Align D-galactono-lactonase (EC 3.1.1.-) (characterized)
to candidate PP_2021 PP_2021 L-alpha-hydroxyglutaric acid gamma-lactonase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3314 (389 letters) >FitnessBrowser__Putida:PP_2021 Length = 376 Score = 424 bits (1089), Expect = e-123 Identities = 222/386 (57%), Positives = 276/386 (71%), Gaps = 11/386 (2%) Query: 1 MRNLWPLLMAGSIGAMGVQVASAEDYQLLVGSYTAGQSQGIYRLAFDSRTGQIDASPLQV 60 M W L+ S+ ++ + SA LLVGSYT G SQGIYR FD + GQI +PLQV Sbjct: 1 MNRTWTSLLTASLMSLTI---SAHAATLLVGSYTDGASQGIYRYHFDDKAGQIGPTPLQV 57 Query: 61 IKSANPSWLTLSKDQRHLFVVNENGPGQTDPVGRVSSFAIDPKTHALSLISQVQSLGNEP 120 +KS +PSWL LS DQR LF VNE P G SSF+I K + ++QV + G+EP Sbjct: 58 VKSVSPSWLVLSADQRQLFAVNET------PQGHASSFSISSKGE-IKPLNQVVTQGDEP 110 Query: 121 THSSLSIDGSHLFVSNYSVAEDPGGTLAVLPVAADGKLKAVVQMSSHPASRVNPERQASA 180 TH+SLS D +LFV+NY+V DPGG+L V+PVA DG LK VVQ + H AS VNPERQA A Sbjct: 111 THASLSRDQRYLFVANYAVNPDPGGSLVVIPVAKDGTLKPVVQQARHKASGVNPERQAGA 170 Query: 181 HVHSTIPSPDGRYVFANDLGADKVFAYRFDPKANPELPLTPATPAFVQLPPGSGPRHLLF 240 HVHS + SPDG++++A+DLGADKVF YR+D A+ + PLT A PA V LPPGSGPRHLLF Sbjct: 171 HVHSLVLSPDGQHLYASDLGADKVFIYRYDG-ASADHPLTAAIPASVALPPGSGPRHLLF 229 Query: 241 SADGKHAWLTMEMSAQVAVFDYHDGQLEQTQMVDLAAGQPVSDKAAAALHASADGKFLYV 300 A G+HA+LT+EM+A+V +FD DG L + Q + L Q + KAA LH SADG+FLYV Sbjct: 230 DAKGRHAYLTLEMNAEVVMFDVQDGNLVERQRLPLTERQEAAAKAAGGLHLSADGRFLYV 289 Query: 301 SNRGTANQLLVFAIDPATGHLSELQRRAVEGDHPREFSLDPSGKFLLIANQKSNQIVVVE 360 SNRGTAN+++ F++ G L+ LQRR EGDHPREF+LDPS FLL+ANQKSNQIVV+ Sbjct: 290 SNRGTANEIVAFSVGKQDGQLTFLQRRPAEGDHPREFALDPSDNFLLVANQKSNQIVVIR 349 Query: 361 RDARTGLLGKTVQKLPMDAPSDLRFL 386 RD R+G L +TVQ L DAPSDL+F+ Sbjct: 350 RDPRSGKLLETVQTLKQDAPSDLKFI 375 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: 592 Number of extensions: 33 Number of successful extensions: 6 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: 376 Length adjustment: 30 Effective length of query: 359 Effective length of database: 346 Effective search space: 124214 Effective search space used: 124214 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