Query 023541
Match_columns 281
No_of_seqs 185 out of 1298
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 04:50:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023541.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023541hhsearch_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 6.8E-57 1.5E-61 398.1 20.1 203 66-281 1-205 (206)
2 COG1878 Kynurenine formamidase 100.0 7.9E-55 1.7E-59 386.3 19.3 209 63-281 2-216 (218)
3 PF04199 Cyclase: Putative cyc 100.0 1.1E-39 2.3E-44 279.3 9.4 153 67-226 1-170 (171)
4 cd05560 Xcc1710_like Xcc1710_l 57.3 26 0.00057 27.8 5.1 55 153-222 35-89 (109)
5 PF06057 VirJ: Bacterial virul 51.1 21 0.00046 31.5 3.9 36 174-222 4-39 (192)
6 cd05125 Mth938_2P1-like Mth938 48.8 42 0.0009 27.0 5.0 57 152-222 34-91 (114)
7 cd00248 Mth938-like Mth938-lik 48.0 39 0.00085 26.7 4.7 54 155-222 36-89 (109)
8 PF04430 DUF498: Protein of un 45.0 35 0.00075 26.9 4.0 57 152-222 33-90 (110)
9 COG3958 Transketolase, C-termi 42.1 39 0.00084 31.9 4.3 46 168-228 189-234 (312)
10 COG3737 Uncharacterized conser 39.9 25 0.00053 28.8 2.3 58 151-225 48-106 (127)
11 COG3946 VirJ Type IV secretory 38.9 37 0.0008 33.6 3.8 25 197-222 273-297 (456)
12 cd05126 Mth938 Mth938 domain. 32.6 83 0.0018 25.3 4.4 53 156-222 44-96 (117)
13 PRK06932 glycerate dehydrogena 23.7 3.5E+02 0.0075 25.3 7.6 33 199-232 238-271 (314)
14 TIGR02153 gatD_arch glutamyl-t 20.9 1.3E+02 0.0028 29.6 4.1 51 194-246 282-333 (404)
15 PRK04183 glutamyl-tRNA(Gln) am 20.2 1.3E+02 0.0028 29.7 4.0 51 194-246 295-346 (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=6.8e-57 Score=398.15 Aligned_cols=203 Identities=25% Similarity=0.393 Sum_probs=180.1
Q ss_pred EEEEcceecCCCCCCCCCCCCCeeeeecceeccCCCeeeeeeEEecCCcccccccccccccCcccCCcccccccccceec
Q 023541 66 QIYDITHRITSDMPSFGSKEGLGQYLWLPKSIKNGSLANNSEMKLPSHTGTHVDAPGHVFDHYFDAGYDVDTLDLGVLNG 145 (281)
Q Consensus 66 ~iiDLS~~i~~~mP~~p~~~~~~~~~~~~~~~~~g~~~~~~~l~~~~HtGTHiDAP~H~~~~~~~~G~~id~l~l~~~~g 145 (281)
|+|||||+++++||.||++|+++. ....+..+++.+|.+.++|++|+|||+|||+||. ++|++++++|++.|+|
T Consensus 1 ~iiDLS~~i~~~~p~~p~~p~~~~--~~~~~~~~~~~~~~~~i~~~~H~GTHiDAP~Hf~----~~g~~id~~pl~~~~g 74 (206)
T TIGR03035 1 RWWDISPPLNNATPTWPGDTPFSQ--EWVWSKEETCPVNVGRITLSPHTGAHADAPLHYD----NDGAPIGDVPLDVYLG 74 (206)
T ss_pred CEEEeccCcCCCCCccCCCCCeeE--EEEEEecCCCcEEEEEEEECCccccccccchhhC----CCCCCccccchHHhee
Confidence 689999999999999999987753 2223333444599999999999999999999999 8999999999999999
Q ss_pred cEEEEE-cCCCccCCHHHHhcCCCCCCCeEEEEEeccCcccccccccccCCCcccCHHHHHHHHhCCCceEEeecCCCcC
Q 023541 146 PALLVD-VPRDKNITAEVMESLNIPRGVRRVIFRTLNTDRKLMFKREFDSSYVGFMKDGARWLVQNTDIKLVGIDYLSAA 224 (281)
Q Consensus 146 ~avvlD-v~~~~~It~edle~~~i~~g~d~VL~rTG~~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~~V~~VGiD~~Svd 224 (281)
+++||| ++.+..||+|||+++.++.+ |+|||||||.. ..++|..++||+++|+|+||+++ +|++||+|++|+|
