Query psy16498
Match_columns 102
No_of_seqs 101 out of 422
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 22:48:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16498.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16498hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05951 Peptidase_M15_2: Bact 99.9 6.2E-23 1.3E-27 150.5 5.8 66 7-75 71-149 (152)
2 PF01085 HH_signal: Hedgehog a 99.9 8.6E-22 1.9E-26 145.2 6.4 71 1-71 90-160 (160)
3 PF08291 Peptidase_M15_3: Pept 99.8 6.3E-22 1.4E-26 136.7 -1.6 67 2-71 38-110 (110)
4 COG3108 Uncharacterized protei 99.8 4.8E-20 1E-24 138.7 6.0 70 7-79 103-183 (185)
5 PF02557 VanY: D-alanyl-D-alan 97.3 4.7E-05 1E-09 53.2 -0.5 35 6-40 23-79 (132)
6 PF13539 Peptidase_M15_4: D-al 96.3 0.0045 9.8E-08 39.1 2.9 49 23-71 5-66 (67)
7 PF06904 Extensin-like_C: Exte 94.0 0.15 3.2E-06 38.4 5.4 67 8-74 78-169 (178)
8 COG3921 Uncharacterized protei 92.3 0.089 1.9E-06 42.7 2.0 68 8-75 200-292 (300)
9 PRK10178 D-alanyl-D-alanine di 89.5 0.22 4.7E-06 37.8 1.7 35 5-39 60-110 (184)
10 COG1876 VanY D-alanyl-D-alanin 81.5 0.68 1.5E-05 36.3 0.9 31 6-36 119-171 (241)
11 KOG3638|consensus 79.9 0.98 2.1E-05 37.7 1.4 78 14-97 137-214 (414)
12 PF01427 Peptidase_M15: D-ala- 69.9 1.3 2.9E-05 33.4 -0.2 33 6-38 60-123 (198)
13 TIGR03292 PhnH_redo phosphonat 53.1 8.1 0.00018 29.0 1.4 17 85-101 144-161 (174)
14 KOG0788|consensus 52.2 15 0.00033 30.5 2.9 57 43-100 89-148 (334)
15 COG3625 PhnH Uncharacterized e 44.2 14 0.0003 28.6 1.5 18 84-101 162-180 (196)
16 PF05845 PhnH: Bacterial phosp 42.7 15 0.00033 27.8 1.5 17 85-101 159-176 (192)
17 PRK10147 phnH carbon-phosphoru 38.1 18 0.00039 27.6 1.2 16 86-101 163-179 (196)
18 PF05445 Pox_ser-thr_kin: Poxv 36.9 19 0.00042 30.8 1.3 16 61-76 291-309 (434)
19 PRK12766 50S ribosomal protein 35.8 74 0.0016 25.1 4.4 69 1-73 145-230 (232)
20 COG1902 NemA NADH:flavin oxido 35.2 34 0.00073 28.2 2.5 19 45-63 151-170 (363)
21 PF00724 Oxidored_FMN: NADH:fl 34.3 37 0.00081 27.1 2.6 19 44-62 150-169 (341)
22 KOG2551|consensus 34.3 33 0.00071 27.1 2.2 43 9-55 140-192 (230)
23 PF08002 DUF1697: Protein of u 31.0 1.1E+02 0.0023 21.6 4.2 35 37-71 13-48 (137)
24 PRK10605 N-ethylmaleimide redu 30.8 53 0.0011 26.7 2.9 24 45-68 161-185 (362)
25 COG3502 Uncharacterized protei 29.6 54 0.0012 23.4 2.4 27 47-73 13-41 (115)
26 PRK08562 rpl32e 50S ribosomal 28.7 74 0.0016 22.9 3.0 56 1-57 46-118 (125)
27 PF12683 DUF3798: Protein of u 28.5 41 0.0009 27.2 1.9 40 31-77 105-144 (275)
28 PHA03111 Ser/Thr kinase; Provi 25.5 30 0.00065 29.7 0.6 16 61-76 295-313 (444)
29 COG1165 MenD 2-succinyl-6-hydr 24.8 54 0.0012 29.1 2.1 70 3-73 94-173 (566)
30 COG2173 DdpX D-alanyl-D-alanin 24.5 47 0.001 26.0 1.5 33 6-38 88-137 (211)
31 PF06108 DUF952: Protein of un 23.1 40 0.00087 22.5 0.8 9 65-73 25-33 (93)
32 PLN02411 12-oxophytodienoate r 22.9 79 0.0017 26.1 2.6 24 45-68 167-191 (391)
33 TIGR00535 SAM_DCase S-adenosyl 21.5 1.3E+02 0.0029 24.9 3.7 56 44-100 83-142 (334)
34 cd00513 Ribosomal_L32_L32e Rib 20.5 32 0.0007 24.1 -0.1 19 1-19 29-47 (107)
No 1
>PF05951 Peptidase_M15_2: Bacterial protein of unknown function (DUF882); InterPro: IPR010275 This family consists of proteins related to metallopeptidases belong to MEROPS peptidase family M15A. They are classed as non-peptidase homologues (M15A.UNA) and include A3D3U2 from SWISSPROT, where the metal ligands (marked by *) are conserved but the catalytic Asn has been replaced by Asp (+): 70 80 90 100 110 120 A3D3U2: QSKVLNDFNHLLRDHRQNVAAPMDKRLFDLLYSLKTTLNVDDEIHVISGYRSPKTNAMLA : .:. .:. : :.: ::.:: . :: . B1W1A6: PELNTCNSTWAGGKVAAGTARANALSSMWKLEALRHALG-DRSIRVTSGFRSASCNAAV- 20 30 40 50 60 70 * 130 * 140 150 160 170 * + A3D3U2: SNSGGVAKKSYHMRGMAMDIAIPSVKLKTLREAALSLKLGGV---GYYPNSGFVHVDCGP :: :..: :: : :.:.. .: :: . : . :. :: .. :::. :: B1W1A6: ---GG-ASNSRHMYGDAVDLGASPHSLCTLAKQARYHGFRGILGPGYVGHNDHVHVNQGP 80 90 100 110 120 B1W1A6 from SWISSPROT belongs to IPR013230 from INTERPRO, whcih contains peptidases belonging to the M15A family. The function of the proteins in this entry are not known.
