Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_013091777.1 BC1002_RS19865 amino acid aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_000092885.1:WP_013091777.1 Length = 399 Score = 446 bits (1146), Expect = e-130 Identities = 225/397 (56%), Positives = 283/397 (71%), Gaps = 1/397 (0%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 MF + AY GDPIL+L E F+ DPR +KVNLSIG+Y+++ G +P + AV AE L Sbjct: 1 MFDHIPAYPGDPILSLNEDFQLDPRPNKVNLSIGIYFDDAGKLPVIDAVRRAETAL-LDA 59 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 G YLPM GL YR L+FGAD + R+AT+QTLGGSGALKVGADFLKRYFP Sbjct: 60 IGPRSYLPMAGLPLYRDTAQALVFGADSAARAEGRIATLQTLGGSGALKVGADFLKRYFP 119 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 S VW+SDP+WENH IF GAG V+TYP+YD T G+RF ++LA + LP +S+VLLH Sbjct: 120 ASQVWISDPSWENHRVIFEGAGLTVNTYPYYDPQTGGLRFAEMLAAIDVLPEKSVVLLHA 179 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTG DL+ QW ++ +L+ R+LI F+D+AYQGFGAG+EEDA +R +A A +P + Sbjct: 180 CCHNPTGVDLSPAQWAELVPVLQRRKLIAFVDMAYQGFGAGLEEDAAPVRMLADANVPLI 239 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 V+NSFSK FSLYGERVG LSV+C+ A+ A RV GQL + VR NYS+PP GA++VA VL Sbjct: 240 VANSFSKNFSLYGERVGALSVVCKSADEAARVAGQLMSAVRANYSNPPTHGARLVANVLA 299 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 D L+ASW AE+ MR RILAMR + L + E + QRGMF+YTGLS +QV+ Sbjct: 300 DATLRASWQAELGAMRERILAMRNVIHAGLDGRVDEVMRARYVAQRGMFTYTGLSESQVE 359 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 RLR E+ VY++ SGRMCVAGLN N VA + AAV+ Sbjct: 360 RLRNEYAVYVLRSGRMCVAGLNARNADYVASSIAAVV 396 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: 476 Number of extensions: 13 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: 399 Length adjustment: 31 Effective length of query: 366 Effective length of database: 368 Effective search space: 134688 Effective search space used: 134688 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