 67888999999999999998665
No 19
>PF02677 DUF208: Uncharacterized BCR, COG1636; InterPro: IPR003828 This entry describes proteins of unknown function.
Probab=41.20 E-value=20 Score=25.80 Aligned_cols=18 Identities=17% Similarity=0.272 Sum_probs=15.5
Q ss_pred eeee--CCCchhHhHhhhcc
Q 037388 7 KFEV--SPDTYPVVSRFLNE 24 (70)
Q Consensus 7 vLHV--GPdTC~VVSkLLkE 24 (70)
+||+ ||+++.++.+|..+
T Consensus 2 LLH~CCaPCs~~~~~~L~~~ 21 (176)
T PF02677_consen 2 LLHICCAPCSTYPLERLREE 21 (176)
T ss_pred eeeecCccccHHHHHHHHHC
Confidence 4776 99999999999866
No 20
>PF08003 Methyltransf_9: Protein of unknown function (DUF1698); InterPro: IPR010017 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. This entry represents a set of bacterial AdoMet-dependent tRNA (mo5U34)-methyltransferases. These enzymes catalyse the conversion of 5-hydroxyuridine (ho5U) to 5-methoxyuridine (mo5U) at the wobble position (34) of tRNA []. The 5-methoxyuridine is subsequently converted to uridine-5-oxyacetic acid, a modified nucleoside that is apparently necessary for the efficient decoding of G-ending Pro, Ala, and Val codons in these organisms [].; GO: 0016300 tRNA (uracil) methyltransferase activity, 0002098 tRNA wobble uridine modification
Probab=39.69 E-value=24 Score=27.74 Aligned_cols=39 Identities=10% Similarity=0.103 Sum_probs=32.9
Q ss_pred ceeeeeeeCCCchhHhHhhhcccccccccccccchhhHH
Q 037388 3 TACTKFEVSPDTYPVVSRFLNEEETKAWGLEPYDTEVAE 41 (70)
Q Consensus 3 ~~~kvLHVGPdTC~VVSkLLkEeeTeAWGVEPYd~edad 41 (70)
+=++||.||+..=+--=+++.++-..+-|++|+..--.+
T Consensus 115 ~gk~VLDIGC~nGY~~frM~~~GA~~ViGiDP~~lf~~Q 153 (315)
T PF08003_consen 115 KGKRVLDIGCNNGYYSFRMLGRGAKSVIGIDPSPLFYLQ 153 (315)
T ss_pred CCCEEEEecCCCcHHHHHHhhcCCCEEEEECCChHHHHH
Confidence 347899999999888889999999999999998775433
No 21
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=39.46 E-value=22 Score=25.30 Aligned_cols=30 Identities=17% Similarity=0.188 Sum_probs=22.2
Q ss_pred eeeeeeCCCchhHhHhhhccccccccccccc
Q 037388 5 CTKFEVSPDTYPVVSRFLNEEETKAWGLEPY 35 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkEeeTeAWGVEPY 35 (70)
.+||.|||+|-.+-..|++.. .+..|+|.-
T Consensus 44 ~~VLEiG~G~G~lt~~L~~~~-~~v~avE~d 73 (272)
T PRK00274 44 DNVLEIGPGLGALTEPLLERA-AKVTAVEID 73 (272)
T ss_pred CeEEEeCCCccHHHHHHHHhC-CcEEEEECC
Confidence 479999999977666666554 477787764
No 22
>TIGR00537 hemK_rel_arch HemK-related putative methylase. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. This model represents an archaeal and eukaryotic protein family that lacks an N-terminal domain found in HemK and its eubacterial homologs. It is found in a single copy in the first six completed archaeal and eukaryotic genomes.
Probab=39.09 E-value=35 Score=22.08 Aligned_cols=40 Identities=10% Similarity=-0.034 Sum_probs=27.4
Q ss_pred eeeeeeCCCchhHhHhhhccccccccccccc--chhhHHHHHH
Q 037388 5 CTKFEVSPDTYPVVSRFLNEEETKAWGLEPY--DTEVAENLCI 45 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkEeeTeAWGVEPY--d~edad~~Ck 45 (70)
.++|.+|+++..+...+.+... +..|+|.- -++-+..+++
T Consensus 21 ~~vLdlG~G~G~~~~~l~~~~~-~v~~vD~s~~~~~~a~~~~~ 62 (179)
T TIGR00537 21 DDVLEIGAGTGLVAIRLKGKGK-CILTTDINPFAVKELRENAK 62 (179)
T ss_pred CeEEEeCCChhHHHHHHHhcCC-EEEEEECCHHHHHHHHHHHH
Confidence 5799999999987777765544 78888753 2334555544
No 23
>PRK14896 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Provisional
Probab=38.39 E-value=22 Score=24.97 Aligned_cols=30 Identities=13% Similarity=0.251 Sum_probs=24.0
Q ss_pred eeeeeeCCCchhHhHhhhccccccccccccc
Q 037388 5 CTKFEVSPDTYPVVSRFLNEEETKAWGLEPY 35 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkEeeTeAWGVEPY 35 (70)
..||.|||++-.+-..|++. ..+..|||.-
T Consensus 31 ~~VLEIG~G~G~lt~~L~~~-~~~v~~vEid 60 (258)
T PRK14896 31 DPVLEIGPGKGALTDELAKR-AKKVYAIELD 60 (258)
T ss_pred CeEEEEeCccCHHHHHHHHh-CCEEEEEECC
Confidence 57999999998887777766 5678888764
No 24
>PF14078 DUF4259: Domain of unknown function (DUF4259)
Probab=38.33 E-value=14 Score=23.16 Aligned_cols=22 Identities=32% Similarity=0.570 Sum_probs=14.8
Q ss_pred cccccccchhhHHHHHHHHHHH
Q 037388 29 AWGLEPYDTEVAENLCIKALYA 50 (70)
Q Consensus 29 AWGVEPYd~edad~~CksLvrk 50 (70)
|||..|||=+.+---.-.|...
