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_012567061.1 RC1_RS09020 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_000016185.1:WP_012567061.1 Length = 401 Score = 501 bits (1289), Expect = e-146 Identities = 251/396 (63%), Positives = 303/396 (76%), Gaps = 1/396 (0%) Query: 15 ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74 ASR+S I S + + ++A A+K G+ VI LGAGEPDFDTP+ +K AA +AI RG TKY Sbjct: 5 ASRLSRIKPSATIAVTSKARALKAAGRDVIGLGAGEPDFDTPDSIKDAAIEAIRRGFTKY 64 Query: 75 TALDGTPELKKAIREKFQRENGLAYE-LDEITVATGAKQILFNAMMASLDPGDEVIIPTP 133 T +DGTPELKKA+ KF+R+NGL Y+ +ITV TG KQ+LFNA++A+LDPGDEVI+P P Sbjct: 65 TDVDGTPELKKAVAAKFRRDNGLEYDPATQITVGTGGKQVLFNALLATLDPGDEVIVPAP 124 Query: 134 YWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSA 193 YW SY D+V + EG PV +AC A +GF+LT LEAAITPRT+W++LNSPSNP+GAAY+A Sbjct: 125 YWVSYPDMVLLAEGTPVPVACPAEAGFKLTPAALEAAITPRTKWLILNSPSNPTGAAYTA 184 Query: 194 ADYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAM 253 A+ L EVLLRHP VW++ DDMYEH+VYDGFRF T AQ+ PGL RTLTVNGVSKAY+M Sbjct: 185 AELTALGEVLLRHPQVWVMSDDMYEHLVYDGFRFATIAQVVPGLLGRTLTVNGVSKAYSM 244 Query: 254 TGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRD 313 TGWRIG+AGGP+ELIKAM V+QSQ+TS P+SISQAA+ ALNGPQD++ + E F RRRD Sbjct: 245 TGWRIGFAGGPKELIKAMGVIQSQSTSNPTSISQAAATEALNGPQDYIPRQAEVFARRRD 304 Query: 314 LVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVV 373 LVV+ LN GL C PEGAFY + CA LG TP G+ I +D DF LLE VAVV Sbjct: 305 LVVSMLNQAKGLSCPNPEGAFYVYPSCAATLGLSTPGGRVIGSDEDFATELLEAEGVAVV 364 Query: 374 PGSAFGLSPFFRISYATSEAELKEALERIAAACDRL 409 G+AFGLSP FRISYATSE L+EA RI C L Sbjct: 365 HGAAFGLSPHFRISYATSETVLEEACRRIQRFCASL 400 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: 589 Number of extensions: 21 Number of successful extensions: 2 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: 401 Length adjustment: 31 Effective length of query: 379 Effective length of database: 370 Effective search space: 140230 Effective search space used: 140230 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