HHsearch alignment for GI: 254781061 and conserved domain: TIGR01981
>TIGR01981 sufD FeS assembly protein SufD; InterPro: IPR011542 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents SufD proteins that form part of the SufBCD complex in the SUF system. No specific functions have been assigned to these proteins.; GO: 0005515 protein binding, 0016226 iron-sulfur cluster assembly.
Probab=100.00 E-value=0 Score=613.57 Aligned_cols=365 Identities=31% Similarity=0.547 Sum_probs=315.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHCCCC----CCCCCCCCC-CC------H--HHCCCCEEEEEECCCCCCCCCCCCCCCCCHH
Q ss_conf 239972474258878977513576----443211111-10------0--0015815999834654200044575410056
Q gi|254781061|r 45 LPTRKIENWHYTDLKNILKVLPTN----KNSIATLQK-KY------K--PLVADSIQLSISQQPSSSILKEKNIEVLPFS 111 (428)
Q Consensus 45 lPtkK~E~WKyT~l~~l~~~~~~~----~~~~~~~~~-~~------~--~~~~d~~~i~~~~~~~~~~l~~~~i~~~~~~ 111 (428)
T Consensus 1 ~~~~~~~~W~~t~l~~~~~~~~~~~LLW~~~~~~~~~~~~~~lvq~~~~~~~~~~~~~~~~~G~~~~~l~~~~~~~~~~~ 80 (397)
T TIGR01981 1 LPTRRIEEWRYTDLSKLLNESFQPPLLWRAKVPDEVKAKGGLLVQVLSETAVSNLVRLVFVNGVFVPDLSDADPLLPELL 80 (397)
T ss_pred CCCCCCCEEEECCCHHCCCCCCCCCEEECCCCCCCCHHCCCEEEEEEEEEECCCCCCHHHCCCEEECHHHHHCCCCCCCC
T ss_conf 98974103630352120001478530002578754210077068986554215663001108732000222034664321
Q ss_pred HH--C----CCC--HHHCCCCCCCCCCHHHHHHHHHCCCCEEEEEECCEEECCCEEEEEECCCCC------CCEEEEEEC
Q ss_conf 52--1----242--010001345554456678875213874877305447702303432022322------210121001
Q gi|254781061|r 112 HI--E----NTD--ENSYCLEPLSEHDTIGYINGILSNDGYKVVIPDECQLNVPLELQAIQCGGQ------MHLRYPISF 177 (428)
Q Consensus 112 ~~--~----~~~--~~~~~~~~~~~~d~f~~LN~A~~~~g~~I~V~~~~~~~~PI~i~~~~~~~~------~~~r~~I~v 177 (428)
T Consensus 81 ~~~~~~~~~~~~e~~~~yL-~~~g~d~~~~~~~~~~~~~g~~~~~~~~~~~~~Pi~~~~~~~~~~~e~~~~~~~~~~i~~ 159 (397)
T TIGR01981 81 EDLLEARAVLSDEIQSKYL-QFEGADERFTALNAALFNDGTVLYVPKGVEVEEPIEIKFIGVAGEGEKKAFVHPRLLIEV 159 (397)
T ss_pred CCCCCCCCCCHHHHHHHCC-CCCCCHHHHHHHHHHHCCCEEEEEECCCCEEECCEEEEEEEECCCCCEEEEEECCEEEEE
T ss_conf 0013772567379998506-745833775665563135159999658947733489999840676750136534538998
Q ss_pred CCCCCEEEEEEC--CCCCCCCE-EECCCEEEEECCCCEEEEEECCCCCCCEEEEE-ECEEEECCCCCEEEEEEECCCCCE
Q ss_conf 798613555303--56675520-10031289964886376630024565301432-000112035514677864256512
