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