Query T0569 PtR41O, , 79 residues
Match_columns 79
No_of_seqs 4 out of 6
Neff 1.6
Searched_HMMs 11830
Date Tue Jun 1 15:13:50 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0569.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0569.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07029 CryBP1: CryBP1 protei 12.2 35 0.003 13.8 1.4 50 27-76 10-66 (161)
2 PF00379 Chitin_bind_4: Insect 11.9 41 0.0035 13.4 2.5 17 53-69 33-49 (51)
3 PF10065 DUF2303: Uncharacteri 10.1 40 0.0034 13.5 1.1 21 29-49 28-48 (276)
4 PF07166 DUF1398: Protein of u 10.1 48 0.0041 13.0 2.2 34 31-64 29-63 (125)
5 PF02554 CstA: Carbon starvati 9.2 52 0.0044 12.9 1.5 24 29-52 33-56 (376)
6 PF12141 DUF3589: Protein of u 8.1 58 0.0049 12.6 4.0 43 35-77 410-454 (498)
7 PF08726 efhand_Ca_insen: Ca2+ 6.0 43 0.0036 13.3 -0.3 12 36-47 51-62 (69)
8 PF07076 DUF1344: Protein of u 6.0 76 0.0064 12.0 5.0 35 36-76 46-80 (81)
9 PF06134 RhaA: L-rhamnose isom 5.7 53 0.0045 12.9 0.1 17 34-50 180-196 (417)
10 PF05415 Peptidase_C36: Beet n 4.7 94 0.0079 11.5 3.2 27 53-79 69-95 (104)
No 1
>PF07029 CryBP1: CryBP1 protein; InterPro: IPR009751 This family consists of several CryBP1 like proteins from Bacillus thuringiensis and Paenibacillus popilliae. Members of this family are thought to be involved in the overall toxicity of the bacteria to their hosts ,.
Probab=12.16 E-value=35 Score=13.79 Aligned_cols=50 Identities=34% Similarity=0.395 Sum_probs=25.7
Q ss_pred CCCCCCEEEEEECCCCCEEECCCC--CE--EECCC---CEEEEEEECCCCCEEEEEE
Q ss_conf 543654125887478810203678--56--41388---4579998308996489988
Q T0569 27 GKTDDSTTYTVTIPDGYEYVGTDG--GV--VSSDG---KTVTITFAADDSDNVVIHL 76 (79)
Q Consensus 27 GktD~~~~~tvtIPDGYeYVga~g--~~--vs~dG---Kt~~~t~~adDsdnv~iHL 76 (79)
++-.-.---.+.||.|++|+.-.- -+ +||=+ .|-+-+..-+|...+-|-|
T Consensus 10 ~~~~vpFcc~vsIP~GF~~~~~~~~klVy~ls~Ls~vKetcrk~i~vddCG~~eIdL 66 (161)
T PF07029_consen 10 EKHKVPFCCVVSIPHGFEYVPPCTPKLVYDLSCLSMVKETCRKTIQVDDCGQVEIDL 66 (161)
T ss_pred CCCCCCEEEEEECCCCEEECCCCCCEEEEECCCEEEEEEEEEEEEEECCCCEEEEEE
T ss_conf 664254689897788769878997059999134078823068999946985578998
No 2
>PF00379 Chitin_bind_4: Insect cuticle protein; InterPro: IPR000618 Insect cuticle is composed of proteins and chitin. The cuticular proteins seem to be specific to the type of cuticle (flexible or stiff) that occur at stages of the insect development. The proteins found in the flexible cuticle of larva and pupa of different insects share a conserved C-terminal section such a region is also found in the soft endocuticle of adults insects as well as in other cuticular proteins including in arachnids . In addition, cuticular proteins share hydrophobic regions dominated by tetrapeptide repeats (A-A-P-A/V), which are presumed to be functionally important , . Many insect cuticle