Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate GFF2981 HP15_2925 adenosylmethionine-8-amino-7-oxononanoate transaminase
Query= SwissProt::Q84P52 (520 letters) >FitnessBrowser__Marino:GFF2981 Length = 450 Score = 222 bits (566), Expect = 2e-62 Identities = 133/413 (32%), Positives = 220/413 (53%), Gaps = 8/413 (1%) Query: 84 PLV-IQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATKQLNELAFYHSFWNR 142 PLV I++ EG ++ D G +++DA++ W G PR+ AA KQ+ EL H Sbjct: 29 PLVPIKRGEGVWLEDFEGNRFIDAVSSWWVNLFGHANPRINAAIQKQIGELE--HVILAG 86 Query: 143 ST-KPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNNALGRPDKKKFIAR 201 T +P ++L++ L+++ T + K F+ ++GS A + +K+ ++Y +P KK F+ Sbjct: 87 FTHEPVVNLSERLIEV-TPPGLNKVFYADNGSSAIEAALKMSFHYWKNHDKPGKKNFVNL 145 Query: 202 TKSYHGSTLISASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGETEEEFSTRLANNL 261 + SYHG TL + +L + + VL P + +PGET+E+++ R + Sbjct: 146 SNSYHGETLGALALGDVSLYKDTYQPLLMEVLTAPSPDAFN-KEPGETDEDYALRQFEAM 204 Query: 262 ENLILKEGPETIAAFIAEPVMG-AGGVIPPPATYFEKVQAILKKYDILFIADEVICGFGR 320 E L L E E I A + EP++ AGG+ Y K++ +Y + IADE+ GFGR Sbjct: 205 EKL-LAEKHEEICAVVVEPLIQCAGGMRMHHPIYHTKLREACDRYGVHLIADEIAVGFGR 263 Query: 321 LGTMFGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSNKLGTFSHGFTYS 380 GT+F CE+ I PD + ++K L++GY+P+ VL + +V + Y L F H +Y+ Sbjct: 264 TGTLFACEQSGITPDFMCLSKGLTAGYLPLSVVLTTDDVYNAFYDDYETLKAFLHSHSYT 323 Query: 381 GHPVSCAVALETLKIYKERNIIEQVNRISPKFQEGLKAFSDSPIIGEIRGTGLLHGTEFT 440 G+P+ CAVAL TL I+++ N+IE +S E + +D P +G+IR G+ E Sbjct: 324 GNPIGCAVALATLDIFRDDNVIESNRALSTCMAESVAHLADHPNVGDIRQHGMTLAVEMV 383 Query: 441 DNKSPNDPFPPEWGIGAYFGARCEKHGVLVRVAGDNIMMSPPYILSLEEIDEL 493 +K+ PFP + G L+R G+ + PPY+++ E+I L Sbjct: 384 KDKASKTPFPWQERRGIRVYQHALTRQALLRPLGNVVYFMPPYVITEEQIRHL 436 Lambda K H 0.317 0.135 0.401 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: 512 Number of extensions: 24 Number of successful extensions: 3 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: 520 Length of database: 450 Length adjustment: 34 Effective length of query: 486 Effective length of database: 416 Effective search space: 202176 Effective search space used: 202176 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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