Query 023836
Match_columns 276
No_of_seqs 186 out of 1287
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 07:00:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023836.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023836hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR03035 trp_arylform arylfor 100.0 3.9E-57 8.5E-62 397.6 21.1 203 61-276 1-205 (206)
2 COG1878 Kynurenine formamidase 100.0 1.4E-55 3E-60 388.9 20.1 209 58-276 2-216 (218)
3 PF04199 Cyclase: Putative cyc 100.0 1.3E-39 2.8E-44 277.6 9.4 152 62-221 1-170 (171)
4 cd05560 Xcc1710_like Xcc1710_l 73.6 7.9 0.00017 30.6 5.0 54 149-216 35-88 (109)
5 cd00248 Mth938-like Mth938-lik 62.2 16 0.00034 28.8 4.5 54 151-217 36-89 (109)
6 cd05125 Mth938_2P1-like Mth938 56.1 27 0.00058 27.9 4.9 56 148-216 34-90 (114)
7 PF04430 DUF498: Protein of un 55.9 17 0.00037 28.5 3.8 56 148-216 33-89 (110)
8 PF06057 VirJ: Bacterial virul 53.9 18 0.0004 31.7 3.9 36 170-217 4-39 (192)
9 cd05126 Mth938 Mth938 domain. 44.7 39 0.00085 27.0 4.2 53 152-217 44-96 (117)
10 COG3946 VirJ Type IV secretory 37.4 43 0.00093 32.9 3.9 26 191-217 272-297 (456)
11 COG3737 Uncharacterized conser 35.0 30 0.00066 28.1 2.1 58 147-220 48-106 (127)
12 PF11256 DUF3055: Protein of u 32.5 34 0.00073 25.9 1.9 25 137-161 30-56 (81)
13 PLN03023 Expansin-like B1; Pro 30.4 52 0.0011 30.0 3.1 31 10-40 4-37 (247)
14 COG3958 Transketolase, C-termi 27.2 85 0.0018 29.5 3.9 45 165-223 190-234 (312)
15 PRK06932 glycerate dehydrogena 22.6 3.9E+02 0.0084 24.9 7.6 57 153-227 214-271 (314)
16 TIGR02153 gatD_arch glutamyl-t 21.0 1.6E+02 0.0034 28.8 4.7 51 189-241 282-333 (404)
17 PRK04183 glutamyl-tRNA(Gln) am 20.3 1.6E+02 0.0035 28.9 4.6 51 189-241 295-346 (419)
No 1
>TIGR03035 trp_arylform arylformamidase. One of several pathways of tryptophan degradation is as follows: tryptophan 2,3-dioxygenase (1.13.11.11) uses 02 to convert Trp to L-formylkynurenine. Arylformamidase (3.5.1.9) hydrolyzes the product to L-kynurenine and formate. Kynureninase (3.7.1.3) hydrolyzes L-kynurenine to anthranilate plus alanine. Members of the seed alignment for this model are bacterial predicted metal-dependent hydrolases. All are supported as arylformamidase (3.5.1.9) by an operon structure in which kynureninase and/or tryptophan 2,3-dioxygenase genes are adjacent. The members from Bacillus cereus, Pseudomonas aeruginosa and Ralstonia metallidurans were characterized. An example from Pseudomonas fluorescens is given the gene symbol qbsH instead of kynB because of its role in quinolobactin biosynthesis, which begins with tryptophan. All members of this family should be arylformamidase (3.5.1.9).
