Query psy960
Match_columns 83
No_of_seqs 102 out of 137
Neff 2.9
Searched_HMMs 46136
Date Fri Aug 16 23:57:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy960.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/960hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02936 COX4: Cytochrome c ox 99.9 4.4E-27 9.4E-32 165.7 2.8 48 4-51 95-142 (142)
2 KOG4075|consensus 99.9 1.2E-24 2.7E-29 159.8 3.5 48 4-51 120-167 (167)
3 cd00922 Cyt_c_Oxidase_IV Cytoc 99.8 2.1E-21 4.6E-26 136.1 3.7 42 4-45 95-136 (136)
4 PF06592 DUF1138: Protein of u 65.5 6 0.00013 26.4 2.2 22 9-30 29-51 (73)
5 PF03037 KMP11: Kinetoplastid 63.4 5.3 0.00012 27.3 1.7 32 1-32 23-58 (90)
6 PF02013 CBM_10: Cellulose or 62.4 2.6 5.5E-05 24.4 0.0 11 40-50 23-33 (36)
7 PF14311 DUF4379: Domain of un 55.7 3 6.6E-05 24.5 -0.4 13 39-52 3-15 (55)
8 PF00101 RuBisCO_small: Ribulo 48.5 16 0.00035 24.7 2.2 44 15-58 10-55 (99)
9 PF13342 Toprim_Crpt: C-termin 46.4 19 0.00041 22.4 2.1 21 22-42 18-39 (62)
10 PLN02289 ribulose-bisphosphate 41.8 27 0.00059 26.5 2.7 26 15-40 75-100 (176)
11 TIGR02574 stabl_TIGR02574 puta 39.7 53 0.0011 19.9 3.3 30 13-42 25-54 (63)
12 CHL00130 rbcS ribulose-1,5-bis 38.8 30 0.00065 25.4 2.4 26 15-40 13-38 (138)
13 PF13239 2TM: 2TM domain 36.9 27 0.0006 21.8 1.8 17 14-30 66-82 (83)
14 PF09720 Unstab_antitox: Putat 35.0 66 0.0014 18.6 3.1 28 14-41 23-50 (54)
15 cd03527 RuBisCO_small Ribulose 34.0 65 0.0014 22.0 3.3 42 16-57 12-55 (99)
16 COG0275 Predicted S-adenosylme 33.9 15 0.00033 29.8 0.3 16 27-42 124-139 (314)
17 PHA00439 exonuclease 24.9 73 0.0016 25.3 2.6 26 15-49 253-280 (286)
18 PF05089 NAGLU: Alpha-N-acetyl 23.9 36 0.00078 27.7 0.8 28 10-37 83-113 (333)
19 PF08793 2C_adapt: 2-cysteine 21.9 42 0.0009 19.2 0.6 13 28-40 7-19 (37)
20 PF06029 AlkA_N: AlkA N-termin 21.8 33 0.0007 23.4 0.2 17 20-36 73-89 (116)
21 TIGR00006 S-adenosyl-methyltra 20.8 37 0.00081 26.9 0.3 15 28-42 121-135 (305)
22 PRK00050 16S rRNA m(4)C1402 me 20.6 37 0.00081 26.6 0.3 15 28-42 119-133 (296)
23 PF01795 Methyltransf_5: MraW 20.5 32 0.0007 27.5 -0.1 15 28-42 122-136 (310)
No 1
>PF02936 COX4: Cytochrome c oxidase subunit IV; InterPro: IPR004203 Cytochrome c oxidase, a 13 sub-unit complex (1.9.3.1 from EC) is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit IV. The Dictyostelium discoideum (Slime mould) member of this family is called COX VI. The Saccharomyces cerevisiae protein YGX6_YEAST appears to be the yeast COX IV subunit.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3ABK_Q 3AG1_Q 3ASN_Q 1OCZ_D 2EIN_Q 2OCC_D 2YBB_O 3AG3_D 1OCO_Q 1V55_Q ....
