From 1897c1f65d098e41667232ab523a284746bf9d74 Mon Sep 17 00:00:00 2001
From: Chris Fields <cjfields@bioperl.org>
Date: Sat, 5 Oct 2013 15:50:31 -0500
Subject: [PATCH] add test case for GenBank tests for bug #3448

---
 t/data/YP_007988852.gp | 100 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 100 insertions(+)
 create mode 100644 t/data/YP_007988852.gp

diff --git a/t/data/YP_007988852.gp b/t/data/YP_007988852.gp
new file mode 100644
index 000000000..01a24b108
--- /dev/null
+++ b/t/data/YP_007988852.gp
@@ -0,0 +1,100 @@
+LOCUS       YP_007988852             205 aa            linear   CON 22-MAY-2013
+DEFINITION  recombinase [Staphylococcus aureus].
+ACCESSION   YP_007988852
+VERSION     YP_007988852.1  GI:502045014
+DBLINK      Project: 178791
+            BioProject: PRJNA178791
+DBSOURCE    REFSEQ: accession NC_021230.1
+KEYWORDS    RefSeq.
+SOURCE      Staphylococcus aureus
+  ORGANISM  Staphylococcus aureus
+            Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcus.
+REFERENCE   1  (residues 1 to 205)
+  AUTHORS   Mendes,R.E., Deshpande,L.M., Bonilla,H.F., Huband,M.D., Jones,R.N.
+            and Quinn,J.P.
+  TITLE     Molecular analysis of cfr-carrying Staphylococcus aureus and
+            Staphylococcus epidermidis clinical isolates recovered from two
+            hospitals in Ohio
+  JOURNAL   Unpublished
+REFERENCE   2  (residues 1 to 205)
+  CONSRTM   NCBI Genome Project
+  TITLE     Direct Submission
+  JOURNAL   Submitted (16-MAY-2013) National Center for Biotechnology
+            Information, NIH, Bethesda, MD 20894, USA
+REFERENCE   3  (residues 1 to 205)
+  AUTHORS   Mendes,R.E., Deshpande,L.M., Bonilla,H.F., Huband,M.D., Jones,R.N.
+            and Quinn,J.P.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (31-JAN-2013) Molecular Studies, JMI Laboratories, 345
+            Beaver Kreek Centre, North Liberty, IA 52317, USA
+COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
+            NCBI review. The reference sequence is identical to AGL42326.
+            Method: conceptual translation.
+FEATURES             Location/Qualifiers
+     source          1..205
+                     /organism="Staphylococcus aureus"
+                     /strain="1"
+                     /isolation_source="blood culture"
+                     /host="Homo sapiens"
+                     /db_xref="taxon:1280"
+                     /plasmid="pSA8589"
+                     /country="USA"
+     Protein         1..205
+                     /product="recombinase"
+                     /calculated_mol_wt=23947
+     Region          4..>155
+                     /region_name="PinR"
+                     /note="Site-specific recombinases, DNA invertase Pin
+                     homologs [DNA replication, recombination, and repair];
+                     COG1961"
+                     /db_xref="CDD:224872"
+     Region          5..126
+                     /region_name="SR_ResInv"
+                     /note="Serine Recombinase (SR) family, Resolvase and
+                     Invertase subfamily, catalytic domain; members contain a
+                     C-terminal DNA binding domain. Serine recombinases
+                     catalyze site-specific recombination of DNA molecules by a
+                     concerted, four-strand cleavage and...; cd03768"
+                     /db_xref="CDD:239737"
+     Site            order(10,12,69..70,73)
+                     /site_type="active"
+                     /note="catalytic residues [active]"
+                     /db_xref="CDD:239737"
+     Site            12
+                     /site_type="active"
+                     /note="catalytic nucleophile [active]"
+                     /db_xref="CDD:239737"
+     Site            order(68,121..122,124..125)
+                     /site_type="other"
+                     /note="Presynaptic Site I dimer interface [polypeptide
+                     binding]"
+                     /db_xref="CDD:239737"
+     Site            order(74,79..80,117,120..121,124..125)
+                     /site_type="other"
+                     /note="Synaptic Antiparallel dimer interface [polypeptide
+                     binding]"
+                     /db_xref="CDD:239737"
+     Site            order(98..100,117..118,121..122,125)
+                     /site_type="other"
+                     /note="Synaptic Flat tetramer interface [polypeptide
+                     binding]"
+                     /db_xref="CDD:239737"
+     Site            order(98,122,125)
+                     /site_type="other"
+                     /note="Synaptic Site I dimer interface [polypeptide
+                     binding]"
+                     /db_xref="CDD:239737"
+     CDS             1..205
+                     /locus_tag="D646_p13002"
+                     /coded_by="NC_021230.1:1774..2391"
+                     /note="ORF1"
+                     /transl_table=11
+                     /db_xref="GeneID:15564138"
+CONTIG      join(WP_015639704.1:1..205)
+ORIGIN      
+        1 menrkfgyir vsskdqnegr qleamrkigi terdiyldkq sgknferany qllkriirkg
+       61 dilyihsldr fgrnkeeilq ewndltknie adivvldmpl ldttqykdsm gtfiadlvlq
+      121 ilswmaeeer erirkrqreg idlalqngiq fgrspvvvsd efkevyrkwk akeltaveam
+      181 qeagvkktsf yklvkahens ikvns
+//
+
-- 
2.11.4.GIT