Query 032320
Match_columns 143
No_of_seqs 166 out of 1155
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 12:33:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032320.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032320hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0545 FkpA FKBP-type peptidy 99.1 8.1E-11 1.8E-15 96.2 5.9 43 99-143 97-139 (205)
2 KOG0544 FKBP-type peptidyl-pro 98.9 2.8E-09 6.1E-14 79.2 5.1 38 104-143 2-40 (108)
3 PRK11570 peptidyl-prolyl cis-t 98.8 8.4E-09 1.8E-13 83.5 5.7 43 99-143 98-140 (206)
4 PRK10902 FKBP-type peptidyl-pr 98.6 6.3E-08 1.4E-12 81.5 5.7 42 100-143 143-184 (269)
5 KOG0552 FKBP-type peptidyl-pro 98.5 1.7E-07 3.7E-12 77.7 5.4 43 100-143 117-159 (226)
6 TIGR03516 ppisom_GldI peptidyl 98.4 6.1E-07 1.3E-11 71.2 5.7 43 99-143 65-109 (177)
7 KOG0549 FKBP-type peptidyl-pro 98.0 1.3E-05 2.9E-10 65.1 5.2 40 102-143 67-108 (188)
8 KOG0543 FKBP-type peptidyl-pro 95.9 0.014 3E-07 52.4 5.3 39 102-143 83-123 (397)
9 TIGR00115 tig trigger factor. 76.6 3 6.5E-05 36.2 3.5 24 116-142 145-168 (408)
10 PRK01490 tig trigger factor; P 74.8 3.6 7.7E-05 36.1 3.5 24 116-142 156-179 (435)
11 KOG0545 Aryl-hydrocarbon recep 64.3 5.5 0.00012 34.9 2.4 42 102-143 9-52 (329)
12 PF10518 TAT_signal: TAT (twin 52.5 16 0.00035 20.6 2.3 15 61-75 3-17 (26)
13 COG0544 Tig FKBP-type peptidyl 46.0 23 0.00049 32.1 3.3 22 118-142 158-179 (441)
14 TIGR03096 nitroso_cyanin nitro 43.4 36 0.00079 26.4 3.7 28 102-129 43-76 (135)
15 PRK13159 cytochrome c-type bio 24.6 72 0.0016 25.4 2.6 13 122-134 83-95 (155)
16 TIGR02811 formate_TAT formate 23.4 1.1E+02 0.0023 20.9 2.9 8 61-68 10-17 (66)
17 PF05984 Cytomega_UL20A: Cytom 20.0 84 0.0018 23.2 2.0 18 61-79 2-19 (100)
No 1
>COG0545 FkpA FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.13 E-value=8.1e-11 Score=96.23 Aligned_cols=43 Identities=37% Similarity=0.619 Sum_probs=40.7
Q ss_pred cCCCCCcEEEEeEcCCCCCCCCCCEEEEEEEEEEcCCCCCcccCC
Q 032320 99 LPNSGGVKALDLRLGRGPVPVDGDQVAIHYYGRLAAKQGWRFDST 143 (143)
Q Consensus 99 l~~~sGL~~~iLk~GsG~~Pk~GDtV~VhYtG~L~d~~GkvFDSS 143 (143)
...++||+|++++.|+|+.|+.||+|.|||+|+|.| |++||||
T Consensus 97 ~~~~sgl~y~~~~~G~G~~~~~~~~V~vhY~G~l~~--G~vFDsS 139 (205)
T COG0545 97 KTLPSGLQYKVLKAGDGAAPKKGDTVTVHYTGTLID--GTVFDSS 139 (205)
T ss_pred eECCCCcEEEEEeccCCCCCCCCCEEEEEEEEecCC--CCccccc
Confidence 457899999999999999999999999999999999 9999997
No 2
>KOG0544 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=98.88 E-value=2.8e-09 Score=79.18 Aligned_cols=38 Identities=39% Similarity=0.726 Sum_probs=35.8
Q ss_pred CcEEEEeEcCCCC-CCCCCCEEEEEEEEEEcCCCCCcccCC
Q 032320 104 GVKALDLRLGRGP-VPVDGDQVAIHYYGRLAAKQGWRFDST 143 (143)
Q Consensus 104 GL~~~iLk~GsG~-~Pk~GDtV~VhYtG~L~d~~GkvFDSS 143 (143)
