Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate AO356_10035 AO356_10035 hypothetical protein
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_10035 Length = 970 Score = 298 bits (763), Expect = 6e-85 Identities = 178/445 (40%), Positives = 246/445 (55%), Gaps = 30/445 (6%) Query: 36 DAPPHIPPFVHQPRPYKGPSADEVLQKRKKFLGPSLFHYYQKPLNIVEGKMQYLYDESGR 95 DA P + P + +L +R S HYY P I G +L D GR Sbjct: 537 DAEPEVDP-------------EALLARRDASFARSQKHYYVDPPRIERGWRNHLIDMQGR 583 Query: 96 RYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTIYLHHAIGDFAEALAAKMPGNLK 155 YLD + + GH HP + Q LL + + + + AI +F+E L A P N+ Sbjct: 584 SYLDMLNNVAVL--GHGHPRMAAVAARQWSLL-NTNSRFHYAAIAEFSERLLALSPSNMD 640 Query: 156 VVYFVNSGSEANELAMMMARLYTGSLEMISLRNAYHGGSSNTIGLTALNTWKYPLPQGE- 214 V+ VNSG+EAN+LA+ +A Y+G +M+S+ AYHG S + A++T PQ Sbjct: 641 RVFLVNSGTEANDLAIRLAWAYSGGRDMLSVLEAYHGWS---VAADAVSTSIADNPQALS 697 Query: 215 -----IHHVVNPDPYRGVFGSDGSL--YAKDVHDHIEYGTSGK--VAGFIAETIQGVGGA 265 +H V P+ YRG F S Y + V ++ K +AGFI E + G G Sbjct: 698 SRPDWVHPVTAPNTYRGEFRGPDSAPDYVRSVEHNLAKIAESKRQLAGFICEPVYGNAGG 757 Query: 266 VELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYWGFQTQDVVPDIVTMAKGIGNG 325 + L PGYLK VY +VR GGVCIADEVQ G+GR G +WGF+ Q VVPDI+TMAKG+GNG Sbjct: 758 IALPPGYLKQVYAMVRERGGVCIADEVQVGYGRMGEFFWGFEEQGVVPDIITMAKGMGNG 817 Query: 326 LPLGAVVTTPEIASVL-ASKILFNTFGGNPVCSAGGLAVLNVIDKEKRQEHCAEVGSHLI 384 PLGAV+T EIA L A F++ GG+PV G+AVL+V++++ E+ VG H Sbjct: 818 QPLGAVITRREIAEALEAEGYFFSSAGGSPVSCQIGMAVLDVMEEDNLWENARVVGGHFK 877 Query: 385 QRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKAETSVLFEQLRELGILVGKGGL 444 RL+ + ++ ++G V G G +G+EL+ DR+ PA ET L +LRELGI + G Sbjct: 878 ARLEALIDQYPLVGAVHGSGFYLGVELIRDRETLEPATEETMALCNRLRELGIFMQPTGD 937 Query: 445 HGNVFRIKPPMCFTKDDADFLVDAL 469 + N+ +IKPPM T+ DF VD L Sbjct: 938 YLNILKIKPPMVTTRQSVDFFVDML 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: 1033 Number of extensions: 53 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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