Align L-arabinonolactonase (characterized, see rationale)
to candidate HSERO_RS05225 HSERO_RS05225 gluconolaconase
Query= uniprot:A0A1I2AUG6 (300 letters) >FitnessBrowser__HerbieS:HSERO_RS05225 Length = 292 Score = 318 bits (815), Expect = 9e-92 Identities = 166/296 (56%), Positives = 201/296 (67%), Gaps = 9/296 (3%) Query: 1 MNARVVHHPANTLGEGILWCEREQALYWTDIQAATLWRHRPADGATRSWEMPERLGCLAL 60 MN +++ + LGEG+LWC+R Q+++WTDI A+ LW H P G TRSW MPERL C A Sbjct: 1 MNVQLLVDGHHELGEGVLWCDRSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYAF 60 Query: 61 CEADGWLLLGLATRLAFFRPEDDLLLPLVSVEPDLP-TRLNDGACDRQGRFVFGTLHEPA 119 LL+GL +RLAFF + P+ +E DLP TRLNDG CDRQGRFVFGTL+E A Sbjct: 61 TADPQQLLIGLESRLAFFNLSTGTIAPICRIEDDLPSTRLNDGRCDRQGRFVFGTLNEDA 120 Query: 120 AGETRQPIGAFYRLNADLTLERLNLPGIGISNSVAFSPDGRTMYFCDSPSRVIQCCDYGD 179 R PI +FYRLN DLTLERL+LP I ISNS+ FS DG+ MY CDS + I CDY Sbjct: 121 G---RAPIASFYRLNTDLTLERLSLPSIAISNSICFSLDGKLMYHCDSMAGKIMVCDYDT 177 Query: 180 RCGE---PRVFARVDDERGEPDGSAVDAQGCLWNAQWGLGRVVRYAPDGRVDRIVEVPAT 236 G RVFA V + G PDGS +DA+G LWNAQWG RVVRYAPDGR+DR+V +P + Sbjct: 178 ASGAVGGQRVFADVA-QPGGPDGSTIDAEGYLWNAQWGGARVVRYAPDGRIDRVVAIPTS 236 Query: 237 QPTRPAFGDSPLDTLYITSARDGLSSAALATQPLAGALFA-ADAGASGLPEPRFRG 291 QP+ AFG + DTLY+T+A +G+S+ A P AGALFA A A GLPE RF G Sbjct: 237 QPSCVAFGGAQFDTLYVTTAHEGMSAEQRAADPQAGALFAVALADVRGLPEVRFAG 292 Lambda K H 0.321 0.139 0.451 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: 342 Number of extensions: 18 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: 300 Length of database: 292 Length adjustment: 26 Effective length of query: 274 Effective length of database: 266 Effective search space: 72884 Effective search space used: 72884 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