Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_089299882.1 CHB84_RS02455 aspartate aminotransferase family protein
Query= BRENDA::H7CE71 (509 letters) >NCBI__GCF_900188115.1:WP_089299882.1 Length = 480 Score = 391 bits (1004), Expect = e-113 Identities = 213/486 (43%), Positives = 289/486 (59%), Gaps = 15/486 (3%) Query: 22 LDPEEFRKQGHMVIDFIADYYQNIEKYPVLSRVEPGYLKKCLPESAPYDPEPISTILKDV 81 + E+FR G ++D+IADY IE +PV + V PG ++ LPESAP E I DV Sbjct: 1 MSAEQFRAHGKQLVDWIADYLAGIESHPVRAPVRPGDIRARLPESAPEHGESWDRIQADV 60 Query: 82 QDHIVPGLTHWQSPNFFAYFSSTASTAGFLGEILTTGFNVVGFNWVSSPAATELENIVMD 141 I+PG+THWQ P+FFAYF + AS LGE+L+ G G W + PA TELE++V+D Sbjct: 61 DRVIMPGITHWQHPSFFAYFPANASGPAILGELLSAGLGAQGMLWETGPACTELESVVVD 120 Query: 142 WLGDMLQLPKSFHFSGNGGGVLHGSTCEAIVCTMVAARDQMLRRIGSENLGK--LVVYGS 199 WL ++L LP ++ G GGGV+ S A + +VAA LRR G + + VY S Sbjct: 121 WLAELLGLPATWRTDGPGGGVIQDSASSAALVALVAA----LRRAGRVDADRTACTVYVS 176 Query: 200 DQTHSTLQKATQIVGINTENFRAIKTTKSTGFALSPEMLRLTISSDLEKGLVPLFLCATI 259 QTHS++ KA +I GI T N R + T A+ P+ L +++D+ G VP +CATI Sbjct: 177 AQTHSSMAKAARIAGITTPNLRTVDVDPDT-LAMRPDHLEELVAADVAAGSVPTMVCATI 235 Query: 260 GTTATTAIDPLEALCHVAKEYGVWVHVDAAYAGSACICPEFRHFING-VEGANSFSFNPH 318 GTT+TTAIDP+ AL V +GVW+HVDAAYAG A +CPE R +G E A+S+ +PH Sbjct: 236 GTTSTTAIDPVGALGEVCSRHGVWLHVDAAYAGVAAVCPELRWINDGAAEYADSYVTDPH 295 Query: 319 KWLFTGMDCCCLWVKNPSVLASSLSTNPEFLRNKASDSKQVVDYKDWQIALSRRFRALKL 378 KWL T DC LWV + L +LS PE+LRN A+ S +V+DY+DWQ+ L RRFRALKL Sbjct: 296 KWLLTNFDCSVLWVADRGPLVDALSILPEYLRNPATASGEVIDYRDWQVPLGRRFRALKL 355 Query: 379 WLVLRSYGVANLRNFIRIHVNMAKTFEGLVRMDKRFEILVPRNFSLVCFRISPSALISSN 438 W+V+R YG +LR IR V +A G R + F +L F LVCFR AL S+ Sbjct: 356 WMVMRWYGATSLREHIRTGVALADELAGWFREHEDFALLEHHPFGLVCFRPLWPAL--SH 413 Query: 439 EDDEIGMVNEVNCKLLEAINASGKAYMTHAVVGGLYVLRCAVGATLSEEKHIVEAWKVVQ 498 D E LL +N SG Y++H +GG LR A+GA + +H+ A++ ++ Sbjct: 414 RDAE-----TATAALLARLNDSGDLYLSHTNIGGRTTLRIAIGAPATTREHVRVAFRRIE 468 Query: 499 DHAKAI 504 A+ Sbjct: 469 QEYLAL 474 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: 576 Number of extensions: 18 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: 480 Length adjustment: 34 Effective length of query: 475 Effective length of database: 446 Effective search space: 211850 Effective search space used: 211850 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