Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate Ac3H11_4340 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
Query= BRENDA::A0A081YAY7 (498 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4340 Length = 505 Score = 723 bits (1867), Expect = 0.0 Identities = 353/496 (71%), Positives = 408/496 (82%) Query: 2 TLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPP 61 T + HLI G+ +AD RT VFNP+TG++ V LA + T++ AI +A+AAFPAWRNTPP Sbjct: 9 TTVGHLIDGKSVADAERTQPVFNPATGQSTTSVALASKATVEAAIASAEAAFPAWRNTPP 68 Query: 62 AKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGE 121 KRA+V+ + K LLE N ++I LI+ EHGK + DA GEL+RGIENVEYA+ APE+LKGE Sbjct: 69 LKRARVMSKLKVLLEENADKIAALITAEHGKVLADAHGELQRGIENVEYASYAPELLKGE 128 Query: 122 YSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSST 181 +SRNVGP+ID+WS+FQ +GV AGITPFNFPAMVPLWM+P+A+ACGNTF+LKPSERDPSST Sbjct: 129 HSRNVGPSIDSWSEFQALGVTAGITPFNFPAMVPLWMWPMAVACGNTFVLKPSERDPSST 188 Query: 182 LLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGK 241 L IA+L EAGLP GVLNVV+GDK AVD L++ P VKA+SFVGSTPIAEYIYSEG K GK Sbjct: 189 LFIAQLALEAGLPPGVLNVVNGDKLAVDTLLQDPRVKAVSFVGSTPIAEYIYSEGCKHGK 248 Query: 242 RVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKL 301 RVQALGGAKNHAVLMPDAD+ NAVSALMGAAYGSCGERCMAI + V VGD + DA++ L Sbjct: 249 RVQALGGAKNHAVLMPDADVGNAVSALMGAAYGSCGERCMAIPLLVAVGDAVGDAVIAGL 308 Query: 302 VPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENG 361 +I +K+G GT DMGPLVT +KV Y+D+GV +GA LVVDGRG KVAGHE G Sbjct: 309 KTEIAKMKVGPGTDNSNDMGPLVTKPHFEKVKAYVDSGVTEGATLVVDGRGVKVAGHEEG 368 Query: 362 FFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEA 421 +FLG LFD V P M IY+EEIFGPVL +VRV +L+EAMQLINDHEYGNGTCIFTRDGEA Sbjct: 369 YFLGACLFDNVKPGMKIYQEEIFGPVLGVVRVKTLQEAMQLINDHEYGNGTCIFTRDGEA 428 Query: 422 ARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRW 481 AR F D I+VGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPD VRFYTKRK ITQRW Sbjct: 429 ARYFTDHIQVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTITQRW 488 Query: 482 PQRKSHEAAQFAFPSN 497 P E A F+FPS+ Sbjct: 489 PSAGVREGAVFSFPSS 504 Lambda K H 0.319 0.137 0.411 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: 828 Number of extensions: 20 Number of successful extensions: 1 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: 498 Length of database: 505 Length adjustment: 34 Effective length of query: 464 Effective length of database: 471 Effective search space: 218544 Effective search space used: 218544 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:
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