Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate WP_057508832.1 ABB28_RS11865 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_001431535.1:WP_057508832.1 Length = 425 Score = 166 bits (421), Expect = 9e-46 Identities = 123/408 (30%), Positives = 197/408 (48%), Gaps = 31/408 (7%) Query: 17 RISSIGVSEILKIGARAAAMKREGKPVIILGAGEPD---FDTPEHVKQAASDAIHRGETK 73 R+S + ++ RA ++ +G+ +I L G P F PEH+++A +D + R + Sbjct: 14 RLSEVRYEIRGELARRARELEAQGRTLIKLNIGNPGNFGFRAPEHLQRAIADDMGRTDP- 72 Query: 74 YTALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTP 133 YT G PE ++AI + R D + + G +++ ++ A L+PGDEV++P+P Sbjct: 73 YTHQQGLPEAREAIAAAYARRGAPDAHPDRVFIGNGVSELIDLSLRALLNPGDEVLVPSP 132 Query: 134 YWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSA 193 + +S + +G+PV C +GF+ ++EA ++ RTR ++L +P+NPSGA+YS Sbjct: 133 DYPLWSAATILNDGRPVYYRCAPENGFQPDPSEIEALVSSRTRAIVLINPNNPSGASYS- 191 Query: 194 ADYRPLLE---VLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKA 250 R LLE + R ++ L+VD++Y+ I+YD F A L +T +G+SK Sbjct: 192 ---RELLERIVAIARKHNLLLMVDEIYDQILYDDAVFQPVAPLAG--DQPCITFSGLSKV 246 Query: 251 YAMTGWRIGYA-----GGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERT 305 + GWR+G+A G +A + S C + Q A AA+NGP T Sbjct: 247 HRACGWRVGWAMLSGDAGRLGEFRAAMDLLSALRLCANVPGQYAIDAAVNGPDTITPLCT 306 Query: 306 ES--FQRRRDLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAY 363 R V++ A + L P GA Y F G K D DF Sbjct: 307 PGGRLYETRRAVIDACAASEHLSLVAPAGALYAFPAVVGDAAKGL-------DDHDFALD 359 Query: 364 LLEDAHVAVVPGSAFGLSPF---FRISYATSEAELKEALERIAAACDR 408 L+ D V VVPGS+F + P+ FR++ ++E RI A R Sbjct: 360 LMTDEGVLVVPGSSFNV-PYRHHFRVTLLPEATVMREVFSRIDRALAR 406 Lambda K H 0.318 0.134 0.393 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: 483 Number of extensions: 21 Number of successful extensions: 5 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: 410 Length of database: 425 Length adjustment: 32 Effective length of query: 378 Effective length of database: 393 Effective search space: 148554 Effective search space used: 148554 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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