Query 040697
Match_columns 61
No_of_seqs 33 out of 35
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 10:52:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040697.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040697hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2366 Alpha-D-galactosidase 98.3 1.9E-07 4.2E-12 72.9 1.2 21 34-54 21-41 (414)
2 PLN02229 alpha-galactosidase 98.1 7.3E-07 1.6E-11 68.9 0.1 26 29-54 46-71 (427)
3 PLN02692 alpha-galactosidase 98.1 8.4E-07 1.8E-11 68.3 0.3 26 29-54 39-64 (412)
4 PLN02808 alpha-galactosidase 97.9 3E-06 6.6E-11 64.4 0.6 21 34-54 20-40 (386)
5 PLN02899 alpha-galactosidase 97.9 4.9E-06 1.1E-10 67.6 1.3 21 35-55 20-40 (633)
6 COG0118 HisH Glutamine amidotr 88.2 0.18 3.9E-06 36.5 0.5 12 43-54 115-126 (204)
7 PF09007 EBP50_C-term: EBP50, 61.7 1.6 3.6E-05 25.2 -0.8 9 44-52 25-33 (41)
8 PF02065 Melibiase: Melibiase; 59.0 2.1 4.6E-05 32.6 -0.9 20 34-53 28-48 (394)
9 KOG1958 Glycosyl hydrolase, fa 58.9 5.5 0.00012 35.3 1.4 22 36-57 269-290 (1129)
10 PRK13142 hisH imidazole glycer 55.1 5.3 0.00012 27.8 0.6 10 45-54 111-120 (192)
11 PF04800 ETC_C1_NDUFA4: ETC co 51.0 10 0.00022 24.6 1.4 9 46-54 36-44 (101)
12 cd08047 TAF7 TATA Binding Prot 47.7 8.1 0.00018 25.9 0.6 9 42-50 112-120 (162)
13 PF04658 TAFII55_N: TAFII55 pr 44.2 7.6 0.00016 26.6 0.0 9 42-50 119-127 (162)
14 PRK14004 hisH imidazole glycer 41.4 15 0.00032 25.4 1.1 9 44-52 120-128 (210)
15 CHL00188 hisH imidazole glycer 37.0 15 0.00032 25.4 0.6 9 44-52 116-124 (210)
16 KOG4026 Uncharacterized conser 37.0 14 0.0003 27.2 0.5 9 46-54 131-139 (207)
17 TIGR02362 dhaK1b probable dihy 35.3 13 0.00028 28.4 0.1 16 33-48 249-264 (326)
18 TIGR02363 dhaK1 dihydroxyaceto 34.3 13 0.00029 28.4 -0.0 16 33-48 253-268 (329)
19 COG2376 DAK1 Dihydroxyacetone 34.2 14 0.0003 28.3 0.1 16 33-48 248-263 (323)
20 PRK14483 DhaKLM operon coactiv 34.1 13 0.00028 28.5 -0.1 16 33-48 252-267 (329)
21 PF10555 MraY_sig1: Phospho-N- 33.6 18 0.00038 16.5 0.4 6 44-49 3-8 (13)
22 PRK14481 dihydroxyacetone kina 33.3 14 0.0003 28.3 -0.0 16 33-48 252-267 (331)
23 PRK11468 dihydroxyacetone kina 32.6 14 0.00031 28.7 -0.0 15 34-48 277-291 (356)
24 PF00372 Hemocyanin_M: Hemocya 28.7 24 0.00051 25.7 0.5 16 38-53 121-136 (278)
25 PRK13435 response regulator; P 27.8 40 0.00087 19.8 1.3 15 39-53 124-138 (145)
26 KOG4011 Transcription initiati 26.7 23 0.00049 27.8 0.1 9 42-50 136-144 (330)
27 PF13910 DUF4209: Domain of un 26.2 32 0.00069 21.3 0.7 9 44-52 55-63 (93)
28 PF10242 L_HGMIC_fpl: Lipoma H 24.4 34 0.00073 23.1 0.6 10 46-55 127-136 (181)
29 PLN02832 glutamine amidotransf 24.2 43 0.00094 24.4 1.2 7 46-52 126-132 (248)
30 PF12475 Amdo_NSP: Amdovirus n 23.0 24 0.00053 20.8 -0.2 7 44-50 11-17 (48)
31 PRK14479 dihydroxyacetone kina 22.4 29 0.00064 28.1 0.0 16 33-48 251-266 (568)
32 TIGR02361 dak_ATP dihydroxyace 22.2 29 0.00063 28.1 -0.0 16 33-48 259-274 (574)
