Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate PP_2180 PP_2180 polyamine:pyruvate transaminase
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >FitnessBrowser__Putida:PP_2180 Length = 452 Score = 778 bits (2008), Expect = 0.0 Identities = 368/453 (81%), Positives = 418/453 (92%), Gaps = 1/453 (0%) Query: 1 MTSKNPQTREWQTLSSEHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGL 60 M+ +N QT WQT+S +HHLAPFSD +QL EKGPRIIT+AKGVYLWDSEGNKILDGMAGL Sbjct: 1 MSEQNSQTLAWQTMSRDHHLAPFSDVRQLAEKGPRIITSAKGVYLWDSEGNKILDGMAGL 60 Query: 61 WCVAIGYGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGS 120 WCVA+GYGR+ELA+ AS+QM++LPYYNLFFQTAHPP LELAKAI+++AP+GMNHVFFTGS Sbjct: 61 WCVAVGYGREELAEVASQQMKQLPYYNLFFQTAHPPALELAKAIAEVAPQGMNHVFFTGS 120 Query: 121 GSEGNDTMLRMVRHYWAIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPG 180 GSEGNDT+LRMVRHYWA+KGQ NKKVII RINGYHGSTVAGA+LGGM+ MH+QG + IP Sbjct: 121 GSEGNDTVLRMVRHYWALKGQKNKKVIIGRINGYHGSTVAGAALGGMSGMHQQGGV-IPD 179 Query: 181 IVHIPQPYWFGEGGDMTPEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPD 240 +VHIPQPYWFGEGGDMT +FG+WAA QLE+KILE+GVD V AFIAEPIQGAGGVIIPP Sbjct: 180 VVHIPQPYWFGEGGDMTEADFGVWAAEQLEKKILEVGVDNVAAFIAEPIQGAGGVIIPPQ 239 Query: 241 SYWPRIKEILAKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGG 300 +YWP+IKEILA+YDILFVADEVICGFGRTGEWFG+D+Y LKPD+MTIAKGLTSGYIPMGG Sbjct: 240 TYWPKIKEILARYDILFVADEVICGFGRTGEWFGTDYYDLKPDLMTIAKGLTSGYIPMGG 299 Query: 301 LIVRDEVVEVLNEGGDFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKR 360 +IVRDEV +V++EGGDFNHGFTYSGHPVAAAV LEN+RILR+E+II+ V +TAPYLQ+R Sbjct: 300 VIVRDEVAKVISEGGDFNHGFTYSGHPVAAAVGLENLRILRDEQIIQQVHDKTAPYLQQR 359 Query: 361 LRELNDHPLVGEVRGVGLLGAIELVQDKATRARYVGKGVGMICRQFCFDNGLIMRAVGDT 420 LREL DHPLVGEVRG+G+LGAIELV+DKATRAR+ GKGVGMICRQ CFDNGLIMRAVGDT Sbjct: 360 LRELADHPLVGEVRGLGMLGAIELVKDKATRARHEGKGVGMICRQHCFDNGLIMRAVGDT 419 Query: 421 MIIAPPLVITKAEIDELVTKARKCLDLTLSALQ 453 MIIAPPLVI+ EIDELV KARKCLDLT A++ Sbjct: 420 MIIAPPLVISIEEIDELVEKARKCLDLTYEAVR 452 Lambda K H 0.320 0.140 0.428 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: 821 Number of extensions: 31 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: 454 Length of database: 452 Length adjustment: 33 Effective length of query: 421 Effective length of database: 419 Effective search space: 176399 Effective search space used: 176399 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