Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate AO356_28705 AO356_28705 hypothetical protein
Query= reanno::SB2B:6938540 (460 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28705 Length = 449 Score = 299 bits (766), Expect = 1e-85 Identities = 171/437 (39%), Positives = 254/437 (58%), Gaps = 13/437 (2%) Query: 22 HPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRKSIADAAYAQL 81 HP + SA + T +I R +G YI D +G+++LD + GLW VNVG+ R S+ A AQL Sbjct: 14 HPMSSSAPANRSKTLIIARGDGNYITDIEGHRMLDGVGGLWNVNVGHNRPSVKAAIAAQL 73 Query: 82 QTLPFYNNFFQCTHEPAIRLASKIASL-APGHMNRVFFTGSGSEANDTNLRMVRRYWDLK 140 L +Y F H LA ++ S+ A +M RV F+ GS+A +T L+M R+YW Sbjct: 74 DELAYYQTFDGIAHPRVFDLAERLTSMFAQENMARVLFSSGGSDAVETALKMARQYWIAS 133 Query: 141 GMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPGIVHIDQPYWFGEGRDM-SP 199 G P + +S +N YHG V G S+GG G H + G +D P+ + D P Sbjct: 134 GEPGRTRFLSLRNGYHGVHVGGTSVGGNGVYHYNHGPLLAGCHLLDTPWLYRNPWDCRDP 193 Query: 200 EAFGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPDSYWNEIKRILEKYNILFI 259 E + LE +I LG +AA IAEP QGAGGVI+PP YW ++ + +++ IL I Sbjct: 194 EELTAHCIRQLEDQIALLGPQTIAALIAEPVQGAGGVIVPPAHYWKRLREVCDRHGILLI 253 Query: 260 LDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVADVLISDGGEF 319 DEV++GFGRTG ++ G+ PD++ +AKG+T+GYIPMG + + R+AD I +G F Sbjct: 254 ADEVVTGFGRTGCMLGSRGWGVAPDVLCLAKGITAGYIPMGATVFNQRIADA-IENGPGF 312 Query: 320 A----HGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTLS-AHPLVGE 374 + HG+TYSGHP A A AL + I+E E L G L ++LQ L+ + +VGE Sbjct: 313 SSVIMHGYTYSGHPTACAAALAVLDIVEAEDLPGNA-GKVGAQLLEQLQPLTERYAVVGE 371 Query: 375 VRGMGMVGAIELVADKHSMVRFGSEISAGMLCR--EACIESGLVMRAVGDTMIISPPLCI 432 VRG G++ A++LVADK + R + + G+ R E +G+++R +G+ +++SPPL + Sbjct: 372 VRGKGLMIAVDLVADK--VTREPLDPANGLASRIAEQARRAGVLVRPIGNKIVMSPPLTL 429 Query: 433 TRDEIDELIFKASQALS 449 T DE ++ AL+ Sbjct: 430 TSDEAAMMVGALDGALA 446 Lambda K H 0.321 0.137 0.408 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: 533 Number of extensions: 23 Number of successful extensions: 4 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: 460 Length of database: 449 Length adjustment: 33 Effective length of query: 427 Effective length of database: 416 Effective search space: 177632 Effective search space used: 177632 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