Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized)
to candidate 7025944 Shewana3_3092 succinate semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::Q9S795 (501 letters) >FitnessBrowser__ANA3:7025944 Length = 482 Score = 301 bits (770), Expect = 4e-86 Identities = 172/482 (35%), Positives = 260/482 (53%), Gaps = 14/482 (2%) Query: 8 RQLFIDGEWREPILKKRIPIVNPATEEVIGDIPAATTEDVDVAVNAARRALSRNKGKDWA 67 +Q +I+G+W + K+ + I NPAT VI +P + A+ AA AL W Sbjct: 11 QQCYINGQWCDAQSKETVAIANPATGAVIASVPVMGQAETQAAIAAAEAALPA-----WR 65 Query: 68 KAPGAVRAKYLRAIAAKVNERKTDLAKLEALDCGKPLDEAVWDMDDVAGCFEFYADLAEG 127 R LR +NE DLA + + GKPL EA ++ A E++A+ Sbjct: 66 ALTAKERGVKLRRWFELLNENSDDLALMMTSEQGKPLAEAKGEVTYAASFIEWFAE---- 121 Query: 128 LDAKQKAPVSLP--MESFKSYVLKQPLGVVGLITPWNYPLLMAVWKVAPSLAAGCTAILK 185 +AK+ ++P + V+KQP+GV ITPWN+P M K AP+LAAGCT ++K Sbjct: 122 -EAKRVYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVK 180 Query: 186 PSELASVTCLELADICREVGLPPGVLNVLTGFGSEAGAPLASHPGVDKIAFTGSFATGSK 245 P+ T L LA + G+P GV +V+TG G + S+P V K++FTGS G K Sbjct: 181 PAPQTPFTALALAVLAERAGIPAGVFSVITGDAIGIGNEMCSNPVVRKLSFTGSTQVGIK 240 Query: 246 VMTAAAQLVKPVSMELGGKSPLIVFDDVDLDKAAEWALFGCFWTNGQICSATSRLLVHES 305 +M A +K +S+ELGG +P IVFDD ++D A E A+ + GQ C +R+ V Sbjct: 241 LMEQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAG 300 Query: 306 IASEFIEKLVKWSKNIKISDPMEEGCRLGPVVSKGQYEKILKFISTAKSEGATILHGGSR 365 + EF KL +K+ + + EG GP+++ EK+ + A S+GAT++ GG Sbjct: 301 VYDEFARKLSIAVGKLKVGEGIGEGVTTGPLINCAAVEKVQSHLEDALSKGATVVAGGK- 359 Query: 366 PEHLEKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFASEDEAIELANDSHYGLGAAV 425 H G F EPT++T+V +SM++ REE FGP+ + F D+ I+ AND+ +GL A Sbjct: 360 -PHSLGGNFFEPTVLTNVDSSMRVAREETFGPLAPLFKFTDVDDVIKQANDTEFGLAAYF 418 Query: 426 ISNDTERCDRISEAFEAGIVWINCSQPCFTQAPWGGVKRSGFGRELGEWGLDNYLSVKQV 485 D +++EA E G+V +N AP+GG+K SG GRE ++G++ YL +K + Sbjct: 419 YGRDISLVWKVTEALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKFGIEEYLEIKYI 478 Query: 486 TL 487 + Sbjct: 479 CM 480 Lambda K H 0.318 0.135 0.416 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: 614 Number of extensions: 22 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: 501 Length of database: 482 Length adjustment: 34 Effective length of query: 467 Effective length of database: 448 Effective search space: 209216 Effective search space used: 209216 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 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