Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate SM_b20423 SM_b20423 hypothetical protein
Query= SwissProt::Q84P52 (520 letters) >FitnessBrowser__Smeli:SM_b20423 Length = 458 Score = 364 bits (934), Expect = e-105 Identities = 183/433 (42%), Positives = 271/433 (62%), Gaps = 9/433 (2%) Query: 76 GWHSTDLEPL-VIQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATKQLNELA 134 G H+ P VI EG Y+ D++GK+ LDA AGL+C ++G ++ A +Q LA Sbjct: 24 GMHARGETPTRVIGGGEGVYITDISGKRSLDAFAGLYCVNVGYGRQKIADAIAEQAKNLA 83 Query: 135 FYHSFWNRSTKPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNNALGRPD 194 +YH++ T+ S+ L+K ++D M++ +F SGS+AN+T +KL+WYYNN LGRP+ Sbjct: 84 YYHAYVGHGTEASIRLSKMIIDR-APEGMSRVYFGLSGSDANETNIKLIWYYNNILGRPE 142 Query: 195 KKKFIARTKSYHGSTLISASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGETEEEFS 254 KKK I+R + YHGS +++ SL+GL H FDLP +LHT+ P+++R +EE+FS Sbjct: 143 KKKIISRWRGYHGSGVMTGSLTGLHLFHNAFDLPRAPILHTEAPYYFRRPDRSMSEEQFS 202 Query: 255 TRLANNLENLILKEGPETIAAFIAEPVMGAGGVIPPPATYFEKVQAILKKYDILFIADEV 314 A+ LE +IL EGP+T+AAFI EP++G GG++PPP Y+EK+QA+L+KYDIL +ADEV Sbjct: 203 QYCADKLEEMILAEGPDTVAAFIGEPILGTGGIVPPPKGYWEKIQAVLQKYDILLVADEV 262 Query: 315 ICGFGRLGTMFGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSNKLGTFS 374 + GFGRLGTMFG + Y IKPDL+++AK L+S Y P+ +VS ++ V+ S++LG Sbjct: 263 VTGFGRLGTMFGSDHYGIKPDLITIAKGLTSAYAPLSGTIVSDKLWQVLVKGSDELGAIG 322 Query: 375 HGFTYSGHPVSCAVALETLKIYKERNIIEQVNRISPKFQEGL-KAFSDSPIIGEIRGTGL 433 HG+TYS HP+ A + L++ E I+E F+ L KA D +GE+RG GL Sbjct: 323 HGWTYSAHPICAAAGIANLELIDELGIVENAGSTGAYFRAELQKAVGDHRHVGEVRGDGL 382 Query: 434 LHGTEFTDNKSPNDPFPPEWGIGAYFGARCEKHGVLVRV--AGDNIMMSPPYILSLEEID 491 + EF +++ F P +G A + GV+ R GD + +PP L+ +E D Sbjct: 383 MAAIEFVEDRDDRAFFDPGRKVGPQVAAALLERGVIGRAMPQGDILGFAPPLCLTRDEAD 442 Query: 492 ELIIKYGKALKDT 504 ++ KA DT Sbjct: 443 IVV----KAAADT 451 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: 628 Number of extensions: 21 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: 458 Length adjustment: 34 Effective length of query: 486 Effective length of database: 424 Effective search space: 206064 Effective search space used: 206064 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