Query gi|255764502|ref|YP_003064963.2| hypothetical protein CLIBASIA_02185 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 100
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 30 00:07:06 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 255764502.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11267 biopolymer transport 85.9 1.8 4.6E-05 22.9 4.9 70 27-97 11-87 (141)
2 COG0848 ExbD Biopolymer transp 85.4 1.4 3.5E-05 23.5 4.1 67 30-97 12-85 (137)
3 PRK11024 colicin uptake protei 75.1 7 0.00018 19.7 5.1 57 30-86 12-76 (142)
4 pfam02472 ExbD Biopolymer tran 65.8 8.6 0.00022 19.3 3.6 69 28-97 2-78 (128)
5 TIGR02801 tolR protein TolR; I 59.9 11 0.00028 18.7 3.3 61 31-91 2-70 (133)
6 TIGR01341 aconitase_1 aconitat 45.2 4.2 0.00011 20.9 -0.8 60 15-96 529-588 (896)
7 pfam09846 DUF2073 Uncharacteri 42.1 30 0.00076 16.4 4.6 83 2-98 2-94 (104)
8 pfam09680 Tiny_TM_bacill Prote 31.4 28 0.00072 16.5 1.6 11 41-51 7-17 (26)
9 cd05479 RP_DDI RP_DDI; retrope 31.1 21 0.00054 17.2 0.9 22 60-81 98-120 (124)
10 pfam10177 DUF2371 Uncharacteri 29.5 49 0.0012 15.2 3.0 53 4-58 5-61 (142)
11 cd05480 NRIP_C NRIP_C; putativ 22.9 27 0.00069 16.6 0.3 22 59-80 81-103 (103)
12 pfam10705 Ycf15 Chloroplast pr 21.0 39 0.00099 15.7 0.8 26 57-82 38-70 (93)
13 COG5116 RPN2 26S proteasome re 20.6 73 0.0019 14.3 2.8 92 5-96 674-791 (926)
No 1
>PRK11267 biopolymer transport protein ExbD; Provisional
Probab=85.86 E-value=1.8 Score=22.88 Aligned_cols=70 Identities=20% Similarity=0.308 Sum_probs=49.7
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHH-------HHCCCCEEEEEECCCCEEEEEEECCCEEEEEHHHHHHHHHH
Q ss_conf 132132001210599999999999967988-------72021056742111150799970377069601566787775
Q gi|255764502|r 27 DGRMNSELQSTSLVGLVLVLFIILIGTVMV-------LIPKAEFILGLDIKRYPIMIDVKRDGEIRVQGQQVLLNEIT 97 (100)
Q Consensus 27 dgrmnselqstslvglvlvlfiiligtvmv-------lipkaefilgldikrypimidvkrdgeirvqgqqvllneit 97 (100)
|+..-||..-|.++-.+++|.|+.+=+... -.|++.-- ...-..-|+.|.+..||.+.+.++.+-+.+..
T Consensus 11 d~~~~~eINltPlIDVvfvLLIfFmvtt~~~~~~i~v~LP~~~~~-~~~~~~~~i~I~I~~dg~i~~~~~~v~~~~L~ 87 (141)
T PRK11267 11 DNGEMHEINVTPFIDVMLVLLIIFMVAAPLATVDVKVNLPASTST-PQPRPEKPVYLSVKADNSMFIGNDPVTDETMI 87 (141)
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-CCCCCCCCEEEEEECCCCEEECCCCCCHHHHH
T ss_conf 777434124765899999999999950564316742438876566-77898876799991698468778035799999
No 2
>COG0848 ExbD Biopolymer transport protein [Intracellular trafficking and secretion]
Probab=85.43 E-value=1.4 Score=23.55 Aligned_cols=67 Identities=34% Similarity=0.513 Sum_probs=50.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHH-------HHHCCCCEEEEEECCCCEEEEEEECCCEEEEEHHHHHHHHHH
Q ss_conf 13200121059999999999996798-------872021056742111150799970377069601566787775
Q gi|255764502|r 30 MNSELQSTSLVGLVLVLFIILIGTVM-------VLIPKAEFILGLDIKRYPIMIDVKRDGEIRVQGQQVLLNEIT 97 (100)
Q Consensus 30 mnselqstslvglvlvlfiiligtvm-------vlipkaefilgldikrypimidvkrdgeirvqgqqvllneit 97 (100)
..+|..-|.++...|||.+|++-|.. |-.|+|.- --.+-..-|+.+.++.+|.+-++.+++-+.+..