Probab=99.93 E-value=4.4e-27 Score=165.74 Aligned_cols=48 Identities=44% Similarity=0.879 Sum_probs=41.2
Q ss_pred ccccccCCCCCCCcHHHHHHHHHHHHHccCCCCcccccccccccCccc
Q psy960 4 KVKKIFPEKAETLSEEHRQEMLQKMIDLRWNPITGTASKWDYEKNDWK 51 (83)
Q Consensus 4 ~k~yVYpp~P~TfseEWkeAQleRMLdmkvNPItG~SSkWDYEkn~WK 51 (83)
+|.|||||+|+|||+|||+||++|||+|++|||+|+||+||||||+||
T Consensus 95 ~r~~~~~~~P~T~~~Ew~ea~~~~m~~~~~nPi~G~ss~wdy~~~~wk 142 (142)
T PF02936_consen 95 QRSYVYPPLPHTFSKEWQEAQNERMLDMKVNPITGFSSKWDYEKNEWK 142 (142)
T ss_dssp HHHHT-----GGGSHHHHHHHHHHHHHTTSSTTTTSGGGEETTTTEE-
T ss_pred HHHHhCCCCCCCcCHHHHHHHHHHHHHcCCCCCCCCcCCcCCCCCcCC
Confidence 688999999999999999999999999999999999999999999997
No 2
>KOG4075|consensus
Probab=99.90 E-value=1.2e-24 Score=159.78 Aligned_cols=48 Identities=40% Similarity=0.828 Sum_probs=46.8
Q ss_pred ccccccCCCCCCCcHHHHHHHHHHHHHccCCCCcccccccccccCccc
Q psy960 4 KVKKIFPEKAETLSEEHRQEMLQKMIDLRWNPITGTASKWDYEKNDWK 51 (83)
Q Consensus 4 ~k~yVYpp~P~TfseEWkeAQleRMLdmkvNPItG~SSkWDYEkn~WK 51 (83)
+++|||||+|+||++|||+||+||||||++|||+|+||+||||+|+||
T Consensus 120 ~~v~vy~~~P~Tf~~Ewq~kq~erml~~~~NPi~Glas~wdye~k~wK 167 (167)
T KOG4075|consen 120 GKVRVYGPLPKTFNKEWQEKQLERMLDLKINPIGGLASKWDYEEKKWK 167 (167)
T ss_pred HhheecCCCCcchhHHHHHHHHHHHHHcccCCccCcccccChhhhccC
Confidence 578999999999999999999999999999999999999999999998
No 3
>cd00922 Cyt_c_Oxidase_IV Cytochrome c oxidase subunit IV. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit IV is the largest of the nuclear-encoded subunits. It binds ATP at the matrix side, leading to an allosteric inhibition of enzyme activity at high intramitochondrial ATP/ADP ratios. In mammals, subunit IV has a lung-specific isoform and a ubiquitously expressed isoform.
Probab=99.83 E-value=2.1e-21 Score=136.09 Aligned_cols=42 Identities=43% Similarity=0.798 Sum_probs=41.2
Q ss_pred ccccccCCCCCCCcHHHHHHHHHHHHHccCCCCccccccccc
Q psy960 4 KVKKIFPEKAETLSEEHRQEMLQKMIDLRWNPITGTASKWDY 45 (83)
Q Consensus 4 ~k~yVYpp~P~TfseEWkeAQleRMLdmkvNPItG~SSkWDY 45 (83)
+|+|+|||+|+||++|||+||++||++|++|||+|+||+|||
T Consensus 95 ~r~~~~~~~P~T~t~Ewqea~~er~~~~~~NPitG~ss~~dy 136 (136)
T cd00922 95 QRAFVYGPKPHTFTEEWQEAQLERMLDMKVNPITGYASKWDY 136 (136)
T ss_pred HHHhccCCCCCCcCHHHHHHHHHHHHHhCCCCCcccccCCcC
Confidence 689999999999999999999999999999999999999998
No 4
>PF06592 DUF1138: Protein of unknown function (DUF1138); InterPro: IPR009515 This family consists of several hypothetical short plant proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.
