Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate WP_008507916.1 BIBO1_RS13055 aspartate aminotransferase family protein
Query= uniprot:A1S8Y2 (425 letters) >NCBI__GCF_000182725.1:WP_008507916.1 Length = 403 Score = 203 bits (517), Expect = 7e-57 Identities = 141/402 (35%), Positives = 199/402 (49%), Gaps = 48/402 (11%) Query: 23 IHPVFT---------ERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEK 73 +HP++ ER E + +G YIDFA GIAV + GH HP + + Q EK Sbjct: 7 VHPLYDTYNRAALRFERGEGIWLITEDGERYIDFAAGIAVNSLGHSHPHLVETLKTQAEK 66 Query: 74 FSHTCFMVLGYESYVAVCEKLNQ-LVPGDFAKKSALFTSGSEAVENAIKVARAYTKRAG- 131 H + YE + EKL + LV FA K SG+EA+E AIK AR Y +G Sbjct: 67 LWHLSNI---YE--IPAQEKLGRRLVENTFADKVFFTNSGAEALECAIKTARRYQYVSGH 121 Query: 132 -----VIAFTSGYHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVSEDDAMA 186 +I F +HGRT+A +A G+ A Y +G G + F ++ A+ Sbjct: 122 PERFRIITFEGAFHGRTLATIAAGGQ-AKYLEGFGPKVEGFDQVPF-------GDEAALR 173 Query: 187 SIERIFKNDAEPSDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIADEVQTGA 246 + A + A I+LEP+QGEGG A F++ +R++CD G++L+ DEVQTG Sbjct: 174 A--------AITPETAGILLEPIQGEGGLRAFPEEFLRLVRQICDENGLLLLLDEVQTGV 225 Query: 247 GRTGTFFAMEQMGVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYGGSPLAC 306 GRTG FFA E G+ DI AK I GGFP+ AE + G G TYGG+PL Sbjct: 226 GRTGKFFAHEWAGIRPDIMAIAKGIGGGFPIGACLATAEAAKGMTAGMHGTTYGGNPLGM 285 Query: 307 AAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQ-IAEVRGLGSMIAIELMENGK 365 A AV++V + +E A +K + L RYP ++E+RG G ++ ++ + Sbjct: 286 AVGNAVLDVVLADGFMENVQATALVMKQGLASLVDRYPNVVSEIRGRGLLMGLKCV---- 341 Query: 366 PAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVP-ITAPDE 406 P R +LS G NV+R+L P IT P+E Sbjct: 342 -----VPNTSLIQALRDEHVLSVGAGDNVVRLLPPLITTPEE 378 Lambda K H 0.319 0.136 0.391 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: 412 Number of extensions: 26 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 425 Length of database: 403 Length adjustment: 31 Effective length of query: 394 Effective length of database: 372 Effective search space: 146568 Effective search space used: 146568 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 (21.8 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