HHsearch alignment for GI: 254780619 and conserved domain: TIGR00143

>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF; InterPro: IPR004421 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesized as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins , , . Members of the HypF family are accessory proteins involved in hydrogenase maturation. They contain the following domains: acylphosphatase, zinc fingers (2 repeats), a YrdC-like domain, and a C-terminal domain with a putative O-carbamoyltransferase motif. The presence of CO and CN- ligands of the active site iron atoms is essential for [NiFe]-hydrogenase enzyme activity . Both ligands have been suggested to originate from carbamoylphosphate , which is required for maturation of [NiFe]-hydrogenases . Escherichia coli HypF interacts with carbamoylphosphate as a substrate and releases inorganic phosphate . In addition, HypF also cleaves ATP into AMP and pyrophosphate in the presence of carbamoylphosphate. This, and the fact that HypF catalyzes a carbamoylphosphate-dependent pyrophosphate ATP exchange reaction, suggest that the protein catalyzes the activation of carbamoylphosphate . The mechanism of action of HypF, as well as of its individual domains, is not yet clear. Mutations in any of the three major signature motifs, the acylphosphatase, the zinc fingers, and the O-carbamoyltransferase motif, can block carbamoylphosphate phosphatase activity. This indicates an integrated cooperativity between these domains in the cleavage reaction . The N-terminal acylphosphatase (ACP) domain is thought to support the conversion of carbamoylphosphate into CO and CN- , . Biochemical results demonstrating its ACP activity are not available , . ACPs are small enzymes that specifically catalyze the hydrolysis of carboxylphosphate bonds in acylphosphates, including carbamoylphosphate . Zinc fingers have been implicated in bivalent cation binding or as part of a chaperone domain interacting with the large subunit precursor, but experimental studies on such a function are lacking thus far. The YrdC-like domain is present in protein families with regulatory functions (IPR012200 from INTERPRO, IPR010923 from INTERPRO) and has been implicated in RNA binding . It is not clear what function it may have in members of the HypF family. A C-terminal domain is distantly related to peptidase M22, but contains a conserved O-carbamoyltransferase motif required for the carbamoylphosphate phosphatase activity . The function of this domain is not clear. Nomenclature note: the following names are used as synonyms of HypF: HupY in Azotobacter chroococcum, HupN in Rhizobium leguminosarum, HydA in Escherichia coli. In other organisms, these names are used to designate various "hydrogenase cluster" proteins unrelated to the members of this family. ; GO: 0030528 transcription regulator activity.
Probab=91.68  E-value=0.096  Score=32.46  Aligned_cols=86  Identities=17%  Similarity=0.240  Sum_probs=52.0

Q ss_pred             HHHHHHHHCCCC--C-EEEEEECCCCCHHHHHHH-----HHHHCCCCEEEEECCHHHH-HHH----CCCEEE-EEEECCC
Q ss_conf             344555430389--7-689962355723566789-----9997199739994001211-001----000136-7740553
Q gi|254780619|r  260 SAILERFQKRFG--V-KPAEWHSSLSTSMREKIW-----RQVARGAISVIVGVRSALF-LPF----KKLGLI-VIDEEHD  325 (731)
Q Consensus       260 ~Q~~~rl~~rF~--~-~v~v~HS~ls~~eR~~~w-----~~i~~G~~~IVIGtRSAif-~P~----~nLglI-IvDEEHd  325 (731)
T Consensus       231 ~~~V~~LR~~k~RP~kPfAvM~~~l~~~~~~A~~~~~E~~~L~S~aaPIVl~~Kk~dy~~~~~~iAp~l~~iGVM-----  305 (799)
T TIGR00143       231 DEVVERLRLRKNRPAKPFAVMSPDLESIEEHAELNNLEKELLLSPAAPIVLLRKKKDYIKLFENIAPNLDTIGVM-----  305 (799)
T ss_pred             HHHHHHHHHHCCCCCCCCEECCCCCCCHHHHHCCCHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCCCEEEE-----
T ss_conf             489999986457889751441530200155505586899851166477677615757443560116796932586-----


Q ss_pred             CCCHHCCCCCCCHHHHHHHHHHHCCCCEECCCCC
Q ss_conf             2100002443224899999751103210000245
Q gi|254780619|r  326 ISYKQEEGILYNARDMSIVRGKIESFPVVLVSAT  359 (731)
Q Consensus       326 ~sykq~~~pry~aRdvA~~Ra~~~~~~lilgSAT  359 (731)
T Consensus       306 --------LPYtPLHhLLL~-~~~~~p~VmTSaN  330 (799)
T TIGR00143       306 --------LPYTPLHHLLLQ-ELLAKPLVMTSAN  330 (799)
T ss_pred             --------CCCCHHHHHHHH-HHCCCCEEEECCC
T ss_conf             --------488645789867-6227771660267