Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA reductase
Query= reanno::acidovorax_3H11:Ac3H11_612 (483 letters) >FitnessBrowser__Dyella79:N515DRAFT_0379 Length = 476 Score = 209 bits (533), Expect = 1e-58 Identities = 153/451 (33%), Positives = 221/451 (49%), Gaps = 19/451 (4%) Query: 35 EVVAEYARADRNQTELAVRAAADALPTWSQSTPQRRADVLDMIGSELLARKDELGALLAR 94 +V A D TE A+ AA A Q P R VL R+DEL L Sbjct: 30 KVATRVAVPDAKATEQAIAAAVKAAEPMRQFKPWERQAVLQHCVQRFTERRDELAYALCV 89 Query: 95 EEGKTLPEGVAEVARSGQIFKFFAGEALRIQGELL----ASVRQGVQVDVTREPVGVVGI 150 E GK + + EV R + F A EA+R GE + A G R P+G V Sbjct: 90 EAGKPIKDSAGEVTRLIETFGIAAEEAVRTNGETINLEIAKRLNGYHGYTRRVPLGPVSF 149 Query: 151 IAPWNFPFAIPAWKIAPALAYGNTVVFKPAELVPACGWALAEIISRSGLPAGAFNLIMGS 210 I P+NFP + A K+APA+A G V KPAE P + E+++ + LP GAF+++ Sbjct: 150 ITPFNFPLNLVAHKVAPAIAAGCPFVLKPAERTPIGALIIGEVLAETDLPKGAFSILNLD 209 Query: 211 GREVGQTLVDHPLVNALSFTGSVATGDRILRAASQRRAKVQLEMGGKNPLIVLAD--ADL 268 G+ LV+ P LSFTGS D RA + KV LE+GG IV AD L Sbjct: 210 GKH-ASPLVEDPRFKLLSFTGSQIGWDLKTRAGHK---KVTLELGGNAACIVDADQLPRL 265 Query: 269 DQAVDCALQGSYFSTGQRCTASSRLIVEAEVHDAFVARLRNRLASLKVGHALERGTEMGP 328 D ++ + G+++ +GQ C + R+ ++D RL + LK G ++ T +GP Sbjct: 266 DHVIERLVFGAFYQSGQSCISVQRIYAHESLYDELKKRLVAAVKGLKAGDPKKKETFLGP 325 Query: 329 VVDDNQLAQNLGYIDIAKSEGAEHVWGGERLERPTPGHYMSPALF-LARPEHRVAREEIF 387 ++D+ + G+I+ A+ G + + GG+R G + L R + +V R+E+F Sbjct: 326 MIDEAAAERLHGWIEEARKGGGKVLCGGKR-----KGPMLEATLMENVRGDAKVNRQEVF 380 Query: 388 GPVACVLRADDYDHALALANDTPFGLCAGICTTSLKRAMHFKRHAAVGMTMVN-LPTAGV 446 GP A + D A+A+ ND+ +GL AGI T SL AM G +VN +P+ V Sbjct: 381 GPFALLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMRAWNELEQGGVIVNDVPSFRV 440 Query: 447 DFHVPFGGRKESSYGAREQGRYAAEFYTTVK 477 D ++P+GG K S G RE RYA E T ++ Sbjct: 441 D-NMPYGGVKLSGAG-REGVRYAIEDMTEIR 469 Lambda K H 0.320 0.135 0.400 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: 493 Number of extensions: 28 Number of successful extensions: 5 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: 483 Length of database: 476 Length adjustment: 34 Effective length of query: 449 Effective length of database: 442 Effective search space: 198458 Effective search space used: 198458 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 (21.8 bits) S2: 51 (24.3 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