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_041100392.1 SUTH_RS15085 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_000828635.1:WP_041100392.1 Length = 388 Score = 149 bits (375), Expect = 2e-40 Identities = 118/399 (29%), Positives = 184/399 (46%), Gaps = 28/399 (7%) Query: 16 SRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYT 75 SR+ ++G + I + +R AA I L G PDF + + + + G +Y Sbjct: 7 SRLPNVGTT-IFTVMSRLAAEHG----AINLSQGFPDFSPSPRLLERVTHHMAAGANQYP 61 Query: 76 ALDGTPELKKAIREKFQRENGLAYELD-EITVATGAKQILFNAMMASLDPGDEVIIPTPY 134 + G L++AI EK R Y+ + E+TV GA Q ++ A+ A + PGDEVI+ P Sbjct: 62 PMAGVASLREAIAEKVARLYLANYDPETEVTVTAGATQAIYTAIAACVRPGDEVIVFAPV 121 Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194 + SY + + G V F+ +++ A ITPRTR +++NSP NPSG+ +SAA Sbjct: 122 YDSYVPGIELNGGHAVHAHLRFPE-FKPDWDEVRALITPRTRMIIINSPHNPSGSVWSAA 180 Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYD----GFRFVTPAQLEPGLKNRTLTVNGVSKA 250 D +LE L+R + ++ D++YEH+V+D G PGL+ R+ V+ K Sbjct: 181 D-MAMLETLVRDTKIVVVSDEVYEHVVFDQQDGGSLRHESVTRYPGLRERSFVVSSFGKT 239 Query: 251 YAMTGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQR 310 Y +TGW++ Y PR L+ +Q A + +F +Q Sbjct: 240 YHVTGWKVAYCLAPRALMGEFRKAHQFIVFTVHHPAQLALADFMREHPEFADTLASFYQA 299 Query: 311 RRDLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKV-TPSGKRIKTDTDFCAYLLEDAH 369 +RD L EG+ + CAG ++ T + + DT F L + Sbjct: 300 KRDFFRQQL-----------EGSRFVLLPCAGTYFQLATYAAISDEPDTSFVQRLTKQHG 348 Query: 370 VAVVPGSAFGL----SPFFRISYATSEAELKEALERIAA 404 VA +P SAF R +A +EA L A ER+ A Sbjct: 349 VAAIPVSAFNPDGDDQRVIRFCFAKNEATLAAAGERLRA 387 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: 360 Number of extensions: 22 Number of successful extensions: 5 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: 388 Length adjustment: 31 Effective length of query: 379 Effective length of database: 357 Effective search space: 135303 Effective search space used: 135303 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