Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate PP_5063 PP_5063 betaine aldehyde dehydrogenase, NAD-dependent
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__Putida:PP_5063 Length = 490 Score = 331 bits (848), Expect = 4e-95 Identities = 184/463 (39%), Positives = 267/463 (57%), Gaps = 8/463 (1%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83 +P V+A V A A+V+ AV +A+ K W M+ QR +L D + R D+ Sbjct: 28 NPATGEVLAHVQRATEADVEKAVESAERGQK-VWAAMTAMQRSRILRRAVDILRERNDEL 86 Query: 84 LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143 E DTGK S R+VDI GA + +A +V + E ++P + + Y R P Sbjct: 87 AMLETLDTGKSYSETRYVDIVTGADVLEYYAGLVPAIEGE--QIPLRES--SFVYTRREP 142 Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203 +GV I WN P+ + WK PALA GN ++ KPSE T T L E+ AG+P GV+ Sbjct: 143 LGVTVGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTTLKLAEIYTEAGLPNGVF 202 Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGA-RPVSLELGGKNAAIV 262 NV+ G G G +LT HP + ++FTG T TG+ +M +A+ + + V++ELGGK+ I+ Sbjct: 203 NVLTGSG-REVGTWLTEHPRIEKVSFTGGTTTGKKVMASASSSSLKEVTMELGGKSPLII 261 Query: 263 FADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDL 322 AD DLDKA + + + F + GQVC RV++ + F +++ + +++G PED Sbjct: 262 CADADLDKAADIAMMANFYSSGQVCTNGTRVFIPAEMKAAFEAKIAERVARIRVGNPEDE 321 Query: 323 ATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDD 382 T GPL+S +H E VL Y K E GA V+ GG + KG A+V PT++T DD Sbjct: 322 NTNFGPLVSFQHMESVLGYIAKGKEEGARVLCGGERLTAGDFAKG-AFVAPTVFTDCTDD 380 Query: 383 SVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAW 442 + +EEIFGP ++ +++EEEVIRRAND DYGLA + T +++RAHR+ +E GI W Sbjct: 381 MTIVKEEIFGPVMSILTYETEEEVIRRANDTDYGLAAGVCTNDITRAHRIIHKLEAGICW 440 Query: 443 VNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485 +N+W GG KQSG+GRE GV SL YT +K+V ++L Sbjct: 441 INAWGESPAEMPVGGYKQSGVGRENGVSSLAQYTRIKSVQVEL 483 Lambda K H 0.318 0.135 0.406 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: 552 Number of extensions: 23 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: 485 Length of database: 490 Length adjustment: 34 Effective length of query: 451 Effective length of database: 456 Effective search space: 205656 Effective search space used: 205656 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