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 16751 b2661 succinate-semialdehyde dehydrogenase I, NADP-dependent (NCBI)
Query= SwissProt::Q64057 (539 letters) >FitnessBrowser__Keio:16751 Length = 482 Score = 231 bits (588), Expect = 6e-65 Identities = 142/469 (30%), Positives = 238/469 (50%), Gaps = 10/469 (2%) Query: 52 EGVFNGSW--GGRGEVITTYCPANNEPIARVRQASMKDYEETIGKAKKAWNIWADIPAPK 109 + + NG W GE I PAN + + V + + I A +A W + A + Sbjct: 12 QALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRALPAWRALTAKE 71 Query: 110 RGEIVRKIGDALREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTL 169 R I+R + + E L RL++LE GK L E GE+ ++ A + I G T+ Sbjct: 72 RATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKRIYGDTI 131 Query: 170 PSERPGHALMEQWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIA 229 P + L+ P+G+ IT +NFP A+ AL G + K A T ++A Sbjct: 132 PGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSALA 191 Query: 230 VTKIIAKVLEDNLLPGAICSLTCGGAD-MGTAMARDERVNLLSFTGSTQVGKQVALMVQE 288 + ++ + +P + ++ G A +G + + V LSFTGST++G+Q+ + Sbjct: 192 LAELAIRAG----VPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQLMEQCAK 247 Query: 289 RFGKSLLELGGNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVD 348 K LELGGN I F+DADL + AL + AGQ C RL++ + ++D + Sbjct: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVYDRFAE 307 Query: 349 RLKNAYSQIRVGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVMDHPGNY 408 +L+ A S++ +G+ D + GPL ++AV+ + + +A ++G VV GGK + GN+ Sbjct: 308 KLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAHERGGNF 367 Query: 409 VEPTIVTGLVHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDLGRIF 468 +PTI+ + +A + +ETF P+ +F+FK+E +V N+ + GL++ + +DL R+F Sbjct: 368 FQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDLSRVF 427 Query: 469 RWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM 517 R +G + + GIV +N E+ FGG K +G GRE + Y+ Sbjct: 428 R-VG-EALEYGIVGINTGIISNEV-APFGGIKASGLGREGSKYGIEDYL 473 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: 609 Number of extensions: 29 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