Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__Cola:Echvi_0481 Length = 509 Score = 271 bits (692), Expect = 5e-77 Identities = 168/480 (35%), Positives = 257/480 (53%), Gaps = 18/480 (3%) Query: 14 YINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERS 73 +I G+++ +G+ V +P G+V V + A+ A++AA KA PAW +A ERS Sbjct: 25 FIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELALDAAHKAFPAWSRTSATERS 84 Query: 74 AKLRRWFELMIENQDDLARLMTTEQGKPLAEA-KGEIAYAASFIEWFAEEAKRIYGDTIP 132 L + + + + LA + T + GKP+ E ++A +FA + G Sbjct: 85 NILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAGVIRAEEGSIAE 144 Query: 133 GHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALAL 192 Q + +K+PIG+ I PWNFP M T K PALAAGC ++KPA QTP S + L Sbjct: 145 LDQHTVS-VNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQTPASIMIL 203 Query: 193 VELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKV 252 +E+ +PAGVL+VV G E G L + + K++FTG T GR +M+ ++++ V Sbjct: 204 MEVIGDL-LPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLIMQYASENLNPV 262 Query: 253 SLELGGNAPFIVF------DDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFA 306 ++ELGG +P + F DD LDK +EGA++ N G+ C C +RI V + +YDAF Sbjct: 263 TMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFAL-NQGEVCTCPSRILVHEKIYDAFM 321 Query: 307 EKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGK------- 359 EK+ A +++G+ L++ T G K+ +I+ +GA+VL+GG+ Sbjct: 322 EKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQEGAEVLTGGEVAKLNSG 381 Query: 360 LIEGNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYAR 419 L G + +PT+L K V +EE FGP+ + FKD E I++SNDT +GL + + R Sbjct: 382 LENGYYVKPTLLKGHNK-MRVFQEEIFGPVCSVATFKDVEEAISISNDTLYGLGAGVWTR 440 Query: 420 DMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCIS 479 D ++V A++ G V +N APFGG K SG GRE + Y + K + IS Sbjct: 441 DAHEAYQVPRAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHLMMLNHYRQNKNMLIS 500 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: 553 Number of extensions: 26 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: 509 Length adjustment: 34 Effective length of query: 446 Effective length of database: 475 Effective search space: 211850 Effective search space used: 211850 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