Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate Pf1N1B4_512 Short-chain dehydrogenase/reductase SDR
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_512 Length = 253 Score = 145 bits (365), Expect = 1e-39 Identities = 92/259 (35%), Positives = 140/259 (54%), Gaps = 25/259 (9%) Query: 1 MTQRLAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDG---------LAGKPVEA 51 M+ +G+ A++T A GIG ATA FA EG +V+ D+ G AG Sbjct: 1 MSMTFSGQVAVVTGAANGIGRATALAFAAEGLKVVVADLDAAGGEGTVALIRTAGGEATF 60 Query: 52 RKLDVRDDAAIKALAAEI----GAVDVLFNCAGF-VHAGNILECSEEDWDFAFDLNVKAM 106 + +V ++ +K L E+ G +D FN AG + G + E + +++D +NVK + Sbjct: 61 VRCNVTVESEVKNLMDEVVNTYGRLDYAFNNAGIEIEKGKLAEGTIDEFDAIMGVNVKGV 120 Query: 107 YRMIRAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRG 166 + ++ LP +L +GGG+I+N +S A + P Y+ASK AVIGLTKS A ++ + Sbjct: 121 WLCMKYQLPLLLAQGGGAIVNTASVAG-LGAAPKMSIYAASKHAVIGLTKSAAIEYAKKK 179 Query: 167 VRCNAICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFV-ARQPMGRIGKPEEIAALALY 225 +R NA+CP + + + A D + F A P+GRIGK EEIA+ LY Sbjct: 180 IRVNAVCPAVIDTDMFRRAYEA---------DPKKGEFANAMHPVGRIGKVEEIASAVLY 230 Query: 226 LGSDESSFTTGHAHVIDGG 244 L SD ++FTTGH+ +DGG Sbjct: 231 LCSDGAAFTTGHSLAVDGG 249 Lambda K H 0.320 0.133 0.381 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: 141 Number of extensions: 5 Number of successful extensions: 4 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: 247 Length of database: 253 Length adjustment: 24 Effective length of query: 223 Effective length of database: 229 Effective search space: 51067 Effective search space used: 51067 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: 46 (22.3 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