Align D-galactono-lactonase (EC 3.1.1.-) (characterized)
to candidate Pf1N1B4_4626 3-carboxymuconate cyclase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3314 (389 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4626 Length = 405 Score = 650 bits (1677), Expect = 0.0 Identities = 322/380 (84%), Positives = 344/380 (90%) Query: 1 MRNLWPLLMAGSIGAMGVQVASAEDYQLLVGSYTAGQSQGIYRLAFDSRTGQIDASPLQV 60 MRN WPLLMAGS+GAMGVQ A + Y+LLVGSYTAGQSQGIYRL FDSRTGQIDA PLQV Sbjct: 3 MRNFWPLLMAGSVGAMGVQAAPVDSYELLVGSYTAGQSQGIYRLNFDSRTGQIDAKPLQV 62 Query: 61 IKSANPSWLTLSKDQRHLFVVNENGPGQTDPVGRVSSFAIDPKTHALSLISQVQSLGNEP 120 +KSANPSWL +SKDQ LF VNENGPGQ DPVGRVSS+AIDPKT+ LSLISQVQ+LGNEP Sbjct: 63 VKSANPSWLVVSKDQHRLFAVNENGPGQADPVGRVSSYAIDPKTNELSLISQVQTLGNEP 122 Query: 121 THSSLSIDGSHLFVSNYSVAEDPGGTLAVLPVAADGKLKAVVQMSSHPASRVNPERQASA 180 THSS+S D SH+FVSNYSVAEDPGGTLAVLPV DGKLK VVQMSSHP+SRVNPERQ SA Sbjct: 123 THSSVSGDASHVFVSNYSVAEDPGGTLAVLPVGTDGKLKPVVQMSSHPSSRVNPERQKSA 182 Query: 181 HVHSTIPSPDGRYVFANDLGADKVFAYRFDPKANPELPLTPATPAFVQLPPGSGPRHLLF 240 HVHS + SPDG+YVF+NDLGADK+F YRFDPKANPELPLT A PA VQLPPGSGPRHLLF Sbjct: 183 HVHSVVSSPDGQYVFSNDLGADKIFVYRFDPKANPELPLTAAKPASVQLPPGSGPRHLLF 242 Query: 241 SADGKHAWLTMEMSAQVAVFDYHDGQLEQTQMVDLAAGQPVSDKAAAALHASADGKFLYV 300 SADGKHAWLTMEMSAQVAVFDY DG+LEQTQ+VDLAAG P S KAAAALHASADGKFLYV Sbjct: 243 SADGKHAWLTMEMSAQVAVFDYRDGKLEQTQLVDLAAGLPTSGKAAAALHASADGKFLYV 302 Query: 301 SNRGTANQLLVFAIDPATGHLSELQRRAVEGDHPREFSLDPSGKFLLIANQKSNQIVVVE 360 SNRGT NQLLVFAIDPATG+L ELQRR+V+GDHPREFSLDPSGKF+LIANQKSNQIVVVE Sbjct: 303 SNRGTTNQLLVFAIDPATGNLKELQRRSVDGDHPREFSLDPSGKFVLIANQKSNQIVVVE 362 Query: 361 RDARTGLLGKTVQKLPMDAP 380 RDA+TGLLGKTVQK P Sbjct: 363 RDAKTGLLGKTVQKTTDGCP 382 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: 753 Number of extensions: 30 Number of successful extensions: 3 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: 405 Length adjustment: 31 Effective length of query: 358 Effective length of database: 374 Effective search space: 133892 Effective search space used: 133892 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