Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate GFF4233 Psest_4306 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__psRCH2:GFF4233 Length = 441 Score = 171 bits (432), Expect = 5e-47 Identities = 120/401 (29%), Positives = 195/401 (48%), Gaps = 43/401 (10%) Query: 30 LIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ-TLPTPM 88 L+ +G ++G + +D G N GHG E+ EAV +Q + P + P+ Sbjct: 30 LLESAEGMYYTASDGRQVLDGTAGLWCCNAGHGRREISEAVSKQIAKMDFAPTFQMGHPL 89 Query: 89 RGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHT------GRKKFVAAMRGFSG 142 E L AI P LNRVF NSG+E+ + ALK A A+ R + + + G Sbjct: 90 PFELAEKLAAISPEGLNRVFFTNSGSESADTALKIALAYQRAIGQGSRTRLIGRELAYHG 149 Query: 143 RTMGSLSVTWEPKYREPFLPLVEPVEFIPYN------------------DVEALKRAVD- 183 G +SV R F P++ V+ +P+ + L+R V Sbjct: 150 VGFGGMSVGGMANNRRAFGPMLPGVDHLPHTLDLQRNAFSRGLPQHGVERADELERLVTL 209 Query: 184 ---EETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAF 240 E AAVI+EP+ G GV +L+ REIT + G LLI DE+ TG GR G+ FA Sbjct: 210 HGAENIAAVIVEPMSGSAGVILPPVGYLQRLREITAKHGILLIFDEVITGFGRVGEAFAA 269 Query: 241 EHFGIVPDILTLAKAL-GGGVPLGVAVMREEVARSMPKGG-------HGTTFGGNPLAMA 292 + +G+ PDILT AK L G +P+G + + + + KG HG T+ G+P+A A Sbjct: 270 QRWGVTPDILTCAKGLTNGAIPMGAVLAADHLFDAFMKGPESVIEFFHGYTYSGHPVACA 329 Query: 293 AGVAAIRYLERTRLWERAAELGPWFMEKLRAIPS-PKIREVRGMGLMVGLELKEKA---- 347 A +A + ++ L+++A +L P++ E L ++ P + ++R +GL+ G++ A Sbjct: 330 AALATQQIYQQENLFQKAIDLEPYWQEALFSLRDLPNVIDIRTVGLVAGIQFAAHADGVG 389 Query: 348 -APYIARLEKEHRVLALQAGPTVIRFLPPLVIEKEDLERVV 387 Y E + L ++A I P L++EK ++++++ Sbjct: 390 KRGYEVFRECFEKGLLVRASGDTIALSPALIVEKAEIDQMM 430 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: 391 Number of extensions: 20 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: 395 Length of database: 441 Length adjustment: 32 Effective length of query: 363 Effective length of database: 409 Effective search space: 148467 Effective search space used: 148467 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 09 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