Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_005453184.1 SACCYDRAFT_RS02235 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_000244975.1:WP_005453184.1 Length = 410 Score = 207 bits (526), Expect = 6e-58 Identities = 126/373 (33%), Positives = 200/373 (53%), Gaps = 19/373 (5%) Query: 19 KFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAI-DENVTSYTPNAGYLELRQAVQLY 77 K L A+ VI GQPDF TP ++ AA A+ D YT AG ELR+A+ Sbjct: 33 KAKALKAEGRPVIGFGAGQPDFPTPEYIVEAAAAAVRDRGNHGYTAAAGLPELREAIAAK 92 Query: 78 MKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKP 137 + + F+ DA S++++T G QA+ +AF T+L PGDEV++ P + Y I L G P Sbjct: 93 TLRDSGFSCDA-SQVLVTNGGKQAVYSAFATLLDPGDEVLLLAPYWTTYPESITLAGGVP 151 Query: 138 VIVDTT-SHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVF 196 V V S G+++T +E A T TK ++ PSNPTG + E++++I +++ Sbjct: 152 VQVTADESTGYRVTVEQLEAARTERTKVLLFNSPSNPTGAVYTREQVEAIGRWAAEHDIW 211 Query: 197 VLSDEIYSELTYDRPHYS----IATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKH 252 V++DEIY L YD + + L D+T+++NG++K++SMTGWR+G++ P+D+ K Sbjct: 212 VITDEIYEHLVYDGVKAASLPTVVPELADRTLILNGVAKTYSMTGWRVGWIVGPQDVIKA 271 Query: 253 ILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKP 311 + +++SQ+AAL AV D MR + R + L + ++ P Sbjct: 272 ASSFQSHLCGNVANVSQRAALAAVEGPLDVVHEMRAAFDSRRKKIVSMLSEIPNVECPTP 331 Query: 312 SGAFYIFPSIKSF---------GMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFA 362 GAFY +PS+K+ + + + +L + VA+VPG +F T GY R S+A Sbjct: 332 EGAFYAYPSVKAVLGKEIRGQRPADTVELADLILREVEVAVVPGEAFGT--PGYFRFSYA 389 Query: 363 CSMDTLREGLDRL 375 + L EG+ R+ Sbjct: 390 LAEKDLVEGVTRV 402 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: 370 Number of extensions: 21 Number of successful extensions: 8 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: 410 Length adjustment: 31 Effective length of query: 362 Effective length of database: 379 Effective search space: 137198 Effective search space used: 137198 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 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