33 PTZ00375 dihydroxyacetone kina 22.1 30 0.00065 28.3 0.1 16 33-48 261-276 (584)
34 PF09701 Cas_Cmr5: CRISPR-asso 21.4 6.6 0.00014 24.9 -3.1 12 34-45 36-47 (122)
35 PF08347 CTNNB1_binding: N-ter 21.1 32 0.0007 25.0 0.0 12 39-50 191-203 (203)
36 COG1408 Predicted phosphohydro 20.6 81 0.0017 23.0 2.0 17 36-52 255-272 (284)
No 1
>KOG2366 consensus Alpha-D-galactosidase (melibiase) [Carbohydrate transport and metabolism]
Probab=98.31 E-value=1.9e-07 Score=72.92 Aligned_cols=21 Identities=48% Similarity=0.564 Sum_probs=19.2
Q ss_pred cceeccCCCCCCCCCCCCCCC
Q 040697 34 GTLQLTNGLASTPQMGGILDY 54 (61)
Q Consensus 34 rR~LL~NGLG~TPQMGWNS~~ 54 (61)
.++.|+||||+||||||||--
T Consensus 21 ~~~~l~NGLg~tP~MGw~sW~ 41 (414)
T KOG2366|consen 21 GRMSLNNGLGRTPQMGWNSWE 41 (414)
T ss_pred hheeeccccccCCCccccccc
Confidence 499999999999999999864
No 2
>PLN02229 alpha-galactosidase
Probab=98.08 E-value=7.3e-07 Score=68.89 Aligned_cols=26 Identities=62% Similarity=0.640 Sum_probs=21.2
Q ss_pred ecCcccceeccCCCCCCCCCCCCCCC
Q 040697 29 YTSNYGTLQLTNGLASTPQMGGILDY 54 (61)
Q Consensus 29 ~~~~~rR~LL~NGLG~TPQMGWNS~~ 54 (61)
....+....++|||++||||||||=.
T Consensus 46 ~~~~~~~~~~~ngla~tPpmGWnSWn 71 (427)
T PLN02229 46 DTSMYGRLQLNNGLARTPQMGWNSWN 71 (427)
T ss_pred hhhhhhhhhccCCccCCCCceEEchh
Confidence 44555778889999999999999853
No 3
>PLN02692 alpha-galactosidase
Probab=98.08 E-value=8.4e-07 Score=68.29 Aligned_cols=26 Identities=31% Similarity=0.173 Sum_probs=21.3
Q ss_pred ecCcccceeccCCCCCCCCCCCCCCC
Q 040697 29 YTSNYGTLQLTNGLASTPQMGGILDY 54 (61)
Q Consensus 29 ~~~~~rR~LL~NGLG~TPQMGWNS~~ 54 (61)
+.+....+.+.||||+||||||||=+
T Consensus 39 ~~~~~~~~~~~ngla~tPpmGWnSW~ 64 (412)
T PLN02692 39 DSEILRRNLLANGLGITPPMGWNSWN 64 (412)
T ss_pred hhhhhhhhcccCcCcCCCcceEEchh
Confidence 33444788899999999999999964
No 4
>PLN02808 alpha-galactosidase
Probab=97.91 E-value=3e-06 Score=64.44 Aligned_cols=21 Identities=43% Similarity=0.329 Sum_probs=17.9
Q ss_pred cceeccCCCCCCCCCCCCCCC
Q 040697 34 GTLQLTNGLASTPQMGGILDY 54 (61)
Q Consensus 34 rR~LL~NGLG~TPQMGWNS~~ 54 (61)
....+.||||+||||||||=.
T Consensus 20 ~~~~~~ngla~tPpmGWnsW~ 40 (386)
T PLN02808 20 SRNLLDNGLGLTPQMGWNSWN 40 (386)
T ss_pred hhhcccCcccCCCcceEEchH
Confidence 456779999999999999853
No 5
>PLN02899 alpha-galactosidase
Probab=97.87 E-value=4.9e-06 Score=67.57 Aligned_cols=21 Identities=29% Similarity=0.033 Sum_probs=17.6
Q ss_pred ceeccCCCCCCCCCCCCCCCC
Q 040697 35 TLQLTNGLASTPQMGGILDYS 55 (61)
Q Consensus 35 R~LL~NGLG~TPQMGWNS~~~ 55 (61)
....+|||++||||||||=.+
T Consensus 20 ~~~~~~glA~TPPMGWNSWn~ 40 (633)
T PLN02899 20 GASSQQQLASFPPRGWNSYDS 40 (633)
T ss_pred cccccCcccCCCCCCCcchhh
Confidence 456799999999999999654
No 6
>COG0118 HisH Glutamine amidotransferase [Amino acid transport and metabolism]
Probab=88.22 E-value=0.18 Score=36.52 Aligned_cols=12 Identities=25% Similarity=0.130 Sum_probs=9.5
Q ss_pred CCCCCCCCCCCC
Q 040697 43 ASTPQMGGILDY 54 (61)
Q Consensus 43 G~TPQMGWNS~~ 54 (61)
=.-|+||||.-.
