Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate NP_661271.1 CT0367 acetylornithine aminotransferase
Query= BRENDA::Q93R93 (395 letters) >NCBI__GCF_000006985.1:NP_661271.1 Length = 400 Score = 241 bits (614), Expect = 3e-68 Identities = 149/390 (38%), Positives = 216/390 (55%), Gaps = 13/390 (3%) Query: 13 LEAEKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKR 72 LE EK L Y + L I G+G+ ++ A G Y+D + G GV +G+G+ + +A+ Sbjct: 8 LETEKQLFFHNYARLPLDIASGKGSFLYTASGERYLDMIAGVGVNAIGYGDKRLEQAITE 67 Query: 73 QAETLMAMPQTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFAR------A 126 QA + + + + L I +++VF NSGTEA EAA+K AR Sbjct: 68 QASKYIHVSNLFMQKPQFDLAAKLLEI--SRMSKVFFCNSGTEAIEAAIKLARRFAARNG 125 Query: 127 HTGRKKFVAAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEET 186 T + + ++ F GRT G+LS+T +PKY + F PLV I +NDVE L+R V T Sbjct: 126 DTDKTQVLSLTNCFHGRTYGALSLTAKPKYVDGFEPLVPETGMIDFNDVEDLERKVSNRT 185 Query: 187 AAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIV 246 AAV +E VQGEGG+ + F+ +E+ +E L++ DEIQ G GRTG F++ F I Sbjct: 186 AAVFVEFVQGEGGIHKVSEAFIAKLKELAKEHDFLIVADEIQAGCGRTGAFFSYMPFDIQ 245 Query: 247 PDILTLAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRL 306 PD++ +AK LGGG+PLG + E+VA G HGTTFGGNP+A AAG+A I + L Sbjct: 246 PDLVCVAKPLGGGLPLGAIIGSEKVAEVFTPGSHGTTFGGNPVACAAGLAMIEAILADGL 305 Query: 307 WERAAELGPWF---MEKLRAIPSPKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLAL 363 + A E+G EK+ A +I E+R GLM+G+ + +A Y+ K VL Sbjct: 306 MQNALEVGSMMRTAFEKM-AEKHAQILEIRQYGLMIGVTVHREAKYYVEEALK-RGVLVN 363 Query: 364 QAGPTVIRFLPPLVIEKEDLERVVEAVRAV 393 VIR LPPL I KE+ + ++ + A+ Sbjct: 364 ATSNNVIRLLPPLSISKEEAQLCLDTLDAI 393 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: 325 Number of extensions: 18 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: 395 Length of database: 400 Length adjustment: 31 Effective length of query: 364 Effective length of database: 369 Effective search space: 134316 Effective search space used: 134316 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