Probab=100.00 E-value=3.9e-57 Score=397.65 Aligned_cols=203 Identities=28% Similarity=0.451 Sum_probs=179.2
Q ss_pred eEEEcceeccCCCCcCCCCCCccceEEeeeeeccCCceeEEeEEEEcCCcccccccccccccCcCCCCccccccCccccc
Q 023836 61 RIFDITHQVTVDLPSYDTEGGRLGQFLRLPVSMKNGSFCNISEMKFTTHTGTHVDAPGHFFDHYFDAGFDADSLDLDVLN 140 (276)
Q Consensus 61 kiiDLS~~i~~~mP~~p~~p~~~~~~~~~~~~~~~G~~~~~~~l~~~~HtGTHvDAP~H~~~~~~~~G~~id~i~l~~~~ 140 (276)
|+|||||+++++||.||++|+ + .+....+..+++.+|.+.++|++|+|||+|||+||. ++|++++++|++.|+
T Consensus 1 ~iiDLS~~i~~~~p~~p~~p~-~--~~~~~~~~~~~~~~~~~~i~~~~H~GTHiDAP~Hf~----~~g~~id~~pl~~~~ 73 (206)
T TIGR03035 1 RWWDISPPLNNATPTWPGDTP-F--SQEWVWSKEETCPVNVGRITLSPHTGAHADAPLHYD----NDGAPIGDVPLDVYL 73 (206)
T ss_pred CEEEeccCcCCCCCccCCCCC-e--eEEEEEEecCCCcEEEEEEEECCccccccccchhhC----CCCCCccccchHHhe
Confidence 699999999999999999987 4 233233444445599999999999999999999998 799999999999999
Q ss_pred ccEEEEEc-CCCCCCCHHHHhcCCCCCCCeEEEEEecCCccccccccCCCCCcccCHHHHHHHHHcCCceEEEecCCCCC
Q 023836 141 GPGLLVDV-PRDKNLTAEVLESLNIPKGVRRVLFRTLNTDRQLMFKKFDTSYVGFMADGAKWLVENTDIKLVGVDYLSVA 219 (276)
Q Consensus 141 g~~vvlDv-~~~~~It~edl~~~~i~~g~diVL~rTg~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~gik~VGiD~~Svd 219 (276)
|+++|||+ +.+..||+|||+++.++.+ |+|||||||.. ...+|..++||++.|+|+||+|+ +|++||+|++|+|
T Consensus 74 g~~~vid~~~~~~~it~edl~~~~~~~~-d~vl~~Tg~~~---~~~~y~~~~Pgls~eaa~~L~e~-~i~~iG~D~~s~d 148 (206)
T TIGR03035 74 GPCRVIHCLGAGELIDPEHLRSALLELP-PRVLLRTYLPA---PANAWPDDFPAVAPDTIELLAEK-GVRLIGIDTPSVD 148 (206)
T ss_pred ecEEEEEEeCCCCccCHHHHHhhhhcCC-CEEEEECCCCC---CccccCCCCCeeCHHHHHHHHHC-CCeEEEECCCccC
Confidence 99999994 4567899999998876655 99999999942 23458889999999999999997 9999999999999
Q ss_pred CCC-CChHHHHHHHhcCCcceEEcccCCCCCCCcEEEEEeccccCCCcccceeeEEEC
Q 023836 220 AFD-DIISAHHELLRNREIIPVEGLKLDHVPAGLYSIHCLPLRMVGAEGSPVRCILIK 276 (276)
Q Consensus 220 ~~~-~~~p~H~~lL~~~gi~iiE~LnLd~L~~~~~~~~~~PLki~G~~GsPvR~vAi~ 276 (276)
... ..+++|+.||+ +||+++||++|++|++++|.|+|+|||++|+||||||+||++
T Consensus 149 ~~~~~~~~~H~~ll~-~gi~iiE~~~L~~l~~~~~~~~~~PLki~g~~GsPvR~va~~ 205 (206)
T TIGR03035 149 PLDSKTLDAHHALFR-HGMAILENVVLDDVAEGDYELIALPLKFTDADASPVRAVLRP 205 (206)
T ss_pred CCCCCchHHHHHHHh-CCeeEEeccccccCCCCCeEEEEeCcccCCCCccCeEEEEec
Confidence 873 56899999997 799999999999999999999999999999999999999984
No 2
>COG1878 Kynurenine formamidase [Amino acid transport and metabolism]
Probab=100.00 E-value=1.4e-55 Score=388.90 Aligned_cols=209 Identities=30% Similarity=0.499 Sum_probs=186.0
Q ss_pred CCceEEEcceeccCCCCcCCCCCCccceEEeeeeeccCCceeEEeEEEEcCCcccccccccccccCcCCCCccccccCcc
