Align galactaro-1,5-lactonase (characterized)
to candidate BPHYT_RS06110 BPHYT_RS06110 3-carboxymuconate cyclase
Query= reanno::HerbieS:HSERO_RS15795 (352 letters) >FitnessBrowser__BFirm:BPHYT_RS06110 Length = 385 Score = 130 bits (327), Expect = 6e-35 Identities = 108/337 (32%), Positives = 161/337 (47%), Gaps = 39/337 (11%) Query: 27 SQDIYVLRLNNDGSVNLIDKVDTGSTVMP--LAISPDRKYLYA--------SLRREPYAV 76 S+ +YV R D +V TV P L +S DR+++YA + + Sbjct: 35 SEGLYVYRF--DTKTGEATRVSAAQTVNPSYLVVSRDRRFVYAVNEMPGDNGPATQRGGI 92 Query: 77 ASYAIDPASGKLKALSKAPLADN-MANIATDRSGRYLLAASYF-----GNKISVNAIGSD 130 +++ D ASG+L L+K N ++ G+YLL A+Y G +V + +D Sbjct: 93 SAFRFDAASGQLTFLNKVSSDGNDPCYLSLSPDGKYLLTANYSVAADPGGSFAVFPLQAD 152 Query: 131 GAVQTPPLAVIPTG----------KNAHSVQVDPANAFVFASNLGSDVILQYRFDP--AS 178 G V L V G + HS P ++FA +LG+D + YR+ P + Sbjct: 153 GQVGASVLTVHHEGGGPVKGRQDNSHVHSTVFSPDGHYLFAQDLGADKLYSYRYTPDGSR 212 Query: 179 GAVTPNTPPSVASKAGAGPRHFVFSPDQRFLYCANELDATVSTYAYDRQAGTLTLLGSDS 238 G P KAG+GPRH VF D + Y +E+ ATVST+ Y+ G LT + + Sbjct: 213 GLFGPTDWRYNQEKAGSGPRHLVFGADGKHAYLTSEMAATVSTFDYN--DGKLTQVQTLP 270 Query: 239 ALPEGFQSSEQLAAADLHLTPDGRFLYATER-TSNTLTGYRVDRASGKLTRILNIPT-ET 296 GF+ + + AA +HL+PDGRFLYAT R +N + + VD +G L ++ + + Sbjct: 271 LTEPGFKGA--VGAAAIHLSPDGRFLYATNRGDANDIVIFSVDPTNGHLKKVGHQSSMGK 328 Query: 297 QPRAFNIDPQGRYLLAVGQKAGLTSYAI--DAASGTL 331 PR F IDP G +L+ VG + T Y D SG L Sbjct: 329 SPREFAIDPTGNWLI-VGNQNSDTVYVFKRDQQSGLL 364 Score = 35.0 bits (79), Expect = 3e-06 Identities = 42/170 (24%), Positives = 59/170 (34%), Gaps = 18/170 (10%) Query: 30 IYVLRLNNDGSVNLIDKVD-------TGSTVMPLAISPDRKYLYASLRREPYAVASYAID 82 +Y R DGS L D GS L D K+ Y L E A S D Sbjct: 201 LYSYRYTPDGSRGLFGPTDWRYNQEKAGSGPRHLVFGADGKHAY--LTSEMAATVS-TFD 257 Query: 83 PASGKLKALSKAPLAD-------NMANIATDRSGRYLLAASYF-GNKISVNAIGSDGAVQ 134 GKL + PL + A I GR+L A + N I + ++ Sbjct: 258 YNDGKLTQVQTLPLTEPGFKGAVGAAAIHLSPDGRFLYATNRGDANDIVIFSVDPTNGHL 317 Query: 135 TPPLAVIPTGKNAHSVQVDPANAFVFASNLGSDVILQYRFDPASGAVTPN 184 GK+ +DP ++ N SD + ++ D SG + N Sbjct: 318 KKVGHQSSMGKSPREFAIDPTGNWLIVGNQNSDTVYVFKRDQQSGLLEAN 367 Lambda K H 0.316 0.131 0.375 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: 486 Number of extensions: 58 Number of successful extensions: 11 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 352 Length of database: 385 Length adjustment: 30 Effective length of query: 322 Effective length of database: 355 Effective search space: 114310 Effective search space used: 114310 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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