Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate HSERO_RS07235 HSERO_RS07235 aldehyde dehydrogenase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1229 (505 letters) >FitnessBrowser__HerbieS:HSERO_RS07235 Length = 477 Score = 243 bits (619), Expect = 1e-68 Identities = 147/476 (30%), Positives = 243/476 (51%), Gaps = 9/476 (1%) Query: 12 VKLLIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHRAFQTWKLTPIG 71 V+L I+GEW S + D++NPAT++V+ K+ A A++D A+ AA + F+TW+ Sbjct: 5 VQLFINGEWTASASGRTIDVINPATEEVIGKIAHADRADLDRALEAASKGFETWRNMSAF 64 Query: 72 ARMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHACSIGSLQMGEF 131 R +IM + L+RE ++ +A +++ EQGK +A+A+ + + ++ G Sbjct: 65 ERSKIMRRAADLLRERAEEVARLMTMEQGKPLAEAKMETLGAADTIDWFAEEARRTYGRL 124 Query: 132 AENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTM 191 G +++P+G A TP+NFP + A+A G + ++K E+ P S Sbjct: 125 VPARVPGAYQMVIKEPVGPVAAFTPWNFPLNQVVRKLSAALAAGCSIIVKAPEETPASPA 184 Query: 192 LLVELAIEAGIPPGVLNVVHG-GKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGK 250 L+ +AG+P GV+N+V+G ++ + L H IK +SF GST VG + LAG+H K Sbjct: 185 ELIRAYADAGVPAGVINLVYGVPAEISEYLIPHPVIKKISFTGSTPVGKQLAALAGQHMK 244 Query: 251 RVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMA-TSVVVLVGAAKQWLPDLK 309 R +G A+V DA+ + A L A F AGQ C++ T +V G ++ Sbjct: 245 RATMELGGHAPAMVFDDADVDVAAKMLATAKFRNAGQVCVSPTRFLVQKGVFNAFVDKFV 304 Query: 310 ALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDISVPGYEKGN 369 A++LKV G E G +GPV +KR + LI+ + +GA+L G+ I KG Sbjct: 305 TYAEQLKVGNGLEAGITMGPVANKRRIPALEALIDDAVSQGAQLRTGGKRIG----NKGY 360 Query: 370 FVGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSGAAA 429 F PT+ + + + + +E FGP+ ++ +TLD+ I N P+G F +S Sbjct: 361 FFQPTVLTNLPLQARAMNEEPFGPLALINSFETLDEVITEANRLPYGLAAYAFAKSAHTK 420 Query: 430 RKFQTEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVT 485 ++ G + IN + + +P F G + S G G G + ++ Y TK VT Sbjct: 421 HALAARVESGMLTIN-HLGLALPELPFGGIKDSGYGSEG--GTEAIEAYINTKLVT 473 Lambda K H 0.319 0.135 0.397 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: 521 Number of extensions: 25 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: 505 Length of database: 477 Length adjustment: 34 Effective length of query: 471 Effective length of database: 443 Effective search space: 208653 Effective search space used: 208653 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: 52 (24.6 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