Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate 5208454 Shew_0966 beta alanine--pyruvate transaminase (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >FitnessBrowser__PV4:5208454 Length = 446 Score = 290 bits (741), Expect = 8e-83 Identities = 165/433 (38%), Positives = 248/433 (57%), Gaps = 24/433 (5%) Query: 17 EHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAA 76 EH+ PF+ +Q K+ PR++ A+G+Y D G +LDG AGLWC G+GR +++A Sbjct: 16 EHYWMPFTANRQFKQS-PRLLAQAEGMYYKDVNGRPVLDGTAGLWCCNAGHGRKAISEAV 74 Query: 77 SKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYW 136 SKQ+ E+ Y F Q HP ELA+ ++ IAP+G+N VFFT SGSE DT L++ +Y Sbjct: 75 SKQIHEMDYAPSF-QMGHPLAFELAERLAAIAPKGINKVFFTNSGSESVDTALKIALNYH 133 Query: 137 AIKGQPNKKVIISRINGYHGSTVAGASLGGM-----TYMHEQGDLPIPGIVHIPQPYWFG 191 +G+ + I R GYHG G S+GG+ T+ + + G+ H+P Sbjct: 134 RARGEATRTRFIGRELGYHGVGFGGISVGGIGGNRRTFSQQL----LQGVDHLPHTLDIQ 189 Query: 192 EGGDMTP-EEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEIL 250 + E G A LE+ + G + + A I EP+ G+ GVI+PP Y R++EI Sbjct: 190 QNAFCKGLPETGAEKAEVLEQLVTLHGAENIAAVIVEPMSGSAGVILPPQGYLKRLREIT 249 Query: 251 AKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEV 310 KY IL + DEVI GFGR G+ F S +G+ PDM+T AK L +G IPMG +++ D + + Sbjct: 250 RKYGILLIFDEVITGFGRVGDAFASQRWGVTPDMITTAKALNNGTIPMGAVLIDDAIYDA 309 Query: 311 ---LNEGG-DFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELND 366 EG + HG+TYSGHPVAAA A+ + I +EE++ E ++ Y +K + L Sbjct: 310 SMDAPEGAIELYHGYTYSGHPVAAAAAIATLDIYQEEQLFERTKS-LEGYFEKAVHSLKG 368 Query: 367 HPLVGEVRGVGLLGAIEL-VQDKATRARYVGKGVGMICRQFCFDNGLIMRAVGDTMIIAP 425 P + ++R GL+ I+ DK R G G+ + CF NG ++RA DT+ ++P Sbjct: 369 LPNLIDIRNTGLVAGIQFSPSDKGIGKR----GFGIF--ETCFKNGTLVRATADTIALSP 422 Query: 426 PLVITKAEIDELV 438 PL++ +A+ID++V Sbjct: 423 PLIVDEAQIDQMV 435 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: 521 Number of extensions: 22 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: 446 Length adjustment: 33 Effective length of query: 421 Effective length of database: 413 Effective search space: 173873 Effective search space used: 173873 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