T Consensus 2 aWg~g~FdnD~a~D~l~el~~~ 23 (128)
T PF14078_consen 2 AWGTGPFDNDTALDFLDELRDA 23 (128)
T ss_pred CCCCCCCCCchHHHHHHHHHHh
Confidence 7999999988754444444333
No 25
>TIGR00755 ksgA dimethyladenosine transferase. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase
Probab=37.83 E-value=26 Score=24.36 Aligned_cols=30 Identities=17% Similarity=0.186 Sum_probs=23.4
Q ss_pred eeeeeeCCCchhHhHhhhccccccccccccc
Q 037388 5 CTKFEVSPDTYPVVSRFLNEEETKAWGLEPY 35 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkEeeTeAWGVEPY 35 (70)
.+||.+||++-.+-..|++.. ....|+|+-
T Consensus 31 ~~VLEiG~G~G~lt~~L~~~~-~~v~~iE~d 60 (253)
T TIGR00755 31 DVVLEIGPGLGALTEPLLKRA-KKVTAIEID 60 (253)
T ss_pred CEEEEeCCCCCHHHHHHHHhC-CcEEEEECC
Confidence 579999999988777777554 568888773
No 26
>cd04449 DEP_DEPDC5-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.
Probab=34.09 E-value=15 Score=22.45 Aligned_cols=30 Identities=27% Similarity=0.299 Sum_probs=22.1
Q ss_pred chhhHHHHHHHHHHHHHHHHhH----hhcCccee
Q 037388 36 DTEVAENLCIKALYAWLISNFL----FHTGQHFF 65 (70)
Q Consensus 36 d~edad~~CksLvrkglvr~~~----~h~g~~~~ 65 (70)
+-++|-..++.|+.+|+|+-.. |.-|..||
T Consensus 48 ~r~eAv~lgq~Ll~~g~I~hv~~~~~F~d~~~~Y 81 (83)
T cd04449 48 TREEAVELGQELMNEGLIEHVSGRHPFLDGFYFY 81 (83)
T ss_pred CHHHHHHHHHHHHHCCCEEecCCCCCccCCCEeE
Confidence 4567999999999999998664 44444444
No 27
>KOG3147 consensus 6-phosphogluconolactonase - like protein [Carbohydrate transport and metabolism]
Probab=33.00 E-value=15 Score=28.31 Aligned_cols=26 Identities=19% Similarity=0.284 Sum_probs=18.8
Q ss_pred eeeeCCC--chhHhHhhhcccccccccc
Q 037388 7 KFEVSPD--TYPVVSRFLNEEETKAWGL 32 (70)
Q Consensus 7 vLHVGPd--TC~VVSkLLkEeeTeAWGV 32 (70)
.|++||| |||+-..=....|+.+|=+
T Consensus 147 LLG~GpDGHtaSLFP~~~~l~e~~~wV~ 174 (252)
T KOG3147|consen 147 LLGMGPDGHTASLFPGHPLLNEKLKWVV 174 (252)
T ss_pred EeccCCCCCeeecCCCchhhhcccCEEE
Confidence 6899999 8999887333556667743
No 28
>TIGR00452 methyltransferase, putative. Known examples to date are restricted to the proteobacteria.
Probab=32.91 E-value=35 Score=25.69 Aligned_cols=33 Identities=18% Similarity=0.150 Sum_probs=28.5
Q ss_pred eeeeeeCCCchhHhHhhhcccccccccccccch
Q 037388 5 CTKFEVSPDTYPVVSRFLNEEETKAWGLEPYDT 37 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkEeeTeAWGVEPYd~ 37 (70)
++||.||=+|=....+++++....+.||+|.+.
T Consensus 123 ~~VLDvGCG~G~~~~~~~~~g~~~v~GiDpS~~ 155 (314)
T TIGR00452 123 RTILDVGCGSGYHMWRMLGHGAKSLVGIDPTVL 155 (314)
T ss_pred CEEEEeccCCcHHHHHHHHcCCCEEEEEcCCHH
Confidence 689999999988888888876667999999874
No 29
>TIGR02469 CbiT precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit. This model recognizes the CbiT methylase which is responsible, in part (along with CbiE), for methylating precorrin-6y (or cobalt-precorrin-6y) at both the 5 and 15 positions as well as the concomitant decarbozylation at C-12. In many organisms, this protein is fused to the CbiE subunit. The fused protein, when found in organisms catalyzing the oxidative version of the cobalamin biosynthesis pathway, is called CobL.
