Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate WP_086510992.1 BZY95_RS16570 SMP-30/gluconolactonase/LRE family protein
Query= reanno::HerbieS:HSERO_RS05225 (292 letters) >NCBI__GCF_002151265.1:WP_086510992.1 Length = 304 Score = 144 bits (362), Expect = 3e-39 Identities = 105/302 (34%), Positives = 146/302 (48%), Gaps = 26/302 (8%) Query: 3 VQLLVDGHHELGEGVLWCD---RSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYA 59 +Q + G +LG G LWC + + + DI L+ HD +G TR W + E C Sbjct: 15 IQRIWRGRAQLGGGPLWCPGQGEAGRLLFVDILRRALYVHDFASGTTRGWPLEEACCWLV 74 Query: 60 FTADPQQLLIGLESRLAFFNLSTGTIAPICRIEDDLPS------TRLNDGRCDRQGRFVF 113 AD + GL SRL L P RI DD + R N+ D GR F Sbjct: 75 PRADGDGFIAGLASRLVHLRLEEH--GP--RIVDDWVTPEEPAGNRFNNAAVDTLGRLWF 130 Query: 114 GTLNE---DAGRAPIASFYRLNTDLTLERLSLPSIAISNSICFSLDGKLMYHCDSMAGKI 170 G+++E ++G + YRL+ L R+ ++N S DG+ +YH D+ AG + Sbjct: 131 GSMSENEQESGEPGQGALYRLD-GAGLRRVD-HGYGVANGPAVSPDGRTLYHSDTAAGIV 188 Query: 171 MVCDYDTASGAVGGQRVFADV-AQPGGPDGSTIDAEGYLWNAQWGGARVVRYAPDGRIDR 229 + A G + G+R G PDG T D EG LW A WGG RV R+ PDG +D Sbjct: 189 YAYEL-AADGELTGRREHLRFHGAQGYPDGMTCDVEGGLWVAHWGGGRVSRFLPDGTLDE 247 Query: 230 VVAIPTSQPSCVAFGGAQFDTLYVTTAHEGMSAEQRAADPQAGALFAVALADVRGLPEVR 289 + +P S+ + AFGG + D LY+TTA +G R + AG+LF VA VRGL Sbjct: 248 TLLLPASRVTSCAFGGPELDQLYITTAADG-----RDQEALAGSLFRVA-PGVRGLASPM 301 Query: 290 FA 291 F+ Sbjct: 302 FS 303 Lambda K H 0.322 0.138 0.437 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: 324 Number of extensions: 14 Number of successful extensions: 5 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: 292 Length of database: 304 Length adjustment: 26 Effective length of query: 266 Effective length of database: 278 Effective search space: 73948 Effective search space used: 73948 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 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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