T Consensus 75 ~~~vid~~~~~~~it~edl~~~~~~~~-d~vl~~Tg~~~----~~~~y~~~~Pgls~eaa~~L~e~-~i~~iG~D~~s~d 148 (206)
T TIGR03035 75 PCRVIHCLGAGELIDPEHLRSALLELP-PRVLLRTYLPA----PANAWPDDFPAVAPDTIELLAEK-GVRLIGIDTPSVD 148 (206)
T ss_pred cEEEEEEeCCCCccCHHHHHhhhhcCC-CEEEEECCCCC----CccccCCCCCeeCHHHHHHHHHC-CCeEEEECCCccC
Confidence 999999 44567899999998877666 89999999942 24678889999999999999995 9999999999999
Q ss_pred CCC-CCcHhHHhhhhCCCeeEEEcccCCCCCCCcEEEEEeccccCCCCccceeeEEEC
Q 023541 225 AHD-DLLPSHYEFLEGREVILVEGLKLDGVPAGLYNIHCLHLRLLGAEGSPIRCILIK 281 (281)
Q Consensus 225 ~~~-~~~p~H~~lL~~~gI~iiE~LnLd~L~~~~~~~~a~PLki~Ga~GsPvR~vAi~ 281 (281)
... ..+++|+.||+ +||+++||+||++|++++|.|+|+||||+|+||||||+||++
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 874 46899999997 799999999999999999999999999999999999999984
No 2
>COG1878 Kynurenine formamidase [Amino acid transport and metabolism]
Probab=100.00 E-value=7.9e-55 Score=386.29 Aligned_cols=209 Identities=28% Similarity=0.450 Sum_probs=184.3
Q ss_pred CCCEEEEcceecCCCCCCCCCCCCCeeeeecceeccCCCeeeeeeEEecCCcccccccccccccCcccCCcccccccccc
Q 023541 63 ENGQIYDITHRITSDMPSFGSKEGLGQYLWLPKSIKNGSLANNSEMKLPSHTGTHVDAPGHVFDHYFDAGYDVDTLDLGV 142 (281)
Q Consensus 63 ~~~~iiDLS~~i~~~mP~~p~~~~~~~~~~~~~~~~~g~~~~~~~l~~~~HtGTHiDAP~H~~~~~~~~G~~id~l~l~~ 142 (281)
+.+++|||||+++++||+||++|++++ +...++++++ |+.+++++++|+|||+|||.||. .+|.++|++|++.
T Consensus 2 ~~~~~iDLS~~l~~~~p~~pg~p~~~i--e~~~~~~~~g-~~~~~i~~~~HtGTHiDAP~Hf~----~~G~~id~ipl~~ 74 (218)
T COG1878 2 GMMKVIDLSHPLEPGMPTWPGDPPVEI--ERIATLAKDG-FNVSIITLGEHTGTHIDAPLHFI----EGGLSIDEIPLES 74 (218)
T ss_pred CcceEEEcccccCCCCCCCCCCCCcEE--EEeEEecCCc-EEEEEEEecCccccccccHHhhc----CCCCccccCCHHH
Confidence 578999999999999999999998753 4445555554 99999999999999999999999 8999999999999
Q ss_pred eeccEEEEEcCC---CccCCHHHHhcCCCCCCCeEEEEEeccCcccccccccccCCCcccCHHHHHHHHhCCCceEEeec
Q 023541 143 LNGPALLVDVPR---DKNITAEVMESLNIPRGVRRVIFRTLNTDRKLMFKREFDSSYVGFMKDGARWLVQNTDIKLVGID 219 (281)
Q Consensus 143 ~~g~avvlDv~~---~~~It~edle~~~i~~g~d~VL~rTG~~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~~V~~VGiD 219 (281)
|+|+++|||++. +..++.++++++.....+++|+|||||.+++. +..+|..++||++.|+|+||++ ++||+||+|
T Consensus 75 ~ig~~~Vid~~~~~~~~~~~~~~~~a~~~~~~g~~v~i~Tgw~~~~~-~~~~f~~~~Pg~~~eaa~~L~e-~~VkaVGiD 152 (218)
T COG1878 75 FIGPGVVIDISGKDPDEVITEDDIEAWDAEHPGDIVLIRTGWSKRWG-DEPAFQYHFPGISIEAAEYLIE-RGVKAVGID 152 (218)
T ss_pred hEeeeEEEEecCCCcccccCHHHhhhhcccCCccEEEEEccchhhcC-CcchhhccCcccCHHHHHHHHH-cCCeEEEec
Confidence 999999999994 55799999999865442389999999987643 2345578999999999999999 599999999
Q ss_pred CCCcCCCC-CCcHhHHhhhhCCCeeEEEcc-cCCCCCCCcE-EEEEeccccCCCCccceeeEEEC
Q 023541 220 YLSAAAHD-DLLPSHYEFLEGREVILVEGL-KLDGVPAGLY-NIHCLHLRLLGAEGSPIRCILIK 281 (281)
Q Consensus 220 ~~Svd~~~-~~~p~H~~lL~~~gI~iiE~L-nLd~L~~~~~-~~~a~PLki~Ga~GsPvR~vAi~ 281 (281)
++|+|+.. ..+++|+.||+ +|++++||| ||++|+.+.+ .+.++|||++|++|||||++|+.
