Align Probable 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized)
to candidate WP_109969430.1 DK846_RS13185 aspartate aminotransferase family protein
Query= curated2:P94427 (436 letters) >NCBI__GCF_003173355.1:WP_109969430.1 Length = 400 Score = 214 bits (546), Expect = 3e-60 Identities = 131/400 (32%), Positives = 209/400 (52%), Gaps = 38/400 (9%) Query: 35 KGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKVVEAVKRQAEELI-HPGFNVMMYPTYI 93 KG+G ++D +G++++DF G +GH++P + EA+ Q++++I +P P Sbjct: 28 KGDGVYVWDENGKQYLDFTSGWGVTCIGHANPIITEALCNQSKKIIQNPNSGATYSPARS 87 Query: 94 ELAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIARKYTKRQGVVSFTRGFHGRTNMTMS 153 L + I P H + F NSGAEA + A+K+ARK T ++ ++S FHGRT T+S Sbjct: 88 RLIQLFHEILP-KHLTRIFFANSGAEANDAAIKLARKVTGKKNIISTEMSFHGRTISTVS 146 Query: 154 MTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMSDESYDDMVIQAFNDFF-IASVAPET 212 T + ++ F P P + PF ND + + + Sbjct: 147 ATGQ-DVHRNKFNPLMPGYFFVPF-----------------------NDISAVKEIIDQD 182 Query: 213 VACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIVFVADEIQTGFARTGTYFAIEHFDV 272 VA V++EP+QGEGG IPS+ ++ ++ C+EHG++F+ADEIQTGF RTG F Sbjct: 183 VAAVIVEPIQGEGGVNIPSESYLLELSEVCREHGVLFIADEIQTGFFRTGPLFYSISKGA 242 Query: 273 VPDLITVSKSLAAGLPLSGVIGRAEMLDAAAPGELGGTYAGSPLGCAAALAVLDIIEEEG 332 PD+IT++K +A G P S E+++ G+ GGTY G+PLGCA + AV+ + + Sbjct: 243 KPDIITMAKGIAGGFPFSAFAVTDEVVNGIQKGDHGGTYNGNPLGCAVSEAVIRYLIDSD 302 Query: 333 LNERSEEIGKIIEDKAYEWKQEFP-FIGDIRRLGAMAAIEIVKDPDTREPDKTKAAAIAA 391 + ++G + WK+++P I ++R G + A+E+ D K+A I Sbjct: 303 IESHVSDLGIDTIKRLNGWKEKYPKAITEVRGQGLLIALELT--------DDLKSAEIVT 354 Query: 392 YANQNGLLLLTAGINGNIIRFLTPLVISDSLLNEGLSILE 431 NGL+L +G+IIR L I+ + GL ILE Sbjct: 355 RCLDNGLILNLK--HGHIIRIFPALTITKQEMQTGLDILE 392 Lambda K H 0.319 0.136 0.393 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: 393 Number of extensions: 18 Number of successful extensions: 4 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: 436 Length of database: 400 Length adjustment: 32 Effective length of query: 404 Effective length of database: 368 Effective search space: 148672 Effective search space used: 148672 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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