Query psy738
Match_columns 62
No_of_seqs 125 out of 422
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 16:44:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy738.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/738hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3738|consensus 100.0 2.8E-33 6E-38 208.1 2.2 61 1-61 331-391 (559)
2 KOG3736|consensus 100.0 3.2E-31 7E-36 200.7 3.5 60 1-61 353-412 (578)
3 KOG3737|consensus 99.9 1.3E-23 2.8E-28 157.0 1.5 61 1-61 371-435 (603)
4 cd02510 pp-GalNAc-T pp-GalNAc- 99.2 1E-11 2.2E-16 84.6 4.4 60 1-61 209-269 (299)
5 PF11407 RestrictionMunI: Type 77.6 1.2 2.7E-05 30.8 1.1 26 34-59 156-183 (202)
6 KOG3629|consensus 59.5 5.7 0.00012 31.9 1.5 28 31-58 126-153 (728)
7 PF03615 GCM: GCM motif protei 59.2 5.2 0.00011 26.5 1.0 24 1-24 89-117 (143)
8 PF12909 DUF3832: Protein of u 56.5 8.8 0.00019 23.3 1.7 25 33-59 41-65 (89)
9 PRK09194 prolyl-tRNA synthetas 56.5 4.2 9.1E-05 31.1 0.3 28 2-29 394-421 (565)
10 TIGR00409 proS_fam_II prolyl-t 51.8 2.7 5.8E-05 32.5 -1.4 27 2-28 399-425 (568)
11 KOG4405|consensus 35.4 17 0.00036 28.6 0.7 17 4-21 172-188 (547)
12 KOG2416|consensus 31.1 14 0.00031 29.9 -0.3 45 10-55 442-486 (718)
13 PF05401 NodS: Nodulation prot 30.1 13 0.00028 25.7 -0.6 16 3-18 139-159 (201)
14 cd08584 PI-PLCc_GDPD_SF_unchar 29.1 13 0.00028 25.4 -0.8 19 36-54 119-137 (192)
15 PF01641 SelR: SelR domain; I 28.9 36 0.00078 21.8 1.3 10 12-21 94-103 (124)
16 PF10906 DUF2697: Protein of u 28.1 23 0.0005 20.7 0.3 18 34-53 51-68 (68)
17 COG0163 UbiX 3-polyprenyl-4-hy 27.0 33 0.00072 23.7 1.0 8 5-12 83-90 (191)
18 PRK05508 methionine sulfoxide 25.3 31 0.00068 22.1 0.6 11 12-22 87-97 (119)
19 smart00037 CNX Connexin homolo 24.8 24 0.00052 18.1 -0.0 13 43-55 1-13 (34)
20 COG0229 Conserved domain frequ 23.2 37 0.00079 22.5 0.6 14 12-26 99-112 (140)
21 COG0350 Ada Methylated DNA-pro 23.2 42 0.0009 22.1 0.9 9 7-15 135-143 (168)
22 PHA02836 putative transmembran 23.1 30 0.00065 23.1 0.2 16 4-20 45-60 (153)
23 PF06326 Vesiculo_matrix: Vesi 22.9 58 0.0013 22.5 1.6 16 36-51 87-102 (228)
24 PF14803 Nudix_N_2: Nudix N-te 22.3 47 0.001 16.7 0.8 8 1-8 5-12 (34)
25 PF13639 zf-RING_2: Ring finge 22.1 90 0.0019 15.4 1.9 14 4-17 14-27 (44)
26 TIGR01913 bet_lambda phage rec 22.0 9.4 0.0002 25.9 -2.4 10 42-51 133-142 (188)
27 PF11672 DUF3268: Protein of u 21.7 1.5E+02 0.0034 18.3 3.2 48 2-49 8-73 (102)
28 KOG1941|consensus 21.4 18 0.0004 28.0 -1.2 13 5-17 381-393 (518)
29 KOG4628|consensus 21.1 48 0.001 24.7 0.9 17 3-19 242-258 (348)
30 PHA02641 hypothetical protein; 20.8 35 0.00076 23.4 0.2 16 4-20 75-90 (188)
31 cd06224 REM Guanine nucleotide 20.7 62 0.0013 18.8 1.2 22 33-54 65-86 (122)
32 PF13854 Kelch_5: Kelch motif 20.6 39 0.00085 16.7 0.3 12 9-20 1-12 (42)
No 1
>KOG3738|consensus
Probab=99.97 E-value=2.8e-33 Score=208.11 Aligned_cols=61 Identities=59% Similarity=1.141 Sum_probs=59.4
Q ss_pred CccceeEEecccceEeeccCCCCCCCCCCcchhhhHHHhHhHHhhccccchhhhhcCCCCC