T Consensus 115 ~kvPHMGWN~l~ 126 (204)
T COG0118 115 LKVPHMGWNQVE 126 (204)
T ss_pred CCCCccccceee
Confidence 467999999753
No 7
>PF09007 EBP50_C-term: EBP50, C-terminal; InterPro: IPR015098 This C-terminal domain allows interaction of EBP50 with FERM (four-point one ERM) domains, resulting in the activation of Ezrin-radixin-moesin (ERM), with subsequent cytoskeletal modulation and cellular growth control []. ; PDB: 2D10_G 2KRG_A 2D11_G.
Probab=61.74 E-value=1.6 Score=25.16 Aligned_cols=9 Identities=33% Similarity=0.268 Sum_probs=3.0
Q ss_pred CCCCCCCCC
Q 040697 44 STPQMGGIL 52 (61)
Q Consensus 44 ~TPQMGWNS 52 (61)
+.|||-|+-
T Consensus 25 rAP~MDW~K 33 (41)
T PF09007_consen 25 RAPQMDWSK 33 (41)
T ss_dssp --S---HHH
T ss_pred cCCCcchHH
Confidence 579999973
No 8
>PF02065 Melibiase: Melibiase; InterPro: IPR000111 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycosyl hydrolase family 27, family 31 and family 36 alpha-galactosidases form the glycosyl hydrolase clan GH-D (acc_GH from CAZY), a superfamily of alpha-galactosidases, alpha-N-acetylgalactosaminidases, and isomaltodextranases which are likely to share a common catalytic mechanism and structural topology. Alpha-galactosidase (3.2.1.22 from EC) (melibiase) [] catalyzes the hydrolysis of melibiose into galactose and glucose. In man, the deficiency of this enzyme is the cause of Fabry's disease (X-linked sphingolipidosis). Alpha-galactosidase is present in a variety of organisms. There is a considerable degree of similarity in the sequence of alpha-galactosidase from various eukaryotic species. Escherichia coli alpha-galactosidase (gene melA), which requires NAD and magnesium as cofactors, is not structurally related to the eukaryotic enzymes; by contrast, an Escherichia coli plasmid encoded alpha-galactosidase (gene rafA P16551 from SWISSPROT) [] contains a region of about 50 amino acids which is similar to a domain of the eukaryotic alpha-galactosidases. Alpha-N-acetylgalactosaminidase (3.2.1.49 from EC) [] catalyzes the hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D- galactosaminides. In man, the deficiency of this enzyme is the cause of Schindler and Kanzaki diseases. The sequence of this enzyme is highly related to that of the eukaryotic alpha-galactosidases.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 1KTC_A 1KTB_A 1UAS_A 3H55_A 3H53_A 3IGU_B 3H54_A 3LRM_A 3LRL_A 3LRK_A ....
Probab=58.96 E-value=2.1 Score=32.64 Aligned_cols=20 Identities=15% Similarity=-0.107 Sum_probs=12.4
Q ss_pred cceecc-CCCCCCCCCCCCCC
Q 040697 34 GTLQLT-NGLASTPQMGGILD 53 (61)
Q Consensus 34 rR~LL~-NGLG~TPQMGWNS~ 53 (61)
|++++. +--..+|||||||=
T Consensus 28 r~~~~~~~~~~~~~pv~~nsW 48 (394)
T PF02065_consen 28 RRHLLRPPWRDKPPPVGWNSW 48 (394)
T ss_dssp HHHTSTTTTTTSS--EEEESH
T ss_pred HHhcCCCccCCCCCceEEEcc
Confidence 455444 34689999999984
No 9
>KOG1958 consensus Glycosyl hydrolase, family 38 - alpha-mannosidase [Carbohydrate transport and metabolism]
Probab=58.89 E-value=5.5 Score=35.34 Aligned_cols=22 Identities=36% Similarity=0.404 Sum_probs=18.2
Q ss_pred eeccCCCCCCCCCCCCCCCCce
Q 040697 36 LQLTNGLASTPQMGGILDYSGV 57 (61)
Q Consensus 36 ~LL~NGLG~TPQMGWNS~~~~~ 57 (61)
.-|+|++|.|||-||.-|--|.
