Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate PfGW456L13_398 4-aminobutyrate aminotransferase (EC 2.6.1.19)
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_398 Length = 970 Score = 294 bits (753), Expect = 8e-84 Identities = 171/422 (40%), Positives = 242/422 (57%), Gaps = 17/422 (4%) Query: 59 VLQKRKKFLGPSLFHYYQKPLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILN 118 +L +R + HYY P I G +L D GR YLD + + GH HP + Sbjct: 547 LLARRDASFARTQKHYYVDPPRIERGWRNHLIDMQGRSYLDMLNNVAVL--GHGHPRMAA 604 Query: 119 AITEQSKLLQHATTIYLHHAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLYT 178 + Q LL + + + + A+ +F+E L P + V+ VNSGSEAN+LA+ +A Y+ Sbjct: 605 VASRQWSLL-NTNSRFNYAAVAEFSERLLKLSPDGMDRVFLVNSGSEANDLAIRLAWAYS 663 Query: 179 GSLEMISLRNAYHGGSSNTIGLTALNTWKYPLPQGE------IHHVVNPDPYRGVFGSDG 232 G +M+S+ AYHG T+G +++T P+ +H V P+ YRG F Sbjct: 664 GGRDMLSVLEAYHGW---TVGADSVSTSIADNPKALSSRPDWVHPVTAPNTYRGEFRGPD 720 Query: 233 SL--YAKDVHDHIEYGTSGK--VAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCI 288 S Y + V ++ K +AGFI E + G G + L PGYLK VY +VR GGVCI Sbjct: 721 SAPDYVRSVEHNLAKIAEQKRQLAGFICEPVYGNAGGISLPPGYLKQVYAMVRARGGVCI 780 Query: 289 ADEVQTGFGRTGSHYWGFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVL-ASKILF 347 ADEVQ G+GR G +WGF+ Q VVPDI+TMAKG+GNG PLGAV+T EIA L A F Sbjct: 781 ADEVQVGYGRMGDFFWGFEEQGVVPDIITMAKGMGNGQPLGAVITRREIAEALEAEGYFF 840 Query: 348 NTFGGNPVCSAGGLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMV 407 ++ GG+PV G+AVL+V+ +EK E+ VG H +RL+ + H ++G V G G + Sbjct: 841 SSAGGSPVSCQVGMAVLDVMQEEKLWENAQVVGGHFKERLEALIDIHPLVGAVHGSGFYL 900 Query: 408 GIELVSDRKDKTPAKAETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDDADFLVD 467 G+EL+ +R+ PA ET+ L ++LRELGI + G + N+ +IKPPM ++ DF VD Sbjct: 901 GVELIRNRETLEPATEETTALCDRLRELGIFMQPTGDYLNILKIKPPMVTSRQSVDFFVD 960 Query: 468 AL 469 L Sbjct: 961 ML 962 Lambda K H 0.320 0.138 0.412 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: 1069 Number of extensions: 50 Number of successful extensions: 4 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: 476 Length of database: 970 Length adjustment: 39 Effective length of query: 437 Effective length of database: 931 Effective search space: 406847 Effective search space used: 406847 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 Aug 03 2021. The underlying query database was built on Aug 03 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, or see changes to Amino acid biosynthesis since the publication.
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