Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate H281DRAFT_06301 H281DRAFT_06301 L-arabinonolactonase (EC 3.1.1.15)
Query= reanno::BFirm:BPHYT_RS16915 (300 letters) >FitnessBrowser__Burk376:H281DRAFT_06301 Length = 307 Score = 530 bits (1365), Expect = e-155 Identities = 254/292 (86%), Positives = 267/292 (91%) Query: 9 TAALLLDTKCTLGEGATWCAQTGHFYWTDIEGARLWRYDPRDCSNMSWHMPERLATFALC 68 +AALLLDTKCTLGEGATWCA+TG FYWTDIEGARLWRYDP D + W MPERLATFALC Sbjct: 16 SAALLLDTKCTLGEGATWCARTGRFYWTDIEGARLWRYDPSDGRSTFWPMPERLATFALC 75 Query: 69 ADPRYLLLGLATHLAFFELATGETRRIIDVEAGLNTRVNDGRCDRQGRFVFGTKDEGAPL 128 ADP YLLLGLA+ LAFF++ATG+TR I+DVEAG+NTRVNDGRCDRQGRFVFGTKDEG+PL Sbjct: 76 ADPHYLLLGLASQLAFFDIATGQTRHIVDVEAGMNTRVNDGRCDRQGRFVFGTKDEGSPL 135 Query: 129 QAIGGFYRLGHDLSLERLPLPAPAISNSIAFSPDGATMYYCDSPTREIRACDYRADGSIA 188 QAIGGFYRL HDLSLERLPLPAPAISNSIAFSPDGATMY+CDSPTREIRACDYRADG IA Sbjct: 136 QAIGGFYRLNHDLSLERLPLPAPAISNSIAFSPDGATMYFCDSPTREIRACDYRADGGIA 195 Query: 189 NDRLFTRLTDATGEPDGSTVDRDGGLWNAQWGGRRVVRYGPDGMETERVDVPTAQPSCVA 248 NDRLF RL DATGEPDGSTVDRDGGLWNAQWGGRRVVRYG DG+ETERV+VPTAQPSCVA Sbjct: 196 NDRLFVRLADATGEPDGSTVDRDGGLWNAQWGGRRVVRYGADGVETERVEVPTAQPSCVA 255 Query: 249 LGGTQLDTLYITSARCDLDAAALANDPHAGGVFIATLGRRGLPEPVFQGAPA 300 LGG QL TLYITSAR LDAAALA D AGGVFI T RRGLPEPVFQGAPA Sbjct: 256 LGGAQLGTLYITSARVGLDAAALAGDLRAGGVFIVTPARRGLPEPVFQGAPA 307 Lambda K H 0.321 0.138 0.443 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: 545 Number of extensions: 21 Number of successful extensions: 1 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: 307 Length adjustment: 27 Effective length of query: 273 Effective length of database: 280 Effective search space: 76440 Effective search space used: 76440 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