Align Gluconolactonase (characterized, see rationale)
to candidate WP_028997352.1 H537_RS0107150 SMP-30/gluconolactonase/LRE family protein
Query= uniprot:A0A165IRV8 (316 letters) >NCBI__GCF_000430725.1:WP_028997352.1 Length = 299 Score = 168 bits (426), Expect = 1e-46 Identities = 106/284 (37%), Positives = 141/284 (49%), Gaps = 13/284 (4%) Query: 35 LGEGVLWSVREQAVYWVDILGRELHRWDPATGAHQRWTFDEEISAIAERAHAPGFIVTLR 94 LGE W E A++WVDI GR L+RW+P G H W+F+ E A A ++ +R Sbjct: 19 LGESPFWHPHEGALWWVDIPGRRLNRWEPGRGRHDHWSFEAE-PGCAAPAQGGRVLLAMR 77 Query: 95 RGFALFDPATDMAPRYLHQPEPDRAGNRFNDGKCDAQGRFWAGSMDFACEAPTGALYRYD 154 G FDP R + QP D A RFNDGK D QGR WAG++D P ALYR+ Sbjct: 78 DGLWCFDPRHGQRQR-VCQPPYDPAQQRFNDGKADPQGRLWAGTID-EQRQPRAALYRF- 134 Query: 155 SDGSCTRHDDGFAVTNGPTWSGTGQGAAMFFNATIEGNTYRYDSDLATGTVSNKTLWKHW 214 DG R DG +NG WS G M+++ T D DL GT+S + ++ + Sbjct: 135 HDGELERMADGITTSNGLAWSPDGH--TMYWSDTRAHEIRALDFDLDLGTLSRQRVFARF 192 Query: 215 LPED------GLPDGMTTDAQGRLWIAHWGGWCVTCHDPVTAAELGRVRLPVSQVTTCAF 268 P G PDG D++G W+A + G C L V LPV T F Sbjct: 193 APRQEGVRYGGRPDGAAVDSEGAYWVAMYEG-CRLLRLSPQGQLLQEVALPVHCPTMPCF 251 Query: 269 GGADLRTLFISSARVGLTPEQLAAEPLAGALFAVDTDSLGLPAH 312 GG DLRTL++++AR ++LA EP AG + + GLP + Sbjct: 252 GGPDLRTLYLTTARDHRPADELAREPWAGCVLEMRVAVPGLPVN 295 Score = 26.9 bits (58), Expect = 6e-04 Identities = 24/107 (22%), Positives = 38/107 (35%), Gaps = 31/107 (28%) Query: 29 IALGNALGEGVLWSVREQAVYWVDILGRELHRWDPATGAHQRWTFDEEISAIAERAHAPG 88 +A G G+ WS +YW D E+ D FD ++ ++ Sbjct: 142 MADGITTSNGLAWSPDGHTMYWSDTRAHEIRALD----------FDLDLGTLSR------ 185 Query: 89 FIVTLRRGFALFDPATDMAPRYLHQPEPDRAGNRFNDGKCDAQGRFW 135 +R FA F P + E R G R + D++G +W Sbjct: 186 -----QRVFARFAP----------RQEGVRYGGRPDGAAVDSEGAYW 217 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: 445 Number of extensions: 34 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 316 Length of database: 299 Length adjustment: 27 Effective length of query: 289 Effective length of database: 272 Effective search space: 78608 Effective search space used: 78608 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 24 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