Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_057507768.1 ABB28_RS05980 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::A6T8Z5 (462 letters) >NCBI__GCF_001431535.1:WP_057507768.1 Length = 454 Score = 424 bits (1091), Expect = e-123 Identities = 212/447 (47%), Positives = 288/447 (64%) Query: 12 VNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRRIGAALRARGEEV 71 VNPTTG V + ++ + AA + W T L +RA LR IGA LR R +++ Sbjct: 6 VNPTTGRVDYRHELLDKAGIEQRLQAAAGAFPAWSATSLQERAAVLRAIGAQLRERKDDI 65 Query: 72 AQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVENNQAVIEYRPLGAIL 131 +T EMGK +A EV K A C++YA+H L + E ++ + Y P+G + Sbjct: 66 QGAMTREMGKLKVEALAEVEKCAAACEYYADHAADYLKPQLIDTEAQRSYVRYEPIGCVF 125 Query: 132 AVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAAGLPDGVFGWVNA 191 AVMPWNFP+WQV R P +AGN LLKHA NV A L+ E+ A GLPDGVF ++ Sbjct: 126 AVMPWNFPIWQVFRFLAPAFMAGNVALLKHASNVPQCADLINEVVRAGGLPDGVFDVLHI 185 Query: 192 TNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPFIVLNDADLDE 251 ND + ++ D R+ AVT+TGS RAG++I A AG LKKCV+ELGGSD F+VL+DADLD+ Sbjct: 186 DNDQAADVLRDRRVKAVTLTGSERAGRSIAANAGDQLKKCVMELGGSDAFVVLDDADLDK 245 Query: 252 AVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGDPRDEQNYVGPMA 311 A+ AAV R+ NSGQ C A+KRFI+ +A+AFT +FV A + GDP D + + PMA Sbjct: 246 AIDAAVKSRFDNSGQTCIAAKRFIVVEAVADAFTERFVAAAGERRYGDPADARTTLAPMA 305 Query: 312 RFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGMTGFRQELFGPVA 371 R DLRDELH+QV A++ +GA +L G E ++G+ Y TVL V GM + +ELFGPVA Sbjct: 306 RADLRDELHKQVQASVAKGARVLAGGEPVDGSHAGYPATVLDQVGPGMPAYDEELFGPVA 365 Query: 372 TLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFLNGYCASDARVAF 431 + +D AL +AND+ FGL +V+TTD A+ + FA+++ECG F+N SD R+ F Sbjct: 366 AVIRVKDEAEALKVANDTRFGLGGSVWTTDAARGEAFAQQMECGAAFVNSIVKSDVRLPF 425 Query: 432 GGVKKSGFGRELSHFGLHEFCNAQTVW 458 GG K+SGFGREL+ G+HEF N +T++ Sbjct: 426 GGSKESGFGRELAEHGIHEFMNIKTIY 452 Lambda K H 0.319 0.133 0.392 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: 510 Number of extensions: 16 Number of successful extensions: 1 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: 462 Length of database: 454 Length adjustment: 33 Effective length of query: 429 Effective length of database: 421 Effective search space: 180609 Effective search space used: 180609 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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