Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate AO356_25485 AO356_25485 aldehyde dehydrogenase
Query= BRENDA::P80668 (499 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25485 Length = 495 Score = 444 bits (1143), Expect = e-129 Identities = 231/495 (46%), Positives = 315/495 (63%), Gaps = 4/495 (0%) Query: 6 VAVLSQVQQFLDRQHGLYIDGRPGPAQSEKRLAIFDPATGQEIASTADANEADVDNAVMS 65 +A+L QV+ FL R+H L+IDG +QS + L + +PATGQ IA +DA+ +D+D AV S Sbjct: 4 IALLPQVEAFLGRRHALFIDGGYVESQSRQTLDVVNPATGQVIAQVSDASPSDIDAAVES 63 Query: 66 AWRAFVSRRWAGRLPAERERILLRFADLVEQHSEELAQLETLEQGKSIAISRAFEVGCTL 125 + R F ++W+ PA R +LL+ ADL+E++ EELAQ+ET + GK I ISRAFEV Sbjct: 64 SRRGF--KQWSQTAPAVRGHVLLKLADLLERNREELAQIETCQSGKIIHISRAFEVDQAA 121 Query: 126 NWMRYTAGLTTKIAGKTLDLSIPLPQGARYQAWTRKEPVGVVAGIVPWNFPLMIGMWKVM 185 +++RY AG TKI G+T+ S+P G RY A+T +EPVGVV GIVPWNF MI +WK+ Sbjct: 122 HFLRYYAGWATKINGETITPSLPSFAGERYTAFTLREPVGVVVGIVPWNFSTMIAIWKLA 181 Query: 186 PALAAGCSIVIKPSETTPLTMLRVAELASEAGIPDGVFNVVTGSGAVCGAALTSHPHVAK 245 AL GCS++IKPSE TPLT+LR+AELA EAG+P G NV+TG G V G L HP K Sbjct: 182 SALVTGCSVIIKPSEFTPLTILRIAELAMEAGLPAGALNVLTGGGQV-GKGLIEHPGTNK 240 Query: 246 ISFTGSTATGKGIARTAADH-LTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQ 304 +SFTGS TG + + A LTR TLELGGKN A L+D DP+ + G++ FL+ GQ Sbjct: 241 VSFTGSVPTGLAVGQAAMGAGLTRATLELGGKNAAGFLRDIDPEVAVNGIIEAGFLHSGQ 300 Query: 305 VCAASSRIYIEAPLFDTLVSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSFLDDA 364 +CAA+ R ++ ++++ Q + L +G + + P+ +R H K+ F A Sbjct: 301 ICAAAERFFVHRSQIESIMDKLAQRLSKLTIGSPLDERTEFGPVTNRQHQHKLAEFFAKA 360 Query: 365 QAQQAELIRGSNGPAGEGYYVAPTLVVNPDAKLRLTREEVFGPVVNLVRVADGEEALQLA 424 +AQ +I G G G YV PT+++ L EE FGP+ EE L+L Sbjct: 361 RAQNNTIIHGGKLIDGPGCYVEPTIILANRRDDALLNEETFGPIATFFPYDTEEELLELM 420 Query: 425 NDTEYGLTASVWTQNLSQALEYSDRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRDFGPD 484 NDT YGL+AS+WT +L +AL ++AGTVWVN HTL+D +PFGG K SG GR+FG Sbjct: 421 NDTPYGLSASLWTNDLGKALRMVPAIEAGTVWVNMHTLLDPAVPFGGSKSSGVGREFGSA 480 Query: 485 WLDGWCETKSVCVRY 499 ++D + E KSV +RY Sbjct: 481 FIDDYTELKSVMIRY 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: 662 Number of extensions: 31 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