Probab=99.88 E-value=6.2e-23 Score=150.49 Aligned_cols=66 Identities=27% Similarity=0.434 Sum_probs=61.0
Q ss_pred CeEEEeeeeCCCCCCC----------CCCcCcceeEEEEEeCCCCcchHHHHHHHHHHcCCCeE-EEcCCC--eEEEeec
Q psy16498 7 VRLRVIEGWDEEGHHA----------SDSLHYEGRAVDITTSDRDSSKYGLLARMAVEAGFDWV-YYESRN--HIHCSVK 73 (102)
Q Consensus 7 ~Pi~VtSGYR~p~~N~----------~~S~H~~GrAaDI~~~~~~~~~~~~L~~~A~~~gFd~v-~Y~~~~--fVHvdv~ 73 (102)
.||.|+||||||++|+ ++|+||.|+|+||++++.+. .+|.++|+.++.++| +||+++ |||||++
T Consensus 71 ~~i~iiSGYRsp~TN~~Lr~~~~gvA~~S~Hm~G~AiDi~ipgv~~---~~l~~~A~~l~~GGVG~Yp~s~~~FVHvDtG 147 (152)
T PF05951_consen 71 NPIQIISGYRSPETNAMLRRRSGGVAKNSLHMQGKAIDIRIPGVPL---RQLRRAALSLQRGGVGYYPRSGSKFVHVDTG 147 (152)
T ss_pred CcEEEEeecCCHHHHHHHHhcCCCccccCccccceEEEEecCCCCH---HHHHHHHHHcCCCeEEeeCCCCCCEEEeCCC
Confidence 5899999999999995 99999999999999998774 588899999999999 999988 9999998
Q ss_pred CC
Q psy16498 74 TV 75 (102)
Q Consensus 74 ~~ 75 (102)
+.
T Consensus 148 ~v 149 (152)
T PF05951_consen 148 PV 149 (152)
T ss_pred CC
Confidence 74
No 2
>PF01085 HH_signal: Hedgehog amino-terminal signalling domain; InterPro: IPR000320 This domain identifies a group of sequences which belong to the MEROPS peptidase family C46 (clan CH). The type example is the hedgehog protein from Drosophila melanogaster (Fruit fly) which self-processes by a one-time cysteine dependent self cleavage. Hedgehog is a family of secreted signal molecules required for embryonic cell differentiation. members of this family are composed of two domains. These proteins are autocatalytically cleaved by the C-terminal domain IPR001767 from INTERPRO. This family is the N-terminal domain that is responsible for both local and long-range signalling activities. The structure of this domain is known [] and reveals a tetrahedrally coordinated zinc ion that appears to be structurally analogous to the zinc coordination sites of zinc hydrolases, such as thermolysin and carboxypeptidase A. This putative catalytic site represents a distinct activity from the autoprocessing activity that resides in the carboxy-terminal domain.; GO: 0007267 cell-cell signaling, 0007275 multicellular organismal development; PDB: 2WFR_A 3N1Q_B 3N1G_B 2WFQ_A 2WG3_A 3MXW_A 3M1N_B 3HO5_H 3K7H_B 3N1O_B ....
Probab=99.85 E-value=8.6e-22 Score=145.20 Aligned_cols=71 Identities=86% Similarity=1.519 Sum_probs=61.0
Q ss_pred CCCCCCCeEEEeeeeCCCCCCCCCCcCcceeEEEEEeCCCCcchHHHHHHHHHHcCCCeEEEcCCCeEEEe
Q psy16498 1 MNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYGLLARMAVEAGFDWVYYESRNHIHCS 71 (102)
Q Consensus 1 ~~e~~G~Pi~VtSGYR~p~~N~~~S~H~~GrAaDI~~~~~~~~~~~~L~~~A~~~gFd~v~Y~~~~fVHvd 71 (102)
|+||+|+.|+|+.||....+.+++|+|++|||+||++++.+..++++|+++|.++|||||+|+++++||||
T Consensus 90 ~nqwpgvkLrV~eaWded~~h~~~sLHyeGRAvdittsd~d~~k~g~LarLAv~AGFDwV~Yes~~hiHcS 160 (160)
T PF01085_consen 90 MNQWPGVKLRVTEAWDEDGHHSPDSLHYEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESRNHIHCS 160 (160)
T ss_dssp HHHSTT--EEEEESS-SSSTSSTT-GGGGT-EEEEEETT--GGGHHHHHHHHHHTT-SEEEEEETTEEEEE
T ss_pred HHhCCCcEEEEEecccCcccCCchhccccceeEEEEeccccchhhHHHHHHHhhcccCeEEecccceEecC
Confidence 68999999999999999989899999999999999999999999999999999999999999999999997
No 3
>PF08291 Peptidase_M15_3: Peptidase M15 ; InterPro: IPR013230 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry represents the C-terminal domain of zinc D-Ala-D-Ala carboxypeptidases from Streptomyces species and non-peptidase homologues that belong to MEROPS peptidase family M15 (subfamily M15A, clan MD) [].; PDB: 1LBU_A.
Probab=99.82 E-value=6.3e-22 Score=136.68 Aligned_cols=67 Identities=27% Similarity=0.398 Sum_probs=45.8
Q ss_pred CCCCCCeEEEeeeeCCCCCCC-----CCCcCcceeEEEEEeCCCCcchHHHHHHHHHHcCCCeE-EEcCCCeEEEe
Q psy16498 2 NEWPGVRLRVIEGWDEEGHHA-----SDSLHYEGRAVDITTSDRDSSKYGLLARMAVEAGFDWV-YYESRNHIHCS 71 (102)
Q Consensus 2 ~e~~G~Pi~VtSGYR~p~~N~-----~~S~H~~GrAaDI~~~~~~~~~~~~L~~~A~~~gFd~v-~Y~~~~fVHvd 71 (102)
|+.+|.||+||||||||.+|+ ++|+|+.|+|+||.+++.+ ..+++++++++++.++ +|..++|||||
T Consensus 38 R~~~g~pi~ItSgyR~~~~N~~vGGa~~S~H~~G~A~Di~~~~~~---~~~~~~~~~~~~~~~~g~~~~~~~vHid 110 (110)
T PF08291_consen 38 RDHFGKPIIITSGYRCPDHNRAVGGAPNSQHMKGRAADIVVSGMS---PEEVAQIARSAGFFGIGIYRYSGFVHID 110 (110)
T ss_dssp HHHTTS---EEE----HHHHHHHT--TT-GGGGT-EEEE--TTT----HHHHHHHGGGTT-SEETSTT-SSSEEE-
T ss_pred HHHHCCCeEEeeeecChhhchhhcCCCCCCCCCCEeEEEecCCCC---HHHHHHHHHHcCCCCeeeccCCCEEEeC
Confidence 567899999999999999997 9999999999999998764 4578899998888777 77778999997
No 4
>COG3108 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.80 E-value=4.8e-20 Score=138.72 Aligned_cols=70 Identities=26% Similarity=0.314 Sum_probs=63.4
Q ss_pred CeEEEeeeeCCCCCCC----------CCCcCcceeEEEEEeCCCCcchHHHHHHHHHHcCCCeE-EEcCCCeEEEeecCC
Q psy16498 7 VRLRVIEGWDEEGHHA----------SDSLHYEGRAVDITTSDRDSSKYGLLARMAVEAGFDWV-YYESRNHIHCSVKTV 75 (102)
Q Consensus 7 ~Pi~VtSGYR~p~~N~----------~~S~H~~GrAaDI~~~~~~~~~~~~L~~~A~~~gFd~v-~Y~~~~fVHvdv~~~ 75 (102)
.||+|+||||+|++|+ +.|+||.|+|+||++++.+ +.+|.++++++.-++| +||.++|||+|++|.