Probab=65.51 E-value=6 Score=26.36 Aligned_cols=22 Identities=18% Similarity=0.056 Sum_probs=18.1
Q ss_pred cCCCCCCCcH-HHHHHHHHHHHH
Q psy960 9 FPEKAETLSE-EHRQEMLQKMID 30 (83)
Q Consensus 9 Ypp~P~Tfse-EWkeAQleRMLd 30 (83)
-+..|+|.++ ||.++.-+||..
T Consensus 29 GGt~p~Tv~~keW~~aT~~K~qa 51 (73)
T PF06592_consen 29 GGTTPHTVSNKEWWKATDKKFQA 51 (73)
T ss_pred CCCCCCccccHHHHHHHHHHHhh
Confidence 3678999965 999999998864
No 5
>PF03037 KMP11: Kinetoplastid membrane protein 11; InterPro: IPR004132 Kinetoplastid membrane protein 11 is a major cell surface glycoprotein of the parasite Leishmania donovani. It stimulates T-cell proliferation and may play a role in the immunlogy of the dieases Leishmaniasis.; GO: 0006952 defense response, 0008284 positive regulation of cell proliferation
Probab=63.42 E-value=5.3 Score=27.33 Aligned_cols=32 Identities=41% Similarity=0.631 Sum_probs=24.8
Q ss_pred CccccccccCCCC--CCCcHHHHH--HHHHHHHHcc
Q psy960 1 MEEKVKKIFPEKA--ETLSEEHRQ--EMLQKMIDLR 32 (83)
Q Consensus 1 ~~~~k~yVYpp~P--~TfseEWke--AQleRMLdmk 32 (83)
|+||..-.|...| .|||.|-++ .-++|||...
T Consensus 23 m~eqn~kffadkpdestlspemkehyekfe~miqeh 58 (90)
T PF03037_consen 23 MQEQNKKFFADKPDESTLSPEMKEHYEKFERMIQEH 58 (90)
T ss_pred HHHHHHhhhcCCCcccccCHHHHHHHHHHHHHHHHH
Confidence 6788777777777 499999986 5688888754
No 6
>PF02013 CBM_10: Cellulose or protein binding domain; InterPro: IPR002883 This domain is found in two distinct sets of proteins with different functions. Those found in aerobic bacteria bind cellulose (or other carbohydrates); but in anaerobic fungi they are protein binding domains, referred to as dockerin domains or docking domains. They are believed to be responsible for the assembly of a multiprotein cellulase/hemicellulase complex, similar to the cellulosome found in certain anaerobic bacteria. The recycling of photosynthetically fixed carbon in plant cell walls is a key microbial process. Enzyme systems that attack the plant cell wall contain noncatalytic carbohydrate-binding modules that mediate attachment to this composite structure and play a pivotal role in maximizing the hydrolytic process. In anaerobes, the degradation is carried out by a high molecular weight, multifunctional complex termed the cellulosome. This consists of a number of independent enzyme components, each of which contains a conserved 40-residue dockerin domain, which functions to bind the enzyme to a cohesin domain within the scaffoldin protein [, ]. In anaerobic bacteria that degrade plant cell walls, exemplified by Clostridium thermocellum, the dockerin domains of the catalytic polypeptides can bind equally well to any cohesin from the same organism. More recently, anaerobic fungi, typified by Piromyces equi, have been suggested to also synthesise a cellulosome complex, although the dockerin sequences of the bacterial and fungal enzymes are completely different []. For example, the fungal enzymes contain one, two or three copies of the dockerin sequence in tandem within the catalytic polypeptide. In contrast, all the C. thermocellum cellulosome catalytic components contain a single dockerin domain. The anaerobic bacterial dockerins are homologous to EF hands (calcium-binding motifs) and require calcium for activity whereas the fungal dockerin does not require calcium. Finally, the interaction between cohesin and dockerin appears to be species specific in bacteria, there is almost no species specificity of binding within fungal species and no identified sites that distinguish different species. The structure of dockerin from P. equi contains two helical stretches and four short beta-strands which form an antiparallel sheet structure adjacent to an additional short twisted parallel strand. The N- and C-termini are adjacent to each other. Aerobic bacteria contain related regions, however these appear to function as cellulose/carbohydrate binding domains.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 2J4M_A 2J4N_A 1E8R_A 1QLD_A 1E8P_A 1E8Q_A.
