Query 537021.9.peg.532_1
Match_columns 38
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Tue May 24 21:21:42 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i peg_532.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 pfam03967 PRCH Photosynthetic 20.8 64 0.0016 15.4 1.9 17 15-31 18-34 (135)
2 cd00226 PRCH Photosynthetic re 16.0 1E+02 0.0026 14.4 2.0 17 15-31 19-35 (246)
3 pfam03656 Pam16 Pam16. The Pam 14.3 55 0.0014 15.7 0.2 16 15-30 79-99 (127)
4 TIGR02509 type_III_yopR type I 13.0 86 0.0022 14.7 0.9 10 10-19 80-89 (137)
5 PRK01844 hypothetical protein; 10.9 1.6E+02 0.004 13.5 1.8 20 13-32 2-21 (72)
6 pfam09743 DUF2042 Uncharacteri 10.8 1.3E+02 0.0034 13.8 1.3 13 22-36 244-256 (272)
7 pfam04333 VacJ VacJ like lipop 10.0 1.7E+02 0.0042 13.4 1.6 14 19-32 184-197 (200)
8 KOG3281 consensus 9.7 1.5E+02 0.0038 13.6 1.3 22 13-34 225-246 (273)
9 TIGR01980 sufB FeS assembly pr 9.3 1.3E+02 0.0033 13.9 0.8 8 23-30 427-434 (469)
10 COG3932 Uncharacterized ABC-ty 8.6 1.4E+02 0.0036 13.7 0.8 16 20-35 160-175 (209)
No 1
>pfam03967 PRCH Photosynthetic reaction centre, H-chain N-terminal region. The family corresponds the N-terminal cytoplasmic domain.
Probab=20.77 E-value=64 Score=15.38 Aligned_cols=17 Identities=29% Similarity=0.817 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHC
Q ss_conf 99999999999887444
Q 537021.9.peg.5 15 FLWIFIIVQSFYLQQRN 31 (38)
Q Consensus 15 flwifiivqsfylqqrn 31 (38)
-.|||...--||||..|
T Consensus 18 ~FwiFFagLv~YL~rE~ 34 (135)
T pfam03967 18 AFWIFFAGLVYYLRRED 34 (135)
T ss_pred HHHHHHHHHHHHHHHCC
T ss_conf 99999999999861046
No 2
>cd00226 PRCH Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce ATP by ATP synthase. Subunit H is positioned mainly in the cytoplasm with one transmembrane alpha helix. Provides proton transfer pathway (water channels) connecting the terminal quinone electron acceptor of RC, to the aqueous phase. Found in photosynthetic bacteria: alpha, beta, and gamma proteobacteria.
Probab=15.97 E-value=1e+02 Score=14.41 Aligned_cols=17 Identities=35% Similarity=0.833 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHC
Q ss_conf 99999999999887444
Q 537021.9.peg.5 15 FLWIFIIVQSFYLQQRN 31 (38)
Q Consensus 15 flwifiivqsfylqqrn 31 (38)
-.|||..---||||..|
T Consensus 19 ~FWiFFagLv~YL~rE~ 35 (246)
T cd00226 19 AFWIFFAGLIYYLRREN 35 (246)
T ss_pred HHHHHHHHHHHHHHCCC
T ss_conf 99999999999861256
No 3
>pfam03656 Pam16 Pam16. The Pam16 protein is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM). In Saccharomyces cerevisiae, Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane. Pam16 has a degenerate J domain. J-domain proteins play important regulatory roles as co-chaperones, recruiting Hsp70 partners and accelerating the ATP-hydrolysis step of the chaperone cycle. Pam16's J-like domain strongly interacts with Pam18's J domain, leading to a productive interaction of Pam18 with mtHsp70 at the mitochondria import channel. Pam18 stimulates the ATPase activity of mtHsp70.
Probab=14.28 E-value=55 Score=15.70 Aligned_cols=16 Identities=38% Similarity=0.731 Sum_probs=8.9
Q ss_pred HHHHHHHH-----HHHHHHHH
Q ss_conf 99999999-----99988744
Q 537021.9.peg.5 15 FLWIFIIV-----QSFYLQQR 30 (38)
Q Consensus 15 flwifiiv-----qsfylqqr 30 (38)
|-..|-+- -|||||-.
T Consensus 79 y~~LF~~Ndk~kGGSFYLQSK 99 (127)
T pfam03656 79 YEHLFEVNDKSKGGSFYLQSK 99 (127)
T ss_pred HHHHHHCCCCCCCCCHHHHHH
T ss_conf 999986379888986469999
No 4
>TIGR02509 type_III_yopR type III secretion effector, YopR family; InterPro: IPR013349 Proteins in this entry are type III secretion system effectors, named differently in different species and designated YopR (Yersinia outer protein R), encoded by the YscH (Yersinia secretion H) gene. This Yop protein is unusual in that it is released to the extracellular environment rather than injected directly into the target cell as are most Yop proteins.; GO: 0009405 pathogenesis, 0030254 protein secretion by the type III secretion system, 0030257 type III protein secretion system complex.
