HHsearch alignment for GI: 254780281 and conserved domain: TIGR01068
>TIGR01068 thioredoxin thioredoxin; InterPro: IPR005746 Thioredoxins , , , are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of 2 cysteine thiol groups to a disulphide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulphide and a dithiol. TR-S_2 + NADPH + H^+ -> TR-(SH)_2 + NADP^+ (1) trx-S_2 + TR-(SH)_2 -> trx-(SH)_2 + TR-S_2 (2) Protein-S_2 + trx-(SH)_2 -> Protein-(SH)_2 + trx-S_2 (3) In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide (steps 1 and 2). Reduced thioredoxin then directly reduces the disulphide in the substrate protein (step 3) . Protein disulphide isomerase (PDI), a resident foldase of the endoplasmic recticulum, is a multi-functional protein that catalyses the formation and isomerisation of disulphide bonds during protein folding , . PDI contains 2 redox active domains, near the N- and C-termini, that are similar to thioredoxin: both contribute to disulphide isomerase activity, but are functionally non-equivalent . Interestingly, a mutant PDI, with all 4 of the active cysteines replaced by serine, displays a low but detectable level of disulphide isomerase activity . Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity . A number of endoplasmic reticulum proteins that differ from the PDI major isozyme contain 2 (ERp60, ERp5) or 3 (ERp72 ) thioredoxin domains; all of them seem to be PDIs. 3D-structures have been determined for a number of thioredoxins . The molecule has a doubly-wound alternating alpha/beta fold, consisting of a 5-stranded parallel beta-sheet core, enclosed by 4 alpha-helices. The active site disulphide is located at the N-terminus of helix 2 in a short segment that is separated from the rest of the helix by a kink caused by a conserved proline. The 4-membered disulphide ring is located on the surface of the protein. A flat hydrophobic surface lies adjacent to the disulphide, which presumably facilitates interaction with other proteins. One invariant feature of all thioredoxins is a cis-proline located in a loop preceding beta-strand 4. This residue is positioned in van der Waals contact with the active site cysteines and is important both for stability and function . Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase . Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0006662 glycerol ether metabolic process, 0045454 cell redox homeostasis.
Probab=98.25 E-value=6.1e-06 Score=56.70 Aligned_cols=89 Identities=24% Similarity=0.274 Sum_probs=66.8
Q ss_pred HCC-CEEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCHHHHHHHHHHCCCCEECCCCCHHHHH
Q ss_conf 499-6799996047776544688887765554302443330588765143333305777775313686422458988989
Q gi|254780281|r 54 LYI-KPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDPTGTLLNAYFITVDPKRDTPEVMKKFVQRFSDRIIGISGDPIDVM 132 (201)
Q Consensus 54 ~~G-k~~li~F~~T~Cpd~Cp~~l~~l~~~~~~l~~~~~~v~~v~IsvDP~rDt~e~l~~y~~~~~~~~~~ltg~~~~i~ 132 (201)
T Consensus 11 ~~~d~~VlVDFWA~WC-GPCKm~aP~lee~a~e~~---~~v~~~KlnvD~~~~~A------------------------- 61 (101)
T TIGR01068 11 ASSDKPVLVDFWAPWC-GPCKMIAPILEELAKEYE---GKVKFVKLNVDENPDIA------------------------- 61 (101)
T ss_pred HHCCCCEEEEEECCCC-CCCCCHHHHHHHHHHHCC---CCCEEEEEECCCCCCCH-------------------------
T ss_conf 7189737887435999-873442468888875416---97468885347883414-------------------------
Q ss_pred HHHHHCCEEEEECCCCCCCCCCCEEEEEEEEEEEECCCCCEEEEECCCCCHHHHHHHHHHH
Q ss_conf 8888609088622565567777525874206999858982999857898889999999999
Q gi|254780281|r 133 RVAKNFRIYVNNVLAEKSGVEEKYFVDHTTALLLFDTAGSIVGVIPYKDDSDSAIEKINRL 193 (201)
Q Consensus 133 ~l~~~~~v~~~~~~~~~~~~~~~y~i~H~~~~~lid~~G~i~~~~~~~~~~~~i~~~i~~l 193 (201)
T Consensus 62 ---~~ygi~S------------------IPTl~lF-K~G~~V~~~vGa~pK~~l~~~~~~~ 100 (101)
T TIGR01068 62 ---AKYGIRS------------------IPTLLLF-KNGKVVDRSVGALPKAALKQLINKN 100 (101)
T ss_pred ---HHCCCCC------------------CCEEEEE-CCCEEEEEEECCCCHHHHHHHHHHH
T ss_conf ---4528540------------------5637775-1982520061356979999999871