T Consensus 269 ~Wl~~~igv~P~s~WaiDPFG~ 290 (1129)
T KOG1958|consen 269 QWLKNNIGVTPQSGWAIDPFGY 290 (1129)
T ss_pred hHHhccCCCCCCcccccCCCCC
Confidence 3469999999999999887653
No 10
>PRK13142 hisH imidazole glycerol phosphate synthase subunit HisH; Provisional
Probab=55.14 E-value=5.3 Score=27.76 Aligned_cols=10 Identities=20% Similarity=0.112 Sum_probs=8.1
Q ss_pred CCCCCCCCCC
Q 040697 45 TPQMGGILDY 54 (61)
Q Consensus 45 TPQMGWNS~~ 54 (61)
=|.||||+-+
T Consensus 111 vph~GWn~~~ 120 (192)
T PRK13142 111 VPHLGWNNLV 120 (192)
T ss_pred CCcccccccC
Confidence 3999999764
No 11
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=51.00 E-value=10 Score=24.58 Aligned_cols=9 Identities=33% Similarity=0.250 Sum_probs=5.9
Q ss_pred CCCCCCCCC
Q 040697 46 PQMGGILDY 54 (61)
Q Consensus 46 PQMGWNS~~ 54 (61)
|=|||.|..
T Consensus 36 PLMGWtss~ 44 (101)
T PF04800_consen 36 PLMGWTSSG 44 (101)
T ss_dssp TTT-SSSS-
T ss_pred CccCCCCCC
Confidence 889999853
No 12
>cd08047 TAF7 TATA Binding Protein (TBP) Associated Factor 7 (TAF7) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 7 (TAF7) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving
Probab=47.67 E-value=8.1 Score=25.94 Aligned_cols=9 Identities=33% Similarity=0.372 Sum_probs=7.1
Q ss_pred CCCCCCCCC
Q 040697 42 LASTPQMGG 50 (61)
Q Consensus 42 LG~TPQMGW 50 (61)
=|+||||=|
T Consensus 112 hGLTPP~~~ 120 (162)
T cd08047 112 HGLTPPMKN 120 (162)
T ss_pred CCCCcCchh
Confidence 378999966
No 13
>PF04658 TAFII55_N: TAFII55 protein conserved region; InterPro: IPR006751 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. TAFII55 binds to TAFII250 and inhibits its acetyltransferase activity. The exact role of TAFII55 is currently unknown. The conserved region is situated towards the N-terminal of the protein [].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005669 transcription factor TFIID complex
Probab=44.19 E-value=7.6 Score=26.58 Aligned_cols=9 Identities=33% Similarity=0.383 Sum_probs=7.0
Q ss_pred CCCCCCCCC
Q 040697 42 LASTPQMGG 50 (61)
Q Consensus 42 LG~TPQMGW 50 (61)
=|+||||=|
T Consensus 119 hGiTPP~kn 127 (162)
T PF04658_consen 119 HGITPPMKN 127 (162)
T ss_pred CCCChhhhh
Confidence 478999965
No 14
>PRK14004 hisH imidazole glycerol phosphate synthase subunit HisH; Provisional
Probab=41.36 E-value=15 Score=25.36 Aligned_cols=9 Identities=22% Similarity=0.335 Sum_probs=7.2
Q ss_pred CCCCCCCCC
Q 040697 44 STPQMGGIL 52 (61)
Q Consensus 44 ~TPQMGWNS 52 (61)
.-|-||||.
T Consensus 120 ~~ph~Gw~~ 128 (210)
T PRK14004 120 KVPHIGWNR 128 (210)
T ss_pred cCCccCccc
Confidence 459999994
No 15
>CHL00188 hisH imidazole glycerol phosphate synthase subunit hisH; Provisional
Probab=36.97 E-value=15 Score=25.37 Aligned_cols=9 Identities=33% Similarity=0.338 Sum_probs=7.2
Q ss_pred CCCCCCCCC
Q 040697 44 STPQMGGIL 52 (61)
Q Consensus 44 ~TPQMGWNS 52 (61)
..|.||||.
T Consensus 116 ~~p~~Gw~~ 124 (210)
T CHL00188 116 VIPHMGWNR 124 (210)
T ss_pred ccCccCCcc
Confidence 469999993
No 16
>KOG4026 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.95 E-value=14 Score=27.17 Aligned_cols=9 Identities=11% Similarity=-0.477 Sum_probs=6.9
Q ss_pred CCCCCCCCC
Q 040697 46 PQMGGILDY 54 (61)
Q Consensus 46 PQMGWNS~~ 54 (61)
=|+||+|+.
