Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate BWI76_RS12820 BWI76_RS12820 NAD-dependent phenylacetaldehyde dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_23175 (500 letters) >FitnessBrowser__Koxy:BWI76_RS12820 Length = 499 Score = 244 bits (622), Expect = 7e-69 Identities = 163/486 (33%), Positives = 252/486 (51%), Gaps = 16/486 (3%) Query: 8 GHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPA--WSEQSS 65 G Y+DG QA+++ + V+NPATG A A A + VD AV SA AF + W+ ++ Sbjct: 21 GLYLDGTQQAAESEQRLTVWNPATGQAIASTADANAADVDRAVMSAWRAFVSRSWAGRTP 80 Query: 66 LRRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHG-EVTRGIEIVEYACG-----AP 119 R R++ +F +L+++H +ELAQ+ + E GK ++ + EV + + Y G + Sbjct: 81 ADRERILLRFADLVEQHGEELAQLETLEQGKSINISRAFEVGCTLNWMRYTAGLTTKISG 140 Query: 120 NLLKTDFSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSE 179 L GG W ++P+GV AG+ P+NFP+M+ +W + AL AG ++KPSE Sbjct: 141 RTLDVSIPFPAGGRYQAWTKKEPVGVVAGIVPWNFPLMIGMWKVMPALAAGCSIVIKPSE 200 Query: 180 RDPSASLLMARLLTEAGLPDGVFNVVQGDKVAVD-ALLQHPDIEAISFVGSTPIAEYIHQ 238 P L +A L TEAG+PDGVFNVV G AL HP + +SF GST + I + Sbjct: 201 TTPLTLLRVAELATEAGVPDGVFNVVTGSGAGCGAALTSHPLVAKVSFTGSTATGKQIAR 260 Query: 239 QGTAQGKRVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGD 298 + RV G KN IV+ DAD + L+ ++ + G+ C A S + D Sbjct: 261 VAADRLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQVCAASSRIYIEAPLFD 320 Query: 299 ELIAKLLPRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKV 358 L++ + L++G G + + P+V+ H AKV ++D + A LI G Sbjct: 321 TLVSGFEQAVKSLQVGPGMLESSQINPVVSQAHCAKVAAYLDEARQQKAELI---SGHAG 377 Query: 359 PGAEQGFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCF 418 P A QG+++ TL A + + ++E+FGPV+ +VRV D A+ L N +FG S + Sbjct: 378 PDA-QGYYIAPTLVINPDAGLRLCREEVFGPVVNLVRVADGEEALLLANDSDFGLTASVW 436 Query: 419 TRDGGIARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYK 478 TRD A ++ ++ G V +N + A FGG K+S G +G + L + K Sbjct: 437 TRDLTQALSYTDRLQAGTVWVNSHTLID-ANLPFGGMKQS--GTGRDFGPDWLDDWCETK 493 Query: 479 SVMQRW 484 SV R+ Sbjct: 494 SVCVRY 499 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: 535 Number of extensions: 23 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: 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 Apr 09 2024. 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