Q psy738 1 MCGGVLEIATCSHVGHVFRKSTPYTFPGGTSNIVNHNNARLAEVWLDEWKHFYYAINPENM 61 (62)
Q Consensus 1 mCGG~ie~~PCSRVGHifr~~~Py~~~~~~~~~~~rN~~RvaevWmDeyk~~~y~~~p~~~ 61 (62)
||||+|||+||||||||||+++||.||+|.+.+..+|.+|+|||||||||.+||+.+|.|+
T Consensus 331 ~CGGslEIvPCSRVGHVFRkrHpy~FP~gs~~ty~~NTkr~AEvWmDEYK~~yyaarPsAr 391 (559)
T KOG3738|consen 331 QCGGSLEIVPCSRVGHVFRKRHPYTFPGGSGNTYIKNTKRAAEVWMDEYKNYYYAARPSAR 391 (559)
T ss_pred eeCCeeEEEeccchhhhhhccCCCcCCCCCCcchhhcchHHHHHHHHHHHHHHHhcCchhh
Confidence 7999999999999999999999999999999999999999999999999999999999885
No 2
>KOG3736|consensus
Probab=99.96 E-value=3.2e-31 Score=200.73 Aligned_cols=60 Identities=55% Similarity=1.027 Sum_probs=57.1
Q ss_pred CccceeEEecccceEeeccCCCCCCCCCCcchhhhHHHhHhHHhhccccchhhhhcCCCCC
Q psy738 1 MCGGVLEIATCSHVGHVFRKSTPYTFPGGTSNIVNHNNARLAEVWLDEWKHFYYAINPENM 61 (62)
Q Consensus 1 mCGG~ie~~PCSRVGHifr~~~Py~~~~~~~~~~~rN~~RvaevWmDeyk~~~y~~~p~~~ 61 (62)
||||+|||+||||||||||++.||++|++. +++.+|++|+|||||||||++||.++|.++
T Consensus 353 qCGG~lei~PCSrVGHifRk~~pY~~p~~~-~~~~~N~~RlAeVWmDeyK~~~y~~~P~~~ 412 (578)
T KOG3736|consen 353 QCGGRLEIVPCSRVGHIFRKRKPYTFPDGT-DTATRNLKRLAEVWMDEYKEQFYKRMPGLR 412 (578)
T ss_pred ccCCeEEecCccceeeeeecCCCccCCCcc-hhhhhchhhhhhhhhHHHHHHHHhhCcccc
Confidence 899999999999999999999999999765 788999999999999999999999999875
No 3
>KOG3737|consensus
Probab=99.87 E-value=1.3e-23 Score=156.99 Aligned_cols=61 Identities=38% Similarity=0.798 Sum_probs=54.1
Q ss_pred CccceeEEecccceEeeccCCCCCCCCCC----cchhhhHHHhHhHHhhccccchhhhhcCCCCC
Q psy738 1 MCGGVLEIATCSHVGHVFRKSTPYTFPGG----TSNIVNHNNARLAEVWLDEWKHFYYAINPENM 61 (62)
Q Consensus 1 mCGG~ie~~PCSRVGHifr~~~Py~~~~~----~~~~~~rN~~RvaevWmDeyk~~~y~~~p~~~ 61 (62)
||||+|+++||||||||||+..||++.+- .+..+..|++||+|+||||||+|||.+.|++.
T Consensus 371 QCGG~i~fVPCSrVGHvYR~~mpy~fgk~~~k~~~p~i~iNy~RVvetW~Ddyk~YfytreP~a~ 435 (603)
T KOG3737|consen 371 QCGGKILFVPCSRVGHVYRSLMPYQFGKPPIKVGSPPILINYVRVVETWWDDYKDYFYTREPEAQ 435 (603)
T ss_pred eeCCEEEEEEccccchhhhccccccCCCCccccCCCceEeehhhHHHHHHHhhhhheeecChhhc
Confidence 79999999999999999999999997321 13467899999999999999999999999874
No 4
>cd02510 pp-GalNAc-T pp-GalNAc-T initiates the formation of mucin-type O-linked glycans. UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferases (pp-GalNAc-T) initiate the formation of mucin-type, O-linked glycans by catalyzing the transfer of alpha-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to hydroxyl groups of Ser or Thr residues of core proteins to form the Tn antigen (GalNAc-a-1-O-Ser/Thr). These enzymes are type II membrane proteins with a GT-A type catalytic domain and a lectin domain located on the lumen side of the Golgi apparatus. In human, there are 15 isozymes of pp-GalNAc-Ts, representing the largest of all glycosyltransferase families. Each isozyme has unique but partially redundant substrate specificity for glycosylation sites on acceptor proteins.
