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 6938534 Sama_2637 succinate-semialdehyde dehydrogenase (NAD(P)(+)) (RefSeq)
Query= SwissProt::Q9DBF1 (539 letters) >FitnessBrowser__SB2B:6938534 Length = 480 Score = 216 bits (551), Expect = 1e-60 Identities = 141/465 (30%), Positives = 227/465 (48%), Gaps = 12/465 (2%) Query: 56 NGSWGGR--GEVITTYCPANNEPIARVRQASLKDYEETIGKAKKAWNIWADIPAPKRGEI 113 NG W GE +T PA NE IA V + E I A+ A W + A +RG Sbjct: 16 NGEWRDALSGETVTIANPATNEAIASVPVMGRDETREAIAAAEAALPAWRALTAKERGAK 75 Query: 114 VRKIGDAFREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPSER 173 +R+ + E L +++ E GK L E GEV ++ A ++ + G T+P + Sbjct: 76 LRRWYELMLENADDLALMMTTEQGKPLAEAKGEVVYAASFIEWFAEEAKRLYGDTIPGHQ 135 Query: 174 PGHALIEMWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSVAVTKI 233 ++ + +G+ IT +NFP A+ AL G + K AP T ++A+ ++ Sbjct: 136 GDKRIMVIKQGVGVTAAITPWNFPAAMITRKAGPALAAGCTMIVKPAPQTPFTALALAEL 195 Query: 234 IAQVLEDNLLPGAICSLVCGGA-DIGTTMARDERVNLLSFTGSTQVGKEVALMVQERFGK 292 A+ +P + S+V G A IG + + V LSFTGST VG ++ K Sbjct: 196 AAEAG----IPPGVFSVVTGDAVAIGNELCENPVVRKLSFTGSTGVGIKLMQQCAPTLKK 251 Query: 293 SLLELGGNNAIIAFEDADLSLVVPSVLFAAVGTAGQRCTTVRRLFLHESIHNEVVDRLRS 352 LELGGN I F DADL V + + AGQ C RL++ + +++ +L + Sbjct: 252 VSLELGGNAPFIVFNDADLDAAVEGAMISKYRNAGQTCVCANRLYVQDGVYDAFAQKLAA 311 Query: 353 AYSQIRVGNPWDPNILYGPLHTKQAVSMFVRAVEEAKKQGGTVVYGGKVMDHPGNYVEPT 412 A ++++VGN +P + GPL A+ +++A +G T+V GGK + GN++EP Sbjct: 312 AVAKLKVGNGAEPGVTTGPLINAAALEKVQSHLQDALDKGATLVAGGKPLG--GNFMEPA 369 Query: 413 IVTGLAHDAPIVHQETFAPILYVFKFQDEEEVFEWNNEVKQGLSSSIFTKDLGRIFRWLG 472 IVT + + +ETF P+ +F+F D ++V N+ + GL++ + +D+ I W Sbjct: 370 IVTNVDASMKVAREETFGPLAPLFRFSDVDDVIRQANDTEFGLAAYFYGRDISLI--WKV 427 Query: 473 PKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM 517 + + G+V VN E+ FGG K +G GRE +Y+ Sbjct: 428 AEALEYGMVGVNTGLISTEV-APFGGMKSSGLGREGSKYGIDEYV 471 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: 647 Number of extensions: 34 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 ( 7.4 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