proteins also include a 35-36 amino acid motif known as the R and R consensus. An extended form of this motif has been shown to bind chitin. It has no sequence similiarity to the cysteine-containing chitin-binding domain of chitinases and some peritrophic membrane proteins, suggesting that arthropods have two distinct classes of chitin-binding proteins, those with the chitin-binding domains found in lectins, chitinases and peritrophic membranes (cysCBD), and those with the type of chitin-binding domains found in cuticular proteins (non-cysCBD) . The cuticle protein signature has been found in locust cuticle proteins 7 (LM-7), 8 (LM-8), 19 (LM-19) and endocuticle structural glycoprotein ABD-4; Hyalophora cecropia (Cecropia moth) cuticle proteins 12 and 66; Drosophila melanogaster (Fruit fly) larval cuticles proteins I, II, III and IV (LCP1 to LCP4); drosophila pupal cuticle proteins PCP, EDG-78E and EDG-84E; Manduca sexta (Tobacco hawkmoth) cuticle protein LCP-14; Tenebrio molitor (Yellow mealworm) cuticle proteins ACP-20, A1A, A2B and A3A; and Araneus diadematus (Spider) cuticle proteins ACP 11.9, ACP 12.4, ACP 12.6, ACP 15.5 and ACP 15.7.; GO: 0042302 structural constituent of cuticle
Probab=11.91 E-value=41 Score=13.40 Aligned_cols=17 Identities=41% Similarity=0.796 Sum_probs=12.6
Q ss_pred EECCCCEEEEEEECCCC
Q ss_conf 41388457999830899
Q T0569 53 VSSDGKTVTITFAADDS 69 (79)
Q Consensus 53 vs~dGKt~~~t~~adDs 69 (79)
++.||+..+++.+||.+
T Consensus 33 ~~pdG~~~~V~Y~Ad~~ 49 (51)
T PF00379_consen 33 VDPDGRRRTVTYTADEN 49 (51)
T ss_pred ECCCCCEEEEEEECCCC
T ss_conf 99999899999988888
No 3
>PF10065 DUF2303: Uncharacterized conserved protein (DUF2303)
Probab=10.15 E-value=40 Score=13.46 Aligned_cols=21 Identities=24% Similarity=0.548 Sum_probs=16.3
Q ss_pred CCCCEEEEEECCCCCEEECCC
Q ss_conf 365412588747881020367
Q T0569 29 TDDSTTYTVTIPDGYEYVGTD 49 (79)
Q Consensus 29 tD~~~~~tvtIPDGYeYVga~ 49 (79)
.+++..+.+-+|+||+++.-+
T Consensus 28 ~~g~~~p~v~~P~g~~i~~Le 48 (276)
T PF10065_consen 28 IEGTDCPAVAVPDGYRIQSLE 48 (276)
T ss_pred CCCCCCCEEECCCCCCEEEHH
T ss_conf 655779868878987510267
No 4
>PF07166 DUF1398: Protein of unknown function (DUF1398); InterPro: IPR009833 This family consists of several hypothetical Enterobacterial proteins of around 130 residues in length. Members of this family seem to be found exclusively in Escherichia coli and Salmonella species. The function of this family is unknown.; PDB: 2hh8_A.
Probab=10.07 E-value=48 Score=13.05 Aligned_cols=34 Identities=29% Similarity=0.555 Sum_probs=24.2
Q ss_pred CCEEEEEECCCC-CEEECCCCCEEECCCCEEEEEE
Q ss_conf 541258874788-1020367856413884579998
Q T0569 31 DSTTYTVTIPDG-YEYVGTDGGVVSSDGKTVTITF 64 (79)
Q Consensus 31 ~~~~~tvtIPDG-YeYVga~g~~vs~dGKt~~~t~ 64 (79)
+...|.|-+-|| |.|++.+|..|+..|+-..+..
