Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate WP_015943022.1 DHAF_RS03890 aspartate aminotransferase family protein
Query= uniprot:A1S8Y2 (425 letters) >NCBI__GCF_000021925.1:WP_015943022.1 Length = 399 Score = 218 bits (556), Expect = 2e-61 Identities = 141/419 (33%), Positives = 214/419 (51%), Gaps = 36/419 (8%) Query: 7 SLMVRRRAAVAGGVGQIHPVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKAA 66 +++ R + V G++ P+ + + TVWD+EG++Y+DF G+AV + GH HP V A Sbjct: 7 TMIQRGQEVVMNTYGRL-PMAIVKGKGTTVWDIEGKQYLDFVTGLAVSSLGHSHPAVVEA 65 Query: 67 VAEQLEKFSHTCFMVLGYESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAIKVARAY 126 + +Q E+ HT + + +A+ EKL V FA + SG+EA E AIK+AR Y Sbjct: 66 IQKQAEEILHTSNLYW-IPNQIALAEKL---VEHSFADQVFFCNSGAEANEAAIKIARKY 121 Query: 127 TK------RAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVS 180 K + ++ + +HGRT+A L TG+ Y KG A P V Sbjct: 122 AKEHYSEDKYEILTLVNSFHGRTLATLTATGQTK-YQKGY---------APLPEGFTYVP 171 Query: 181 EDDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIAD 240 +D +A +E +AA++LEP+QGEGG + F+ + R+LCD G +LI D Sbjct: 172 IND-LAQLEEKMN-----PKVAAVMLEPIQGEGGVFPLEVEFLAKARKLCDDYGALLIFD 225 Query: 241 EVQTGAGRTGTFFAMEQMGVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYG 300 E+Q G GRTG FA E V DI T AK++ GG P+ + + +V PG T+G Sbjct: 226 EIQVGLGRTGKLFAYEWSNVVPDIMTLAKALGGGVPIGVMLAKEKVASTFKPGDHASTFG 285 Query: 301 GSPLACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIEL 360 G+PLA A AV++V EE LE Q K + +LA +Y E+RG G ++ Sbjct: 286 GNPLATAVGCAVMDVLTEEGFLEDVQKRAQYFKQELQKLADKYQTGTEIRGQGFIL---- 341 Query: 361 MENGKPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECF 419 G P +++ AR +GL++ G G LR L P+ ++I + I+ + F Sbjct: 342 ---GWPLDRLGAEIVEGAREKGLLINFVG--GKALRFLPPLNVSYQEIDEAITILDQIF 395 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: 382 Number of extensions: 19 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: 425 Length of database: 399 Length adjustment: 31 Effective length of query: 394 Effective length of database: 368 Effective search space: 144992 Effective search space used: 144992 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