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_004222844.1 KVAR_RS20445 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_000025465.1:WP_004222844.1 Length = 400 Score = 398 bits (1023), Expect = e-115 Identities = 195/392 (49%), Positives = 268/392 (68%) Query: 15 ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74 A R+ ++ VS + + +A + +G V+ L GEPDF TP HV AA A G+T+Y Sbjct: 5 ADRLKNVTVSASVAMTQKARDLAAQGIDVVGLSTGEPDFPTPPHVIDAAYAAACAGDTRY 64 Query: 75 TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134 DGTP L+ AI+ KF R+N L Y++ +I A GA+QI+FNAMMA+++PGDEV+IP P Sbjct: 65 PPTDGTPALRAAIQRKFLRDNELRYDISQILTAGGARQIIFNAMMATINPGDEVLIPMPS 124 Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194 W SY+DIV G PV + C GF+ + +EAAITP+T+W+LLN PSNP+G+ + A Sbjct: 125 WISYADIVKFAGGTPVPVPCHEEYGFKPLPQDVEAAITPKTKWLLLNYPSNPTGSVATHA 184 Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254 + L E LLRHPH+W++ DD+YEH++YDG +F T AQ+EP L +R LTVNGVSKAY+MT Sbjct: 185 ELLALGETLLRHPHIWIMTDDIYEHLLYDGVKFWTLAQVEPRLYDRVLTVNGVSKAYSMT 244 Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314 GWR+G+ GGP LIKAM+ V +Q + ++++QA SVAAL+GPQ L ER E +++RRD Sbjct: 245 GWRLGFCGGPLTLIKAMSNVNTQNSGGVTTLAQAGSVAALDGPQGLLAERAEIYRQRRDY 304 Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374 V+ L I GL C P+GAFY F +GK + SG I +D DF L+E+ HV V Sbjct: 305 VLERLAGIPGLRCHKPQGAFYLFVNIEAFIGKTSASGHFIASDADFVMALIEEQHVVTVQ 364 Query: 375 GSAFGLSPFFRISYATSEAELKEALERIAAAC 406 G+A+G+SP+FR+SYATS L+ +R+AA C Sbjct: 365 GAAYGMSPYFRLSYATSMERLQTGCDRLAAFC 396 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: 494 Number of extensions: 19 Number of successful extensions: 1 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: 400 Length adjustment: 31 Effective length of query: 379 Effective length of database: 369 Effective search space: 139851 Effective search space used: 139851 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 Jul 25 2024. The underlying query database was built on Jul 25 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