HHsearch alignment for GI: 254780229 and conserved domain: TIGR01587
>TIGR01587 cas3_core CRISPR-associated helicase Cas3; InterPro: IPR006474 This entry represents a highly conserved core region of the Cas3 sequences. The proteins are found in association with CRISPR repeat elements in a broad range of bacteria and Archaea . Cas3 appears to be a helicase, containing a DEAD/DEAH box region and conserved C-terminal domain. Some but not all members have an N-terminal HD domain region (IPR006674 from INTERPRO), these sequences are not included within this group..
Probab=94.56 E-value=0.25 Score=28.77 Aligned_cols=72 Identities=31% Similarity=0.493 Sum_probs=36.3
Q ss_pred EEEECCCCCCCHHHHHHHHHHH---HHC-C--CEEEEEECCHHHHHHHHHHHHH----CCCCC--EEEECCCCCHHHHHH
Q ss_conf 5994287877038999999999---967-9--8289960105899999986443----58441--365402661108999
Q gi|254780229|r 422 LIIEGPPGTGKSQTITNIIAAA---MLH-G--KKILFCAQKMAAIEVVRHRLEK----AGLGE--FCLELHSHKVHKRAI 489 (1775)
Q Consensus 422 ~vi~GPPGTGKSQTIaNlIa~~---la~-G--k~VLfVaeK~aALdVV~~RL~~----~gLg~--~cleLHs~ka~k~~v 489 (1775)
T Consensus 2 ~v~~APTG~GKT-e~aL~~A~~sah~~k~~~~~~~I~alP~r~~~na~~~r~~~sash~-Fg~P~~~~~~~ssrfnh~~~ 79 (424)
T TIGR01587 2 LVIEAPTGYGKT-EAALLWALKSAHLIKKQKADKVIFALPTRVTINAMYRRLKESASHL-FGSPELVLLLHSSRFNHLAS 79 (424)
T ss_pred EEEECCCCCCHH-HHHHHHHHHHHHHHHHHHHCCEEEECCHHHHHHHHHHHHHHHHHHH-CCCCCCCCCCCCCHHHHHHH
T ss_conf 688617899878-9999999863666422444010122026888999999999867754-17854323345522678999
Q ss_pred HHHHHH
Q ss_conf 999999
Q gi|254780229|r 490 LDDLRK 495 (1775)
Q Consensus 490 l~~L~~ 495 (1775)
T Consensus 80 ~ik~~~ 85 (424)
T TIGR01587 80 SIKLRK 85 (424)
T ss_pred HHHHHH
T ss_conf 999877