Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_066048767.1 C0029_RS01835 aldehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >NCBI__GCF_002869505.1:WP_066048767.1 Length = 497 Score = 335 bits (858), Expect = 3e-96 Identities = 182/471 (38%), Positives = 272/471 (57%), Gaps = 9/471 (1%) Query: 12 QAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALP--AWRALTA 69 +AFI+G VDA +GQT NPATG+ L V A+ A+ A + W + A Sbjct: 21 RAFINGRRVDAASGQTRTTYNPATGQALAEVANCAPADADEAVRIARETFEQGTWAGMPA 80 Query: 70 KERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKG-EIVYAASFIEWFAEEAKRIYG 128 ER L RW ELI ++ D+LA L TL+ GKP+A+ ++ + I W E ++Y Sbjct: 81 AERKMVLVRWAELIEQHADELALLETLDVGKPIADTVNVDVPSSVRTIRWTGEAIDKVYD 140 Query: 129 DVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFS 188 + P LI + P+GV AAI PWNFP + K PALA G +++LKPAS TP + Sbjct: 141 QISPTRDNCMGLIT-RLPLGVVAAIVPWNFPLSTTAWKLAPALATGNSVILKPASNTPLT 199 Query: 189 AFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAK- 247 A +A+LA +AG+P GV V+ G G +G + ++ + L+FTGST +G+QLM + Sbjct: 200 ALRIADLATQAGLPDGVLHVLPGPGGSLGEHIATHMGIDGLTFTGSTPVGKQLMVYSGQS 259 Query: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAE 307 ++K+V LELGG +P IVF DAD+DKA A ++ Y N GQTC RL + + ++D F E Sbjct: 260 NLKRVFLELGGKSPNIVFPDADIDKAASAAALAVYYNGGQTCTAGTRLIVHESIHDTFIE 319 Query: 308 KLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGG----KPMEG 363 K+ A + GN L+ T GP++D+ V E++A +GA ++AGG + G Sbjct: 320 KVIEAASGWAPGNPLDPATAMGPMVDKGQCDTVAEYVAIGRDEGAKLVAGGGTVMEDTGG 379 Query: 364 NFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGR 423 ++ EPTI V N +A+EE FGP+ + F E++ +A++ND+ +GLA +++++ Sbjct: 380 HYHEPTIFAGVNNQMRIAQEEIFGPVLAVIPFSTESEAVAIANDSIYGLAGAVWSQNINT 439 Query: 424 VFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 RVAE + G +G+N + PFGG K SG GR+ S + +DY E+K Sbjct: 440 AHRVAEQVRVGTMGINNYFGGDITVPFGGFKESGNGRDKSMHAFDDYTELK 490 Lambda K H 0.317 0.135 0.390 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: 623 Number of extensions: 28 Number of successful extensions: 6 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: 497 Length adjustment: 34 Effective length of query: 446 Effective length of database: 463 Effective search space: 206498 Effective search space used: 206498 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 24 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