T Consensus 103 ~~i~V~SGYRSPatNr~lr~~s~gvAk~S~Hm~g~AmD~~i~gV~---l~~lr~~~~~~~~GGVGyYp~s~sVH~DvGpv 179 (185)
T COG3108 103 RPVQVTSGYRSPATNRMLRSRSRGVAKKSLHMLGQAMDFQIPGVS---LWELRNAALSMQGGGVGYYPHSNSVHMDVGPV 179 (185)
T ss_pred cceEEEeeccChhhhHHHHhhcccchhccccccceeeeeecCCcc---HHHHHHHHHhCcCCceeeccCCCceEeccCcc
Confidence 6999999999999997 9999999999999999876 5688899999988999 999999999999986
Q ss_pred cccc
Q psy16498 76 LDMV 79 (102)
Q Consensus 76 ~~~~ 79 (102)
.+=+
T Consensus 180 R~W~ 183 (185)
T COG3108 180 RDWN 183 (185)
T ss_pred ccCC
Confidence 5433
No 5
>PF02557 VanY: D-alanyl-D-alanine carboxypeptidase; InterPro: IPR003709 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. These proteins are metallopeptidases belonging to MEROPS peptidase family M15 (clan MD), subfamily M15B (vanY D-Ala-D-Ala carboxypeptidase) and M15C (Ply, L-alanyl-D-glutamate peptidase). Acquired VanA- and VanB-type glycopeptide resistance in enterococci is due to synthesis of modified peptidoglycan precursors terminating in D-lactate. As opposed to VanA-type strains which are resistant to both vancomycin and teicoplanin, VanB-type strains remain teicoplanin susceptible []. The vanY gene was necessary for synthesis of the vancomycin-inducible D,D-carboxypeptidase 3.4.16.4 from EC activity previously proposed to be responsible for glycopeptide resistance. However, this activity was not required for peptidoglycan synthesis in the presence of glycopeptides []. Bacteriophage lysins (Ply) or endolysins are phage-encoded cell wall lytic enzymes which are synthesised late during virus multiplication and mediate the release of progeny virions. Bacteriophages of the pathogen Listeria monocytogenes encode endolysin enzymes which specifically hydrolyse the cross-linking peptide bridges in Listeria peptidoglycan. Ply118 is a 30.8kDa L-alanoyl-D-glutamate peptidase and Ply511 (36.5 kDa) acts as N-acetylmuramoyl-L-alanine amidase (IPR002502 from INTERPRO). ; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 4F78_A 2VO9_C.
Probab=97.28 E-value=4.7e-05 Score=53.19 Aligned_cols=35 Identities=31% Similarity=0.507 Sum_probs=23.8
Q ss_pred CCeEEEeeeeCCCCCC-------------C---------CCCcCcceeEEEEEeCCC
Q psy16498 6 GVRLRVIEGWDEEGHH-------------A---------SDSLHYEGRAVDITTSDR 40 (102)
Q Consensus 6 G~Pi~VtSGYR~p~~N-------------~---------~~S~H~~GrAaDI~~~~~ 40 (102)
|.+|.|+||||+.+.. . -.|.|-.|.|+||...+.
T Consensus 23 G~~l~i~SgyRs~~~Q~~ly~~~~~~~~~~~~~~~~a~pG~SeH~~GlAiDi~~~~~ 79 (132)
T PF02557_consen 23 GINLKITSGYRSYEEQQQLYDKYAQEYGKAGARVYVAPPGYSEHQTGLAIDIGIGDA 79 (132)
T ss_dssp TTSEEEEE----HHHHHHHHHHHHCCCSCCCHHHHS--TTSSGGGGT-EEEEEEC-T
T ss_pred CCCEEEEeecCCHHHHHHHHHHHHHhhhHhhhheecCCCCCCcccceeEEEeccCCC
Confidence 8899999999996531 1 589999999999998754
No 6
>PF13539 Peptidase_M15_4: D-alanyl-D-alanine carboxypeptidase
Probab=96.27 E-value=0.0045 Score=39.06 Aligned_cols=49 Identities=22% Similarity=0.394 Sum_probs=31.9
Q ss_pred CCCcCcceeEEEEEeCCC------------CcchHHHHHHHHHHcCCCeE-EEcCCCeEEEe
Q psy16498 23 SDSLHYEGRAVDITTSDR------------DSSKYGLLARMAVEAGFDWV-YYESRNHIHCS 71 (102)
Q Consensus 23 ~~S~H~~GrAaDI~~~~~------------~~~~~~~L~~~A~~~gFd~v-~Y~~~~fVHvd 71 (102)
..|.|..|.|+||..... ......+++++++++||.|= -+...++.|.+
T Consensus 5 ~~S~H~~G~AiDin~~~np~~~~~~~~~~~~~~~~~~~~~~~~~~G~~WGG~W~~~D~~HFe 66 (67)
T PF13539_consen 5 KLSNHSYGLAIDINPDENPYIQWNGDVDGYKIADYKEVVAIFEKLGFRWGGDWKFKDYMHFE 66 (67)
T ss_pred cccccccEEEEEEccccCCeeeeCCccchhhhhhHHHHHHHHHhCCCEeCCCCCCCCCcCCc
Confidence 479999999999983211 12345567777778888554 22345666654
No 7
>PF06904 Extensin-like_C: Extensin-like protein C-terminus; InterPro: IPR009683 This entry represents the C terminus (approx. 120 residues) of a number of bacterial extensin-like proteins. Extensins are cell wall glycoproteins normally associated with plants, where they strengthen the cell wall in response to mechanical stress []. Many proteins in this entry are hypothetical.
Probab=94.04 E-value=0.15 Score=38.43 Aligned_cols=67 Identities=19% Similarity=0.231 Sum_probs=44.3
Q ss_pred eEEEeeeeCCCCCCC----CCCcCcceeEEEEE---eCC---------CC-cchHHHHHHHHH---HcCCCeEEEcC---
Q psy16498 8 RLRVIEGWDEEGHHA----SDSLHYEGRAVDIT---TSD---------RD-SSKYGLLARMAV---EAGFDWVYYES--- 64 (102)
Q Consensus 8 Pi~VtSGYR~p~~N~----~~S~H~~GrAaDI~---~~~---------~~-~~~~~~L~~~A~---~~gFd~v~Y~~--- 64 (102)
.|...++|-|..-|. +-|.|-.|.|+||. +.+ .. ...-.++++.+. +.-|+-|+-|.
T Consensus 78 ~I~~~gsY~CR~~n~~~~~rlSEHA~gnAiDI~gf~ladG~~i~V~~~w~~~~~~~~fl~~v~~~AC~~F~tVLgP~~na 157 (178)
T PF06904_consen 78 RIEHAGSYACRNRNGRAGGRLSEHARGNAIDIAGFRLADGRRISVLRDWRGGGPEAAFLRAVRAGACGRFGTVLGPDYNA 157 (178)
T ss_pred EEeeccceecCCcCCCCCCCcCccccccceeeeeeEecCCCEEEecCCCCCCchHHHHHHHHHHHHHhcCCcccCCCCch
Confidence 478889999999775 88999999999994 221 11 111122223222 44588885443
Q ss_pred --CCeEEEeecC
Q psy16498 65 --RNHIHCSVKT 74 (102)
Q Consensus 65 --~~fVHvdv~~ 74 (102)
.+++|+|+..
