Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate WP_015798369.1 AFER_RS04845 aspartate aminotransferase family protein
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_000023265.1:WP_015798369.1 Length = 431 Score = 182 bits (463), Expect = 1e-50 Identities = 144/408 (35%), Positives = 195/408 (47%), Gaps = 37/408 (9%) Query: 23 VYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQ-AETLMAMP 81 +Y + + RG+G VWDA G Y+DC GG ++GH PE+V A+ Q A + + Sbjct: 17 LYYDEPIELDRGEGCWVWDAHGERYLDCFGGILTTSVGHNVPEIVSAISDQAARVIHSST 76 Query: 82 QTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFS 141 L PM R A P+ +VF SGTEAN+AAL A A G + A + Sbjct: 77 LYLNRPMIELAERLAKASGIPDA-KVFFTTSGTEANDAALLLATAALGSNQVFALRNSYH 135 Query: 142 GRTMGSLSV----TWEPKYREPF--------------LPLVEPVEFIPYN--DVE-ALKR 180 GR+ ++V TW P P L + E++ D+E AL Sbjct: 136 GRSFTEIAVTGNRTWSPTSYSPLSVSWLQGGSRLRGPLAGLSDAEYVARGVADLEDALLT 195 Query: 181 AVDEETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRF-A 239 AA+I EP+QG GG + +TQ +G L I DE+QTG GRTG+ F Sbjct: 196 TTAGRVAALIAEPIQGVGGFCLPPDGYFGELWRVTQREGILWISDEVQTGFGRTGEHFWG 255 Query: 240 FEHFGIVPDILTLAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIR 299 +E GI PD++T AK +G G+ L + R EV ++ +TFGG+P+ AAGVA Sbjct: 256 YEAHGITPDLITFAKGVGNGMSLAGVIGRAEVMDALGTNSI-STFGGSPITAAAGVATFD 314 Query: 300 YLERTRLWERAAELGPWFMEKLRAI--PSPKIREVRGMGLMVGLEL----KEKAAPYIA- 352 Y+ L A G E L AI +P I EVRG GLM G+EL + AP +A Sbjct: 315 YIIDHDLMANARARGAELREGLDAIARSTPAIGEVRGKGLMQGVELVWPGTVEPAPELAT 374 Query: 353 -RLEKEHR--VLALQAG--PTVIRFLPPLVIEKEDLERVVEAVRAVLA 395 LE R VL + G V+R PP+ I E +E +EA R A Sbjct: 375 RALEAARREGVLIGKGGLHGNVLRIAPPMTISAEQIEHALEAFRRSFA 422 Lambda K H 0.319 0.137 0.403 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: 429 Number of extensions: 22 Number of successful extensions: 7 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: 395 Length of database: 431 Length adjustment: 31 Effective length of query: 364 Effective length of database: 400 Effective search space: 145600 Effective search space used: 145600 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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