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 36899999997 799999999 7999998766 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=1.1e-39 Score=279.34 Aligned_cols=153 Identities=32% Similarity=0.487 Sum_probs=105.6
Q ss_pred EEEcceecCCCCCCCCCCCCCeeeeec----ceeccCCCeeeeeeEEecCCcccccccccc-cccCcccCCccccccccc
Q 023541 67 IYDITHRITSDMPSFGSKEGLGQYLWL----PKSIKNGSLANNSEMKLPSHTGTHVDAPGH-VFDHYFDAGYDVDTLDLG 141 (281)
Q Consensus 67 iiDLS~~i~~~mP~~p~~~~~~~~~~~----~~~~~~g~~~~~~~l~~~~HtGTHiDAP~H-~~~~~~~~G~~id~l~l~ 141 (281)
||||||+|+++||+|| ++++...... ....++|..++.+.++|++|+|||+|||+| |. ++|.+++++|++
T Consensus 1 iiDLS~~i~~~~p~~p-~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~H~GTHiDap~H~~~----~~g~~i~~~pl~ 75 (171)
T PF04199_consen 1 IIDLSHPISNGMPVWP-DPPFEFETISSIEKDGSYPEGDGFNVDSITMSTHTGTHIDAPAHYFI----PDGATIDEIPLE 75 (171)
T ss_dssp EEE----B-TT---GG--GGGS-EEE-------EEEEECTCEEEEEEEETTSSSEEE-GGGC-S----TTT-TGGGSSCC
T ss_pred cEEcceEcCCCCCCCC-CCCcEEEEEeeecccccccccceEEEEEEEeCCCccCCCcccccccC----CCCCCHHHhhhh
Confidence 7999999999999999 7766432221 112345566999999999999999999999 77 899999999999
Q ss_pred ceeccEEEEEcCC-----CccCCHHHHhcC------CCCCCCeEEEEEeccC-cccccccccccCCCcccCHHHHHHHHh
Q 023541 142 VLNGPALLVDVPR-----DKNITAEVMESL------NIPRGVRRVIFRTLNT-DRKLMFKREFDSSYVGFMKDGARWLVQ 209 (281)
Q Consensus 142 ~~~g~avvlDv~~-----~~~It~edle~~------~i~~g~d~VL~rTG~~-~~~~~~~~~y~~~~Pgls~eaA~~L~e 209 (281)
.|+|+|+|||+++ +..||.+||+++ .+++| |+|||||||. +++...+++|...+|||++|+|+||++
T Consensus 76 ~~~g~~vviD~~~~~~~~~~~It~~dl~~~~~~~~~~i~~g-divlirTG~~~~~~~~~~~~y~~~~p~ls~eaa~~L~~ 154 (171)
T PF04199_consen 76 RFIGPAVVIDVSHDKQPPGEAITAEDLEAAWEAQGVEIRPG-DIVLIRTGWNDKRWEMGTEEYFNDFPGLSPEAAEWLAE 154 (171)
T ss_dssp CCEEEEEEEETTT------SEE-HHHHTT------S---TT-SEEEEE-CG-GGGT--TSGCGGCT--EE-HCCHHHHHH
T ss_pred hccCcEEEEeccccccCCCceEcHHHHHhhhcccccccCCC-cEEEEECCchhhhcccCCHhHccCCCcCCHHHHHHHHH
Confidence 9999999999998 457999999865 67777 9999999994 443334578888999999999999999
Q ss_pred CCCceEEeecCCCcCCC
Q 023541 210 NTDIKLVGIDYLSAAAH 226 (281)
Q Consensus 210 ~~~V~~VGiD~~Svd~~ 226 (281)
+ +|++||+|++|+|++
T Consensus 155 ~-~v~~vG~D~~s~d~~ 170 (171)
T PF04199_consen 155 R-GVKAVGIDTPSVDPP 170 (171)
T ss_dssp C-T-SEEEESSSSS--S
T ss_pred C-CCCEEEECCCCCCCC
Confidence 4 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=57.28 E-value=26 Score=27.77 Aligned_cols=55 Identities=18% Similarity=0.138 Sum_probs=39.2
Q ss_pred CCCccCCHHHHhcCCCCCCCeEEEEEeccCcccccccccccCCCcccCHHHHHHHHhCCCceEEeecCCC