Probab=32.71 E-value=38 Score=19.50 Aligned_cols=32 Identities=3% Similarity=0.092 Sum_probs=23.1
Q ss_pred eeeeeeCCCchhHhHhhhcc-cccccccccccc
Q 037388 5 CTKFEVSPDTYPVVSRFLNE-EETKAWGLEPYD 36 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkE-eeTeAWGVEPYd 36 (70)
.++|.+|+++=.....+++. .+.+.+|+|+.+
T Consensus 21 ~~vldlG~G~G~~~~~l~~~~~~~~v~~vD~s~ 53 (124)
T TIGR02469 21 DVLWDIGAGSGSITIEAARLVPNGRVYAIERNP 53 (124)
T ss_pred CEEEEeCCCCCHHHHHHHHHCCCceEEEEcCCH
Confidence 47999999985555556654 247899999753
No 30
>PRK00121 trmB tRNA (guanine-N(7)-)-methyltransferase; Reviewed
Probab=31.56 E-value=62 Score=21.87 Aligned_cols=33 Identities=12% Similarity=0.131 Sum_probs=26.0
Q ss_pred eeeeeeeCCCchhHhHhhhcc-cccccccccccc
Q 037388 4 ACTKFEVSPDTYPVVSRFLNE-EETKAWGLEPYD 36 (70)
Q Consensus 4 ~~kvLHVGPdTC~VVSkLLkE-eeTeAWGVEPYd 36 (70)
..++|.+|.+|-.....|.+. .....+|||+.+
T Consensus 41 ~~~VLDiGcGtG~~~~~la~~~p~~~v~gVD~s~ 74 (202)
T PRK00121 41 APIHLEIGFGKGEFLVEMAKANPDINFIGIEVHE 74 (202)
T ss_pred CCeEEEEccCCCHHHHHHHHHCCCccEEEEEech
Confidence 457999999998887777654 356899999876
No 31
>PRK00304 hypothetical protein; Provisional
Probab=30.99 E-value=53 Score=21.13 Aligned_cols=37 Identities=16% Similarity=0.038 Sum_probs=29.4
Q ss_pred hHhHhhhcccccccccccccchhhHHHHHHHHHHHHHHH
Q 037388 16 PVVSRFLNEEETKAWGLEPYDTEVAENLCIKALYAWLIS 54 (70)
Q Consensus 16 ~VVSkLLkEeeTeAWGVEPYd~edad~~CksLvrkglvr 54 (70)
+++..++-+|.| .+|- -..+++.-..|+..+++|-+.
T Consensus 15 nLIeefv~ReGT-Dyg~-E~sL~~kv~qv~~qL~~G~~v 51 (75)
T PRK00304 15 RLIEDFVTRDGT-DNGD-ETPLETRVLRVRQALTKGQAV 51 (75)
T ss_pred HHHHHHHhccCc-cCcc-cccHHHHHHHHHHHHHcCCEE
Confidence 466777778888 5787 677999999999999999654
No 32
>PF10959 DUF2761: Protein of unknown function (DUF2761); InterPro: IPR024249 Members of this family of proteins are annotated as KleF [,]. Their function is known.
Probab=28.02 E-value=22 Score=24.17 Aligned_cols=15 Identities=27% Similarity=0.849 Sum_probs=11.3
Q ss_pred cccccccccccchhh
Q 037388 25 EETKAWGLEPYDTEV 39 (70)
Q Consensus 25 eeTeAWGVEPYd~ed 39 (70)
.+.|-||++|+.+-+
T Consensus 37 aqseewgldpwrlve 51 (95)
T PF10959_consen 37 AQSEEWGLDPWRLVE 51 (95)
T ss_pred ccchhcCCChhhhhc
Confidence 356889999997643
No 33
>KOG0820 consensus Ribosomal RNA adenine dimethylase [RNA processing and modification]
Probab=27.97 E-value=43 Score=26.79 Aligned_cols=21 Identities=24% Similarity=0.309 Sum_probs=18.1
Q ss_pred eeeeeeCCCchhHhHhhhccc
Q 037388 5 CTKFEVSPDTYPVVSRFLNEE 25 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkEe 25 (70)
..||+|||+|=+.--+||+-.
T Consensus 60 D~VLEvGPGTGnLT~~lLe~~ 80 (315)
T KOG0820|consen 60 DVVLEVGPGTGNLTVKLLEAG 80 (315)
T ss_pred CEEEEeCCCCCHHHHHHHHhc
Confidence 469999999999999999543
No 34
>PF14217 DUF4327: Domain of unknown function (DUF4327)
Probab=27.82 E-value=26 Score=22.24 Aligned_cols=20 Identities=10% Similarity=0.157 Sum_probs=17.6
Q ss_pred cchhhHHHHHHHHHHHHHHH
Q 037388 35 YDTEVAENLCIKALYAWLIS 54 (70)
Q Consensus 35 Yd~edad~~CksLvrkglvr 54 (70)
|+|+.....=.+||++|+|+
T Consensus 2 ysi~~iq~ear~LV~~g~v~ 21 (68)
T PF14217_consen 2 YSIDKIQDEARSLVESGVVS 21 (68)
T ss_pred CcHHHHHHHHHHHHHcCCCC
Confidence 78888888899999999875
No 35
>PF12140 DUF3588: Protein of unknown function (DUF3588); InterPro: IPR021987 This family of proteins is found in eukaryotes. Proteins in this family are typically between 129 and 866 amino acids in length, and the family is found in association with PF02820 from PFAM. The exact function of this family is not known.
