Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_012647687.1 GEOB_RS12935 L-glutamate gamma-semialdehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >NCBI__GCF_000022265.1:WP_012647687.1 Length = 1004 Score = 238 bits (607), Expect = 8e-67 Identities = 151/454 (33%), Positives = 241/454 (53%), Gaps = 23/454 (5%) Query: 55 PTVNPST-GEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIE 113 P++NPS E++ V + ++V +A+ AAR +F+ WR + R L + ++ Sbjct: 524 PSMNPSDPSEIVGWVCQAGTDEVAQAIGAARKSFET---WRDITPEIRAEFLLKACTVVR 580 Query: 114 RDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAG-----WADKYHGKTIPIDGDFF 168 R L+AL+ L+ GK + +Y D+ + L YYA + + GK +F Sbjct: 581 RRIYELSALQVLEIGKQWDQAY-ADVTEAIDFLEYYAREMIRLGSPRSMGKVAGETNQYF 639 Query: 169 SYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEA 228 +EP GV I PWNFPL + + A+ TGN VV K + T + + ++ +E Sbjct: 640 ----YEPKGVAAVIAPWNFPLAISMGMVSAAIVTGNCVVFKPSGLTSIIGWQLVDIFREV 695 Query: 229 GFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIG-RVIQVAA----GSSNLKRVT 283 G P GV N VPG G + H V +AFTGS E+G R+I+ AA G +K+V Sbjct: 696 GLPDGVFNFVPGRSGIMGDYLVDHPHVSLIAFTGSMEVGLRIIERAAKVQPGQEMVKKVI 755 Query: 284 LELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARA 343 E+GGK+ II DAD+D AV + F QGQ C A SR V + IYD+FV+R A A Sbjct: 756 CEMGGKNAIIIDDDADLDEAVPHVFNSAFGFQGQKCSACSRVIVLDGIYDKFVQRLTALA 815 Query: 344 KSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGYFIQPTVF 403 ++ VG D G +E K+I+ YI G+QEG +LL G + + G+F+ T+ Sbjct: 816 EAVPVGPVEDPANLIGAVAEENAQKRIMNYIEVGRQEG-RLLYQGHV-PEVGFFVPLTII 873 Query: 404 GDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQAL 463 GD++ +A+EEIFGP++ +++ + E + AN++ Y L +F++ + ++ Sbjct: 874 GDIRPEHRLAQEEIFGPLLAVMRARDFNEALVWANSTRYALTGGLFSRSPEHIAIATKRF 933 Query: 464 QAGTVWV--NCYDVFGAQSPFGGYKMSGSGRELG 495 + G +++ NC + PFGG+++SG+G + G Sbjct: 934 RVGNLYLNRNCTGALVGRQPFGGFRLSGAGTKAG 967 Lambda K H 0.319 0.136 0.409 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: 1159 Number of extensions: 49 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: 517 Length of database: 1004 Length adjustment: 40 Effective length of query: 477 Effective length of database: 964 Effective search space: 459828 Effective search space used: 459828 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 55 (25.8 bits)
This GapMind analysis is from Sep 24 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