Probab=62.36 E-value=2.6 Score=24.35 Aligned_cols=11 Identities=36% Similarity=1.087 Sum_probs=9.7
Q ss_pred ccccccccCcc
Q psy960 40 ASKWDYEKNDW 50 (83)
Q Consensus 40 SSkWDYEkn~W 50 (83)
+.+|.+||++|
T Consensus 23 ~g~WGvEN~~w 33 (36)
T PF02013_consen 23 DGGWGVENGDW 33 (36)
T ss_dssp TEEEEEETTEE
T ss_pred CCCEeeECCce
Confidence 56899999998
No 7
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=55.74 E-value=3 Score=24.46 Aligned_cols=13 Identities=54% Similarity=0.989 Sum_probs=11.1
Q ss_pred cccccccccCcccC
Q psy960 39 TASKWDYEKNDWKK 52 (83)
Q Consensus 39 ~SSkWDYEkn~WKK 52 (83)
|+.+|||++|. ..
T Consensus 3 l~~eW~~~~N~-~~ 15 (55)
T PF14311_consen 3 LAKEWDYEKNK-LD 15 (55)
T ss_pred HHHHhChhhcC-CC
Confidence 68899999999 55
No 8
>PF00101 RuBisCO_small: Ribulose bisphosphate carboxylase, small chain; InterPro: IPR000894 RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP) [], thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown []. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [], which results in RuBisCO being more abundant during the day when it is required. The RuBisCo small subunit consists of a central four-stranded beta-sheet, with two helices packed against it [].; PDB: 1BWV_W 1IWA_P 3AXM_X 1WDD_S 3AXK_T 1IR2_K 1RBL_N 1UZH_J 1RSC_P 1UW9_C ....
Probab=48.53 E-value=16 Score=24.74 Aligned_cols=44 Identities=14% Similarity=0.268 Sum_probs=34.2
Q ss_pred CCcHHHHHHHHHHHHHccCCCCcccccccccccCccc--CCCCccc
Q psy960 15 TLSEEHRQEMLQKMIDLRWNPITGTASKWDYEKNDWK--KGDSINS 58 (83)
Q Consensus 15 TfseEWkeAQleRMLdmkvNPItG~SSkWDYEkn~WK--K~~~~~~ 58 (83)
.|+++-..+|++.+|.++-.|-.=++.+=.|.++-|. +...|.+
T Consensus 10 ~l~~~~i~~Qv~~ll~qG~~i~iE~ad~r~~r~~~W~mW~~p~~~~ 55 (99)
T PF00101_consen 10 PLTDEEIAKQVRYLLSQGWIIGIEHADPRRFRTSYWQMWKLPMFGC 55 (99)
T ss_dssp ---HHHHHHHHHHHHHTT-EEEEEEESCGGSTSSS-EEESSEBTTB
T ss_pred CCCHHHHHHHHHhhhhcCceeeEEecCCCCCCCCEeecCCCCCcCC
Confidence 4678889999999999999998888888899999999 8666544
No 9
>PF13342 Toprim_Crpt: C-terminal repeat of topoisomerase
Probab=46.35 E-value=19 Score=22.39 Aligned_cols=21 Identities=24% Similarity=0.311 Sum_probs=17.0
Q ss_pred HHHHHHHH-HccCCCCcccccc
Q psy960 22 QEMLQKMI-DLRWNPITGTASK 42 (83)
Q Consensus 22 eAQleRML-dmkvNPItG~SSk 42 (83)
++|++.+| .=+.++|.||-|+
T Consensus 18 ~~~~~~Ll~~gkT~~ikGF~SK 39 (62)
T PF13342_consen 18 DEEVKELLEKGKTGLIKGFKSK 39 (62)
T ss_pred HHHHHHHHHcCCccCccCcccC
Confidence 46788888 5677889999996
No 10
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=41.81 E-value=27 Score=26.51 Aligned_cols=26 Identities=15% Similarity=0.371 Sum_probs=22.3
Q ss_pred CCcHHHHHHHHHHHHHccCCCCcccc
Q psy960 15 TLSEEHRQEMLQKMIDLRWNPITGTA 40 (83)
Q Consensus 15 TfseEWkeAQleRMLdmkvNPItG~S 40 (83)
.|++|-..+|+++||+++..|---|+
T Consensus 75 pLtdeqI~kQVeYli~~GW~pclEf~ 100 (176)
