Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate GFF3179 PGA1_c32300 aminotransferase class-III
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >FitnessBrowser__Phaeo:GFF3179 Length = 448 Score = 285 bits (728), Expect = 3e-81 Identities = 152/414 (36%), Positives = 241/414 (58%), Gaps = 6/414 (1%) Query: 34 PRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAASKQMRELPYYNLFFQTA 93 P+IIT A+GV++ D +G++++DG+ GLW V +GY + DA + Q+ +LPYY+ F T+ Sbjct: 30 PKIITGAEGVFITDIDGHRVIDGVGGLWNVNLGYSCQPVKDAMAAQLDKLPYYSTFRGTS 89 Query: 94 HPPVLELAKAISDI-APEGMNHVFFTGSGSEGNDTMLRMVRHYWAIKGQPNKKVIISRIN 152 + +EL+ +S P+G++ FFT GS+ +T LR+ R Y ++G + +S Sbjct: 90 NDAAIELSYELSRFFEPDGLSRAFFTSGGSDSVETALRLARQYHKLRGDSGRTKFLSLKK 149 Query: 153 GYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWFGEGGDMT-PEEFGIWAANQLEE 211 GYHG+ + GAS+ G + +PG HIP PY + D + PE A LE+ Sbjct: 150 GYHGTHIGGASVNGNANFRTAYEPLLPGCFHIPAPYTYRNPFDESDPERLAQLCAAALED 209 Query: 212 KILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEILAKYDILFVADEVICGFGRTGE 271 +I G +T+ A I EPI GAGGVI P S+ P ++EI + IL + DEVI +GRTG Sbjct: 210 EIAFQGANTIAAMIMEPILGAGGVIPPHPSFAPMVQEICNRNGILLITDEVITAYGRTGA 269 Query: 272 WFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEGGD--FNHGFTYSGHPVA 329 W G+ +G++PDMM AK +T+GY P G +++ ++EV + D HG+TYSGHPV Sbjct: 270 WSGARLWGIQPDMMCTAKAITNGYFPFGAVMLGARMIEVFEDNPDAKIGHGYTYSGHPVG 329 Query: 330 AAVALENIRILREEKIIEHVRAETAPYLQKRLRELNDHPLVGEVR-GVGLLGAIELVQDK 388 AA AL + ++ + A A + L ++G+VR G GL+ A+ELV D+ Sbjct: 330 AAAALTCLAEMQRLNVTATAAARGAQLYEGCLALKERFDVIGDVRGGYGLMIALELVSDR 389 Query: 389 ATRARYVGKGVGMICRQFCFDNGLIMRAVGDTMIIAPPLVITKAEIDELVTKAR 442 TRA G+ + ++ C++ G ++R G +I++PPL++++A+ L+ R Sbjct: 390 QTRAPLDGRR-ALALQEACYEAGALIRVSGPNVILSPPLIMSEADTRGLLDALR 442 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: 554 Number of extensions: 28 Number of successful extensions: 6 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: 448 Length adjustment: 33 Effective length of query: 421 Effective length of database: 415 Effective search space: 174715 Effective search space used: 174715 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