Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate 7025944 Shewana3_3092 succinate semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::P49419 (539 letters) >FitnessBrowser__ANA3:7025944 Length = 482 Score = 212 bits (540), Expect = 2e-59 Identities = 141/465 (30%), Positives = 220/465 (47%), Gaps = 10/465 (2%) Query: 56 NGSW--GGRGEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEI 113 NG W E + PA IA V A+ + + A A W + A +RG Sbjct: 16 NGQWCDAQSKETVAIANPATGAVIASVPVMGQAETQAAIAAAEAALPAWRALTAKERGVK 75 Query: 114 VRQIGDALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSER 173 +R+ + L E L +++ E GK L E GEV ++ ++ + G +P + Sbjct: 76 LRRWFELLNENSDDLALMMTSEQGKPLAEAKGEVTYAASFIEWFAEEAKRVYGDTIPGHQ 135 Query: 174 SGHALIEQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKI 233 ++ PVG+ IT +NFP A+ A A+ G + K AP T ++A Sbjct: 136 GDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPFTALA---- 191 Query: 234 IAKVLEDNKLPGAICSLTCGGA-DIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGR 292 +A + E +P + S+ G A IG M + V LSFTGSTQVG ++ + Sbjct: 192 LAVLAERAGIPAGVFSVITGDAIGIGNEMCSNPVVRKLSFTGSTQVGIKLMEQCAPTLKK 251 Query: 293 SLLELGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKK 352 LELGGN I F+DA++ V A+ A AGQ C A R+++ ++DE +L Sbjct: 252 LSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDEFARKLSI 311 Query: 353 AYAQIRVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPT 412 A +++VG V GPL AV +E+A +G TVV GGK GN+ EPT Sbjct: 312 AVGKLKVGEGIGEGVTTGPLINCAAVEKVQSHLEDALSKGATVVAGGKPHSLGGNFFEPT 371 Query: 413 IVTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLG 472 ++T + +A ETF P+ +FKF + ++V N+ + GL++ + +D+ + W Sbjct: 372 VLTNVDSSMRVAREETFGPLAPLFKFTDVDDVIKQANDTEFGLAAYFYGRDISLV--WKV 429 Query: 473 PKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM 517 + + G+V VN E+ FGG K +G GRE ++Y+ Sbjct: 430 TEALEYGMVGVNTGLISTEV-APFGGMKSSGLGREGSKFGIEEYL 473 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: 654 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 ( 7.3 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