Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate N515DRAFT_3729 N515DRAFT_3729 aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde dehydrogenase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1229 (505 letters) >lcl|FitnessBrowser__Dyella79:N515DRAFT_3729 N515DRAFT_3729 aminomuconate-semialdehyde/2-hydroxymuconate-6- semialdehyde dehydrogenase Length = 483 Score = 246 bits (628), Expect = 1e-69 Identities = 166/482 (34%), Positives = 251/482 (52%), Gaps = 15/482 (3%) Query: 15 LIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHRAFQTWKLTPIGARM 74 LIDG + W ++ PAT +V A P ++ A+VDAA++AA A W TP R Sbjct: 9 LIDGRLQAPRQERWLEVFEPATGEVFAHCPESSFADVDAAVAAAVAAAPGWAATPSEQRA 68 Query: 75 RIMLKLQALIREHSKRIAVVLSNEQGKTIADAEG-DIFRGLEVVEH-ACSIGSLQMGEFA 132 R++ +L LI A + S + GK ++ A DI R + + + A +I A Sbjct: 69 RLLQRLADLIEARLDEFAALESRDSGKPLSLARSLDIPRAVSNLRYFAAAIVPWSSESHA 128 Query: 133 ENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTML 192 + G YTLRQP+GV A I+P+N P + W A+A GN V KPSE P + L Sbjct: 129 MEL--GAINYTLRQPLGVVACISPWNLPLYLFTWKIAPALAAGNAVVAKPSEITPCTAAL 186 Query: 193 LVELAIEAGIPPGVLNVVHG-GKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGKR 251 L EL+IEAG PPGVLN+V G G +V AL H+D+KAVSF GST G + A K+ Sbjct: 187 LGELSIEAGFPPGVLNIVQGRGPEVGQALVEHRDVKAVSFTGSTRTGAQIAAAAAPRFKK 246 Query: 252 VQSMMGAKNHAVVLPDANREQA-LNALVGAGFGAAGQRCMATS-VVVLVGAAKQWLPDLK 309 + +G KN A+V DA+ A L+ +V +GF G+ C+ S ++V + Sbjct: 247 LSLELGGKNPAIVFADADLSDANLDTIVRSGFANQGEICLCGSRLLVQRSIYDAFRERYL 306 Query: 310 ALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDISVPGYEKGN 369 A + L+V E TD+G ++S+ ++ I EG ++ G +++PG G Sbjct: 307 AKVRALRVGDPREAATDLGALVSREHFDKVTGCIAQARAEGGRVLCGGDALALPGPLAGG 366 Query: 370 -FVGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSGAA 428 +V PT+ G+ PE QEIFGPV+ ++ D QA+A+ N +G L+T + Sbjct: 367 WYVAPTVIEGLGPETATNQQEIFGPVVTLIPFDDEAQALAIANGTGYGLAASLWTTDLSR 426 Query: 429 ARKFQTEIDVGQVGINIPI--PVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTA 486 A +F ++D G V IN + + P F G++ S +G G G + ++F+T+ K + Sbjct: 427 AHRFGAQLDFGIVWINCWLLRDLRTP---FGGAKQSGVGREG--GVEALRFFTEPKNICI 481 Query: 487 RW 488 R+ Sbjct: 482 RY 483 Lambda K H 0.319 0.135 0.397 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: 566 Number of extensions: 30 Number of successful extensions: 5 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: 505 Length of database: 483 Length adjustment: 34 Effective length of query: 471 Effective length of database: 449 Effective search space: 211479 Effective search space used: 211479 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 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