Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate Ac3H11_1480 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= BRENDA::P80668 (499 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1480 Length = 486 Score = 318 bits (816), Expect = 2e-91 Identities = 183/475 (38%), Positives = 275/475 (57%), Gaps = 8/475 (1%) Query: 23 YIDGRPGPAQSEKRLAIFDPATGQEIASTADANEADVDNAVMSAWRAFVSRRWAGRLPAE 82 YIDG+ A + LA+ +PA G I + +A A A+ +A RAF W R + Sbjct: 17 YIDGQWVDADNGATLAVNNPANGALIGTIPNAGAAQTQTAIAAADRAFGP--WKDRTAED 74 Query: 83 RERILLRFADLVEQHSEELAQLETLEQGKSIAISRAFEVGCTLNWMRYTAGLTTKIAGKT 142 R RIL R+ +L+ QH E+LA + T EQGK +A +R E+ +++ + A +I G+ Sbjct: 75 RARILRRWFELMLQHQEDLALIMTSEQGKPLAEARG-EIAYAASYIEWFAEEARRIYGEV 133 Query: 143 LDLSIPLPQGARYQAWTRKEPVGVVAGIVPWNFPLMIGMWKVMPALAAGCSIVIKPSETT 202 IP P + TR EPVGV A I PWNFP + KV PALAAGC+I++KP+ T Sbjct: 134 ----IPSPWLDKRIVVTR-EPVGVCAAITPWNFPAAMITRKVAPALAAGCTIIVKPATQT 188 Query: 203 PLTMLRVAELASEAGIPDGVFNVVTGSGAVCGAALTSHPHVAKISFTGSTATGKGIARTA 262 PL+ L +AELA+ AG+P GVF+V+TG GA LT+ P V K++FTGST G+ +A Sbjct: 189 PLSALAMAELAARAGVPAGVFSVITGDARPIGAELTASPVVRKLTFTGSTEIGRVLAAQC 248 Query: 263 ADHLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQVCAASSRIYIEAPLFDTL 322 A L +++LELGG P IV +DAD + G M + N GQ C ++R+ ++ ++D Sbjct: 249 APTLKKMSLELGGNAPFIVFEDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGVYDAF 308 Query: 323 VSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSFLDDAQAQQAELIRGSNGPAGEG 382 + V +L+VG G+ + PL+ A KV + + DA+A+ A ++ G A G Sbjct: 309 AEKLARTVAALKVGHGLEEGVEQGPLIDEASLTKVEALVADAKARGARVVTGGRRHALGG 368 Query: 383 YYVAPTLVVNPDAKLRLTREEVFGPVVNLVRVADGEEALQLANDTEYGLTASVWTQNLSQ 442 + PT++ + +R+ REE+FGPV L R EA+Q+ANDTE+GL A +++++ + Sbjct: 369 TFYEPTILADITPDMRMAREEIFGPVAPLFRFHTEAEAIQMANDTEFGLAAYFYSRDVGR 428 Query: 443 ALEYSDRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRDFGPDWLDGWCETKSVCV 497 S LQ G V +N+ + A PFGG+KQSG GR+ ++ + +TK +C+ Sbjct: 429 VWRVSGALQYGMVGINAGVISTAVAPFGGVKQSGMGREGSVHGIEEYVDTKYLCM 483 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: 615 Number of extensions: 37 Number of successful extensions: 3 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: 486 Length adjustment: 34 Effective length of query: 465 Effective length of database: 452 Effective search space: 210180 Effective search space used: 210180 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 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