T PLN02289 75 DLTDEELAKEVDYLLRNKWVPCLEFE 100 (176)
T ss_pred CCCHHHHHHHHHHHHhCCCeeeeeec
Confidence 58999999999999999999865444
No 11
>TIGR02574 stabl_TIGR02574 putative addiction module component, TIGR02574 family. Members of this family are bacterial proteins, typically are about 75 amino acids long, always found as part of a pair (at least) of two small genes. The other in the pair always belongs to a subfamily of the larger family pfam05016 (although not necessarily scoring above the designated cutoff), which contains plasmid stabilization proteins. It is likely that this protein and its pfam05016 member partner comprise some form of addiction module, although these gene pairs usually are found on the bacterial main chromosome.
Probab=39.65 E-value=53 Score=19.90 Aligned_cols=30 Identities=17% Similarity=0.327 Sum_probs=24.5
Q ss_pred CCCCcHHHHHHHHHHHHHccCCCCcccccc
Q psy960 13 AETLSEEHRQEMLQKMIDLRWNPITGTASK 42 (83)
Q Consensus 13 P~TfseEWkeAQleRMLdmkvNPItG~SSk 42 (83)
...++..|++.--+|+-..+.|++.|++..
T Consensus 25 ~~~~~~~~~~el~~R~~~~~~g~~~~i~~e 54 (63)
T TIGR02574 25 HLILTEAQKAELDRRLADYKADPSKASPWE 54 (63)
T ss_pred cCCCCHHHHHHHHHHHHHHHcCCcCCCCHH
Confidence 345678888888899999999999998643
No 12
>CHL00130 rbcS ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed
Probab=38.82 E-value=30 Score=25.36 Aligned_cols=26 Identities=15% Similarity=0.256 Sum_probs=22.3
Q ss_pred CCcHHHHHHHHHHHHHccCCCCcccc
Q psy960 15 TLSEEHRQEMLQKMIDLRWNPITGTA 40 (83)
Q Consensus 15 TfseEWkeAQleRMLdmkvNPItG~S 40 (83)
.||+|-..+|+++||+++.+|---|+
T Consensus 13 pLTdeqI~kQI~Y~i~~GW~p~iEft 38 (138)
T CHL00130 13 DLTDQQIEKQIQYAISKGWALNVEWT 38 (138)
T ss_pred CCCHHHHHHHHHHHHhcCCeEEEEec
Confidence 48999999999999999999955444
No 13
>PF13239 2TM: 2TM domain
Probab=36.86 E-value=27 Score=21.81 Aligned_cols=17 Identities=12% Similarity=0.362 Sum_probs=14.3
Q ss_pred CCCcHHHHHHHHHHHHH
Q psy960 14 ETLSEEHRQEMLQKMID 30 (83)
Q Consensus 14 ~TfseEWkeAQleRMLd 30 (83)
..|.++|.++++|+.++
T Consensus 66 ~~~~~~We~rki~k~m~ 82 (83)
T PF13239_consen 66 YFFGKDWEERKIQKLME 82 (83)
T ss_pred ccccchHHHHHHHHHhc
Confidence 67788999999998764
No 14
>PF09720 Unstab_antitox: Putative addiction module component; InterPro: IPR013406 This entry defines several short bacterial proteins, typically about 75 amino acids long, which are always found as part of a pair (at least) of small genes. The other protein in the pair always belongs to a family of plasmid stabilisation proteins (IPR007712 from INTERPRO). It is likely that this protein and its partner comprise some form of addiction module - a pair of genes consisting of a stable toxin and an unstable antitoxin which mediate programmed cell death [] - although these gene pairs are usually found on the bacterial main chromosome.
