Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >NCBI__GCF_002115805.1:WP_085640679.1 Length = 485 Score = 325 bits (832), Expect = 3e-93 Identities = 180/473 (38%), Positives = 277/473 (58%), Gaps = 6/473 (1%) Query: 14 YVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKERA 73 ++DGA+V+ G I V PATGE I +V A +A+ AA +A AW A++ ER Sbjct: 12 FIDGAYVEDTTGTPIPVIYPATGEQIATVYAATPAIVDKALAAAHRAQKAWAAMSGTERG 71 Query: 74 NKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKG-EIAYAASFLEWFGEEAKRIYGDTIP 132 LRR D+M E DL+ L T + GKP E + A LE+FG A + G+ I Sbjct: 72 RILRRAADMMRERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGLAGSLTGEHI- 130 Query: 133 GHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALAL 192 + + ++P+GV I WN+P+ + K PALA G MV KP+ TP AL + Sbjct: 131 -QLGEDWVYTRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPLCALKV 189 Query: 193 AELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKKV 252 AE+ AG+P G+++VV G GEVG L ++P V K++ TGS G+++ A A+ +K V Sbjct: 190 AEILHEAGLPAGIYNVVQG-LGEVGASLVTDPRVAKVSLTGSVPTGKKVYAAAAEQMKHV 248 Query: 253 SLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDKLKAA 312 ++ELGG +P ++FDDADL+ AV GA++ + ++GQ C R++VQ G+ +AF+ +L Sbjct: 249 TMELGGKSPLLIFDDADLENAVGGAILGNFYSSGQVCSNGTRVFVQKGIKEAFLKRLTER 308 Query: 313 VAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGTFFEPTI 372 ++ +G+ L+ GP++ K + V ++I ++GA++V+GG+ G + +PT+ Sbjct: 309 LSTAVVGDPLDEATNFGPMVSEKQMKIVLDYIEKGENEGARLVAGGRRLNRDGFYLQPTV 368 Query: 373 LVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARVFRVAEQ 432 DV + +++++E FGP+ V F+ E E I +N TEFGL++ + RDL+R RV Q Sbjct: 369 FADVKDDMIIAREEIFGPVMAVLDFETEEEAITRANSTEFGLSAGVFTRDLSRAHRVIAQ 428 Query: 433 LEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK--YLCLGGI 483 LE G IN+ + APFGG K SG+GRE SK I Y E+K Y+ +G + Sbjct: 429 LEAGSCFINSYNDAPVEAPFGGTKMSGVGRENSKAAINHYSEMKSVYVRMGDV 481 Lambda K H 0.317 0.135 0.391 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: 601 Number of extensions: 28 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: 483 Length of database: 485 Length adjustment: 34 Effective length of query: 449 Effective length of database: 451 Effective search space: 202499 Effective search space used: 202499 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 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