Q 023836 58 GGGRIFDITHQVTVDLPSYDTEGGRLGQFLRLPVSMKNGSFCNISEMKFTTHTGTHVDAPGHFFDHYFDAGFDADSLDLD 137 (276)
Q Consensus 58 ~~~kiiDLS~~i~~~mP~~p~~p~~~~~~~~~~~~~~~G~~~~~~~l~~~~HtGTHvDAP~H~~~~~~~~G~~id~i~l~ 137 (276)
+.+++|||||+++++||+||++|+ ..++...++++++ |+.+.+++++|+|||||||.||. +||.++|++|++
T Consensus 2 ~~~~~iDLS~~l~~~~p~~pg~p~---~~ie~~~~~~~~g-~~~~~i~~~~HtGTHiDAP~Hf~----~~G~~id~ipl~ 73 (218)
T COG1878 2 GMMKVIDLSHPLEPGMPTWPGDPP---VEIERIATLAKDG-FNVSIITLGEHTGTHIDAPLHFI----EGGLSIDEIPLE 73 (218)
T ss_pred CcceEEEcccccCCCCCCCCCCCC---cEEEEeEEecCCc-EEEEEEEecCccccccccHHhhc----CCCCccccCCHH
Confidence 568999999999999999999997 4555666677666 99999999999999999999999 899999999999
Q ss_pred cccccEEEEEcCC---CCCCCHHHHhcCCCCCCCeEEEEEecCCccccccccCCCCCcccCHHHHHHHHHcCCceEEEec
Q 023836 138 VLNGPGLLVDVPR---DKNLTAEVLESLNIPKGVRRVLFRTLNTDRQLMFKKFDTSYVGFMADGAKWLVENTDIKLVGVD 214 (276)
Q Consensus 138 ~~~g~~vvlDv~~---~~~It~edl~~~~i~~g~diVL~rTg~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~gik~VGiD 214 (276)
.|+|+++|||++. +..++.++++++.....+++|++||||.+++....+|..++||++.|+|+||+|+ +||+||+|
T Consensus 74 ~~ig~~~Vid~~~~~~~~~~~~~~~~a~~~~~~g~~v~i~Tgw~~~~~~~~~f~~~~Pg~~~eaa~~L~e~-~VkaVGiD 152 (218)
T COG1878 74 SFIGPGVVIDISGKDPDEVITEDDIEAWDAEHPGDIVLIRTGWSKRWGDEPAFQYHFPGISIEAAEYLIER-GVKAVGID 152 (218)
T ss_pred HhEeeeEEEEecCCCcccccCHHHhhhhcccCCccEEEEEccchhhcCCcchhhccCcccCHHHHHHHHHc-CCeEEEec
Confidence 9999999999995 4579999999886544359999999998875433336789999999999999996 99999999
Q ss_pred CCCCCCCC-CChHHHHHHHhcCCcceEEcc-cCCCCCCCcE-EEEEeccccCCCcccceeeEEEC
Q 023836 215 YLSVAAFD-DIISAHHELLRNREIIPVEGL-KLDHVPAGLY-SIHCLPLRMVGAEGSPVRCILIK 276 (276)
Q Consensus 215 ~~Svd~~~-~~~p~H~~lL~~~gi~iiE~L-nLd~L~~~~~-~~~~~PLki~G~~GsPvR~vAi~ 276 (276)
++|+|+.. ..+++|+.||. +|++++|+| ||++|+.+.+ .+.++|||++|++|||||++|+.
T Consensus 153 t~s~d~~~~~~~~~H~~lL~-~~~~i~E~l~nl~~l~~~~~~~~~~lPlk~~g~~g~PvRv~a~~ 216 (218)
T COG1878 153 TPSTDPGLSEDFPAHRLLLS-AGILIVENLTNLDKLPAGGAYLFLALPLKIKGGDGSPVRVLALV 216 (218)
T ss_pred CCccCcccccchHHHHHHHh-CCCEEEEeeccccccCCCceEEEEecCceecCCCCCceEEEEEc
Confidence 99999874 46999999997 899999999 7999998765 89999999999999999999974
No 3
>PF04199 Cyclase: Putative cyclase; InterPro: IPR007325 Proteins in this family are thought to be cyclase enzymes. They are found in proteins involved in antibiotic synthesis. However they are also found in organisms that do not make antibiotics pointing to a wider role for these proteins. The proteins contain a conserved motif HXGTHXDXPXH that is likely to form a part of the active site.; PDB: 2B0A_A 3KRV_A 1R61_A.
