Align D-mannonate dehydratase Caul1835; ManD; EC 4.2.1.8 (characterized)
to candidate CA265_RS13665 CA265_RS13665 galactonate dehydratase
Query= SwissProt::B0T4L2 (403 letters) >FitnessBrowser__Pedo557:CA265_RS13665 Length = 388 Score = 140 bits (353), Expect = 6e-38 Identities = 119/393 (30%), Positives = 186/393 (47%), Gaps = 28/393 (7%) Query: 3 KITAARV-VVTCPGRNFVTLKIETSDGVYGVGDATLNGRELPVVSYLTDHVIPCLIGRDA 61 KIT +V +V N+ LKI T G GVG+AT N P+V T HV +IG D Sbjct: 2 KITDVKVWLVEGVKYNWTLLKIYTDTGHTGVGEAT-NWPGSPIVFEATKHVGQRIIGLDP 60 Query: 62 HRIEDIWQYLYKGAYWRRGP--VTMAAIAAVDMALWDIKAKIAGLPLYQLLGGACREGIM 119 + + IW LY+ W GP +M AI+ +DMAL D+KAK+ G+P Y+LLGGA R+ I+ Sbjct: 61 MKTDFIWTKLYRDLNWM-GPFGASMCAISGIDMALLDLKAKVLGVPCYELLGGAFRKDIL 119 Query: 120 VYGH---ANGATIEETLENAAVYAAQGYKAIRLQSGVPGLKGVYGVSKDKFFYEPADGDL 176 +Y + G N A YAAQ K ++G GLK + + Y G+ Sbjct: 120 LYANYWFTGGG------HNTADYAAQAKKV--KEAGFTGLK-FDPFAHTNYLY----GED 166 Query: 177 PTESLWSTEKYLRSAPGLFEAARDKLGWDLHLLHDVHHRLTPIEAGRLGKDLEPYRPFWM 236 + +L T A + +A RD +G + ++ + H L A + + L W Sbjct: 167 LSSNLQLTAPQQDLAFNVSKAVRDAVGPEFDIMIETHAMLNYRVAVTMAQRLSELNITWY 226 Query: 237 EDAVPAENQASFRLIRQH--TTTPLAVGEVFNSIWDCKQLIEEQLIDYIRATVVHAGGIT 294 E+ EN + + +R + + VGE + + ++E+ + D + + GG + Sbjct: 227 EEPAGPENANTLKAMRDRIPSNVSICVGERHYTRHGIRDVLEKHICDIMMPDITRCGGPS 286 Query: 295 HLRKIASFADLHHVRTGCHGATDLSPIAMAAALHFDLSIPNFGIQEYM-RHTEATDTVFP 353 ++++A+ + ++V H P++ A+ S+PNF QE+M D V Sbjct: 287 EMKRMATMMEAYNVLLAPHNPN--GPLSTLASAQVCASVPNFFRQEFMFNDVPWRDEVIS 344 Query: 354 H--AYTFNDGMLHPGDAVGLGVDINETEAAKYP 384 H A +G L D GLGVD+ E E K+P Sbjct: 345 HPIADMVQNGHLKLSDRPGLGVDLIEEEMEKHP 377 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: 388 Number of extensions: 26 Number of successful extensions: 7 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: 388 Length adjustment: 31 Effective length of query: 372 Effective length of database: 357 Effective search space: 132804 Effective search space used: 132804 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