Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate 353284 BT3758 acetylornithine aminotransferase (NCBI ptt file)
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__Btheta:353284 Length = 373 Score = 247 bits (630), Expect = 5e-70 Identities = 142/373 (38%), Positives = 218/373 (58%), Gaps = 6/373 (1%) Query: 23 VYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ 82 VY +D+ IV+GQG +VWD G EY+D GG+ V ++GH +P VE + Q TL Sbjct: 6 VYPLYDINIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGFYSN 65 Query: 83 TLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSG 142 ++ ++ + L I E +F +NSG EANE ALK A + GR K ++ + F G Sbjct: 66 SVINKLQQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFSKAFHG 125 Query: 143 RTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDE-ETAAVILEPVQGEGGVR 201 RT ++ T P P + V ++P ND+EA+K+ + + + AVI+E +QG GG++ Sbjct: 126 RTSLAVEATNNPTIIAP-INNNGHVTYLPLNDIEAMKQELAKGDVCAVIIEGIQGVGGIK 184 Query: 202 PATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVP 261 T EF++ R++ E G +LILDEIQ+G GR+GK FA ++ I PDI+T+AK +G G P Sbjct: 185 IPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITVAKGIGNGFP 244 Query: 262 LGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKL 321 + V+ + + + G GTTFGGN LA +A +A + +E+ L E A +G + +E+L Sbjct: 245 M-AGVLISPMFKPV-YGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVGDYLLEEL 302 Query: 322 RAIPSPKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLALQAGPTVIRFLPPLVIEKE 381 + P+I+EVRG GLM+GLE +E +RL + V +G V+R LPPL + E Sbjct: 303 KKF--PQIKEVRGRGLMIGLEFEEPIKELRSRLIYDEHVFTGASGTNVLRLLPPLCLSME 360 Query: 382 DLERVVEAVRAVL 394 + + + + VL Sbjct: 361 EADEFLARFKRVL 373 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: 329 Number of extensions: 11 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: 373 Length adjustment: 30 Effective length of query: 365 Effective length of database: 343 Effective search space: 125195 Effective search space used: 125195 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