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/usr/include/genometools/gt_config.h is in libgenometools0-dev 1.5.3-2.

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#ifndef GT_CONFIG_H
#define GT_CONFIG_H
#define GT_BUILT "2014-09-05 13:33:55"
#define GT_CC "gcc-4.9.real (Debian 4.9.1-11) 4.9.1"
#define GT_CFLAGS "-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -O3"
#define GT_CPPFLAGS "-D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP -DHAVE_SQLITE -I/tmp/buildd/genometools-1.5.3/src -I/tmp/buildd/genometools-1.5.3/obj -I/tmp/buildd/genometools-1.5.3/src/external/zlib-1.2.8 -I/tmp/buildd/genometools-1.5.3/src/external/md5-1.1.2/src -I/tmp/buildd/genometools-1.5.3/src/external/lua-5.1.5/src -I/tmp/buildd/genometools-1.5.3/src/external/luafilesystem-1.5.0/src -I/tmp/buildd/genometools-1.5.3/src/external/lpeg-0.10.2 -I/tmp/buildd/genometools-1.5.3/src/external/expat-2.0.1/lib -I/tmp/buildd/genometools-1.5.3/src/external/bzip2-1.0.6 -I/tmp/buildd/genometools-1.5.3/src/external/samtools-0.1.18 -I/tmp/buildd/genometools-1.5.3/src/external/sqlite-3.8.0.1 -I/tmp/buildd/genometools-1.5.3/src/external/tre/include/tre -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libdrm -I/usr/include/libpng12  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libdrm -I/usr/include/libpng12  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include "
#define GT_VERSION "1.5.3"
#define GT_MAJOR_VERSION 1
#define GT_MINOR_VERSION 5
#define GT_MICRO_VERSION 3
#endif