Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate PP_0213 PP_0213 succinate-semialdehyde dehydrogenase (NADP+)
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__Putida:PP_0213 Length = 480 Score = 538 bits (1386), Expect = e-157 Identities = 267/478 (55%), Positives = 356/478 (74%), Gaps = 8/478 (1%) Query: 44 ADLLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWK 101 A L R +++ G WL T V +PA+G +GTV G E R A+ AA A +W+ Sbjct: 6 AQLFRQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWR 65 Query: 102 EISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARR 161 ++ KERS+ LR+W++LMI+N+D+LA+++T E GKPL EA+GEI Y+A F+EWF+EEA+R Sbjct: 66 ALTAKERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKR 125 Query: 162 VYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDT 221 +YGD I DKR +V+KQP+GV + ITPWNFP+AMITRK G ALAAGCT+V+KPA T Sbjct: 126 IYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQT 185 Query: 222 PYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILL 281 PYSALAL +LA++AGIP GV +V+ S A EVG L + LV K+SFTGST G+ L+ Sbjct: 186 PYSALALVELAHRAGIPAGVLSVVTGS---AGEVGGELTGNSLVRKLSFTGSTEIGRQLM 242 Query: 282 HHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIH 341 A +K+VS+ELGG APFIVFD A++D+AV GA+ SK+RN GQTCVC+NR VQ G++ Sbjct: 243 EECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVY 302 Query: 342 DSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRH 401 D+F K A A+ K L++GNG EEGTT GPLI+ KAV KV++H+ DAV+KGA V++GGK Sbjct: 303 DAFAEKLAAAVAK-LKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLI 361 Query: 402 QSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQ 461 + GNFFEPT+L +V + EETFGP+AP+ +F E E +A++N + GLA YFY++ Sbjct: 362 E--GNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYAR 419 Query: 462 DPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVC 519 D ++++RVAE LE GMVG+N GLIS+ PFGG+K SGLGREGSKYGI++YLE+KY+C Sbjct: 420 DMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLC 477 Lambda K H 0.318 0.135 0.400 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: 624 Number of extensions: 23 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: 523 Length of database: 480 Length adjustment: 34 Effective length of query: 489 Effective length of database: 446 Effective search space: 218094 Effective search space used: 218094 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