T Consensus 12 ~~~eINvtPlIDVmLVLLiiFmvtap~~t~~i~V~LP~a~~-~~~~~~~~~i~v~i~~~G~~~l~~~~v~~~~l~ 85 (137)
T COG0848 12 EKSEINVTPLIDVMLVLLIIFMVTAPFITQSIKVDLPKASA-KPAPQDKKPIIVSVDADGQIYLNDKPVSLEELE 85 (137)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC-CCCCCCCCCEEEEEECCCCEEECCCCCCHHHHH
T ss_conf 55866655379999999999998511311462332798767-776678987799991898689878132589999
No 3
>PRK11024 colicin uptake protein TolR; Provisional
Probab=75.15 E-value=7 Score=19.73 Aligned_cols=57 Identities=25% Similarity=0.486 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHH-------CCCCEEEEEEC-CCCEEEEEEECCCEEEE
Q ss_conf 13200121059999999999996798872-------02105674211-11507999703770696
Q gi|255764502|r 30 MNSELQSTSLVGLVLVLFIILIGTVMVLI-------PKAEFILGLDI-KRYPIMIDVKRDGEIRV 86 (100)
Q Consensus 30 mnselqstslvglvlvlfiiligtvmvli-------pkaefilgldi-krypimidvkrdgeirv 86 (100)
.+||..-|.++..+|||.||..=|...+- |++..--...- ..-|+.+++..+|+..+
T Consensus 12 ~~~EINvtPlIDVmlVLLIiFMvtap~~~~~i~V~LP~a~~~~~~~~~~~~~vii~i~~~g~~~~ 76 (142)
T PRK11024 12 LKSEINIVPLLDVLLVLLLIFMATAPIITQSVEVDLPDATESQAVSSNDNPPVIVEVSGVGQYTV 76 (142)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCEEEEEECCCCEEE
T ss_conf 66634553179999999999996124210653500899877787888888977999936875799
No 4
>pfam02472 ExbD Biopolymer transport protein ExbD/TolR. This group of proteins are membrane bound transport proteins essential for ferric ion uptake in bacteria. The Pfam family consists of ExbD, and TolR which are involved in TonB-dependent transport of various receptor bound substrates including colicins.
Probab=65.84 E-value=8.6 Score=19.27 Aligned_cols=69 Identities=26% Similarity=0.439 Sum_probs=43.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHH-HHH-------HCCCCEEEEEECCCCEEEEEEECCCEEEEEHHHHHHHHHH
Q ss_conf 321320012105999999999999679-887-------2021056742111150799970377069601566787775
Q gi|255764502|r 28 GRMNSELQSTSLVGLVLVLFIILIGTV-MVL-------IPKAEFILGLDIKRYPIMIDVKRDGEIRVQGQQVLLNEIT 97 (100)
Q Consensus 28 grmnselqstslvglvlvlfiiligtv-mvl-------ipkaefilgldikrypimidvkrdgeirvqgqqvllneit 97 (100)
.+.++|+.-|+++-.+++|.|.++=|. +.- .|.++--- ..-..-++.+-++++|++.+.|+.+-.+++.
T Consensus 2 ~~~~~~initPliDv~flLLiFFmvt~~~~~~~~~~v~lP~~~~~~-~~~~~~~v~i~i~~~g~~~~~~~~~~~~~L~ 78 (128)
T pfam02472 2 KEEEPEINLTPLIDVVFLLLIFFMVTATFIKESVLKVELPSASSTA-PVEEKEELIISVDADGKIYLDGEPVDLEELE 78 (128)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC-CCCCCCCEEEEECCCCCEEECCEEECHHHHH
T ss_conf 8656664653289999999999986053133355323478876676-6677742156686778777899970899999
No 5
>TIGR02801 tolR protein TolR; InterPro: IPR014168 This entry describes the inner membrane protein TolR, part of the TolR/TolQ complex that transduces energy from the proton-motive force, through TolA, to an outer membrane complex made up of TolB and Pal (peptidoglycan-associated lipoprotein). The complex is required to maintain outer membrane integrity, and defects may cause a defect in the import of some organic compounds. While several gene pairs homologous to talR and tolQ may be found in a single genome, the members of this entry should be bone fide TolR, supported by operon structure..
Probab=59.91 E-value=11 Score=18.72 Aligned_cols=61 Identities=31% Similarity=0.422 Sum_probs=44.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHH-------HHHCCCCEEEEEECC-CCEEEEEEECCCEEEEEHHHH
Q ss_conf 3200121059999999999996798-------872021056742111-150799970377069601566
Q gi|255764502|r 31 NSELQSTSLVGLVLVLFIILIGTVM-------VLIPKAEFILGLDIK-RYPIMIDVKRDGEIRVQGQQV 91 (100)
Q Consensus 31 nselqstslvglvlvlfiiligtvm-------vlipkaefilgldik-rypimidvkrdgeirvqgqqv 91 (100)
-||.--|-++-.-|||.||+.=|-- |=.|++.-----.-. .-||.+.+++||++-++....
