Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate H281DRAFT_01082 H281DRAFT_01082 putrescine aminotransferase
Query= reanno::BFirm:BPHYT_RS23155 (482 letters) >FitnessBrowser__Burk376:H281DRAFT_01082 Length = 478 Score = 877 bits (2266), Expect = 0.0 Identities = 422/482 (87%), Positives = 456/482 (94%), Gaps = 4/482 (0%) Query: 1 MSYRTEEVAYVQPAQPAASAQASQAAQQQRSTAEYRALDAAHHIHPFSDMGSLNRSGSRV 60 MSYRTEE+AY+QPA+PAA A+ +Q QR+TAEYRALDAAHHIHPFSDMG LNRSGSRV Sbjct: 1 MSYRTEEIAYMQPAEPAAGARTAQ----QRTTAEYRALDAAHHIHPFSDMGELNRSGSRV 56 Query: 61 IVKAQGVYLWDSEGNKVIDGMAGLWCVNVGYGRKELADAAYKQMQELPYYNTFFKTTHPP 120 IV+A GVYLWDSEGNK+IDGMAGLWCVNVGYGRKELA+AAY+QM+ELPYYNTFFKTTHPP Sbjct: 57 IVRAHGVYLWDSEGNKIIDGMAGLWCVNVGYGRKELANAAYRQMEELPYYNTFFKTTHPP 116 Query: 121 VIELSALLAELAPEAFNHFFYCNSGSEGNDTVLRIVHQYWATQGKHSKKFVISRKNGYHG 180 VIELSALLAELAPE FNHFFYCNSGSE NDTVLRIVH+YW TQGKHSKK VISR+NGYHG Sbjct: 117 VIELSALLAELAPEPFNHFFYCNSGSEANDTVLRIVHRYWTTQGKHSKKVVISRRNGYHG 176 Query: 181 STIAGGTLGGMGYMHEQMPSKVENIVHIDQPYFFGEAQGNLTPEEFALARAQQLEAKILE 240 STIAGGTLGGMGYMHEQMPSKVENIVHIDQPYFF EA + TPEEFALARAQQLE KILE Sbjct: 177 STIAGGTLGGMGYMHEQMPSKVENIVHIDQPYFFAEANSSQTPEEFALARAQQLEMKILE 236 Query: 241 IGADNVAAFIGEPFQGAGGVIFPASTYWPEIQRICRKYDILLVADEVIGGFGRTGEWFAH 300 IGA NVAAFIGEPFQGAGGVIFPASTYWPEI+RICRKYD+LLVADEVIGGFGRTGEWFAH Sbjct: 237 IGAHNVAAFIGEPFQGAGGVIFPASTYWPEIERICRKYDVLLVADEVIGGFGRTGEWFAH 296 Query: 301 QHFGFEPDLITLAKGLTSGYVPMGAVGLHDRVAKAIIENGDFNHGLTYSGHPVAAAVAVA 360 QHFGF+PDLIT+AKGLTSGYVPMGAVGL+DR+AKAIIENG+FNHGLTYSGHPVAAAVAVA Sbjct: 297 QHFGFQPDLITMAKGLTSGYVPMGAVGLNDRIAKAIIENGEFNHGLTYSGHPVAAAVAVA 356 Query: 361 NLKLLRDEKIVDRVKNDTGPYFQKQLRETFANHPIIGEISGTGLVAGLQLAQDPKARKRF 420 NLKLLRDEKIV+RVK DTGPYFQK+LR+TFA HPI+GEI+G GLVAGLQLA++P +RKRF Sbjct: 357 NLKLLRDEKIVERVKTDTGPYFQKKLRDTFARHPIVGEIAGAGLVAGLQLAEEPASRKRF 416 Query: 421 ANGGDVGTICRDFCFNGNLIMRATGDRMLLSPPLVINKLEIDEIVSKAKKAIDATAQQLG 480 ANGGDVG +CRDFCFNGNLIMRA+GDRMLLSPPLVI+K EID++VSKAK AIDATA QLG Sbjct: 417 ANGGDVGGVCRDFCFNGNLIMRASGDRMLLSPPLVISKQEIDDLVSKAKNAIDATATQLG 476 Query: 481 IS 482 IS Sbjct: 477 IS 478 Lambda K H 0.319 0.136 0.408 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: 834 Number of extensions: 18 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: 482 Length of database: 478 Length adjustment: 34 Effective length of query: 448 Effective length of database: 444 Effective search space: 198912 Effective search space used: 198912 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