T Consensus 131 yP~GW~s~~ 139 (207)
T KOG4026|consen 131 YPDGWDSPE 139 (207)
T ss_pred cCCccCCHH
Confidence 379999874
No 17
>TIGR02362 dhaK1b probable dihydroxyacetone kinase DhaK1b subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form with a phosphoprotein donor related to PTS transport proteins. This family represents a protein, unique to the Firmicutes (low GC Gram-positives), that appears to be a divergent second copy of the K subunit of that complex; its gene is always found in operons with the other three proteins of the complex.
Probab=35.31 E-value=13 Score=28.39 Aligned_cols=16 Identities=31% Similarity=0.231 Sum_probs=13.5
Q ss_pred ccceeccCCCCCCCCC
Q 040697 33 YGTLQLTNGLASTPQM 48 (61)
Q Consensus 33 ~rR~LL~NGLG~TPQM 48 (61)
.+-.+|-||||-||+|
T Consensus 249 d~v~vlvN~LG~t~~l 264 (326)
T TIGR02362 249 DHYAVLVNNLGGTTPM 264 (326)
T ss_pred CEEEEEecCCCCCCHH
Confidence 3567889999999987
No 18
>TIGR02363 dhaK1 dihydroxyacetone kinase, DhaK subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form (EC 2.7.1.-) with a phosphoprotein donor related to PTS transport proteins. This family represents the DhaK subunit of the latter type of dihydroxyacetone kinase, but it specifically excludes the DhaK paralog DhaK2 (TIGR02362) found in the same operon as DhaK and DhaK in the Firmicutes.
Probab=34.26 E-value=13 Score=28.41 Aligned_cols=16 Identities=38% Similarity=0.607 Sum_probs=13.6
Q ss_pred ccceeccCCCCCCCCC
Q 040697 33 YGTLQLTNGLASTPQM 48 (61)
Q Consensus 33 ~rR~LL~NGLG~TPQM 48 (61)
.+--+|-||||-||+|
T Consensus 253 d~v~vlvN~LG~ts~l 268 (329)
T TIGR02363 253 DRVIVLVNGMGATPLM 268 (329)
T ss_pred CeEEEEEeCCCCCCHH
Confidence 3567889999999987
No 19
>COG2376 DAK1 Dihydroxyacetone kinase [Carbohydrate transport and metabolism]
Probab=34.16 E-value=14 Score=28.26 Aligned_cols=16 Identities=44% Similarity=0.553 Sum_probs=13.6
Q ss_pred ccceeccCCCCCCCCC
Q 040697 33 YGTLQLTNGLASTPQM 48 (61)
Q Consensus 33 ~rR~LL~NGLG~TPQM 48 (61)
.+--+|-||||-||.|
T Consensus 248 ~~v~~lvn~lG~tp~~ 263 (323)
T COG2376 248 DEVAVLVNGLGATPLM 263 (323)
T ss_pred CcEEEEecCCCCCcHH
Confidence 4567889999999987
No 20
>PRK14483 DhaKLM operon coactivator DhaQ; Provisional
Probab=34.12 E-value=13 Score=28.46 Aligned_cols=16 Identities=38% Similarity=0.445 Sum_probs=13.5
Q ss_pred ccceeccCCCCCCCCC
Q 040697 33 YGTLQLTNGLASTPQM 48 (61)
Q Consensus 33 ~rR~LL~NGLG~TPQM 48 (61)
.+-.+|-||||-||+|
T Consensus 252 d~v~vlVN~LG~ts~~ 267 (329)
T PRK14483 252 DNFILLINGLGATTLM 267 (329)
T ss_pred CeEEEEEeCCCCCcHH
Confidence 3567889999999987
No 21
>PF10555 MraY_sig1: Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1 ; InterPro: IPR018480 Phospho-N-acetylmuramoyl-pentapeptide-transferase (2.7.8.13 from EC) (MraY) is a bacterial enzyme responsible for the formation of the first lipid intermediate of the cell wall peptidoglycan synthesis []. It catalyses the formation of undecaprenyl-pyrophosphoryl-N-acetylmuramoyl-pentapeptide from UDP-MurNAc-pentapeptide and undecaprenyl-phosphate. MraY is an integral membrane protein with probably ten transmembrane domains. It belongs to family 4 of glycosyl transferases. Homologues of MraY have been found in archaebacteria Methanobacterium thermoautotrophicum and in Arabidopsis thaliana (Mouse-ear cress). This entry represents two conserved sites found in these proteins. The first site is located at the end of the first cytoplasmic loop and the beginning of the second transmembrane domain. The second site is located in the third cytoplasmic loop.