Probab=100.00 E-value=1.3e-39 Score=277.61 Aligned_cols=152 Identities=32% Similarity=0.522 Sum_probs=104.0
Q ss_pred EEEcceeccCCCCcCCCCCCccceEEe----eeeeccCCceeEEeEEEEcCCcccccccccc-cccCcCCCCccccccCc
Q 023836 62 IFDITHQVTVDLPSYDTEGGRLGQFLR----LPVSMKNGSFCNISEMKFTTHTGTHVDAPGH-FFDHYFDAGFDADSLDL 136 (276)
Q Consensus 62 iiDLS~~i~~~mP~~p~~p~~~~~~~~----~~~~~~~G~~~~~~~l~~~~HtGTHvDAP~H-~~~~~~~~G~~id~i~l 136 (276)
||||||+|+++||.|| +|+ +..... .....++|..++.+.++|++|+|||+|||+| |. ++|.+++++|+
T Consensus 1 iiDLS~~i~~~~p~~p-~~~-~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~H~GTHiDap~H~~~----~~g~~i~~~pl 74 (171)
T PF04199_consen 1 IIDLSHPISNGMPVWP-DPP-FEFETISSIEKDGSYPEGDGFNVDSITMSTHTGTHIDAPAHYFI----PDGATIDEIPL 74 (171)
T ss_dssp EEE----B-TT---GG--GG-GS-EEE-------EEEEECTCEEEEEEEETTSSSEEE-GGGC-S----TTT-TGGGSSC
T ss_pred cEEcceEcCCCCCCCC-CCC-cEEEEEeeecccccccccceEEEEEEEeCCCccCCCcccccccC----CCCCCHHHhhh
Confidence 7999999999999999 776 433222 1112345566999999999999999999999 77 79999999999
Q ss_pred ccccccEEEEEcCC-----CCCCCHHHHhcC------CCCCCCeEEEEEecCCcccc--ccccCCCCCcccCHHHHHHHH
Q 023836 137 DVLNGPGLLVDVPR-----DKNLTAEVLESL------NIPKGVRRVLFRTLNTDRQL--MFKKFDTSYVGFMADGAKWLV 203 (276)
Q Consensus 137 ~~~~g~~vvlDv~~-----~~~It~edl~~~------~i~~g~diVL~rTg~~~~~~--~~~~y~~~~Pgls~eaA~~L~ 203 (276)
+.|+|||+|||+++ +..||.+||+++ .+++| |+|||||||.++++ ...+|..++|||++|+|+||+
T Consensus 75 ~~~~g~~vviD~~~~~~~~~~~It~~dl~~~~~~~~~~i~~g-divlirTG~~~~~~~~~~~~y~~~~p~ls~eaa~~L~ 153 (171)
T PF04199_consen 75 ERFIGPAVVIDVSHDKQPPGEAITAEDLEAAWEAQGVEIRPG-DIVLIRTGWNDKRWEMGTEEYFNDFPGLSPEAAEWLA 153 (171)
T ss_dssp CCCEEEEEEEETTT------SEE-HHHHTT------S---TT-SEEEEE-CG-GGGT--TSGCGGCT--EE-HCCHHHHH
T ss_pred hhccCcEEEEeccccccCCCceEcHHHHHhhhcccccccCCC-cEEEEECCchhhhcccCCHhHccCCCcCCHHHHHHHH
Confidence 99999999999998 457999999865 56665 99999999954433 223488889999999999999
Q ss_pred HcCCceEEEecCCCCCCC
Q 023836 204 ENTDIKLVGVDYLSVAAF 221 (276)
Q Consensus 204 e~~gik~VGiD~~Svd~~ 221 (276)
++ +|++||+|++|+|++
T Consensus 154 ~~-~v~~vG~D~~s~d~~ 170 (171)
T PF04199_consen 154 ER-GVKAVGIDTPSVDPP 170 (171)
T ss_dssp HC-T-SEEEESSSSS--S
T ss_pred HC-CCCEEEECCCCCCCC
Confidence 97 999999999999974
No 4
>cd05560 Xcc1710_like Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. Their three-dimensional structures have been determined, but their functions are unknown.
Probab=73.56 E-value=7.9 Score=30.60 Aligned_cols=54 Identities=22% Similarity=0.153 Sum_probs=40.3
Q ss_pred CCCCCCCHHHHhcCCCCCCCeEEEEEecCCccccccccCCCCCcccCHHHHHHHHHcCCceEEEecCC
Q 023836 149 PRDKNLTAEVLESLNIPKGVRRVLFRTLNTDRQLMFKKFDTSYVGFMADGAKWLVENTDIKLVGVDYL 216 (276)
Q Consensus 149 ~~~~~It~edl~~~~i~~g~diVL~rTg~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~gik~VGiD~~ 216 (276)
.+-..++.++++.+...+ .++|++-||-+.+ +| +++..++|.++ ||.+--.||.
T Consensus 35 ~~~~~l~~e~l~~l~~~~-peiliiGTG~~~~----------~~--~~~~~~~l~~~-gi~vE~m~T~ 88 (109)
T cd05560 35 ARFEDLTAAHFEALLALQ-PEVILLGTGERQR----------FP--PPALLAPLLAR-GIGVEVMDTQ 88 (109)
T ss_pred CCcccCCHHHHHHHHhcC-CCEEEEecCCCCC----------cC--CHHHHHHHHHc-CCeEEEECHH
Confidence 334589999998764434 3899999996532 33 78999999997 9888777775
No 5
>cd00248 Mth938-like Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. 2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and known to be alternately spliced. Xcr35 and Rpa2829 are hypothetical proteins of unknown function from the Xanthomonas campestris and Rhodopseudomonas palustris genomes, respectively, for which the crystal structures have been determined.
