Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate Ac3H11_4342 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)
Query= reanno::WCS417:GFF5299 (454 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4342 Length = 454 Score = 272 bits (695), Expect = 2e-77 Identities = 161/454 (35%), Positives = 243/454 (53%), Gaps = 24/454 (5%) Query: 6 PQTREWQALSSDHHLAPFSDFKQLKEKGPRIITKAHGVYLWDSEGNKILDGMAGLWCVAI 65 P + A D H PF+ + K K PR+I G Y D++G KI DG++GLWC + Sbjct: 13 PDSPRMDAEWLDAHWMPFTGNRNFKAK-PRMIVSGQGAYYTDADGRKIFDGLSGLWCSGL 71 Query: 66 GYGRDELADAAAKQMKELPYYNLFFQTAHPPVLELAKAISDIAPAGMNHVFFTGSGSEGN 125 G+GR ++A+A K L Y + FQ HP LA + ++ PAG+++VFFTGSGSE Sbjct: 72 GHGRKDVAEAIGKAAATLDY-SPAFQFGHPASFALANKLKELTPAGLDYVFFTGSGSESA 130 Query: 126 DTMLRMVRHYWAIKGQPNKKTIISRKNGYHGSTVAGASLGGMTYMHE---QGDLPIPGIT 182 DT L+M R YW KGQ +K +I R+ GYHG G S+GG+ + QG + + Sbjct: 131 DTSLKMARAYWRAKGQASKTRLIGREKGYHGVNYGGISVGGIVGNRKTFGQG-IEADHLP 189 Query: 183 HIAQPYWFGEGGDMSPEEFGVWAANQLEEKILELGVDNVGAFIAEPIQGAGGVIVPPATY 242 H P + G E+ G A++L + I N+ A I EP G+ GV++PP Y Sbjct: 190 HTQPPAGTFQKG--MAEDGGRALADKLLDVIALHDASNIAAVIVEPFSGSAGVVIPPKGY 247 Query: 243 WPRIKEILAKYDILFIADEVICGFGRTGEWFGSDFYDLKPHMMTIAKGLTSGYIPMGGLI 302 RI+EI + +IL I DEVI GFGR G W G++ + + P ++ AK +T+G P+GG+I Sbjct: 248 LERIREICTQNNILLIFDEVITGFGRCGAWTGAEAFGVTPDILNFAKQVTNGAQPLGGVI 307 Query: 303 VRDEVVEV-LNEGG-----DFNHGFTYSGHPVAAAVALENIRIMRDEKIVNRVHDETAPY 356 E+ + +++GG +F HG+TYS HPVA A + I++ E + RV AP+ Sbjct: 308 ATKEIYDTFISQGGPEYMLEFPHGYTYSAHPVACAAGNAVLDILQKEDMPGRV-KALAPH 366 Query: 357 LQKRLRELADHPLVGEVRGVGMLGAIEL--VQDKATRKRYEGKGVGMICRTFCFENGLIM 414 + + L V ++R G+ I + + + ++ YE C+E G + Sbjct: 367 FENAVHGLKGAKHVADIRNYGLAAGITISALPSEPAKRPYE-------IAMKCWEKGFYV 419 Query: 415 RAVGDTMIISPPLVISKAEIDELVTKARQCLDLT 448 R GDT+ ++PP + + AEID +V+ L T Sbjct: 420 RYGGDTIQLAPPFISTSAEIDRMVSALGDALHET 453 Lambda K H 0.320 0.139 0.426 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: 626 Number of extensions: 32 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: 454 Length of database: 454 Length adjustment: 33 Effective length of query: 421 Effective length of database: 421 Effective search space: 177241 Effective search space used: 177241 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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