Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 200453 SO1275 succinate-semialdehyde dehydrogenase (NCBI ptt file)
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__MR1:200453 Length = 482 Score = 530 bits (1365), Expect = e-155 Identities = 261/476 (54%), Positives = 346/476 (72%), Gaps = 6/476 (1%) Query: 46 LLRGDSFVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103 LLR ++ G+W + T + +PA+GA + V G E +AA+ AA A +W+ + Sbjct: 8 LLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALPAWRAL 67 Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163 + KER + LR+W++L+ +N D+LA ++T+E GKPL EA+GE+ Y+A F+EWF+EEA+R+Y Sbjct: 68 TAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAEEAKRIY 127 Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223 GD I DKR +V+KQPVGV + ITPWNFP+AMITRK ALAAGCT+VVKPA TP+ Sbjct: 128 GDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPF 187 Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283 +ALALA LA +AGIP GV++VI A +G +CT+P+V K+SFTGST G L+ Sbjct: 188 TALALAVLAERAGIPAGVFSVI---TGDAIAIGNEMCTNPIVRKLSFTGSTNVGIKLMAQ 244 Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343 A ++K++S+ELGG APFIVFD AN+D AV GAM +K+RNAGQTCVC+NR VQ G++D Sbjct: 245 CAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDE 304 Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403 F K + A+ K L+VG G G T GPLIN AVEKV+ H+ DA+ KGATV+ GGK H+ Sbjct: 305 FAEKLSMAVAK-LKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKVHEL 363 Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463 GGNFFEPT+L+N + M EETFGP+AP+ KF+ ++ + AN + GLA YFY +D Sbjct: 364 GGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYGRDI 423 Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVC 519 + +W+VAE LE GMVGVN GLIS+ PFGG+K SGLGREGSKYGI+EYLE+KY+C Sbjct: 424 SLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIKYIC 479 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: 646 Number of extensions: 30 Number of successful extensions: 3 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: 482 Length adjustment: 34 Effective length of query: 489 Effective length of database: 448 Effective search space: 219072 Effective search space used: 219072 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 Apr 09 2024. 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