Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate GFF4233 Psest_4306 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >FitnessBrowser__psRCH2:GFF4233 Length = 441 Score = 305 bits (782), Expect = 1e-87 Identities = 173/433 (39%), Positives = 257/433 (59%), Gaps = 21/433 (4%) Query: 15 SSEHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELAD 74 S +H PF+ +Q K PR++ +A+G+Y S+G ++LDG AGLWC G+GR E+++ Sbjct: 10 SPDHFWMPFTANRQFKAS-PRLLESAEGMYYTASDGRQVLDGTAGLWCCNAGHGRREISE 68 Query: 75 AASKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRH 134 A SKQ+ ++ + F Q HP ELA+ ++ I+PEG+N VFFT SGSE DT L++ Sbjct: 69 AVSKQIAKMDFAPTF-QMGHPLPFELAEKLAAISPEGLNRVFFTNSGSESADTALKIALA 127 Query: 135 YWAIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIP-----QPYW 189 Y GQ ++ +I R YHG G S+GGM +PG+ H+P Q Sbjct: 128 YQRAIGQGSRTRLIGRELAYHGVGFGGMSVGGMANNRRAFGPMLPGVDHLPHTLDLQRNA 187 Query: 190 FGEGGDMTPEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEI 249 F G + G+ A++LE + G + + A I EP+ G+ GVI+PP Y R++EI Sbjct: 188 FSRG----LPQHGVERADELERLVTLHGAENIAAVIVEPMSGSAGVILPPVGYLQRLREI 243 Query: 250 LAKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVE 309 AK+ IL + DEVI GFGR GE F + +G+ PD++T AKGLT+G IPMG ++ D + + Sbjct: 244 TAKHGILLIFDEVITGFGRVGEAFAAQRWGVTPDILTCAKGLTNGAIPMGAVLAADHLFD 303 Query: 310 VLNEGG----DFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELN 365 +G +F HG+TYSGHPVA A AL +I ++E + + + PY Q+ L L Sbjct: 304 AFMKGPESVIEFFHGYTYSGHPVACAAALATQQIYQQENLFQKA-IDLEPYWQEALFSLR 362 Query: 366 DHPLVGEVRGVGLLGAIELVQDKATRARYVGKGVGMICRQFCFDNGLIMRAVGDTMIIAP 425 D P V ++R VGL+ I+ A A VGK + R+ CF+ GL++RA GDT+ ++P Sbjct: 363 DLPNVIDIRTVGLVAGIQF----AAHADGVGKRGYEVFRE-CFEKGLLVRASGDTIALSP 417 Query: 426 PLVITKAEIDELV 438 L++ KAEID+++ Sbjct: 418 ALIVEKAEIDQMM 430 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: 525 Number of extensions: 26 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: 441 Length adjustment: 33 Effective length of query: 421 Effective length of database: 408 Effective search space: 171768 Effective search space used: 171768 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