Probab=62.24 E-value=16 Score=28.82 Aligned_cols=54 Identities=15% Similarity=-0.093 Sum_probs=39.6
Q ss_pred CCCCCHHHHhcCCCCCCCeEEEEEecCCccccccccCCCCCcccCHHHHHHHHHcCCceEEEecCCC
Q 023836 151 DKNLTAEVLESLNIPKGVRRVLFRTLNTDRQLMFKKFDTSYVGFMADGAKWLVENTDIKLVGVDYLS 217 (276)
Q Consensus 151 ~~~It~edl~~~~i~~g~diVL~rTg~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~gik~VGiD~~S 217 (276)
-..++.++|+.....+..|+|+|-||-..+ -++++..++|.++ ||.+--.||.+
T Consensus 36 ~~~l~~~~l~~~~~~~~peiliiGTG~~~~------------~~~~~~~~~l~~~-gI~vE~m~T~a 89 (109)
T cd00248 36 LSDLDPEALLPLLAEDRPDILLIGTGAEIA------------FLPRALRAALRAA-GIGVEVMSTGA 89 (109)
T ss_pred cccCCHHHHHHHHhhCCCCEEEEcCCCCCC------------cCCHHHHHHHHHc-CCeEEEeCcHH
Confidence 457999999865322224899999996432 2479999999997 99888777753
No 6
>cd05125 Mth938_2P1-like Mth938_2P1-like domain. This model contains sequences that are similar to 2P1, a partially characterized nuclear protein, which is homologous to E3-3 from rat and known to be alternatively spliced. Its function is unknown. This family is part of the Mth938 family, for which structures, but no functional data are available.
Probab=56.06 E-value=27 Score=27.91 Aligned_cols=56 Identities=16% Similarity=0.121 Sum_probs=41.1
Q ss_pred cCCCCCCCHHHHhcCC-CCCCCeEEEEEecCCccccccccCCCCCcccCHHHHHHHHHcCCceEEEecCC
Q 023836 148 VPRDKNLTAEVLESLN-IPKGVRRVLFRTLNTDRQLMFKKFDTSYVGFMADGAKWLVENTDIKLVGVDYL 216 (276)
Q Consensus 148 v~~~~~It~edl~~~~-i~~g~diVL~rTg~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~gik~VGiD~~ 216 (276)
+.+-..++.++++.+. ..+..|+|++-||-+. --++++..++|.++ ||.+--.||.
T Consensus 34 ~~~~~~l~~~~l~~l~~~~~~peiliiGtG~~~------------~~~~~~~~~~l~~~-gi~vevm~T~ 90 (114)
T cd05125 34 VSSFEDITEESLSLFELLEPRPEILVIGTGRKS------------RPLSPELRKYFKKL-GIAVEVVDTR 90 (114)
T ss_pred CCChhhCCHHHHHHHHhccCCCCEEEEccCCCC------------CcCCHHHHHHHHHc-CCEEEEECHH
Confidence 4445689999988653 3334589999999642 13578899999997 9988877775
No 7
>PF04430 DUF498: Protein of unknown function (DUF498/DUF598); InterPro: IPR007523 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This is entry represents an essential factor for the assembly of mitochondrial NADH:ubiquinone oxidoreductase complex (complex I) []. The crystal structure of this protein revealed a 3-layer beta+alpha/beta/alpha topology [].; PDB: 2K2E_A 2Q4Q_B 2AB1_A 2FVT_A 2CYJ_A 1IHN_B 2GM2_A 3CPK_A 2FI9_A.
Probab=55.88 E-value=17 Score=28.47 Aligned_cols=56 Identities=20% Similarity=0.189 Sum_probs=38.8
Q ss_pred cCCCCCCCHHHHhcC-CCCCCCeEEEEEecCCccccccccCCCCCcccCHHHHHHHHHcCCceEEEecCC
Q 023836 148 VPRDKNLTAEVLESL-NIPKGVRRVLFRTLNTDRQLMFKKFDTSYVGFMADGAKWLVENTDIKLVGVDYL 216 (276)
Q Consensus 148 v~~~~~It~edl~~~-~i~~g~diVL~rTg~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~gik~VGiD~~ 216 (276)
+.+...++.++++.+ ...+..|+|+|-||-.. --++++..++|.++ ||.+--.||.