T Consensus 158 aH~dHfHlD~~~ 169 (178)
T PF06904_consen 158 AHADHFHLDMAR 169 (178)
T ss_pred hHhhcccccccc
Confidence 5899999963
No 8
>COG3921 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.30 E-value=0.089 Score=42.71 Aligned_cols=68 Identities=25% Similarity=0.326 Sum_probs=45.5
Q ss_pred eEEEeeeeCCCCCCC----CCCcCcceeEEEEE---eCCC----------CcchHHHHHHHH---HHcCCCeEEEcC---
Q psy16498 8 RLRVIEGWDEEGHHA----SDSLHYEGRAVDIT---TSDR----------DSSKYGLLARMA---VEAGFDWVYYES--- 64 (102)
Q Consensus 8 Pi~VtSGYR~p~~N~----~~S~H~~GrAaDI~---~~~~----------~~~~~~~L~~~A---~~~gFd~v~Y~~--- 64 (102)
.|.=.|+|=|...|. +-|.|-.|.|+||. +++. ....=+.+++.. -+.=|.-|+-|.
T Consensus 200 ~I~~~g~Y~CR~~n~r~~gk~SEHA~gNAlDIssf~LsdGk~i~v~~~~~~~~~eg~flraVr~aaC~yF~TVLGPg~da 279 (300)
T COG3921 200 RIEHAGGYSCRNRNSRRDGKISEHARGNALDISSFTLSDGKKIEVRSRGEGAFREGAFLRAVRAAACLYFNTVLGPGSDA 279 (300)
T ss_pred eeeccccceeecccCCCCCccchhhcccceeeeeEEecCCcEEEeecCCCCcccchHHHHHHHHHHHHHhhcccCCCCCh
Confidence 466679999999885 88999999999994 3321 111111233332 255688885554
Q ss_pred --CCeEEEeecCC
Q psy16498 65 --RNHIHCSVKTV 75 (102)
Q Consensus 65 --~~fVHvdv~~~ 75 (102)
.++.|+|++..
T Consensus 280 aH~dHfHlDl~~r 292 (300)
T COG3921 280 AHADHFHLDLRTR 292 (300)
T ss_pred hhhhhceecchhc
Confidence 58999999864
No 9
>PRK10178 D-alanyl-D-alanine dipeptidase; Provisional
Probab=89.47 E-value=0.22 Score=37.80 Aligned_cols=35 Identities=29% Similarity=0.524 Sum_probs=28.0
Q ss_pred CCCeEEEeeeeCCCCCCC----------------CCCcCcceeEEEEEeCC
Q psy16498 5 PGVRLRVIEGWDEEGHHA----------------SDSLHYEGRAVDITTSD 39 (102)
Q Consensus 5 ~G~Pi~VtSGYR~p~~N~----------------~~S~H~~GrAaDI~~~~ 39 (102)
.|-.|+|-.|||+...-. +.|.|..|.|+|+++-+
T Consensus 60 ~G~~L~I~D~yRP~~aq~~~w~~~~~~~yVA~p~~~S~HsrG~AVDLTL~d 110 (184)
T PRK10178 60 AGLTLRIYDAYRPQQAQQVLWDACPDPQYVADLGRGSNHSRGTAIDLTLVD 110 (184)
T ss_pred CCCeEEEEeccCCHHHHHHHHHhCCCcCeeeCCCCCCCCCCceEEEEEEEC
Confidence 378899999999954221 45999999999999865
No 10
>COG1876 VanY D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]
Probab=81.53 E-value=0.68 Score=36.35 Aligned_cols=31 Identities=32% Similarity=0.355 Sum_probs=25.6
Q ss_pred CCeEEEeeeeCCCCCC--------------------C--CCCcCcceeEEEEE
Q psy16498 6 GVRLRVIEGWDEEGHH--------------------A--SDSLHYEGRAVDIT 36 (102)
Q Consensus 6 G~Pi~VtSGYR~p~~N--------------------~--~~S~H~~GrAaDI~ 36 (102)
|+-|.+.||||+-... + ..|.|-.|.|+||.
T Consensus 119 g~~l~~~S~yrs~~~q~~lf~~~v~~~~~~~~~~~sa~pg~SeH~tG~A~Di~ 171 (241)
T COG1876 119 GVALLRWSAYRSYSRQHWLFDNDVFDPGLLPAATYSALPGWSEHQTGLAIDIS 171 (241)
T ss_pred CcEEeeeecchhHHHHHhhhhhhhcCchhhhhhhhccCCCccccccceeEeec
Confidence 6678999999994421 0 89999999999998
No 11
>KOG3638|consensus
Probab=79.94 E-value=0.98 Score=37.68 Aligned_cols=78 Identities=31% Similarity=0.453 Sum_probs=56.8
Q ss_pred eeCCCCCCCCCCcCcceeEEEEEeCCCCcchHHHHHHHHHHcCCCeEEEcCCCeEEEeecCCcccchhhhhhhhcCCCcC
Q psy16498 14 GWDEEGHHASDSLHYEGRAVDITTSDRDSSKYGLLARMAVEAGFDWVYYESRNHIHCSVKTVLDMVGIASALWALGRGFP 93 (102)
Q Consensus 14 GYR~p~~N~~~S~H~~GrAaDI~~~~~~~~~~~~L~~~A~~~gFd~v~Y~~~~fVHvdv~~~~~~~~~~~~~~~~~~~~~ 93 (102)
+|+--.+-+..+.|..+++.|+.+...+......+++.+.+.++++..|+..+.+|.+++....-+ ... ..|||
T Consensus 137 ~fD~i~ni~~~~~~~g~~~y~~tv~r~~c~~~~~~~r~~~e~~~~~~~~~~~~~~~~~~~~~~~~~--~~~----~~cf~ 210 (414)
T KOG3638|consen 137 AFDYISNVSKSVDEYGGVAYEVTVSRMNCLDYPQAARLAVEAGFDWETYRVVEHAHNSAKASSSVA--HQP----PVCFP 210 (414)
T ss_pred eeeeecceeeccCCCCceeccceeeecccCCccccccccccccccccceeecccccceeeccCccc--cCC----CCCCC
Confidence 333333334888999999999988665555566778889999999999999999999998655554 211 48888
Q ss_pred Ccce
Q psy16498 94 PGVD 97 (102)
Q Consensus 94 ~~~~ 97 (102)
...-
T Consensus 211 ~~~~ 214 (414)
T KOG3638|consen 211 TDAT 214 (414)
T ss_pred CCCE
Confidence 7643
No 12
>PF01427 Peptidase_M15: D-ala-D-ala dipeptidase This is family M15 in the peptidase classification. ; InterPro: IPR000755 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M15 (clan MD), subfamily M15D (vanX D-Ala-D-Ala dipeptidase). The D-alanyl-D-alanine dipeptidase enzyme from Enterococcus faecalis is also known as the vancomycin resistance protein VanX, and hydrolyses D-ala-D-ala. It has a 250-fold differential in catalytic efficiency for hydrolysis of D-ala-D-ala versus D-ala-D-lactate. The latter therefore remains intact for subsequent incorporation into peptidoglycan precursors that terminate in the dipeptide D-ala-D-lactate rather than the dipeptide D-ala-D-ala, thereby preventing vancomycin from binding. The enzyme requires a metal cofactor, and is induced by vancomycin through regulation by VanS and VanR.; GO: 0008237 metallopeptidase activity, 0016805 dipeptidase activity, 0006508 proteolysis, 0005618 cell wall; PDB: 1R44_B.
