Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_013420785.1 RVAN_RS16200 amino acid decarboxylase
Query= BRENDA::H7CE71 (509 letters) >NCBI__GCF_000166055.1:WP_013420785.1 Length = 472 Score = 326 bits (835), Expect = 1e-93 Identities = 177/486 (36%), Positives = 275/486 (56%), Gaps = 22/486 (4%) Query: 22 LDPEEFRKQGHMVIDFIADYYQNIEKYPVLSRVEPGYLKKCLPESAPYDPEPISTILKDV 81 +D ++FR+ GH +ID++ADY + + PV+S +PG ++ P P + + + Sbjct: 1 MDAQDFRRFGHQLIDWVADYREGLASRPVMSEAQPGDIRAKFPAHPPQKGGRLDEAVAAL 60 Query: 82 QDHIVPGLTHWQSPNFFAYFSSTASTAGFLGEILTTGFNVVGFNWVSSPAATELENIVMD 141 ++PG+THW P+FFAYF S S A L +++ G G +W +SPAATE+E +VMD Sbjct: 61 DRDVLPGITHWNHPSFFAYFPSNTSYASILADLVIAGLGAQGMSWQTSPAATEVEEVVMD 120 Query: 142 WLGDMLQLPKSFHFSGNGGGVLHGSTCEAIVCTMVAARD------QMLRRIGSENLGKLV 195 WL M+ L ++F GV+H + A + +++AR+ Q R + S + LV Sbjct: 121 WLRQMVGLGEAF------TGVIHDTASTATLTALLSARERASNFSQNGRGLQSGD-APLV 173 Query: 196 VYGSDQTHSTLQKATQIVGINTENFRAIKTTKSTGFALSPEMLRLTISSDLEKGLVPLFL 255 VY SDQ+HS+++KA + G ++ R I+T A+ ++L I+ D+ +GL P + Sbjct: 174 VYASDQSHSSIEKAALLAGFGRDHLRLIET--DDDHAIRLDLLEAAIAEDVRRGLRPCAV 231 Query: 256 CATIGTTATTAIDPLEALCHVAKEYGVWVHVDAAYAGSACICPEFRHFINGVEGANSFSF 315 A IGTT TTA+DPL + +A +G W+HVDAA AG+A + PE R G+E A+S F Sbjct: 232 IACIGTTGTTAVDPLAKIADIAARFGPWLHVDAAMAGTAMVLPECRDHWTGIERADSLVF 291 Query: 316 NPHKWLFTGMDCCCLWVKNPSVLASSLSTNPEFLRNKASDSKQVVDYKDWQIALSRRFRA 375 NPHKW+ G D +V++P L +STNP +L+ K + V +Y+DW I L RRFRA Sbjct: 292 NPHKWMGVGFDFSAYYVRDPEHLIRVMSTNPSYLQTKQDGA--VKNYRDWHIQLGRRFRA 349 Query: 376 LKLWLVLRSYGVANLRNFIRIHVNMAKTFEGLVRMDKRFEILVPRNFSLVCFRISPSALI 435 LKLW L GV ++ +R + A+ F+ V +E L P F +C R P+AL Sbjct: 350 LKLWFHLMDVGVEGVQALVRRDLGNAQWFKDRVDAAADWERLAPVPFQTICVRHVPAAL- 408 Query: 436 SSNEDDEIGMVNEVNCKLLEAINASGKAYMTHAVVGGLYVLRCAVGATLSEEKHIVEAWK 495 + DE + N +L +N G+AY+T A++ G +LR ++GAT +E + W Sbjct: 409 ---KGDEAAL-KAHNLELARRVNEGGEAYITPALLKGKQILRVSIGATATERAEVQALWV 464 Query: 496 VVQDHA 501 ++ + A Sbjct: 465 LLNEAA 470 Lambda K H 0.321 0.135 0.416 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: 563 Number of extensions: 26 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: 509 Length of database: 472 Length adjustment: 34 Effective length of query: 475 Effective length of database: 438 Effective search space: 208050 Effective search space used: 208050 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 (21.9 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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