Probab=99.23 E-value=1e-11 Score=84.58 Aligned_cols=60 Identities=55% Similarity=1.132 Sum_probs=53.3
Q ss_pred CccceeEEecccceEeecc-CCCCCCCCCCcchhhhHHHhHhHHhhccccchhhhhcCCCCC
Q psy738 1 MCGGVLEIATCSHVGHVFR-KSTPYTFPGGTSNIVNHNNARLAEVWLDEWKHFYYAINPENM 61 (62)
Q Consensus 1 mCGG~ie~~PCSRVGHifr-~~~Py~~~~~~~~~~~rN~~RvaevWmDeyk~~~y~~~p~~~ 61 (62)
+||+++..+|+|+|.|+++ ...||..+.+.. .+.+|.+|.++.|+|+++.++|..+|++.
T Consensus 209 ~~G~~i~~~p~a~v~H~~~~~~~~~~~~~~~~-~~~~n~~r~~~~w~~~~~~~~~~~~~~~~ 269 (299)
T cd02510 209 QCGGSIEIVPCSRVGHIFRRKRKPYTFPGGSG-TVLRNYKRVAEVWMDEYKEYFYKARPELR 269 (299)
T ss_pred HcCCeEEEeeccEEEEeccccCCCCCCCCccc-HHHHHHHHHHHHHHHHHHHHHHhcCcccc
Confidence 5899999999999999999 788998875432 57899999999999999999999998764
No 5
>PF11407 RestrictionMunI: Type II restriction enzyme MunI; InterPro: IPR022725 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. Type II restriction enzyme MunI recognises the palindromic sequence C/AATTG. It makes contact with the DNA via the major groove []. ; PDB: 1D02_B.
Probab=77.63 E-value=1.2 Score=30.82 Aligned_cols=26 Identities=27% Similarity=0.763 Sum_probs=17.0
Q ss_pred hhHHHhHhHH--hhccccchhhhhcCCC
Q psy738 34 VNHNNARLAE--VWLDEWKHFYYAINPE 59 (62)
Q Consensus 34 ~~rN~~Rvae--vWmDeyk~~~y~~~p~ 59 (62)
+.|--+|+-| -|.|||.+.||-++|.
T Consensus 156 ITRDpkR~REIt~Wf~~y~~nyF~Wr~~ 183 (202)
T PF11407_consen 156 ITRDPKRVREITFWFDEYDKNYFMWRPT 183 (202)
T ss_dssp GGG-HHHHHHHHHHHTT-CCCEEEE-TT
T ss_pred cccCcccceeeeeehhhcccceEEecCC
Confidence 4555566655 5999999988888775
No 6
>KOG3629|consensus
Probab=59.47 E-value=5.7 Score=31.86 Aligned_cols=28 Identities=21% Similarity=0.538 Sum_probs=23.4
Q ss_pred chhhhHHHhHhHHhhccccchhhhhcCC
Q psy738 31 SNIVNHNNARLAEVWLDEWKHFYYAINP 58 (62)
Q Consensus 31 ~~~~~rN~~RvaevWmDeyk~~~y~~~p 58 (62)
...+.+|++|+...|+|.|-+-||.-.|
T Consensus 126 s~~~v~naI~il~~WL~~~pEDF~~~~~ 153 (728)
T KOG3629|consen 126 SALLVQNAIRILMCWLETYPEDFYDSDK 153 (728)
T ss_pred HHHHHHHHHHHHHHHHHhChHhhcCccH
Confidence 4457799999999999999998887543
No 7
>PF03615 GCM: GCM motif protein; InterPro: IPR003902 GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologs [, , , ]. IN GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3' [, , ]. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues []. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding []. The GCM domain as a new class of Zn-containing DNA-binding domain with no similarity to any other DNA-binding domain []. The GCM domain consists of a large and a small domain tethered together by one of the two Zn ions present in the structure. The large and the small domains comprise five- and three-stranded beta-sheets, respectively, with three small helical segments packed against the same side of the two beta-sheets. The GCM domain exercises a novel mode of sequence-specific DNA recognition, where the five-stranded beta-pleated sheet inserts into the major groove of the DNA. Residues protruding from the edge strand of the beta-pleated sheet and the following loop and strand contact the bases and backbone of both DNA strands, providing specificity for its DNA target site. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ODH_A.
