Align NADH-dependent aldehyde reductase (EC 1.1.1.77; EC 1.1.1.244; EC 1.1.1.1) (characterized)
to candidate BPHYT_RS28580 BPHYT_RS28580 3-beta hydroxysteroid dehydrogenase
Query= metacyc::G3O-32155-MONOMER (298 letters) >FitnessBrowser__BFirm:BPHYT_RS28580 Length = 323 Score = 208 bits (530), Expect = 1e-58 Identities = 129/317 (40%), Positives = 175/317 (55%), Gaps = 29/317 (9%) Query: 1 MKVFITGASGFIGSAVLSELISSGHEVVGLARSDEAAAKIKSIDPAAKILRGDLKDLEIL 60 M VF+TG +G GS ++ +L+++GHEV LAR+DE+AA + ++ AK RGDL DL L Sbjct: 1 MHVFVTGGTGHAGSHIIPDLVAAGHEVTALARTDESAATVSAL--GAKARRGDLSDLAGL 58 Query: 61 KKGATESDGVIHLGFVHDFKNFEQCCEI---DRQATVAMLESLKGSNKPFLYTNGTLSLR 117 K A ESDGVIH+G+ D + + +A E+L G+ KP L G++ Sbjct: 59 KAAAAESDGVIHVGYRADLLQAGGIAALGDSELSIVLAFGEALAGTGKP-LVVAGSIGAP 117 Query: 118 PN--------------KVANEQD----GIDEDSKILRA--VTEQVALSYKDKGVSARIVR 157 N + A E D G D+ LRA V E + ++GV + +VR Sbjct: 118 TNVGRGAPLVAPVSLGRPATEDDPALPGRPLDAGTLRARNVVETAVVGLAEQGVRSSVVR 177 Query: 158 LPFSVHGKGDKA-FVPILMNIAKAAGKSGYVGQGTNAWAAVHRLDTAPLFRLVLEKGKTG 216 +P H D+ F+ IL+ +AK G GY G G N W AVH D A LFRL LEKG G Sbjct: 178 IPLIAHSTADRVGFLQILIGLAKEKGVIGYPGDGENRWPAVHIRDLASLFRLALEKGPAG 237 Query: 217 QVYHCVGEQGIPFKDIARVIGEILNVPVASIPVDD--AESHFGFLTCFVTRDGPVSSEGT 274 + +H V ++GI F++IA I L VP SIP D+ +FGFL+ VT D P S+ T Sbjct: 238 KTWHAVADEGIRFREIAEAIAARLGVPAVSIPADELMVPGYFGFLSAVVTGDFPASNAIT 297 Query: 275 RKELGWQPQQIGLLEDI 291 RK LGW+P Q GLLED+ Sbjct: 298 RKSLGWEPAQPGLLEDM 314 Lambda K H 0.318 0.136 0.393 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: 248 Number of extensions: 12 Number of successful extensions: 5 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: 298 Length of database: 323 Length adjustment: 27 Effective length of query: 271 Effective length of database: 296 Effective search space: 80216 Effective search space used: 80216 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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