Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate WP_012101318.1 CKL_RS04610 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= SwissProt::Q84P52 (520 letters) >NCBI__GCF_000016505.1:WP_012101318.1 Length = 451 Score = 239 bits (609), Expect = 2e-67 Identities = 138/425 (32%), Positives = 238/425 (56%), Gaps = 6/425 (1%) Query: 81 DLEPLVIQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATKQLNELAFYHSFW 140 + P+VI+K EG ++YD+ G +YLD ++ W +LG + R+ KQ++ + + F Sbjct: 24 EFNPIVIEKGEGVWLYDIEGNRYLDCVSSWWTNTLGHSNKRINETIKKQIDNIE-HVIFA 82 Query: 141 NRSTKPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNNALGRPDKKKFIA 200 N S KP++DL+++L+++ T +++AK FF+++GS A + +K+ ++Y+ G KK+F A Sbjct: 83 NFSNKPAVDLSEKLVNI-TPDRLAKVFFSDNGSSAVEIALKMSFHYHMQKGNTKKKRFAA 141 Query: 201 RTKSYHGSTLISASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGETEEEFSTRLANN 260 + +YHG TL + S+ + ++ ++ + + P +R G T + + + Sbjct: 142 LSDAYHGETLGALSVCDIDEYNKIYNPLLLDTIRVEGPDCYRCRY-GCTRDNCNAECFAD 200 Query: 261 LENLILKEGPETIAAFIAEP-VMGAGGVIPPPATYFEKVQAILKKYDILFIADEVICGFG 319 +E ++E + I+A I EP V GA G+ Y EK++ I KYD+ IADE+ GFG Sbjct: 201 MEKC-MEEKHDEISAVIIEPMVQGAAGMKIYSPNYLEKLRKICDKYDVHLIADEIAVGFG 259 Query: 320 RLGTMFGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSNKLGTFSHGFTY 379 R G MF C I PD + ++K +S+GYMP+ V+ + E+ D Y N+ F H TY Sbjct: 260 RAGEMFACNHAQISPDFMCLSKGISAGYMPMSVVMTTDEIYDCFYGDYNEQKAFLHSHTY 319 Query: 380 SGHPVSCAVALETLKIYKERNIIEQVNRISPKFQE-GLKAFSDSPIIGEIRGTGLLHGTE 438 +G+ SCA+ALE+LKI +E NIIE + ++ L+ S IGE+R G++ E Sbjct: 320 AGNATSCAIALESLKILEEDNIIENNRKKGNLIKKLTLEKAKVSKHIGEVRNIGMITAVE 379 Query: 439 FTDNKSPNDPFPPEWGIGAYFGARCEKHGVLVRVAGDNIMMSPPYILSLEEIDELIIKYG 498 +K +P E +G G+L+R G+ + PPYI++ EEI ++ K Sbjct: 380 IVKDKFTKKNYPWEMRVGYEIYKIALSKGLLLRPIGNVLYFIPPYIINEEEIKFMVNKCF 439 Query: 499 KALKD 503 +++++ Sbjct: 440 QSIEE 444 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: 553 Number of extensions: 27 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: 520 Length of database: 451 Length adjustment: 34 Effective length of query: 486 Effective length of database: 417 Effective search space: 202662 Effective search space used: 202662 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 24 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