Probab=59.18 E-value=5.2 Score=26.50 Aligned_cols=24 Identities=33% Similarity=0.643 Sum_probs=10.8
Q ss_pred CccceeEEeccc-----ceEeeccCCCCC
Q psy738 1 MCGGVLEIATCS-----HVGHVFRKSTPY 24 (62)
Q Consensus 1 mCGG~ie~~PCS-----RVGHifr~~~Py 24 (62)
.|.|+||++||- =|-|+.|....+
T Consensus 89 ~C~g~L~~~pCrGh~GYPVThFWr~~~~~ 117 (143)
T PF03615_consen 89 NCKGRLELIPCRGHCGYPVTHFWRHDGNA 117 (143)
T ss_dssp -S--BEEEE---TBTTB--EEEEEE-SSB
T ss_pred ccCCceeEEeccCcCCCceeEEEecCCCE
Confidence 399999999995 255666655443
No 8
>PF12909 DUF3832: Protein of unknown function (DUF3832); InterPro: IPR024308 This domain found in bacteria and Acanthamoeba polyphaga mimivirus (APMV) L591 protein has no known function. In Q0AZ30 from SWISSPROT and other uncharacterised proteins this domain is found C-terminal, while the N terminus shows remote homology to the bacterial toxin/antitoxin 'addiction module' (PF12910 from PFAM).; PDB: 3K6Q_C.
Probab=56.53 E-value=8.8 Score=23.31 Aligned_cols=25 Identities=16% Similarity=0.432 Sum_probs=18.9
Q ss_pred hhhHHHhHhHHhhccccchhhhhcCCC
Q psy738 33 IVNHNNARLAEVWLDEWKHFYYAINPE 59 (62)
Q Consensus 33 ~~~rN~~RvaevWmDeyk~~~y~~~p~ 59 (62)
.+..+++-.|+.|||+++ +|++ .|+
T Consensus 41 ~lie~l~dYAedy~~~~~-~~~~-apn 65 (89)
T PF12909_consen 41 DLIEDLRDYAEDYMNRFP-LFYN-APN 65 (89)
T ss_dssp HHHHHHHHHHHHHHHTHH-HHHT-STT
T ss_pred HHHHHHHHHHHHHHHHHH-HHhc-CCC
Confidence 356889999999999987 4444 554
No 9
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=56.48 E-value=4.2 Score=31.05 Aligned_cols=28 Identities=39% Similarity=0.591 Sum_probs=24.2
Q ss_pred ccceeEEecccceEeeccCCCCCCCCCC
Q psy738 2 CGGVLEIATCSHVGHVFRKSTPYTFPGG 29 (62)
Q Consensus 2 CGG~ie~~PCSRVGHifr~~~Py~~~~~ 29 (62)
|||.|++...=-|||+|+-...|+.+-+
T Consensus 394 c~~~l~~~~~iEvGh~f~lG~~ys~~~~ 421 (565)
T PRK09194 394 GGGTLKIARGIEVGHIFQLGTKYSEAMN 421 (565)
T ss_pred CCceeEEeeeEEEEEEecCCcchhhccC
Confidence 8999999999999999999888886543
No 10
>TIGR00409 proS_fam_II prolyl-tRNA synthetase, family II. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent groups. This group includes enzymes from Escherichia coli, Bacillus subtilis, Aquifex aeolicus, the spirochete Treponema pallidum, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae. The other group includes the Pro-specific domain of a human multifunctional tRNA ligase and the prolyl-tRNA synthetases from the Archaea, the Mycoplasmas, and the spirochete Borrelia burgdorferi.
