Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_23175 (500 letters) >NCBI__GCF_000009985.1:WP_011383257.1 Length = 499 Score = 211 bits (537), Expect = 5e-59 Identities = 141/456 (30%), Positives = 228/456 (50%), Gaps = 11/456 (2%) Query: 10 YIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSLRRS 69 Y+DG +D+ R +V +PATG + A V + A+ +A AA+ W ++++ R+ Sbjct: 28 YVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWNPWRQRTAKDRA 87 Query: 70 RVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSDN 129 VM + +L+ H D LA+++S E GK L++A GE++ G + + D Sbjct: 88 AVMMAWHDLIMAHQDALARLLSAEQGKPLAEAMGEISYGASFISWFAEEGKRAYGDLIPT 147 Query: 130 IGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLMA 189 ++QP+GV A VTP+NFP+ + AL AG ++KP+E P ++L +A Sbjct: 148 TASDRRLLVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPAEDTPLSALALA 207 Query: 190 RLLTEAGLPDGVFNVVQGDKVAV--DALLQHPDIEAISFVGSTPIAEYIHQQGTAQGKRV 247 L AGLP G+FN+V + A + + + +SF GST + + + Q K+V Sbjct: 208 ELAHRAGLPKGLFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRVGKLLMAQCAETVKKV 267 Query: 248 QALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLPR 307 G IV D DLD A + + Y ++G+ C+ + + + ++ KL + Sbjct: 268 SLELGGNAPFIVFDDCDLDAAVAGALASKYRNSGQTCICTNRFLVQAGIYEDFAVKLAEK 327 Query: 308 IDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQGFFV 367 + +G+ GPL+ A AKV + V++GAR++ GR P A G F Sbjct: 328 AAAMAVGHALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTGGR----PHALGGGFW 383 Query: 368 GATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARA 427 T+ VT M +++E FGPV ++R A A+AL NA EFG ++RD +AR Sbjct: 384 QPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYFYSRD--VARV 441 Query: 428 F--ARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFG 461 F A +++ GMVG+N + + FGG K S G Sbjct: 442 FRVAEALECGMVGVNESL-ISNEVAPFGGIKESGLG 476 Lambda K H 0.320 0.137 0.412 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: 553 Number of extensions: 27 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: 500 Length of database: 499 Length adjustment: 34 Effective length of query: 466 Effective length of database: 465 Effective search space: 216690 Effective search space used: 216690 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: 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