Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate PP_1817 PP_1817 Oxidoreductase, short-chain dehydrogenase/reductase family
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__Putida:PP_1817 Length = 253 Score = 154 bits (390), Expect = 1e-42 Identities = 101/260 (38%), Positives = 142/260 (54%), Gaps = 27/260 (10%) Query: 1 MTQRLAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGLAGKPVEAR-------- 52 M+ +G+ AL+T AG GIG ATA FA EG +V+ D+ D + G+ A+ Sbjct: 1 MSMTFSGQVALVTGAGAGIGRATALAFAHEGMKVVVADL--DPVGGEATVAQIHAAGGEA 58 Query: 53 ---KLDVRDDAAIKAL----AAEIGAVDVLFNCAGF-VHAGNILECSEEDWDFAFDLNVK 104 DV DA ++ L A G +D FN AG + + E SE ++D +NVK Sbjct: 59 LFIACDVTRDAEVRQLHERLMAAYGRLDYAFNNAGIEIEQHRLAEGSEAEFDAIMGVNVK 118 Query: 105 AMYRMIRAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFIT 164 ++ ++ LP +L +GGG+I+N +S A + P YSASK AVIGLTKS A ++ Sbjct: 119 GVWLCMKYQLPLLLAQGGGAIVNTASVAG-LGAAPKMSIYSASKHAVIGLTKSAAIEYAK 177 Query: 165 RGVRCNAICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALAL 224 +G+R NA+CP + + R QA + A A A P+GRIGK EEIA+ L Sbjct: 178 KGIRVNAVCPAVIDTDMF--RRAYQADPRKAEFAA------AMHPVGRIGKVEEIASAVL 229 Query: 225 YLGSDESSFTTGHAHVIDGG 244 YL SD ++FTTGH +DGG Sbjct: 230 YLCSDGAAFTTGHCLTVDGG 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: 156 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