Q 023541 153 PRDKNITAEVMESLNIPRGVRRVIFRTLNTDRKLMFKREFDSSYVGFMKDGARWLVQNTDIKLVGIDYLS 222 (281)
Q Consensus 153 ~~~~~It~edle~~~i~~g~d~VL~rTG~~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~~V~~VGiD~~S 222 (281)
.+-..++.++++.....+. |+|+|=||.... +| +++..++|.++ ||.+--.|+.+
T Consensus 35 ~~~~~l~~e~l~~l~~~~p-eiliiGTG~~~~-----------~~--~~~~~~~l~~~-gi~vE~m~T~~ 89 (109)
T cd05560 35 ARFEDLTAAHFEALLALQP-EVILLGTGERQR-----------FP--PPALLAPLLAR-GIGVEVMDTQA 89 (109)
T ss_pred CCcccCCHHHHHHHHhcCC-CEEEEecCCCCC-----------cC--CHHHHHHHHHc-CCeEEEECHHH
Confidence 3445799999987643343 899999996432 23 68899999995 88776666643
No 5
>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=51.13 E-value=21 Score=31.50 Aligned_cols=36 Identities=22% Similarity=0.312 Sum_probs=28.7
Q ss_pred EEEEEeccCcccccccccccCCCcccCHHHHHHHHhCCCceEEeecCCC
Q 023541 174 RVIFRTLNTDRKLMFKREFDSSYVGFMKDGARWLVQNTDIKLVGIDYLS 222 (281)
Q Consensus 174 ~VL~rTG~~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~~V~~VGiD~~S 222 (281)
.++|.+|-.. +.+++.+.|+.|+++ |+..||+|++.
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 5677776432 347899999999995 99999999866
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=48.82 E-value=42 Score=26.98 Aligned_cols=57 Identities=14% Similarity=0.161 Sum_probs=41.0
Q ss_pred cCCCccCCHHHHhcCC-CCCCCeEEEEEeccCcccccccccccCCCcccCHHHHHHHHhCCCceEEeecCCC
Q 023541 152 VPRDKNITAEVMESLN-IPRGVRRVIFRTLNTDRKLMFKREFDSSYVGFMKDGARWLVQNTDIKLVGIDYLS 222 (281)
Q Consensus 152 v~~~~~It~edle~~~-i~~g~d~VL~rTG~~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~~V~~VGiD~~S 222 (281)
+.+-..++.++++... +.+..|+|++=||-... -++++.-++|.++ ||.+--.||..
T Consensus 34 ~~~~~~l~~~~l~~l~~~~~~peiliiGtG~~~~-------------~~~~~~~~~l~~~-gi~vevm~T~~ 91 (114)
T cd05125 34 VSSFEDITEESLSLFELLEPRPEILVIGTGRKSR-------------PLSPELRKYFKKL-GIAVEVVDTRN 91 (114)
T ss_pred CCChhhCCHHHHHHHHhccCCCCEEEEccCCCCC-------------cCCHHHHHHHHHc-CCEEEEECHHH
Confidence 4455689999998763 33445899999996421 3678889999985 88877776643
No 7
>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=47.99 E-value=39 Score=26.70 Aligned_cols=54 Identities=9% Similarity=-0.097 Sum_probs=38.5
Q ss_pred CccCCHHHHhcCCCCCCCeEEEEEeccCcccccccccccCCCcccCHHHHHHHHhCCCceEEeecCCC
Q 023541 155 DKNITAEVMESLNIPRGVRRVIFRTLNTDRKLMFKREFDSSYVGFMKDGARWLVQNTDIKLVGIDYLS 222 (281)
Q Consensus 155 ~~~It~edle~~~i~~g~d~VL~rTG~~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~~V~~VGiD~~S 222 (281)