Probab=26.54 E-value=35 Score=23.11 Aligned_cols=13 Identities=31% Similarity=0.332 Sum_probs=10.2
Q ss_pred eeeCCCchhHhHh
Q 037388 8 FEVSPDTYPVVSR 20 (70)
Q Consensus 8 LHVGPdTC~VVSk 20 (70)
-|+||+++++|-|
T Consensus 29 ~~fGPg~~~~Vlr 41 (118)
T PF12140_consen 29 DHFGPGPVSVVLR 41 (118)
T ss_pred cccCCCcHHHHHH
Confidence 4799999988744
No 36
>PRK07402 precorrin-6B methylase; Provisional
Probab=26.03 E-value=96 Score=20.40 Aligned_cols=42 Identities=7% Similarity=0.094 Sum_probs=28.7
Q ss_pred eeeeeeCCCchhHhHhhhcc-cccccccccccc--hhhHHHHHHH
Q 037388 5 CTKFEVSPDTYPVVSRFLNE-EETKAWGLEPYD--TEVAENLCIK 46 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkE-eeTeAWGVEPYd--~edad~~Cks 46 (70)
.+||.+|..|-.+-..+.+. .+.+..|||+.. ++.+..|++.
T Consensus 42 ~~VLDiG~G~G~~~~~la~~~~~~~V~~vD~s~~~~~~a~~n~~~ 86 (196)
T PRK07402 42 SVLWDIGAGTGTIPVEAGLLCPKGRVIAIERDEEVVNLIRRNCDR 86 (196)
T ss_pred CEEEEeCCCCCHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHHHHH
Confidence 47899999998875555432 347899999753 3445666653
No 37
>PF12129 Phtf-FEM1B_bdg: Male germ-cell putative homeodomain transcription factor; InterPro: IPR021980 This domain is found in bacteria and eukaryotes, and is typically between 101 and 140 amino acids in length. Phtf proteins do not display any sequence similarity to known or predicted proteins, but their conservation among species suggests an essential function. The 84 kDa Phtf1 protein is an integral membrane protein, anchored to a cell membrane by six to eight trans-membrane domains, that is associated with a domain of the endoplasmic reticulum (ER) juxtaposed to the Golgi apparatus. It is present during meiosis and spermiogenesis, and, by the end of spermiogenesis, is released from the mature spermatozoon within the residual bodies []. Phtf1 enhances the binding of FEM1B -feminisation homologue 1B - to cell membranes. Fem-1 was initially identified in the signaling pathway for sex determination, as well as being implicated in apoptosis, but its biochemical role is still unclear, and neither FEM1B nor PHTF1 is directly implicated in apoptosis in spermatogenesis. It is the ANK domain of FEM1B that is necessary for the interaction with the N-terminal region of Phtf1 [].
Probab=25.30 E-value=57 Score=23.71 Aligned_cols=15 Identities=13% Similarity=0.124 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHhHh
Q 037388 44 CIKALYAWLISNFLF 58 (70)
Q Consensus 44 CksLvrkglvr~~~~ 58 (70)
=.+++||||+|...+
T Consensus 68 ~~~l~~kgl~R~lf~ 82 (159)
T PF12129_consen 68 WTSLTRKGLVRVLFF 82 (159)
T ss_pred hhHHHHHHHHHHHHH
Confidence 357999999998765
No 38
>TIGR03587 Pse_Me-ase pseudaminic acid biosynthesis-associated methylase. Members of this small clade are methyltransferases of the pfam08241 family and are observed within operons for the biosynthesis of pseudaminic acid, a component of exopolysaccharide and flagellin glycosyl modifications. Notable among these genomes is Pseudomonas fluorescens PfO-1. Possibly one of the two hydroxyl groups of pseudaminic acid, at positions 4 and 8 is converted to a methoxy group by this enzyme
Probab=23.86 E-value=52 Score=22.61 Aligned_cols=32 Identities=9% Similarity=0.117 Sum_probs=25.9
Q ss_pred eeeeeeCCCchhHhHhhhcc-cccccccccccc
Q 037388 5 CTKFEVSPDTYPVVSRFLNE-EETKAWGLEPYD 36 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkE-eeTeAWGVEPYd 36 (70)
.+||.||-+|=.....|.+. ...+..|||+.+
T Consensus 45 ~~VLDiGCG~G~~~~~L~~~~~~~~v~giDiS~ 77 (204)
T TIGR03587 45 ASILELGANIGMNLAALKRLLPFKHIYGVEINE 77 (204)
T ss_pred CcEEEEecCCCHHHHHHHHhCCCCeEEEEECCH
Confidence 57999999998888888765 467899998764
No 39
>smart00828 PKS_MT Methyltransferase in polyketide synthase (PKS) enzymes.
Probab=23.62 E-value=1.5e+02 Score=19.51 Aligned_cols=30 Identities=3% Similarity=-0.066 Sum_probs=22.4
Q ss_pred eeeeeeCCCchhHhHhhhccc-ccccccccc
Q 037388 5 CTKFEVSPDTYPVVSRFLNEE-ETKAWGLEP 34 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkEe-eTeAWGVEP 34 (70)
++||.||..+-.....+.++- ..+..|+++
T Consensus 1 ~~vLDiGcG~G~~~~~la~~~~~~~v~gid~ 31 (224)
T smart00828 1 KRVLDFGCGYGSDLIDLAERHPHLQLHGYTI 31 (224)
T ss_pred CeEEEECCCCCHHHHHHHHHCCCCEEEEEEC
Confidence 579999999988777776553 456778776
No 40
>PRK00312 pcm protein-L-isoaspartate O-methyltransferase; Reviewed
Probab=23.32 E-value=1.4e+02 Score=19.88 Aligned_cols=30 Identities=10% Similarity=0.093 Sum_probs=20.6
Q ss_pred eeeeeeCCCchhHhHhhhccccccccccccc
Q 037388 5 CTKFEVSPDTYPVVSRFLNEEETKAWGLEPY 35 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkEeeTeAWGVEPY 35 (70)
.+||.||..|=.... +|.+-..+..|+|..
