Align Gamma aminobutyrate transaminase 1, mitochondrial; Gamma-aminobutyrate transaminase isozyme 1; LeGABA-TP1; SlGABA-T1; EC 2.6.1.96 (characterized)
to candidate GFF919 PGA1_c09350 aminotransferase class-III
Query= SwissProt::Q84P54 (515 letters) >FitnessBrowser__Phaeo:GFF919 Length = 450 Score = 374 bits (959), Expect = e-108 Identities = 197/438 (44%), Positives = 278/438 (63%), Gaps = 9/438 (2%) Query: 80 TDVDPLIIEKSEGSHVYDMQGRKYIDTLAGLWCTALGGNEPRLVDAATKQLNTLPFYHSF 139 T + L +E+ EG +V+D GRKYI+ LAGLWCT+LG + ++DA T+QL+ LPF H+F Sbjct: 12 TATEQLCLERGEGIYVFDSDGRKYIEGLAGLWCTSLGYSNTEVMDAITEQLHKLPFTHTF 71 Query: 140 WNRTTKPSLDLAKELLDMFTAKKMAKAFFTNSGSEANDTQVKLVWYYNNALGRPNKKKFI 199 +T +P DLA +L M + A FF NSGS+ANDT K++ YY NA+G+P K+K I Sbjct: 72 GGKTHQPIQDLADKLAAMVPVED-AYIFFGNSGSDANDTHYKMLRYYFNAIGKPEKRKII 130 Query: 200 ARAKAYHGSTLISASLTGLPALHQNFDLP--APFVLHTDCPHYWRYHLPGETEEEFSTRL 257 R + YHG T+ + SLT LPA +FD P A +L D PHY+ ETE +F R+ Sbjct: 131 TRERGYHGVTVAAGSLTSLPANLAHFDAPLEALSILRADSPHYYTARQGNETEAQFVERI 190 Query: 258 AKNLEDLILKEGPETIAAFIAEPVMGAGGVIPPPATYFDKIQAVVKKYDILFIADEVICA 317 +NLED I+ E P+TIAA I EP+ GA GVI PP Y++ +QA+++KY IL ADEVIC Sbjct: 191 LQNLEDQIISEDPDTIAAMIVEPITGASGVIVPPDGYYEGLQALLRKYGILIWADEVICG 250 Query: 318 FGRLGTMFGSDMYNIKPDLVTLAKALSSAYMPIGAVLVSPEVSDVIHSQSNKLGSFSHGF 377 FGR G FG I PDL+T AK LSSAY PI A ++ + + + Q+N++G F HG+ Sbjct: 251 FGRTGADFGCTTMGITPDLMTFAKQLSSAYFPISASVIPGWMYEAMVDQTNEVGVFGHGY 310 Query: 378 TYSGHPVACAVALEAIKIYKERNMVERVNRISPKFQEGLK-AFSDSPIIGEIRGLGLILA 436 TYSGHP ACA AL+ ++IY+ N+ + + Q L+ F+D P++GE+RG GLI A Sbjct: 311 TYSGHPAACAAALKTLEIYERDNLFDHAAEVGSYLQTQLREIFTDHPLVGEVRGKGLIAA 370 Query: 437 TEFANNKSPNDHFPPEWGVGAYFGAQCQKNGMLVR-VAGDTIMMSPPFVVTPEELDELIR 495 E +NK+ F + GA CQ NG+++R VAG+ + + PP ++T EE+D+++ Sbjct: 371 LELVSNKTTGASF-DKGRAGATAQRLCQDNGLILRAVAGNAVALCPPLIITREEVDDMLT 429 Query: 496 IYGKALRETEKRVEELKS 513 A+ + EELK+ Sbjct: 430 RLKTAI---DASYEELKA 444 Lambda K H 0.318 0.135 0.402 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: 561 Number of extensions: 16 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: 515 Length of database: 450 Length adjustment: 34 Effective length of query: 481 Effective length of database: 416 Effective search space: 200096 Effective search space used: 200096 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 (21.7 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