Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate Pf6N2E2_462 Aspartate aminotransferase (EC 2.6.1.1)
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_462 Length = 394 Score = 187 bits (476), Expect = 3e-52 Identities = 110/354 (31%), Positives = 189/354 (53%), Gaps = 5/354 (1%) Query: 26 QHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFN 85 Q DV+ L++G PDF TP + AA ++ T Y+ G LR ++ + + Sbjct: 30 QGMDVLLLSVGDPDFDTPRAIVDAAVGSLRAGETHYSDIRGLHTLRTSIARRHRLRCGQP 89 Query: 86 YDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDTT-S 144 AE ++++ GA A+ A + +L+PGDEVI+ P+Y YE + CGA V V Sbjct: 90 AGAE-QVVVLPGAQCAVYAVAQCLLNPGDEVIVAEPMYVTYEAVFGACGATVVPVAVRPE 148 Query: 145 HGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYS 204 +GF++ + +TP T+ ++L P+NP+G +L +++A L +++++SDE+YS Sbjct: 149 NGFRVEPADVARLVTPRTRAMLLNSPNNPSGASLPMPTWQALARLCIEHDLWLISDEVYS 208 Query: 205 ELTYDRPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVS 262 +L YD H S A+ + ++T IN LSKSH+MTGWRIG++ P+ +A H+ + + Sbjct: 209 DLLYDGEHISPASLPGMAERTATINSLSKSHAMTGWRIGWVIGPESLADHLANLSLCMLF 268 Query: 263 CASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAFYIFPSI 321 Q+AA A+ + M ++Y++R D V L GL V+P G ++ + Sbjct: 269 GLPDFVQRAAQVALEQALPEVAQMHDEYRQRRDLVCAMLDDCPGLKPVRPDGGMFVMVDV 328 Query: 322 KSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRL 375 + G+ + F+ LL+D GV+++ G +F G++RL L + R+ Sbjct: 329 RRTGLDAQAFAERLLDDYGVSVLAGEAFGPSAAGHIRLGLVVDQVKLADACQRI 382 Lambda K H 0.319 0.135 0.388 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: 327 Number of extensions: 15 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: 393 Length of database: 394 Length adjustment: 31 Effective length of query: 362 Effective length of database: 363 Effective search space: 131406 Effective search space used: 131406 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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