Align D-galactonate dehydratase family member PC1_0802; EC 4.2.1.-; D-mannonate dehydratase; EC 4.2.1.8 (uncharacterized)
to candidate H281DRAFT_01518 H281DRAFT_01518 D-mannonate dehydratase (EC 4.2.1.8)
Query= curated2:C6D9S0 (404 letters) >FitnessBrowser__Burk376:H281DRAFT_01518 Length = 402 Score = 671 bits (1731), Expect = 0.0 Identities = 315/404 (77%), Positives = 352/404 (87%), Gaps = 2/404 (0%) Query: 1 MKIVSAEVFVTCPGRNFVTLKITTDSGLTGLGDATLNGRELPVASYLNDHVCPQLIGRDA 60 MKIV A+V VTCPGRNFVTLKI TD G+ G+GDATLNGREL VASYL DHVCP LIGRD Sbjct: 1 MKIVRADVIVTCPGRNFVTLKIVTDEGVHGIGDATLNGRELAVASYLKDHVCPLLIGRDP 60 Query: 61 HQIEDIWQYFYKGAYWRRGPVTMSAISAVDMALWDIKAKAANMPLYQLLGGASRTGVMVY 120 +IED WQY YKGAYWRRGPVTM+AI+AVDMALWDI K MPLY+LLGGASR GVMVY Sbjct: 61 GRIEDTWQYLYKGAYWRRGPVTMTAIAAVDMALWDILGKVTGMPLYKLLGGASREGVMVY 120 Query: 121 CHTTGHSIDEVLDDYAKHRDQGFKAIRVQCGVPGMETTYGMAKGKGLAYEPATKGSLPEE 180 H TG I E LD YA+H + G++AIR+QCGVP M + YG++KG G+ YEPATKG++ EE Sbjct: 121 GHATGRDIPEALDRYAEHIEAGYQAIRIQCGVPNMRSVYGVSKGSGM-YEPATKGAV-EE 178 Query: 181 QLWSTEKYLDFTPKLFEAVRDKFGFNEHLLHDMHHRLTPIEAARFGKSVEDYRLFWMEDP 240 Q WS+EKYLDF PKLFEAVR+KFGF+ HLLHD+HHRLTPIEAAR GKSVE YRLFWMEDP Sbjct: 179 QSWSSEKYLDFVPKLFEAVREKFGFDTHLLHDVHHRLTPIEAARLGKSVEPYRLFWMEDP 238 Query: 241 TPAENQACFRLIRQHTVTPIAVGEVFNSIWDCKQLIEEQLIDYIRTTITHAGGITGMRRI 300 TPAENQA FRLIR+HTVTPIAVGEVFNSIWDCKQLIEEQLIDYIR T+THAGGI+ +RRI Sbjct: 239 TPAENQAGFRLIREHTVTPIAVGEVFNSIWDCKQLIEEQLIDYIRATLTHAGGISHLRRI 298 Query: 301 ADFASLYQVRTGSHGPSDLSPICMAAALHFDLWVPNFGVQEYMGYSEQMLEVFPHSWTFD 360 ADFASLYQVRTG HGPSDLSP+CM AALHFDLWVPNFGVQEYMG+ E+ LEVFPH+W FD Sbjct: 299 ADFASLYQVRTGCHGPSDLSPVCMGAALHFDLWVPNFGVQEYMGFPEEALEVFPHAWRFD 358 Query: 361 NGYMHPGEKPGLGIEFDEKLAAKYPYDPAYLPVARLEDGTLWNW 404 +G MHPG+ PG G++ DE AA++PYDPAYLPVARLEDGTLW+W Sbjct: 359 HGMMHPGDAPGHGVDIDEAAAARFPYDPAYLPVARLEDGTLWSW 402 Lambda K H 0.321 0.138 0.442 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: 722 Number of extensions: 35 Number of successful extensions: 3 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: 404 Length of database: 402 Length adjustment: 31 Effective length of query: 373 Effective length of database: 371 Effective search space: 138383 Effective search space used: 138383 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 Sep 17 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