Probab=33.55 E-value=18 Score=16.49 Aligned_cols=6 Identities=67% Similarity=1.187 Sum_probs=5.0
Q ss_pred CCCCCC
Q 040697 44 STPQMG 49 (61)
Q Consensus 44 ~TPQMG 49 (61)
-||-||
T Consensus 3 gTPTMG 8 (13)
T PF10555_consen 3 GTPTMG 8 (13)
T ss_pred CCccce
Confidence 489998
No 22
>PRK14481 dihydroxyacetone kinase subunit DhaK; Provisional
Probab=33.28 E-value=14 Score=28.28 Aligned_cols=16 Identities=44% Similarity=0.636 Sum_probs=13.8
Q ss_pred ccceeccCCCCCCCCC
Q 040697 33 YGTLQLTNGLASTPQM 48 (61)
Q Consensus 33 ~rR~LL~NGLG~TPQM 48 (61)
.+-.+|-||||-||+|
T Consensus 252 d~v~lLvN~LG~ts~l 267 (331)
T PRK14481 252 DEVLVLVNGMGATPLM 267 (331)
T ss_pred CeEEEEEeCCCCCcHH
Confidence 3567889999999997
No 23
>PRK11468 dihydroxyacetone kinase subunit DhaK; Provisional
Probab=32.59 E-value=14 Score=28.65 Aligned_cols=15 Identities=33% Similarity=0.501 Sum_probs=12.9
Q ss_pred cceeccCCCCCCCCC
Q 040697 34 GTLQLTNGLASTPQM 48 (61)
Q Consensus 34 rR~LL~NGLG~TPQM 48 (61)
+-.+|-||||-||+|
T Consensus 277 ~v~vLVNgLG~t~~~ 291 (356)
T PRK11468 277 RVIALVNNLGATPLS 291 (356)
T ss_pred eEEEEEeCCCCCCHH
Confidence 456789999999987
No 24
>PF00372 Hemocyanin_M: Hemocyanin, copper containing domain; InterPro: IPR000896 Haemocyanins are copper-containing oxygen transport proteins found in the haemolymph of many invertebrates. They are divided into 2 main groups, arthropodan and molluscan. These have structurally similar oxygen-binding centres, which are similar to the oxygen-binding centre of tyrosinases [], but their quaternary structures are arranged differently. The arthropodan proteins exist as hexamers comprising 3 heterogeneous subunits (a, b and c) and possess 1 oxygen-binding centre per subunit; and the molluscan proteins exist as cylindrical oligomers of 10 to 20 subunits and possess 7 or 8 oxygen-binding centres per subunit []. Although the proteins have similar amino acid compositions, the only real similarity in their primary sequences is in the region corresponding to the second copper-binding domain, which also shows similarity to the copper-binding domain of tyrosinases []. Larval storage proteins (LSP) [] are proteins from the hemolymph of insects, which may serve as a store of amino acids for synthesis of adult proteins. There are two classes of LSP's, arylphorins, which are rich in aromatic amino acids, and methionine-rich LSP's. LSP's forms hexameric complexes. LSP's are structurally related to arthropods hemocyanins. This entry represents the copper-containg domain that usually occurs in the centre of haemocyanin proteins.; GO: 0005344 oxygen transporter activity, 0006810 transport; PDB: 1HCY_A 1HC1_C 3IXV_E 3IXW_L 3GWJ_F 3HHS_A 1NOL_A 1LLA_A 1OXY_A 1LL1_A.
Probab=28.75 E-value=24 Score=25.70 Aligned_cols=16 Identities=31% Similarity=0.412 Sum_probs=7.1
Q ss_pred ccCCCCCCCCCCCCCC
Q 040697 38 LTNGLASTPQMGGILD 53 (61)
Q Consensus 38 L~NGLG~TPQMGWNS~ 53 (61)
|.||||..|+..|+..
T Consensus 121 lSngL~~v~~~~~~~p 136 (278)
T PF00372_consen 121 LSNGLGEVPPFSWNEP 136 (278)
T ss_dssp HHTT--S-----TTSS
T ss_pred hccCCCCcccccCCCc
Confidence 4899999999999854
No 25
>PRK13435 response regulator; Provisional
Probab=27.78 E-value=40 Score=19.80 Aligned_cols=15 Identities=20% Similarity=0.284 Sum_probs=11.6
Q ss_pred cCCCCCCCCCCCCCC
Q 040697 39 TNGLASTPQMGGILD 53 (61)
Q Consensus 39 ~NGLG~TPQMGWNS~ 53 (61)
++-...-|||+||-.