T Consensus 33 ~~~~~~l~~~~l~~l~~~~p~pe~liiGtG~~~------------~~~~~~~~~~l~~~-GI~ve~m~T~ 89 (110)
T PF04430_consen 33 VKSPHDLTPEDLEELLELEPKPEVLIIGTGKRQ------------LFLPPELREYLRKK-GIGVEVMDTP 89 (110)
T ss_dssp HSSTTCEETHHHHHHHCTCCS-SEEEEEETTS-------------SECTHHHHHHHHTT-T-EEEEE-HH
T ss_pred CCCcccCCHHHHHHHHhccCCCcEEEEccCCcc------------ccCCHHHHHHHHHc-CCeEEEECHH
Confidence 345678999999865 23223489999999642 23579999999997 9888777764
No 8
>PF06057 VirJ: Bacterial virulence protein (VirJ); InterPro: IPR010333 This entry contains several bacterial VirJ virulence proteins. VirJ is thought to be involved in the type IV secretion system. It is thought that the substrate proteins localised to the periplasm may associate with the pilus in a manner that is mediated by VirJ, and suggest a two-step process for type IV secretion in Agrobacterium [].
Probab=53.86 E-value=18 Score=31.67 Aligned_cols=36 Identities=22% Similarity=0.274 Sum_probs=28.6
Q ss_pred EEEEEecCCccccccccCCCCCcccCHHHHHHHHHcCCceEEEecCCC
Q 023836 170 RVLFRTLNTDRQLMFKKFDTSYVGFMADGAKWLVENTDIKLVGVDYLS 217 (276)
Q Consensus 170 iVL~rTg~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~gik~VGiD~~S 217 (276)
.++|-+|-.. +.+++.+.|+.|+++ |+-.||+|++.
T Consensus 4 ~~v~~SGDgG-----------w~~~d~~~a~~l~~~-G~~VvGvdsl~ 39 (192)
T PF06057_consen 4 LAVFFSGDGG-----------WRDLDKQIAEALAKQ-GVPVVGVDSLR 39 (192)
T ss_pred EEEEEeCCCC-----------chhhhHHHHHHHHHC-CCeEEEechHH
Confidence 5667776332 346899999999997 99999999975
No 9
>cd05126 Mth938 Mth938 domain. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. The function of the protein has not been determined.
Probab=44.67 E-value=39 Score=27.04 Aligned_cols=53 Identities=17% Similarity=0.161 Sum_probs=38.1
Q ss_pred CCCCHHHHhcCCCCCCCeEEEEEecCCccccccccCCCCCcccCHHHHHHHHHcCCceEEEecCCC
Q 023836 152 KNLTAEVLESLNIPKGVRRVLFRTLNTDRQLMFKKFDTSYVGFMADGAKWLVENTDIKLVGVDYLS 217 (276)
Q Consensus 152 ~~It~edl~~~~i~~g~diVL~rTg~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~gik~VGiD~~S 217 (276)
..++.+|++.+--. ..++|+|-||-..+. -++++..+.|.++ ||.+.-.||.+
T Consensus 44 ~~l~~~~l~~ll~~-~peivliGTG~~~~~-----------~~~~~~~~~l~~~-Gi~ve~m~T~a 96 (117)
T cd05126 44 HGLQPEELEELLEE-GVEVIVIGTGQSGAL-----------KVPPETVEKLEKR-GVEVLVLPTEE 96 (117)
T ss_pred ccCCHHHHHHHHhc-CCCEEEEcCCCCccc-----------cCCHHHHHHHHhc-CCEEEEcChHH
Confidence 36889998875322 247999999965331 1468899999996 99888777753
No 10
>COG3946 VirJ Type IV secretory pathway, VirJ component [Intracellular trafficking and secretion]
Probab=37.43 E-value=43 Score=32.91 Aligned_cols=26 Identities=27% Similarity=0.373 Sum_probs=22.7
Q ss_pred CcccCHHHHHHHHHcCCceEEEecCCC
Q 023836 191 YVGFMADGAKWLVENTDIKLVGVDYLS 217 (276)
Q Consensus 191 ~Pgls~eaA~~L~e~~gik~VGiD~~S 217 (276)
|-.|++|.++||.++ ||-+||+|++-
T Consensus 272 Wr~lDk~v~~~l~~~-gvpVvGvdsLR 297 (456)
T COG3946 272 WRDLDKEVAEALQKQ-GVPVVGVDSLR 297 (456)
T ss_pred hhhhhHHHHHHHHHC-CCceeeeehhh
Confidence 346889999999997 99999999863
No 11
>COG3737 Uncharacterized conserved protein [Function unknown]
Probab=34.99 E-value=30 Score=28.10 Aligned_cols=58 Identities=22% Similarity=0.152 Sum_probs=35.5
Q ss_pred EcCCCCCCCHHHHhcC-CCCCCCeEEEEEecCCccccccccCCCCCcccCHHHHHHHHHcCCceEEEecCCCCCC
