Align Gluconolactonase (characterized, see rationale)
to candidate GFF363 Psest_0364 Gluconolactonase
Query= uniprot:A0A165IRV8 (316 letters) >FitnessBrowser__psRCH2:GFF363 Length = 296 Score = 168 bits (425), Expect = 2e-46 Identities = 111/295 (37%), Positives = 146/295 (49%), Gaps = 15/295 (5%) Query: 28 VIALGNALGEGVLWSVREQAVYWVDILGRELHRWDPATGAHQRWTFDEEISAIAERAHAP 87 ++ LG A GE +W EQA+YWVDI REL RW+ A G RW DE ++ IA H Sbjct: 8 IVDLGCATGESPVWVAAEQALYWVDIPNRELLRWNAADGQISRWQGDEMLACIAR--HGD 65 Query: 88 GFIVTLRRGFALFDPATD--MAPRYLHQPEPDRAGNRFNDGKCDAQGRFWAGSM--DFAC 143 G++ + GF D + L + R NDG+CD +GRFWAGSM D A Sbjct: 66 GWVAGMESGFFSLQTRPDGRLDSHLLATIDHQLPAMRMNDGRCDREGRFWAGSMALDMAA 125 Query: 144 EAPTGALYRYDS---DGSCTRHDDGFAVTNGPTWSGTGQGAAMFFNATIEGNTYRYDSDL 200 P GALYR DS D DGF V NG +S G+ + + + +D D+ Sbjct: 126 GHPVGALYRLDSKSIDAPLVPQLDGFIVPNGLAFSPDGRTMYLSDSHPSVQKIWAFDYDI 185 Query: 201 ATGTVSNKTLWKHWLPEDGLPDGMTTDAQGRLWIAHWGGWCVTCHDPVTAAELGR-VRLP 259 +GT S + L+ L G PDG DA G WI G H L R + +P Sbjct: 186 DSGTPSRRRLFVDMLDHPGRPDGAAVDADGCYWIC--GNDAGFIHRFTPDGRLDRSLAVP 243 Query: 260 VSQVTTCAFGGADLRTLFISSARVGLTPEQLAAEPLAGALFAVDTDSLGLPAHPF 314 V + + CAFGGA L TLF++S R G L+ +PLAG +FA++ GL F Sbjct: 244 VKKPSMCAFGGARLDTLFVTSIRPG---GDLSDQPLAGGVFALNPGVTGLEEPAF 295 Lambda K H 0.321 0.137 0.457 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: 409 Number of extensions: 32 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: 316 Length of database: 296 Length adjustment: 27 Effective length of query: 289 Effective length of database: 269 Effective search space: 77741 Effective search space used: 77741 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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