Q gi|254781061|r 178 GMNSRTTVVERY--TTLTNDNS-FVSSIADIKVGEGADITWVIVLDQGIEDTHLG-QLRVILEKKSSLKVFVLNIGQGLS 253 (428)
Q Consensus 178 ~~ns~~~iiE~~--~~~~~~~~-~~n~~~ei~l~~~A~l~~~~iq~~~~~s~~~~-~~~~~~~~~S~~~~~~~~~Gg~~~ 253 (428)
T Consensus 160 ~~~~~~~v~e~~~~~~~~~~~~Y~~n~v~~i~~~~~A~v~~~~~~~~~~~~~~~~W~~~~~~~~~a~~~~~~~~~Gg~~~ 239 (397)
T TIGR01981 160 EKGSKITVIERFEGISLNESKAYFTNSVVEITVGANASVSFVRVQDFSKNSTHFSWNHRAKIGKDARLRLAVVNLGGKLS 239 (397)
T ss_pred CCCCEEEEEEEEECCCCCCCCEEEEECEEEEEECCCCEEEEEEEECCCCCEEEEEEEEEEEEECCCEEEEEEEECCCCEE
T ss_conf 68980799998325788864314650408999744878999996158981699865577765128658999999278579
Q ss_pred EEEEEEEEECCCCEEEEEEEEECCCCCCHHHHHHHHHCCCCCEEEEEEEEEECCCCEEEEECCCCCCCCCCCCCCCEEEE
Q ss_conf 44335665135412466334422744100111222212777526888730004885278741010136641000000000
Q gi|254781061|r 254 RRELSIDVKGEESQFMLRGINLLSGKAHSDLSMFLRHKVPNTCSTSVIRNIVLEKSTGVFQGAVHVSSEAQGSNARMTAN 333 (428)
Q Consensus 254 R~~i~i~L~Ge~a~~~~~g~~l~~~~q~~D~~~~i~H~~~~t~S~~~~k~vl~d~s~~vf~G~i~V~~~a~~t~~~q~~~ 333 (428)
T Consensus 240 ~~~~~~~l~G~~s~~~~~gl~~~~~~~~~D~~~~v~h~~~~~~S~~~~~g~~~d~a~~vF~G~~~i~~~A~~tda~~~~~ 319 (397)
T TIGR01981 240 RHNLDVDLEGEGSKLEVKGLAIGAGRQHVDVRTLVEHNGPDTKSNILHRGILDDRAHGVFRGIIRIPKGAKGTDAEQLNR 319 (397)
T ss_pred EEEEEEEEECCCEEEEEEEEEEECCCCEEEEEEEEEECCCCCEEEEEEEEEECCCCEEEEEEEEEECCCCCCCCEEEEEE
T ss_conf 99987888246407999998751798157777568871666243289977992684299998788465574863365631
Q ss_pred EEEECCCEEEEEEEEEEEECCCCEEE-EEEEECCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
Q ss_conf 46612871798121247713873365-542212389999999994688989999999999999998858978999999
Q gi|254781061|r 334 TLLFSNEGSFYVKPELEIFADDVQCG-HGATISDINPEHLYYLMARGISKNQACSMLSHAFMSEIVEDLNDQVLQFSI 410 (428)
Q Consensus 334 ~llLs~~a~~~s~P~LeI~~ddV~~~-Hgatvg~id~e~lfYl~sRGi~~~~A~~lli~gF~~~~i~~i~~~~~~~~~ 410 (428)
T Consensus 320 ~LlLs~~A~~d~~P~LeI~~ddV~~~gHgAtVg~iD~e~LFYLrSRGi~~~~A~~L~i~gF~~e~i~~i~~~~l~~~~ 397 (397)
T TIGR01981 320 NLLLSDKARADTKPQLEIDADDVKCSGHGATVGQIDDEQLFYLRSRGIDEEEARRLLIRGFLGEIIEEIPDESLKEEL 397 (397)
T ss_pred EEEECCCCEEEECEEEEEECCCEEECCEECCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHCC
T ss_conf 575478762871216799758243211011003357446576763788989999999998864333213881565229