HHsearch alignment for GI: 254781059 and conserved domain: TIGR01980

>TIGR01980 sufB FeS assembly protein SufB; InterPro: IPR010231 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 SufB, which is part of the SUF system and forms a complex with SufBCD.; GO: 0005515 protein binding, 0016226 iron-sulfur cluster assembly.
Probab=100.00  E-value=0  Score=1252.75  Aligned_cols=458  Identities=51%  Similarity=0.851  Sum_probs=448.1

Q ss_pred             CCCCCCCCCCCC-EECCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEECCC---
Q ss_conf             221257413531-0204888899999999863299889999999999999968877866587665682000310056---
Q gi|254781059|r   17 DQYKYGFETNIQ-VDKAPKGLNEDIIRFISAKKNEPDWMLEWRLLAYRRWLTMKDPSWARIRYPAIDFDDLYYYAAP---   92 (489)
Q Consensus        17 ~~y~~~~~~~~~-~~~~~~gl~~~~i~~iS~~k~EP~Wl~e~R~~Al~~f~~l~~P~W~~~~l~~i~~~~i~~~~~p---   92 (489)
T Consensus         1 ~~~~yGf~~~~~~~~~~~kGLt~~VV~~IS~~K~EP~WMLd~RLrale~f~k~p~P~Wg~~dl~~iD~~~~vyY~~PdCn   80 (469)
T TIGR01980         1 TEYKYGFHDEDKYAYETEKGLTEEVVREISEKKGEPDWMLDFRLRALELFLKMPMPTWGRPDLSGIDIEDIVYYSKPDCN   80 (469)
T ss_pred             CCCCCCCCCCCCHHHHCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHCCCCCCCCCH
T ss_conf             97667751222224440789888999999730588868999999999988428889888888886786453434377703


Q ss_pred             ---C-CCC--CCCCCCCCCHHHHHHHHHCCCCHHHHHHHCCCCCCCCEEEEEECCEEEECCCHHHHHHCCEEEEEHHHHH
Q ss_conf             ---5-333--4332101587888877651765111111023444431000121350220200567874790885589987
Q gi|254781059|r   93 ---K-SIV--GPQSLDDVDPELLRTYEKLGIPIREQEILAGVQTSKVAVDAVFDSVSVVTTFKEELKKSGVIFMPISEAI  166 (489)
Q Consensus        93 ---~-~~~--~~~sld~v~~ei~~tf~kLgip~~e~~~l~g~~~~~v~v~~~~ds~~v~~~l~~~L~~~GVi~~~l~eA~  166 (489)
T Consensus        81 efkKq~~~~r~~~sWdevP~eIk~TFEkLGIPeaE~k~LaG-----vav~AQYdSEviY~~~Ke~L~~~GVIF~d~d~Al  155 (469)
T TIGR01980        81 EFKKQSKKTRKATSWDEVPDEIKDTFEKLGIPEAERKALAG-----VAVGAQYDSEVIYHNIKEDLEEKGVIFCDMDTAL  155 (469)
T ss_pred             HHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHCC-----CEEEEEEEEEEEECCCHHHHHHCCEEECCHHHHH
T ss_conf             33101234215678234678999876444861799987425-----3577886204462220467562987863859986


Q ss_pred             HHHHHHHHHHCCCE-ECCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCEEEEEEECCCCCEECCEEEEEEECCCEEEEEE
Q ss_conf             77789886202211-24565314668876423843887347741342127999965888400221489972772499996
Q gi|254781059|r  167 CEHPDLVKKYLSTV-VPVGDNFYAALNSAVFTDGSFVYIPKGVRCPMELSTYFRINEKGTGQFERTLIIADEGSYVSYLE  245 (489)
Q Consensus       167 ~~~p~lv~~~~~~~-~~~~~~~f~aLn~A~~~~G~fi~Vp~gv~v~~PI~~~~~~~~~~~~~f~r~lIi~ee~S~v~~iE  245 (489)
T Consensus       156 ~~YPdLVKeYF~~v~VPp~DnKFAALn~AVWSGGsFvYVPkGV~v~~PLqtYFRIN~~~~GQFErTLiIadeGa~VhYiE  235 (469)
T TIGR01980       156 KEYPDLVKEYFGKVCVPPSDNKFAALNGAVWSGGSFVYVPKGVRVDMPLQTYFRINSENTGQFERTLIIADEGASVHYIE  235 (469)
T ss_pred             HHCHHHHHHHCCCCCCCCCCCHHHHHHHHEEECCEEEEECCCCEECCCCCCCEECCCCCCCCCEEEEEEEEECCEEEEEE
T ss_conf             51725678662700258763414664021102785798478986666300000028477886325889995177488870


