Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate 6938540 Sama_2643 putative aminotransferase (RefSeq)
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__SB2B:6938540 Length = 460 Score = 160 bits (406), Expect = 6e-44 Identities = 128/414 (30%), Positives = 207/414 (50%), Gaps = 36/414 (8%) Query: 88 YLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTIY--LHHAIGDFAEA 145 Y++D G + LDA AG+ V+ G+ I +A Q + L + H A Sbjct: 45 YIWDAKGNKLLDAMAGLWCVNVGYGRKSIADAAYAQLQTLPFYNNFFQCTHEPAIRLASK 104 Query: 146 LAAKMPGNLKVVYFVNSGSEANELAMMMARLY------TGSLEMISLRNAYHGGSSNTIG 199 +A+ PG++ V+F SGSEAN+ + M R Y +IS +NAYHG +T+ Sbjct: 105 IASLAPGHMNRVFFTGSGSEANDTNLRMVRRYWDLKGMPSKKTIISRKNAYHG---STVA 161 Query: 200 LTALNTWKYPLPQGE--IHHVVNPD-PYRGVFGSDGSLYAKDVHDH-------IEYGTSG 249 +L + QG+ I +V+ D PY G D S A + +E G Sbjct: 162 GASLGGMGFMHQQGDLPIPGIVHIDQPYWFGEGRDMSPEAFGIKTAQALEAKILELGED- 220 Query: 250 KVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYWGFQTQ 309 KVA FIAE QG GG + Y + I+ + I DEV +GFGRTG +++ QT Sbjct: 221 KVAAFIAEPFQGAGGVIIPPDSYWNEIKRILEKYNILFILDEVISGFGRTG-NWFAAQTL 279 Query: 310 DVVPDIVTMAKGIGNG-LPLGAVVTTPEIASVLASK----ILFNTFGGNPVCSAGGLAVL 364 + PD++T+AKG+ +G +P+G V+ + +A VL S T+ G+PV +A L + Sbjct: 280 GLKPDLITIAKGMTSGYIPMGGVIVSDRVADVLISDGGEFAHGFTYSGHPVAAAVALENI 339 Query: 365 NVIDKEKRQEHC-AEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKA 423 ++++E+ + + G +L RL+ + H ++G+VRG G++ IELV+D+ + Sbjct: 340 RILEEERLVDKVRTDTGPYLQDRLQTL-SAHPLVGEVRGMGMVGAIELVADKHSMVRFGS 398 Query: 424 ETS---VLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDDADFLVDALDYSIS 474 E S + E E G+++ G+ I PP+C T+D+ D L+ ++S Sbjct: 399 EISAGMLCREACIESGLVM---RAVGDTMIISPPLCITRDEIDELIFKASQALS 449 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: 511 Number of extensions: 26 Number of successful extensions: 7 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: 460 Length adjustment: 33 Effective length of query: 443 Effective length of database: 427 Effective search space: 189161 Effective search space used: 189161 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 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