Probab=34.99 E-value=66 Score=18.60 Aligned_cols=28 Identities=7% Similarity=0.203 Sum_probs=24.8
Q ss_pred CCCcHHHHHHHHHHHHHccCCCCccccc
Q psy960 14 ETLSEEHRQEMLQKMIDLRWNPITGTAS 41 (83)
Q Consensus 14 ~TfseEWkeAQleRMLdmkvNPItG~SS 41 (83)
...+..|.+---+|.-+++.|+++|++.
T Consensus 23 ~~~~~~w~~el~rR~~~~~~G~~~~i~~ 50 (54)
T PF09720_consen 23 SEVEAWWKEELERRLAEYESGKVQGIPW 50 (54)
T ss_pred ccCcHHHHHHHHHHHHHHHcCCCCCCcH
Confidence 3788999999999999999999999864
No 15
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=34.03 E-value=65 Score=21.97 Aligned_cols=42 Identities=19% Similarity=0.389 Sum_probs=36.1
Q ss_pred CcHHHHHHHHHHHHHccCCCCcccccccccccCccc--CCCCcc
Q psy960 16 LSEEHRQEMLQKMIDLRWNPITGTASKWDYEKNDWK--KGDSIN 57 (83)
Q Consensus 16 fseEWkeAQleRMLdmkvNPItG~SSkWDYEkn~WK--K~~~~~ 57 (83)
||+|--.+|++.+|.++-.|=.=++..=-|.+.-|. |...+.
T Consensus 12 lt~~~i~~QI~yll~qG~~~~lE~ad~~~~~~~yW~mwklP~f~ 55 (99)
T cd03527 12 LTDEQIAKQIDYIISNGWAPCLEFTEPEHYDNRYWTMWKLPMFG 55 (99)
T ss_pred CCHHHHHHHHHHHHhCCCEEEEEcccCCCCCCCEEeeccCCCCC
Confidence 679999999999999999999888888889999998 555443
No 16
>COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]
Probab=33.87 E-value=15 Score=29.83 Aligned_cols=16 Identities=19% Similarity=0.397 Sum_probs=14.3
Q ss_pred HHHHccCCCCcccccc
Q psy960 27 KMIDLRWNPITGTASK 42 (83)
Q Consensus 27 RMLdmkvNPItG~SSk 42 (83)
-.|||||||-+|+|+.
