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_110206897.1 DNK54_RS10510 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_003194585.1:WP_110206897.1 Length = 394 Score = 190 bits (483), Expect = 6e-53 Identities = 126/370 (34%), Positives = 192/370 (51%), Gaps = 23/370 (6%) Query: 44 IILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKKAIREKFQRENGLAYELD- 102 I LG G PD D P V +AA A+ G +Y G EL++AI R GL + D Sbjct: 29 INLGQGFPDADGPASVVEAAVSALRNGRNQYAPGIGVRELREAIARHQHRHYGLDLDPDT 88 Query: 103 EITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHICEG--KPVLIACDASSGF 160 E+ V TGA + + A++ +DPGDEV++ PY+ SY ++ G +PV + + + Sbjct: 89 EVVVTTGATEGIAAALLGLVDPGDEVVVLEPYYDSYLAMIAFAGGVRRPVTLR---APDY 145 Query: 161 RLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLRHPHVWLLVDDMYEHI 220 RL L+AA+T RTR +LLNSP NP+G + + + ++ + H V ++ D++YEH+ Sbjct: 146 RLDVAALQAAVTDRTRVILLNSPHNPTGTVLRPEELQAIADLAIEHDLV-VVTDEVYEHL 204 Query: 221 VYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGPRELIKAMAVVQSQATS 280 V+DG R V L PG+ RT+T++ K+++ TGW++G+A GP +L+ A+ + + Sbjct: 205 VFDGHRHVPLCTL-PGMFERTVTLSSAGKSFSFTGWKVGWATGPADLVGAVLAAKQWLSF 263 Query: 281 CPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAIDGLDCRVPEGAFYTFSGC 340 S Q A AL+ +E Q RRDL+ +GL A+D LD R+PEG ++ + Sbjct: 264 TSGSPLQPAIAHALDHEWRAYEELAADLQLRRDLLCSGLAALD-LDVRIPEGTYFALT-- 320 Query: 341 AGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAF-----GLSPFFRISYATSEAEL 395 V P G+ FC L E A V +P F R ++ A Sbjct: 321 -DVRALGWPDGRA------FCLALPERAGVVAIPTQGFHDDQEAGRHLVRWAFCKDAAVT 373 Query: 396 KEALERIAAA 405 E LER+A A Sbjct: 374 TEGLERLARA 383 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: 380 Number of extensions: 22 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: 410 Length of database: 394 Length adjustment: 31 Effective length of query: 379 Effective length of database: 363 Effective search space: 137577 Effective search space used: 137577 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