T Consensus 80 ~~VLeiG~GsG~~t~-~la~~~~~v~~vd~~ 109 (212)
T PRK00312 80 DRVLEIGTGSGYQAA-VLAHLVRRVFSVERI 109 (212)
T ss_pred CEEEEECCCccHHHH-HHHHHhCEEEEEeCC
Confidence 579999999876543 333333468888876
No 41
>PRK13942 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=23.17 E-value=63 Score=22.08 Aligned_cols=32 Identities=9% Similarity=-0.003 Sum_probs=23.5
Q ss_pred eeeeeeCCCchhHhHhhhcc--cccccccccccc
Q 037388 5 CTKFEVSPDTYPVVSRFLNE--EETKAWGLEPYD 36 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkE--eeTeAWGVEPYd 36 (70)
.+||.||..|-+....|.+. ...+..|||+.+
T Consensus 78 ~~VLdIG~GsG~~t~~la~~~~~~~~V~~vE~~~ 111 (212)
T PRK13942 78 MKVLEIGTGSGYHAAVVAEIVGKSGKVVTIERIP 111 (212)
T ss_pred CEEEEECCcccHHHHHHHHhcCCCCEEEEEeCCH
Confidence 58999999998866444332 346899999864
No 42
>PRK15068 tRNA mo(5)U34 methyltransferase; Provisional
Probab=23.12 E-value=1.1e+02 Score=22.67 Aligned_cols=35 Identities=17% Similarity=0.140 Sum_probs=29.0
Q ss_pred eeeeeeCCCchhHhHhhhcccccccccccccchhh
Q 037388 5 CTKFEVSPDTYPVVSRFLNEEETKAWGLEPYDTEV 39 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkEeeTeAWGVEPYd~ed 39 (70)
++||.||-++=.....+++.....+.||+|....-
T Consensus 124 ~~VLDIGCG~G~~~~~la~~g~~~V~GiD~S~~~l 158 (322)
T PRK15068 124 RTVLDVGCGNGYHMWRMLGAGAKLVVGIDPSQLFL 158 (322)
T ss_pred CEEEEeccCCcHHHHHHHHcCCCEEEEEcCCHHHH
Confidence 68999999999888888877656799999887543
No 43
>PRK05134 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional
Probab=23.05 E-value=64 Score=21.47 Aligned_cols=29 Identities=7% Similarity=0.015 Sum_probs=20.5
Q ss_pred eeeeeeCCCchhHhHhhhcccccccccccc
Q 037388 5 CTKFEVSPDTYPVVSRFLNEEETKAWGLEP 34 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkEeeTeAWGVEP 34 (70)
.++|.+|..+=...+.+.+ ...+.+|+|+
T Consensus 50 ~~vLdiG~G~G~~~~~l~~-~~~~v~~iD~ 78 (233)
T PRK05134 50 KRVLDVGCGGGILSESMAR-LGADVTGIDA 78 (233)
T ss_pred CeEEEeCCCCCHHHHHHHH-cCCeEEEEcC
Confidence 4799999988555555554 4556888876
No 44
>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=22.96 E-value=40 Score=28.03 Aligned_cols=22 Identities=32% Similarity=0.578 Sum_probs=19.1
Q ss_pred CchhHhHhhhcccccccccccccchhhH
Q 037388 13 DTYPVVSRFLNEEETKAWGLEPYDTEVA 40 (70)
Q Consensus 13 dTC~VVSkLLkEeeTeAWGVEPYd~eda 40 (70)
|..+++.||++ ||||||.+..+
T Consensus 363 da~~ai~RL~~------mGv~~~~l~s~ 384 (500)
T COG2804 363 DAPGAITRLLE------MGVEPYLLASS 384 (500)
T ss_pred chHHHHHHHHH------cCCCHHHHHHH
Confidence 67889999984 99999999875
No 45
>PF01135 PCMT: Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT); InterPro: IPR000682 Protein-L-isoaspartate(D-aspartate) O-methyltransferase (2.1.1.77 from EC) (PCMT) [] (which is also known as L-isoaspartyl protein carboxyl methyltransferase) is an enzyme that catalyses the transfer of a methyl group from S-adenosylmethionine to the free carboxyl groups of D-aspartyl or L-isoaspartyl residues in a variety of peptides and proteins. The enzyme does not act on normal L-aspartyl residues L-isoaspartyl and D-aspartyl are the products of the spontaneous deamidation and/or isomerisation of normal L-aspartyl and L-asparaginyl residues in proteins. PCMT plays a role in the repair and/or degradation of these damaged proteins; the enzymatic methyl esterification of the abnormal residues can lead to their conversion to normal L-aspartyl residues. The SAM domain is present in most of these proteins.; GO: 0004719 protein-L-isoaspartate (D-aspartate) O-methyltransferase activity, 0006464 protein modification process; PDB: 3LBF_A 1DL5_B 1JG3_B 1JG2_A 1JG1_A 1JG4_A 2YXE_A 2PBF_B 1VBF_C 1R18_A ....
