Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-15732 (497 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1496 Length = 500 Score = 513 bits (1320), Expect = e-150 Identities = 257/487 (52%), Positives = 338/487 (69%), Gaps = 2/487 (0%) Query: 8 LPATRAFLERKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQ 67 L + ER++ IG A SGR L +PAT V+ E P +DA D+ RAV +A++ Sbjct: 11 LQGAKFLSERRVGNVIGGVSGPALSGRWLPVTDPATEMVVAEAPDSDAADIARAVASAQR 70 Query: 68 AFDDSPWSRLRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFL 127 AFD W LRP +R+ LL+RL++L+ER A +L+ LE L +GK +A+ +DVQ +F+ Sbjct: 71 AFDSHVWRGLRPADREKLLFRLSELIERHADELSALETLQSGKLQGIARAIDVQAGAEFV 130 Query: 128 RYMAGWATKIEGSTVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPAL 187 RYMAGWATK+EG T++ S+P+ P Q+ + RRE +GVVGAIV WNFPL +A WK+ PAL Sbjct: 131 RYMAGWATKLEGQTLDNSIPI-PGPQWVTYTRREPVGVVGAIVPWNFPLAIALWKIAPAL 189 Query: 188 ATGCTIVLKPADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTF 247 A GCT+VLKP+++TPL+ L+LA L EAG P GV NVV G G AGAAL HPGV KL+F Sbjct: 190 AAGCTVVLKPSEDTPLTALRLAHLALEAGIPEGVLNVVCGRGATAGAALIAHPGVRKLSF 249 Query: 248 TGSTEVGKLIGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCA 307 TGST VGK++G AA++NM R TLELGGKSP +VM DA+ + A G AT IFF+QGQVC A Sbjct: 250 TGSTAVGKVVGHAAVENMARFTLELGGKSPAVVMEDADPSQVAQGIATGIFFHQGQVCTA 309 Query: 308 GSRLYVHRKHFDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELG 367 SRL VHR + V+ ++AGIA GM++G+G D A Q GPL S RV +I + G Sbjct: 310 SSRLLVHRSLYRRVLDELAGIAQGMRIGSGFDAATQFGPLTSKAHFARVMDFIASAKAEG 369 Query: 368 ATVACGGEG-FGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNP 426 AT+ GGE G FV+PT+ D + R+V+EE+FGPVL PFDD+++ I AND P Sbjct: 370 ATLVAGGERVHDAGCFVQPTIFADTTAQMRVVREEVFGPVLAVAPFDDVEDAIAAANDTP 429 Query: 427 YGLGASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEH 486 YGL AS+W+ L+ HR++PR+++G VWVN H+ LD LP GG K SG GR++G AA+E Sbjct: 430 YGLAASLWTQSLSHAHRIVPRLQAGVVWVNAHNVLDAGLPLGGIKQSGTGRDLGRAAVEG 489 Query: 487 YTELKSV 493 +TELKSV Sbjct: 490 FTELKSV 496 Lambda K H 0.320 0.137 0.413 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: 656 Number of extensions: 29 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: 497 Length of database: 500 Length adjustment: 34 Effective length of query: 463 Effective length of database: 466 Effective search space: 215758 Effective search space used: 215758 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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