Align Gluconolactonase (characterized, see rationale)
to candidate CCNA_00863 CCNA_00863 xylonolactonase xylC
Query= uniprot:A0A165IRV8 (316 letters) >FitnessBrowser__Caulo:CCNA_00863 Length = 289 Score = 176 bits (447), Expect = 5e-49 Identities = 115/295 (38%), Positives = 159/295 (53%), Gaps = 14/295 (4%) Query: 21 VTGAVRCVIALGNALGEGVLWSVREQAVYWVDILGRELHRWDPATGAHQRWTFD--EEIS 78 +T V CV L LGEG +W +++VDI R++H + PATG +R++FD ++++ Sbjct: 1 MTAQVTCVWDLKATLGEGPIW--HGDTLWFVDIKQRKIHNYHPATG--ERFSFDAPDQVT 56 Query: 79 AIAERAHAPGFIVTLRRGFALFDPATDMAPRYLHQPEPDRAGNRFNDGKCDAQGRFWAGS 138 +A A GF+V L+ G F PAT + L + E NR ND DAQGR W G+ Sbjct: 57 FLAPIVGATGFVVGLKTGIHRFHPATGFS--LLLEVEDAALNNRPNDATVDAQGRLWFGT 114 Query: 139 MDFACEAPTGALYRYDSDGSCTRHDDGFAVTNGPTWSGTGQGAAMFFNATIEGNTYRYDS 198 M E +G+LYR D G R D +TNGP S G+ + T+E Y +D Sbjct: 115 MHDGEENNSGSLYRMDLTG-VARMDRDICITNGPCVSPDGK--TFYHTDTLEKTIYAFDL 171 Query: 199 DLATGTVSNKTLWKHW-LPEDGLPDGMTTDAQGRLWIAHWGGWCVTCHDPVTAAELGRVR 257 G +SNK ++ + L +D PDG D++G LW A WGG+ P A + R+ Sbjct: 172 -AEDGLLSNKRVFVQFALGDDVYPDGSVVDSEGYLWTALWGGFGAVRFSPQGDA-VTRIE 229 Query: 258 LPVSQVTTCAFGGADLRTLFISSARVGLTPEQLAAEPLAGALFAVDTDSLGLPAH 312 LP VT FGG DL+TL+ ++AR GL+ E LA PLAG +FAV D G P H Sbjct: 230 LPAPNVTKPCFGGPDLKTLYFTTARKGLSDETLAQYPLAGGVFAVPVDVAGQPQH 284 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: 366 Number of extensions: 22 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: 289 Length adjustment: 27 Effective length of query: 289 Effective length of database: 262 Effective search space: 75718 Effective search space used: 75718 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