Q 023836 147 DVPRDKNLTAEVLESL-NIPKGVRRVLFRTLNTDRQLMFKKFDTSYVGFMADGAKWLVENTDIKLVGVDYLSVAA 220 (276)
Q Consensus 147 Dv~~~~~It~edl~~~-~i~~g~diVL~rTg~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~gik~VGiD~~Svd~ 220 (276)
++++-+.+|++++++. ..-+..++||+-||..-+ +| .++.-.=|.. +.||+|++|.++
T Consensus 48 ~v~~~~~Lt~e~f~~vl~~a~~~EilliGTG~~~r----------f~--p~~l~aal~~----~gIsve~Mst~A 106 (127)
T COG3737 48 EVATLSDLTPEDFERVLAEAPDVEILLIGTGARLR----------FP--PPKLRAALKA----AGISVEPMSTGA 106 (127)
T ss_pred cccChhhCCHHHHHHHHhcCCCceEEEEecCcccc----------CC--CHHHHHHHHH----cCCccccccchh
Confidence 4444568999999864 222235899999997543 22 2333333333 346789988775
No 12
>PF11256 DUF3055: Protein of unknown function (DUF3055); InterPro: IPR021415 This family of proteins with unknown function appear to be restricted to Firmicutes.
Probab=32.48 E-value=34 Score=25.86 Aligned_cols=25 Identities=20% Similarity=0.290 Sum_probs=20.1
Q ss_pred ccccccEEEEEcCCCC--CCCHHHHhc
Q 023836 137 DVLNGPGLLVDVPRDK--NLTAEVLES 161 (276)
Q Consensus 137 ~~~~g~~vvlDv~~~~--~It~edl~~ 161 (276)
++|+|+.+|+|+..+. .|..+|+++
T Consensus 30 ~rF~GK~LV~~mQtgr~ailg~dDlee 56 (81)
T PF11256_consen 30 NRFYGKPLVLCMQTGRFAILGPDDLEE 56 (81)
T ss_pred ccccCceEEEEecCCceEEEChhhccc
Confidence 4799999999998753 578888764
No 13
>PLN03023 Expansin-like B1; Provisional
Probab=30.44 E-value=52 Score=29.99 Aligned_cols=31 Identities=13% Similarity=0.140 Sum_probs=16.3
Q ss_pred hhHHHHHHHHHHHhhhhcCCCCCCC---CCCCCC
Q 023836 10 QFLLPFVIFTLLALTVAANDEAYPT---TTTAPD 40 (276)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~ 40 (276)
++++.+|+++++++++++..+|.++ .||..|
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~W~~a~AT~Yg~~~ 37 (247)
T PLN03023 4 SHYCCFLCVIVLLPLLCKSQDFTYSRATYYGSPD 37 (247)
T ss_pred hhhHHHHHHHHHhhhhhhcCCcccceEEEeCCCC
Confidence 3444444444444556666667763 455444
No 14
>COG3958 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]
Probab=27.16 E-value=85 Score=29.51 Aligned_cols=45 Identities=13% Similarity=0.166 Sum_probs=34.4
Q ss_pred CCCCeEEEEEecCCccccccccCCCCCcccCHHHHHHHHHcCCceEEEecCCCCCCCCC
Q 023836 165 PKGVRRVLFRTLNTDRQLMFKKFDTSYVGFMADGAKWLVENTDIKLVGVDYLSVAAFDD 223 (276)
Q Consensus 165 ~~g~diVL~rTg~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~gik~VGiD~~Svd~~~~ 223 (276)
++|.|+.++-||-.- .-+.++|+-|.++ ||.+--+|.+++.+.++
T Consensus 190 rdG~D~tiiA~G~mv-------------~~al~AA~~L~~~-GIsa~Vi~m~tIKPiD~ 234 (312)
T COG3958 190 RDGSDLTIIATGVMV-------------AEALEAAEILKKE-GISAAVINMFTIKPIDE 234 (312)
T ss_pred ecCCceEEEecCcch-------------HHHHHHHHHHHhc-CCCEEEEecCccCCCCH
Confidence 345566666666421 2368999999998 99999999999998764
No 15
>PRK06932 glycerate dehydrogenase; Provisional
Probab=22.61 E-value=3.9e+02 Score=24.86 Aligned_cols=57 Identities=16% Similarity=-0.019 Sum_probs=35.4
Q ss_pred CCCHHHHhcCCCCCCCeEEEEEecCCccccccccCCCCCcccC-HHHHHHHHHcCCceEEEecCCCCCCCCCChHH
Q 023836 153 NLTAEVLESLNIPKGVRRVLFRTLNTDRQLMFKKFDTSYVGFM-ADGAKWLVENTDIKLVGVDYLSVAAFDDIISA 227 (276)
Q Consensus 153 ~It~edl~~~~i~~g~diVL~rTg~~~~~~~~~~y~~~~Pgls-~eaA~~L~e~~gik~VGiD~~Svd~~~~~~p~ 227 (276)
-|+.+.|..+ ++| .+|++|+... -++ .+..+.|.+. .+...|.|.+..|+.....|.
