Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate PP_3463 PP_3463 phenylacetaldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Putida:PP_3463 Length = 497 Score = 418 bits (1075), Expect = e-121 Identities = 220/495 (44%), Positives = 311/495 (62%), Gaps = 10/495 (2%) Query: 7 VPIKLPNGTTYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEA 66 +PI E+ + I ++ + S +T +P+T E + +V A +ED+D AV A Sbjct: 5 LPILPATRAFLERKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAAEAEDVDRAVRA 64 Query: 67 ATAAFHSS-WSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTA 124 A AF S WS P+ R +L++LADL++ A LA +E L+NGKS ++ DV L Sbjct: 65 ARQAFDDSPWSRMRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQMMDVQLAI 124 Query: 125 AYFRSCAGWTDKIKGSVIETG------DTHFNYTRREPIGVCGQIIPWNFPLLMASWKLG 178 + R AGW KI+GS +E D + RRE +GV G I+ WNFPLL+A WKLG Sbjct: 125 DFLRYMAGWATKIEGSTVEASMPLMPNDQFHGFVRREAVGVVGAIVAWNFPLLLACWKLG 184 Query: 179 PVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKK 238 P L TGCT VLK A+ TPLS L LA L+ EAG P GV NVV+G G AGA +S HP + K Sbjct: 185 PALATGCTVVLKPADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDK 244 Query: 239 VAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGE 298 + FTGST G+ I KAA + N+ +VTLELGGKSP IV DA+++ T IF+N G+ Sbjct: 245 LTFTGSTEVGKLIGKAAMD-NMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQ 303 Query: 299 VCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIG 358 VCCAGSR+YV +D +V++ A ++K+G+ MG S Q D++ YI++G Sbjct: 304 VCCAGSRLYVHRKHFDNVVADIAGIANAMKLGNGLDPAVQMGPLISAKQQDRVTGYIELG 363 Query: 359 KKEGATVITGGERFGNKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALA 418 ++ GAT+ GGE FG GYF+KPT+ DV + H++V++EIFGPV+ F ++EVI +A Sbjct: 364 RELGATIACGGEGFG-PGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDIDEVIGMA 422 Query: 419 NDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEE 478 ND+ YGL A + + +L+ + +I SG++WVN ++ P +PFGGY SG+GREMG Sbjct: 423 NDNPYGLGASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGSA 482 Query: 479 ALDNYTQVKAVRIGL 493 A+++YT++K+V I L Sbjct: 483 AIEHYTELKSVLIKL 497 Lambda K H 0.316 0.133 0.389 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: 646 Number of extensions: 41 Number of successful extensions: 7 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: 495 Length of database: 497 Length adjustment: 34 Effective length of query: 461 Effective length of database: 463 Effective search space: 213443 Effective search space used: 213443 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 (21.6 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