Q ss_pred             CCCCCCCCCCCCCCEEEEEEECCCCEEEEEEEEECCCCCCCCCCCEEEEEEEEEEEECCCEEEEEEEEEECCCEEEEEEE
Q ss_conf             15676544444433058998669958999996304755311448746401467863046303899887514634788538
Q gi|254781059|r  246 GCTAPQRDENQLHAAVVELVALDNAEIKYSTVQNWYPGDSQGKGGIYNFVTKRGDCRGMRSKISWTQLETGSAITWKYPS  325 (489)
Q Consensus       246 ~~~s~~~~~~~~~~~v~Ei~vg~nA~v~~~~iQn~~~~~~~~~~~~~~~~t~r~~~~~~~a~~~~~~~~lG~~~~r~~~~  325 (489)
T Consensus       236 GCsAP~Y~~~sLHAa~VE~~v~~~A~~rYtTvQNWs~N~-~~KGGvyNlvTKRA~veG~ng~meWv~Gs~GSK~Tm~YPs  314 (469)
T TIGR01980       236 GCSAPVYSTNSLHAAVVELIVKEDARVRYTTVQNWSKND-KNKGGVYNLVTKRALVEGENGTMEWVDGSIGSKITMKYPS  314 (469)
T ss_pred             CCCCCCCCCCCCEEEEEEEEECCCCEEEEEEEEECCCCC-CCCCCEEECCCCEEEEECCCCEEEEEECCHHHHHHHHCCE
T ss_conf             232665688871335899998378758984687303788-9985448668723789626877999602400024412552


Q ss_pred             EEEECCCCEEEEEEEEEECCCEEEEEEEEEEEECCCCCCEEEEEEEECCCCEEEEEEEEEECCCCCCCCCEEEEEEEEEC
Q ss_conf             99827872799998776259868997218998367661101000010589468994014733886587430221058845
Q gi|254781059|r  326 CLLRGEQSCGEFYSIAISNGFQQIDSGTKMLHLAKNTTSRIVSKGISAGFSNNTYRGKVSVHRGAAHSRNFTQCDSLLIG  405 (489)
Q Consensus       326 ~~L~G~~a~~~~~gi~l~~~~Q~~D~~~~v~H~~p~t~S~~~~K~i~~d~s~~~f~G~i~v~~~A~~t~~~~~~~~LlLs  405 (489)
T Consensus       315 ~iL~G~~A~~e~~sIa~A~~gQ~~DTGaK~~H~AP~TSStI~sKSIS~ggG~~~YRGLVk~~~~A~~~k~~v~CD~Ll~D  394 (469)
T TIGR01980       315 SILKGEGAKTEFLSIALAGKGQHLDTGAKMIHLAPNTSSTIISKSISKGGGKSSYRGLVKIGKGAKGAKSHVQCDSLLLD  394 (469)
T ss_pred             EEECCCCCCCCCEEEEEECCCCCEECCCEEEEECCCCEEEEEEEEEECCCCEEEEEEEEEECCCCCCCCCEEEEEEEEEC
T ss_conf             47828862114227787247630000753687089962488987887588744302578865765577111256655657


Q ss_pred             CCCEEEEEEEEEEECCCCEEEEEEEECCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             985486223689834875688753202479999999983788989999999999899998858968999999999
Q gi|254781059|r  406 NNCGAHTIPYIESKNSSCNLEHEATTSKISDEHLFYCLQRGIPEEAAIALIVNGFVREVLQKLPMEFAVEAQKLI  480 (489)
Q Consensus       406 ~~a~~~s~P~LeI~~ddv~~~H~Atvg~id~e~LFYL~sRGi~~~~A~~liv~gF~~~v~~~ip~e~~~e~~~li  480 (489)
T Consensus       395 d~S~SdT~P~~ei~n~~v~~~HEAtvsKIsEeqlfYL~sRGl~EedA~~MIV~GF~~pI~keLPmEYAVElnrLi  469 (469)
T TIGR01980       395 DESASDTIPYIEIFNDTVSVEHEATVSKISEEQLFYLMSRGLSEEDARAMIVRGFVEPITKELPMEYAVELNRLI  469 (469)
T ss_pred             CCCCCCCCCEEEEECCCCCEEEEEEECCCCHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHCCHHHHHHHCCCC
T ss_conf             842213243055526833247855520012456889773788889999997515802565523357889840359