Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate WP_012709840.1 NGR_RS27930 NADP-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P49419 (539 letters) >NCBI__GCF_000018545.1:WP_012709840.1 Length = 484 Score = 215 bits (547), Expect = 3e-60 Identities = 141/449 (31%), Positives = 222/449 (49%), Gaps = 10/449 (2%) Query: 71 PANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALREKIQVLGS 130 PA E I RV + A+ + ++ A K WA A +R I+R+ + + E LG Sbjct: 33 PATGEIIGRVPKLGAAETKVAIETAARVQKEWAGRTAKERAAILRRWYELMIENKDDLGQ 92 Query: 131 LVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSERSGHALIEQWNPVGLVGI 190 ++++E GK L E GE+ ++ R + G ++P + ++ P+G+V Sbjct: 93 ILTIEQGKPLAEATGEIVYGASFIEWFAEEGRRVYGDLVPGHQKDKRILVMKQPIGVVAA 152 Query: 191 ITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVLEDNKLPGAICSL 250 IT +NFP A+ A G + K A T ++A IA + E +P + S+ Sbjct: 153 ITPWNFPNAMITRKAGPAFAAGCAMVLKPAAQTPYSAIA----IAVLAERAGMPKGLFSV 208 Query: 251 TCGGA-DIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLELGGNNAIIAFEDA 309 G A +IG M + V L+FTGST+VG ++ + LELGGN I F+DA Sbjct: 209 ITGSAREIGAEMTSNPTVRKLTFTGSTEVGAELYRQSAATIKKLGLELGGNAPFIVFDDA 268 Query: 310 DLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQIRVGNPWDPNVLY 369 DL V AL A GQ C A RL++ E ++D +L A A+++ GN + + Sbjct: 269 DLDAAVEGALIAKFRNNGQTCVCANRLYVQEGVYDAFSEKLAAAVAKLKTGNGMEDGTIL 328 Query: 370 GPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPTIVTGLGHDASIAHTETF 429 GPL K A+ V +A +G V+ GG+ G++ E T++ + ++A ETF Sbjct: 329 GPLIDKPALEKVEEHVADALAKGARVIQGGRRHALGGSFFEATVLADVTQAMAVAREETF 388 Query: 430 APILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCGIVNVNIP-TS 488 P+ +F+FK+E +V N+ + GL+S + KDL R+FR + + G+V VN S Sbjct: 389 GPVAPLFRFKDEADVIRQANDTEFGLASYFYAKDLARVFR--VAEALEYGMVGVNTGLIS 446 Query: 489 GAEIGGAFGGEKHTGGGRESGSDAWKQYM 517 AE FGG K +G GRE +++M Sbjct: 447 TAE--APFGGVKFSGLGREGSKYGIEEFM 473 Lambda K H 0.318 0.136 0.417 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: 689 Number of extensions: 39 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: 539 Length of database: 484 Length adjustment: 35 Effective length of query: 504 Effective length of database: 449 Effective search space: 226296 Effective search space used: 226296 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