Query 029179
Match_columns 197
No_of_seqs 31 out of 33
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 08:46:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029179.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029179hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01134 GIDA: Glucose inhibit 79.5 5.4 0.00012 37.5 6.3 64 75-172 282-347 (392)
2 PRK05192 tRNA uridine 5-carbox 77.6 2.2 4.7E-05 42.3 3.2 72 65-170 271-349 (618)
3 TIGR00137 gid_trmFO tRNA:m(5)U 73.5 6.1 0.00013 37.5 4.9 60 75-168 255-316 (433)
4 PRK05335 tRNA (uracil-5-)-meth 72.8 4.2 9.1E-05 38.8 3.7 58 76-167 257-316 (436)
5 TIGR00136 gidA glucose-inhibit 65.6 8.9 0.00019 38.2 4.4 72 64-169 268-346 (617)
6 PF07447 VP40: Matrix protein 46.3 9.4 0.0002 35.0 1.0 34 84-117 88-128 (295)
7 PRK13781 paaB phenylacetate-Co 35.7 84 0.0018 24.9 4.6 40 74-113 4-43 (95)
8 PF06243 PaaB: Phenylacetic ac 34.3 83 0.0018 24.4 4.4 38 76-113 3-40 (94)
9 COG1169 MenF Isochorismate syn 31.9 49 0.0011 31.8 3.3 49 70-150 364-417 (423)
10 TIGR02157 PA_CoA_Oxy2 phenylac 31.7 81 0.0018 24.7 3.9 38 77-114 2-39 (90)
11 COG0445 GidA Flavin-dependent 26.9 1.2E+02 0.0026 30.9 5.1 72 65-170 271-349 (621)
12 PF07005 DUF1537: Protein of u 22.9 49 0.0011 27.1 1.4 16 96-111 200-215 (223)
13 KOG2292 Oligosaccharyltransfer 22.9 33 0.00071 35.0 0.5 13 89-101 78-90 (751)
14 PRK11436 biofilm-dependent mod 22.3 52 0.0011 24.7 1.3 19 106-124 43-61 (71)
15 PF07024 ImpE: ImpE protein; 20.7 69 0.0015 25.9 1.8 22 76-99 16-37 (123)
No 1
>PF01134 GIDA: Glucose inhibited division protein A; InterPro: IPR002218 GidA is a tRNA modification enzyme found in bacteria and mitochondria. Though its precise molecular function of these proteins is not known, it is involved in the 5-carboxymethylaminomethyl modification of the wobble uridine base in some tRNAs [, ]. Sequence variations in the human mitochondrial protein may influence the severity of aminoglycoside-induced deafness []. This entry is found in GidA and related proteins, such as the methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase enzyme TrmFO.; GO: 0050660 flavin adenine dinucleotide binding, 0008033 tRNA processing; PDB: 3CES_C 3CP2_A 3G05_A 2CUL_A 3CP8_A 2ZXI_B 2ZXH_A 3G5S_A 3G5R_A 3G5Q_A.
