Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_057507768.1 ABB28_RS05980 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q8VWZ1 (503 letters) >NCBI__GCF_001431535.1:WP_057507768.1 Length = 454 Score = 236 bits (603), Expect = 1e-66 Identities = 146/458 (31%), Positives = 230/458 (50%), Gaps = 12/458 (2%) Query: 28 INPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRDWSAASGSLRARYLRAIAAKIKE 87 +NP+T + K ++ + AA A WSA S RA LRAI A+++E Sbjct: 6 VNPTTGRVDYRHELLDKAGIEQRLQAAAGAFPA-----WSATSLQERAAVLRAIGAQLRE 60 Query: 88 KKDELGKLESIDCGKPLEEALADLDDVVACFEYYAGLAEELDSKQKAPISLPMDTFKSYI 147 +KD++ + + GK EALA+++ A EYYA A + P + + +SY+ Sbjct: 61 RKDDIQGAMTREMGKLKVEALAEVEKCAAACEYYADHAADY----LKPQLIDTEAQRSYV 116 Query: 148 LKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPSELASVTCLELGEICKEVGLP 207 EPIG V + PWN+P +APA AG A+LK + + E+ + GLP Sbjct: 117 RYEPIGCVFAVMPWNFPIWQVFRFLAPAFMAGNVALLKHASNVPQCADLINEVVRAGGLP 176 Query: 208 RGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIMTTAAQLVKPVSLELGGKSPI 267 GV +++ + ++ A + V ++ TGS G I A +K +ELGG Sbjct: 177 DGVFDVLH-IDNDQAADVLRDRRVKAVTLTGSERAGRSIAANAGDQLKKCVMELGGSDAF 235 Query: 268 VVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIVHESIAVEFVDKLVKWAENIKISDPL 327 VV +D DLDK + V F +GQ C A R IV E++A F ++ V A + DP Sbjct: 236 VVLDDADLDKAIDAAVKSRFDNSGQTCIAAKRFIVVEAVADAFTERFVAAAGERRYGDPA 295 Query: 328 EEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTGGRRPEHLKKGYFVEPTIITDVTTSM 387 + L P+ ++ + ++ ++GA +L GG + GY T++ V M Sbjct: 296 DARTTLAPMARADLRDELHKQVQASVAKGARVLAGGEPVDGSHAGY--PATVLDQVGPGM 353 Query: 388 QIWREEVFGPVLAVKTFSTEEEAINLANDTHYGLGSAVMSNDLERCERLSKALQAGIVWI 447 + EE+FGPV AV E EA+ +ANDT +GLG +V + D R E ++ ++ G ++ Sbjct: 354 PAYDEELFGPVAAVIRVKDEAEALKVANDTRFGLGGSVWTTDAARGEAFAQQMECGAAFV 413 Query: 448 NCAQPSFIQAPWGGIKRSGFGRELGEWGLENYLSVKQV 485 N S ++ P+GG K SGFGREL E G+ ++++K + Sbjct: 414 NSIVKSDVRLPFGGSKESGFGRELAEHGIHEFMNIKTI 451 Lambda K H 0.317 0.134 0.402 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: 428 Number of extensions: 17 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: 503 Length of database: 454 Length adjustment: 34 Effective length of query: 469 Effective length of database: 420 Effective search space: 196980 Effective search space used: 196980 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 (21.6 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