Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate PfGW456L13_3737 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::P80668 (499 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3737 Length = 496 Score = 512 bits (1319), Expect = e-149 Identities = 253/495 (51%), Positives = 346/495 (69%), Gaps = 1/495 (0%) Query: 5 HVAVLSQVQQFLDRQHGLYIDGRPGPAQSEKRLAIFDPATGQEIASTADANEADVDNAVM 64 +V +L QV FL+R+HG +IDG+ A+ + +A+ +PATGQ + T DA V+ AV Sbjct: 3 NVEILPQVAAFLERRHGCFIDGQWVLAEGDS-IAVVNPATGQTLCETLDAPLELVERAVQ 61 Query: 65 SAWRAFVSRRWAGRLPAERERILLRFADLVEQHSEELAQLETLEQGKSIAISRAFEVGCT 124 S+ +AF S W+ PA+RERILL F LVE+H+EELAQLETL QGKSI ++RA ++ T Sbjct: 62 SSHKAFKSGVWSSLRPADRERILLNFTRLVEEHAEELAQLETLSQGKSINMARALDLNAT 121 Query: 125 LNWMRYTAGLTTKIAGKTLDLSIPLPQGARYQAWTRKEPVGVVAGIVPWNFPLMIGMWKV 184 + +MRY +G TKI G+T D+SIPLP GA++ A+T++EPVGVV GIVPWNFPL+I WK+ Sbjct: 122 VEFMRYMSGWATKIEGQTFDVSIPLPPGAKFTAFTKREPVGVVVGIVPWNFPLLIAAWKL 181 Query: 185 MPALAAGCSIVIKPSETTPLTMLRVAELASEAGIPDGVFNVVTGSGAVCGAALTSHPHVA 244 MPALA GC+++IKP+ TPLT +R+AELA EAGIP GVFNVVTG GA G LT HP V+ Sbjct: 182 MPALATGCTVIIKPAMETPLTAMRLAELALEAGIPAGVFNVVTGGGASVGGVLTQHPLVS 241 Query: 245 KISFTGSTATGKGIARTAADHLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQ 304 K+SFTGSTA GK + +++TR +LELGGKNP IVL DAD + ++G + G LN GQ Sbjct: 242 KVSFTGSTAVGKSVGVACMENMTRFSLELGGKNPMIVLADADIEKAVQGAILGGLLNNGQ 301 Query: 305 VCAASSRIYIEAPLFDTLVSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSFLDDA 364 VCAA+SR Y+ + D V AV S+ +G GM+ A INPLVSR V ++ A Sbjct: 302 VCAAASRFYVHRSIHDQFVEALAAAVSSMPIGAGMNCDAAINPLVSRKQQQSVLKHIELA 361 Query: 365 QAQQAELIRGSNGPAGEGYYVAPTLVVNPDAKLRLTREEVFGPVVNLVRVADGEEALQLA 424 + Q A ++ G G+G++V PT++ + D + + REEVFGPV+ ++ D + ++LA Sbjct: 362 RQQGARVVTGGELLEGDGFFVQPTILADIDHSMAVAREEVFGPVLGVMPFDDEDAVIELA 421 Query: 425 NDTEYGLTASVWTQNLSQALEYSDRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRDFGPD 484 ND YGL AS+WT +L +A+ R++AGTVWVN+H L+D +PFGG+KQSG GR+FG Sbjct: 422 NDNRYGLAASLWTNDLGKAMNLVPRIEAGTVWVNAHVLLDPAMPFGGVKQSGMGREFGRA 481 Query: 485 WLDGWCETKSVCVRY 499 ++ + E KSVC+ + Sbjct: 482 VIEAYTELKSVCIAH 496 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: 712 Number of extensions: 24 Number of successful extensions: 2 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: 496 Length adjustment: 34 Effective length of query: 465 Effective length of database: 462 Effective search space: 214830 Effective search space used: 214830 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