Align D-galactonate dehydratase; EC 4.2.1.6 (characterized)
to candidate WP_053939463.1 WG78_RS19245 galactonate dehydratase
Query= CharProtDB::CH_024133 (382 letters) >NCBI__GCF_001294205.1:WP_053939463.1 Length = 382 Score = 665 bits (1716), Expect = 0.0 Identities = 313/382 (81%), Positives = 349/382 (91%) Query: 1 MKITKITTYRLPPRWMFLKIETDEGVVGWGEPVIEGRARTVEAAVHELGDYLIGQDPSRI 60 MKIT+ITTYR+PPRWMFLKIETDEG+VGWGEPV+EGRA+TVEAAVHE+ +YLIGQDP+RI Sbjct: 1 MKITRITTYRVPPRWMFLKIETDEGIVGWGEPVLEGRAKTVEAAVHEMSEYLIGQDPARI 60 Query: 61 NDLWQVMYRAGFYRGGPILMSAIAGIDQALWDIKGKVLNAPVWQLMGGLVRDKIKAYSWV 120 NDLWQV+YRAGFYRGG ILMSAIAGIDQALWDIKGK L PV+QL+GGLVRD++K YSWV Sbjct: 61 NDLWQVLYRAGFYRGGGILMSAIAGIDQALWDIKGKALGVPVYQLLGGLVRDRVKTYSWV 120 Query: 121 GGDRPADVIDGIKTLREIGFDTFKLNGCEELGLIDNSRAVDAAVNTVAQIREAFGNQIEF 180 GGDRPAD+I I+ ++GFDTFK+NGCEEL +IDNSRA+DAAV VA+IREAFGN+IEF Sbjct: 121 GGDRPADIIRDIQARVDVGFDTFKMNGCEELAVIDNSRAIDAAVRKVAEIREAFGNKIEF 180 Query: 181 GLDFHGRVSAPMAKVLIKELEPYRPLFIEEPVLAEQAEYYPKLAAQTHIPLAAGERMFSR 240 GLDFHGRV+APMA+VLIKELEPYRPLFIEEPVLAEQAEYYPKLAAQTHIPLAAGERM+SR Sbjct: 181 GLDFHGRVTAPMARVLIKELEPYRPLFIEEPVLAEQAEYYPKLAAQTHIPLAAGERMYSR 240 Query: 241 FDFKRVLEAGGISILQPDLSHAGGITECYKIAGMAEAYDVTLAPHCPLGPIALAACLHID 300 F+FK VL AGG+SILQPDLSHAGGITEC KIA MAEAYDV LAPHCPLGPIALAACL +D Sbjct: 241 FEFKNVLAAGGLSILQPDLSHAGGITECMKIASMAEAYDVALAPHCPLGPIALAACLQVD 300 Query: 301 FVSYNAVLQEQSMGIHYNKGAELLDFVKNKEDFSMVGGFFKPLTKPGLGVEIDEAKVIEF 360 FVS+NA +QEQSMGIHYNKG E+LD+V NK DF++ G KP TKPGLGVE+DEA +IE Sbjct: 301 FVSWNAFIQEQSMGIHYNKGGEVLDYVLNKADFALENGHIKPFTKPGLGVELDEALIIER 360 Query: 361 SKNAPDWRNPLWRHEDNSVAEW 382 SKNAPDWRNPLWRH D SVAEW Sbjct: 361 SKNAPDWRNPLWRHADGSVAEW 382 Lambda K H 0.321 0.140 0.433 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 646 Number of extensions: 17 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 382 Length of database: 382 Length adjustment: 30 Effective length of query: 352 Effective length of database: 352 Effective search space: 123904 Effective search space used: 123904 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory