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 BWI76_RS05620 BWI76_RS05620 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q64057 (539 letters) >FitnessBrowser__Koxy:BWI76_RS05620 Length = 482 Score = 241 bits (614), Expect = 6e-68 Identities = 143/468 (30%), Positives = 242/468 (51%), Gaps = 8/468 (1%) Query: 52 EGVFNGSWGGRG--EVITTYCPANNEPIARVRQASMKDYEETIGKAKKAWNIWADIPAPK 109 + + NG W E + PAN +P+ V + + E I A +A W + A + Sbjct: 12 QAMINGRWRDASGKETLAVTNPANGQPLGNVPKMGAGETREAIDAAARALPAWRALTAKE 71 Query: 110 RGEIVRKIGDALREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTL 169 R I+R+ + + E L RL++LE GK L E GE+ ++ A + I G T+ Sbjct: 72 RSSILRRWFELMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKRIYGDTI 131 Query: 170 PSERPGHALMEQWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIA 229 P + L+ P+G+ IT +NFP A+ AL G + K A T ++A Sbjct: 132 PGHQADKRLLVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPFSALA 191 Query: 230 VTKIIAKVLEDNLLPGAICSLTCGGADMGTAMARDERVNLLSFTGSTQVGKQVALMVQER 289 + ++ + + G +T +++G + + V LSFTGST++G+Q+ + Sbjct: 192 LAELANRA---GIPEGVFNVVTGSASEVGGELTGNPLVRKLSFTGSTEIGRQLMEQCAKD 248 Query: 290 FGKSLLELGGNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVDR 349 K LELGGN I F+DADL + AL + AGQ C RL++ +S++D ++ Sbjct: 249 IKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDSVYDRFAEK 308 Query: 350 LKNAYSQIRVGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVMDHPGNYV 409 L+ A S++++G+ PN+ GPL ++A++ + + +A +G VV GGK + GN+ Sbjct: 309 LQQAVSKLQIGDGLQPNVTIGPLIDEKAIAKVQEHIADALGKGARVVTGGKAHELGGNFF 368 Query: 410 EPTIVTGLVHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDLGRIFR 469 +PTI+ + DA + +ETF P+ +F+FK+E +V N+ + GL++ + +DLGR+FR Sbjct: 369 QPTILVDVPGDAKVAKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDLGRVFR 428 Query: 470 WLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM 517 +G + + GI+ +N E+ FGG K +G GRE + Y+ Sbjct: 429 -VG-EALEYGIIGINTGLISTEV-APFGGVKSSGLGREGSKYGIEDYL 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: 669 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: 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