HHsearch alignment for GI: 254780417 and conserved domain: TIGR00580

>TIGR00580 mfd transcription-repair coupling factor; InterPro: IPR004576 All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by TcrF, which releases RNAP and the truncated transcript. The TcrF may replace RNAP at the lesion site and then recruit the UvrA/B/C repair system.; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair.
Probab=99.84  E-value=4.3e-21  Score=155.92  Aligned_cols=147  Identities=16%  Similarity=0.229  Sum_probs=109.4

Q ss_pred             HHCCCCCEEECCCCCCEEEEEEEE-EEECCCCHHHEEEECCCCCCE-EEEECCCHHHCCCCCCCCCHHHHHHHHHCCCCC
Q ss_conf             313899869748785099976789-864873025302202488856-998052012104543344102467898507866
Q gi|254780417|r   12 QGFRTGEHIVYPAHGVGTITEIKE-QEVAGMKLEFFVIAFDKDKMC-LKVPVGKAIDIGMRKLSEAHFVERALKLVRGKA   89 (188)
Q Consensus        12 ~~FkvGD~VVy~~~GVg~i~~I~~-~~i~g~~~eyy~L~~~~~~~~-l~vPv~~~~~~~~R~~~~~~e~~~l~~~l~~~~   89 (188)
T Consensus       381 ~~L~~Gd~VVH~~hGIG~F~~l~~~~~~~g~~~DYL~l~Ya-~~~k~LyvPve~~~li~rY~G~~~~~p~--L~kL----  453 (997)
T TIGR00580       381 NELKPGDYVVHKDHGIGKFLGLEKKLKVLGIERDYLVLEYA-GEDKKLYVPVEQLDLISRYVGGEGKNPE--LDKL----  453 (997)
T ss_pred             HCCCCCCEEEECCCCCCEEHHHHHHHHHCCCCCCEEEEEEC-CCCCEEEECCCHHHHHHHHCCCCCCCCC--CCCC----
T ss_conf             03799887775335850214223214424765241244402-7786686033124455332067889764--1027----


Q ss_pred             CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             44665503899999998516899999999999984101000001268999999999997746774899899999999985
Q gi|254780417|r   90 RVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNL  169 (188)
Q Consensus        90 ~~~~~~~~~R~~~~~~~lksgd~~~~a~vik~L~~~~~~k~l~~~e~~~l~~A~~~L~~Efa~~l~i~~eea~~~I~~~L  169 (188)
T Consensus       454 ------Gg~~W~~~K~kv~~~v~~iA~~Li~lyA~R~~~~G~af~~D~---e~~~~Fe~~FPfeeT~DQ~~AI~eik~Dm  524 (997)
T TIGR00580       454 ------GGKSWEKTKAKVKKSVKEIAAKLIELYAKRKASKGHAFPPDD---EWQAEFEDSFPFEETPDQLKAIEEIKADM  524 (997)
T ss_pred             ------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCH---HHHHHHHHHCCCCCCHHHHHHHHHHHHHH
T ss_conf             ------838899999999999999999999999987515898898880---89999998387889778999999999974


Q ss_pred             HCCCC
Q ss_conf             04675
Q gi|254780417|r  170 SSKSS  174 (188)
Q Consensus       170 ~~~~~  174 (188)
T Consensus       525 ~~~~~  529 (997)
T TIGR00580       525 ESPRP  529 (997)
T ss_pred             CCCCC
T ss_conf             06898