Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate N515DRAFT_1751 N515DRAFT_1751 adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= SwissProt::Q84P52 (520 letters) >FitnessBrowser__Dyella79:N515DRAFT_1751 Length = 467 Score = 222 bits (566), Expect = 2e-62 Identities = 126/420 (30%), Positives = 224/420 (53%), Gaps = 9/420 (2%) Query: 78 HSTDLEPLVIQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATKQLNELAFYH 137 H+ + L I + EG ++ D +G++YLD ++ W G PR+ AA +QL+ L + Sbjct: 41 HAGTVPMLPIVRGEGPWLVDADGRRYLDGISSWWTNLFGHANPRIGAALKQQLDTLE-HV 99 Query: 138 SFWNRSTKPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNNALGRPDKKK 197 F + +P+++LA+ L + A + + F ++GS A + +K+ ++Y G K + Sbjct: 100 IFAGFTHEPAIELAERLAQITPAG-LERVFLADNGSAAIEVALKMSFHYWLNQGAGQKTR 158 Query: 198 FIARTKSYHGSTLISASLSGLPALHQQFDLPAPFVLH---TDCPHFWRFHQPGETEEEFS 254 FIA T SYHG TL + S+S + + + AP +L P + +PGE+ E + Sbjct: 159 FIALTGSYHGETLGALSVSDVALYRKTY---APLLLTPVLAPSPDAYEA-EPGESAEACA 214 Query: 255 TRLANNLENLILKEGPETIAAFIAEPVMGAGGVIPPPATYFEKVQAILKKYDILFIADEV 314 R L L+ + ET A + V AGG+ +Y ++A+ ++ + FIADE+ Sbjct: 215 ARRLGELRVLLEQHAHETCAVIVEPLVQCAGGMRMYHPSYLTGLRALCDEFGVHFIADEI 274 Query: 315 ICGFGRLGTMFGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSNKLGTFS 374 GFGR GT+F CE+ + PD + ++K L+ G++P+ AVL + V + Y++ N F Sbjct: 275 AVGFGRTGTLFACEQAGVSPDFMCLSKGLTGGFLPLSAVLTTTPVYEAFYAEYNAGKAFL 334 Query: 375 HGFTYSGHPVSCAVALETLKIYKERNIIEQVNRISPKFQEGLKAFSDSPIIGEIRGTGLL 434 H +Y+G+P++C AL TL I+++ ++E+ ++ L + P + ++R TG++ Sbjct: 335 HSHSYTGNPLACRAALATLDIFRDEPVLERNRELAAHLARRLAPLREHPQVADVRQTGMI 394 Query: 435 HGTEFTDNKSPNDPFPPEWGIGAYFGARCEKHGVLVRVAGDNIMMSPPYILSLEEIDELI 494 E +K+ P+P E G +HG L+R G+ + PPY++S +E+D L+ Sbjct: 395 AAVELVRDKATRAPYPSEERRGLRVYLHGLEHGALLRPLGNVVYFMPPYVVSTDELDHLV 454 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: 519 Number of extensions: 22 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: 520 Length of database: 467 Length adjustment: 34 Effective length of query: 486 Effective length of database: 433 Effective search space: 210438 Effective search space used: 210438 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