Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate AZOBR_RS03635 AZOBR_RS03635 aminotransferase
Query= SwissProt::Q84P52 (520 letters) >FitnessBrowser__azobra:AZOBR_RS03635 Length = 471 Score = 469 bits (1207), Expect = e-136 Identities = 229/433 (52%), Positives = 308/433 (71%), Gaps = 3/433 (0%) Query: 70 LAPFTAGWHSTDLE-PLVIQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATK 128 L P+T H+ + + PL+I++ EG V+D +GK+Y++ LA LWC SLG E RLV AAT+ Sbjct: 32 LHPYT-NLHAHETQGPLIIERGEGVRVFDDSGKEYIEGLASLWCVSLGWGEERLVEAATR 90 Query: 129 QLNELAFYHSFWNRSTKPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNN 188 Q+ +L YH F ++S +P +DLA+ L+ L M+K FF NSGSEANDT VKLVWYYNN Sbjct: 91 QMRKLPTYHVFGHKSHEPGIDLAERLIKLAPV-PMSKVFFANSGSEANDTAVKLVWYYNN 149 Query: 189 ALGRPDKKKFIARTKSYHGSTLISASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGE 248 ALGRP+KKK ++R K+YHG T+ +ASL+GL H+ FDLP + HTDCPH +RF +PGE Sbjct: 150 ALGRPEKKKILSRVKAYHGVTVATASLTGLVNNHRDFDLPIARIQHTDCPHHYRFAEPGE 209 Query: 249 TEEEFSTRLANNLENLILKEGPETIAAFIAEPVMGAGGVIPPPATYFEKVQAILKKYDIL 308 +EE+F+TRLA +LE LIL EGPETIAA AEPVMGAGGVI PPATYF K+Q ILKKYDIL Sbjct: 210 SEEDFATRLAESLEALILAEGPETIAAMFAEPVMGAGGVIVPPATYFAKIQPILKKYDIL 269 Query: 309 FIADEVICGFGRLGTMFGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSN 368 +ADEVICGFGR G +G + ++PD+++ AK LSSGY+PI AV+VS V +S Sbjct: 270 LVADEVICGFGRTGNFWGSQTMGMQPDILTCAKQLSSGYLPISAVMVSDAVYRACVEESK 329 Query: 369 KLGTFSHGFTYSGHPVSCAVALETLKIYKERNIIEQVNRISPKFQEGLKAFSDSPIIGEI 428 K+GTF HG+TYS HPV+ AVA+ETLKIY+ER+++ V ++P FQ LKA +D P++GE Sbjct: 330 KIGTFGHGYTYSAHPVAAAVAIETLKIYEERDLVGHVRAVAPLFQRRLKALADHPLVGEA 389 Query: 429 RGTGLLHGTEFTDNKSPNDPFPPEWGIGAYFGARCEKHGVLVRVAGDNIMMSPPYILSLE 488 RG GL+ E +K PF P GA +++G+++R GD++ + PP ++ E Sbjct: 390 RGVGLIGALELVADKETKTPFDPVGRAGAVVNGLSQENGLIIRAMGDSVAVCPPLVIGEE 449 Query: 489 EIDELIIKYGKAL 501 +I+ + + AL Sbjct: 450 DINRMFDRLTTAL 462 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: 645 Number of extensions: 18 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: 471 Length adjustment: 34 Effective length of query: 486 Effective length of database: 437 Effective search space: 212382 Effective search space used: 212382 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