T Consensus 214 li~~~~l~~m--k~g--a~lIN~aRG~-------------~Vde~AL~~aL~~g-~i~gAaLDV~~~EP~~~~~pl 271 (314)
T PRK06932 214 LINAETLALM--KPT--AFLINTGRGP-------------LVDEQALLDALENG-KIAGAALDVLVKEPPEKDNPL 271 (314)
T ss_pred ccCHHHHHhC--CCC--eEEEECCCcc-------------ccCHHHHHHHHHcC-CccEEEEecCCCCCCCCCChh
Confidence 3455555442 232 6777776432 234 4556788875 999999999998876443343
No 16
>TIGR02153 gatD_arch glutamyl-tRNA(Gln) amidotransferase, subunit D. This peptide is found only in the Archaea. It is part of a heterodimer, with GatE (TIGR00134), that acts as an amidotransferase on misacylated Glu-tRNA(Gln) to produce Gln-tRNA(Gln). The analogous amidotransferase found in bacteria is the GatABC system, although GatABC homologs in the Archaea appear to act instead on Asp-tRNA(Asn).
Probab=20.97 E-value=1.6e+02 Score=28.79 Aligned_cols=51 Identities=14% Similarity=0.167 Sum_probs=36.9
Q ss_pred CCCcccCHHHHHHHHHcCCceEEEecCCCCCCCCC-ChHHHHHHHhcCCcceEE
Q 023836 189 TSYVGFMADGAKWLVENTDIKLVGVDYLSVAAFDD-IISAHHELLRNREIIPVE 241 (276)
Q Consensus 189 ~~~Pgls~eaA~~L~e~~gik~VGiD~~Svd~~~~-~~p~H~~lL~~~gi~iiE 241 (276)
+-|||++.+..+++.+. +++.+-+.+........ ..+.=+.+.+ +||+++=
T Consensus 282 ~~~pG~d~~~l~~~~~~-g~~GiVleg~G~G~vp~~~~~~l~~a~~-~GipVV~ 333 (404)
T TIGR02153 282 KFYPGISPEIIEFLVDK-GYKGIVIEGTGLGHVSEDWIPSIKRATD-DGVPVVM 333 (404)
T ss_pred EeCCCCCHHHHHHHHhC-CCCEEEEeeECCCCCCHHHHHHHHHHHH-CCCEEEE
Confidence 46899999999999997 89999888888776543 2333333443 6777764
No 17
>PRK04183 glutamyl-tRNA(Gln) amidotransferase subunit D; Validated
Probab=20.31 E-value=1.6e+02 Score=28.91 Aligned_cols=51 Identities=14% Similarity=0.146 Sum_probs=37.3
Q ss_pred CCCcccCHHHHHHHHHcCCceEEEecCCCCCCCCC-ChHHHHHHHhcCCcceEE
Q 023836 189 TSYVGFMADGAKWLVENTDIKLVGVDYLSVAAFDD-IISAHHELLRNREIIPVE 241 (276)
Q Consensus 189 ~~~Pgls~eaA~~L~e~~gik~VGiD~~Svd~~~~-~~p~H~~lL~~~gi~iiE 241 (276)
+-|||++.+..+++.++ +++.+-+.......... ..+.=+.+.+ +||+++=
T Consensus 295 ~~~PG~~~~~l~~~~~~-g~~GiVleg~G~Gnvp~~~~~~l~~a~~-~Gi~VV~ 346 (419)
T PRK04183 295 KFYPGMDPEILDFYVDK-GYKGIVIEGTGLGHVSTDLIPSIKRATD-DGIPVVM 346 (419)
T ss_pred EEcCCCCHHHHHHHHhC-CCCEEEEEeECCCCCCHHHHHHHHHHHH-CCCEEEE
Confidence 46899999999999997 89999898888776543 2333344444 6787764
Done!