|+.++++.+|+|. .|++||+|+|||+|.|.| |++||||
T Consensus 2 Gv~~~~i~~Gdg~tfpK~Gqtvt~hYtg~L~d--G~kfDSs 40 (108)
T KOG0544|consen 2 GVEKQVISPGDGRTFPKKGQTVTVHYTGTLQD--GKKFDSS 40 (108)
T ss_pred CceeEEeeCCCCcccCCCCCEEEEEEEeEecC--CcEeecc
Confidence 7899999999995 799999999999999998 9999997
No 3
>PRK11570 peptidyl-prolyl cis-trans isomerase; Provisional
Probab=98.80 E-value=8.4e-09 Score=83.50 Aligned_cols=43 Identities=35% Similarity=0.614 Sum_probs=40.0
Q ss_pred cCCCCCcEEEEeEcCCCCCCCCCCEEEEEEEEEEcCCCCCcccCC
Q 032320 99 LPNSGGVKALDLRLGRGPVPVDGDQVAIHYYGRLAAKQGWRFDST 143 (143)
Q Consensus 99 l~~~sGL~~~iLk~GsG~~Pk~GDtV~VhYtG~L~d~~GkvFDSS 143 (143)
..+++||+|+++++|+|..|+.||.|.|||+|++.| |++||||
T Consensus 98 ~~t~sGl~y~vi~~G~G~~p~~~d~V~v~Y~g~l~d--G~vfdss 140 (206)
T PRK11570 98 NSTESGLQFRVLTQGEGAIPARTDRVRVHYTGKLID--GTVFDSS 140 (206)
T ss_pred EECCCCcEEEEEeCCCCCCCCCCCEEEEEEEEEECC--CCEEEec
Confidence 356899999999999999999999999999999988 9999986
No 4
>PRK10902 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=98.61 E-value=6.3e-08 Score=81.50 Aligned_cols=42 Identities=33% Similarity=0.529 Sum_probs=39.4
Q ss_pred CCCCCcEEEEeEcCCCCCCCCCCEEEEEEEEEEcCCCCCcccCC
Q 032320 100 PNSGGVKALDLRLGRGPVPVDGDQVAIHYYGRLAAKQGWRFDST 143 (143)
Q Consensus 100 ~~~sGL~~~iLk~GsG~~Pk~GDtV~VhYtG~L~d~~GkvFDSS 143 (143)
.+++||+|+++++|+|..|+.||.|.|||+|++.| |++||+|
T Consensus 143 ~t~sGl~y~Vi~~G~G~~p~~gD~V~V~Y~g~l~d--G~vfdss 184 (269)
T PRK10902 143 TTSTGLLYKVEKEGTGEAPKDSDTVVVNYKGTLID--GKEFDNS 184 (269)
T ss_pred ECCCccEEEEEeCCCCCCCCCCCEEEEEEEEEeCC--CCEeecc
Confidence 46899999999999999999999999999999988 9999985
No 5
>KOG0552 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=98.50 E-value=1.7e-07 Score=77.75 Aligned_cols=43 Identities=40% Similarity=0.757 Sum_probs=39.5
Q ss_pred CCCCCcEEEEeEcCCCCCCCCCCEEEEEEEEEEcCCCCCcccCC
Q 032320 100 PNSGGVKALDLRLGRGPVPVDGDQVAIHYYGRLAAKQGWRFDST 143 (143)
Q Consensus 100 ~~~sGL~~~iLk~GsG~~Pk~GDtV~VhYtG~L~d~~GkvFDSS 143 (143)
+.+.||+|++++.|+|+.++.|+.|.|||.|+|.+ +|++||++
T Consensus 117 tl~~Gl~y~D~~vG~G~~a~~G~rV~v~Y~Gkl~~-~GkvFd~~ 159 (226)
T KOG0552|consen 117 TLPGGLRYEDLRVGSGPSAKKGKRVSVRYIGKLKG-NGKVFDSN 159 (226)
T ss_pred ecCCCcEEEEEEecCCCCCCCCCEEEEEEEEEecC-CCeEeecc
Confidence 45799999999999999999999999999999984 39999984
No 6
>TIGR03516 ppisom_GldI peptidyl-prolyl isomerase, gliding motility-associated. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldI is a FKBP-type peptidyl-prolyl cis-trans isomerase (pfam00254) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockout of this gene abolishes the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. This family is only found in Bacteroidetes containing the suite of genes proposed to confer the gliding motility phenotype.
