Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized)
to candidate 6938534 Sama_2637 succinate-semialdehyde dehydrogenase (NAD(P)(+)) (RefSeq)
Query= BRENDA::Q9S795 (501 letters) >FitnessBrowser__SB2B:6938534 Length = 480 Score = 300 bits (769), Expect = 6e-86 Identities = 173/479 (36%), Positives = 256/479 (53%), Gaps = 16/479 (3%) Query: 11 FIDGEWREPILKKRIPIVNPATEEVIGDIPAATTEDVDVAVNAARRALSRNKGKDWAKAP 70 +I+GEWR+ + + + I NPAT E I +P ++ A+ AA AL W Sbjct: 14 YINGEWRDALSGETVTIANPATNEAIASVPVMGRDETREAIAAAEAALPA-----WRALT 68 Query: 71 GAVRAKYLRAIAAKVNERKTDLAKLEALDCGKPLDEAVWDMDDVAGCFEFYADLAEGLDA 130 R LR + E DLA + + GKPL EA ++ A E++A+ +A Sbjct: 69 AKERGAKLRRWYELMLENADDLALMMTTEQGKPLAEAKGEVVYAASFIEWFAE-----EA 123 Query: 131 KQKAPVSLP--MESFKSYVLKQPLGVVGLITPWNYPLLMAVWKVAPSLAAGCTAILKPSE 188 K+ ++P + V+KQ +GV ITPWN+P M K P+LAAGCT I+KP+ Sbjct: 124 KRLYGDTIPGHQGDKRIMVIKQGVGVTAAITPWNFPAAMITRKAGPALAAGCTMIVKPAP 183 Query: 189 LASVTCLELADICREVGLPPGVLNVLTGFGSEAGAPLASHPGVDKIAFTGSFATGSKVMT 248 T L LA++ E G+PPGV +V+TG G L +P V K++FTGS G K+M Sbjct: 184 QTPFTALALAELAAEAGIPPGVFSVVTGDAVAIGNELCENPVVRKLSFTGSTGVGIKLMQ 243 Query: 249 AAAQLVKPVSMELGGKSPLIVFDDVDLDKAAEWALFGCFWTNGQICSATSRLLVHESIAS 308 A +K VS+ELGG +P IVF+D DLD A E A+ + GQ C +RL V + + Sbjct: 244 QCAPTLKKVSLELGGNAPFIVFNDADLDAAVEGAMISKYRNAGQTCVCANRLYVQDGVYD 303 Query: 309 EFIEKLVKWSKNIKISDPMEEGCRLGPVVSKGQYEKILKFISTAKSEGATILHGGSRPEH 368 F +KL +K+ + E G GP+++ EK+ + A +GAT++ GG Sbjct: 304 AFAQKLAAAVAKLKVGNGAEPGVTTGPLINAAALEKVQSHLQDALDKGATLVAGGKP--- 360 Query: 369 LEKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFASEDEAIELANDSHYGLGAAVISN 428 G F+EP I+T+V SM++ REE FGP+ + F+ D+ I AND+ +GL A Sbjct: 361 -LGGNFMEPAIVTNVDASMKVAREETFGPLAPLFRFSDVDDVIRQANDTEFGLAAYFYGR 419 Query: 429 DTERCDRISEAFEAGIVWINCSQPCFTQAPWGGVKRSGFGRELGEWGLDNYLSVKQVTL 487 D +++EA E G+V +N AP+GG+K SG GRE ++G+D Y+ +K + L Sbjct: 420 DISLIWKVAEALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIDEYVEIKYICL 478 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: 621 Number of extensions: 25 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: 480 Length adjustment: 34 Effective length of query: 467 Effective length of database: 446 Effective search space: 208282 Effective search space used: 208282 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