Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate 6938534 Sama_2637 succinate-semialdehyde dehydrogenase (NAD(P)(+)) (RefSeq)
Query= metacyc::MONOMER-15732 (497 letters) >FitnessBrowser__SB2B:6938534 Length = 480 Score = 311 bits (796), Expect = 4e-89 Identities = 179/480 (37%), Positives = 262/480 (54%), Gaps = 9/480 (1%) Query: 18 KLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFDDSPWSRL 77 K K I +W+DA SG T++ NPAT E + VP ++ A+ AA A W L Sbjct: 10 KTKCYINGEWRDALSGETVTIANPATNEAIASVPVMGRDETREAIAAAEAALP--AWRAL 67 Query: 78 RPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATKI 137 +ER L R +LM +A LA + GK A A+ +V A F+ + A A ++ Sbjct: 68 TAKERGAKLRRWYELMLENADDLALMMTTEQGKPLAEAKG-EVVYAASFIEWFAEEAKRL 126 Query: 138 EGSTVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATGCTIVLKP 197 G T+ P D+ V ++ +GV AI WNFP + K GPALA GCT+++KP Sbjct: 127 YGDTI----PGHQGDK-RIMVIKQGVGVTAAITPWNFPAAMITRKAGPALAAGCTMIVKP 181 Query: 198 ADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGKLI 257 A +TP + L LAEL EAG P GVF+VVTG + G L +P V KL+FTGST VG + Sbjct: 182 APQTPFTALALAELAAEAGIPPGVFSVVTGDAVAIGNELCENPVVRKLSFTGSTGVGIKL 241 Query: 258 GKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGSRLYVHRKH 317 + + +V+LELGG +P IV DA+L A GA + + N GQ C +RLYV Sbjct: 242 MQQCAPTLKKVSLELGGNAPFIVFNDADLDAAVEGAMISKYRNAGQTCVCANRLYVQDGV 301 Query: 318 FDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATVACGGEGF 377 +D +A +K+GNG +P V GPLI+A ++V +++ + GAT+ GG+ Sbjct: 302 YDAFAQKLAAAVAKLKVGNGAEPGVTTGPLINAAALEKVQSHLQDALDKGATLVAGGKPL 361 Query: 378 GPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNPYGLGASIWSND 437 G G F++P ++ +VD ++ +EE FGP+ F D+D+VI AND +GL A + D Sbjct: 362 G-GNFMEPAIVTNVDASMKVAREETFGPLAPLFRFSDVDDVIRQANDTEFGLAAYFYGRD 420 Query: 438 LAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEHYTELKSVLIKL 497 ++ + ++ ++ G V VN PFGG K SG+GRE I+ Y E+K + + + Sbjct: 421 ISLIWKVAEALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIDEYVEIKYICLSV 480 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: 576 Number of extensions: 28 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: 497 Length of database: 480 Length adjustment: 34 Effective length of query: 463 Effective length of database: 446 Effective search space: 206498 Effective search space used: 206498 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