Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate Echvi_3728 Echvi_3728 3-carboxymuconate cyclase
Query= uniprot:Q9HWH7 (388 letters) >FitnessBrowser__Cola:Echvi_3728 Length = 392 Score = 229 bits (585), Expect = 8e-65 Identities = 129/357 (36%), Positives = 196/357 (54%), Gaps = 10/357 (2%) Query: 25 ASLYNLLVGTYTEGSSEGIQVYRFDGADGSVKGPLRVAHTSNPSYLTFAPDQRTLFVVNE 84 AS +GTYT S+G + ++ + L + +NPS++ + +F V E Sbjct: 36 ASPITFWLGTYTSKPSDGFHLIQYHPETSTFDSVLMESDINNPSFVISNLKRDLVFTVQE 95 Query: 85 NGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSLSHDGRYLFVANYSVQPE 144 G G+ G S+RFD + L+++S + P Y +LS D +++F NY Sbjct: 96 EG----GENGGSVCSFRFDRSANSLKKLSTSASQGSGPCYITLSPDEKFIFAGNYG---S 148 Query: 145 GSVAVLPVRADGSLAPVVQVESHQASKVHP-RQVSGHVHSVVSSPDGQYLFAPDLGADKV 203 G +AVLP+ DG+L VQ H S V+ RQ S HVHS+V P+G+ LF DLG DKV Sbjct: 149 GDLAVLPINEDGTLGEAVQTIQHTGSSVNEGRQSSPHVHSLVFHPNGKQLFVADLGTDKV 208 Query: 204 FVYRYAPEQAERPLQAADPAFVPTPPGSGPRHLIFSADGRFAYLTLELSGQVMVFAHE-G 262 +Y Y P++ E PL A+ PA GSGPRHL F+ G YL E++ +V ++ + Sbjct: 209 SIYNYDPDRKE-PLTASSPASFTVKAGSGPRHLAFNQSGDKIYLIHEITSEVGLYDYNLD 267 Query: 263 NGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRGDDNQLVTFAVDPASGQLRF 322 ++ L ++ L P GF+G+ GA + +S DG+FL NRGD N+++ F+++ +G L Sbjct: 268 ENKITHLDSYALTPQGFEGEKGAAEIKISDDGQFLYASNRGDSNEIIVFSINAQTGTLDK 327 Query: 323 VERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSGQVGKTLQSVEVGSP 379 ++ S G PR FA SP G F+ V NQNSD + + R+P+SG + KT + + P Sbjct: 328 IQAISSGGKTPRNFALSPDGTFLFVGNQNSDSILAYERNPRSGIIKKTNAKLPIHRP 384 Lambda K H 0.318 0.135 0.395 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: 469 Number of extensions: 42 Number of successful extensions: 13 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: 388 Length of database: 392 Length adjustment: 31 Effective length of query: 357 Effective length of database: 361 Effective search space: 128877 Effective search space used: 128877 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 (21.7 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