Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate 7025957 Shewana3_3105 aldehyde dehydrogenase (acceptor) (RefSeq)
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__ANA3:7025957 Length = 498 Score = 286 bits (731), Expect = 1e-81 Identities = 175/478 (36%), Positives = 265/478 (55%), Gaps = 10/478 (2%) Query: 12 QAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPA--WRALTA 69 +AYINGE+ DA G T +P G V+ V + A+ A + + W Sbjct: 22 KAYINGEYRDAAAGSTFDCVSPIDGRVLAKVASCDQMDANIAVANAREVFESGVWSKTAP 81 Query: 70 KERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKG-EIAYAASFIEWFAEEAKRIYG 128 +R + R+ EL+ EN ++LA L T + GKP+ +K +IA AA I W E ++Y Sbjct: 82 VKRKQVMIRFAELLEENANELALLETLDMGKPIRFSKAVDIAGAARAIRWSGEAVDKLYD 141 Query: 129 DTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYS 188 + P + +I ++P+GV AAI PWNFP M K GPALA G +++LKP+ ++P + Sbjct: 142 ELAPTAHNEIGMIT-REPVGVVAAIVPWNFPLLMACWKLGPALATGNSVILKPSEKSPLT 200 Query: 189 ALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAK- 247 A+ + ELA +AGIP GVL+V+ G VG L + V L FTGST+I +QLM + Sbjct: 201 AIRIAELAVQAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGES 260 Query: 248 DIKKVSLELGGNAPFIVFDDA-DLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFA 306 ++K+V LE GG +P IVF+DA DL A A + N G+ C +R+ V+ GV D Sbjct: 261 NMKRVWLEAGGKSPNIVFNDAPDLKAAAVAAAEAIAFNQGEVCTAGSRLLVESGVKDQLI 320 Query: 307 EKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLI----E 362 E +A +A + G+ L+ T +G ++D + + + +I+ +GA ++ GG+ + Sbjct: 321 ELIAEELASWQPGHPLDPATVSGAVVDKQQLDTILSYIKAGQDEGASLVHGGQQVLAETG 380 Query: 363 GNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMS 422 G + +PTI V +A EE FGP+ + F E IA++NDT +GLA+ + D+S Sbjct: 381 GVYVQPTIFSQVNNKMKIASEEIFGPVLSVIEFNGMEEAIAIANDTIYGLAAGVWTADIS 440 Query: 423 RVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCISV 480 + + A+AL GMV IN + APFGG K SG GR+ S + + Y EIK I++ Sbjct: 441 KAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSMHSFDKYTEIKATWIAL 498 Lambda K H 0.317 0.134 0.384 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: 592 Number of extensions: 29 Number of successful extensions: 7 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: 480 Length of database: 498 Length adjustment: 34 Effective length of query: 446 Effective length of database: 464 Effective search space: 206944 Effective search space used: 206944 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 (21.6 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