Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate PfGW456L13_3206 Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::D2Z0I0 (402 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3206 Length = 396 Score = 154 bits (389), Expect = 4e-42 Identities = 113/375 (30%), Positives = 184/375 (49%), Gaps = 17/375 (4%) Query: 28 LRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHGYSASKGIPRLRKAICDFYKRR 87 LR +GEDI+ L +G+PD Q I+ + N H Y+ +G LR+AI +++R Sbjct: 27 LREQGEDILLLSVGDPDFDTPQPIVQGAIDSLLNGNTH-YAEVRGKRALREAIARRHQQR 85 Query: 88 YGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPNPTYPIHYYAPIICGGDAISVP 147 G + ++ ++ GA+ + +L PGD VIV P Y + CG + VP Sbjct: 86 SGQSVSADQVTVLA-GAQCALFSVAQCVLNPGDEVIVAEPMYVTYEAVFGACGAVVVPVP 144 Query: 148 ILPEEDF---PEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTTLCVDLEFFQEVVKLAKQE 204 + E F PE R+ + +A+ L+ PHNP+ + + + +L Sbjct: 145 VRSENGFRVLPEDVAARITP-------RTRALALNSPHNPSGASLPRSTWAALAELCIAH 197 Query: 205 GIWIVHDFAYADLGFDG-YTPPSILQVEGALDVAVELYSMSKGFSMAGWRVAFVVGNEML 263 +W++ D Y++L F+G + P+ L G + L S+SK +M GWRV +VV L Sbjct: 198 DLWLISDEVYSELLFEGEHVSPASLP--GMAERTATLNSLSKSHAMTGWRVGWVVAPPSL 255 Query: 264 IKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRRRRDVLVEGL-NRVGWEV 322 +L +L + YG IQ A+++ALES +E RE YR+RRD++ + L + G Sbjct: 256 AAHLENLALCMLYGSPDFIQDAAVVALESNLPELEAMREAYRQRRDLVCDSLADCPGVRA 315 Query: 323 KKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVSPGIGFGEYGEGYVRFALVENEHR 382 KP G MFV + + G+++ F+ LL V+V G FG G++R LV Sbjct: 316 LKPDGGMFVMLDI-RQTGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVVGAEP 374 Query: 383 IRQAVRGIKKALDKI 397 +R A + I + ++ Sbjct: 375 LRDACQRIARCAQEL 389 Lambda K H 0.322 0.141 0.425 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: 352 Number of extensions: 21 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: 402 Length of database: 396 Length adjustment: 31 Effective length of query: 371 Effective length of database: 365 Effective search space: 135415 Effective search space used: 135415 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 (21.9 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