Probab=69.91 E-value=1.3 Score=33.41 Aligned_cols=33 Identities=33% Similarity=0.529 Sum_probs=20.1
Q ss_pred CCeEEEeeeeCCCCCC-------------C------------------CCCcCcceeEEEEEeC
Q psy16498 6 GVRLRVIEGWDEEGHH-------------A------------------SDSLHYEGRAVDITTS 38 (102)
Q Consensus 6 G~Pi~VtSGYR~p~~N-------------~------------------~~S~H~~GrAaDI~~~ 38 (102)
|-.|.|-.|||+...- . ..|.|..|-|+|+++-
T Consensus 60 g~~L~I~DayRP~~~Q~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~H~tG~AVDlTL~ 123 (198)
T PF01427_consen 60 GYRLKIFDAYRPQSAQDAFKMWAAVPDPQYVAYPYYPRFWASPLFDPASPSPHSTGGAVDLTLV 123 (198)
T ss_dssp TEEEEEEE----HHHHHHHHHHHTS----TTHHHH-TTS-CCHHCCS-SS-GGGGT-EEEEEEE
T ss_pred CcEEEEEEEeCcHHHHHHHHHHHcCCchhhhhcccccccccccccccCCCCCccCCCCCCccce
Confidence 6679999999983322 0 2499999999999986
No 13
>TIGR03292 PhnH_redo phosphonate C-P lyase system protein PhnH. PhnH is a component of the C-P lyase system (GenProp0232) for the catabolism of phosphonate compounds. The specific function of this component is unknown. This model is based on Pfam model pfam05845.2, and has been broadened to include sequences missed by that model which are clearly true positive hits based on genome context.
Probab=53.06 E-value=8.1 Score=28.96 Aligned_cols=17 Identities=41% Similarity=0.614 Sum_probs=13.5
Q ss_pred hhhcC-CCcCCcceeeec
Q psy16498 85 LWALG-RGFPPGVDFILN 101 (102)
Q Consensus 85 ~~~~~-~~~~~~~~~~~~ 101 (102)
.|..| .-||-|+|+||-
T Consensus 144 ~~~~n~~~FP~GvDlil~ 161 (174)
T TIGR03292 144 ELQENRAAFPLGVDLILT 161 (174)
T ss_pred HHHHccccCCcceEEEEe
Confidence 35555 899999999984
No 14
>KOG0788|consensus
Probab=52.23 E-value=15 Score=30.45 Aligned_cols=57 Identities=21% Similarity=0.289 Sum_probs=43.6
Q ss_pred chHHHHHHHHHHcCCCeE---EEcCCCeEEEeecCCcccchhhhhhhhcCCCcCCcceeee
Q psy16498 43 SKYGLLARMAVEAGFDWV---YYESRNHIHCSVKTVLDMVGIASALWALGRGFPPGVDFIL 100 (102)
Q Consensus 43 ~~~~~L~~~A~~~gFd~v---~Y~~~~fVHvdv~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (102)
..+..|.++|.+++|+.| .|.+++|+-=+-.+.+.++. ..|.=-++.-||-|.-+.+
T Consensus 89 ~sL~pLlkLA~~~~~~~v~~v~YSRknFl~P~~Q~~pH~sf-~eEV~~L~~~F~~g~ay~m 148 (334)
T KOG0788|consen 89 KALVPLLKLAGELSFDSVQSVFYSRKNFLFPGAQPYPHTSF-DEEVEYLDKFFPNGKAYCM 148 (334)
T ss_pred HHHHHHHHHHHHhcccchHhheeccccccCcccCCCCCcCH-HHHHHHHHHhcCCCceEEe
Confidence 346788899999999987 89999999888888777774 5555556778887765543
No 15
>COG3625 PhnH Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=44.23 E-value=14 Score=28.57 Aligned_cols=18 Identities=44% Similarity=0.870 Sum_probs=15.8
Q ss_pred hhhhcC-CCcCCcceeeec
Q psy16498 84 ALWALG-RGFPPGVDFILN 101 (102)
Q Consensus 84 ~~~~~~-~~~~~~~~~~~~ 101 (102)
+.|..| .-||.|+|+||.
T Consensus 162 ~~w~~n~~~fPrGiDvilt 180 (196)
T COG3625 162 HFWAENRAIFPRGIDVILT 180 (196)
T ss_pred HHHHhCccccCCcceEEEe
Confidence 589999 789999999983
No 16
>PF05845 PhnH: Bacterial phosphonate metabolism protein (PhnH); InterPro: IPR008772 This family consists of several bacterial PhnH sequences, which is a component of the C-P lyase system (GenProp0232 from GENPROP) for the catabolism of phosphonate compounds []. The specific function of this component is unknown.; GO: 0015716 phosphonate transport; PDB: 2FSU_A.
Probab=42.74 E-value=15 Score=27.79 Aligned_cols=17 Identities=41% Similarity=0.479 Sum_probs=11.6
Q ss_pred hhhcC-CCcCCcceeeec
Q psy16498 85 LWALG-RGFPPGVDFILN 101 (102)
Q Consensus 85 ~~~~~-~~~~~~~~~~~~ 101 (102)
.|..+ .-||-|+|+||-
T Consensus 159 ~~~~~~~~fPlGvDlil~ 176 (192)
T PF05845_consen 159 ARQENNALFPLGVDLILV 176 (192)
T ss_dssp HHHH--STTTTS-EEEEE
T ss_pred HHHHccccCCCceeEEEE
Confidence 45555 679999999973
No 17
>PRK10147 phnH carbon-phosphorus lyase complex subunit; Validated
Probab=38.13 E-value=18 Score=27.64 Aligned_cols=16 Identities=38% Similarity=0.601 Sum_probs=12.7
Q ss_pred hhcC-CCcCCcceeeec
Q psy16498 86 WALG-RGFPPGVDFILN 101 (102)
Q Consensus 86 ~~~~-~~~~~~~~~~~~ 101 (102)
|..| .-||-|+|+||-
T Consensus 163 ~~~n~~~FPlGvD~il~ 179 (196)
T PRK10147 163 RTENPALFPLGIDLILT 179 (196)
T ss_pred HHHccccCCcceeEEEe
Confidence 4445 889999999984
No 18
>PF05445 Pox_ser-thr_kin: Poxvirus serine/threonine protein kinase; InterPro: IPR008790 This family of proteins contain poxvirus serine/threonine protein kinases, which are essential for phosphorylation of virion proteins during virion assembly. ; GO: 0004672 protein kinase activity, 0005524 ATP binding
Probab=36.87 E-value=19 Score=30.77 Aligned_cols=16 Identities=31% Similarity=0.430 Sum_probs=13.0
Q ss_pred EEcC---CCeEEEeecCCc
Q psy16498 61 YYES---RNHIHCSVKTVL 76 (102)
Q Consensus 61 ~Y~~---~~fVHvdv~~~~ 76 (102)
+|+. .+|+|+|.+||.
