Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase
Query= BRENDA::P80668 (499 letters) >FitnessBrowser__PS:Dsui_0105 Length = 476 Score = 290 bits (743), Expect = 6e-83 Identities = 186/484 (38%), Positives = 267/484 (55%), Gaps = 21/484 (4%) Query: 18 RQHG-LYIDGRPGPAQSEKRLAIFDPATGQEIASTADANEADVDNAVMSAWRAFVSRRWA 76 +QH YI G+ + + +PAT IA + D D A +A AF + WA Sbjct: 2 QQHSRFYIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPA--WA 59 Query: 77 GRLPAERERILLRFADLVEQHSEELAQLETLEQGKSIAISRAFEVGCTLNWMRYTAGLTT 136 AER L + AD ++ +EL +L E G + ++ + G + +T Sbjct: 60 ALSGAERGAFLQKIADGLKARQDELGRLIASEVGMPVKLATRVQAGNPI----FTFAACA 115 Query: 137 KIAGKTLDLSIPLPQGARYQAWTRKEPVGVVAGIVPWNFPLMIGMWKVMPALAAGCSIVI 196 +IA + + Q+ K P G VA I PWNFPL KV ALAAGC++V+ Sbjct: 116 RIAAEGF------AEERIGQSLVLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVL 169 Query: 197 KPSETTPLTMLRVAELASEAGIPDGVFNVVTGSGAVCGAALTSHPHVAKISFTGSTATGK 256 KPSE PL +AE+ AG+P GVFN+VTG G V G AL +HP +A +SFTGSTA GK Sbjct: 170 KPSEVAPLNAFLLAEVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGK 229 Query: 257 GIARTAADHLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQVCAASSRIYIEA 316 +A AA + RV+LELGGK+ ++VL DAD ++G + G FLN GQ C+A +R+ + Sbjct: 230 RVAAVAAATVKRVSLELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQ 289 Query: 317 PLFDTLVSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSFLDDAQAQQAELI-RGS 375 + + QA + +G ++ +++ PLVS +V + ++ A A AEL+ GS Sbjct: 290 ERYAEAAALAVQAAAAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGS 349 Query: 376 NGPAG--EGYYVAPTLV--VNPDAKLRLTREEVFGPVVNLVRVADGEEALQLANDTEYGL 431 P G GYYV PT+ V PDA L REEVFGPV+ ++ D EA +AN T+YGL Sbjct: 350 AAPEGLPTGYYVRPTVFGRVRPDA--ALAREEVFGPVLAILTYRDEAEAEAIANGTDYGL 407 Query: 432 TASVWTQNLSQALEYSDRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRDFGPDWLDGWCE 491 A+VW+ ++AL ++ RL+AG V +N + PFGG KQSG GR+ G ++ + E Sbjct: 408 AAAVWSAEEARALAFARRLRAGQVDING-AFFNLLAPFGGFKQSGYGRELGRHGVEDFLE 466 Query: 492 TKSV 495 T+S+ Sbjct: 467 TQSI 470 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: 599 Number of extensions: 29 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: 499 Length of database: 476 Length adjustment: 34 Effective length of query: 465 Effective length of database: 442 Effective search space: 205530 Effective search space used: 205530 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