Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_029134199.1 A3GO_RS0115615 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::A6T8Z5 (462 letters) >NCBI__GCF_000428045.1:WP_029134199.1 Length = 454 Score = 404 bits (1037), Expect = e-117 Identities = 206/448 (45%), Positives = 284/448 (63%) Query: 11 SVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRRIGAALRARGEE 70 S+NP TG + S S ++ A+ W + RA LR + L + Sbjct: 5 SINPATGHEIQSYEQLSADDLSTLCVNASHAQGDWMALTIDQRAALLREVARQLETGKRQ 64 Query: 71 VAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVENNQAVIEYRPLGAI 130 +A++IT EMGK I +A EV K A +C +YA+ LA E + +++++ +PLG + Sbjct: 65 LAKLITSEMGKLIGEAESEVEKCAWVCHYYADTANQFLADEVIESDASRSMLVKQPLGLV 124 Query: 131 LAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAAGLPDGVFGWVN 190 LA+MPWNFP WQV R A P L+AGN LLKHA NV G A +L ++F AG P VF + Sbjct: 125 LAIMPWNFPFWQVFRCAAPALMAGNGVLLKHASNVPGCALMLEQLFQDAGFPSSVFSTLL 184 Query: 191 ATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPFIVLNDADLD 250 ++ V+ ++ D +I A+++TGS AG+++ + AG LKK VLELGGSD F+VL+DADLD Sbjct: 185 ISSGQVADLVADAQIHAISLTGSEAAGRSVASVAGKNLKKLVLELGGSDAFVVLDDADLD 244 Query: 251 EAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGDPRDEQNYVGPM 310 AVKAAV R+ N GQ C A+KRF++ GI + F KF A+ L++GDP D + +GPM Sbjct: 245 AAVKAAVQSRFLNCGQSCIAAKRFVVVDGIGDRFVEKFHAAINNLRVGDPLDAETTLGPM 304 Query: 311 ARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGMTGFRQELFGPV 370 AR DLR+ LH+QVT ++D+GA LL G + + G +YA T+L VT GM + +ELFGPV Sbjct: 305 ARDDLRETLHRQVTDSIDQGALLLAGGQFLPRPGWFYAATLLDQVTPGMPAYEEELFGPV 364 Query: 371 ATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFLNGYCASDARVA 430 A + A D AL +ANDS FGL +V+T D A+ + FAR + CG F+NG SD R+ Sbjct: 365 AAVIRATDEQDALRIANDSRFGLGGSVWTGDAARGEEFARRMACGSAFVNGLVKSDPRLP 424 Query: 431 FGGVKKSGFGRELSHFGLHEFCNAQTVW 458 FGG+K SG+GRELS G+ EF NA+TVW Sbjct: 425 FGGIKHSGYGRELSRLGIQEFINAKTVW 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: 491 Number of extensions: 21 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 Sep 24 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