-..++.++++.....+..|+|+|=||-..+ -++++..++|.++ ||.+--.|+.+
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 457999999875322224899999996432 2578999999995 88777766643
No 8
>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=45.03 E-value=35 Score=26.87 Aligned_cols=57 Identities=18% Similarity=0.181 Sum_probs=38.9
Q ss_pred cCCCccCCHHHHhcC-CCCCCCeEEEEEeccCcccccccccccCCCcccCHHHHHHHHhCCCceEEeecCCC
Q 023541 152 VPRDKNITAEVMESL-NIPRGVRRVIFRTLNTDRKLMFKREFDSSYVGFMKDGARWLVQNTDIKLVGIDYLS 222 (281)
Q Consensus 152 v~~~~~It~edle~~-~i~~g~d~VL~rTG~~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~~V~~VGiD~~S 222 (281)
..+...++.++++.. ...+..|+|+|=||... --++++..++|.++ ||.+--.|+.+
T Consensus 33 ~~~~~~l~~~~l~~l~~~~p~pe~liiGtG~~~-------------~~~~~~~~~~l~~~-GI~ve~m~T~~ 90 (110)
T PF04430_consen 33 VKSPHDLTPEDLEELLELEPKPEVLIIGTGKRQ-------------LFLPPELREYLRKK-GIGVEVMDTPA 90 (110)
T ss_dssp HSSTTCEETHHHHHHHCTCCS-SEEEEEETTS--------------SECTHHHHHHHHTT-T-EEEEE-HHH
T ss_pred CCCcccCCHHHHHHHHhccCCCcEEEEccCCcc-------------ccCCHHHHHHHHHc-CCeEEEECHHH
Confidence 345678999999875 33234489999999642 13679999999985 88777666643
No 9
>COG3958 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]
Probab=42.07 E-value=39 Score=31.91 Aligned_cols=46 Identities=20% Similarity=0.177 Sum_probs=34.3
Q ss_pred CCCCCeEEEEEeccCcccccccccccCCCcccCHHHHHHHHhCCCceEEeecCCCcCCCCC
Q 023541 168 IPRGVRRVIFRTLNTDRKLMFKREFDSSYVGFMKDGARWLVQNTDIKLVGIDYLSAAAHDD 228 (281)
Q Consensus 168 i~~g~d~VL~rTG~~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~~V~~VGiD~~Svd~~~~ 228 (281)
++.|.|+.+|-||-. ..-.-++|+-|.++ ||++=-+|.+++-+.|+
T Consensus 189 LrdG~D~tiiA~G~m--------------v~~al~AA~~L~~~-GIsa~Vi~m~tIKPiD~ 234 (312)
T COG3958 189 LRDGSDLTIIATGVM--------------VAEALEAAEILKKE-GISAAVINMFTIKPIDE 234 (312)
T ss_pred eecCCceEEEecCcc--------------hHHHHHHHHHHHhc-CCCEEEEecCccCCCCH
Confidence 344556666666642 22357899999996 99999999999998764
No 10
>COG3737 Uncharacterized conserved protein [Function unknown]
Probab=39.90 E-value=25 Score=28.82 Aligned_cols=58 Identities=17% Similarity=0.069 Sum_probs=35.9
Q ss_pred EcCCCccCCHHHHhcC-CCCCCCeEEEEEeccCcccccccccccCCCcccCHHHHHHHHhCCCceEEeecCCCcCC
Q 023541 151 DVPRDKNITAEVMESL-NIPRGVRRVIFRTLNTDRKLMFKREFDSSYVGFMKDGARWLVQNTDIKLVGIDYLSAAA 225 (281)
Q Consensus 151 Dv~~~~~It~edle~~-~i~~g~d~VL~rTG~~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~~V~~VGiD~~Svd~ 225 (281)
++++.+.+|+++++.. ..-+..++|||-||...+. +.++.-.=|.. ..||+|++|.+.