Probab=79.46 E-value=5.4 Score=37.47 Aligned_cols=64 Identities=22% Similarity=0.321 Sum_probs=48.3
Q ss_pred CCCeEEEEEEecCc--cceeeeeeeecchhHHHHHHhhhcchhhhhhhhHHHHHHHHHHhhCHHHHHHHHHhhccccccc
Q 029179 75 GNPRFVIFIRMANV--YLWYPLSIITGGTTAKIMVAAKDNFLGKYIYKDTLARNLAAVIYRDEKEIQKTAFKQFRVLQSA 152 (197)
Q Consensus 75 GnP~FvIFVR~k~~--~~WYPl~vV~Ggt~Ak~lV~a~dn~lgk~iyk~tL~~nIa~aIYkDe~~L~k~a~r~yP~Lk~a 152 (197)
..|.=+||+|--+. +.|||.|+=|.=. .++|+.++|..|=|.++
T Consensus 282 ~~~~h~v~Lepe~~~~~~~y~~G~stslp----------------------------------~~~Q~~~~r~IpGLe~a 327 (392)
T PF01134_consen 282 DRPYHQVFLEPEGLNTNEYYPNGFSTSLP----------------------------------WDVQKRIFRSIPGLENA 327 (392)
T ss_dssp STSSEEEEEEESSTTS-EEEEETS-CSS-----------------------------------HHHHHHHHTTSTTTTT-
T ss_pred CCCCEEEEEEecCCCCceEEecCCcCCCC----------------------------------HHHHHHHhhcCCChhcC
Confidence 37889999999754 4899999877653 77899999999999999
Q ss_pred cceeeeEEEeeeeccccccc
Q 029179 153 TEFRYGYKLVVMLLYLLSIL 172 (197)
Q Consensus 153 kefEYGYKl~dk~lnp~s~~ 172 (197)
+=++|||.+.+.-++|..-+
T Consensus 328 ~~~r~Gy~~ey~~v~~~~l~ 347 (392)
T PF01134_consen 328 EILRPGYAHEYDFVDPPQLL 347 (392)
T ss_dssp -EEE--EEEEEEEE-GGGBB
T ss_pred hhhheEEeeeeeEEehhhcc
Confidence 99999999999998887543
No 2
>PRK05192 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated
Probab=77.61 E-value=2.2 Score=42.31 Aligned_cols=72 Identities=25% Similarity=0.327 Sum_probs=59.0
Q ss_pred CCCCCCCCCC-----CCCeEEEEEEecCcc--ceeeeeeeecchhHHHHHHhhhcchhhhhhhhHHHHHHHHHHhhCHHH
Q 029179 65 PPSLPKIEDD-----GNPRFVIFIRMANVY--LWYPLSIITGGTTAKIMVAAKDNFLGKYIYKDTLARNLAAVIYRDEKE 137 (197)
Q Consensus 65 ~p~~Pki~dD-----GnP~FvIFVR~k~~~--~WYPl~vV~Ggt~Ak~lV~a~dn~lgk~iyk~tL~~nIa~aIYkDe~~ 137 (197)
|-+-|.|||+ +-+.-+||+|--|.. .|||.|+=|.=. .+
T Consensus 271 pRYCpsiE~k~~rf~~~~~h~v~lepeg~~~~~~y~~G~stslp----------------------------------~~ 316 (618)
T PRK05192 271 PRYCPSIEDKIVRFADKDRHQIFLEPEGLDTNEVYPNGISTSLP----------------------------------ED 316 (618)
T ss_pred CCCCCCHHHHhhhcCCCCCceEEEecCCCCCCEEeccCccCCCC----------------------------------HH
Confidence 4467777743 123349999988655 999999887654 78
Q ss_pred HHHHHHhhccccccccceeeeEEEeeeeccccc
Q 029179 138 IQKTAFKQFRVLQSATEFRYGYKLVVMLLYLLS 170 (197)
Q Consensus 138 L~k~a~r~yP~Lk~akefEYGYKl~dk~lnp~s 170 (197)
+|+.++|..|=|.+++=++|||.+.+.-+||+.
T Consensus 317 ~Q~~~~r~ipGle~a~i~r~gy~ieyd~i~p~~ 349 (618)
T PRK05192 317 VQLEMLRSIPGLENAEILRPGYAIEYDYVDPRQ 349 (618)
T ss_pred HHHHHHhcCcCccceeEeecccceeecccChhh
Confidence 899999999999999999999999999988887
No 3
>TIGR00137 gid_trmFO tRNA:m(5)U-54 methyltransferase. This model represents an orthologous set of proteins present in relatively few bacteria but very tightly conserved where it occurs. It is closely related to gidA (glucose-inhibited division protein A), which appears to be present in all complete eubacterial genomes so far and in Saccharomyces cerevisiae. It was designated gid but is now recognized as a tRNA:m(5)U-54 methyltransferase and is now designated trmFO.