Probab=51.79 E-value=2.7 Score=32.50 Aligned_cols=27 Identities=37% Similarity=0.503 Sum_probs=23.0
Q ss_pred ccceeEEecccceEeeccCCCCCCCCC
Q psy738 2 CGGVLEIATCSHVGHVFRKSTPYTFPG 28 (62)
Q Consensus 2 CGG~ie~~PCSRVGHifr~~~Py~~~~ 28 (62)
|||.|.+-..=-|||+|+-..-|+.+-
T Consensus 399 c~~~l~~~rgIEvGhiF~LG~kYS~~~ 425 (568)
T TIGR00409 399 GQGTLKIARGIEVGHIFQLGTKYSEAL 425 (568)
T ss_pred CCCcccccceEEEEEeccchhhhHHhc
Confidence 899999988889999999887777653
No 11
>KOG4405|consensus
Probab=35.41 E-value=17 Score=28.56 Aligned_cols=17 Identities=41% Similarity=0.720 Sum_probs=13.9
Q ss_pred ceeEEecccceEeeccCC
Q psy738 4 GVLEIATCSHVGHVFRKS 21 (62)
Q Consensus 4 G~ie~~PCSRVGHifr~~ 21 (62)
|.++-||||| |-||.+.
T Consensus 172 g~l~~VPcSR-advFnsk 188 (547)
T KOG4405|consen 172 GELEQVPCSR-ADVFNSK 188 (547)
T ss_pred CeeeecCchH-Hhhhccc
Confidence 7999999999 4577664
No 12
>KOG2416|consensus
Probab=31.14 E-value=14 Score=29.86 Aligned_cols=45 Identities=22% Similarity=0.440 Sum_probs=33.6
Q ss_pred cccceEeeccCCCCCCCCCCcchhhhHHHhHhHHhhccccchhhhh
Q psy738 10 TCSHVGHVFRKSTPYTFPGGTSNIVNHNNARLAEVWLDEWKHFYYA 55 (62)
Q Consensus 10 PCSRVGHifr~~~Py~~~~~~~~~~~rN~~RvaevWmDeyk~~~y~ 55 (62)
+-|.|-||-.--.||... .....|.||-.-|.+-|||--|.+-|-
T Consensus 442 ~~SnvlhI~nLvRPFTlg-QLkelL~rtgg~Vee~WmDkIKShCyV 486 (718)
T KOG2416|consen 442 EPSNVLHIDNLVRPFTLG-QLKELLGRTGGNVEEFWMDKIKSHCYV 486 (718)
T ss_pred CccceEeeecccccchHH-HHHHHHhhccCchHHHHHHHhhcceeE
Confidence 357888998777888863 123446688888999999998886664
No 13
>PF05401 NodS: Nodulation protein S (NodS); InterPro: IPR008715 This entry consists of nodulation S (NodS) proteins. The products of the rhizobial nodulation genes are involved in the biosynthesis of lipochitin oligosaccharides (LCOs), which are host-specific signal molecules required for nodule formation. NodS is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase involved in N methylation of LCOs. NodS uses N-deacetylated chitooligosaccharides, the products of the NodBC proteins, as its methyl acceptors [].; GO: 0008757 S-adenosylmethionine-dependent methyltransferase activity, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3OFK_D 3OFJ_A.
Probab=30.07 E-value=13 Score=25.71 Aligned_cols=16 Identities=44% Similarity=0.769 Sum_probs=9.9
Q ss_pred cceeEE-----ecccceEeec
Q psy738 3 GGVLEI-----ATCSHVGHVF 18 (62)
Q Consensus 3 GG~ie~-----~PCSRVGHif 18 (62)
||.+.+ .+|+|.||.|
T Consensus 139 gG~LV~g~~rd~~c~~wgh~~ 159 (201)
T PF05401_consen 139 GGHLVFGHARDANCRRWGHAA 159 (201)
T ss_dssp EEEEEEEEE-HHHHHHTT-S-
T ss_pred CCEEEEEEecCCcccccCccc
Confidence 455544 3899999987
No 14
>cd08584 PI-PLCc_GDPD_SF_unchar2 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues.
Probab=29.12 E-value=13 Score=25.42 Aligned_cols=19 Identities=16% Similarity=0.478 Sum_probs=13.8
Q ss_pred HHHhHhHHhhccccchhhh
Q psy738 36 HNNARLAEVWLDEWKHFYY 54 (62)
Q Consensus 36 rN~~RvaevWmDeyk~~~y 54 (62)
+=+-++.-||+|+|....+
T Consensus 119 ~~~~~~~~VW~D~f~~~~~ 137 (192)
T cd08584 119 SLYEKADWVWIDSFTSLWL 137 (192)
T ss_pred HhhccccEEEEecccccCC
Confidence 3345788899999877544
No 15
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=28.89 E-value=36 Score=21.79 Aligned_cols=10 Identities=60% Similarity=1.119 Sum_probs=7.8
Q ss_pred cceEeeccCC
Q psy738 12 SHVGHVFRKS 21 (62)
Q Consensus 12 SRVGHifr~~ 21 (62)
|++||||...
