Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_084931116.1 HA51_RS00225 SDR family oxidoreductase
Query= uniprot:B2T9V3 (247 letters) >NCBI__GCF_002095475.1:WP_084931116.1 Length = 258 Score = 132 bits (332), Expect = 7e-36 Identities = 88/255 (34%), Positives = 137/255 (53%), Gaps = 14/255 (5%) Query: 4 RLAGKTALITAAGQGIGLATAELFAREGARVIATDIR--IDGLA-----GKPVEARKLDV 56 R GK LIT A G+G A +AREGA + D D +A G+ A K DV Sbjct: 2 RYQGKNVLITGAAAGLGQTIATSYAREGASIAIIDFADASDTVAKVQASGQQAVAFKADV 61 Query: 57 RDDAAIKAL---AAEI--GAVDVLFNCAGFVHAGNILECSE-EDWDFAFDLNVKAMYRMI 110 RD A++A AA + G +DVL N AGF N++E W D+N+ + Sbjct: 62 RDQDAVQAAVNQAANVFAGRIDVLINNAGFNGHYNLVENMPLAQWRETLDINLTGTLLVT 121 Query: 111 RAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCN 170 +A +P M +GGG+I ++++ + +G+P R Y SK A++GL +++A + + +R N Sbjct: 122 QAVIPFMKAQGGGAI-GITASNVARRGLPYRADYVCSKWALLGLNQTLALELVDHHIRVN 180 Query: 171 AICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDE 230 A+CPG + +E +V QA+A+G +L ++ A+ PM R EE+ A ++L SD Sbjct: 181 AVCPGPIEGDRIEDVMVRQAEAEGKSLKEMRKAWEEAAPMKRFVTAEEVTAAMMFLTSDA 240 Query: 231 SSFTTGHAHVIDGGW 245 +S TG A + GG+ Sbjct: 241 ASAMTGQALNVTGGF 255 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: 137 Number of extensions: 10 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: 258 Length adjustment: 24 Effective length of query: 223 Effective length of database: 234 Effective search space: 52182 Effective search space used: 52182 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 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