Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate Ac3H11_3954 hypothetical protein, not 6-phosphogluconolactonase
Query= uniprot:Q9HWH7 (388 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3954 Length = 343 Score = 112 bits (281), Expect = 1e-29 Identities = 92/297 (30%), Positives = 138/297 (46%), Gaps = 24/297 (8%) Query: 70 LTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSLSH 129 + +PD + L+V + D + T D +GR + + + L + + Sbjct: 44 MALSPDGKRLYVAR------RSDPLAVVT-LAVDARAGRAEVLGEA-ALPASMAHVATDG 95 Query: 130 DGRYLFVANYSVQPEGSVAVLPVRADGSLAPVVQVESHQASKVHPRQVSGHVHSVVSSPD 189 GR+L A+Y VAV + ADG +A ++ + H HS ++SP Sbjct: 96 TGRWLLSASYGAD---LVAVQAIAADGVVAAGRGATTYATGR--------HAHSALASPG 144 Query: 190 GQYLFAPDLGADKVFVYRYAPEQAERPLQAADPAFVPTPPGSGPRHLIFSADGRFAYLTL 249 +++ A LG ++ YR+ + A LQ DPA P G+GPRHL F+A G YL Sbjct: 145 NRFVLAASLGGGQLHRYRF--DAATGALQPTDPAVFALPAGTGPRHLRFNARGDRIYLLG 202 Query: 250 ELSGQVMVFA-HEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRGDDNQL 308 EL V V E +G L LQ+ P G G LHLSADG +L R + + L Sbjct: 203 ELDACVHVLGWDEASGGLELLQSLPTLPPGSTGPAWGADLHLSADGHWLYTSER-NSHTL 261 Query: 309 VTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSG 365 FAVD +G+L ++ S + +PR F +P GR ++ A Q S ++ V P SG Sbjct: 262 AGFAVDAVTGRLAPIDYWSTQ-LQPRGFVITPDGRHLIAAGQISHRVGVHLIAPGSG 317 Score = 28.5 bits (62), Expect = 3e-04 Identities = 44/159 (27%), Positives = 59/159 (37%), Gaps = 21/159 (13%) Query: 249 LELSGQVMVFAHEGNG-RLRQLQTHDL---------APAGFQGKVGAGAL-----HLSAD 293 L L GQ+M A +G RL + D A AG +G AL H++ D Sbjct: 35 LALGGQLMPMALSPDGKRLYVARRSDPLAVVTLAVDARAGRAEVLGEAALPASMAHVATD 94 Query: 294 GRFLGVLNRGDDNQLVTFAVDPASGQLRFVERRSV--EGTEPREFAFSPGGRFVLVANQN 351 G +L+ LV A G + + G SPG RFVL A+ Sbjct: 95 GTGRWLLSASYGADLVAVQAIAADGVVAAGRGATTYATGRHAHSALASPGNRFVLAASLG 154 Query: 352 SDQLRVFARDPQSGQVGKTLQSVEV----GSPSDLRFVA 386 QL + D +G + T +V P LRF A Sbjct: 155 GGQLHRYRFDAATGALQPTDPAVFALPAGTGPRHLRFNA 193 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: 488 Number of extensions: 40 Number of successful extensions: 5 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: 388 Length of database: 343 Length adjustment: 30 Effective length of query: 358 Effective length of database: 313 Effective search space: 112054 Effective search space used: 112054 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 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