T Consensus 94 ~HLGHVF~DG 103 (124)
T PF01641_consen 94 SHLGHVFDDG 103 (124)
T ss_dssp CEEEEEESTS
T ss_pred CccccEeCCC
Confidence 4799999843
No 16
>PF10906 DUF2697: Protein of unknown function (DUF2697); InterPro: IPR020301 This entry contains proteins with no known function.
Probab=28.09 E-value=23 Score=20.67 Aligned_cols=18 Identities=28% Similarity=0.444 Sum_probs=13.7
Q ss_pred hhHHHhHhHHhhccccchhh
Q psy738 34 VNHNNARLAEVWLDEWKHFY 53 (62)
Q Consensus 34 ~~rN~~RvaevWmDeyk~~~ 53 (62)
..-|+-|+. |.||.|..|
T Consensus 51 ~k~~AFr~l--f~DE~K~~f 68 (68)
T PF10906_consen 51 QKFNAFRIL--FWDELKNSF 68 (68)
T ss_pred HHHHHHHHH--HHHHHHhcC
Confidence 456777776 999998754
No 17
>COG0163 UbiX 3-polyprenyl-4-hydroxybenzoate decarboxylase [Coenzyme metabolism]
Probab=27.04 E-value=33 Score=23.71 Aligned_cols=8 Identities=50% Similarity=0.708 Sum_probs=6.6
Q ss_pred eeEEeccc
Q psy738 5 VLEIATCS 12 (62)
Q Consensus 5 ~ie~~PCS 12 (62)
.|.|+|||
T Consensus 83 gMiI~PCS 90 (191)
T COG0163 83 GMIIAPCS 90 (191)
T ss_pred cEEEEeCc
Confidence 47899998
No 18
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=25.35 E-value=31 Score=22.08 Aligned_cols=11 Identities=45% Similarity=0.897 Sum_probs=8.5
Q ss_pred cceEeeccCCC
Q psy738 12 SHVGHVFRKST 22 (62)
Q Consensus 12 SRVGHifr~~~ 22 (62)
|+.||||....
T Consensus 87 ~HLGHVF~d~g 97 (119)
T PRK05508 87 GHLGHVFEGEG 97 (119)
T ss_pred CccCcccCCCC
Confidence 57999998543
No 19
>smart00037 CNX Connexin homologues. Connexin channels participate in the regulation of signaling between developing and differentiated cell types.
Probab=24.76 E-value=24 Score=18.12 Aligned_cols=13 Identities=38% Similarity=0.631 Sum_probs=9.9
Q ss_pred Hhhccccchhhhh
Q psy738 43 EVWLDEWKHFYYA 55 (62)
Q Consensus 43 evWmDeyk~~~y~ 55 (62)
.||-||-+++.-.
T Consensus 1 ~vw~DEq~~FvCn 13 (34)
T smart00037 1 SVWGDEQSDFVCN 13 (34)
T ss_pred Cccccchhhceec
Confidence 3799998887653
No 20
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=23.21 E-value=37 Score=22.46 Aligned_cols=14 Identities=50% Similarity=0.842 Sum_probs=10.4
Q ss_pred cceEeeccCCCCCCC
Q psy738 12 SHVGHVFRKSTPYTF 26 (62)
Q Consensus 12 SRVGHifr~~~Py~~ 26 (62)
|+.||||... |...
T Consensus 99 sHLGHVF~DG-P~~t 112 (140)
T COG0229 99 SHLGHVFPDG-PPPT 112 (140)
T ss_pred CccccccCCC-CCCC
Confidence 7899999654 6554
No 21
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=23.19 E-value=42 Score=22.08 Aligned_cols=9 Identities=33% Similarity=0.423 Sum_probs=7.6
Q ss_pred EEecccceE
Q psy738 7 EIATCSHVG 15 (62)
Q Consensus 7 e~~PCSRVG 15 (62)
.++||=||=
T Consensus 135 IiIPCHRVi 143 (168)
T COG0350 135 IIIPCHRVI 143 (168)
T ss_pred EEecCeEeE
Confidence 589999984
No 22
>PHA02836 putative transmembrane protein; Provisional
Probab=23.07 E-value=30 Score=23.06 Aligned_cols=16 Identities=25% Similarity=0.544 Sum_probs=12.5
Q ss_pred ceeEEecccceEeeccC
Q psy738 4 GVLEIATCSHVGHVFRK 20 (62)
Q Consensus 4 G~ie~~PCSRVGHifr~ 20 (62)
|+|.++| |.||.+|=.