T Consensus 291 IYelp~c~nF~H~DLKPdN 309 (434)
T PF05445_consen 291 IYELPCCTNFLHVDLKPDN 309 (434)
T ss_pred eecCCCcceeeecccCcCc
Confidence 6766 489999999974
No 19
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=35.83 E-value=74 Score=25.15 Aligned_cols=69 Identities=16% Similarity=0.134 Sum_probs=43.7
Q ss_pred CCCCCCCeEEEeeeeCCCCCCC-----------------CCCcCcceeEEEEEeCCCCcchHHHHHHHHHHcCCCeEEEc
Q psy16498 1 MNEWPGVRLRVIEGWDEEGHHA-----------------SDSLHYEGRAVDITTSDRDSSKYGLLARMAVEAGFDWVYYE 63 (102)
Q Consensus 1 ~~e~~G~Pi~VtSGYR~p~~N~-----------------~~S~H~~GrAaDI~~~~~~~~~~~~L~~~A~~~gFd~v~Y~ 63 (102)
|+.+-|.|..+.-|||||.-=+ -..+|..=.||-|.-.= ...+=.++.+-|.++|+.- -
T Consensus 145 Rr~~kg~~~mp~iGYgS~k~~R~l~PsG~~~vlV~N~~eLe~l~~~~~aa~Ia~~V-g~rKR~~I~erA~el~ikV---~ 220 (232)
T PRK12766 145 RRGIKGKGDTVEAGFRTPTAVRGKHPSGFEEVRVHNTDDLEGVDGDTEAVRIASKV-GARKRERIEEVAEEQGIRV---L 220 (232)
T ss_pred hcccCCCCCCCcCCCCCChhhcccCCCCCeeEEecCHHHHhhccCcceEEEeeccc-cchhHHHHHHHHHHhCCcc---c
Confidence 4678899999999999976211 23345555688885432 2222336667788887543 3
Q ss_pred CCCeEEEeec
Q psy16498 64 SRNHIHCSVK 73 (102)
Q Consensus 64 ~~~fVHvdv~ 73 (102)
+.++|-|.|.
T Consensus 221 N~~~~~~~~~ 230 (232)
T PRK12766 221 NPTYVEVEVE 230 (232)
T ss_pred CCCceEEecc
Confidence 5677777764
No 20
>COG1902 NemA NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]
Probab=35.18 E-value=34 Score=28.23 Aligned_cols=19 Identities=47% Similarity=0.497 Sum_probs=14.2
Q ss_pred HHHHHHHHHHcCCCeE-EEc
Q psy16498 45 YGLLARMAVEAGFDWV-YYE 63 (102)
Q Consensus 45 ~~~L~~~A~~~gFd~v-~Y~ 63 (102)
+.+-++.|+++|||+| +.-
T Consensus 151 f~~AA~rA~~AGFDgVEIH~ 170 (363)
T COG1902 151 FARAARRAKEAGFDGVEIHG 170 (363)
T ss_pred HHHHHHHHHHcCCCEEEEee
Confidence 4555666889999999 643
No 21
>PF00724 Oxidored_FMN: NADH:flavin oxidoreductase / NADH oxidase family; InterPro: IPR001155 The TIM-barrel fold is a closed barrel structure composed of an eight-fold repeat of beta-alpha units, where the eight parallel beta strands on the inside are covered by the eight alpha helices on the outside []. It is a widely distributed fold which has been found in many enzyme families that catalyse completely unrelated reactions []. The active site is always found at the C-terminal end of this domain. Proteins in this entry are a variety of NADH:flavin oxidoreductase/NADH oxidase enzymes, found mostly in bacteria or fungi, that contain a TIM-barrel fold. They commonly use FMN/FAD as cofactor and include: dimethylamine dehydrogenase trimethylamine dehydrogenase 12-oxophytodienoate reductase NADPH dehydrogenase NADH oxidase ; GO: 0010181 FMN binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3GKA_B 3P67_A 3F03_K 2ABA_A 1VYR_A 1GVO_A 3KFT_B 3P8I_A 1GVQ_A 3P74_A ....
Probab=34.33 E-value=37 Score=27.10 Aligned_cols=19 Identities=47% Similarity=0.530 Sum_probs=13.0
Q ss_pred hHHHHHHHHHHcCCCeE-EE
Q psy16498 44 KYGLLARMAVEAGFDWV-YY 62 (102)
Q Consensus 44 ~~~~L~~~A~~~gFd~v-~Y 62 (102)
.+.+-++.|+++|||+| +-
T Consensus 150 ~f~~AA~~A~~AGfDGVEIH 169 (341)
T PF00724_consen 150 DFAQAARRAKEAGFDGVEIH 169 (341)
T ss_dssp HHHHHHHHHHHTT-SEEEEE
T ss_pred HHHHHHHHHHHhccCeEeec
Confidence 35556667889999999 53
No 22
>KOG2551|consensus
Probab=34.32 E-value=33 Score=27.15 Aligned_cols=43 Identities=23% Similarity=0.221 Sum_probs=28.4
Q ss_pred EEEeeeeCCCC-------CCC---CCCcCcceeEEEEEeCCCCcchHHHHHHHHHHc
Q psy16498 9 LRVIEGWDEEG-------HHA---SDSLHYEGRAVDITTSDRDSSKYGLLARMAVEA 55 (102)
Q Consensus 9 i~VtSGYR~p~-------~N~---~~S~H~~GrAaDI~~~~~~~~~~~~L~~~A~~~ 55 (102)
+++.|||+.+. +++ --|+|..|.. |-.++... -..|++....+
T Consensus 140 ~v~~SGf~~~~~~~~~~~~~~~i~~PSLHi~G~~-D~iv~~~~---s~~L~~~~~~a 192 (230)
T KOG2551|consen 140 AVFISGFKFPSKKLDESAYKRPLSTPSLHIFGET-DTIVPSER---SEQLAESFKDA 192 (230)
T ss_pred EEEEecCCCCcchhhhhhhccCCCCCeeEEeccc-ceeecchH---HHHHHHhcCCC
Confidence 67899999982 222 5599999998 77665322 23565655443
No 23
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=31.04 E-value=1.1e+02 Score=21.62 Aligned_cols=35 Identities=17% Similarity=0.236 Sum_probs=23.7
Q ss_pred eCCCCcchHHHHHHHHHHcCCCeE-EEcCCCeEEEe
Q psy16498 37 TSDRDSSKYGLLARMAVEAGFDWV-YYESRNHIHCS 71 (102)
Q Consensus 37 ~~~~~~~~~~~L~~~A~~~gFd~v-~Y~~~~fVHvd 71 (102)
+.+....+..+|.+++..+||..| -|-++|=|=++
T Consensus 13 VGG~nki~MaeLr~~l~~~Gf~~V~Tyi~SGNvvf~ 48 (137)
T PF08002_consen 13 VGGKNKIKMAELREALEDLGFTNVRTYIQSGNVVFE 48 (137)
T ss_dssp BTTBS---HHHHHHHHHHCT-EEEEEETTTTEEEEE
T ss_pred cCCCCcccHHHHHHHHHHcCCCCceEEEeeCCEEEe
Confidence 344444456788888999999999 88888766666
No 24
>PRK10605 N-ethylmaleimide reductase; Provisional
Probab=30.76 E-value=53 Score=26.75 Aligned_cols=24 Identities=29% Similarity=0.360 Sum_probs=15.7
Q ss_pred HHHHHHHHHHcCCCeE-EEcCCCeE
Q psy16498 45 YGLLARMAVEAGFDWV-YYESRNHI 68 (102)
Q Consensus 45 ~~~L~~~A~~~gFd~v-~Y~~~~fV 68 (102)
+.+-++.|+++|||+| +.-..+|+
T Consensus 161 f~~AA~rA~~AGfDGVEIh~ahGyL 185 (362)
T PRK10605 161 FRQAIANAREAGFDLVELHSAHGYL 185 (362)
T ss_pred HHHHHHHHHHcCCCEEEEcccccch
Confidence 4445566779999999 64434444
No 25
>COG3502 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.63 E-value=54 Score=23.41 Aligned_cols=27 Identities=30% Similarity=0.289 Sum_probs=18.3
Q ss_pred HHHHHHHHcC-CCeE-EEcCCCeEEEeec
Q psy16498 47 LLARMAVEAG-FDWV-YYESRNHIHCSVK 73 (102)
Q Consensus 47 ~L~~~A~~~g-Fd~v-~Y~~~~fVHvdv~ 73 (102)
.+++.|+..| |.+- +....||||+|..
