Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate GFF262 PS417_01335 hypothetical protein
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__WCS417:GFF262 Length = 966 Score = 301 bits (770), Expect = 9e-86 Identities = 179/448 (39%), Positives = 253/448 (56%), Gaps = 19/448 (4%) Query: 33 SIADAPPHIPPFVHQPRPYKGPSADEVLQKRKKFLGPSLFHYYQKPLNIVEGKMQYLYDE 92 S+ +P + P P A +L +R S HYY P I G +L D Sbjct: 519 SLCPSPAALLGLACDAEPELDPEA--LLARRDASFARSQKHYYADPPRIERGWRNHLIDM 576 Query: 93 SGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTIYLHHAIGDFAEALAAKMPG 152 GR YLD + + GH HP + Q LL + + + + A+ +F+E L A P Sbjct: 577 QGRSYLDMLNNVAVL--GHGHPRMAAVAARQWSLL-NTNSRFHYAAVTEFSERLLALAPE 633 Query: 153 NLKVVYFVNSGSEANELAMMMARLYTGSLEMISLRNAYHGGSSNTIGLTALNTWKYPLPQ 212 + V+ VNSG+EAN+LA+ +A Y+G +M+S+ AYHG S + A++T PQ Sbjct: 634 GMDRVFLVNSGTEANDLAIRLAWAYSGGRDMLSVLEAYHGWS---VAADAVSTSIADNPQ 690 Query: 213 GE------IHHVVNPDPYRGVFGSDGSL--YAKDVHDHIEY--GTSGKVAGFIAETIQGV 262 +H V P+ YRG F S Y + V ++ + ++AGFI E + G Sbjct: 691 ALSSRPDWVHPVTAPNTYRGEFRGQDSAPDYVRSVEHNLAKIAASQRQLAGFICEPVYGN 750 Query: 263 GGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYWGFQTQDVVPDIVTMAKGI 322 G + L PGYL+ VY +VR GGVCIADEVQ G+GR G +WGF+ Q VVPDI+TMAKG+ Sbjct: 751 AGGISLPPGYLQQVYGLVRAQGGVCIADEVQVGYGRMGHFFWGFEEQGVVPDIITMAKGM 810 Query: 323 GNGLPLGAVVTTPEIASVL-ASKILFNTFGGNPVCSAGGLAVLNVIDKEKRQEHCAEVGS 381 GNG PLGAV+T EIA L A F++ GG+PV G+AVL+V+++EK E+ VG Sbjct: 811 GNGQPLGAVITRREIAEALEAEGYFFSSSGGSPVSCRIGMAVLDVMEEEKLWENARVVGG 870 Query: 382 HLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKAETSVLFEQLRELGILVGK 441 H RL+++ RH ++G V G G +G+ELV DR+ PA ET++L ++LRELGI + Sbjct: 871 HFKARLEELIDRHPLVGAVHGSGFYLGLELVRDRQTLEPATEETTLLCDRLRELGIFMQP 930 Query: 442 GGLHGNVFRIKPPMCFTKDDADFLVDAL 469 G + N+ +IKPPM ++ DF VD L Sbjct: 931 TGDYLNILKIKPPMVTSRHSVDFFVDML 958 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: 1051 Number of extensions: 53 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: 966 Length adjustment: 39 Effective length of query: 437 Effective length of database: 927 Effective search space: 405099 Effective search space used: 405099 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