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_005453184.1 SACCYDRAFT_RS02235 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_000244975.1:WP_005453184.1 Length = 410 Score = 323 bits (827), Expect = 7e-93 Identities = 164/390 (42%), Positives = 246/390 (63%), Gaps = 3/390 (0%) Query: 15 ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIH-RGETK 73 ++RI+ I S L + A+A A+K EG+PVI GAG+PDF TPE++ +AA+ A+ RG Sbjct: 16 SARIAGITPSATLAVDAKAKALKAEGRPVIGFGAGQPDFPTPEYIVEAAAAAVRDRGNHG 75 Query: 74 YTALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTP 133 YTA G PEL++AI K R++G + + ++ V G KQ +++A LDPGDEV++ P Sbjct: 76 YTAAAGLPELREAIAAKTLRDSGFSCDASQVLVTNGGKQAVYSAFATLLDPGDEVLLLAP 135 Query: 134 YWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSA 193 YWT+Y + + + G PV + D S+G+R+T E+LEAA T RT+ +L NSPSNP+GA Y+ Sbjct: 136 YWTTYPESITLAGGVPVQVTADESTGYRVTVEQLEAARTERTKVLLFNSPSNPTGAVYTR 195 Query: 194 ADYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAM 253 + H +W++ D++YEH+VYDG + + + P L +RTL +NGV+K Y+M Sbjct: 196 EQVEAIGRWAAEHD-IWVITDEIYEHLVYDGVKAASLPTVVPELADRTLILNGVAKTYSM 254 Query: 254 TGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRD 313 TGWR+G+ GP+++IKA + QS +++SQ A++AA+ GP D + E +F RR Sbjct: 255 TGWRVGWIVGPQDVIKAASSFQSHLCGNVANVSQRAALAAVEGPLDVVHEMRAAFDSRRK 314 Query: 314 LVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVV 373 +V+ L+ I ++C PEGAFY + VLGK G+R + +L + VAVV Sbjct: 315 KIVSMLSEIPNVECPTPEGAFYAYPSVKAVLGKEI-RGQRPADTVELADLILREVEVAVV 373 Query: 374 PGSAFGLSPFFRISYATSEAELKEALERIA 403 PG AFG +FR SYA +E +L E + R+A Sbjct: 374 PGEAFGTPGYFRFSYALAEKDLVEGVTRVA 403 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: 18 Number of successful extensions: 4 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: 410 Length adjustment: 31 Effective length of query: 379 Effective length of database: 379 Effective search space: 143641 Effective search space used: 143641 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 10 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