T Consensus 13 ~~W~~A~~~G~f~~~svd~~dGfIH~St~ 41 (115)
T COG3502 13 ALWAAARAAGSFEGASVDDADGFIHLSTA 41 (115)
T ss_pred HHHHHHHHcCCcCCCCcccccceEEechH
Confidence 5777888766 4443 3344699999975
No 26
>PRK08562 rpl32e 50S ribosomal protein L32e; Validated
Probab=28.66 E-value=74 Score=22.90 Aligned_cols=56 Identities=20% Similarity=0.119 Sum_probs=34.9
Q ss_pred CCCCCCCeEEEeeeeCCCCCCC-----------------CCCcCcceeEEEEEeCCCCcchHHHHHHHHHHcCC
Q psy16498 1 MNEWPGVRLRVIEGWDEEGHHA-----------------SDSLHYEGRAVDITTSDRDSSKYGLLARMAVEAGF 57 (102)
Q Consensus 1 ~~e~~G~Pi~VtSGYR~p~~N~-----------------~~S~H~~GrAaDI~~~~~~~~~~~~L~~~A~~~gF 57 (102)
++.+-|.|..++-||+||.-=+ -..+|-.-.||-|.-.=... +=.++.+-|.++|+
T Consensus 46 Rrr~kg~~~mp~iGYgS~k~tR~l~PsG~~~vlV~N~keLe~l~~~~~aa~Ia~~Vg~r-KR~~I~~rA~el~i 118 (125)
T PRK08562 46 RLKLKGKPAIVEVGYRSPKAVRGLHPSGYEEVLVHNVKELEKLDPETQAARIASTVGKR-KRLEILKKARELGI 118 (125)
T ss_pred hccccCCCCCCcCCcCCChhhcccCCCCCeeEEecCHHHhhhccCCceEEEEeccccch-hHHHHHHHHHHhCC
Confidence 4667888999999999976211 33445566688775321122 22356677777775
No 27
>PF12683 DUF3798: Protein of unknown function (DUF3798); InterPro: IPR024258 This entry represents functionally uncharacterised proteins that are found in bacteria. They are typically between 247 and 417 amino acids in length. Most of the proteins in this entry have an N-terminal lipoprotein attachment site. These proteins have distant similarity to periplasmic ligand binding families suggesting that this family has a similar role.; PDB: 3QI7_A.
Probab=28.45 E-value=41 Score=27.23 Aligned_cols=40 Identities=20% Similarity=0.235 Sum_probs=24.7
Q ss_pred eEEEEEeCCCCcchHHHHHHHHHHcCCCeEEEcCCCeEEEeecCCcc
Q psy16498 31 RAVDITTSDRDSSKYGLLARMAVEAGFDWVYYESRNHIHCSVKTVLD 77 (102)
Q Consensus 31 rAaDI~~~~~~~~~~~~L~~~A~~~gFd~v~Y~~~~fVHvdv~~~~~ 77 (102)
.++||.+.......-..+.++|+.+|. +.|||+|.-+.-.
T Consensus 105 ~~aDi~~~~D~~~~G~~i~~~Ak~mGA-------ktFVh~sfprhms 144 (275)
T PF12683_consen 105 SAADIVVNPDEISRGYTIVWAAKKMGA-------KTFVHYSFPRHMS 144 (275)
T ss_dssp HHSSEEEE--HHHHHHHHHHHHHHTT--------S-EEEEEETTGGG
T ss_pred hccCeEeccchhhccHHHHHHHHHcCC-------ceEEEEechhhcc
Confidence 578888754333334467788889883 5788988865443
No 28
>PHA03111 Ser/Thr kinase; Provisional
Probab=25.50 E-value=30 Score=29.66 Aligned_cols=16 Identities=31% Similarity=0.428 Sum_probs=12.5
Q ss_pred EEcC---CCeEEEeecCCc
Q psy16498 61 YYES---RNHIHCSVKTVL 76 (102)
Q Consensus 61 ~Y~~---~~fVHvdv~~~~ 76 (102)
+|+. .+|||+|.+||.
