HHsearch alignment for GI: 254780897 and conserved domain: TIGR01462
>TIGR01462 greA transcription elongation factor GreA; InterPro: IPR006359 Bacterial GreA and GreB IPR006358 from INTERPRO promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase (RNAP) , allowing RNA transcription to continue past template-encoded arresting sites. GreA and GreB are sequence homologues and have homologues in every known bacterial genome. GreA and GreB stimulate transcript cleavage in different ways; GreA induces cleavage of 3'-RNA fragments 23 nt in length and can only prevent the formation of arrested complexes, whereas GreB induces cleavage of fragments up to 18 nt in length and can rescue pre-existing arrested complexes. The 2.2 Å resolution crystal structure of Escherichia coli GreA comprises an N-terminal antiparallel alpha-helical coiled coil, and a C-terminal globular domain. While the C-terminal domain binds RNAP, the N-terminal coiled coil interacts with the transcript 3' end and is responsible for stimulating the transcript cleavage reaction . Functional differences between GreA and GreB correlate with the distribution of positively charged residues on one face of the N-terminal coiled coil. Because members of the family outside the Proteobacteria resemble GreA more closely than GreB, the GreB clade (IPR006358 from INTERPRO) forms a plausible outgroup and the remainder of the GreA/B family, included in this family, is designated GreA. In the Chlamydias and some spirochetes, the conserved region of these proteins is found as the C-terminal region of a much larger protein. ; GO: 0003677 DNA binding, 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent.
Probab=91.45 E-value=0.64 Score=25.99 Aligned_cols=93 Identities=24% Similarity=0.366 Sum_probs=52.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCC--EEEEEEEEEECCCCCCCCCCCCEEE-EEC-------CC--C--CCC
Q ss_conf 11115789999997643100002343322111--1344456664265346665442036-517-------86--6--563
Q gi|254780897|r 140 EVDEKEIDRQMAEIAKNNVAFEVKETESEIGD--KVTVDYTVSVDNVILEDQSKKNVQF-IVG-------SA--D--LFS 205 (473)
Q Consensus 140 ~vtd~~Id~~i~~l~~~~~~~~~~~~~~~~gD--~v~id~~~~~dg~~~~~~~~~~~~~-~lg-------~~--~--~~~ 205 (473)
T Consensus 48 Ke~Q~~~E~RI~~le~~l~~A~vi~~~~~~~~gd~V~~G~~V~~~~~~----~~e~~~y~IVG~~EaD~~~giekIS~~S 123 (155)
T TIGR01462 48 KEEQGFIEGRIAELEDLLANAEVIDDSKLSTDGDKVSFGSTVTIKDED----TGEEETYTIVGSWEADPKEGIEKISIES 123 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHCEEECCHHHCCCCCCEEECCCEEEEEECC----CCCEEEEEEECCCCCCHHCCCEEEECCC
T ss_conf 999999988999999887620623601004788377157589999838----9964899983452055330807822677
Q ss_pred CHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHHHH
Q ss_conf 10342068878875433234444444100038730467610110
Q gi|254780897|r 206 ETTEILVGLKTGDQKEIERFFPEDHSIKDLAGKKVRLNFSIKEV 249 (473)
Q Consensus 206 ~f~~~liG~k~Gd~~~~~~~~P~d~~~~~laGk~v~f~v~v~~I 249 (473)
T Consensus 124 Plg~aL~Gkk~GD~~~v~~--P~g-----------~~~~~Il~i 154 (155)
T TIGR01462 124 PLGKALIGKKVGDEVEVQV--PKG-----------EKEYEILKI 154 (155)
T ss_pred HHHHHHCCCCCCCEEEEEE--CCC-----------EEEEEEEEE
T ss_conf 0235333762587789985--892-----------379988873