Query 537021.9.peg.1107_1
Match_columns 40
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Wed May 25 07:21:09 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i peg_1107.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01997 sufA_proteo FeS asse 42.7 13 0.00034 19.0 1.4 18 13-30 84-101 (110)
2 cd01237 Unc112 Unc-112 pleckst 32.4 25 0.00062 17.8 1.5 18 9-26 7-31 (106)
3 cd01220 PH_CDEP Chondrocyte-de 31.3 26 0.00066 17.7 1.5 11 15-25 17-27 (99)
4 cd01218 PH_phafin2 Phafin2 Pl 26.3 34 0.00086 17.2 1.3 11 15-25 19-29 (104)
5 pfam08533 Glyco_hydro_42C Beta 17.6 81 0.0021 15.5 1.8 15 14-28 10-24 (58)
6 pfam02723 NS3_envE Non-structu 14.0 38 0.00098 16.9 -0.6 19 20-38 4-22 (82)
7 cd01221 PH_ephexin Ephexin Ple 10.5 1.5E+02 0.0037 14.3 1.5 11 15-25 28-38 (125)
8 pfam05780 consensus 8.5 57 0.0015 16.2 -1.3 17 23-39 4-20 (75)
9 cd01457 vWA_ORF176_type VWA OR 7.8 2.4E+02 0.0061 13.4 1.7 15 14-28 1-15 (199)
10 pfam00243 NGF Nerve growth fac 7.3 2.1E+02 0.0053 13.7 1.1 7 15-21 46-52 (116)
No 1
>TIGR01997 sufA_proteo FeS assembly scaffold SufA; InterPro: IPR011298 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents the SufA protein of the SUF system of iron-sulphur cluster biosynthesis. SufA acts as a scaffold in which Fe and S are assembled into FeS clusters . This system performs FeS biosynthesis even during oxidative stress and tends to be absent in obligate anaerobic and microaerophilic bacteria..
Probab=42.65 E-value=13 Score=19.03 Aligned_cols=18 Identities=39% Similarity=0.539 Sum_probs=14.8
Q ss_pred EECCEEEEEEECCCCCCH
Q ss_conf 103059999906771148
Q 537021.9.peg.1 13 REKRQYFFVFNDTNQMNI 30 (40)
Q Consensus 13 rekrqyffvfndtnqmni 30 (40)
..-|||-|.||..||.+-
T Consensus 84 ~~L~~y~f~FnNPn~~~a 101 (110)
T TIGR01997 84 TTLRQYGFKFNNPNATSA 101 (110)
T ss_pred CCCCEEEEEECCCCCCCC
T ss_conf 354122227428554678
No 2
>cd01237 Unc112 Unc-112 pleckstrin homology (PH) domain. Unc-112 and related proteins contain two FERM domains with a PH domain between them. Both the PH and FERM domains have a PH-like fold. The FERM domains are likely responsible for the role of Unc-112 in organizing beta-integrin. The specific role of the Unc-112 PH domain is not known, but it is predicted to be involved in mediating membrane interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=32.44 E-value=25 Score=17.82 Aligned_cols=18 Identities=50% Similarity=1.062 Sum_probs=13.1
Q ss_pred HHHEEEC-------CEEEEEEECCC
Q ss_conf 4630103-------05999990677
Q 537021.9.peg.1 9 LFFFREK-------RQYFFVFNDTN 26 (40)
Q Consensus 9 lfffrek-------rqyffvfndtn 26 (40)
|-|||.| .||+|+|.||.
T Consensus 7 Lk~~kpkk~tLK~yK~ywf~fkD~~ 31 (106)
T cd01237 7 LKYFKPKKLTLKGYKQYWFTFRDTS 31 (106)
T ss_pred HHHHCCHHHHHHHHEEEEEEEECCE
T ss_conf 4642700230200123899982359
No 3
>cd01220 PH_CDEP Chondrocyte-derived ezrin-like domain containing protein (CDEP) Pleckstrin homology (PH) domain. CDEP consists of a Ferm domain, a rhoGEF (DH) domain followed by two PH domains. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=31.33 E-value=26 Score=17.70 Aligned_cols=11 Identities=36% Similarity=0.951 Sum_probs=8.7
Q ss_pred CCEEEEEEECC
Q ss_conf 30599999067
Q 537021.9.peg.1 15 KRQYFFVFNDT 25 (40)
Q Consensus 15 krqyffvfndt 25 (40)
+..|||.|||.
T Consensus 17 q~R~ffLFnD~ 27 (99)
T cd01220 17 QQRMFFLFSDL 27 (99)
T ss_pred CCEEEEEEEEE
T ss_conf 82699997148
No 4
>cd01218 PH_phafin2 Phafin2 Pleckstrin Homology (PH) domain. Phafin contains a PH domain and a FYVE domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=26.34 E-value=34 Score=17.20 Aligned_cols=11 Identities=55% Similarity=1.065 Sum_probs=8.7
Q ss_pred CCEEEEEEECC
Q ss_conf 30599999067
Q 537021.9.peg.1 15 KRQYFFVFNDT 25 (40)
Q Consensus 15 krqyffvfndt 25 (40)
|..+||.|||.
