Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate CCNA_01648 CCNA_01648 adenosylmethionine-8-amino-7-oxononanoate
Query= reanno::BFirm:BPHYT_RS23155 (482 letters) >FitnessBrowser__Caulo:CCNA_01648 Length = 420 Score = 139 bits (349), Expect = 2e-37 Identities = 97/312 (31%), Positives = 146/312 (46%), Gaps = 21/312 (6%) Query: 61 IVKAQGVYLWDSEGNKVIDGMAGLWCVNVGYGRKELADAAYKQMQELPYYNTFFKTTHPP 120 +V +G L +G +++DG+A W GY +A A KQ++ +P+ F H P Sbjct: 30 VVATRGARLILEDGRELVDGLASWWTACHGYNHPHIAGALRKQIETMPHV-MFGGLAHEP 88 Query: 121 VIELSALLAELAPEAFNHFFYCNSGSEGNDTVLRIVHQYWATQGKHSKKFVISRKNGYHG 180 L+ LA L P +H F+ SGS + +++ QY +G + ++ + GYHG Sbjct: 89 AYRLAKRLARLLPGDLDHVFFAESGSVAVEIAMKMALQYQINRGVGGRTRFLAFRGGYHG 148 Query: 181 STIAGGTL-GGMGYMHEQMPSKVENIVHIDQPYFFGEAQGNLTPEEFALARAQQLEAKIL 239 T+A T+ MH + V D P P A A +L Sbjct: 149 DTLATMTVCDPEEGMHSLFAGVMPAQVIADLP---------RDPASEAALDA------LL 193 Query: 240 EIGADNVAAFIGEP-FQGAGGVIFPASTYWPEIQRICRKYDILLVADEVIGGFGRTGEWF 298 +AA + EP QGAGG++ ++R+ K+ +LL+ DE+ GFGRTG F Sbjct: 194 AARGHEIAAMLVEPLIQGAGGMLPHPPEVLRTLRRLADKHGVLLIFDEIFTGFGRTGSLF 253 Query: 299 AHQHFGFEPDLITLAKGLTSGYVPMGAVGLHDRVAKAIIEN---GDFNHGLTYSGHPVAA 355 A Q G EPD++TL+K LT G +P+ A V +A + HG TY +P+A Sbjct: 254 AMQAAGVEPDIVTLSKALTGGTLPLSAAVARRHVFEAFWSDDPAAALMHGPTYMANPLAC 313 Query: 356 AVAVANLKLLRD 367 A A A+L L D Sbjct: 314 AAANASLDLFED 325 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: 466 Number of extensions: 20 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 482 Length of database: 420 Length adjustment: 33 Effective length of query: 449 Effective length of database: 387 Effective search space: 173763 Effective search space used: 173763 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