HHsearch alignment for GI: 254780601 and conserved domain: TIGR03117
>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.
Probab=99.55 E-value=1.2e-11 Score=97.49 Aligned_cols=87 Identities=23% Similarity=0.227 Sum_probs=56.1
Q ss_pred HHCCCCCCCCEEEEECCCHHHHHHHHHHHHHC-CCCCCCCCCCCC-HHHHHHHHHHHHCCCEEEEEECCCCCCCCCCC--
Q ss_conf 20010235641677513023345655555422-666301048999-99999998665448814998538650014578--
Q gi|254780601|r 236 VNILRYHGAKNAIVFCSTRASVSRFTKVLAEH-LFQVVALSGELS-QQERSNALQMMRDGRARVCIATDVAARGIDLP-- 311 (573)
Q Consensus 236 ~~ll~~~~~~~~ivF~~t~~~~~~l~~~L~~~-g~~~~~lhg~~~-q~~R~~~~~~fr~g~~~vLV~TDvaaRGiDi~-- 311 (573)
T Consensus 463 ~~li~~~-~Gr~LvLFTS~r~~~~~ae~l~~~l~~~~l~Qge~~~~~~l~~~~~~~f~~~~~svLfGT~SfWEGVDvpG~ 541 (636)
T TIGR03117 463 AAILRKA-QGGTLVLTTAFSHISAIGQLVELGIPAEIVIQSEKNRLASAEQQFLALYANGIQPVLIAAGGAWTGIDLTHK 541 (636)
T ss_pred HHHHHHC-CCCEEEEECCHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCC
T ss_conf 9999870-798899704099999999999722788658745764035689999998727899689867764066257886
Q ss_pred ------C--CCEEEEECCCC
Q ss_conf ------8--73389705887
Q gi|254780601|r 312 ------D--LELVIHAELSS 323 (573)
Q Consensus 312 ------~--v~~Vin~d~P~ 323 (573)
T Consensus 542 ~~~~~~Gd~Ls~VII~rLPF 561 (636)
T TIGR03117 542 PVSPDKDNLLTDLIITCAPF 561 (636)
T ss_pred CCCCCCCCCCEEEEEECCCC
T ss_conf 66788777420665756998