HHsearch alignment for GI: 254781110 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=98.40 E-value=0.0001 Score=49.24 Aligned_cols=172 Identities=17% Similarity=0.169 Sum_probs=123.5
Q ss_pred CEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCC-CCCCCCCC
Q ss_conf 20122102232422335787666675346766530678899989999851046787655430223204876-43124457
Q gi|254781110|r 192 LIELVVDLSGSMHCAMNSDPEDVNSAPICQDKKRTKMAALKNALLLFLDSIDLLSHVKEDVYMGLIGYTTR-VEKNIEPS 270 (420)
Q Consensus 192 ~~~~~~d~s~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~lt 270 (420)
T Consensus 5 ~l~iiiD~S~am~~~D---------------~~PtRl~~~~~~l~~Fi~effdqNPi---sqlGii~~rn~~a~~ls~ls 66 (183)
T cd01453 5 HLIIVIDCSRSMEEQD---------------LKPSRLAVVLKLLELFIEEFFDQNPI---SQLGIISIKNGRAEKLTDLT 66 (183)
T ss_pred EEEEEEECCHHHHHCC---------------CCCCHHHHHHHHHHHHHHHHHCCCCC---CEEEEEEEECCEEEEEEECC
T ss_conf 9999998837677565---------------89549999999999999998707974---04899999468169976468
Q ss_pred CCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCHH
Q ss_conf 78488999999864046788765388999999861310123345543347767787766624899606867777765348
Q gi|254781110|r 271 WGTEKVRQYVTRDMDSLILKPTDSTPAMKQAYQILTSDKKRSFFTNFFRQGVKIPSLPFQKFIIFLTDGENNNFKSNVNT 350 (420)
Q Consensus 271 ~~~~~~~~~i~~~~~~~~~g~T~~~~gl~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~k~iil~TDG~~~~~~~~~~~ 350 (420)
T Consensus 67 gn~~~hi~~l~~~~--~~~G~~SLqN~Le~A~~~L~~~----------------P~~~sREILiI-~~Sl~t~Dpg--dI 125 (183)
T cd01453 67 GNPRKHIQALKTAR--ECSGEPSLQNGLEMALESLKHM----------------PSHGSREVLII-FSSLSTCDPG--NI 125 (183)
T ss_pred CCHHHHHHHHHHCC--CCCCCHHHHHHHHHHHHHHHHC----------------CCCCCEEEEEE-ECCCCCCCCC--CH
T ss_conf 99899999998545--8999813999999999998208----------------98784489999-7565347976--49
Q ss_pred HHHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHCCCCCEEEECCHHHHHHHHHH
Q ss_conf 999999997898799999548977899999862189827981798999999999
Q gi|254781110|r 351 IKICDKAKENFIKIVTISINASPNGQRLLKTCVSSPEYHYNVVNADSLIHVFQN 404 (420)
Q Consensus 351 ~~~c~~~k~~gi~i~tIgf~~~~~~~~~l~~cas~~~~yf~a~~~~~L~~aF~~ 404 (420)
T Consensus 126 ~~ti~~lk~~~IrvsvI~l~aE--v~I~k~l~~~TgG~y~V~lde~H~~~ll~~ 177 (183)
T cd01453 126 YETIDKLKKENIRVSVIGLSAE--MHICKEICKATNGTYKVILDETHLKELLLE 177 (183)
T ss_pred HHHHHHHHHCCCEEEEEEECHH--HHHHHHHHHHHCCEEEEECCHHHHHHHHHH
T ss_conf 9999999983978999974278--999999999839976875399999999995