Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_011384974.1 AMB_RS13050 aldehyde dehydrogenase family protein
Query= BRENDA::Q88RC0 (480 letters) >lcl|NCBI__GCF_000009985.1:WP_011384974.1 AMB_RS13050 aldehyde dehydrogenase family protein Length = 479 Score = 296 bits (759), Expect = 8e-85 Identities = 185/479 (38%), Positives = 264/479 (55%), Gaps = 30/479 (6%) Query: 14 YINGEWLDADNG-QTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKER 72 Y++G W+ G + + V NPAT +V G V G + RAI+AA KA PAW A ER Sbjct: 8 YVDGAWVKPAKGSRLLDVINPATEQVSGRVALGGADDAVRAIQAAAKAFPAWAATPLAER 67 Query: 73 SAKLRRWFELMIENQDDLARLMTTEQGKPL------AEAK---GEIAYAASFIEWFAEEA 123 L + D++A ++ E G PL A+A+ G A S + +A E Sbjct: 68 LEILAKVTAGYERRLDEIAEAISLEMGAPLERLAKPAQARAGLGHFKTALSLAKTYAFER 127 Query: 124 KRIYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPAS 183 ++ G T+ V+K+P+GV + ITPWN+P I K PALAAGC MVLKP+ Sbjct: 128 RQ--GTTL----------VVKEPVGVVSLITPWNWPMNQIACKVAPALAAGCAMVLKPSE 175 Query: 184 QTPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLME 243 PYSA L E+ H AG+PAGV ++V G E+G L+ + LV +S TGS G +M Sbjct: 176 FAPYSARILAEIIHEAGVPAGVFNMVFGDGAEIGPVLSSHPLVDMVSLTGSNLAGSSVMR 235 Query: 244 ECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYD 303 E A IKKVSLELGG + I+ D AD KA+ A+ + N GQ+C +R++V D Sbjct: 236 EGAATIKKVSLELGGKSANIICDSADFKKAIGHAVKAMMGNTGQSCNAPSRLFVPAHRLD 295 Query: 304 AFAEKLAAAV-AKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGK--- 359 AE LAA + A++K+G+ + T GP+ +G+ KV+ I + +GAK++ GG Sbjct: 296 E-AEGLAAELCAQIKVGDPSDPETVMGPIANGRQFDKVRRMIRTGMEEGAKLVCGGPERP 354 Query: 360 --LIEGNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFY 417 L +G F PT+ V + +EE FGP+ + + D + +A +ND +GL+ Y Y Sbjct: 355 EGLDKGYFVRPTVFSRVTDAMTIMREEIFGPVLSMRGYADLDDAVAGANDCVYGLSGYVY 414 Query: 418 ARDMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYL 476 A D+ VA L GMV +N G +S+ PFGGI+ SG+GRE + G E++LE K L Sbjct: 415 AGDLDEARAVARRLRTGMVHLN-GALSHPGGPFGGIRQSGVGREWGEAGFEEFLESKTL 472 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: 601 Number of extensions: 23 Number of successful extensions: 4 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: 479 Length adjustment: 34 Effective length of query: 446 Effective length of database: 445 Effective search space: 198470 Effective search space used: 198470 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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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