T Consensus 2 ~sEINVvPyiDVMLVLLiIFMVTAP~lt~Gv~VdLP~~~~~~~~~~~~~~pi~v~v~~~G~~~l~~~~~ 70 (133)
T TIGR02801 2 MSEINVVPYIDVMLVLLIIFMVTAPLLTQGVKVDLPKAGAKPLQSPDDKKPITVSVDADGKIFLNDKKV 70 (133)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCCCCEEEEEECCEEEEEECCCC
T ss_conf 876565661788899999986323113488321158877667786335876689970580588650556
No 6
>TIGR01341 aconitase_1 aconitate hydratase 1; InterPro: IPR006249 Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop , . Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) . Below is a description of some of the multi-functional activities associated with different aconitases. Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway . The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA. Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) , . As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated . IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis . Although IRP2 is homologous to IRP1, IPR2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes . In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system. Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica , . In S.enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress. This entry represents bacterial aconitase A (AcnA), eukaryotic cytosolic aconitase (cAcn/IRP1), iron regulatory protein 2 (IRP2), and a few mitochondrial aconitases (certain mAcn proteins, but not the majority of these enzymes). More information about these proteins can be found at Protein of the Month: Aconitase .; GO: 0051539 4 iron 4 sulfur cluster binding, 0008152 metabolic process.
Probab=45.20 E-value=4.2 Score=20.92 Aligned_cols=60 Identities=32% Similarity=0.517 Sum_probs=47.8
Q ss_pred HHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCEEEEEHHHHHHH
Q ss_conf 21336860489713213200121059999999999996798872021056742111150799970377069601566787
Q gi|255764502|r 15 SRSKGNRNLTILDGRMNSELQSTSLVGLVLVLFIILIGTVMVLIPKAEFILGLDIKRYPIMIDVKRDGEIRVQGQQVLLN 94 (100)
Q Consensus 15 srskgnrnltildgrmnselqstslvglvlvlfiiligtvmvlipkaefilgldikrypimidvkrdgeirvqgqqvlln 94 (100)
|---||||. .||.+.-+..+-|.---||.---|-|++- .|.+.-||-.|. .|++|.|+
T Consensus 529 aVLSGNRNF---EGRIHPLvK~NyLASPPLVVAYALAG~~~-----------Inl~~~PIG~d~--------~Gk~VYl~ 586 (896)
T TIGR01341 529 AVLSGNRNF---EGRIHPLVKANYLASPPLVVAYALAGNVD-----------INLETDPIGTDK--------DGKPVYLK 586 (896)
T ss_pred EEEECCCCC---CCEECCCCCCCCCCCCHHHHHHHHCCCEE-----------ECCCCCCEEECC--------CCCEEEEE
T ss_conf 983155463---32016001235345725798985148135-----------545778710687--------79778862
Q ss_pred HH
Q ss_conf 77
Q gi|255764502|r 95 EI 96 (100)
Q Consensus 95 ei 96 (100)
.|
T Consensus 587 DI 588 (896)
T TIGR01341 587 DI 588 (896)
T ss_pred CC
T ss_conf 44
No 7
>pfam09846 DUF2073 Uncharacterized protein conserved in archaea (DUF2073). This archaeal protein has no known function.
Probab=42.14 E-value=30 Score=16.35 Aligned_cols=83 Identities=29% Similarity=0.440 Sum_probs=57.7
Q ss_pred CCCHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEE----
Q ss_conf 6411167789976213368604897132132001210599999999999967988720210567421111507999----
Q gi|255764502|r 2 MNIRSQEGIRKIRSRSKGNRNLTILDGRMNSELQSTSLVGLVLVLFIILIGTVMVLIPKAEFILGLDIKRYPIMID---- 77 (100)
Q Consensus 2 mnirsqegirkirsrskgnrnltildgrmnselqstslvglvlvlfiiligtvmvlipkaefilgldikrypimid---- 77 (100)
-+..|-|-||+|-..-+++ |.-+|.|+...|-++. ||-..|.-|-..+| -|.+|.-||---.
