Align D-galactono-lactonase (EC 3.1.1.-) (characterized)
to candidate GFF4068 Psest_4141 3-carboxymuconate cyclase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3314 (389 letters) >FitnessBrowser__psRCH2:GFF4068 Length = 397 Score = 377 bits (967), Expect = e-109 Identities = 202/393 (51%), Positives = 270/393 (68%), Gaps = 12/393 (3%) Query: 2 RNLWPLLM----AGSIGAM--GVQVASAEDYQLLVGSYTA-GQSQGIYRLAFDSRTGQID 54 R WP L+ A +GA+ G A +D +L+GSYT S GI RL FD TGQID Sbjct: 6 RGNWPTLLRLVFALLVGALLAGGARAETDDMHILIGSYTHDSDSPGILRLRFDPATGQID 65 Query: 55 ASPLQVIKSANPSWLTLSKDQRHLFVVNENGPGQTDPVGRVSSFAIDPKTHALSLISQVQ 114 P+Q + S NPSWL L + L+ NENGP DPVGRVS++ +D + LI Q Sbjct: 66 PKPVQTLTSDNPSWLVLDDKRGRLYATNENGPAHADPVGRVSAWQLDSSSEH-QLIGQNI 124 Query: 115 SLGNEPTHSSLSIDGSHLFVSNYSVAEDPGGTLAVLPVAADGKLKAVVQMSSHPASRVNP 174 SLG+EPTH+SLS DG +LF+SNY +PGG+LAV+P+A DG V Q+ +H +S V+P Sbjct: 125 SLGDEPTHASLSHDGRYLFISNYGSRPNPGGSLAVMPLAEDGHPLPVTQILAHQSSGVHP 184 Query: 175 ERQASAHVHSTIPSPDGRYVFANDLGADKVFAYRFDPKANPELPLTPATPAFVQLPPGSG 234 ERQ SAHVHS +PSPDG+ + +DLGAD+VF YR+DP+ N E PL PA ++LPPGSG Sbjct: 185 ERQRSAHVHSAVPSPDGKRLLVSDLGADRVFVYRYDPQ-NAERPLQADEPASIELPPGSG 243 Query: 235 PRHLLFSADGKHAWLTMEMSAQVAVFDYHDGQLEQTQMVDLA-AGQPVSDKAAAALHASA 293 PRHL+F +GKHA+L +E+SAQVA FDY +G L + Q++DL AG V + A+H+SA Sbjct: 244 PRHLVFHPNGKHAYLALELSAQVASFDYTNGTLTRRQLLDLKDAGNDVR-HSPGAIHSSA 302 Query: 294 DGKFLYVSNRGTANQLLVFAIDPATGHLSELQRRAVEGDHPREFSLDPSGKFLLIANQKS 353 DG+FLYVS+RG N ++VFAI+ A G L E+QRR+ EG PREF++ G+F+LIANQ S Sbjct: 303 DGRFLYVSDRGDYNHIIVFAIE-ADGTLREIQRRSSEGREPREFAITADGRFMLIANQLS 361 Query: 354 NQIVVVERDARTGLLGKTVQKLPMDAPSDLRFL 386 +++VV+ RD +G LG+ +Q L + PSD++ L Sbjct: 362 DELVVIRRDPDSGQLGEKLQTLTVGRPSDIKLL 394 Lambda K H 0.316 0.132 0.382 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: 629 Number of extensions: 42 Number of successful extensions: 11 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: 389 Length of database: 397 Length adjustment: 31 Effective length of query: 358 Effective length of database: 366 Effective search space: 131028 Effective search space used: 131028 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: 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