Probab=73.48 E-value=6.1 Score=37.50 Aligned_cols=60 Identities=22% Similarity=0.212 Sum_probs=52.6
Q ss_pred CCCeEEEEEEecCcc--ceeeeeeeecchhHHHHHHhhhcchhhhhhhhHHHHHHHHHHhhCHHHHHHHHHhhccccccc
Q 029179 75 GNPRFVIFIRMANVY--LWYPLSIITGGTTAKIMVAAKDNFLGKYIYKDTLARNLAAVIYRDEKEIQKTAFKQFRVLQSA 152 (197)
Q Consensus 75 GnP~FvIFVR~k~~~--~WYPl~vV~Ggt~Ak~lV~a~dn~lgk~iyk~tL~~nIa~aIYkDe~~L~k~a~r~yP~Lk~a 152 (197)
+.|.=|||+|--|.. .|||.|.=|.=. .+.|+.++|..|=|.++
T Consensus 255 ~~~~~~v~l~~e~~~~~~~~~~G~~t~l~----------------------------------~~~Q~~~~r~ipgle~a 300 (433)
T TIGR00137 255 KKPYAVVQLRQEDKAGTLWNMVGFQTNLR----------------------------------WGEQKRVFRLIPGLENA 300 (433)
T ss_pred CCCceEEEEeccccCCCEEecccccCCCC----------------------------------HHHHHHHHhcCcCccce
Confidence 478899999998665 999999877653 67788899999999999
Q ss_pred cceeeeEEEeeeeccc
Q 029179 153 TEFRYGYKLVVMLLYL 168 (197)
Q Consensus 153 kefEYGYKl~dk~lnp 168 (197)
+=++|||.+++.=+||
T Consensus 301 ~~~r~g~~~~~~~i~~ 316 (433)
T TIGR00137 301 EFVRMGVMHRNTFINS 316 (433)
T ss_pred EEeecceEEeeeeeCC
Confidence 9999999999988885
No 4
>PRK05335 tRNA (uracil-5-)-methyltransferase Gid; Reviewed
Probab=72.76 E-value=4.2 Score=38.81 Aligned_cols=58 Identities=24% Similarity=0.236 Sum_probs=49.0
Q ss_pred CCeEEEEEEecCcc--ceeeeeeeecchhHHHHHHhhhcchhhhhhhhHHHHHHHHHHhhCHHHHHHHHHhhcccccccc
Q 029179 76 NPRFVIFIRMANVY--LWYPLSIITGGTTAKIMVAAKDNFLGKYIYKDTLARNLAAVIYRDEKEIQKTAFKQFRVLQSAT 153 (197)
Q Consensus 76 nP~FvIFVR~k~~~--~WYPl~vV~Ggt~Ak~lV~a~dn~lgk~iyk~tL~~nIa~aIYkDe~~L~k~a~r~yP~Lk~ak 153 (197)
.|-=|||+|--|.. .||++|.=|.=. .+.|+.++|..|-|.++.
T Consensus 257 ~~~a~v~L~~e~~~~~~~~~~Gfqt~l~----------------------------------~~~Q~~~~r~Ipgle~a~ 302 (436)
T PRK05335 257 RPYAVVQLRQDNAAGTLYNIVGFQTKLK----------------------------------WGEQKRVFRMIPGLENAE 302 (436)
T ss_pred CcceEEEEecCCCCCCeEecccccCCCC----------------------------------HHHHHHHHhcccchhceE
Confidence 55559999988655 999999877653 677889999999999999
Q ss_pred ceeeeEEEeeeecc
Q 029179 154 EFRYGYKLVVMLLY 167 (197)
Q Consensus 154 efEYGYKl~dk~ln 167 (197)
=.+|||.+++.=+|
T Consensus 303 ~~r~G~~~~~~~i~ 316 (436)
T PRK05335 303 FVRYGVMHRNTFIN 316 (436)
T ss_pred EEeceEEeeccccC
Confidence 99999999887765
No 5
>TIGR00136 gidA glucose-inhibited division protein A. GidA, the longer of two forms of GidA-related proteins, appears to be present in all complete eubacterial genomes so far, as well as Saccharomyces cerevisiae. A subset of these organisms have a closely related protein. GidA is absent in the Archaea. It appears to act with MnmE, in an alpha2/beta2 heterotetramer, in the 5-carboxymethylaminomethyl modification of uridine 34 in certain tRNAs. The shorter, related protein, previously called gid or gidA(S), is now called TrmFO (see model TIGR00137).