T Consensus 2 ~~m~SmEkIr~ILd~V~~G-~IVvLE~gL~PeEEa~------------LIE~TM~eI~~~~F-~GIEi~typ~~~~~~~~ 67 (104)
T pfam09846 2 ERMSSMEKIRLILDDVRDG-NIVVLEGGLTPEEEAK------------LIEMTMTEIDPDEF-SGIEIETYPSKEKDKGL 67 (104)
T ss_pred CCCCHHHHHHHHHHHHCCC-CEEEECCCCCHHHHHH------------HHHHHHHHCCCCCC-CCEEEEEECCCCCCCHH
T ss_conf 8542789999999861469-6899828989289999------------99999985484664-40799971765665448
Q ss_pred -----EECC-CEEEEEHHHHHHHHHHH
Q ss_conf -----7037-70696015667877752
Q gi|255764502|r 78 -----VKRD-GEIRVQGQQVLLNEITK 98 (100)
Q Consensus 78 -----vkrd-geirvqgqqvllneitk 98 (100)
-|+. ..+.|-|..--+.++.|
T Consensus 68 ~~rl~gk~~~~~lTVIGPAn~lktlkk 94 (104)
T pfam09846 68 LGRLLGKQSSERLTVIGPANQLKTLKK 94 (104)
T ss_pred HHHHHCCCCCCCEEEECCHHHHHHHHC
T ss_conf 999837887676689861898888760
No 8
>pfam09680 Tiny_TM_bacill Protein of unknown function (Tiny_TM_bacill). This entry represents a family of hypothetical proteins, half of which are 40 residues or less in length. Members are found only in spore-forming species. A Gly-rich variable region is followed by a strongly conserved, highly hydrophobic region, predicted to form a transmembrane helix, ending with an invariant Gly. The consensus for this stretch is FALLVVFILLIIV.
Probab=31.39 E-value=28 Score=16.50 Aligned_cols=11 Identities=64% Similarity=1.168 Sum_probs=8.4
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999999
Q gi|255764502|r 41 GLVLVLFIILI 51 (100)
Q Consensus 41 glvlvlfiili 51 (100)
.|..||||.||
T Consensus 7 aLiVVLFILLI 17 (26)
T pfam09680 7 ALIVVLFILLI 17 (26)
T ss_pred EHHHHHHHHHH
T ss_conf 26999999999
No 9
>cd05479 RP_DDI RP_DDI; retropepsin-like domain of DNA damage inducible protein. The family represents the retropepsin-like domain of DNA damage inducible protein. DNA damage inducible protein has a retropepsin-like domain and an amino-terminal ubiquitin-like domain and/or a UBA (ubiquitin-associated) domain. This CD represents the retropepsin-like domain of DDI.
Probab=31.05 E-value=21 Score=17.18 Aligned_cols=22 Identities=41% Similarity=0.853 Sum_probs=18.3
Q ss_pred CCCEEEEEE-CCCCEEEEEEECC
Q ss_conf 210567421-1115079997037
Q gi|255764502|r 60 KAEFILGLD-IKRYPIMIDVKRD 81 (100)
Q Consensus 60 kaefilgld-ikrypimidvkrd 81 (100)
..+|+||+| .+||-..||.|+.
T Consensus 98 ~~d~ilGlD~L~~h~~~IDl~~~ 120 (124)
T cd05479 98 DVDFLIGLDMLKRHQCVIDLKEN 120 (124)
T ss_pred CCCEEECHHHHHHCCEEEECHHC
T ss_conf 81478407799871948872008
No 10
>pfam10177 DUF2371 Uncharacterized conserved protein (DUF2371). This is a family of proteins conserved from nematodes to humans. The function is not known.
Probab=29.53 E-value=49 Score=15.21 Aligned_cols=53 Identities=26% Similarity=0.533 Sum_probs=34.7
Q ss_pred CHHH----HHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1116----778997621336860489713213200121059999999999996798872
Q gi|255764502|r 4 IRSQ----EGIRKIRSRSKGNRNLTILDGRMNSELQSTSLVGLVLVLFIILIGTVMVLI 58 (100)
Q Consensus 4 irsq----egirkirsrskgnrnltildgrmnselqstslvglvlvlfiiligtvmvli 58 (100)
.||| +--||-+.+++..-+.-...|++ .|-|.|-.-+++-+.+++.|..|..+
T Consensus 5 lrs~~~~~~~~rk~k~~~~~~~dVvVVrGKl--rl~S~sg~~~~lG~lVllVGiaMAvl 61 (142)
T pfam10177 5 LRSQIHAAGRKKKAKRKPRATWDVVVVRGKL--RLVSASGRALILGVLILLVGIAMAVL 61 (142)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCEEEEEEEE--EECCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 6786556521132455778877689995378--97168689999839999985888621
No 11
>cd05480 NRIP_C NRIP_C; putative nuclear receptor interacting protein. Proteins in this family have been described as probable nuclear receptor interacting proteins. The C-terminal domain of this family is homologous to the retroviral aspartyl protease domain. The domain is structurally related to one lobe of the pepsin molecule. The conserved active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.
