Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate PfGW456L13_2943 Aspartate aminotransferase (EC 2.6.1.1)
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2943 Length = 395 Score = 194 bits (494), Expect = 3e-54 Identities = 111/363 (30%), Positives = 198/363 (54%), Gaps = 5/363 (1%) Query: 26 QHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFN 85 Q DV+ L+IG PDF TP + AA ++ T Y G LR ++ + ++++ Sbjct: 30 QGVDVLLLSIGDPDFDTPQPIVQAAIGSLLAGDTHYPAVRGSQGLRDSIARHHRRRSGQA 89 Query: 86 YDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDTTS- 144 DA+ +I+ GA A+ + + +L PGDEV++ P+Y YE + CGAK V V S Sbjct: 90 VDAQ-HVIVFPGAQCAVYSVAQCLLDPGDEVLVAEPMYVTYEGVFGACGAKVVPVPVRSQ 148 Query: 145 HGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYS 204 +GF++ + +TPNT+ ++L P+NP+G +L K++AAL +++++SDE+YS Sbjct: 149 NGFRVDPADVAALITPNTRAMLLNSPNNPSGASLPLTAWKALAALCIRHDLWLISDEVYS 208 Query: 205 ELTYDRPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVS 262 EL ++ H S A+ + ++T IN LSKSH+M+GWR+G++ P+ + +H++ + + Sbjct: 209 ELLFEGEHISPASLPGMAERTATINSLSKSHAMSGWRVGWVIGPQSLCEHLVNLSLCMLF 268 Query: 263 CASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRL-VSMGLDVVKPSGAFYIFPSI 321 Q AA A+ MRE+Y++R D V L + G+ ++P G ++ + Sbjct: 269 GIPDFIQNAAQLALDENLPHVAQMREEYRQRRDLVCASLNLCPGIQAIRPDGGMFVMVDV 328 Query: 322 KSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRLELFVLK 381 + G+++ F+ LL+ GV+++ G +F G++R+ L + R+ + V Sbjct: 329 RQTGLSAQHFAERLLDGYGVSVLAGEAFGPSAAGHIRIGLVVDRPKLADACRRIVMCVTN 388 Query: 382 KRE 384 E Sbjct: 389 MLE 391 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: 347 Number of extensions: 16 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: 395 Length adjustment: 31 Effective length of query: 362 Effective length of database: 364 Effective search space: 131768 Effective search space used: 131768 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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