HHsearch alignment for GI: 254780148 and conserved domain: pfam03439
>pfam03439 Spt5-NGN Early transcription elongation factor of RNA pol II, NGN section. Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit.
Probab=97.86 E-value=2.5e-05 Score=51.94 Aligned_cols=79 Identities=20% Similarity=0.284 Sum_probs=54.3
Q ss_pred EEEEECCCCHHHHHHHHHHHHHHC-CCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHHCCCE
Q ss_conf 899952885389999999999977-9811143266313101277202035664120330999999618652244420330
Q gi|254780148|r 6 YIVQVYSNCEKKAVESIGGRLSRS-GLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDTPK 84 (177)
Q Consensus 6 yvv~t~~~~E~~v~~~L~~~~~~~-~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t~g 84 (177)
T Consensus 2 ~~Vk~~~G~E~~va~~l~~k~~~~~~~~l~I~Si~~p-----------------~~lkGyIyVEA~~~~~v~~ai~gi~~ 64 (82)
T pfam03439 2 WAVKCTAGQEREVAISLMNKAEALKKENLEIYSIFVP-----------------DGLKGYIYVEADRQADVERALEGLPH 64 (82)
T ss_pred EEEECCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEEC-----------------CCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf 7587389819999999999998704688745999954-----------------89846999987988999999960377
Q ss_pred EEEEECCCCCCCCCCHHHHHHH
Q ss_conf 3664327886100258899999
Q gi|254780148|r 85 VIGFLGTGENPSPVTDSEIEHI 106 (177)
Q Consensus 85 V~~~l~~~~~P~~i~~~ei~~l 106 (177)
T Consensus 65 v~~~-----~~~~Vp~~E~~~~ 81 (82)
T pfam03439 65 VRGV-----VMGLVPIKEMEHL 81 (82)
T ss_pred HHCC-----CCCCCCHHHHHCC
T ss_conf 7465-----7752888997510