T Consensus 29 gV~~Y~y~Va~G~~~y~~~~~~~v~~~~~~~~~~V 63 (125)
T PF07166_consen 29 GVSHYIYYVADGNYTYVGQNDYTVSIKGNKKPVPV 63 (125)
T ss_dssp -SSEEEEETTTS-EEEE-SSS-EEEE---TT----
T ss_pred CCEEEEEEEECCCEEEEEECCCEEEEECCCCEEEE
T ss_conf 97368999734848999718989998436524874
No 5
>PF02554 CstA: Carbon starvation protein CstA; InterPro: IPR003706 Escherichia coli induces the synthesis of at least 30 proteins at the onset of carbon starvation, two-thirds of which are positively regulated by the cyclic AMP (cAMP) and cAMP receptor protein (CRP) complex. This family consists of carbon starvation protein CstA a predicted membrane protein. It has been suggested that CstA is involved in peptide utilization .; GO: 0009267 cellular response to starvation, 0016020 membrane
Probab=9.22 E-value=52 Score=12.87 Aligned_cols=24 Identities=29% Similarity=0.371 Sum_probs=18.8
Q ss_pred CCCCEEEEEECCCCCEEECCCCCE
Q ss_conf 365412588747881020367856
Q T0569 29 TDDSTTYTVTIPDGYEYVGTDGGV 52 (79)
Q Consensus 29 tD~~~~~tvtIPDGYeYVga~g~~ 52 (79)
-|+..||-++.-||-|||-+.--+
T Consensus 33 d~~r~TPA~~~~DGvDYVPt~k~v 56 (376)
T PF02554_consen 33 DPNRPTPAHRLNDGVDYVPTNKWV 56 (376)
T ss_pred CCCCCCCCEECCCCCCCCCCCCCE
T ss_conf 999999853746797501078513
No 6
>PF12141 DUF3589: Protein of unknown function (DUF3589)
Probab=8.13 E-value=58 Score=12.62 Aligned_cols=43 Identities=28% Similarity=0.365 Sum_probs=30.2
Q ss_pred EEEECCCCCEEECCCC--CEEECCCCEEEEEEECCCCCEEEEEEE
Q ss_conf 5887478810203678--564138845799983089964899884
Q T0569 35 YTVTIPDGYEYVGTDG--GVVSSDGKTVTITFAADDSDNVVIHLK 77 (79)
Q Consensus 35 ~tvtIPDGYeYVga~g--~~vs~dGKt~~~t~~adDsdnv~iHLK 77 (79)
.-|-||.|-.|-..+. +--...--.+++||...|.++-+||+|
T Consensus 410 ~nvLIPNgIssW~i~~~~~~~~~~~DymtlTlS~aD~tv~iI~ik 454 (498)
T PF12141_consen 410 KNVLIPNGISSWDIESHDGEDGSFEDYMTLTLSEADRTVDIIHIK 454 (498)
T ss_pred CCEECCCCCCEEEECCCCCCCCCCCCEEEEEEEECCCCCEEEEEH
T ss_conf 757787872426652565666664424899998325640589846
No 7
>PF08726 efhand_Ca_insen: Ca2+ insensitive EF hand; InterPro: IPR014837 EF hands are helix-loop-helix binding motifs involved in the regulation of many cellular processes. EF hands usually bind to Ca2+ ions, which cause a major conformational change that allows the protein to interact with its designated targets. This protein corresponds to an EF hand which has partially or entirely lost its calcium-binding properties. The calcium insensitive EF hand is still able to mediate protein-protein recognition . ; PDB: 1h8b_A 1sjj_B.
