Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 200843 SO1678 methylmalonate-semialdehyde dehydrogenase (NCBI ptt file)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_805 (497 letters) >lcl|FitnessBrowser__MR1:200843 SO1678 methylmalonate-semialdehyde dehydrogenase (NCBI ptt file) Length = 499 Score = 199 bits (507), Expect = 1e-55 Identities = 155/496 (31%), Positives = 234/496 (47%), Gaps = 42/496 (8%) Query: 23 YINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQRAVENARATFNSGVWSRLAPTK 82 YI+GE+T +P + + I S A + A+ +A+A F + W + ++ Sbjct: 8 YIDGEFTAGTGTSQIVVTNPANNATIAVINSATADEVHAAIASAKAAFKT--WKEVPVSE 65 Query: 83 RKSTMIRFAGLLKQHAEELALLETLDMGKPISDS---LYIDVPGAAQALSWS----GEAI 135 R M+R+ LLK+H +ELA + + GK D+ ++ + A A + + GE + Sbjct: 66 RARVMLRYQHLLKEHHDELATILAHETGKTFEDAKGDVWRGIEVAEHACNIASLLMGETV 125 Query: 136 DKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEK 195 + + + + Q P+GV I P+NFP M+ W A++ GN+ ILKPSE+ Sbjct: 126 ENVARSIDTYSYTQ-------PLGVCAGITPFNFPAMIPLWMFPLAIACGNTFILKPSEQ 178 Query: 196 SPLTAIRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTLVFTGSTKIAKQLLIY 255 P+T R+ EL VEAG PKGVL ++ G T L V + F GS + Q + Sbjct: 179 DPMTPQRLVELFVEAGAPKGVLQLIHG-DKTAVDILLADPAVKAISFVGSVAVG-QYIYK 236 Query: 256 SGESNMKRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGEVCTAGSRLLVERSIK 315 +G N+KRV AG K+ ++ DA N Q GA G+ C A S + + K Sbjct: 237 TGTDNLKRVQAFAGAKNHCVIMPDA-NKQQVINNLVGASVGAAGQRCMAISVAVFVGAAK 295 Query: 316 DKFLPLVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESGHADGARLVAGGK--R 373 + ++P + EAL +PG D G L+ VL I G +GA+ + G Sbjct: 296 E-WIPELKEALAKVRPGLWDDKDAGYGPLISPAAKVRVLKLIAQGKEEGAQCLLDGSDFT 354 Query: 374 TLQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIAIANDTPYGLAAAV 433 G +V PT+F V+ M I +EEIFGPVL +E DS E+AI + N +PYG ++ Sbjct: 355 VAGFESGNWVGPTMFTKVTTDMSIYKEEIFGPVLCCMESDSLEDAIELVNASPYGNGTSI 414 Query: 434 WTADISKAHLTARALRAGSVWVNQYDGGDMTAP-----FGGFKQSGNGRDKSLHAFDK-- 486 +TA + A + G V +N + P F G+K S G HA+ K Sbjct: 415 FTASGAAARKYQHEIEVGQVGINV----PIPVPLPFFSFTGWKGSFYG---DQHAYGKQA 467 Query: 487 ---YTELK---ATWIK 496 YTE K A W + Sbjct: 468 VRFYTETKTITARWFE 483 Lambda K H 0.316 0.132 0.390 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: 580 Number of extensions: 30 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: 497 Length of database: 499 Length adjustment: 34 Effective length of query: 463 Effective length of database: 465 Effective search space: 215295 Effective search space used: 215295 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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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