T Consensus 295 IYelp~c~nF~H~DLKPdN 313 (444)
T PHA03111 295 IYELPCCDNFLHVDLKPDN 313 (444)
T ss_pred hhcCCCcceeeeccCCCCc
Confidence 4665 489999999964
No 29
>COG1165 MenD 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase [Coenzyme metabolism]
Probab=24.77 E-value=54 Score=29.08 Aligned_cols=70 Identities=19% Similarity=0.124 Sum_probs=43.6
Q ss_pred CCCCCeEEEeeeeCCCCCCC------CCCcCcceeEE----EEEeCCCCcchHHHHHHHHHHcCCCeEEEcCCCeEEEee
Q psy16498 3 EWPGVRLRVIEGWDEEGHHA------SDSLHYEGRAV----DITTSDRDSSKYGLLARMAVEAGFDWVYYESRNHIHCSV 72 (102)
Q Consensus 3 e~~G~Pi~VtSGYR~p~~N~------~~S~H~~GrAa----DI~~~~~~~~~~~~L~~~A~~~gFd~v~Y~~~~fVHvdv 72 (102)
.+.++|++|.++=|+|++-. .+-.||+|-.+ |+-.+..+....-.+..++..+ ..+..-+..|=||+.+
T Consensus 94 ~~srvpLIVLTADRP~EL~~~GAnQaI~Q~~lfgs~v~~~~~L~~P~~~~~~~~~~~~~~~~~-~~~a~~~~~GpVHiN~ 172 (566)
T COG1165 94 NLSRVPLIVLTADRPPELRGCGANQAIDQTGLFGSYVRASIDLPLPEDDIEALWYLRTIASAA-AQQARTPHAGPVHINV 172 (566)
T ss_pred hhcCCceEEEeCCCCHHHhcCCCchhhhhhhhhcccchhhccCCCCCCCHHHHHHHHHHHHHH-HHhccCCCCCceEecC
Confidence 35689999999999999653 77788998554 5545544433233333333322 2223335678888887
Q ss_pred c
Q psy16498 73 K 73 (102)
Q Consensus 73 ~ 73 (102)
-
T Consensus 173 P 173 (566)
T COG1165 173 P 173 (566)
T ss_pred C
Confidence 4
No 30
>COG2173 DdpX D-alanyl-D-alanine dipeptidase [Cell envelope biogenesis, outer membrane]
Probab=24.46 E-value=47 Score=25.98 Aligned_cols=33 Identities=27% Similarity=0.458 Sum_probs=24.1
Q ss_pred CCeEEEeeeeCCCCCC-----------------CCCCcCcceeEEEEEeC
Q psy16498 6 GVRLRVIEGWDEEGHH-----------------ASDSLHYEGRAVDITTS 38 (102)
Q Consensus 6 G~Pi~VtSGYR~p~~N-----------------~~~S~H~~GrAaDI~~~ 38 (102)
|.-+.|-.-||..+-- +..|-|-.|.|+|+++-
T Consensus 88 g~~lvi~d~yrP~q~q~i~w~~~p~~a~~~~~~~~~s~HsrG~avDvTl~ 137 (211)
T COG2173 88 GLTLVIYDCYRPQQAQAILWQVYPDPAVVADYVKTGSPHSRGAAVDVTLA 137 (211)
T ss_pred ccceEEeeccCHHHhhhhhhhccCChhhhcCCCCCCCCCCCCceeeEEEE
Confidence 5556777777774311 16799999999999985
No 31
>PF06108 DUF952: Protein of unknown function (DUF952); InterPro: IPR009297 This family consists of several hypothetical bacterial and plant proteins of unknown function.; PDB: 2O0Q_A 2O0P_A 2JQN_A.
Probab=23.06 E-value=40 Score=22.47 Aligned_cols=9 Identities=33% Similarity=0.383 Sum_probs=6.8
Q ss_pred CCeEEEeec
Q psy16498 65 RNHIHCSVK 73 (102)
Q Consensus 65 ~~fVHvdv~ 73 (102)
.||||+|..
T Consensus 25 dGFIH~St~ 33 (93)
T PF06108_consen 25 DGFIHLSTA 33 (93)
T ss_dssp HTSEE-EEH
T ss_pred CCEEEcCCH
Confidence 599999985
No 32
>PLN02411 12-oxophytodienoate reductase
Probab=22.87 E-value=79 Score=26.05 Aligned_cols=24 Identities=29% Similarity=0.372 Sum_probs=14.9
Q ss_pred HHHHHHHHHHcCCCeE-EEcCCCeE
Q psy16498 45 YGLLARMAVEAGFDWV-YYESRNHI 68 (102)
Q Consensus 45 ~~~L~~~A~~~gFd~v-~Y~~~~fV 68 (102)
+.+-++.|+++|||+| +--..+|+
T Consensus 167 f~~AA~rA~~AGFDGVEIH~AhGYL 191 (391)
T PLN02411 167 YRQAALNAIRAGFDGIEIHGAHGYL 191 (391)
T ss_pred HHHHHHHHHHcCCCEEEEccccchH
Confidence 4444555779999999 54333443
No 33
>TIGR00535 SAM_DCase S-adenosylmethionine decarboxylase proenzyme, eukaryotic form. This protein is a pyruvoyl-dependent enzyme. The proenzyme is cleaved at a Ser residue that becomes a pyruvoyl group active site.
Probab=21.45 E-value=1.3e+02 Score=24.89 Aligned_cols=56 Identities=11% Similarity=0.204 Sum_probs=39.8
Q ss_pred hHHHHHHHHHHc-CCCe---EEEcCCCeEEEeecCCcccchhhhhhhhcCCCcCCcceeee
Q psy16498 44 KYGLLARMAVEA-GFDW---VYYESRNHIHCSVKTVLDMVGIASALWALGRGFPPGVDFIL 100 (102)
Q Consensus 44 ~~~~L~~~A~~~-gFd~---v~Y~~~~fVHvdv~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (102)
.+..|.++|.++ |++. |.|.+++|+.=+..+....+ ...|+=-++.=||.|.-+++
T Consensus 83 ~l~~ll~~a~~~~g~~~v~~v~YsRksf~fP~~Q~~pH~s-f~eEV~~L~~~F~~g~AY~~ 142 (334)
T TIGR00535 83 ALPKILQLAEQLSSWYKVFSVFYSRGCFLFPCAQPAIHRN-FSEEVAYLNKFFGNGKAYVV 142 (334)
T ss_pred HHHHHHHHHHHhcCcCceeEEEEecccccCcccCCCcCCC-HHHHHHHHHHhcCCCceEEe
Confidence 355677888654 7754 58999999988887766665 25566567777888877665
No 34
>cd00513 Ribosomal_L32_L32e Ribosomal_L32_L32e: L32 is a protein from the large subunit that contains a surface-exposed globular domain and a finger-like projection that extends into the RNA core to stabilize the tertiary structure. L32 does not appear to play a role in forming the A (aminacyl), P (peptidyl) or E (exit) sites of the ribosome, but does interact with 23S rRNA, which has a "kink-turn" secondary structure motif. L32 is overexpressed in human prostate cancer and has been identified as a stably expressed housekeeping gene in macrophages of human chronic obstructive pulmonary disease (COPD) patients. In Schizosaccharomyces pombe, L32 has also been suggested to play a role as a transcriptional regulator in the nucleus. Found in archaea and eukaryotes, this protein is known as L32 in eukaryotes and L32e in archaea.
Probab=20.45 E-value=32 Score=24.10 Aligned_cols=19 Identities=11% Similarity=0.106 Sum_probs=16.3
Q ss_pred CCCCCCCeEEEeeeeCCCC
Q psy16498 1 MNEWPGVRLRVIEGWDEEG 19 (102)
Q Consensus 1 ~~e~~G~Pi~VtSGYR~p~ 19 (102)
++.+-|.|..++-||++|.
T Consensus 29 Rrr~kg~~~mp~iGYgS~k 47 (107)
T cd00513 29 RRRFKGKPAMPKIGYGSPK 47 (107)
T ss_pred hccccCCCCCCcccCCCCh
Confidence 4677899999999999987
Done!