TABLE 2.

ORFs and other loci affected by insertion of ISs

Family/group/CLa	Comment
IS4/ISPepr1/CL ISAcma11	IS(all7115) interrupts a GNAT superfamily protein gene, with alignment of homologs Npun_R0240 and PCC7424_2037 across the mutation site.
IS5/IS1031/CL 1	IS(alr4438, alr4439) is within a questionably significant, 55-aa ORF. IS(all4817, all4816) is within a Bpu10I RE Superfamily protein gene (19). IS(alr5157, alr5158) is within a gene that fuses the start of alr5156 and the end of alr5159 and that has homologs in diverse cyanobacteria and other bacteria. BLASTn shows that IS(all7002, all7001) can be computationally excised from a sequence closely matching that of alr8016. Computational removal of all of these ISs leads to no shift in the reading frame.
IS5/IS1031/CL 2	IS(alr7025) revises the N terminus of a membrane protein presumptively encoded by all7024.
IS110/(−)/IS1594	Removing IS(all0306) destroys asl0305, and removing IS(all1099) destroys asl1098.IS(alr3636) is inserted within an ORF that may encode a DNA mismatch repair protein.
IS200-IS605/IS1341/IS891	Each of IS(all3986) and IS(alr4104) splits a two-component His kinase family gene, and IS(alr7231) splits a Ser/Thr kinase family gene.
IS200-IS605/IS1341/IS891-related CL 2	BLASTn localizes IS(all0315, all0314)-, IS(alr1157)-, and IS(all4465)-flanking regions between ava4874 and ava4875, ava4411 and ava4412, and ava3329 and ava3330, respectively.
IS200-IS605/IS1341/IS891-related CL 6	IS(all7085, alr7086) revises the 5′ terminus of all7084.
IS630/(−)/IS895-related CL 1	IS(alr1726, alr1727) is within a 102-aa ORF that may not be a gene. IS(alr1853, alr1854) is within a 68-aa ORF that may encode a protein. Removal of IS(all1972, all1971) extends the 5′ end of all1973 to 37 bp from all1970.
IS630/(−)/IS895-related CL 3	IS(alr1858, alr1859) splits an 88-aa ORF that putatively encodes a protein with a PIN (PilT N terminus) domain in diverse cyanobacteria and other bacteria.
IS630/(−)/IS895-related CL 5	BLASTn and BLASTp localize IS(all7564, all7563) in an ORF that encodes an E1 enzyme (super)family protein.
IS892	IS(all7178, all7177) is inserted within an unannotated, 417-bp ORF that overlaps all7178 and has strong homologs, including a close match within N. punctiforme ORF npR1908. IS(all7005, all7004), IS(all7106, all7105), IS(all7268), IS(all7303, all7302), IS(alr7323), and IS(alr8510) are inserted in genes that, respectively, encode a transposase, and—presumptively—a phage resistance protein, a 315-aa ORF with a HAD domain, a member of the DUF 1392 superfamily, a 444-aa ORF with a peptidase domain, and a Mob-Pre plasmid recombination enzyme. Ends of all of these ISs were confirmed by alignment with homologs of proteins whose genes the ISs mutated. IS(all7112, all7111) is inserted 19 bp 5′ from all7110, presumably affecting its transcription.
IS982/(−)/CL 1	Removal of IS(all2664) led to the finding of a 266-aa ORF (Table S1 in the supplemental material) that fuses the 3′ end of asr2665 to and through asr2666. IS(all3624) is positioned within a fusion of alr3623 and alr3625 that encodes a type I restriction modification system DNA specificity subunit. Removing ISNsp1 (aka IS[alr1569]) extends asr1570 5′, predicting a DUF 196 superfamily protein. BLASTn and BLASTp show that ISNSp1 is inserted in a sequence that closely matches, across the mutation site, that of the start of ava4176.
IS982/(−)/CL 3	IS(alr4082) sits in an ORF whose predicted product has tBLASTn scores of >6e−25 in other strains.
ISAzo13/(−)/CL ISNsp4	The sequence intercepted by IS(alr8019) is highly similar to (89% amino acid identity predicted) but only 63% as long as all7355, with alignment across the mutation site. A 426-bp, unannotated ORF that fuses the ends of alr2144 and all2145 is highly homologous to A. variabilis predicted protein AvaC0094. IS(all2145) ends, truncated, 49 bp 3′ from that 426-bp ORF.
ISL3/(−)/CL 1	IS(alr2698) is inserted five codons before the end of alr2697.

^aCL, cluster; −, not assigned by ISfinder.