Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate PP_3463 PP_3463 phenylacetaldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Putida:PP_3463 Length = 497 Score = 389 bits (1000), Expect = e-112 Identities = 217/481 (45%), Positives = 290/481 (60%), Gaps = 13/481 (2%) Query: 24 INGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKR 83 I ++ DA SG T +P G L +V + + D +RAV AR F+ WS++ P +R Sbjct: 23 IGADWQDAASGRTLSFRNPATGEVLGEVPAAEAEDVDRAVRAARQAFDDSPWSRMRPRER 82 Query: 84 KAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVA 143 + L R ADL+ ++ +LA LE L+ GK + +D+ A + + A K+ Sbjct: 83 QNLLWRLADLMERDARQLAELECLNNGKSAAVAQMMDVQLAIDFLRYMAGWATKIEGSTV 142 Query: 144 PT-----PHDQL-GLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSP 197 P+DQ G V RE VGVVGAIV WNFPLL+ACWKLGPALATG +VVLKP++++P Sbjct: 143 EASMPLMPNDQFHGFVRREAVGVVGAIVAWNFPLLLACWKLGPALATGCTVVLKPADETP 202 Query: 198 LTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAG 257 L+ +++A+L EAG PAGV NV+ G G G AL+ H VD L FTGST++ K L+ A Sbjct: 203 LSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGK-LIGKAA 261 Query: 258 ESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317 NM R+ LE GGKSP IV DA +LQ AA AA+AI FNQG+VC AGSRL V R D Sbjct: 262 MDNMTRVTLELGGKSPTIVMPDA-NLQEAAAGAATAIFFNQGQVCCAGSRLYVHRKHFDN 320 Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE 377 + + K GN LDP +G L+ +Q + V YIE G + GA + GG E Sbjct: 321 VVADIAGIANAMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATIACGG----EG 376 Query: 378 TG-GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTS 436 G G +V+PT+ V R+ QEEIFGPVL + FD +E + +AND PYGL A IW++ Sbjct: 377 FGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDIDEVIGMANDNPYGLGASIWSN 436 Query: 437 DISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIK 496 D++ H+ +++GSVWVN + D PFGG+K SG GR+ A+E YTELK+ IK Sbjct: 437 DLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGSAAIEHYTELKSVLIK 496 Query: 497 L 497 L Sbjct: 497 L 497 Lambda K H 0.316 0.132 0.390 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: 623 Number of extensions: 30 Number of successful extensions: 5 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: 497 Length adjustment: 34 Effective length of query: 463 Effective length of database: 463 Effective search space: 214369 Effective search space used: 214369 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