Probab=22.76 E-value=96 Score=21.89 Aligned_cols=31 Identities=6% Similarity=0.125 Sum_probs=21.4
Q ss_pred eeeeeeCCCc---hhHhHhhhcccccccccccccc
Q 037388 5 CTKFEVSPDT---YPVVSRFLNEEETKAWGLEPYD 36 (70)
Q Consensus 5 ~kvLHVGPdT---C~VVSkLLkEeeTeAWGVEPYd 36 (70)
.+||+||-+| ..++|+|... ....-+||.++
T Consensus 74 ~~VLeIGtGsGY~aAlla~lvg~-~g~Vv~vE~~~ 107 (209)
T PF01135_consen 74 DRVLEIGTGSGYQAALLAHLVGP-VGRVVSVERDP 107 (209)
T ss_dssp -EEEEES-TTSHHHHHHHHHHST-TEEEEEEESBH
T ss_pred CEEEEecCCCcHHHHHHHHhcCc-cceEEEECccH
Confidence 5899999876 4577777743 34667899876
No 46
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=22.41 E-value=14 Score=21.87 Aligned_cols=35 Identities=14% Similarity=0.098 Sum_probs=25.5
Q ss_pred cccccccccchhhHHHHHHHHHHHHHHHHhHhhcC
Q 037388 27 TKAWGLEPYDTEVAENLCIKALYAWLISNFLFHTG 61 (70)
Q Consensus 27 TeAWGVEPYd~edad~~CksLvrkglvr~~~~h~g 61 (70)
.+.+|++|.......+.|+.|--.|||+.-...+|
T Consensus 29 c~~~~~~pls~~r~~~~l~eL~~~gli~~~~~~~G 63 (85)
T PF09079_consen 29 CESLGVDPLSYRRFSDYLSELEMLGLIESERKGRG 63 (85)
T ss_dssp HHHTTS----HHHHHHHHHHHHHTTSEEEEEEE-T
T ss_pred HHHcCCCCCCHHHHHHHHHHHHhCCCeEEEeecCC
Confidence 45689999999999999999999999987665555
No 47
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=22.06 E-value=71 Score=17.70 Aligned_cols=24 Identities=21% Similarity=0.279 Sum_probs=13.8
Q ss_pred ccccccchhh-HHHHHHHHHHHHHH
Q 037388 30 WGLEPYDTEV-AENLCIKALYAWLI 53 (70)
Q Consensus 30 WGVEPYd~ed-ad~~CksLvrkglv 53 (70)
.+++|-+++. +..--..|.++|||
T Consensus 43 y~~~~~~~~~dv~~fl~~L~~~glI 67 (68)
T PF05402_consen 43 YDVDPEEAEEDVEEFLEQLREKGLI 67 (68)
T ss_dssp TT--HHHHHHHHHHHHHHHHHTT--
T ss_pred cCCCHHHHHHHHHHHHHHHHHCcCc
Confidence 5777765543 77777777777776
No 48
>TIGR00417 speE spermidine synthase. the SpeE subunit of spermidine synthase catalysesthe reaction (putrescine + S-adenosylmethioninamine = spermidine + 5'-methylthioadenosine) and is involved in polyamine biosynthesis and in the biosynthesis of spermidine from arganine. The region between residues 77 and 120 of the seed alignment is thought to be involved in binding to decarboxylated SAM.
Probab=21.83 E-value=1.2e+02 Score=21.39 Aligned_cols=31 Identities=13% Similarity=0.019 Sum_probs=22.2
Q ss_pred eeeeeeeCCCchhHhHhhhccc-ccccccccc
Q 037388 4 ACTKFEVSPDTYPVVSRFLNEE-ETKAWGLEP 34 (70)
Q Consensus 4 ~~kvLHVGPdTC~VVSkLLkEe-eTeAWGVEP 34 (70)
.++||.+|..+-.+...+++.. ..+.-+||.
T Consensus 73 p~~VL~iG~G~G~~~~~ll~~~~~~~v~~vei 104 (270)
T TIGR00417 73 PKHVLVIGGGDGGVLREVLKHKSVEKATLVDI 104 (270)
T ss_pred CCEEEEEcCCchHHHHHHHhCCCcceEEEEeC
Confidence 4689999999999888888754 233444443
No 49
>cd01986 Alpha_ANH_like Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases and ATP sulphurylases. The domain forms a apha/beta/apha fold which binds to Adenosine group..
Probab=21.50 E-value=1.5e+02 Score=17.67 Aligned_cols=45 Identities=20% Similarity=0.161 Sum_probs=26.5
Q ss_pred CCCchhHhHhhhccc--ccccc----cccccchhhHHHHHHHHHHHHHHHHhH
Q 037388 11 SPDTYPVVSRFLNEE--ETKAW----GLEPYDTEVAENLCIKALYAWLISNFL 57 (70)
Q Consensus 11 GPdTC~VVSkLLkEe--eTeAW----GVEPYd~edad~~CksLvrkglvr~~~ 57 (70)
|+|| +++..++++- +..+. |..| +.+.+...|+...++-+.+.+.
