Align xylono-1,5-lactonase (EC 3.1.1.110) (characterized)
to candidate Pf6N2E2_5966 L-arabinolactonase (EC 3.1.1.15)
Query= metacyc::MONOMER-20628 (289 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5966 Length = 291 Score = 137 bits (346), Expect = 2e-37 Identities = 104/291 (35%), Positives = 143/291 (49%), Gaps = 27/291 (9%) Query: 6 TCVWDLKATLGEGPIWHGDT--LWFVDIKQRKIHNYHPATGERFSFDAPDQVTFLAPIVG 63 T V + +A LGEGP W T L++VDI ++ A + + P+ V+ P Sbjct: 4 TAVTEHRAILGEGPFWDEPTQALYWVDIAGKQALRLIGANVQIWQM--PEHVSAFIPTQS 61 Query: 64 ATGFVVGLKTGIHRFH-PATGFS---LLLEVEDAALNNRPNDATVDAQGRLWFGTMHD-- 117 V L +G++R + G LL + D L NR N+A DA G+LW GTM + Sbjct: 62 GDALVT-LSSGVYRLDLDSPGLEPRLTLLCMADPQLGNRANEARCDALGQLWLGTMQNNI 120 Query: 118 GE-------ENNSGSLYRMDLTG-VARMDRDICITNGPCVSPDGKTFYHTDTLEKTIYAF 169 GE E SG L+R+ G V + R + I N SPDG T Y ++L+ T+Y Sbjct: 121 GENAEDLPIERRSGGLFRVSGDGRVMPLLRGLGIPNTLLWSPDGTTVYFGESLDGTLYRH 180 Query: 170 DLAEDGLLSNKRVFVQFALGDDVYPDGSVVDSEGYLWTALWGGFGAVRFSPQGDAVTRIE 229 + DG L+ V+ F PDGS +D+ GY+W A W G +R +PQG IE Sbjct: 181 FIHPDGSLAPAEVW--FGPHPRGGPDGSAMDARGYIWNARWDGSCLLRLNPQGQVDRVIE 238 Query: 230 LPAPNVTKPCFGGPDLKTLYFTTARKGLSDETLAQYPLAGGVFAVPVDVAG 280 LP T FGG DLKTLY T+A L +PL G V ++ VD+ G Sbjct: 239 LPVSRPTSCVFGGDDLKTLYITSAASPLG------HPLDGAVLSMRVDIPG 283 Lambda K H 0.321 0.139 0.442 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: 353 Number of extensions: 28 Number of successful extensions: 4 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: 289 Length of database: 291 Length adjustment: 26 Effective length of query: 263 Effective length of database: 265 Effective search space: 69695 Effective search space used: 69695 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