Align Short-chain dehydrogenase (characterized, see rationale)
to candidate Pf6N2E2_1577 Glucose 1-dehydrogenase (EC 1.1.1.47)
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1577 Length = 254 Score = 102 bits (255), Expect = 6e-27 Identities = 88/250 (35%), Positives = 125/250 (50%), Gaps = 14/250 (5%) Query: 5 LQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQLEL 64 ++ KV +VTG ASGIG AI+L L A GA VV P AR GL P A ++ Sbjct: 12 VEGKVALVTGAASGIGKAIALLLHARGA-KVVAEDINPAVHELAR-PGLVPLEA----DI 65 Query: 65 QDEARCGEAVAETVRRFGRLDGLVNNAGV--NDSVGLDAGRNEFVASLERNLIHYYVMAH 122 ++ AV V +FGRLD LVNNAG+ N V +D R ++ N ++ + Sbjct: 66 TEDGAAERAVGLAVEQFGRLDILVNNAGIIINKRV-IDMTRQDWERIQAVNATAAFLHSR 124 Query: 123 YCVPHLKATR-GAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNAL 181 V + + GAI+N++S + + Y ASKGA LTR A + +DG+RVNA+ Sbjct: 125 EAVKAMMPNKAGAIVNIASYASYFAFPTIAAYTASKGALAQLTRTLALEVIEDGIRVNAV 184 Query: 182 IPAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSHTTG 241 +V+T + + E+ L P+G R EE+A++ FL S R+S G Sbjct: 185 GVGDVVTNILNDVV---EDGPAFLAQHGEAAPIG-RAAQPEEIAEVVAFLASDRASFIVG 240 Query: 242 QWVFVDGGYT 251 V DGG T Sbjct: 241 SVVMADGGMT 250 Lambda K H 0.318 0.134 0.394 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: 130 Number of extensions: 5 Number of successful extensions: 3 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: 258 Length of database: 254 Length adjustment: 24 Effective length of query: 234 Effective length of database: 230 Effective search space: 53820 Effective search space used: 53820 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 (21.7 bits) S2: 47 (22.7 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