Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate 3608649 Dshi_2042 aminotransferase class-III (RefSeq)
Query= BRENDA::P73133 (429 letters) >FitnessBrowser__Dino:3608649 Length = 460 Score = 185 bits (470), Expect = 2e-51 Identities = 141/421 (33%), Positives = 209/421 (49%), Gaps = 40/421 (9%) Query: 43 PIAIARGQGSTLWDTEGKSYLDFVAG-IATCTLGHAHPALVRAVSDQIQKLHHVSN-LYY 100 P I G+G +WD GK +LD V+G + T +G+ + AV DQ+ ++ SN L Sbjct: 36 PRIIVEGKGMRVWDALGKEHLDAVSGGLWTVNVGYGRERIANAVRDQLMQMCFFSNSLGT 95 Query: 101 IPEQGELAKWIVEHSCADRVFFCNSGAEANEAAIKLVRKYAHTVLDFLEQPVILTAKASF 160 IP I + RV++ +SG+EANE A K+VR+ AH V + IL + + Sbjct: 96 IPGAIFSEMLIDKMPGMSRVYYASSGSEANEKAFKMVRQIAHKVHGG-RKTKILYRERDY 154 Query: 161 HGRTLATITATGQPKYQQYFDPLVPGFDYVPYN-------DIRSLENKVAD------LDE 207 HG TLAT++A GQ + + + P P F VP+ + + + AD L E Sbjct: 155 HGSTLATMSAGGQWERKAQYGPFAPDFVEVPHCLEYRAQWEGENYGERAADAIEEVILRE 214 Query: 208 GNSRVAAIFLEPLQGEGGVRPGDLAYFKRVREICDQNDILLVFDEVQVGVGRTGKLWGYE 267 G V A+ LEP+ GGV Y+ RV+EIC + D+LL DEV G+GRTGK +GY+ Sbjct: 215 GPDTVGALCLEPVTAGGGVITPPEGYWPRVQEICRKYDVLLHIDEVVCGLGRTGKWFGYQ 274 Query: 268 HLGVEPDIFTSAKGLAGGVPIGAMM--CKKFCDVF--EPG------NHASTFGGNPLACA 317 H G+EPD T AKG+A G + M ++ ++F EPG STFGG A Sbjct: 275 HYGIEPDFVTMAKGVASGYAAISCMVTTERVFEMFKSEPGAPLDYFRDISTFGGCTAGPA 334 Query: 318 AGLAVLKTIEGDRLLDNVQARGEQLRSGLAEIKNQYPTLFTEVRGWGLINGLEISAESSL 377 A + +K IE + LL N +QL LA + ++ + ++RG GL G E+ A+ + Sbjct: 335 AAIENMKIIEEEDLLGNTDRMHDQLMGNLAGLMEKH-RVIGDIRGKGLFCGAELVADRTT 393 Query: 378 TS-------VEIVKAAMEQGLLLA------PAGPKVLRFVPPLVVTEAEIAQAVEILRQA 424 +V M QG+++ P L F P L+ T +I Q + + A Sbjct: 394 KEPAPEALVQAVVADCMAQGVIIGATNRSLPGYNNTLCFSPALIATADDIDQITDAVDGA 453 Query: 425 I 425 + Sbjct: 454 L 454 Lambda K H 0.320 0.137 0.405 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: 476 Number of extensions: 19 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: 429 Length of database: 460 Length adjustment: 32 Effective length of query: 397 Effective length of database: 428 Effective search space: 169916 Effective search space used: 169916 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: 51 (24.3 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