Align Gluconolactonase (characterized, see rationale)
to candidate HSERO_RS19370 HSERO_RS19370 gluconolactonase
Query= uniprot:A0A165IRV8 (316 letters) >FitnessBrowser__HerbieS:HSERO_RS19370 Length = 302 Score = 155 bits (392), Expect = 1e-42 Identities = 106/297 (35%), Positives = 143/297 (48%), Gaps = 14/297 (4%) Query: 19 APVTGAVRCVIALGNALGEGVLWSVREQAVYWVDILGRELHRWDPATGAHQRWTFDEEIS 78 +P AV LGE LW +E A+YW+DI G+ +HR P +G H+RW EE Sbjct: 5 SPSAAAVTVAFPEPMLLGESPLWHAQEAALYWIDIPGKAVHRLHPESGQHKRWDLPEEPG 64 Query: 79 AIAERAHAPGFIVTLRRGFALFDPATDMAPRYLHQPEP-DRAGNRFNDGKCDAQGRFWAG 137 +I A G +V +R G +F TD L P D + RFNDG+CDA GRFW G Sbjct: 65 SIVRHAQG-GLVVAIRTG--MFHLNTDTGALTLLLAAPYDSSRIRFNDGRCDASGRFWCG 121 Query: 138 SMDFACEAPTGALYRYDSDGSCTRHDDGFAVTNGPTWSGTGQGAAMFFNATIEGNTYRYD 197 ++ + G LY ++ + H +NG +S + M+ T YD Sbjct: 122 TIYEPRDRDGGTLYCFERNALRDAH-HAVVTSNGLAFSSDQR--LMYHANTPAHRINLYD 178 Query: 198 SDLATGTVSNKTLWKHWLPE------DGLPDGMTTDAQGRLWIAHWGGWCVTCHDPVTAA 251 DLATG SN L + + + G PDG D+QG W A + G V P Sbjct: 179 YDLATGATSNCRLLRQFDSDKSAPDYGGRPDGAAVDSQGAYWCAMFEGGRVLRLSP-QGE 237 Query: 252 ELGRVRLPVSQVTTCAFGGADLRTLFISSARVGLTPEQLAAEPLAGALFAVDTDSLG 308 L +RLP T AFGG DLRTL+I++ R G +P +LA P +G + AV D G Sbjct: 238 ILQEIRLPARCPTMVAFGGDDLRTLYITTGRNGRSPAELAQYPESGCVLAVRVDVPG 294 Lambda K H 0.321 0.137 0.457 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: 368 Number of extensions: 22 Number of successful extensions: 6 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: 316 Length of database: 302 Length adjustment: 27 Effective length of query: 289 Effective length of database: 275 Effective search space: 79475 Effective search space used: 79475 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