Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate WP_035241269.1 Q366_RS17050 NADP-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P49419 (539 letters) >NCBI__GCF_000745975.1:WP_035241269.1 Length = 485 Score = 205 bits (522), Expect = 3e-57 Identities = 135/447 (30%), Positives = 212/447 (47%), Gaps = 6/447 (1%) Query: 71 PANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALREKIQVLGS 130 PA E + V + + A + W A +R I+R+ D L E + L Sbjct: 34 PATGEVLGTVPFCGADETRRAIDAANGSLPAWRSKTAAQRSAILRRWHDLLMENQEDLAL 93 Query: 131 LVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSERSGHALIEQWNPVGLVGI 190 L++ E GK L E GE+ ++ ++ I G I+P + L+ PVG+V Sbjct: 94 LMTAEQGKPLAESRGEIAYAASFFEWFAEEAKRIYGDIIPQTIASQRLVVIKQPVGVVAA 153 Query: 191 ITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVLEDNKLPGAICSL 250 IT +NFP A+ A+ G + K A T ++A+ K+ E PG + Sbjct: 154 ITPWNFPSAMITRKAGAALAAGCTMVVKPATATPFSALAIAKLAQ---EAGMPPGVFNVV 210 Query: 251 TCGGADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLELGGNNAIIAFEDAD 310 T + IG + + V L+FTGST+VGK++ R +ELGGN I F+DAD Sbjct: 211 TGSSSAIGGELTANPIVRKLTFTGSTEVGKKLMQDCAGTMKRVSMELGGNAPFIVFDDAD 270 Query: 311 LSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQIRVGNPWDPNVLYG 370 L V AL +GQ C A RL++ ++D+ +L +A A ++VGN + V+ G Sbjct: 271 LDAAVEGALSCKYRNSGQTCVCANRLYVQAGVYDQFCEKLARAVATLKVGNGIEEGVVQG 330 Query: 371 PLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPTIVTGLGHDASIAHTETFA 430 PL +AV + +A +G V+ GGK G + PT++ + D +A E F Sbjct: 331 PLIDMKAVESVERHINDALDKGAKVLAGGKRHALGGTFFSPTVLADVTDDMLVAKEEIFG 390 Query: 431 PILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCGIVNVNIPTSGA 490 P +FKF++E EV N+ + GL++ FT+D+ R +R +G K + G++ +N Sbjct: 391 PFAPIFKFESEAEVVQKANDTEYGLAAYFFTRDMARTWR-VGEK-LEYGLIGINSGIISN 448 Query: 491 EIGGAFGGEKHTGGGRESGSDAWKQYM 517 + FGG K +G GRE Y+ Sbjct: 449 AV-APFGGVKESGNGREGSKYGLDDYL 474 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: 674 Number of extensions: 24 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: 539 Length of database: 485 Length adjustment: 35 Effective length of query: 504 Effective length of database: 450 Effective search space: 226800 Effective search space used: 226800 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