T Consensus 124 ~pLDMRMd~~~~lsA~ 139 (314)
T COG0275 124 GPLDMRMDQTQGLSAA 139 (314)
T ss_pred CCcccCcCCCCCCCHH
Confidence 3689999999999986
No 17
>PHA00439 exonuclease
Probab=24.86 E-value=73 Score=25.33 Aligned_cols=26 Identities=19% Similarity=0.562 Sum_probs=19.9
Q ss_pred CCcHHH--HHHHHHHHHHccCCCCcccccccccccCc
Q psy960 15 TLSEEH--RQEMLQKMIDLRWNPITGTASKWDYEKND 49 (83)
Q Consensus 15 TfseEW--keAQleRMLdmkvNPItG~SSkWDYEkn~ 49 (83)
.|+||- ++||+-|+|. ++.||+++++
T Consensus 253 g~~e~~~~~q~~~ari~r---------~~d~d~~~k~ 280 (286)
T PHA00439 253 GMTEEDAIKQAQMARILR---------AEDYDFIDKE 280 (286)
T ss_pred CCCHHHHHHHHHHHHHhh---------ccccCcccCc
Confidence 477776 5788888886 6889998765
No 18
>PF05089 NAGLU: Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain; InterPro: IPR024733 Alpha-N-acetylglucosaminidase is a lysosomal enzyme that is required for the stepwise degradation of heparan sulphate []. Mutations on the alpha-N-acetylglucosaminidase gene can lead to mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B), characterised by neurological dysfunction but relatively mild somatic manifestations []. Alpha-N-acetylglucosaminidase is composed of three domains. This entry represents the central domain, which has a tim barrel fold [].; PDB: 4A4A_A 2VC9_A 2VCC_A 2VCB_A 2VCA_A.
Probab=23.88 E-value=36 Score=27.72 Aligned_cols=28 Identities=18% Similarity=0.382 Sum_probs=16.5
Q ss_pred CCCCCCCcH---HHHHHHHHHHHHccCCCCc
Q psy960 10 PEKAETLSE---EHRQEMLQKMIDLRWNPIT 37 (83)
Q Consensus 10 pp~P~Tfse---EWkeAQleRMLdmkvNPIt 37 (83)
+|+|..+=+ |=|.+-++||..++|-||-
T Consensus 83 GPLp~~w~~~q~~Lq~kIl~RmreLGm~PVL 113 (333)
T PF05089_consen 83 GPLPQSWIDQQAELQKKILDRMRELGMTPVL 113 (333)
T ss_dssp ----TTHHHHHHHHHHHHHHHHHHHT-EEEE
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHcCCcccC
Confidence 567766533 3356678899999999983
No 19
>PF08793 2C_adapt: 2-cysteine adaptor domain; InterPro: IPR014901 The virus-specific 2-cysteine adaptor is found fused to OTU/A20-like peptidases and S/T protein kinases. The associations to these proteins indicate that they might function as viral adaptors connecting the kinases and OTU/A20 peptidases to specific targets [].
Probab=21.93 E-value=42 Score=19.17 Aligned_cols=13 Identities=38% Similarity=0.445 Sum_probs=9.2
Q ss_pred HHHccCCCCcccc
Q psy960 28 MIDLRWNPITGTA 40 (83)
Q Consensus 28 MLdmkvNPItG~S 40 (83)
..+-.+||+||=.
T Consensus 7 ~~np~~NP~Tgr~ 19 (37)
T PF08793_consen 7 HRNPTVNPITGRK 19 (37)
T ss_pred HhCCCCCCCCCCc
Confidence 3456799999844
No 20
>PF06029 AlkA_N: AlkA N-terminal domain; InterPro: IPR010316 This domain is found at the N terminus of bacterial AlkA 3.2.2.21 from EC. AlkA (3-methyladenine-DNA glycosylase II) is a base excision repair glycosylase from Escherichia coli. It removes a variety of alkylated bases from DNA, primarily by removing alkylation damage from duplex and single stranded DNA. AlkA flips a 1-azaribose abasic nucleotide out of DNA. This produces a 66 degrees bend in the DNA and a marked widening of the minor groove []. This groove is a large hydrophobic cleft, which is unusually rich in aromatic residues. AlkA recognises electron-deficient methylated bases through pi-donor/acceptor interactions involving the electron-rich aromatic cleft. AlkA is similar in fold and active site location to the bifunctional glycosylase/lyase endonuclease III. This suggests that the two may use similar mechanisms for base excision []. The structural analysis of the AlkA and AlkA-hypoxanthine structures indicate that free hypoxanthine binding in the active site may inhibit glycosylase activity [].; GO: 0003905 alkylbase DNA N-glycosylase activity; PDB: 1MPG_B 3CWS_D 3CW7_C 3CWA_B 3D4V_A 3CWT_C 3CWU_B 3OGD_A 3CVS_C 1PVS_A ....