Probab=98.39 E-value=6.1e-07 Score=71.18 Aligned_cols=43 Identities=26% Similarity=0.200 Sum_probs=38.4
Q ss_pred cCCCCCcEEEEeEc--CCCCCCCCCCEEEEEEEEEEcCCCCCcccCC
Q 032320 99 LPNSGGVKALDLRL--GRGPVPVDGDQVAIHYYGRLAAKQGWRFDST 143 (143)
Q Consensus 99 l~~~sGL~~~iLk~--GsG~~Pk~GDtV~VhYtG~L~d~~GkvFDSS 143 (143)
.++++|++|.++++ |+|..|+.||.|.+||+|++.| |++||++
T Consensus 65 ~~t~sGl~Y~v~~~~~g~g~~p~~gd~V~v~Y~~~~~d--G~v~~ss 109 (177)
T TIGR03516 65 ETSQNGFWYYYNQKDTGEGTTPEFGDLVTFEYDIRALD--GDVIYSE 109 (177)
T ss_pred eECCCccEEEEEEecCCCCCcCCCCCEEEEEEEEEeCC--CCEEEeC
Confidence 46789999998876 7778999999999999999988 9999985
No 7
>KOG0549 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=97.96 E-value=1.3e-05 Score=65.09 Aligned_cols=40 Identities=28% Similarity=0.415 Sum_probs=33.5
Q ss_pred CCCcEEEEeEc--CCCCCCCCCCEEEEEEEEEEcCCCCCcccCC
Q 032320 102 SGGVKALDLRL--GRGPVPVDGDQVAIHYYGRLAAKQGWRFDST 143 (143)
Q Consensus 102 ~sGL~~~iLk~--GsG~~Pk~GDtV~VhYtG~L~d~~GkvFDSS 143 (143)
.++|++.+++. .+..+.+.||+|.+||+|.|.| |++||||
T Consensus 67 ~~~l~I~v~~~p~~C~~kak~GD~l~~HY~g~leD--Gt~fdSS 108 (188)
T KOG0549|consen 67 DEELQIGVLKKPEECPEKAKKGDTLHVHYTGSLED--GTKFDSS 108 (188)
T ss_pred CCceeEEEEECCccccccccCCCEEEEEEEEEecC--CCEEeee
Confidence 35667766663 3778999999999999999998 9999997
No 8
>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=95.94 E-value=0.014 Score=52.36 Aligned_cols=39 Identities=36% Similarity=0.617 Sum_probs=34.5
Q ss_pred CCCcEEEEeEcCCC--CCCCCCCEEEEEEEEEEcCCCCCcccCC
Q 032320 102 SGGVKALDLRLGRG--PVPVDGDQVAIHYYGRLAAKQGWRFDST 143 (143)
Q Consensus 102 ~sGL~~~iLk~GsG--~~Pk~GDtV~VhYtG~L~d~~GkvFDSS 143 (143)
+.+|..+++++|.| ..|.+|..|.|||.|++.| + +||++
T Consensus 83 Dg~iiKriir~G~gd~~~P~~g~~V~v~~~G~~~~--~-~f~~~ 123 (397)
T KOG0543|consen 83 DGGIIKRIIREGEGDYSRPNKGAVVKVHLEGELED--G-VFDQR 123 (397)
T ss_pred CCceEEeeeecCCCCCCCCCCCcEEEEEEEEEECC--c-ceecc
Confidence 67899999999999 6899999999999999976 5 78763
No 9
>TIGR00115 tig trigger factor. Trigger factor is a ribosome-associated molecular chaperone and is the first chaperone to interact with nascent polypeptide. Trigger factor can bind at the same time as the signal recognition particle (SRP), but is excluded by the SRP receptor (FtsY). The central domain of trigger factor has peptidyl-prolyl cis/trans isomerase activity. This protein is found in a single copy in virtually every bacterial genome.