T Consensus 45 GRI~~vP-~~vGkLyl~ 60 (153)
T PHA02836 45 GRIGFVP-VGIGNLFLK 60 (153)
T ss_pred cceeeee-cchhhhhHH
Confidence 7888888 788887754
No 23
>PF06326 Vesiculo_matrix: Vesiculovirus matrix protein; InterPro: IPR009397 This family consists of several Vesiculovirus matrix proteins. The matrix (M) protein of vesicular stomatitis virus (VSV) expressed in the absence of other viral components causes many of the cytopathic effects of VSV, including an inhibition of host gene expression and the induction of cell rounding. It has been shown that M protein also induces apoptosis in the absence of other viral components. It is thought that the activation of apoptotic pathways causes the inhibition of host gene expression and cell rounding by M protein [].; GO: 0005198 structural molecule activity, 0019031 viral envelope; PDB: 1LG7_A 2W2R_A.
Probab=22.85 E-value=58 Score=22.53 Aligned_cols=16 Identities=19% Similarity=0.544 Sum_probs=11.9
Q ss_pred HHHhHhHHhhccccch
Q psy738 36 HNNARLAEVWLDEWKH 51 (62)
Q Consensus 36 rN~~RvaevWmDeyk~ 51 (62)
....++++.|.|+|.-
T Consensus 87 ~d~~~il~~w~d~Y~G 102 (228)
T PF06326_consen 87 SDLYKILSNWLDNYDG 102 (228)
T ss_dssp HHHHHHHGGGGTT--S
T ss_pred HHHHHHHHHHHHhCCC
Confidence 4678999999999963
No 24
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=22.26 E-value=47 Score=16.65 Aligned_cols=8 Identities=63% Similarity=1.128 Sum_probs=3.6
Q ss_pred CccceeEE
Q psy738 1 MCGGVLEI 8 (62)
Q Consensus 1 mCGG~ie~ 8 (62)
+||+.++.
T Consensus 5 ~CG~~l~~ 12 (34)
T PF14803_consen 5 QCGGPLER 12 (34)
T ss_dssp TT--B-EE
T ss_pred cccChhhh
Confidence 58888776
No 25
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=22.10 E-value=90 Score=15.40 Aligned_cols=14 Identities=29% Similarity=0.342 Sum_probs=9.2
Q ss_pred ceeEEecccceEee
Q psy738 4 GVLEIATCSHVGHV 17 (62)
Q Consensus 4 G~ie~~PCSRVGHi 17 (62)
..+..+||.++-|.
T Consensus 14 ~~~~~l~C~H~fh~ 27 (44)
T PF13639_consen 14 EKVVKLPCGHVFHR 27 (44)
T ss_dssp SCEEEETTSEEEEH
T ss_pred CeEEEccCCCeeCH
Confidence 45678899655553
No 26
>TIGR01913 bet_lambda phage recombination protein Bet. This model represents the phage recombination protein Bet from a number of phage, including phage lambda. All members of this family are found in phage genomes or in putative prophage regions of bacterial genomes.
Probab=21.99 E-value=9.4 Score=25.85 Aligned_cols=10 Identities=30% Similarity=0.351 Sum_probs=7.9
Q ss_pred HHhhccccch
Q psy738 42 AEVWLDEWKH 51 (62)
Q Consensus 42 aevWmDeyk~ 51 (62)
+++|+|||..
T Consensus 133 ~~~~~~eY~~ 142 (188)
T TIGR01913 133 ISVPFDAYKM 142 (188)
T ss_pred EEEehhHhhh
Confidence 6789999854
No 27
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.69 E-value=1.5e+02 Score=18.28 Aligned_cols=48 Identities=25% Similarity=0.339 Sum_probs=29.1
Q ss_pred ccceeEEecccceEeeccCCCCC----------------C-CCCC-cchhhhHHHhHhHHhhcccc
Q psy738 2 CGGVLEIATCSHVGHVFRKSTPY----------------T-FPGG-TSNIVNHNNARLAEVWLDEW 49 (62)
Q Consensus 2 CGG~ie~~PCSRVGHifr~~~Py----------------~-~~~~-~~~~~~rN~~RvaevWmDey 49 (62)
|||..++++=|.|---.-...|| + .|-| ..+.-.|+....|+-.+|..
