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_012706371.1 NGR_RS01505 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_000018545.1:WP_012706371.1 Length = 400 Score = 416 bits (1069), Expect = e-121 Identities = 206/393 (52%), Positives = 273/393 (69%) Query: 17 RISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTA 76 R SI S + + A AM+ +G+ V+ L GEPDF+TP+ + +AA A+ G+T+YT Sbjct: 7 RAGSIKSSPSMAVSLAAKAMRAKGESVVDLSLGEPDFETPDFIVEAAIAAMRGGKTRYTG 66 Query: 77 LDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWT 136 DGT EL+ AI KF+REN L Y +DEI++ GAKQILFNA + +L+ GDEVI+P PYW Sbjct: 67 PDGTEELRAAIVAKFKRENRLDYAMDEISIGNGAKQILFNAFLGTLEAGDEVIVPAPYWV 126 Query: 137 SYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADY 196 SY+DIV + G P +IAC F+LT E+LE AITP+TRWVL NSPSNP+GA Y++A+ Sbjct: 127 SYTDIVILHGGVPRIIACGVEDDFKLTPERLEHAITPKTRWVLFNSPSNPTGAIYTSAEL 186 Query: 197 RPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGW 256 L EVL RHPHV ++ D++YEHIV D F + A P ++ RTL +NGVSKAYAMTGW Sbjct: 187 AALGEVLERHPHVLVMSDEIYEHIVADDVPFTSFANACPQVRERTLIINGVSKAYAMTGW 246 Query: 257 RIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVV 316 R+GYA GP+ L + + +QSQ+T+CPSSISQAA+ AALNGPQ+F+ E ++ R +LV Sbjct: 247 RLGYAAGPKSLTRVLNKMQSQSTTCPSSISQAAAAAALNGPQNFVAEAVAEYKARGELVT 306 Query: 317 NGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGS 376 G +AI GL+ R P+GAFY F CAG +GK P G I+ DT ++LL VA VPG+ Sbjct: 307 RGFSAIPGLEVRAPDGAFYLFPKCAGYIGKTAPDGTVIENDTALASFLLTAGKVATVPGA 366 Query: 377 AFGLSPFFRISYATSEAELKEALERIAAACDRL 409 AFG+ P+ R+S+ATS L A+ERI A +L Sbjct: 367 AFGVEPYIRLSFATSRENLHIAIERIGEALAKL 399 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: 457 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 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