Probab=6.01 E-value=43 Score=13.32 Aligned_cols=12 Identities=33% Similarity=0.850 Sum_probs=8.6
Q ss_pred EEECCCCCEEEC
Q ss_conf 887478810203
Q T0569 36 TVTIPDGYEYVG 47 (79)
Q Consensus 36 tvtIPDGYeYVg 47 (79)
..-+|++|+|++
T Consensus 51 ~~~~~~~~DY~s 62 (69)
T PF08726_consen 51 GDAIPGAYDYIS 62 (69)
T ss_dssp -------EECHH
T ss_pred CCCCCCCCCHHH
T ss_conf 678988748999
No 8
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=5.99 E-value=76 Score=12.02 Aligned_cols=35 Identities=23% Similarity=0.575 Sum_probs=24.6
Q ss_pred EEECCCCCEEECCCCCEEECCCCEEEEEEECCCCCEEEEEE
Q ss_conf 88747881020367856413884579998308996489988
Q T0569 36 TVTIPDGYEYVGTDGGVVSSDGKTVTITFAADDSDNVVIHL 76 (79)
Q Consensus 36 tvtIPDGYeYVga~g~~vs~dGKt~~~t~~adDsdnv~iHL 76 (79)
+|+.|.+.+|-|- ..|..+.++|...|..++.--|
T Consensus 46 ty~lp~e~~~~~L------~~G~kV~V~yd~~~g~rvitd~ 80 (81)
T PF07076_consen 46 TYQLPEEFDFEGL------KPGVKVVVTYDEVDGKRVITDI 80 (81)
T ss_pred EEECCCCCCHHHC------CCCCEEEEEEECCCCEEEECCC
T ss_conf 6656876564242------6899899999855880761116
No 9
>PF06134 RhaA: L-rhamnose isomerase (RhaA); InterPro: IPR009308 This family consists of several bacterial L-rhamnose isomerase proteins (5.3.1.14 from EC). This enzyme interconverts L-rhamnose and L-rhamnulose. In some species, including Escherichia coli, this is the first step in rhamnose catabolism. Sequential steps are catalyzed by rhamnulose kinase (rhaB), then rhamnulose-1-phosphate aldolase (rhaD) to yield glycerone phosphate and (S)-lactaldehyde. ; GO: 0008740 L-rhamnose isomerase activity, 0030145 manganese ion binding, 0019299 rhamnose metabolic process; PDB: 1de6_A 1de5_D 1d8w_D.
Probab=5.70 E-value=53 Score=12.85 Aligned_cols=17 Identities=29% Similarity=0.386 Sum_probs=12.3
Q ss_pred EEEEECCCCCEEECCCC
Q ss_conf 25887478810203678
Q T0569 34 TYTVTIPDGYEYVGTDG 50 (79)
Q Consensus 34 ~~tvtIPDGYeYVga~g 50 (79)
....=||||+.|.+.|-
T Consensus 180 v~niWipDG~kd~p~Dr 196 (417)
T PF06134_consen 180 VMNIWIPDGTKDPPQDR 196 (417)
T ss_dssp EEEE-------S--S-S
T ss_pred CEEEECCCCCCCCCCCC
T ss_conf 12466588888887442
No 10
>PF05415 Peptidase_C36: Beet necrotic yellow vein furovirus-type papain-like endopeptidase; InterPro: IPR008746 Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. 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-, 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. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad . This group of cysteine peptidases correspond to MEROPS peptidase family C36 (clan CA). The type example is beet necrotic yellow vein furovirus-type papain-like endopeptidase (beet necrotic yellow vein virus), which is involved in processing the viral polyprotein.
Probab=4.66 E-value=94 Score=11.54 Aligned_cols=27 Identities=22% Similarity=0.149 Sum_probs=0.0
Q ss_pred EECCCCEEEEEEECCCCCEEEEEEECC
Q ss_conf 413884579998308996489988439
Q T0569 53 VSSDGKTVTITFAADDSDNVVIHLKHG 79 (79)
Q Consensus 53 vs~dGKt~~~t~~adDsdnv~iHLKH~ 79 (79)
|-+|--+.-.-|.+++-.+++.||.|+
T Consensus 69 V~~~~~~~l~~~~D~~~s~v~~y~~~K 95 (104)
T PF05415_consen 69 VLSDKPYDLLYFVDGAVSVVTLYLEGK 95 (104)
T ss_pred ECCCCCCEEEEEECCCCCEEEEEEECC
T ss_conf 837998314786147743565333155
Done!