Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate 3607832 Dshi_1240 SMP-30/Gluconolaconase/LRE domain protein (RefSeq)
Query= reanno::HerbieS:HSERO_RS05225 (292 letters) >FitnessBrowser__Dino:3607832 Length = 286 Score = 169 bits (427), Expect = 9e-47 Identities = 112/290 (38%), Positives = 145/290 (50%), Gaps = 8/290 (2%) Query: 1 MNVQLLVDGHHELGEGVLWCDRSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYAF 60 M+ L D LGEG LW Q +FW DI R+ + D T L W E + + Sbjct: 1 MSATLYDDRPCALGEGPLWHPERQQLFWFDITGQRMLSRDGDTPL--EWQFDEMVSAAGW 58 Query: 61 TADPQQLLIGLESRLAFFNLSTGTIAPICRIEDDLPSTRLNDGRCDRQGRFVFGTLNEDA 120 D LLI E+ L F+L+ G + +E D P TR NDGR D G F GT+ + A Sbjct: 59 V-DHDTLLIASETALVTFDLAEGESRFVAPLEADRPETRSNDGRADPWGGFWIGTMGKSA 117 Query: 121 GRAPIASFYRLNTDLTLERLSLPSIAISNSICFSLDGKLMYHCDSMAGKIMVCDYDTASG 180 + YRL D TL R+ + + ISN++CF Y+ D+ ++M D Sbjct: 118 -EPGAGAIYRL-FDGTLRRV-VRDVTISNALCFDAAQSCAYYADTPTRQVMRLPLDGDGW 174 Query: 181 AVGGQRVFADVAQPG-GPDGSTIDAEGYLWNAQWGGARVVRYAPDGRIDRVVAIPTSQPS 239 G V D+ G PDG+ DA G LW AQWG RV +APDG R +A S Sbjct: 175 PSGPATVAVDLRAEGLNPDGAVTDAAGNLWIAQWGAGRVACHAPDGTFLRALACGGRHSS 234 Query: 240 CVAFGGAQFDTLYVTTAHEGMSAEQRAADPQAGALFAVALADVRGLPEVR 289 C AFGG D L++TTA EG+SA+ AA P+ G +FA A RGLPE R Sbjct: 235 CPAFGGPDLDQLFITTAREGLSADDIAAAPENGCVFA-AEGVARGLPEPR 283 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: 302 Number of extensions: 19 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: 292 Length of database: 286 Length adjustment: 26 Effective length of query: 266 Effective length of database: 260 Effective search space: 69160 Effective search space used: 69160 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 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