T Consensus 124 ~~~~~~~~~~~~~~~ 138 (145)
T PRK13435 124 GDRASGPTPMGVFLA 138 (145)
T ss_pred cccCCCCCCCCcCCC
Confidence 566777889999864
No 26
>KOG4011 consensus Transcription initiation factor TFIID, subunit TAF7 [Transcription]
Probab=26.68 E-value=23 Score=27.79 Aligned_cols=9 Identities=33% Similarity=0.383 Sum_probs=7.4
Q ss_pred CCCCCCCCC
Q 040697 42 LASTPQMGG 50 (61)
Q Consensus 42 LG~TPQMGW 50 (61)
=|+||||=|
T Consensus 136 HGiTPPmKn 144 (330)
T KOG4011|consen 136 HGITPPMKN 144 (330)
T ss_pred cCCCcchhH
Confidence 488999966
No 27
>PF13910 DUF4209: Domain of unknown function (DUF4209)
Probab=26.23 E-value=32 Score=21.26 Aligned_cols=9 Identities=33% Similarity=0.194 Sum_probs=7.0
Q ss_pred CCCCCCCCC
Q 040697 44 STPQMGGIL 52 (61)
Q Consensus 44 ~TPQMGWNS 52 (61)
.+||.|||-
T Consensus 55 ~~~p~GlNL 63 (93)
T PF13910_consen 55 FGPPRGLNL 63 (93)
T ss_pred HCCCCCccH
Confidence 468999984
No 28
>PF10242 L_HGMIC_fpl: Lipoma HMGIC fusion partner-like protein; InterPro: IPR019372 This is a group of proteins expressed from a series of genes referred to as Lipoma HGMIC fusion partner-like. The proteins carry four highly conserved transmembrane domains. In certain instances, as in LHFPL5, mutations cause deafness in humans [] or hypospadias []. LHFPL1 is transcribed in six liver tumour cell lines [].
Probab=24.39 E-value=34 Score=23.09 Aligned_cols=10 Identities=10% Similarity=-0.386 Sum_probs=7.2
Q ss_pred CCCCCCCCCC
Q 040697 46 PQMGGILDYS 55 (61)
Q Consensus 46 PQMGWNS~~~ 55 (61)
=|.||+|+.-
T Consensus 127 yP~Gw~s~~v 136 (181)
T PF10242_consen 127 YPAGWDSPEV 136 (181)
T ss_pred ecCccCCcHH
Confidence 3788988753
No 29
>PLN02832 glutamine amidotransferase subunit of pyridoxal 5'-phosphate synthase complex
Probab=24.17 E-value=43 Score=24.36 Aligned_cols=7 Identities=14% Similarity=0.406 Sum_probs=6.2
Q ss_pred CCCCCCC
Q 040697 46 PQMGGIL 52 (61)
Q Consensus 46 PQMGWNS 52 (61)
|.||||.
T Consensus 126 p~~gwn~ 132 (248)
T PLN02832 126 PELAASE 132 (248)
T ss_pred Ccccccc
Confidence 9999994
No 30
>PF12475 Amdo_NSP: Amdovirus non-structural protein ; InterPro: IPR020960 This domain family is found in viruses, and is approximately 50 amino acids in length. This family contains proteins of each of the three types of Amdovirus non-structural protein [].
Probab=23.01 E-value=24 Score=20.84 Aligned_cols=7 Identities=29% Similarity=0.311 Sum_probs=6.1
Q ss_pred CCCCCCC
Q 040697 44 STPQMGG 50 (61)
Q Consensus 44 ~TPQMGW 50 (61)
.|||.||
T Consensus 11 ~t~sL~w 17 (48)
T PF12475_consen 11 VTKSLGW 17 (48)
T ss_pred cccchHH
Confidence 5899999
No 31
>PRK14479 dihydroxyacetone kinase; Provisional
Probab=22.44 E-value=29 Score=28.06 Aligned_cols=16 Identities=38% Similarity=0.418 Sum_probs=13.8
Q ss_pred ccceeccCCCCCCCCC
Q 040697 33 YGTLQLTNGLASTPQM 48 (61)
Q Consensus 33 ~rR~LL~NGLG~TPQM 48 (61)
.+-.+|-||||-||+|
T Consensus 251 d~v~~lvN~lG~t~~~ 266 (568)
T PRK14479 251 ERVAVLVNGLGATPYE 266 (568)
T ss_pred CeEEEEecCCCCCcHH
Confidence 3567889999999987
No 32
>TIGR02361 dak_ATP dihydroxyacetone kinase, ATP-dependent. This family consists of examples of the form of dihydroxyacetone kinase (also called glycerone kinase) that uses ATP (2.7.1.29) as the phosphate donor, rather than a phosphoprotein as in E. coli. This form is composed of a single chain with separable domains homologous to the K and L subunits of the E. coli enzyme, and is found in yeasts and other eukaryotes and in some bacteria, including Citrobacter freundii. The member from tomato has been shown to phosphorylate dihydroxyacetone, 3,4-dihydroxy-2-butanone, and some other aldoses and ketoses (PubMed:11985845).
