Align D-mannonate dehydratase Caul1835; ManD; EC 4.2.1.8 (characterized)
to candidate WP_085125981.1 B9O00_RS27750 mandelate racemase/muconate lactonizing enzyme family protein
Query= SwissProt::B0T4L2 (403 letters) >NCBI__GCF_900177295.1:WP_085125981.1 Length = 400 Score = 155 bits (393), Expect = 2e-42 Identities = 120/400 (30%), Positives = 187/400 (46%), Gaps = 44/400 (11%) Query: 15 GRNFVTLKIETSDGVYGVGDA-TLNGRELPVVSYLTDHVIPCLIGRDAHRIEDIWQYLYK 73 GR FV +K+ T GV G+G+ L VV+ + D L+G+D RIE +W+ +Y Sbjct: 20 GRYFVFVKLVTDGGVEGLGEVYCLPFHPRVVVAMIEDLAGRYLVGQDPTRIESLWRRVYS 79 Query: 74 GAYWRRGPVTMAAI-AAVDMALWDIKAKIAGLPLYQLLGGACREGIMVYGH---ANGATI 129 Y +R +++A I + ++MA WDI K G P++ LLGG E + Y + G T Sbjct: 80 AGYGQRPDLSVAGILSGLEMACWDILGKETGKPVHALLGGRVHERLRSYTYLYPGEGETA 139 Query: 130 ------EETLENAAVYAAQGYKAIRLQSGVPGLKGVYGVSKDKFFYEPADGDLPT-ESLW 182 E + E AA Y QG+ AI+ P Y D +P ESL Sbjct: 140 DFYHDAERSAERAAEYVRQGFTAIKFDPAGP--------------YSAFDPRMPDQESLA 185 Query: 183 STEKYLRSAPGLFEAARDKLGWDLHLLHDVHHRLTPIEAGRLGKDLEPYRPFWMEDAVPA 242 +E++ R L AA +G LL H + TP A RL + LEPY P W+E+ P Sbjct: 186 RSEQFCR----LIRAA---VGGGADLLFGTHGQFTPAGALRLARRLEPYDPLWLEEPTPP 238 Query: 243 ENQASFRLIRQHTTTPLAVGEVFNSIWDCKQLIEEQLIDYIRATVVHAGGITHLRKIASF 302 E L+ + TT P+A GE + ++ +L++ ++ + GG+ +KIA Sbjct: 239 EMPEQMALVARGTTIPVAAGERLATKYEFARLLDAGAAAILQPNLGRVGGLLEAKKIAGL 298 Query: 303 ADLHHVRTGCHGATDLSPIAMAAALHFDLSIPNFGIQEYMR-----HTEATDTVFPHAYT 357 A+ + + H P+ AA + ++PNF I E ++ H E T Sbjct: 299 AEARYAQVAPH--LYCGPVVGAANIQLAATLPNFLILESIQTWGGFHAELLKT----PIR 352 Query: 358 FNDGMLHPGDAVGLGVDINETEAAKYPYKRAYLPIARRED 397 + +G + DA GLGV+++E A +PY+ L + +D Sbjct: 353 WQEGYVLVPDAPGLGVELDEAVALAHPYEGEELHLDMAQD 392 Lambda K H 0.321 0.138 0.434 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: 414 Number of extensions: 21 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: 403 Length of database: 400 Length adjustment: 31 Effective length of query: 372 Effective length of database: 369 Effective search space: 137268 Effective search space used: 137268 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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