T Consensus 8 G~DS-~~ll~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~r~~~~~~~a~ 58 (103)
T cd01986 8 GKDS-SVAAALLKKLGYQVIAVTVDHGISP-RLEDAKEIAKEAREEAAKRIAK 58 (103)
T ss_pred cHHH-HHHHHHHHHhCCCEEEEEEcCCCcc-cHHHHHHHHHHHHHHHHHHHHH
Confidence 4555 3445555543 34444 4444 5677888888866666666654
No 50
>PRK11036 putative S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=21.36 E-value=75 Score=21.87 Aligned_cols=31 Identities=0% Similarity=-0.138 Sum_probs=25.0
Q ss_pred eeeeeeCCCchhHhHhhhcccccccccccccc
Q 037388 5 CTKFEVSPDTYPVVSRFLNEEETKAWGLEPYD 36 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkEeeTeAWGVEPYd 36 (70)
.+||.+|-++-.....|.+. ..++.|+|+.+
T Consensus 46 ~~vLDiGcG~G~~a~~la~~-g~~v~~vD~s~ 76 (255)
T PRK11036 46 LRVLDAGGGEGQTAIKLAEL-GHQVILCDLSA 76 (255)
T ss_pred CEEEEeCCCchHHHHHHHHc-CCEEEEEECCH
Confidence 47999999999877777654 67899998864
No 51
>PF15488 DUF4645: Domain of unknown function (DUF4645)
Probab=21.31 E-value=33 Score=27.22 Aligned_cols=16 Identities=25% Similarity=0.742 Sum_probs=12.2
Q ss_pred hHhhhcccccccccccc
Q 037388 18 VSRFLNEEETKAWGLEP 34 (70)
Q Consensus 18 VSkLLkEeeTeAWGVEP 34 (70)
.|++| +++.|+||--.
T Consensus 37 ~SS~l-kddae~WG~p~ 52 (294)
T PF15488_consen 37 LSSML-KDDAEPWGHPR 52 (294)
T ss_pred ccccc-ccccccccCCC
Confidence 37778 48899999654
No 52
>COG0469 PykF Pyruvate kinase [Carbohydrate transport and metabolism]
Probab=21.28 E-value=35 Score=28.00 Aligned_cols=30 Identities=27% Similarity=0.258 Sum_probs=23.2
Q ss_pred ccccccccchh-------h-HHHHHHHHHHHHHHHHhH
Q 037388 28 KAWGLEPYDTE-------V-AENLCIKALYAWLISNFL 57 (70)
Q Consensus 28 eAWGVEPYd~e-------d-ad~~CksLvrkglvr~~~ 57 (70)
-.|||.|+=++ + ....|+.++++|++..-|
T Consensus 416 l~~GV~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~gD 453 (477)
T COG0469 416 LVWGVYPLLVEEKPTSTDEMVEEAVEKLLESGLVKKGD 453 (477)
T ss_pred eeecceeEEecCCCCcHHHHHHHHHHHHHhcCcccCCC
Confidence 36999998775 2 667888898888876655
No 53
>PRK03612 spermidine synthase; Provisional
Probab=21.28 E-value=72 Score=25.26 Aligned_cols=31 Identities=3% Similarity=-0.072 Sum_probs=25.9
Q ss_pred eeeeeeeCCCchhHhHhhhcccc-cccccccc
Q 037388 4 ACTKFEVSPDTYPVVSRFLNEEE-TKAWGLEP 34 (70)
Q Consensus 4 ~~kvLHVGPdTC~VVSkLLkEee-TeAWGVEP 34 (70)
.++||.+|.++..+...+++... .+..+||.
T Consensus 298 ~~rVL~IG~G~G~~~~~ll~~~~v~~v~~VEi 329 (521)
T PRK03612 298 PRRVLVLGGGDGLALREVLKYPDVEQVTLVDL 329 (521)
T ss_pred CCeEEEEcCCccHHHHHHHhCCCcCeEEEEEC
Confidence 46899999999999999998755 67888875
No 54
>PF00610 DEP: Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP); InterPro: IPR000591 This entry represents the DEP (Dishevelled, Egl-10 and Pleckstrin) domain, a globular domain of about 80 residues that is found in over 50 proteins involved in G-protein signalling pathways. It was named after the three proteins it was initially found in: Dishevelled (Dsh and Dvl), which play a key role in the transduction of the Wg/Wnt signal from the cell surface to the nucleus; it is a segment polarity protein required to establish coherent arrays of polarized cells and segments in embryos, and plays a role in wingless signalling. Egl-10, which regulates G-protein signalling in the central nervous system. Pleckstrin, the major substrate of protein kinase C in platelets; Pleckstrin contains two PH domains flanking the DEP domain. Mammalian regulators of G-protein signalling also contain these domains, and regulate signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving them into their inactive GDP-bound form. It has been proposed that the DEP domain could play a selective role in targeting DEP domain-containing proteins to specific subcellular membranous sites, perhaps even to specific G protein-coupled signaling pathways [, ]. Nuclear magnetic resonance spectroscopy has revealed that the DEP domain comprises a three-helix bundle, a beta-hairpin 'arm' composed of two beta-strands and two short beta-strands in the C-terminal region [].; GO: 0035556 intracellular signal transduction; PDB: 1UHW_A 1V3F_A 2YSR_A 2CSO_A 1W4M_A 2PBI_C 1O7F_A 2BYV_E 1FSH_A 3ML6_D ....
