Align Gluconolactonase (characterized, see rationale)
to candidate RR42_RS30140 RR42_RS30140 gluconolaconase
Query= uniprot:A0A165IRV8 (316 letters) >FitnessBrowser__Cup4G11:RR42_RS30140 Length = 292 Score = 196 bits (499), Expect = 4e-55 Identities = 119/284 (41%), Positives = 155/284 (54%), Gaps = 7/284 (2%) Query: 27 CVIALGNALGEGVLWSVREQAVYWVDILGRELHRWDPATGAHQRWTFDEEISAIAERAHA 86 CV LG LGEG +W AVY+VDI GR +HR+ ATGA + W D + I Sbjct: 8 CVWQLGAELGEGPVWHQGSSAVYFVDIKGRRIHRFAIATGAMRSWPVDSQPGFIVPLDDG 67 Query: 87 PGFIVTLRRGFALFDPATDMAPRYLHQPEPDRAGNRFNDGKCDAQGRFWAGSMDFACEAP 146 GF+ ++ G FDPA D A R L + EPD GNR NDG D GR W G+MD AP Sbjct: 68 -GFLCGMQDGLYRFDPA-DGACRRLKEVEPDLPGNRINDGFVDPAGRLWFGTMDDGEAAP 125 Query: 147 TGALYRYDSDGSCTRHDDGFAVTNGPTWSGTGQGAAMFFNATIEGNTYRYDSDLATGTVS 206 +G+LY+ DG R D G+ +TNGP S + ++ T++ Y +D G +S Sbjct: 126 SGSLYQVGDDGRTWRRDSGYVITNGPAMSPDAR--TLYHADTVKRLVYAFDVG-QDGALS 182 Query: 207 NKTLWKHWLPEDGLPDGMTTDAQGRLWIAHWGGWCVTCHDPVTAAELGRVRLPVSQVTTC 266 + + L G PDGM DA G LWIA +GG + P G VR P VT Sbjct: 183 RRREFAR-LCGTGYPDGMAVDADGHLWIAVFGGARIERWSP-DGRLAGVVRFPCDNVTKL 240 Query: 267 AFGGADLRTLFISSARVGLTPEQLAAEPLAGALFAVDTDSLGLP 310 AFGG DLRT+++++AR GL+P LA +PLAG LF+ + GLP Sbjct: 241 AFGGDDLRTVYVTTARKGLSPAALALQPLAGGLFSFRAPTRGLP 284 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: 425 Number of extensions: 35 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: 316 Length of database: 292 Length adjustment: 27 Effective length of query: 289 Effective length of database: 265 Effective search space: 76585 Effective search space used: 76585 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