Probab=76.57 E-value=3 Score=36.16 Aligned_cols=24 Identities=29% Similarity=0.548 Sum_probs=20.1
Q ss_pred CCCCCCCEEEEEEEEEEcCCCCCcccC
Q 032320 116 PVPVDGDQVAIHYYGRLAAKQGWRFDS 142 (143)
Q Consensus 116 ~~Pk~GDtV~VhYtG~L~d~~GkvFDS 142 (143)
..++.||.|.+||+|+. + |+.|++
T Consensus 145 ~~~~~gD~V~v~~~~~~-d--g~~~~~ 168 (408)
T TIGR00115 145 RAAEKGDRVTIDFEGFI-D--GEAFEG 168 (408)
T ss_pred cccCCCCEEEEEEEEEE-C--CEECcC
Confidence 45789999999999987 5 777775
No 10
>PRK01490 tig trigger factor; Provisional
Probab=74.77 E-value=3.6 Score=36.07 Aligned_cols=24 Identities=29% Similarity=0.623 Sum_probs=20.1
Q ss_pred CCCCCCCEEEEEEEEEEcCCCCCcccC
Q 032320 116 PVPVDGDQVAIHYYGRLAAKQGWRFDS 142 (143)
Q Consensus 116 ~~Pk~GDtV~VhYtG~L~d~~GkvFDS 142 (143)
..++.||.|.+||+|.+ + |+.|+.
T Consensus 156 ~~~~~gD~V~vd~~~~~-~--g~~~~~ 179 (435)
T PRK01490 156 RPAENGDRVTIDFVGSI-D--GEEFEG 179 (435)
T ss_pred ccCCCCCEEEEEEEEEE-C--CEECcC
Confidence 35799999999999998 5 777764
No 11
>KOG0545 consensus Aryl-hydrocarbon receptor-interacting protein [Posttranslational modification, protein turnover, chaperones]
Probab=64.34 E-value=5.5 Score=34.88 Aligned_cols=42 Identities=26% Similarity=0.346 Sum_probs=33.3
Q ss_pred CCCcEEEEeEcCCCCC--CCCCCEEEEEEEEEEcCCCCCcccCC
Q 032320 102 SGGVKALDLRLGRGPV--PVDGDQVAIHYYGRLAAKQGWRFDST 143 (143)
Q Consensus 102 ~sGL~~~iLk~GsG~~--Pk~GDtV~VhYtG~L~d~~GkvFDSS 143 (143)
..|++..++..|.|+. -..|..|..||.-...+..+++.|.|
T Consensus 9 ~~gv~Kril~~G~g~l~e~~dGTrv~FHfrtl~~~e~~tviDDs 52 (329)
T KOG0545|consen 9 VEGVKKRILHGGTGELPEFIDGTRVIFHFRTLKCDEERTVIDDS 52 (329)
T ss_pred chhhhHhhccCCCccCccccCCceEEEEEEecccCcccccccch
Confidence 4689999999999974 58999999999987655336666654
No 12
>PF10518 TAT_signal: TAT (twin-arginine translocation) pathway signal sequence; InterPro: IPR019546 The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []. Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state []. It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases []. In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength []. The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].
Probab=52.48 E-value=16 Score=20.56 Aligned_cols=15 Identities=20% Similarity=0.255 Sum_probs=10.7
Q ss_pred hhHHHHHHHhhhhHH
Q 032320 61 TRREALTVSIVTTTL 75 (143)
Q Consensus 61 ~RR~~l~~s~~~~~l 75 (143)
+||++|-.++.++..
T Consensus 3 sRR~fLk~~~a~~a~ 17 (26)
T PF10518_consen 3 SRRQFLKGGAAAAAA 17 (26)
T ss_pred cHHHHHHHHHHHHHH
Confidence 899999776665333
No 13
>COG0544 Tig FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones]
Probab=45.98 E-value=23 Score=32.13 Aligned_cols=22 Identities=32% Similarity=0.681 Sum_probs=18.3
Q ss_pred CCCCCEEEEEEEEEEcCCCCCcccC
Q 032320 118 PVDGDQVAIHYYGRLAAKQGWRFDS 142 (143)
Q Consensus 118 Pk~GDtV~VhYtG~L~d~~GkvFDS 142 (143)
++.||.|+++|.|+. | |+.|..
