Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate BWI76_RS12820 BWI76_RS12820 NAD-dependent phenylacetaldehyde dehydrogenase
Query= BRENDA::P80668 (499 letters) >FitnessBrowser__Koxy:BWI76_RS12820 Length = 499 Score = 858 bits (2217), Expect = 0.0 Identities = 423/499 (84%), Positives = 459/499 (91%) Query: 1 MTEPHVAVLSQVQQFLDRQHGLYIDGRPGPAQSEKRLAIFDPATGQEIASTADANEADVD 60 M+ VA+L+ VQQFLDRQHGLY+DG A+SE+RL +++PATGQ IASTADAN ADVD Sbjct: 1 MSTSQVALLASVQQFLDRQHGLYLDGTQQAAESEQRLTVWNPATGQAIASTADANAADVD 60 Query: 61 NAVMSAWRAFVSRRWAGRLPAERERILLRFADLVEQHSEELAQLETLEQGKSIAISRAFE 120 AVMSAWRAFVSR WAGR PA+RERILLRFADLVEQH EELAQLETLEQGKSI ISRAFE Sbjct: 61 RAVMSAWRAFVSRSWAGRTPADRERILLRFADLVEQHGEELAQLETLEQGKSINISRAFE 120 Query: 121 VGCTLNWMRYTAGLTTKIAGKTLDLSIPLPQGARYQAWTRKEPVGVVAGIVPWNFPLMIG 180 VGCTLNWMRYTAGLTTKI+G+TLD+SIP P G RYQAWT+KEPVGVVAGIVPWNFPLMIG Sbjct: 121 VGCTLNWMRYTAGLTTKISGRTLDVSIPFPAGGRYQAWTKKEPVGVVAGIVPWNFPLMIG 180 Query: 181 MWKVMPALAAGCSIVIKPSETTPLTMLRVAELASEAGIPDGVFNVVTGSGAVCGAALTSH 240 MWKVMPALAAGCSIVIKPSETTPLT+LRVAELA+EAG+PDGVFNVVTGSGA CGAALTSH Sbjct: 181 MWKVMPALAAGCSIVIKPSETTPLTLLRVAELATEAGVPDGVFNVVTGSGAGCGAALTSH 240 Query: 241 PHVAKISFTGSTATGKGIARTAADHLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFL 300 P VAK+SFTGSTATGK IAR AAD LTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFL Sbjct: 241 PLVAKVSFTGSTATGKQIARVAADRLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFL 300 Query: 301 NQGQVCAASSRIYIEAPLFDTLVSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSF 360 NQGQVCAASSRIYIEAPLFDTLVSGFEQAVKSLQVGPGM +QINP+VS+AHC KV ++ Sbjct: 301 NQGQVCAASSRIYIEAPLFDTLVSGFEQAVKSLQVGPGMLESSQINPVVSQAHCAKVAAY 360 Query: 361 LDDAQAQQAELIRGSNGPAGEGYYVAPTLVVNPDAKLRLTREEVFGPVVNLVRVADGEEA 420 LD+A+ Q+AELI G GP +GYY+APTLV+NPDA LRL REEVFGPVVNLVRVADGEEA Sbjct: 361 LDEARQQKAELISGHAGPDAQGYYIAPTLVINPDAGLRLCREEVFGPVVNLVRVADGEEA 420 Query: 421 LQLANDTEYGLTASVWTQNLSQALEYSDRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRD 480 L LAND+++GLTASVWT++L+QAL Y+DRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRD Sbjct: 421 LLLANDSDFGLTASVWTRDLTQALSYTDRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRD 480 Query: 481 FGPDWLDGWCETKSVCVRY 499 FGPDWLD WCETKSVCVRY Sbjct: 481 FGPDWLDDWCETKSVCVRY 499 Lambda K H 0.318 0.133 0.402 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: 931 Number of extensions: 22 Number of successful extensions: 1 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: 499 Length of database: 499 Length adjustment: 34 Effective length of query: 465 Effective length of database: 465 Effective search space: 216225 Effective search space used: 216225 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: 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