Align D-galactono-lactonase (EC 3.1.1.-) (characterized)
to candidate WP_084931726.1 HA51_RS02640 lactonase family protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3314 (389 letters) >NCBI__GCF_002095475.1:WP_084931726.1 Length = 369 Score = 202 bits (514), Expect = 1e-56 Identities = 134/379 (35%), Positives = 209/379 (55%), Gaps = 30/379 (7%) Query: 22 SAEDYQL-LVGSYTA-----------GQSQGIYRLAFDSRTGQIDASPLQVIKSANPSWL 69 +AE +Q LVG++T+ S+G+YRL +S G + +PL VIK +PSW+ Sbjct: 4 AAEHHQTALVGTWTSIPDAPSEQKPDHPSEGLYRLKVNS-DGTL--TPLDVIKMKSPSWI 60 Query: 70 TLSKDQRHLFVVNENGPGQTDPVGRVSSFAIDPKTHALSLISQVQSLGNEPTHSSLSIDG 129 S+D R + NE G V++ +ID ++ + +++ V S G +PTH+++S DG Sbjct: 61 VKSRDGRFAYTTNEEN------AGAVTALSID-RSGKVQVLNVVDSHGQQPTHATISPDG 113 Query: 130 SHLFVSNYSVAEDPGGTLAVLPVAADGKLKAVVQMSS--HPASRVNPERQASAHVHSTIP 187 LFV+NYSVA+ G ++V P+ DGKL VQ + H V RQ H HST Sbjct: 114 KFLFVANYSVAKGGAG-VSVFPIHHDGKLGEQVQHFAFEHGTGAVKG-RQDGGHAHSTTF 171 Query: 188 SPDGRYVFANDLGADKVFAYRFDPKANPELPLTPATPAFVQLPPGSGPRHLLFSADGKHA 247 + DG+Y++A DLG DK+ AYR+ A+ PL + V GSGPRH++F+ +G+HA Sbjct: 172 THDGKYLYAADLGGDKLHAYRYH--ADKAQPLEADSARDVNFTAGSGPRHMVFAPNGQHA 229 Query: 248 WLTMEMSAQVAVFDYHDGQLEQTQMVDL-AAGQPVSDKAAAALHASADGKFLYVSNRGTA 306 ++T EM+ ++ VF +LE + L + + ++ + S +GKF+ +NRG+ Sbjct: 230 YVTTEMAGEIVVFAVKQDRLEPAAHIKLNSENNSEAYRSGGGIILSPNGKFVIAANRGSD 289 Query: 307 NQLLVFAIDPATGHLSELQRRAVEGDHPREFSLDPSGKFLLIANQKSNQIVVVERDARTG 366 N+LLVF I+ A G L + G PR F+ D SGK+L + N +N I + DA +G Sbjct: 290 NKLLVFKIE-ADGMLGKPMSYKANGIEPRAFAFDSSGKYLYVTNVFTNNISLFHFDANSG 348 Query: 367 LLGKTVQKLPMDAPSDLRF 385 L + P+D++F Sbjct: 349 ELKAAGDAAKISTPTDIKF 367 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: 476 Number of extensions: 45 Number of successful extensions: 15 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: 369 Length adjustment: 30 Effective length of query: 359 Effective length of database: 339 Effective search space: 121701 Effective search space used: 121701 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 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