Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_028997211.1 H537_RS0106295 amino acid aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_000430725.1:WP_028997211.1 Length = 394 Score = 430 bits (1105), Expect = e-125 Identities = 221/396 (55%), Positives = 281/396 (70%), Gaps = 2/396 (0%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 M Q V A+AGDPIL+L E F++D R +K+NLSIG+Y +E +P + AV EAEARL A+ Sbjct: 1 MLQHVPAFAGDPILSLNEAFQQDARPNKINLSIGVYADESLRLPAMAAVLEAEARLTAR- 59 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 A YLPMEG +R A+ L+FGA HP + Q RVAT+QT+G SGALK+GA+F++++ P Sbjct: 60 RDARPYLPMEGDAAFREAVRALVFGAAHPAVTQGRVATVQTIGSSGALKLGAEFIRQWLP 119 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 S VWVSDPTW+NH AIF AG V YP++D A GV F+ +L TL++LPARS+VLLH Sbjct: 120 GSEVWVSDPTWDNHRAIFESAGLAVHAYPYHDPA-RGVAFDAMLDTLRSLPARSVVLLHG 178 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTG DL QW A+ + R LIPF+D+AYQGFG G++ DA +RA+A AG+ Sbjct: 179 CCHNPTGEDLDAAQWGALTALCAQRGLIPFVDLAYQGFGEGVDADAGPVRALAEAGITGF 238 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 V+NS SK LYGER G LSV+C DA A VLGQLK VRR+YSSPP +V A VL Sbjct: 239 VANSLSKNMGLYGERCGALSVVCGDAGQAEHVLGQLKLAVRRSYSSPPLHAGRVAAQVLG 298 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 L+A+W E++ MR RIL+MR+ L L P +++ YLL QRGMFSYTGLSAAQVD Sbjct: 299 APELRAAWAQELDGMRQRILSMRRALHAALVQRRPAQDWSYLLRQRGMFSYTGLSAAQVD 358 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAV 396 RLREE +YL+ SGR+C+AGLN + VA+A A + Sbjct: 359 RLREEHAIYLVRSGRICLAGLNATCIGTVAQAIAGL 394 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: 436 Number of extensions: 11 Number of successful extensions: 3 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: 394 Length adjustment: 31 Effective length of query: 366 Effective length of database: 363 Effective search space: 132858 Effective search space used: 132858 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 Jul 25 2024. The underlying query database was built on Jul 25 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