Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate WP_000665611.1 HK29_RS05400 lactonase family protein
Query= uniprot:Q9HWH7 (388 letters) >NCBI__GCF_000382825.1:WP_000665611.1 Length = 337 Score = 142 bits (357), Expect = 2e-38 Identities = 104/337 (30%), Positives = 157/337 (46%), Gaps = 24/337 (7%) Query: 33 GTYTEGSSEGIQVYRFDGADGSVKGPLRVAHTSNPSYLTFAPDQRTLFVVNENGRGGKGD 92 GTYT SS+GI FD G + A +P+YL F Q V +++G GG Sbjct: 8 GTYTRRSSKGIYKADFDTETGQLANLELFAAEPSPTYLAFDQQQHLYTVGSQDGLGG--- 64 Query: 93 TVGRATSYRFDPISGRLQQISQVQTLADHPTYSSLSHDGRYLFVANYSVQPEGSVAVLPV 152 +Y+ D G L V+ A H Y ++ ++ ANY +G + V Sbjct: 65 ----IAAYKTD---GTLLN-HVVEEGAPH-CYVAVDEKRSLVYGANYH---KGQILVYQR 112 Query: 153 RADGSLAPVVQVESHQASKVHPRQVSGHVHSVVSSPDGQYLFAPDLGADKVFVYRYAPEQ 212 + DGSL ++ H H Q S HVH +PD QYL DLG D+V Y +PE Sbjct: 113 QTDGSLIQT-DLDQHSGQGPHENQTSPHVHFTDLTPD-QYLVTCDLGTDEVTTYDVSPEG 170 Query: 213 AERPLQAADPAFVPTPPGSGPRHLIFSADGRFAYLTLELSGQVMVFAHEGNGRLRQLQTH 272 L + PG+G RH++F + AYL EL+ + V ++G G ++Q Sbjct: 171 KLSKLHTYH-----SQPGAGARHIVFHHHYKIAYLICELNSTIEVLIYDGVGEFERMQVI 225 Query: 273 DLAPAGFQGKVGAGALHLSADGRFLGVLNRGDDNQLVTFAVDPASGQLRFVERRSVEGTE 332 P ++ A+ LS DG++L NRG D+ V + A G L +E G Sbjct: 226 STLPDRYEDFNATAAIRLSKDGKYLYASNRGHDSIAVYTIL--ADGSLELLEIVPTHGQN 283 Query: 333 PREFAFSPGGRFVLVANQNSDQLRVFARDPQSGQVGK 369 PR+F +P F++ +Q+SD VF R+P++G++ + Sbjct: 284 PRDFDLTPDQEFLIAVHQDSDNATVFKRNPETGRLAE 320 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: 406 Number of extensions: 38 Number of successful extensions: 9 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: 337 Length adjustment: 29 Effective length of query: 359 Effective length of database: 308 Effective search space: 110572 Effective search space used: 110572 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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