Probab=65.58 E-value=8.9 Score=38.18 Aligned_cols=72 Identities=24% Similarity=0.327 Sum_probs=57.8
Q ss_pred CCCCCCCCCCC----CCC-eEEEEEEecCc--cceeeeeeeecchhHHHHHHhhhcchhhhhhhhHHHHHHHHHHhhCHH
Q 029179 64 PPPSLPKIEDD----GNP-RFVIFIRMANV--YLWYPLSIITGGTTAKIMVAAKDNFLGKYIYKDTLARNLAAVIYRDEK 136 (197)
Q Consensus 64 ~~p~~Pki~dD----GnP-~FvIFVR~k~~--~~WYPl~vV~Ggt~Ak~lV~a~dn~lgk~iyk~tL~~nIa~aIYkDe~ 136 (197)
.|-|-|.||++ +.+ .-+||+|--+. ..|||.|+=|.=- .
T Consensus 268 GpRYCpsIe~k~~~f~~~~~h~v~lepe~~~~~~~~~~G~st~lp----------------------------------~ 313 (617)
T TIGR00136 268 GPRYCPSIEDKVVRFADKERHQIFLEPEGLNSDEIYPNGLSTSLP----------------------------------E 313 (617)
T ss_pred CCCCCCCHHHHHhhcCCCCCceEEEeecCCCCCeEEecCeecCCC----------------------------------H
Confidence 45678988865 334 46999998654 4799988876543 6
Q ss_pred HHHHHHHhhccccccccceeeeEEEeeeecccc
Q 029179 137 EIQKTAFKQFRVLQSATEFRYGYKLVVMLLYLL 169 (197)
Q Consensus 137 ~L~k~a~r~yP~Lk~akefEYGYKl~dk~lnp~ 169 (197)
++++.+++..|-|.++.-+.|||-+.++-++|+
T Consensus 314 ~~q~~i~~~ipGle~a~~~r~gy~~e~~~i~p~ 346 (617)
T TIGR00136 314 DVQLQIVRSIPGLENAEILRPGYAIEYDFFDPR 346 (617)
T ss_pred HHHHHHHHcCcCcccceEeccccceEEeEEChh
Confidence 677888889999999999999999999998886
No 6
>PF07447 VP40: Matrix protein VP40; InterPro: IPR008986 Ebola virus sp. are non-segmented, negative-strand RNA viruses that causes severe haemorrhagic fever in humans with high rates of mortality. The virus matrix protein VP40 is a major structural protein that plays a central role in virus assembly and budding at the plasma membrane of infected cells. VP40 proteins associate with cellular membranes, interact with the cytoplasmic tails of glycoproteins, and bind to the ribonucleoprotein complex. The VP40 monomer consists of two domains, the N-terminal oligomerization domain and the C-terminal membrane-binding domain, connected by a flexible linker. Both the N- and C-terminal domains fold into beta sandwich structures of similar topology []. Within the N-terminal domain are two overlapping L-domains with the sequences PTAP and PPEY at residues 7 to13, which are required for efficient budding []. L-domains are thought to mediate their function in budding through their interaction with specific host cellular proteins, such as tsg101 and vps-4 []. ; PDB: 1H2D_B 1H2C_A 1ES6_A.