T Consensus 158 a~~gD~v~IDf~g~i-D--g~~feg 179 (441)
T COG0544 158 AENGDRVTIDFEGSV-D--GEEFEG 179 (441)
T ss_pred cccCCEEEEEEEEEE-c--CeeccC
Confidence 899999999999977 5 666653
No 14
>TIGR03096 nitroso_cyanin nitrosocyanin. Nitrosocyanin, as described from the obligate chemolithoautotroph Nitrosomonas europaea, is a red copper protein of unknown function with sequence similarity to a number of blue copper redox proteins.
Probab=43.40 E-value=36 Score=26.41 Aligned_cols=28 Identities=21% Similarity=0.158 Sum_probs=23.0
Q ss_pred CCCcEEEEeEcCCCC------CCCCCCEEEEEEE
Q 032320 102 SGGVKALDLRLGRGP------VPVDGDQVAIHYY 129 (143)
Q Consensus 102 ~sGL~~~iLk~GsG~------~Pk~GDtV~VhYt 129 (143)
..|+.+..++.|++- .+++||.|+++++
T Consensus 43 ~~~~~~~~i~a~n~~~~P~~I~VkaGD~Vtl~vt 76 (135)
T TIGR03096 43 VEGVTVKNIRAFNVLNEPEALVVKKGTPVKVTVE 76 (135)
T ss_pred eCCEEEEEEEeeeeEEcCCEEEECCCCEEEEEEE
Confidence 568888899888762 4799999999886
No 15
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=24.60 E-value=72 Score=25.35 Aligned_cols=13 Identities=23% Similarity=0.434 Sum_probs=10.9
Q ss_pred CEEEEEEEEEEcC
Q 032320 122 DQVAIHYYGRLAA 134 (143)
Q Consensus 122 DtV~VhYtG~L~d 134 (143)
..|.|+|+|-+.|
T Consensus 83 ~~v~V~Y~GilPD 95 (155)
T PRK13159 83 AATQVEYTGILPD 95 (155)
T ss_pred cEEEEEEccCCCc
Confidence 4899999998865
No 16
>TIGR02811 formate_TAT formate dehydrogenase region TAT target. Members of this uncharacterized protein family are all small, extending 70 or fewer residues from their respective likely start codons. All have the twin-arginine-dependent tranport (TAT) signal sequence at the N-terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal sequence suggests a bound cofactor. All members are encoded near genes for subunits of formate dehydrogenase, and may themselves be a subunit or accessory protein.
Probab=23.39 E-value=1.1e+02 Score=20.89 Aligned_cols=8 Identities=38% Similarity=0.551 Sum_probs=6.2
Q ss_pred hhHHHHHH
Q 032320 61 TRREALTV 68 (143)
Q Consensus 61 ~RR~~l~~ 68 (143)
+||++|..
T Consensus 10 sRR~Flk~ 17 (66)
T TIGR02811 10 SRRDLLKG 17 (66)
T ss_pred cHHHHHHH
Confidence 79999843
No 17
>PF05984 Cytomega_UL20A: Cytomegalovirus UL20A protein; InterPro: IPR009245 This family consists of several Cytomegalovirus UL20A proteins. UL20A is thought to be a glycoprotein [].
Probab=20.03 E-value=84 Score=23.25 Aligned_cols=18 Identities=28% Similarity=0.516 Sum_probs=12.4
Q ss_pred hhHHHHHHHhhhhHHHHHH
Q 032320 61 TRREALTVSIVTTTLEILI 79 (143)
Q Consensus 61 ~RR~~l~~s~~~~~l~~~~ 79 (143)
.|| ++.+|+++-.|.++|
T Consensus 2 aRR-lwiLslLAVtLtVAL 19 (100)
T PF05984_consen 2 ARR-LWILSLLAVTLTVAL 19 (100)
T ss_pred chh-hHHHHHHHHHHHHHh
Confidence 577 777777776666655
Done!