Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate Pf1N1B4_1734 Succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16)
Query= BRENDA::P49419 (539 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1734 Length = 480 Score = 236 bits (601), Expect = 2e-66 Identities = 147/465 (31%), Positives = 242/465 (52%), Gaps = 12/465 (2%) Query: 56 NGSW--GGRGEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEI 113 +G+W G+ I PA E + V + A+ ++ A +A W + A +R Sbjct: 16 DGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRGLTAKERANK 75 Query: 114 VRQIGDALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSER 173 +R+ + + E L L++LE GK L E GE+ ++ ++ + G ++P + Sbjct: 76 LRRWFELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRVYGDVIPGHQ 135 Query: 174 SGHALIEQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKI 233 LI P+G+ IT +NFP A+ A+ G + K A T + A Sbjct: 136 PDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFA---- 191 Query: 234 IAKVLEDNKLPGAICSLTCGGA-DIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGR 292 +A++ + +P + S+ G A DIG+ + + V LSFTGST++G+Q+ + + Sbjct: 192 LAELAQRAGIPNGVFSVVTGSAGDIGSELTGNPIVRKLSFTGSTEIGRQLMTECAKDIKK 251 Query: 293 SLLELGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKK 352 LELGGN I F+DADL V A+ + GQ C A RL+I +S++D +LK Sbjct: 252 VSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSVYDAFAEKLKV 311 Query: 353 AYAQIRVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPT 412 A A++++GN + GPL ++AV+ + +A +G TV+ GGK M GN+ EPT Sbjct: 312 AVAKLKIGNGLEDGTTTGPLIDEKAVAKVQEHIADAVGKGATVLAGGKSMQ--GNFFEPT 369 Query: 413 IVTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLG 472 I+T + ++A++A ETF P+ +F+FK+E +V A +N+ + GL+S + +DLGR+FR Sbjct: 370 ILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFR--V 427 Query: 473 PKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM 517 + + G+V VN E+ FGG K +G GRE + Y+ Sbjct: 428 AEALEYGMVGVNTGLISNEV-APFGGIKASGLGREGSKYGIEDYL 471 Lambda K H 0.318 0.136 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: 678 Number of extensions: 29 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: 480 Length adjustment: 34 Effective length of query: 505 Effective length of database: 446 Effective search space: 225230 Effective search space used: 225230 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 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