Probab=46.26 E-value=9.4 Score=35.04 Aligned_cols=34 Identities=35% Similarity=0.556 Sum_probs=24.5
Q ss_pred EecCccceeeeeeeecc------hhHHHHHHhh-hcchhhh
Q 029179 84 RMANVYLWYPLSIITGG------TTAKIMVAAK-DNFLGKY 117 (197)
Q Consensus 84 R~k~~~~WYPl~vV~Gg------t~Ak~lV~a~-dn~lgk~ 117 (197)
=+|+++.|.||||..-. |+|.+|.++. ..-|||-
T Consensus 88 lmK~iP~WLPLGva~q~~YsfdsT~aAim~aSYTIThFg~~ 128 (295)
T PF07447_consen 88 LMKQIPIWLPLGVADQKTYSFDSTTAAIMLASYTITHFGKT 128 (295)
T ss_dssp EEEEEEEEEEEEEEETTTS-HHHHHHHHHCS-EEEEEES-T
T ss_pred hhhcCceeeeccccccceecchhHHHHHhhhceeeeeeccC
Confidence 35688999999998765 6788888874 6666653
No 7
>PRK13781 paaB phenylacetate-CoA oxygenase subunit PaaB; Provisional
Probab=35.66 E-value=84 Score=24.87 Aligned_cols=40 Identities=13% Similarity=0.219 Sum_probs=29.0
Q ss_pred CCCCeEEEEEEecCccceeeeeeeecchhHHHHHHhhhcc
Q 029179 74 DGNPRFVIFIRMANVYLWYPLSIITGGTTAKIMVAAKDNF 113 (197)
Q Consensus 74 DGnP~FvIFVR~k~~~~WYPl~vV~Ggt~Ak~lV~a~dn~ 113 (197)
+.-|.|+||||.+..--=-=+|.|--.+..-+|..|-|.+
T Consensus 4 ~~w~~wEVFvr~~~g~~h~HvGSvhApd~e~Al~~Ar~~y 43 (95)
T PRK13781 4 KEWPLWEVFVRSKQGLSHKHVGSLHAADAEMALRNARDVY 43 (95)
T ss_pred CcCceEEEEEecCCCCCcceEeeeeCCCHHHHHHHHHHHh
Confidence 3469999999999776666688888776555555555444
No 8
>PF06243 PaaB: Phenylacetic acid degradation B; InterPro: IPR009359 Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation [, ]. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA [].; PDB: 3EGR_A.
Probab=34.28 E-value=83 Score=24.44 Aligned_cols=38 Identities=16% Similarity=0.223 Sum_probs=23.6
Q ss_pred CCeEEEEEEecCccceeeeeeeecchhHHHHHHhhhcc
Q 029179 76 NPRFVIFIRMANVYLWYPLSIITGGTTAKIMVAAKDNF 113 (197)
Q Consensus 76 nP~FvIFVR~k~~~~WYPl~vV~Ggt~Ak~lV~a~dn~ 113 (197)
-|.|+||+|.+..-.=-=+|.|--.+..-+|..|-+.+
T Consensus 3 ~~~~EVF~r~~~g~~~~HvGsV~A~d~e~Al~~Ar~~f 40 (94)
T PF06243_consen 3 WPLWEVFVRSKPGLPHQHVGSVHAPDPEMALQQARDVF 40 (94)
T ss_dssp --EEEEEEE-TT-SS-EEEEEEE-SSHHHHHHHHHHHC
T ss_pred CceEEEEEECCCCCCceEEeeeeCCCHHHHHHHHHHHh
Confidence 47899999999666556788888776655555555443
No 9
>COG1169 MenF Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=31.89 E-value=49 Score=31.83 Aligned_cols=49 Identities=33% Similarity=0.480 Sum_probs=38.8
Q ss_pred CCCCCCCCeEEEEEEec-----CccceeeeeeeecchhHHHHHHhhhcchhhhhhhhHHHHHHHHHHhhCHHHHHHHHHh
Q 029179 70 KIEDDGNPRFVIFIRMA-----NVYLWYPLSIITGGTTAKIMVAAKDNFLGKYIYKDTLARNLAAVIYRDEKEIQKTAFK 144 (197)
Q Consensus 70 ki~dDGnP~FvIFVR~k-----~~~~WYPl~vV~Ggt~Ak~lV~a~dn~lgk~iyk~tL~~nIa~aIYkDe~~L~k~a~r 144 (197)
=+|..||-+|++=||++ .+.+|==+|||.|-+ -++|.+|+=.|
T Consensus 364 w~D~~GngEf~VaIRsA~i~~~~~rlfAGaGIV~~Sd--------------------------------P~~E~~Et~~K 411 (423)
T COG1169 364 WCDSEGNGEFVVAIRSALISGNQVRLFAGAGIVAGSD--------------------------------PEEEWRETDLK 411 (423)
