Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate RR42_RS26160 RR42_RS26160 4-aminobutyrate aminotransferase
Query= reanno::Marino:GFF3099 (404 letters) >FitnessBrowser__Cup4G11:RR42_RS26160 Length = 424 Score = 198 bits (504), Expect = 2e-55 Identities = 131/391 (33%), Positives = 199/391 (50%), Gaps = 32/391 (8%) Query: 28 RGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLS-NVMTNEPALR 86 R E + +WD EGR++ D GIAV GH HP ++ A+ Q E+ H + ++ E + Sbjct: 28 RAENATLWDVEGRQYTDFACGIAVLNTGHRHPRVMQAVIAQLERFTHTAYQIVPYESYVA 87 Query: 87 LAK---TLCDLTFAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHGRT 143 LA+ L + ++ +GAEA E A K+AR H G+ +I+F FHGRT Sbjct: 88 LAERINALVPIDGLKKTALFTTGAEAVENAVKIARA----HTGRPG--VIAFSGGFHGRT 141 Query: 144 LFTVSVGGQ-PKYLEGFEPAPGGIHHAEF-------------NDLESVKKL-ISKEKTCA 188 L +++ G+ Y GF P P I+HA F LES+ K I ++ A Sbjct: 142 LLGMALTGKVAPYKVGFGPFPSDIYHAPFPCDLHGVSTEQSIQALESLFKTDIDPQRVAA 201 Query: 189 IVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGVVPD 248 I++EP+QGEGG P F+Q LR LCD++ LL+ DEVQ+G GR+G +A Y V PD Sbjct: 202 IIIEPVQGEGGFHPAPVDFMQTLRALCDKHGILLIADEVQTGFGRTGKLFAMSHYPVAPD 261 Query: 249 ILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPEILK 308 +++ AK L GG P++A+ A + + G G TY GN LA A A V++T+ Q + + Sbjct: 262 LITMAKSLAGGMPLSAVCGRASIMDAPLPGGLGGTYAGNPLAVAAAHAVIETIEQERLCE 321 Query: 309 GVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGK-----AKDFLNAGLEE 363 A +L+ + + ++RG G ++ + G+ AK +E Sbjct: 322 RATALGKQLKAALQQASQTCPGIADIRGLGSMVAVEFHDPATGQPSAELAKRVQLRAMEA 381 Query: 364 GVMVLVAG--ANVIRLAPSLIIPEPDIELAL 392 G+++L G N IR L IP+ + AL Sbjct: 382 GLILLTCGTYGNTIRFLYPLTIPQAQFDAAL 412 Lambda K H 0.318 0.137 0.406 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: 438 Number of extensions: 19 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: 404 Length of database: 424 Length adjustment: 31 Effective length of query: 373 Effective length of database: 393 Effective search space: 146589 Effective search space used: 146589 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 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