HHsearch alignment for GI: 254780934 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=99.15 E-value=8.5e-09 Score=70.96 Aligned_cols=171 Identities=16% Similarity=0.225 Sum_probs=126.8
Q ss_pred EEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEECCC-CEEEEECCCCHHHHHHHHHHC
Q ss_conf 2499996578645113135313799999988763221002366567348999982685-056102047868999998601
Q gi|254780934|r 172 LDMMIVLDVSRSMESFFDSSITKIDMAIKSINAMLEEVKLIPDVNNVVQSGLVTFSNK-IEEFFLLEWGVSHLQRKIKYL 250 (374)
Q Consensus 172 ~di~~VlD~SgSM~~~~~~~~~ki~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~t~~~~~~~~~i~~l 250 (374)
T Consensus 4 R~l~iiiD~S~am~~~-D~~PtRl~~~~~~l~~Fi~effdqNPi---sqlGii~~rn~~a~~ls~lsgn~~~hi~~l~~~ 79 (183)
T cd01453 4 RHLIIVIDCSRSMEEQ-DLKPSRLAVVLKLLELFIEEFFDQNPI---SQLGIISIKNGRAEKLTDLTGNPRKHIQALKTA 79 (183)
T ss_pred EEEEEEEECCHHHHHC-CCCCCHHHHHHHHHHHHHHHHHCCCCC---CEEEEEEEECCEEEEEEECCCCHHHHHHHHHHC
T ss_conf 6999999883767756-589549999999999999998707974---048999994681699764689989999999854
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCC
Q ss_conf 33687744420367677643222333310257886564279998068778888806899999999978987999992482
Q gi|254780934|r 251 SKFGVSTNSTPGLKYAYNQIFDMQGMRQHCNTEDANYKKIIVFMTDGENLSTKEDQQSLYYCNEAKKRGAIVYAIGIRVI 330 (374)
Q Consensus 251 ~~~g~~T~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~k~iillTDG~~~~~~~~~~~~~~~~~~k~~gi~IytIg~~~~ 330 (374)
T Consensus 80 ~~~~G~~SLqN~Le~A~~~L~~~P---------~~~sREILiI-~~Sl~t~--DpgdI~~ti~~lk~~~IrvsvI~l~aE 147 (183)
T cd01453 80 RECSGEPSLQNGLEMALESLKHMP---------SHGSREVLII-FSSLSTC--DPGNIYETIDKLKKENIRVSVIGLSAE 147 (183)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHCC---------CCCCEEEEEE-ECCCCCC--CCCCHHHHHHHHHHCCCEEEEEEECHH
T ss_conf 589998139999999999982089---------8784489999-7565347--976499999999983978999974278
Q ss_pred CCHHHHHHHC--CCCCEEEECCHHHHHHHHHH
Q ss_conf 2278899823--89817983898999999999
Q gi|254780934|r 331 RSHEFLRACA--SPNSFYLVENPHSMYDAFSH 360 (374)
Q Consensus 331 ~~~~~L~~~A--s~~~~~~a~~~~~L~~~f~~ 360 (374)
T Consensus 148 v--~I~k~l~~~TgG~y~V~lde~H~~~ll~~ 177 (183)
T cd01453 148 M--HICKEICKATNGTYKVILDETHLKELLLE 177 (183)
T ss_pred H--HHHHHHHHHHCCEEEEECCHHHHHHHHHH
T ss_conf 9--99999999839976875399999999995