Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate Ac3H11_1332 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= BRENDA::Q9SR86 (481 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1332 Length = 398 Score = 187 bits (474), Expect = 7e-52 Identities = 139/419 (33%), Positives = 209/419 (49%), Gaps = 49/419 (11%) Query: 71 FLSPALFHFYNT----PLNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCHPEVVNSVV 126 F+ A H NT P+ + + V+D NG+ Y+D GGIA + GH H ++V ++ Sbjct: 4 FIEAASPHVMNTYGRVPIALERGQGCRVWDVNGKEYIDGLGGIAVNTLGHNHGKLVPALQ 63 Query: 127 KQLKLINHSTILYLNHTISDFAEALVSTLPGDLKVVFFTNSGTEANELAMMMARLY---- 182 Q+ + H++ Y A LV ++ VFF NSG EANE A+ +AR + Sbjct: 64 DQIAKLIHTSNYYHVPLQEKLATKLVEL--SGMQNVFFCNSGLEANEAALKIARKFGVDK 121 Query: 183 -TGCNDIVSLRNSYHGNAAATMGATAQSNWKFNVVQSGVHHAINPDPYRGIFGSDGEKYA 241 +IV ++HG + ATM AT NP + G FG E + Sbjct: 122 GIAKPEIVVYEKAFHGRSIATMSATG-----------------NPKIHNG-FGPLVEGFV 163 Query: 242 ----SDVHDLIQF--GTSGQVAGFIGESIQGVGGIVELAPGYLPAAYDIVRKAGGVCIAD 295 +D+ + Q G VA F E+IQG GGI + YL + + G + + D Sbjct: 164 RVPMNDIEAIKQATEGNPNVVAVFF-ETIQGEGGINGMRIEYLQQLRKLCDERGWLMMID 222 Query: 296 EVQSGFARTGTHFWGFQSHGVIPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRRSYFNTF 355 EVQ G RTG F Q G++PD++ +AKG+G+G+P+GAVV P+ A VL ++ TF Sbjct: 223 EVQCGMGRTGKWF-AHQWAGIVPDVMPLAKGLGSGVPIGAVVAGPKAANVLQPGNHGTTF 281 Query: 356 GGNPMCTAAGHAVLRVLHEEKLQENANLVGSHLKRRLTLLKNKYELIGDVRGRGLMLGVE 415 GGNP+ AG +R++ E+ L NA VG HL+ L + ++RG+GLMLG+E Sbjct: 282 GGNPLAMRAGVETIRIMEEDGLLHNAAQVGDHLRAALQRELGSLPGVKEIRGQGLMLGIE 341 Query: 416 FVKDRDLKTPAKAETLHLMDQMKEMGVLVGKGGFYGNVFRITPPLCFTLSDADFLVDVM 474 L P A L+ + E G+L+ +V R+ PPL T ++AD +V ++ Sbjct: 342 ------LNKPCGA----LIGRAAEAGLLLSVTA--DSVIRLVPPLILTTAEADAIVAIL 388 Lambda K H 0.320 0.136 0.406 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: 465 Number of extensions: 23 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: 481 Length of database: 398 Length adjustment: 32 Effective length of query: 449 Effective length of database: 366 Effective search space: 164334 Effective search space used: 164334 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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