Probab=22.23 E-value=29 Score=28.13 Aligned_cols=16 Identities=19% Similarity=0.285 Sum_probs=13.6
Q ss_pred ccceeccCCCCCCCCC
Q 040697 33 YGTLQLTNGLASTPQM 48 (61)
Q Consensus 33 ~rR~LL~NGLG~TPQM 48 (61)
.+-.+|-||||-||+|
T Consensus 259 d~v~~lvN~lG~t~~~ 274 (574)
T TIGR02361 259 DEVVLLVNNLGGVSNL 274 (574)
T ss_pred CeEEEEEeCCCCCCHH
Confidence 3567889999999987
No 33
>PTZ00375 dihydroxyacetone kinase-like protein; Provisional
Probab=22.14 E-value=30 Score=28.29 Aligned_cols=16 Identities=31% Similarity=0.316 Sum_probs=13.7
Q ss_pred ccceeccCCCCCCCCC
Q 040697 33 YGTLQLTNGLASTPQM 48 (61)
Q Consensus 33 ~rR~LL~NGLG~TPQM 48 (61)
.+--+|-||||-||+|
T Consensus 261 d~v~vlvN~LG~t~~~ 276 (584)
T PTZ00375 261 AKVALLVNNLGSTTDL 276 (584)
T ss_pred CeEEEEEcCCCCCcHH
Confidence 3567889999999987
No 34
>PF09701 Cas_Cmr5: CRISPR-associated protein (Cas_Cmr5); InterPro: IPR010160 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a family of Cas proteins as represented by TM1791.1 from Thermotoga maritima. This family of Cas proteins are found in both archaeal and bacterial species.; PDB: 2OEB_A 2ZOP_A.
Probab=21.35 E-value=6.6 Score=24.88 Aligned_cols=12 Identities=42% Similarity=0.598 Sum_probs=8.3
Q ss_pred cceeccCCCCCC
Q 040697 34 GTLQLTNGLAST 45 (61)
Q Consensus 34 rR~LL~NGLG~T 45 (61)
.-+++.||||+|
T Consensus 36 Pa~I~~nGL~qt 47 (122)
T PF09701_consen 36 PAMILQNGLGQT 47 (122)
T ss_dssp HHHHHHH-HHHH
T ss_pred HHHHHHcCHHHH
Confidence 456789999875
No 35
>PF08347 CTNNB1_binding: N-terminal CTNNB1 binding; InterPro: IPR013558 This region tends to appear at the N terminus of proteins also containing DNA-binding HMG (high mobility group) boxes (IPR000910 from INTERPRO) and appears to bind the armadillo repeat of CTNNB1 (beta-catenin), forming a stable complex. Signalling by Wnt through TCF/LCF is involved in developmental patterning, induction of neural tissues, cell fate decisions and stem cell differentiation []. Isoforms of HMG T-cell factors lacking the N-terminal CTNNB1-binding domain cannot fulfil their role as transcriptional activators in T-cell differentiation [, ]. ; PDB: 1JPW_E 2GL7_B 1JDH_B 1G3J_D 3OUW_B 3OUX_B.
Probab=21.06 E-value=32 Score=24.99 Aligned_cols=12 Identities=17% Similarity=0.385 Sum_probs=0.0
Q ss_pred cCCCCC-CCCCCC
Q 040697 39 TNGLAS-TPQMGG 50 (61)
Q Consensus 39 ~NGLG~-TPQMGW 50 (61)
-.|+|+ |+||||
T Consensus 191 pg~vgQi~~plgw 203 (203)
T PF08347_consen 191 PGGVGQIPHPLGW 203 (203)
T ss_dssp -------------
T ss_pred CCccCccCCCCCC
Confidence 456664 678888
No 36
>COG1408 Predicted phosphohydrolases [General function prediction only]
Probab=20.59 E-value=81 Score=22.98 Aligned_cols=17 Identities=29% Similarity=0.383 Sum_probs=13.1
Q ss_pred eeccCCCCCC-CCCCCCC
Q 040697 36 LQLTNGLAST-PQMGGIL 52 (61)
Q Consensus 36 ~LL~NGLG~T-PQMGWNS 52 (61)
+..++|||.| ||+=--+
T Consensus 255 lyVSrGlG~~~~p~R~~~ 272 (284)
T COG1408 255 LYVSRGLGTTGPPIRLGC 272 (284)
T ss_pred EEEeCCcCCCCCCcccCC
Confidence 6789999999 8874433
Done!