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) >NCBI__GCF_000009985.1:WP_011384974.1 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:
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