Probab=22.94 E-value=27 Score=16.59 Aligned_cols=22 Identities=27% Similarity=0.593 Sum_probs=17.1
Q ss_pred CCCCEEEEEE-CCCCEEEEEEEC
Q ss_conf 0210567421-111507999703
Q gi|255764502|r 59 PKAEFILGLD-IKRYPIMIDVKR 80 (100)
Q Consensus 59 pkaefilgld-ikrypimidvkr 80 (100)
..-+|++||| .|||--.||.++
T Consensus 81 ~~~d~llGLdmLkr~qC~IdL~k 103 (103)
T cd05480 81 NEKNFSLGLQTLKSLKCVINLEK 103 (103)
T ss_pred CCCCEEHHHHHHHHCCEEECCCC
T ss_conf 98524200888865445760569
No 12
>pfam10705 Ycf15 Chloroplast protein precursor Ycf15 putative. In some species of plants the ycf15 gene is probably not a protein-coding gene because the protein in these species has premature stop codons. Most of the members of the family are hypothetical or uncharacterized.
Probab=21.02 E-value=39 Score=15.75 Aligned_cols=26 Identities=31% Similarity=0.618 Sum_probs=18.4
Q ss_pred HHCCCCEEEE-------EECCCCEEEEEEECCC
Q ss_conf 7202105674-------2111150799970377
Q gi|255764502|r 57 LIPKAEFILG-------LDIKRYPIMIDVKRDG 82 (100)
Q Consensus 57 lipkaefilg-------ldikrypimidvkrdg 82 (100)
-.||.||.-+ -.||+||+|-++....
T Consensus 38 elpkqeflnseqp~~i~~~ikk~~~~~~igp~~ 70 (93)
T pfam10705 38 ELPKQEFLNSEQPEPITHYIKKFPLMKRIGPES 70 (93)
T ss_pred CCCHHHHHCCCCCEEEEEEECCCEEEEECCCHH
T ss_conf 076867427679714456300000000148022
No 13
>COG5116 RPN2 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=20.65 E-value=73 Score=14.26 Aligned_cols=92 Identities=32% Similarity=0.390 Sum_probs=51.6
Q ss_pred HHHHHHHHHHH------HCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHH----HHHHHHH--------------HHHCC
Q ss_conf 11677899762------133686048971321320012105999999999----9996798--------------87202
Q gi|255764502|r 5 RSQEGIRKIRS------RSKGNRNLTILDGRMNSELQSTSLVGLVLVLFI----ILIGTVM--------------VLIPK 60 (100)
Q Consensus 5 rsqegirkirs------rskgnrnltildgrmnselqstslvglvlvlfi----iligtvm--------------vlipk 60 (100)
..|+|.-|.-. -..|.||.||---.|..-+...+.||+|+.+-. -|+.-+- .-|||
T Consensus 674 Khe~glaklGA~laqGi~~aGGRNvti~l~natG~l~~~~ivGlv~FlqyWYWfPL~hf~SLsf~Pttvigi~~s~~~pk 753 (926)
T COG5116 674 KHESGLAKLGAVLAQGISEAGGRNVTISLRNATGILSADRIVGLVLFLQYWYWFPLIHFVSLSFLPTTVIGIRGSQAIPK 753 (926)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCE
T ss_conf 44767999888998655634886389997315675217788899999999998789988866327512340346566752
Q ss_pred CCEEEEEEC--CCCEEEEEEECCCEEEEEHHHHHHHHH
Q ss_conf 105674211--115079997037706960156678777
Q gi|255764502|r 61 AEFILGLDI--KRYPIMIDVKRDGEIRVQGQQVLLNEI 96 (100)
Q Consensus 61 aefilgldi--krypimidvkrdgeirvqgqqvllnei 96 (100)
-.|+-.+.- -.||-|-.-...-+.|--...|+...+
T Consensus 754 F~fn~~~~e~~f~yP~~~~e~s~k~v~kv~tavlstti 791 (926)
T COG5116 754 FCFNEDLEEEEFEYPRMYEEASGKSVRKVNTAVLSTTI 791 (926)
T ss_pred EEECCCCCHHHHCCCCCCCCCCCCHHHHHHHHEECHHH
T ss_conf 54523467766238842245554212333220033457
Done!