Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate RR42_RS26155 RR42_RS26155 succinate-semialdehyde dehydrogenase
Query= BRENDA::P49419 (539 letters) >FitnessBrowser__Cup4G11:RR42_RS26155 Length = 487 Score = 235 bits (599), Expect = 3e-66 Identities = 144/465 (30%), Positives = 233/465 (50%), Gaps = 10/465 (2%) Query: 56 NGSWGGR--GEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEI 113 +G W G G V+ + PA ++ + V + A+ + V+ A A W D+ R + Sbjct: 20 DGEWTGAAGGAVLMVHNPATHDVVGTVPRCGAAETRQAVEAAARALPAWRDLTGKARAAV 79 Query: 114 VRQIGDALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSER 173 +R+ D + + L L++ E GK L E GE+ ++ ++ + G +L S R Sbjct: 80 LRRWADLMLVHQEDLAQLMTAEQGKPLAEARGEIAYAASFLEWFGEEAKRVDGDVLSSPR 139 Query: 174 SGHALIEQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKI 233 +G ++ PVG+ IT +NFP A+ A+ G + K A T L ++A Sbjct: 140 AGQKMLVLRQPVGVCAAITPWNFPAAMITRKAGPALAAGCTMIVKPAEQTPLTALA---- 195 Query: 234 IAKVLEDNKLPGAICSLTCGG-ADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGR 292 +A + E+ +P + + G IG + + V LSFTGST +GK + + Sbjct: 196 LAALAEEAGVPRGVLQVVTGDPVQIGGVLCESPVVRKLSFTGSTAIGKLLMAQCAGTVKK 255 Query: 293 SLLELGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKK 352 LELGGN +I FEDADL V L + +GQ C A R+++H++++DEV +RL + Sbjct: 256 LSLELGGNAPLIVFEDADLDRAVDGILASKFRNSGQTCVCANRIYVHDAVYDEVASRLVR 315 Query: 353 AYAQIRVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPT 412 A + +R G+ D +V GPL AV+ + +A G V+ GGK G + EPT Sbjct: 316 AVSALRPGHGIDSDVTQGPLIDADAVAKVESHIADALAHGARVLTGGKRHALGGTFFEPT 375 Query: 413 IVTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLG 472 +V G +A ETF P+ +F+FK ++EV A N+ + GL++ F+KD+ R+ W Sbjct: 376 VVAGATAAMRVAREETFGPLAPLFRFKGDQEVIAMANDTESGLAAYFFSKDMARV--WRV 433 Query: 473 PKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM 517 + + G+V +N E+ FGG K +G GRE S +Y+ Sbjct: 434 AEALEYGMVGINTGLISNEV-APFGGVKQSGLGREGSSYGIDEYL 477 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: 704 Number of extensions: 17 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: 487 Length adjustment: 35 Effective length of query: 504 Effective length of database: 452 Effective search space: 227808 Effective search space used: 227808 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