T ss_pred eeccCCCeEEEEEEEEEEEeCCEEEEEccCcccCCCC--------------------------------hHHHHHHHHHH
Confidence 36788999999999998 455888899999876 56777777777
Q ss_pred hccccc
Q 029179 145 QFRVLQ 150 (197)
Q Consensus 145 ~yP~Lk 150 (197)
.-++|+
T Consensus 412 l~tml~ 417 (423)
T COG1169 412 LATMLR 417 (423)
T ss_pred HHHHHH
Confidence 766665
No 10
>TIGR02157 PA_CoA_Oxy2 phenylacetate-CoA oxygenase, PaaH subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=31.66 E-value=81 Score=24.70 Aligned_cols=38 Identities=16% Similarity=0.308 Sum_probs=27.8
Q ss_pred CeEEEEEEecCccceeeeeeeecchhHHHHHHhhhcch
Q 029179 77 PRFVIFIRMANVYLWYPLSIITGGTTAKIMVAAKDNFL 114 (197)
Q Consensus 77 P~FvIFVR~k~~~~WYPl~vV~Ggt~Ak~lV~a~dn~l 114 (197)
|.|+||||.+..-.=-=+|.|--.+.--+|..|-|.+.
T Consensus 2 p~wEVFvr~~~g~~h~HvGSvhA~d~e~Al~~Ard~y~ 39 (90)
T TIGR02157 2 PLYEVFVRGKSGLPHQHVGSLHAPDEEMALMMARDNYT 39 (90)
T ss_pred CceEEEEecCCCCCcceEeeeeCCCHHHHHHHHHHHhc
Confidence 78999999997766666788887766666666655443
No 11
>COG0445 GidA Flavin-dependent tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA [Cell cycle control, cell division, chromosome partitioning]
Probab=26.92 E-value=1.2e+02 Score=30.92 Aligned_cols=72 Identities=24% Similarity=0.333 Sum_probs=60.2
Q ss_pred CCCCCCCCCC-----CCCeEEEEEEecCc--cceeeeeeeecchhHHHHHHhhhcchhhhhhhhHHHHHHHHHHhhCHHH
Q 029179 65 PPSLPKIEDD-----GNPRFVIFIRMANV--YLWYPLSIITGGTTAKIMVAAKDNFLGKYIYKDTLARNLAAVIYRDEKE 137 (197)
Q Consensus 65 ~p~~Pki~dD-----GnP~FvIFVR~k~~--~~WYPl~vV~Ggt~Ak~lV~a~dn~lgk~iyk~tL~~nIa~aIYkDe~~ 137 (197)
|-|-|-|||. +-++-.||+---+. +-|||=|+=|.=- ++
T Consensus 271 PRYCPSIEDKIvrF~dK~~HqIFlEPEGl~~~evY~nGlSTSlP----------------------------------~d 316 (621)
T COG0445 271 PRYCPSIEDKIVRFADKERHQIFLEPEGLDTDEVYPNGLSTSLP----------------------------------ED 316 (621)
T ss_pred CCCCCCHHHhhccCCCCccceEEecCCCCCCceEecCcccccCC----------------------------------HH
Confidence 4577888853 36788999987754 4899988877654 88
Q ss_pred HHHHHHhhccccccccceeeeEEEeeeeccccc
Q 029179 138 IQKTAFKQFRVLQSATEFRYGYKLVVMLLYLLS 170 (197)
Q Consensus 138 L~k~a~r~yP~Lk~akefEYGYKl~dk~lnp~s 170 (197)
+|..+.|..|=|-++.=+++||-|-|.-++|+.
T Consensus 317 VQ~~~irsipGlEna~i~rpgYAIEYD~v~p~q 349 (621)
T COG0445 317 VQEQIIRSIPGLENAEILRPGYAIEYDYVDPRQ 349 (621)
T ss_pred HHHHHHHhCcccccceeeccceeeeecccChhh
Confidence 999999999999999999999999999977776
No 12
>PF07005 DUF1537: Protein of unknown function, DUF1537; InterPro: IPR010737 This entry represents a conserved region found in a range of Proteobacteria as well as the Gram-positive Oceanobacillus iheyensis. This entry includes YgbK from Escherichia coli, which is dependent upon FlhDC, the master regulator of the flagellar genes. The ygbK gene appears to be regulated by sigmaF [].; PDB: 3DQQ_B 1YZY_B.