Probab=21.02 E-value=33 Score=19.50 Aligned_cols=22 Identities=27% Similarity=0.147 Sum_probs=18.1
Q ss_pred cchhhHHHHHHHHHHHHHHHHh
Q 037388 35 YDTEVAENLCIKALYAWLISNF 56 (70)
Q Consensus 35 Yd~edad~~CksLvrkglvr~~ 56 (70)
-+-++|-..|+.|+++|+|.-.
T Consensus 36 ~~r~eA~~l~q~Ll~~g~i~~v 57 (74)
T PF00610_consen 36 RDREEAVQLGQELLDHGFIEHV 57 (74)
T ss_dssp SSHHHHHHHHHHHHHCTSEEES
T ss_pred cCHHHHHHHHHHHHHCCCEEEC
Confidence 4567899999999999998643
No 55
>cd04448 DEP_PIKfyve DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol phosphate kinase) domain. PIKfyve-like proteins are important phosphatidylinositol (3)-monophosphate (PtdIns(3)P)-5-kinases, producing PtdIns(3,5)P2, which plays a major role in multivesicular body (MVB) sorting and control of retrograde traffic from the vacuole back to the endosome and/or Golgi. PIKfyve itself has been shown to be play a role in regulating early-endosome-to-trans-Golgi network (TGN) retrograde trafficking.
Probab=20.75 E-value=55 Score=20.19 Aligned_cols=34 Identities=15% Similarity=0.040 Sum_probs=25.6
Q ss_pred hHhHhhhcccccccccccccchhhHHHHHHHHHHHHHHHHh
Q 037388 16 PVVSRFLNEEETKAWGLEPYDTEVAENLCIKALYAWLISNF 56 (70)
Q Consensus 16 ~VVSkLLkEeeTeAWGVEPYd~edad~~CksLvrkglvr~~ 56 (70)
.+|.=|++..+ --+-++|-..|+.|+.+|+|+-.
T Consensus 33 elVdWL~~~~~-------~~~R~eAv~~gq~Ll~~g~i~hV 66 (81)
T cd04448 33 ELVNWLIRQGK-------AATRVQAIAIGQALLDAGWIECV 66 (81)
T ss_pred HHHHHHHHcCC-------CCCHHHHHHHHHHHHHCCCEEec
Confidence 46777775532 24567899999999999999754
No 56
>PF01281 Ribosomal_L9_N: Ribosomal protein L9, N-terminal domain; InterPro: IPR020070 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=20.28 E-value=47 Score=19.27 Aligned_cols=17 Identities=24% Similarity=0.276 Sum_probs=13.2
Q ss_pred HHHHHHHHhHhhcCcce
Q 037388 48 LYAWLISNFLFHTGQHF 64 (70)
Q Consensus 48 vrkglvr~~~~h~g~~~ 64 (70)
|+.|+.||+++=+|+--
T Consensus 21 V~~Gy~RN~L~p~~~A~ 37 (48)
T PF01281_consen 21 VKPGYARNFLIPQGLAV 37 (48)
T ss_dssp -SHHHHHHTTTTTTSEE
T ss_pred EccceeeehccCCCcee
Confidence 67899999999887643
No 57
>TIGR00438 rrmJ cell division protein FtsJ.
Probab=20.22 E-value=85 Score=20.53 Aligned_cols=33 Identities=3% Similarity=-0.041 Sum_probs=23.7
Q ss_pred eeeeeeCCCchhHhHhhhcc--cccccccccccch
Q 037388 5 CTKFEVSPDTYPVVSRFLNE--EETKAWGLEPYDT 37 (70)
Q Consensus 5 ~kvLHVGPdTC~VVSkLLkE--eeTeAWGVEPYd~ 37 (70)
.+||.+|-+|-.+...+.+. ...+.+|+|+-++
T Consensus 34 ~~VLDiG~GtG~~~~~l~~~~~~~~~v~~vDis~~ 68 (188)
T TIGR00438 34 DTVLDLGAAPGGWSQVAVEQVGGKGRVIAVDLQPM 68 (188)
T ss_pred CEEEEecCCCCHHHHHHHHHhCCCceEEEEecccc
Confidence 46899998888765555443 3557899988764
No 58
>smart00049 DEP Domain found in Dishevelled, Egl-10, and Pleckstrin. Domain of unknown function present in signalling proteins that contain PH, rasGEF, rhoGEF, rhoGAP, RGS, PDZ domains. DEP domain in Drosophila dishevelled is essential to rescue planar polarity defects and induce JNK signalling (Cell 94, 109-118).
Probab=20.21 E-value=34 Score=19.56 Aligned_cols=34 Identities=26% Similarity=0.174 Sum_probs=24.5
Q ss_pred HhHhhhcccccccccccccchhhHHHHHHHHHHHHHHHHhH
Q 037388 17 VVSRFLNEEETKAWGLEPYDTEVAENLCIKALYAWLISNFL 57 (70)
Q Consensus 17 VVSkLLkEeeTeAWGVEPYd~edad~~CksLvrkglvr~~~ 57 (70)
+|.-|++... --+-++|...|..|++.|+|+-..
T Consensus 26 ~v~wL~~~~~-------~~~r~eA~~l~~~ll~~g~i~~v~ 59 (77)
T smart00049 26 LVDWLMDNLE-------IIDREEAVHLGQLLLDEGLIHHVN 59 (77)
T ss_pred HHHHHHHcCC-------cCCHHHHHHHHHHHHHCCCEEEeC
Confidence 4555554443 134578999999999999998765
Done!