Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_019557014.1 F612_RS0106825 aldehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000381085.1:WP_019557014.1 Length = 498 Score = 206 bits (524), Expect = 2e-57 Identities = 156/479 (32%), Positives = 230/479 (48%), Gaps = 29/479 (6%) Query: 34 FGRHYPLYIGGEWVDTKERMVSLNPSAPS-EVVGTTAKAGKAEAEAALEAAWKAFKTWKD 92 F Y +IGG+WV + N S S E + ++ + + A+ AA KA W Sbjct: 8 FKEQYENFIGGKWVPPVDGKYFENTSPVSGEFINRIPRSSNKDIDLAVAAATKASTAWGK 67 Query: 93 WPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEA-SADVAEAIDFIEYYARAALR 151 DRS +LLK A M + + ++ GK E +AD+ +ID Y+A Sbjct: 68 TSATDRSNILLKIADAMEQNLEAIAHAETWDNGKAIRETMAADIPLSIDHFRYFAGVI-- 125 Query: 152 YRYPAVEVVPYPGED-NESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAE 210 R + E+ + + PLG I PWNFP+ + I +A GN V+ KPAE Sbjct: 126 -RADSGEISDLDANTVSMEVHEPLGVVAQIIPWNFPILMACWKIAPALAAGNCVVLKPAE 184 Query: 211 DAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYE 270 + EI + P GV+N + G G E G L HP R + FTG G I + Sbjct: 185 QTPSSILVMMEIIQDL-LPQGVLNIVNGFGLEAGKPLATHPDIRKVAFTGETTTGRLIMQ 243 Query: 271 AAGRLAPGQTWFKRAYVETGGK------DAIIVDETADFDLAAEGVVVSAYGFQGQKCSA 324 A T +E GGK ++I+ ++ A FD A EG+V+ A+ QG+ C+ Sbjct: 244 YASENIVPVT------LELGGKSPNVFFESIMEEDDAFFDKAIEGLVLFAFN-QGEVCTC 296 Query: 325 ASRLILTQGAYEPVLERVLKRAERLSVGPA-EENPDLGPVVSAEQERKVLSYIEIGKNEG 383 SR ++ + YE + R L+R + +G + + +G S++Q K+L+YIEIGK EG Sbjct: 297 PSRALIQESIYEKFMARCLERISAIKMGDTLDSSTMMGAQASSDQYEKILNYIEIGKAEG 356 Query: 384 -QLVLGGKRLEGE----GYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVA 438 +++ GG + + GY+I PT+ + R+ QEEIFGPVL V KD EAL++A Sbjct: 357 AEILCGGGAFKNKTFPNGYYIQPTLL-KGNNNMRVFQEEIFGPVLCVTTFKDEDEALKIA 415 Query: 439 NDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKT 497 NDT YGL GV++R + R G ++ N T FGG K SG +T Sbjct: 416 NDTMYGLGAGVWTRDVHQMHKMTRGIDAGRVWANCYHT--YPAHASFGGHKKSGIGRET 472 Lambda K H 0.319 0.137 0.403 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: 521 Number of extensions: 28 Number of successful extensions: 6 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: 516 Length of database: 498 Length adjustment: 34 Effective length of query: 482 Effective length of database: 464 Effective search space: 223648 Effective search space used: 223648 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 (21.7 bits) S2: 52 (24.6 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