Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate SM_b20379 SM_b20379 aminotransferase
Query= SwissProt::Q84P52 (520 letters) >FitnessBrowser__Smeli:SM_b20379 Length = 461 Score = 497 bits (1280), Expect = e-145 Identities = 239/436 (54%), Positives = 315/436 (72%), Gaps = 1/436 (0%) Query: 69 MLAPFTAGWHSTDLEPLVIQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATK 128 ++ P+T + P VI +G YV D GK+Y++ LAGL+C LG +E RLV AAT+ Sbjct: 16 LVHPYTNLAVHQETGPHVITGGDGIYVVDDEGKRYIEGLAGLFCAGLGFSEQRLVEAATR 75 Query: 129 QLNELAFYHSFWNRSTKPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNN 188 QL + FYHSF ++ST+P + LA++LL + M+K FF SGSEANDT +KL+WYYNN Sbjct: 76 QLKTMPFYHSFAHKSTEPGIRLAEKLLSIAPV-PMSKVFFAGSGSEANDTAIKLIWYYNN 134 Query: 189 ALGRPDKKKFIARTKSYHGSTLISASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGE 248 ALGRP+KKK I+R K+YHG T+ +ASL+GLP H+ FDLP +LHTDCPH+WRF + GE Sbjct: 135 ALGRPEKKKIISRRKAYHGVTVATASLTGLPFNHRDFDLPIANILHTDCPHYWRFAETGE 194 Query: 249 TEEEFSTRLANNLENLILKEGPETIAAFIAEPVMGAGGVIPPPATYFEKVQAILKKYDIL 308 TEE+F+TR+ANNLE +IL+EGPETIAAF AEPVM +GGVI PP TYFEKVQA+L+KYDIL Sbjct: 195 TEEDFATRMANNLEAIILEEGPETIAAFFAEPVMVSGGVITPPKTYFEKVQAVLRKYDIL 254 Query: 309 FIADEVICGFGRLGTMFGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSN 368 IADEVICGFGR G MFG E Y +KPD++S AK LS+ YMPI A++++ +++D + QS Sbjct: 255 LIADEVICGFGRTGNMFGSETYGLKPDMISCAKQLSAAYMPISALMINAKIADALVDQSR 314 Query: 369 KLGTFSHGFTYSGHPVSCAVALETLKIYKERNIIEQVNRISPKFQEGLKAFSDSPIIGEI 428 K+GTFSHGFTY GHPV+ AVALE L IY+E +I+ V ++P FQ+ ++ + P+IGE Sbjct: 315 KIGTFSHGFTYGGHPVAAAVALEALTIYEEIDIVGHVRSVAPAFQDRVRKLGEHPLIGEA 374 Query: 429 RGTGLLHGTEFTDNKSPNDPFPPEWGIGAYFGARCEKHGVLVRVAGDNIMMSPPYILSLE 488 RG GL+ G EF +K+ + FPP W + G GVL R GD + + P I+ E Sbjct: 375 RGVGLVAGLEFVKDKATRENFPPAWQVANQAGKFATARGVLTRGLGDMVSLCPAMIIDDE 434 Query: 489 EIDELIIKYGKALKDT 504 +ID+L+ + G AL DT Sbjct: 435 QIDDLMTRMGLALDDT 450 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: 608 Number of extensions: 20 Number of successful extensions: 2 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: 461 Length adjustment: 34 Effective length of query: 486 Effective length of database: 427 Effective search space: 207522 Effective search space used: 207522 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