Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000009985.1:WP_011383257.1 Length = 499 Score = 545 bits (1404), Expect = e-159 Identities = 267/485 (55%), Positives = 361/485 (74%), Gaps = 5/485 (1%) Query: 41 DLHADLLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFS 98 DL L++ ++V G W+ F V DPA+G + +V D G E R A+ AA A++ Sbjct: 17 DLDPSLIKSHAYVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWN 76 Query: 99 SWKEISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEE 158 W++ + K+R++++ W+DL++ ++D LA++++AE GKPL EA GEI Y A F+ WF+EE Sbjct: 77 PWRQRTAKDRAAVMMAWHDLIMAHQDALARLLSAEQGKPLAEAMGEISYGASFISWFAEE 136 Query: 159 ARRVYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPA 218 +R YGD+I T+A D+R LV+KQP+GV + +TPWNFP AMITRK ALAAGC VVVKPA Sbjct: 137 GKRAYGDLIPTTASDRRLLVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPA 196 Query: 219 EDTPYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGK 278 EDTP SALALA+LA++AG+P G++N++ + A VG + + V K+SFTGST GK Sbjct: 197 EDTPLSALALAELAHRAGLPKGLFNIVTTRQPAA--VGGEMTGNAKVRKLSFTGSTRVGK 254 Query: 279 ILLHHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQR 338 +L+ A +VK+VS+ELGG APFIVFD ++D AVAGA+ASK+RN+GQTC+C+NRFLVQ Sbjct: 255 LLMAQCAETVKKVSLELGGNAPFIVFDDCDLDAAVAGALASKYRNSGQTCICTNRFLVQA 314 Query: 339 GIHDSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGG 398 GI++ F K AE ++ VG+ QGPLIN AV KV HV DAV+KGA V+TGG Sbjct: 315 GIYEDFAVKLAEKAA-AMAVGHALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTGG 373 Query: 399 KRHQSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYF 458 + H GG F++PT+L++VT MLC EETFGPVAP+++F+ E EA+A+ANA++ GLAGYF Sbjct: 374 RPHALGGGFWQPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYF 433 Query: 459 YSQDPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYV 518 YS+D A+++RVAE LE GMVGVNE LIS+ PFGG+K+SGLGREGSKYG+D+++E KYV Sbjct: 434 YSRDVARVFRVAEALECGMVGVNESLISNEVAPFGGIKESGLGREGSKYGLDDFMETKYV 493 Query: 519 CYGGL 523 C GGL Sbjct: 494 CIGGL 498 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: 665 Number of extensions: 22 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: 499 Length adjustment: 35 Effective length of query: 488 Effective length of database: 464 Effective search space: 226432 Effective search space used: 226432 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