HHsearch alignment for GI: 254781108 and conserved domain: cd01453

>cd01453 vWA_transcription_factor_IIH_type Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.
Probab=98.23  E-value=0.0003  Score=43.89  Aligned_cols=173  Identities=15%  Similarity=0.207  Sum_probs=114.3

Q ss_pred             CCCEEEECCCCCCCCCCCCCCCCHHHHHCCCEECCCCCCCCEEEECCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf             43135750556666667666310123310230126887654031013432201125553334100024566554102202
Q gi|254781108|r  148 ISICMVLDVSRSMEDLYLQKHNDNNNMTSNKYLLPPPPKKSFWSKNTTKSKYAPAPAPANRKIDVLIESAGNLVNSIQKA  227 (398)
Q Consensus       148 ~di~lvlD~SgSm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~  227 (398)
T Consensus         4 R~l~iiiD~S~am~~~D----------------------------------------~~PtRl~~~~~~l~~Fi~effdq   43 (183)
T cd01453           4 RHLIIVIDCSRSMEEQD----------------------------------------LKPSRLAVVLKLLELFIEEFFDQ   43 (183)
T ss_pred             EEEEEEEECCHHHHHCC----------------------------------------CCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             69999998837677565----------------------------------------89549999999999999998707


Q ss_pred             CCCCCCCCEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHCC-CCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCE
Q ss_conf             768776521346541267765431123568999999997357-7888744588999999961134666665667666651
Q gi|254781108|r  228 IQEKKNLSVRIGTIAYNIGIVGNQCTPLSNNLNEVKSRLNKL-NPYENTNTYPAMHHAYRELYNEKESSHNTIGSTRLKK  306 (398)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lt~~~~~~~~~I~~l-~~~G~T~~~~gl~~a~~~l~~~~~~~~~~~~~~~~~k  306 (398)
T Consensus        44 NP-----isqlGii~~rn~~-a~~ls~lsgn~~~hi~~l~~~~~~~G~~SLqN~Le~A~~~L~~~P~--------~~sRE  109 (183)
T cd01453          44 NP-----ISQLGIISIKNGR-AEKLTDLTGNPRKHIQALKTARECSGEPSLQNGLEMALESLKHMPS--------HGSRE  109 (183)
T ss_pred             CC-----CCEEEEEEEECCE-EEEEEECCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCC--------CCCEE
T ss_conf             97-----4048999994681-6997646899899999998545899981399999999999820898--------78448


Q ss_pred             EEEECCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHCCCCCEEEECCHHHHHHHHHH
Q ss_conf             6998158877877777663148999999997898899999547975589999985199818994698999999999
Q gi|254781108|r  307 FVIFITDGENSGASAYQNTLNTLQICEYMRNAGMKIYSVAVSAPPEGQDLLRKCTDSSGQFFAVNDSRELLESFDK  382 (398)
Q Consensus       307 ~iillTDG~~~~~~~~~~~~~~~~~c~~~K~~gi~IytIg~~~~~~~~~~l~~cAs~~~~yy~a~~~~~L~~aF~~  382 (398)
T Consensus       110 ILiI~-~Sl~t~-----DpgdI~~ti~~lk~~~IrvsvI~l~aE--v~I~k~l~~~TgG~y~V~lde~H~~~ll~~  177 (183)
T cd01453         110 VLIIF-SSLSTC-----DPGNIYETIDKLKKENIRVSVIGLSAE--MHICKEICKATNGTYKVILDETHLKELLLE  177 (183)
T ss_pred             EEEEE-CCCCCC-----CCCCHHHHHHHHHHCCCEEEEEEECHH--HHHHHHHHHHHCCEEEEECCHHHHHHHHHH
T ss_conf             99997-565347-----976499999999983978999974278--999999999839976875399999999995