Probab=22.90 E-value=49 Score=27.13 Aligned_cols=16 Identities=44% Similarity=0.628 Sum_probs=12.7
Q ss_pred eeecchhHHHHHHhhh
Q 029179 96 IITGGTTAKIMVAAKD 111 (197)
Q Consensus 96 vV~Ggt~Ak~lV~a~d 111 (197)
++|||+||..+++++.
T Consensus 200 i~tGGDTa~av~~~Lg 215 (223)
T PF07005_consen 200 ILTGGDTASAVLKALG 215 (223)
T ss_dssp EEESHHHHHHHHHHCT
T ss_pred EEeCChHHHHHHHHhC
Confidence 4679999999888763
No 13
>KOG2292 consensus Oligosaccharyltransferase, STT3 subunit [Posttranslational modification, protein turnover, chaperones]
Probab=22.86 E-value=33 Score=35.04 Aligned_cols=13 Identities=62% Similarity=1.221 Sum_probs=11.8
Q ss_pred cceeeeeeeecch
Q 029179 89 YLWYPLSIITGGT 101 (197)
Q Consensus 89 ~~WYPl~vV~Ggt 101 (197)
-.|||||=|.|||
T Consensus 78 RaWYPLGRiiGGT 90 (751)
T KOG2292|consen 78 RAWYPLGRIIGGT 90 (751)
T ss_pred ccccccceeeccc
Confidence 4799999999997
No 14
>PRK11436 biofilm-dependent modulation protein; Provisional
Probab=22.29 E-value=52 Score=24.66 Aligned_cols=19 Identities=37% Similarity=0.419 Sum_probs=15.9
Q ss_pred HHHhhhcchhhhhhhhHHH
Q 029179 106 MVAAKDNFLGKYIYKDTLA 124 (197)
Q Consensus 106 lV~a~dn~lgk~iyk~tL~ 124 (197)
-|.|.||+...+||+.|+.
T Consensus 43 wvea~dndilsdiyqqtin 61 (71)
T PRK11436 43 WVEASDNDILSDIYQQTIN 61 (71)
T ss_pred HHHhccccHHHHHHHHHHH
Confidence 3778999999999988864
No 15
>PF07024 ImpE: ImpE protein; InterPro: IPR009211 This entry contains proteins of unknown function that occur in bacteria that interact with and manipulate eukaryotic cells []. Salmonella enterica protein SciE is encoded in the centisome 7 genomic island (SCI) []. Deletion of the entire island affects the ability of bacteria to enter eukaryotic cells []. Therefore, SciE and other SCI proteins may be involved in virulence. Interestingly, another member of this family, Rhizobium leguminosarum protein ImpE, has been reported to be encoded by an avirulence locus involved in temperature-dependent protein secretion []. It is believed that the imp locus is involved in the secretion to the environment of proteins, including periplasmic RbsB protein, that cause blocking of R. leguminosarum infection in plants [].; PDB: 1ZBP_A.
Probab=20.74 E-value=69 Score=25.95 Aligned_cols=22 Identities=27% Similarity=0.652 Sum_probs=17.9
Q ss_pred CCeEEEEEEecCccceeeeeeeec
Q 029179 76 NPRFVIFIRMANVYLWYPLSIITG 99 (197)
Q Consensus 76 nP~FvIFVR~k~~~~WYPl~vV~G 99 (197)
.|.+++| +.|.|.|.|.+-|..
T Consensus 16 GpvlE~~--~~G~Y~WvPf~~I~~ 37 (123)
T PF07024_consen 16 GPVLEVI--TNGRYYWVPFSRIAS 37 (123)
T ss_dssp TTEEEEE--TTS-EEEEEGGGEEE
T ss_pred ceeEEEE--ECCEEEEEEHHHccc
Confidence 6888998 999999999987763
Done!