Align galactonate dehydratase (EC 4.2.1.6) (characterized)
to candidate WP_068172340.1 HTA01S_RS13450 D-galactonate dehydratase family protein
Query= BRENDA::G3Y8T6 (383 letters) >NCBI__GCF_001592305.1:WP_068172340.1 Length = 403 Score = 180 bits (457), Expect = 5e-50 Identities = 131/395 (33%), Positives = 192/395 (48%), Gaps = 41/395 (10%) Query: 19 VKVTDSEDKFGWGEATLEGHTQAVEGAL-DEIIGRIVGYEADDIEHVWQTIWRLGFYRGG 77 +K+ E G G+ATL G AV L D +I ++G + IE +WQ +++ ++R G Sbjct: 20 LKIETDEGLTGIGDATLNGRELAVASYLTDHVIPCLIGRDPQQIEDIWQYLYKGAYWRRG 79 Query: 78 PVFMSALSGIDIALWDLKGRRLNVPVYQLLGGKVRNKVQVYAWIGGDRPSDV-------- 129 PV MSA++G+D ALWD+K + N+P+YQLLGGK R V VY G S Sbjct: 80 PVTMSAIAGVDTALWDIKAKAANMPLYQLLGGKSRTGVMVYGHANGKDISQTVDEVLRYK 139 Query: 130 EVAAKARIAQ----GLKCVKMNATEDMNW----LDSPSVLDSCIERI---------KQVK 172 E+ KA AQ GL+ V M + D PS D E+ K Sbjct: 140 EMGYKAIRAQSGVPGLEKVYGVGRGTMFYEPADADLPSEHDWSTEKYLRHTPELFDKVRA 199 Query: 173 ALGLDAGL--DFHGRLHRPMAKQLAKALEPYRPLFIEEPLLVEHPEAIKQLSQHTTIPIA 230 A+G D L D H RL A +L K LEP+R ++E+ E+ E+ + + QHTT P+A Sbjct: 200 AVGPDIHLLHDAHHRLTPIEAARLGKDLEPFRLFWLEDTTPAENQESFRLIRQHTTTPLA 259 Query: 231 FGERLYTRWDVKRFLEDASVDVLQPDIAHAGGISETKRIATMAETYDVAIAPH--CPLGP 288 GE T WD K +++ +D ++ + HAGGI+ +RIA +A Y V H L P Sbjct: 260 VGEIFNTIWDCKDLIQNQLIDYIRTTVVHAGGITHLRRIADLAALYQVRTGSHGATDLSP 319 Query: 289 IALAASMQVALSTPNFVIQEMSLGMHYNVEAGDIDLTSYLTNPTVFNIEEGYVPAPTGAG 348 + + A++ L PNF IQE M + E + P ++ ++G++ G Sbjct: 320 VCMGAALNFDLWVPNFGIQEY---MRHTDETDAV-------FPHAYSFKDGFMHPGEAPG 369 Query: 349 LGVEIDEELVRRISRETEPWLPKEFYGVDGGIREW 383 GV IDE L + + +LP DG + W Sbjct: 370 HGVTIDEALAAKYPYK-RAYLPVNRLQHDGTLTNW 403 Lambda K H 0.320 0.138 0.425 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: 393 Number of extensions: 18 Number of successful extensions: 4 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: 383 Length of database: 403 Length adjustment: 31 Effective length of query: 352 Effective length of database: 372 Effective search space: 130944 Effective search space used: 130944 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