HHsearch alignment for GI: 254780942 and conserved domain: cd03359
>cd03359 LbH_Dynactin_5 Dynactin 5 (or subunit p25); Dynactin is a major component of the activator complex that stimulates dynein-mediated vesicle transport. Dynactin is a heterocomplex of at least eight subunits, including a 150,000-MW protein called Glued, the actin-capping protein Arp1, and dynamatin. In vitro binding experiments show that dynactin enhances dynein-dependent motility, possibly through interaction with microtubules and vesicles. Subunit p25 is part of the pointed-end subcomplex in dynactin that also includes p26, p27, and Arp11. This subcomplex interacts with membranous cargoes. p25 and p27 contain imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X), indicating a left-handed parallel beta helix (LbH) structural domain. Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity.
Probab=99.48 E-value=2.3e-13 Score=94.47 Aligned_cols=119 Identities=20% Similarity=0.266 Sum_probs=66.6
Q ss_pred EEEECCCCCEECCCCCCCC---CCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCC------CEEECCCCCCCCEEEEEC
Q ss_conf 1233178410012232234---4200021116313433212111210021344320------000025864432023102
Q gi|254780942|r 267 DTIIQPDTVIEPHVFFGCG---VSIENYVQIRAFSYLEGVHIGKKTIIGPFARIRQ------ETTIEKNVRIGNFCEVKK 337 (442)
Q Consensus 267 ~~~I~~~~~I~~~~~Ig~~---~~Ig~~~~I~~~~~i~~~~Ig~~~~Ig~~~~i~~------~s~i~~~~~Ig~~~ei~~ 337 (442)
T Consensus 21 nI~IG~~ssI~~~avirGD~~~I~IG~~~~I~d~~~I-----------~~~~~~~~~~~~~~p~~IGd~v~Ig~~~~i~- 88 (161)
T cd03359 21 NIVLNGKTIIQSDVIIRGDLATVSIGRYCILSEGCVI-----------RPPFKKFSKGVAFFPLHIGDYVFIGENCVVN- 88 (161)
T ss_pred CEEECCCCEECCCCEEECCCCCEEECCCCEECCCCEE-----------ECCCCCCCCCCCCCCCEECCCEEECCCEEEE-
T ss_conf 7599998789999689678865499998588899899-----------2464435778888772848987989982884-
Q ss_pred CCCCCCCCCCCCCCCCCCEECCCCEECCCEEECCCCCCCCCCCEECCCCEECCCCEEECCEEECCCCEECCC-CEECCCC
Q ss_conf 112478544874555663988998997980883445775456298788798869989378398899899778-3576643
Q gi|254780942|r 338 ATIKEGSKINHLSYVGDSVVGKNVNIGAGTITCNYDGTHKYKTHINENAFIGSNSSLIAPITIGQGTYVASG-SIITQDT 416 (442)
Q Consensus 338 s~i~~g~~i~~~~~igd~~iG~~~~ig~g~i~~n~~g~~~~~~~ig~~~~iG~~~~i~~gv~ig~~~~i~ag-~~v~~dv 416 (442)
T Consensus 89 ----------------~~~Ig~~v~IG~~~~I~~-------g~~Ig~~~~I~~gsvV~~~~~ip~~~~~~G~Pak~i~~l 145 (161)
T cd03359 89 ----------------AAQIGSYVHIGKNCVIGR-------RCIIKDCVKILDGTVVPPDTVIPPYSVVSGRPARFIGEL 145 (161)
T ss_pred ----------------CCEECCCEEECCCCEECC-------CCEECCCCEECCCCEECCCCEECCCCEEEECCEEEEEEC
T ss_conf ----------------889667715579819949-------979999989988989889989899819985180895769
Q ss_pred CCCC
Q ss_conf 6986
Q gi|254780942|r 417 PENS 420 (442)
Q Consensus 417 ~~~~ 420 (442)
T Consensus 146 ~e~~ 149 (161)
T cd03359 146 PECT 149 (161)
T ss_pred CHHH
T ss_conf 9999