Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate 3608039 Dshi_1446 aminotransferase class-III (RefSeq)
Query= SwissProt::Q84P52 (520 letters) >FitnessBrowser__Dino:3608039 Length = 444 Score = 240 bits (612), Expect = 9e-68 Identities = 140/422 (33%), Positives = 222/422 (52%), Gaps = 15/422 (3%) Query: 92 GSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATKQLNELAFYHSFWNRSTKPSLDLA 151 G Y+ D +GK+YLD G + LG + P + AA Q++++AF H+ + T ++ Sbjct: 21 GCYIIDADGKRYLDGSGGAAVSCLGHDHPAVRAALHAQIDKIAFAHTGF--FTSEPAEVL 78 Query: 152 KELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNNALGRPDKKKFIARTKSYHGSTLI 211 + L + K + + GSE+ + +KL + G P + + IAR +SYHG+TL Sbjct: 79 CDALIAAAPKGIEKVYLLSGGSESVEAALKLARQFFLETGEPRRHRVIARRQSYHGNTLG 138 Query: 212 SASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGETEEEFSTRLANNLENLILKEGPE 271 + + G +++ H D + +R GE++ + R A+ L I + GPE Sbjct: 139 ALAAGGNAWRREKYAPLLVETYHIDPCYAYRHQAVGESDAAYGRRAADALRTEIERLGPE 198 Query: 272 TIAAFIAEPVMGA-GGVIPPPATYFEKVQAILKKYDILFIADEVICGFGRLGTMFGCEKY 330 T+ AFIAEPV+GA G +PP YFE+++ I +Y +L I DEV+CG GR GT+F CE+ Sbjct: 199 TVMAFIAEPVVGATAGAVPPAPGYFERIREICDEYGVLLILDEVMCGMGRTGTLFACEQD 258 Query: 331 NIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSNKLGTFSHGFTYSGHPVSCAVAL 390 I PD+V++AK L +GY PIGA+L S + D I S G+F HG TY GHP++ A A Sbjct: 259 GISPDIVTIAKGLGAGYAPIGAMLASGRIYDAIAQGS---GSFQHGHTYHGHPLAAAAAG 315 Query: 391 ETLKIYKERNIIEQVNRISPKFQEGLK-AFSDSPIIGEIRGTGLLHGTEFTDNKSPNDPF 449 ++ + + QV Q L+ A +G+IRG GL G E +++ P Sbjct: 316 AVVETLRAPGTMAQVRAKGATLQSRLEAALGQHSHVGDIRGRGLFRGIELVEDRDTKRPL 375 Query: 450 PPEWGIGAYFGARCEKHGVLVRVA--------GDNIMMSPPYILSLEEIDELIIKYGKAL 501 P + A A G++ GD+I+++PP+I+ ++ID L+ +A+ Sbjct: 376 DPARKVSARIKAAAMARGLICYPGSGTIDGKHGDHILLAPPFIIEDKQIDALVHMLAEAI 435 Query: 502 KD 503 D Sbjct: 436 DD 437 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: 531 Number of extensions: 23 Number of successful extensions: 7 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: 444 Length adjustment: 34 Effective length of query: 486 Effective length of database: 410 Effective search space: 199260 Effective search space used: 199260 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: 51 (24.3 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