Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate PfGW456L13_4910 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4910 Length = 413 Score = 197 bits (501), Expect = 6e-55 Identities = 128/403 (31%), Positives = 211/403 (52%), Gaps = 41/403 (10%) Query: 74 YYQKPLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTI 133 Y L+ +G L+D++GR YLDA AG+ + GH HP I+ AITEQ+ LL H + + Sbjct: 32 YQPLALSFNKGLGTRLWDQAGREYLDAVAGVAVTNVGHSHPKIVAAITEQAGLLLHTSNL 91 Query: 134 YLHHAIGDFAEALAAKMP--GNLKVVYFVNSGSEANELAMMMARLYTG--SLE---MISL 186 Y D+ + LA K+ + +F NSG+EANE A+ +ARL+ +E ++ + Sbjct: 92 YSI----DWQQRLAQKLTQLAGMDRAFFNNSGAEANETALKIARLHGWHKGIEQPLVVVM 147 Query: 187 RNAYHGGSSNTIGLT---ALNTWKYPLPQGEIHHVVNPDPYRGVFGSDGSLYAKDVHDHI 243 NA+HG + T+ + A+ LP D + FG G+L D + Sbjct: 148 ENAFHGRTLGTLSASDGPAVRLGFNKLPG---------DFVKVPFGDLGAL------DKV 192 Query: 244 EYGTSGKVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHY 303 + ++ + E IQG G PGYL +V E+ + + DE+QTG GRTG + Sbjct: 193 QQAFGSRIVAVLMEPIQGESGVQLAPPGYLSAVRELCNRRSWLLMLDEIQTGIGRTGQ-W 251 Query: 304 WGFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVLASKILFNTFGGNPVCSAGGLAV 363 + FQ + +VPD++T+AKG+GNG+P+GA + + A + +TFGGNP+ G V Sbjct: 252 FAFQHEGIVPDVMTLAKGLGNGVPIGACLARGKAAELFTPGSHGSTFGGNPLACRVGCTV 311 Query: 364 LNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKA 423 L++++++ E+ G+ L++RL+ + + +RG+GLM+GIEL +D + A Sbjct: 312 LDIVEEQGLLENARLQGARLLERLRTELAGNPNVSQIRGQGLMIGIELKQPIRDLSLIAA 371 Query: 424 ETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDDADFLV 466 R+ G+L+ GN R+ PP+ + + + +V Sbjct: 372 ---------RDHGLLINV--TRGNTIRLLPPLTLDEREVEMIV 403 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: 437 Number of extensions: 19 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: 413 Length adjustment: 32 Effective length of query: 444 Effective length of database: 381 Effective search space: 169164 Effective search space used: 169164 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 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:
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