Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate 201494 SO2350 aspartate aminotransferase (NCBI ptt file)
Query= BRENDA::P04693 (397 letters) >FitnessBrowser__MR1:201494 Length = 397 Score = 357 bits (915), Expect = e-103 Identities = 181/397 (45%), Positives = 252/397 (63%), Gaps = 1/397 (0%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 +F +V DPIL L + FK DPR DKVNL +G+Y +E G P LQ+V +AEA L Q Sbjct: 2 IFSQVVLAPADPILGLTDTFKADPRQDKVNLGVGIYKDEAGQTPVLQSVKKAEAILLEQE 61 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 + YL +EG+ Y + LLFG ++ R AT Q GG+GAL++ A+FL R P Sbjct: 62 KTKN-YLGIEGVQTYNRVVQELLFGEGSELVASGRAATAQAPGGTGALRIAAEFLLRNTP 120 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 +WVS+PTW NH IF AG V + +Y+ + + + F+ ++ L A I+LLH Sbjct: 121 SRTIWVSNPTWANHQNIFETAGLTVKEFGYYNASAHDIDFDGMMTDLANAQAGDIILLHG 180 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTG DLT QWD V + ++L+P D AYQGFG G+EEDA +R +AS L Sbjct: 181 CCHNPTGIDLTLAQWDLVANLCADKQLVPLFDFAYQGFGTGIEEDAAGLRLVASKVPELL 240 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 V+NSFSK F LY ER+G ++V+ +A+ A R Q+K T+R NYS+PP GA +V+ +L+ Sbjct: 241 VANSFSKNFGLYNERIGAVTVVAHNADEAVRAFSQVKRTIRANYSNPPAHGALIVSTILS 300 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 D ALKA W+ E+ EMR RI MR V+ L E ++F ++ Q GMFS++GL+ +QV Sbjct: 301 DAALKALWVQELTEMRERIALMRTLFVQSLKDEGVTQDFSFISRQNGMFSFSGLNKSQVA 360 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 RL++EFGVY++ SGR+ VAG+ AN+ + KA A V+ Sbjct: 361 RLKDEFGVYIVGSGRISVAGMTKANMPAICKAIAQVV 397 Lambda K H 0.320 0.135 0.401 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: 424 Number of extensions: 15 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: 397 Length of database: 397 Length adjustment: 31 Effective length of query: 366 Effective length of database: 366 Effective search space: 133956 Effective search space used: 133956 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