Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate Pf1N1B4_1239 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1239 Length = 449 Score = 273 bits (699), Expect = 6e-78 Identities = 160/442 (36%), Positives = 243/442 (54%), Gaps = 17/442 (3%) Query: 4 KNPQTREWQTLSSEHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCV 63 +N T L + H P++ + ++ PR+I A+G +L D +G K+ D ++GLW Sbjct: 5 ENAPTSLASQLKLDAHWMPYTANRNF-QRDPRLIVAAEGSWLTDDKGRKVYDSLSGLWTC 63 Query: 64 AIGYGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSE 123 G+ R E+ +A +KQ+ L Y + FQ HP +LA+ I+D+ P +NHVFFT SGSE Sbjct: 64 GAGHTRKEIQEAVAKQLGTLDY-SPGFQYGHPLSFQLAEKITDLTPGNLNHVFFTDSGSE 122 Query: 124 GNDTMLRMVRHYWAIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVH 183 DT ++MVR YW +KGQ K +I R GYHG +AG SLGG+ + + + H Sbjct: 123 CADTAVKMVRAYWRLKGQATKTKMIGRARGYHGVNIAGTSLGGVNGNRKLFGQAMMDVDH 182 Query: 184 IPQPYWFGEGGDM-TPEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSY 242 +P PE+ GI A++L + I + A EP+ G+ GV++PP Y Sbjct: 183 LPHTLLASNAFTRGMPEQGGIALADELLKLIELHDASNIAAVFVEPLAGSAGVLVPPQGY 242 Query: 243 WPRIKEILAKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLI 302 R++EI +++IL V DEVI GFGRTG FG+D +G+ PD+M IAK +T+G IPMG +I Sbjct: 243 LKRLREICDQHNILLVFDEVITGFGRTGSMFGADSFGVTPDLMCIAKQVTNGAIPMGAVI 302 Query: 303 VRDEVVEV-LNEGG-----DFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPY 356 E+ + +N+ +F HG+TYS HPVA A L + +L++E +++ V AE AP+ Sbjct: 303 ASSEIYQTFMNQATPEYAVEFPHGYTYSAHPVACAAGLAALDLLQKENLVQSV-AEVAPH 361 Query: 357 LQKRLRELNDHPLVGEVRGVGLLGAIELV-QDKATRARYVGKGVGMICRQFCFDNGLIMR 415 + L L V ++R GL GAI++ +D R G+ + + G +R Sbjct: 362 FENALHGLKGSKNVIDIRNYGLAGAIQIAPRDGDAIVRPFEAGMAL------WKAGFYVR 415 Query: 416 AVGDTMIIAPPLVITKAEIDEL 437 GDT+ P ++D L Sbjct: 416 FGGDTLQFGPTFNSKPQDLDRL 437 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: 541 Number of extensions: 30 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: 449 Length adjustment: 33 Effective length of query: 421 Effective length of database: 416 Effective search space: 175136 Effective search space used: 175136 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