Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 353284 BT3758 acetylornithine aminotransferase (NCBI ptt file)
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Btheta:353284 Length = 373 Score = 199 bits (507), Expect = 1e-55 Identities = 127/373 (34%), Positives = 207/373 (55%), Gaps = 24/373 (6%) Query: 78 DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137 D G E++D GG + ++GH +P V + NQ+A +S +++ L+ +A+ L ++ Sbjct: 24 DENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGFYSNSVINKLQQQVAERLGKIS 83 Query: 138 PGKLKYSFFC-NSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTF 196 G YS F NSG E+ E ALKLA Y G+ I+ S AFHG++ A+ AT T Sbjct: 84 -GYEDYSLFLINSGAEANENALKLASFYN---GRTKVISFSKAFHGRTSLAVEATNNPTI 139 Query: 197 RKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTA 256 P ++P +IEAM+ L + DV AVI+E IQG GG+ +P ++ Sbjct: 140 IAPINNN-GHVTYLPLNDIEAMKQELAK-----GDVCAVIIEGIQGVGGIKIPTTEFMQE 193 Query: 257 VRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATE 316 +RK+C E G ++ILDE+Q+G GR+GK FA ++ ++QPDI+ +AK +G G G I+ Sbjct: 194 LRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITVAKGIGNGFPMAGVLIS-- 251 Query: 317 EVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLARE 376 +F ++ TTFGGN LAC+AALA ++V+ + NL A+ GD LL+ ++ + Sbjct: 252 PMFKPVYGQ---LGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVGDYLLEELKKFPQ- 307 Query: 377 YPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLTLTIE 436 ++E RG+G+++ +EF E S + + G + +R+ PPL L++E Sbjct: 308 ----IKEVRGRGLMIGLEF--EEPIKELRSRLIYDEHVFTGA-SGTNVLRLLPPLCLSME 360 Query: 437 QCELVIKAARKAL 449 + + + ++ L Sbjct: 361 EADEFLARFKRVL 373 Lambda K H 0.320 0.135 0.393 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: 348 Number of extensions: 14 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: 459 Length of database: 373 Length adjustment: 31 Effective length of query: 428 Effective length of database: 342 Effective search space: 146376 Effective search space used: 146376 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 (21.8 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