T Consensus 19 k~R~FfLFnDi 29 (104)
T cd01218 19 KQRQFFLFNDI 29 (104)
T ss_pred CCEEEEEECEE
T ss_conf 86799970338
No 5
>pfam08533 Glyco_hydro_42C Beta-galactosidase C-terminal domain. This domain is found at the C-terminus of beta-galactosidase enzymes that belong to the glycosyl hydrolase 42 family.
Probab=17.56 E-value=81 Score=15.49 Aligned_cols=15 Identities=47% Similarity=0.842 Sum_probs=11.6
Q ss_pred ECCEEEEEEECCCCC
Q ss_conf 030599999067711
Q 537021.9.peg.1 14 EKRQYFFVFNDTNQM 28 (40)
Q Consensus 14 ekrqyffvfndtnqm 28 (40)
+...|.|++|-++.-
T Consensus 10 ~~~~y~Fv~N~s~~~ 24 (58)
T pfam08533 10 ERGRYLFVFNFSNEP 24 (58)
T ss_pred CCCEEEEEECCCCCC
T ss_conf 991799999478987
No 6
>pfam02723 NS3_envE Non-structural protein NS3/Small envelope protein E. This is a family of small non-structural proteins, well conserved among Coronavirus strains. This protein is also found in murine hepatitis virus as small envelope protein E.
Probab=13.96 E-value=38 Score=16.94 Aligned_cols=19 Identities=26% Similarity=0.726 Sum_probs=16.6
Q ss_pred EEEECCCCCCHHHHEEEEE
Q ss_conf 9990677114865034626
Q 537021.9.peg.1 20 FVFNDTNQMNIESFLWILF 38 (40)
Q Consensus 20 fvfndtnqmniesflwilf 38 (40)
|.+.|++-+-..+++|.+.
T Consensus 4 l~~~d~~~~Vvn~il~~lv 22 (82)
T pfam02723 4 LFLEDDNGLVVNIILWLLV 22 (82)
T ss_pred EEEECCCEEEHHHHHHHHH
T ss_conf 5985277254359999999
No 7
>cd01221 PH_ephexin Ephexin Pleckstrin homology (PH) domain. Ephexin contains a RhoGEF (DH) followed by a PH domain and an SH3 domain. The ephexin PH domain is believed to act with the DH domain in mediating protein-protein interactions with the Eph receptor. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=10.55 E-value=1.5e+02 Score=14.32 Aligned_cols=11 Identities=45% Similarity=1.011 Sum_probs=8.4
Q ss_pred CCEEEEEEECC
Q ss_conf 30599999067
Q 537021.9.peg.1 15 KRQYFFVFNDT 25 (40)
Q Consensus 15 krqyffvfndt 25 (40)
+--|+|.|||-
T Consensus 28 ~~vylfLFnD~ 38 (125)
T cd01221 28 RTIYLFLFNDL 38 (125)
T ss_pred CCEEEEEECCE
T ss_conf 84899884435
No 8
>pfam05780 consensus
Probab=8.46 E-value=57 Score=16.17 Aligned_cols=17 Identities=24% Similarity=0.690 Sum_probs=12.9
Q ss_pred ECCCCCCHHHHEEEEEE
Q ss_conf 06771148650346265
Q 537021.9.peg.1 23 NDTNQMNIESFLWILFM 39 (40)
Q Consensus 23 ndtnqmniesflwilfm 39 (40)
-|.|.|-+.++||.+.+
T Consensus 4 vdD~GlVvn~ilWllv~ 20 (75)
T pfam05780 4 VDDHGLVVNVILWLLVL 20 (75)
T ss_pred ECCCCEEHHHHHHHHHH
T ss_conf 70687326999999999
No 9
>cd01457 vWA_ORF176_type VWA ORF176 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most
Probab=7.85 E-value=2.4e+02 Score=13.38 Aligned_cols=15 Identities=27% Similarity=0.656 Sum_probs=0.0
Q ss_pred ECCEEEEEEECCCCC
Q ss_conf 030599999067711
Q 537021.9.peg.1 14 EKRQYFFVFNDTNQM 28 (40)
Q Consensus 14 ekrqyffvfndtnqm 28 (40)
|+|+|.|+..|..-|
T Consensus 1 ~~rD~v~lIDdSgSM 15 (199)
T cd01457 1 ENRDYTLLIDKSGSM 15 (199)
T ss_pred CCCCEEEEEECCCCC
T ss_conf 997779999688876
No 10
>pfam00243 NGF Nerve growth factor family.
Probab=7.27 E-value=2.1e+02 Score=13.66 Aligned_cols=7 Identities=57% Similarity=1.103 Sum_probs=0.0
Q ss_pred CCEEEEE
Q ss_conf 3059999
Q 537021.9.peg.1 15 KRQYFFV 21 (40)
Q Consensus 15 krqyffv 21 (40)
.+||||.
T Consensus 46 ~kQyFfE 52 (116)
T pfam00243 46 LKQYFFE 52 (116)
T ss_pred EEEEEEE
T ss_conf 8999999
Done!