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 GFF4164 Psest_4237 succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9DBF1 (539 letters) >FitnessBrowser__psRCH2:GFF4164 Length = 482 Score = 229 bits (585), Expect = 1e-64 Identities = 141/465 (30%), Positives = 236/465 (50%), Gaps = 10/465 (2%) Query: 56 NGSW--GGRGEVITTYCPANNEPIARVRQASLKDYEETIGKAKKAWNIWADIPAPKRGEI 113 +G+W G+ I+ PA E + V + + I A++A W D+ A +R + Sbjct: 16 DGAWLDADSGQTISVNNPATGETLGTVPKMGAAETRRAIDAAERALPAWRDLTAKERSQK 75 Query: 114 VRKIGDAFREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPSER 173 +R+ + E LGRL++LE GK L E GE+ ++ A ++ I G T+P + Sbjct: 76 LRRWFELLMENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIPGHQ 135 Query: 174 PGHALIEMWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSVAVTKI 233 +I + P+G+ IT +NFP A+ AL G + K A T ++A+ ++ Sbjct: 136 KDKRIIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPASQTPFSALAMVEL 195 Query: 234 IAQVLEDNLLPGAICSLVCGGA-DIGTTMARDERVNLLSFTGSTQVGKEVALMVQERFGK 292 E +P + S+V G A DIG + + +V +SFTGST+VG ++ K Sbjct: 196 A----ERAGIPKGVLSVVTGSAGDIGNELTANPKVRKISFTGSTEVGAKLMEQCAPGIKK 251 Query: 293 SLLELGGNNAIIAFEDADLSLVVPSVLFAAVGTAGQRCTTVRRLFLHESIHNEVVDRLRS 352 LELGGN I F+DADL V + + AGQ C V R+++ + +++ ++ ++ Sbjct: 252 VSLELGGNAPFIVFDDADLDEAVKGAVQSKYRNAGQTCVCVNRIYVQDGVYDTFAEKFQA 311 Query: 353 AYSQIRVGNPWDPNILYGPLHTKQAVSMFVRAVEEAKKQGGTVVYGGKVMDHPGNYVEPT 412 A +++RVGN + GPL +A + +E+A QG +V GG+ G+Y EPT Sbjct: 312 AVAKLRVGNGLEEGTDLGPLIDDRAAAKVREHIEDAVAQGARLVAGGQAHALGGSYFEPT 371 Query: 413 IVTGLAHDAPIVHQETFAPILYVFKFQDEEEVFEWNNEVKQGLSSSIFTKDLGRIFRWLG 472 ++ + A + +ETF P+ +F+F+DE + N+ + GL+S + +DLGR+FR Sbjct: 372 VLVNVPDSAKVAKEETFGPLAPLFRFKDEADAIAKANDTEFGLASYFYARDLGRVFR--V 429 Query: 473 PKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM 517 + + G+V +N E+ FGG K +G GRE + Y+ Sbjct: 430 AEALEYGMVGINTGLISTEV-APFGGVKSSGLGREGSKYGIEDYL 473 Lambda K H 0.319 0.137 0.421 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: 650 Number of extensions: 30 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: 482 Length adjustment: 34 Effective length of query: 505 Effective length of database: 448 Effective search space: 226240 Effective search space used: 226240 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