Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate Pf1N1B4_1663 4-aminobutyrate aminotransferase (EC 2.6.1.19)
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1663 Length = 970 Score = 293 bits (751), Expect = 1e-83 Identities = 172/422 (40%), Positives = 243/422 (57%), Gaps = 17/422 (4%) Query: 59 VLQKRKKFLGPSLFHYYQKPLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILN 118 +L +R S HYY P I G +L D GR YLD + + GH HP + Sbjct: 547 LLARRDASFARSQKHYYVDPPRIERGWRNHLIDMQGRSYLDMLNNVAVL--GHGHPRMAA 604 Query: 119 AITEQSKLLQHATTIYLHHAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLYT 178 + Q LL + + + + AI +F+E L P N+ V+ VNSG+EAN+LA+ +A Y+ Sbjct: 605 VASRQWSLL-NTNSRFHYAAIAEFSERLLKLAPDNMDRVFLVNSGTEANDLAIRLAWAYS 663 Query: 179 GSLEMISLRNAYHGGSSNTIGLTALNTWKYPLPQGE------IHHVVNPDPYRGVFGSDG 232 G +M+S+ AYHG S + A++T P+ +H V P+ YRG F Sbjct: 664 GGRDMLSVLEAYHGWS---VAADAVSTSIADNPKALSSRPDWVHPVTAPNTYRGEFRGID 720 Query: 233 SL--YAKDVHDHIEYGTSGK--VAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCI 288 S Y + V ++ K +AGFI E + G G + L PGYLK VY +VR GGVCI Sbjct: 721 SAPDYVRSVEHNLAKIAEQKRQLAGFICEPVYGNAGGISLPPGYLKQVYALVRAQGGVCI 780 Query: 289 ADEVQTGFGRTGSHYWGFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVL-ASKILF 347 ADEVQ G+GR G +WGF+ Q VVPDI+TMAKG+GNG PLGAV+T EIA L A F Sbjct: 781 ADEVQVGYGRMGKFFWGFEEQGVVPDIITMAKGMGNGQPLGAVITRREIAEALEAEGYFF 840 Query: 348 NTFGGNPVCSAGGLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMV 407 ++ GG+PV G+AVL+V+++EK E+ VG + +RL+ + +H ++G V G G + Sbjct: 841 SSAGGSPVSCQIGMAVLDVMEEEKLWENAQVVGGYFKERLEALIDQHPLVGAVHGSGFYL 900 Query: 408 GIELVSDRKDKTPAKAETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDDADFLVD 467 G+EL+ +R+ PA ET+ L ++LRELGI + G + N+ +IKPPM + DF VD Sbjct: 901 GVELIRNRETLEPATEETTALCDRLRELGIFMQPTGDYLNILKIKPPMVTSHQSVDFFVD 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: 1023 Number of extensions: 46 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 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