Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate GFF3502 PS417_17930 aldehyde dehydrogenase
Query= BRENDA::P80668 (499 letters) >FitnessBrowser__WCS417:GFF3502 Length = 495 Score = 428 bits (1101), Expect = e-124 Identities = 226/495 (45%), Positives = 310/495 (62%), Gaps = 4/495 (0%) Query: 6 VAVLSQVQQFLDRQHGLYIDGRPGPAQSEKRLAIFDPATGQEIASTADANEADVDNAVMS 65 + +L QV+ FL R HGL+IDG + S + LA+ +PATG IA +DA+ AD+D AV S Sbjct: 4 IPLLPQVEAFLRRPHGLFIDGVNIRSHSSQTLAVTNPATGDVIAQVSDADLADIDAAVNS 63 Query: 66 AWRAFVSRRWAGRLPAERERILLRFADLVEQHSEELAQLETLEQGKSIAISRAFEVGCTL 125 A R F + W+ LPA R +LL+ ADL+E++ EELAQ+ET + GK I I+RAFEV Sbjct: 64 ANRGF--QVWSQALPATRGNVLLKLADLLERNREELAQIETCQSGKIIQIARAFEVDQAA 121 Query: 126 NWMRYTAGLTTKIAGKTLDLSIPLPQGARYQAWTRKEPVGVVAGIVPWNFPLMIGMWKVM 185 +++RY AG TK++G+TL S+P G RY A+T +EPVGVV GIVPWNF MI +WK+ Sbjct: 122 HFLRYYAGWATKLSGQTLTPSLPSFNGERYTAFTLREPVGVVVGIVPWNFSTMIAIWKLA 181 Query: 186 PALAAGCSIVIKPSETTPLTMLRVAELASEAGIPDGVFNVVTGSGAVCGAALTSHPHVAK 245 AL GCSI+IKPSE TPLT+LR+AELA EAG+P GV NV+TG G V G L HP K Sbjct: 182 SALVTGCSIIIKPSEFTPLTVLRIAELAVEAGLPPGVLNVLTGGGHV-GKGLVEHPGTHK 240 Query: 246 ISFTGSTATGKGIARTA-ADHLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQ 304 +SFTGS TG + R+A LTR TLELGGKN A L+D D + G++ FL+ GQ Sbjct: 241 VSFTGSVPTGIAVGRSAMGAGLTRATLELGGKNAAGFLRDVDVDTAVNGIIEAGFLHSGQ 300 Query: 305 VCAASSRIYIEAPLFDTLVSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSFLDDA 364 +CAA+ R ++ D ++ Q + L +G + + P+ H K+ + + A Sbjct: 301 ICAAAERFFVHRSQIDAVLDTLSQRLSRLNIGSPLDERTEFGPVTHHQHQLKLLGYFNQA 360 Query: 365 QAQQAELIRGSNGPAGEGYYVAPTLVVNPDAKLRLTREEVFGPVVNLVRVADGEEALQLA 424 +A+ +I G G YV PT+++ L EE FGP+ + +E L L Sbjct: 361 RAENNTIIHGGTLIDRPGCYVEPTVILANSINDTLLNEETFGPIATFLPYDSEDELLALM 420 Query: 425 NDTEYGLTASVWTQNLSQALEYSDRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRDFGPD 484 N+ YGL+AS+WT +L +AL +QAGT+WVN HTL+D +PFGG + SG GR+FG Sbjct: 421 NNGPYGLSASLWTNDLGKALRMVPAIQAGTLWVNMHTLLDPAVPFGGNRSSGVGREFGSA 480 Query: 485 WLDGWCETKSVCVRY 499 +++ + E KSV +RY Sbjct: 481 FIEDYTELKSVMIRY 495 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: 648 Number of extensions: 22 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: 499 Length of database: 495 Length adjustment: 34 Effective length of query: 465 Effective length of database: 461 Effective search space: 214365 Effective search space used: 214365 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