Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate Ac3H11_4184 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= SwissProt::Q64057 (539 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4184 Length = 498 Score = 218 bits (555), Expect = 4e-61 Identities = 147/472 (31%), Positives = 221/472 (46%), Gaps = 13/472 (2%) Query: 52 EGVFNGSWGGRGEVITTYCPANNEPIARVRQASMKDYEETIGKAKKAWNIWADIPAPKRG 111 +G+ NG W PA +A V D E I A AW W A +R Sbjct: 20 DGLINGQWVVGSSRFDVNDPATGLKLADVANLGPADAEAAIAAANAAWGPWKTKTAKERS 79 Query: 112 EIVRKIGDALREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPS 171 I+RK D L LGR+++ E GK L E GEV ++ A ++ I G TLP Sbjct: 80 IILRKWFDLLMANQDDLGRIMTAEQGKPLAEAKGEVAYGASFVEWFAEEAKRINGETLPQ 139 Query: 172 ERPGHALMEQWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIAVT 231 LM P+G+ IT +NFP+A+ A AL G + K A T L ++A Sbjct: 140 FDNNRRLMVLKQPIGVCAAITPWNFPLAMITRKVAPALAAGCPVVIKPAELTPLTALAAA 199 Query: 232 KIIAKVLEDNLLPGAICSLTCGGAD----MGTAMARDERVNLLSFTGSTQVGKQVALMVQ 287 ++ + +P + ++ +D +G + + V +SFTGST+VG+ + Sbjct: 200 ELAIRAG----IPAGVFNILPADSDNSIAIGKVLCASDVVRHISFTGSTEVGRILMAQSA 255 Query: 288 ERFGKSLLELGGNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVV 347 K LELGGN I F+DAD+ + A + AGQ C R ++ E ++DE V Sbjct: 256 PTVKKMSLELGGNAPFIVFDDADIDSAVEGAFASKYRNAGQTCVCTNRFYVQEGVYDEFV 315 Query: 348 DRLKNAYSQIRVGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVMD--HP 405 + +VGN ++ + GPL + A++ + V++A +GG VV GG+ + Sbjct: 316 AKFAAKVKTAKVGNGFEAGVNQGPLIEEAALTKVQRHVDDALAKGGQVVAGGQRLTALGS 375 Query: 406 GNYVEPTIVTGLVHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDLG 465 G + EPT+V D +ETF P VFKFK E+E + N + GL+S +++D+G Sbjct: 376 GQFFEPTVVANATADMLCAREETFGPFAPVFKFKTEQEAIDAANNTEFGLASYFYSRDVG 435 Query: 466 RIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM 517 RIFR + + G+V N+ E FGG K +G GRE Y+ Sbjct: 436 RIFR--VTEALEYGMVGANVGILATE-HVPFGGVKQSGLGREGSHHGMDDYV 484 Lambda K H 0.319 0.137 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: 645 Number of extensions: 31 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: 498 Length adjustment: 35 Effective length of query: 504 Effective length of database: 463 Effective search space: 233352 Effective search space used: 233352 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 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