T Consensus 8 Cg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG~H~~t~~PlGtLAd~~lR~~R~~ah~~fd~l 73 (102)
T PF11672_consen 8 CGGPAELVDGSEIYGHRYDDGPYLYVCTPCDAYVGCHPGTDIPLGTLADAELRRARKAAHRAFDPL 73 (102)
T ss_pred CCCeeEEcccchhcCccCCCCceeEECCCCCceeeeeCCCCCcCcccCCHHHHHHHHHHHHHHHHH
Confidence 89999988876664311122344 1 2322 33455688888888877763
No 28
>KOG1941|consensus
Probab=21.35 E-value=18 Score=28.04 Aligned_cols=13 Identities=38% Similarity=0.697 Sum_probs=11.5
Q ss_pred eeEEecccceEee
Q psy738 5 VLEIATCSHVGHV 17 (62)
Q Consensus 5 ~ie~~PCSRVGHi 17 (62)
+++.+|||+|-|.
T Consensus 381 ~LqALpCsHIfH~ 393 (518)
T KOG1941|consen 381 RLQALPCSHIFHL 393 (518)
T ss_pred cccccchhHHHHH
Confidence 6889999999986
No 29
>KOG4628|consensus
Probab=21.10 E-value=48 Score=24.74 Aligned_cols=17 Identities=47% Similarity=0.573 Sum_probs=13.9
Q ss_pred cceeEEecccceEeecc
Q psy738 3 GGVLEIATCSHVGHVFR 19 (62)
Q Consensus 3 GG~ie~~PCSRVGHifr 19 (62)
|-++-++||+|.-|.-.
T Consensus 242 GdklRiLPC~H~FH~~C 258 (348)
T KOG4628|consen 242 GDKLRILPCSHKFHVNC 258 (348)
T ss_pred CCeeeEecCCCchhhcc
Confidence 56788999999999743
No 30
>PHA02641 hypothetical protein; Provisional
Probab=20.84 E-value=35 Score=23.35 Aligned_cols=16 Identities=19% Similarity=0.505 Sum_probs=12.6
Q ss_pred ceeEEecccceEeeccC
Q psy738 4 GVLEIATCSHVGHVFRK 20 (62)
Q Consensus 4 G~ie~~PCSRVGHifr~ 20 (62)
|+|.++| +.||.+|=.
T Consensus 75 GRI~~vP-~~VGKLyld 90 (188)
T PHA02641 75 SKIDILP-KNVGKLYLD 90 (188)
T ss_pred cceeeee-cchhhhhHH
Confidence 7888888 788888754
No 31
>cd06224 REM Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few.
Probab=20.68 E-value=62 Score=18.83 Aligned_cols=22 Identities=5% Similarity=0.360 Sum_probs=17.1
Q ss_pred hhhHHHhHhHHhhccccchhhh
Q psy738 33 IVNHNNARLAEVWLDEWKHFYY 54 (62)
Q Consensus 33 ~~~rN~~RvaevWmDeyk~~~y 54 (62)
.++...+.+...|+++|-.-|+
T Consensus 65 ~~~~~v~~~l~~Wv~~~~~df~ 86 (122)
T cd06224 65 PIRLRVLNVLRTWVENYPYDFF 86 (122)
T ss_pred HHHHHHHHHHHHHHHhCCCccc
Confidence 3566778889999999877664
No 32
>PF13854 Kelch_5: Kelch motif
Probab=20.65 E-value=39 Score=16.75 Aligned_cols=12 Identities=17% Similarity=0.138 Sum_probs=8.4
Q ss_pred ecccceEeeccC
Q psy738 9 ATCSHVGHVFRK 20 (62)
Q Consensus 9 ~PCSRVGHifr~ 20 (62)
+|+.|-+|-.=.
T Consensus 1 ~P~~R~~hs~~~ 12 (42)
T PF13854_consen 1 IPSPRYGHSAVV 12 (42)
T ss_pred CCCCccceEEEE
Confidence 588888886543
Done!