T Consensus 48 ~v~~~~~Lt~e~f~~vl~~a~~~EilliGTG~~~rf-------------~p~~l~aal~~----~gIsve~Mst~A 106 (127)
T COG3737 48 EVATLSDLTPEDFERVLAEAPDVEILLIGTGARLRF-------------PPPKLRAALKA----AGISVEPMSTGA 106 (127)
T ss_pred cccChhhCCHHHHHHHHhcCCCceEEEEecCccccC-------------CCHHHHHHHHH----cCCccccccchh
Confidence 4555678999999874 2223458999999974431 12233222333 346889988775
No 11
>COG3946 VirJ Type IV secretory pathway, VirJ component [Intracellular trafficking and secretion]
Probab=38.94 E-value=37 Score=33.56 Aligned_cols=25 Identities=28% Similarity=0.371 Sum_probs=21.9
Q ss_pred cccCHHHHHHHHhCCCceEEeecCCC
Q 023541 197 VGFMKDGARWLVQNTDIKLVGIDYLS 222 (281)
Q Consensus 197 Pgls~eaA~~L~e~~~V~~VGiD~~S 222 (281)
-.|++|.++||.++ ||-.||+|++-
T Consensus 273 r~lDk~v~~~l~~~-gvpVvGvdsLR 297 (456)
T COG3946 273 RDLDKEVAEALQKQ-GVPVVGVDSLR 297 (456)
T ss_pred hhhhHHHHHHHHHC-CCceeeeehhh
Confidence 46899999999995 99999999654
No 12
>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=32.65 E-value=83 Score=25.31 Aligned_cols=53 Identities=13% Similarity=0.149 Sum_probs=37.1
Q ss_pred ccCCHHHHhcCCCCCCCeEEEEEeccCcccccccccccCCCcccCHHHHHHHHhCCCceEEeecCCC
Q 023541 156 KNITAEVMESLNIPRGVRRVIFRTLNTDRKLMFKREFDSSYVGFMKDGARWLVQNTDIKLVGIDYLS 222 (281)
Q Consensus 156 ~~It~edle~~~i~~g~d~VL~rTG~~~~~~~~~~~y~~~~Pgls~eaA~~L~e~~~V~~VGiD~~S 222 (281)
..++.+|++..--. +.++|||=||-..+. -++++..+.|.++ ||.+.-.||.+
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 36889999875322 247999999964321 2578888999985 88877766643
No 13
>PRK06932 glycerate dehydrogenase; Provisional
Probab=23.72 E-value=3.5e+02 Score=25.32 Aligned_cols=33 Identities=15% Similarity=0.022 Sum_probs=24.2
Q ss_pred cCH-HHHHHHHhCCCceEEeecCCCcCCCCCCcHh
Q 023541 199 FMK-DGARWLVQNTDIKLVGIDYLSAAAHDDLLPS 232 (281)
Q Consensus 199 ls~-eaA~~L~e~~~V~~VGiD~~Svd~~~~~~p~ 232 (281)
+.+ +..+.|.+. .+...|.|.+..|+.+...|.
T Consensus 238 Vde~AL~~aL~~g-~i~gAaLDV~~~EP~~~~~pl 271 (314)
T PRK06932 238 VDEQALLDALENG-KIAGAALDVLVKEPPEKDNPL 271 (314)
T ss_pred cCHHHHHHHHHcC-CccEEEEecCCCCCCCCCChh
Confidence 444 457888874 999999999998876544444
No 14
>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=20.88 E-value=1.3e+02 Score=29.56 Aligned_cols=51 Identities=20% Similarity=0.169 Sum_probs=36.9
Q ss_pred CCCcccCHHHHHHHHhCCCceEEeecCCCcCCCCCC-cHhHHhhhhCCCeeEEE
Q 023541 194 SSYVGFMKDGARWLVQNTDIKLVGIDYLSAAAHDDL-LPSHYEFLEGREVILVE 246 (281)
Q Consensus 194 ~~~Pgls~eaA~~L~e~~~V~~VGiD~~Svd~~~~~-~p~H~~lL~~~gI~iiE 246 (281)
.-|||++.+..+++.+. +++.|-+...+....+.. .+.=+.+.+ +||+++=
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 35899999999999995 999999988888776532 233333333 5777665
No 15
>PRK04183 glutamyl-tRNA(Gln) amidotransferase subunit D; Validated
Probab=20.20 E-value=1.3e+02 Score=29.68 Aligned_cols=51 Identities=16% Similarity=0.110 Sum_probs=37.2
Q ss_pred CCCcccCHHHHHHHHhCCCceEEeecCCCcCCCCCC-cHhHHhhhhCCCeeEEE
Q 023541 194 SSYVGFMKDGARWLVQNTDIKLVGIDYLSAAAHDDL-LPSHYEFLEGREVILVE 246 (281)
Q Consensus 194 ~~~Pgls~eaA~~L~e~~~V~~VGiD~~Svd~~~~~-~p~H~~lL~~~gI~iiE 246 (281)
.-|||++.+..+++.++ +++.+-+...+....+.. .+.=+.+.+ +||+++=
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 35899999999999995 999999988888766532 233344443 6777665
Done!