Probab=13.05 E-value=86 Score=14.75 Aligned_cols=10 Identities=30% Similarity=0.106 Sum_probs=7.3
Q ss_pred HHHHHHHHHH
Q ss_conf 6356899999
Q 537021.9.peg.5 10 LQWETFLWIF 19 (38)
Q Consensus 10 lqwetflwif 19 (38)
-||||+||-.
T Consensus 80 ~q~E~~LL~~ 89 (137)
T TIGR02509 80 RQQEAALLQL 89 (137)
T ss_pred HHHHHHHHHH
T ss_conf 7899999999
No 5
>PRK01844 hypothetical protein; Provisional
Probab=10.89 E-value=1.6e+02 Score=13.46 Aligned_cols=20 Identities=20% Similarity=0.173 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHHHCC
Q ss_conf 68999999999998874447
Q 537021.9.peg.5 13 ETFLWIFIIVQSFYLQQRNG 32 (38)
Q Consensus 13 etflwifiivqsfylqqrng 32 (38)
.+.+||++++-.+-.----|
T Consensus 2 ~~~~~Ili~i~~li~G~~~G 21 (72)
T PRK01844 2 PIWLGILVGVVALVAGVALG 21 (72)
T ss_pred CHHHHHHHHHHHHHHHHHHH
T ss_conf 05999999999999999999
No 6
>pfam09743 DUF2042 Uncharacterized conserved protein (DUF2042). This entry is the conserved N-terminal 300 residues of a group of proteins found from protozoa to Humans. The function is unknown.
Probab=10.77 E-value=1.3e+02 Score=13.80 Aligned_cols=13 Identities=46% Similarity=0.984 Sum_probs=8.6
Q ss_pred HHHHHHHHHCCEEEE
Q ss_conf 999988744472423
Q 537021.9.peg.5 22 VQSFYLQQRNGFLSI 36 (38)
Q Consensus 22 vqsfylqqrngflsi 36 (38)
|.|||.| |||+..
T Consensus 244 V~~fy~q--Ngyle~ 256 (272)
T pfam09743 244 VDNFYKQ--NGYIEY 256 (272)
T ss_pred HHHHHHH--CCCEEH
T ss_conf 9999996--795878
No 7
>pfam04333 VacJ VacJ like lipoprotein. VacJ is required for the intercellular spreading of Shigella flexneri. It is attached to the outer membrane by a lipid anchor.
Probab=9.98 E-value=1.7e+02 Score=13.35 Aligned_cols=14 Identities=43% Similarity=0.626 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHCC
Q ss_conf 99999998874447
Q 537021.9.peg.5 19 FIIVQSFYLQQRNG 32 (38)
Q Consensus 19 fiivqsfylqqrng 32 (38)
+..+.+.|+|.|+-
T Consensus 184 Y~~~R~~Y~Q~R~~ 197 (200)
T pfam04333 184 YITTRSAYLQRREF 197 (200)
T ss_pred HHHHHHHHHHHHHH
T ss_conf 79999999999998
No 8
>KOG3281 consensus
Probab=9.68 E-value=1.5e+02 Score=13.57 Aligned_cols=22 Identities=27% Similarity=0.418 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHHCCEE
Q ss_conf 6899999999999887444724
Q 537021.9.peg.5 13 ETFLWIFIIVQSFYLQQRNGFL 34 (38)
Q Consensus 13 etflwifiivqsfylqqrngfl 34 (38)
+.--||-.-||+||+..+++-+
T Consensus 225 qeAQ~l~~~vQ~FY~~~~~~t~ 246 (273)
T KOG3281 225 QEAQLLALAVQKFYLADEEETL 246 (273)
T ss_pred HHHHHHHHHHHHHHCCCCCHHH
T ss_conf 9999999999998747850277
No 9
>TIGR01980 sufB FeS assembly protein SufB; InterPro: IPR010231 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 SufB, which is part of the SUF system and forms a complex with SufBCD.; GO: 0005515 protein binding, 0016226 iron-sulfur cluster assembly.
Probab=9.30 E-value=1.3e+02 Score=13.89 Aligned_cols=8 Identities=63% Similarity=0.970 Sum_probs=0.0
Q ss_pred HHHHHHHH
Q ss_conf 99988744
Q 537021.9.peg.5 23 QSFYLQQR 30 (38)
Q Consensus 23 qsfylqqr 30 (38)
|-|||++|
T Consensus 427 qlfYL~sR 434 (469)
T TIGR01980 427 QLFYLMSR 434 (469)
T ss_pred HHHHHHHC
T ss_conf 68897737
No 10
>COG3932 Uncharacterized ABC-type transport system, permease components [General function prediction only]
Probab=8.58 E-value=1.4e+02 Score=13.67 Aligned_cols=16 Identities=31% Similarity=0.584 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHCCEEE
Q ss_conf 9999998874447242
Q 537021.9.peg.5 20 IIVQSFYLQQRNGFLS 35 (38)
Q Consensus 20 iivqsfylqqrngfls 35 (38)
|.+-++-++||||++.
T Consensus 160 I~ll~lgllerDGll~ 175 (209)
T COG3932 160 ILLLGLGLLERDGLLV 175 (209)
T ss_pred HHHHHHHHHHCCCHHH
T ss_conf 9999877874255699
Done!