Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate PP_4154 PP_4154 putative class 3 aminotransferase
Query= BRENDA::Q9SR86 (481 letters) >FitnessBrowser__Putida:PP_4154 Length = 976 Score = 285 bits (729), Expect = 5e-81 Identities = 167/430 (38%), Positives = 239/430 (55%), Gaps = 11/430 (2%) Query: 59 PSTAEIIAKRREFLSPALFHFYNTPLNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCH 118 P ++A+R + + H+Y P +I Y+ D GR YLD +A + GH H Sbjct: 548 PDPQALLARRDASFARSQKHYYAQPPHIERGWRNYLIDMQGRSYLDMLNNVAVL--GHGH 605 Query: 119 PEVVNSVVKQLKLINHSTILYLNHTISDFAEALVSTLPGDLKVVFFTNSGTEANELAMMM 178 P +V +Q L+N ++ + I++F+E L+ P VF NSGTEAN+LA+ + Sbjct: 606 PRMVAESARQWSLLNTNSRFHYA-AITEFSERLLDLAPEGFDRVFMVNSGTEANDLAIRL 664 Query: 179 ARLYTGCNDIVSLRNSYHGNAAATMGAT---AQSNWKFNVVQSGVHHAINPDPYRGIF-G 234 A Y+G D++S+ +YHG + AT + A + VH P+ +RG F G Sbjct: 665 AWAYSGGRDLLSVLEAYHGWSVATDAISTSIADNPQALETRPDWVHPVEAPNTFRGRFRG 724 Query: 235 SDGEK-YASDVH-DLIQFGTSG-QVAGFIGESIQGVGGIVELAPGYLPAAYDIVRKAGGV 291 +D Y DV L G Q+AG I E + G G + L GYL AAY VR GGV Sbjct: 725 ADSAADYLQDVDAKLADLDARGRQLAGIICEPVYGNAGGISLPAGYLRAAYAKVRARGGV 784 Query: 292 CIADEVQSGFARTGTHFWGFQSHGVIPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRRSY 351 CIADEVQ G+ R G +FWGF+ GV+PDI+TMAKG+GNG PLG V+T EIA L Y Sbjct: 785 CIADEVQVGYGRLGEYFWGFEEQGVVPDIITMAKGMGNGQPLGVVITRREIAEALEAEGY 844 Query: 352 -FNTFGGNPMCTAAGHAVLRVLHEEKLQENANLVGSHLKRRLTLLKNKYELIGDVRGRGL 410 F++ GG+P+ G AVL V+ EE L +NA G + K RL L +K+ L G G G Sbjct: 845 FFSSAGGSPVSCRIGMAVLDVMQEEGLWDNARDTGRYFKARLQALVDKHPLAGAAHGSGF 904 Query: 411 MLGVEFVKDRDLKTPAKAETLHLMDQMKEMGVLVGKGGFYGNVFRITPPLCFTLSDADFL 470 LG+E V+DR PA ET+ L D+++++G+ + G Y N+ +I PP+C + + D+ Sbjct: 905 YLGLELVRDRTTLEPATEETMMLCDRLRDLGIFMQPTGDYLNILKIKPPMCTSRASVDYF 964 Query: 471 VDVMDHAMSK 480 VD +D + + Sbjct: 965 VDSIDRVLGE 974 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: 991 Number of extensions: 42 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: 481 Length of database: 976 Length adjustment: 39 Effective length of query: 442 Effective length of database: 937 Effective search space: 414154 Effective search space used: 414154 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: 54 (25.4 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