Probab=21.81 E-value=33 Score=23.37 Aligned_cols=17 Identities=18% Similarity=0.317 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHccCCCC
Q psy960 20 HRQEMLQKMIDLRWNPI 36 (83)
Q Consensus 20 WkeAQleRMLdmkvNPI 36 (83)
.-.++++||+|+..||-
T Consensus 73 ~~~~rvRrlfDLdaDp~ 89 (116)
T PF06029_consen 73 AVIARVRRLFDLDADPQ 89 (116)
T ss_dssp HHHHHHHHHTTTT--HH
T ss_pred HHHHHHHHHhCCCCCHH
Confidence 45689999999999984
No 21
>TIGR00006 S-adenosyl-methyltransferase MraW. Genetics paper in 1972 links mra cluster to peptidoglycan biosynthesis in E. coli. Seems to be common in proteobacteria.wn.
Probab=20.83 E-value=37 Score=26.89 Aligned_cols=15 Identities=13% Similarity=0.251 Sum_probs=13.2
Q ss_pred HHHccCCCCcccccc
Q psy960 28 MIDLRWNPITGTASK 42 (83)
Q Consensus 28 MLdmkvNPItG~SSk 42 (83)
-|||||||=+|+|+.
T Consensus 121 pLDMRMd~~~~~tA~ 135 (305)
T TIGR00006 121 PLDMRMDQSQKLSAA 135 (305)
T ss_pred CcccccCCCCCCCHH
Confidence 589999999998875
No 22
>PRK00050 16S rRNA m(4)C1402 methyltranserfase; Provisional
Probab=20.58 E-value=37 Score=26.62 Aligned_cols=15 Identities=20% Similarity=0.410 Sum_probs=13.3
Q ss_pred HHHccCCCCcccccc
Q psy960 28 MIDLRWNPITGTASK 42 (83)
Q Consensus 28 MLdmkvNPItG~SSk 42 (83)
.|||||||=.|+|+.
T Consensus 119 pLDMRmd~~~~~sA~ 133 (296)
T PRK00050 119 PLDMRMDQSQGLTAA 133 (296)
T ss_pred CCcCCcCCCCCCCHH
Confidence 699999999998776
No 23
>PF01795 Methyltransf_5: MraW methylase family; InterPro: IPR002903 This is a family of S-adenosyl-L-methionine-dependent methyltransferases, which are found primarily, though not exclusively, in bacteria. The Escherichia coli protein is essential and has been linked to peptidoglycan biosynthesis [, ].; GO: 0008168 methyltransferase activity; PDB: 1N2X_A 1M6Y_A 1WG8_A 3TKA_A.
Probab=20.50 E-value=32 Score=27.46 Aligned_cols=15 Identities=27% Similarity=0.583 Sum_probs=8.5
Q ss_pred HHHccCCCCcccccc
Q psy960 28 MIDLRWNPITGTASK 42 (83)
Q Consensus 28 MLdmkvNPItG~SSk 42 (83)
-|||||||=.|+++.
T Consensus 122 pLDMRMd~~~~~tAa 136 (310)
T PF01795_consen 122 PLDMRMDPSQGLTAA 136 (310)
T ss_dssp BS---SSTTSS--HH
T ss_pred CCcccccccccccHH
Confidence 589999999999775
Done!