Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate WP_011879617.1 aspartate aminotransferase family protein
Query= SwissProt::Q940M2 (476 letters) >NCBI__GCF_000016205.1:WP_011879617.1 Length = 464 Score = 181 bits (460), Expect = 4e-50 Identities = 137/455 (30%), Positives = 226/455 (49%), Gaps = 36/455 (7%) Query: 55 SADEVLQK-RKKFLGPSLFHYYQK----PLNIVEGKMQ-YLYDESGRRYLDAFAGIVTVS 108 S D +L+ R F+ PS Y + P IV G ++ D GRRY+DAFAG+ V+ Sbjct: 4 SIDALLRADRAHFMHPSTHAYDHESGALPGRIVRGAHGIHIEDHEGRRYIDAFAGLYCVN 63 Query: 109 CGHCHPDILNAITEQSKLLQHATTIYLH--HAIGDFAEALAAKMPGNLKVVYFVNSGSEA 166 G+ ++ +A+ EQ+K L + T H AI + + + P +K VY+ SGS+A Sbjct: 64 IGYGRTEVADAMHEQAKQLAYYHTYVGHASDAIIELSSRIIECAPVGMKKVYYGMSGSDA 123 Query: 167 NELAMMMARLYTGSL------EMISLRNAYHGGSSNTIGLTALNTWK--YPLPQGEIHHV 218 NE + + Y L ++IS YHG T LT L ++ + LP + H Sbjct: 124 NETQVKLVWYYNNVLGRPNKKKIISRERGYHGSGIVTGSLTGLPSFHQHFDLPIDRVKHT 183 Query: 219 VNPDPYRGV-FGSDGSLYAKDVHDHIEYGTSGK----VAGFIAETIQGVGGAVELAPGYL 273 V P YR G + + D +E + + +A FIAE + G GG + GY Sbjct: 184 VCPHWYRNAPVGMSEAQFVAYCVDELEKLIAREGADTIAAFIAEPVMGTGGIIAPPAGYW 243 Query: 274 KSVYEIVRNAGGVCIADEVQTGFGRTGSHYWGFQTQDVVPDIVTMAKGIGNGL-PLGAVV 332 ++ ++R + I+DEV GFGR GS G Q + PD++T+AKG+ + PL V+ Sbjct: 244 PAIQAVLRQHDILLISDEVVCGFGRLGSKM-GAQHFGIEPDLITVAKGLTSAYAPLSGVI 302 Query: 333 TTPEIASVLASKILFN-------TFGGNPVCSAGGLAVLNVIDKEKRQEHCAEVGSHLIQ 385 ++ V+A + T+ G+PVC+A LA L ++++E + AEVG++ Sbjct: 303 VGDKVWDVIARGSQAHGPMGHGWTYSGHPVCAAAALANLAILERENLVGNAAEVGAYFGA 362 Query: 386 RLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTP----AKAETSVLFEQLRELGILVGK 441 +L+D H ++G+VR G++ +E ++DR +TP K V LR G+ + + Sbjct: 363 KLRDAFGAHPLVGEVRSVGMLAALEFMADRDARTPFDPALKIGAQVSAAALRR-GV-IAR 420 Query: 442 GGLHGNVFRIKPPMCFTKDDADFLVDALDYSISRL 476 HG++ PP+ T+ +AD +V + ++ + Sbjct: 421 AMPHGDILGFAPPLVMTRAEADEIVGIVKEAVDEV 455 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: 550 Number of extensions: 34 Number of successful extensions: 6 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: 464 Length adjustment: 33 Effective length of query: 443 Effective length of database: 431 Effective search space: 190933 Effective search space used: 190933 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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