Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate WP_012385547.1 BIND_RS13140 aspartate aminotransferase family protein
Query= uniprot:A1S8Y2 (425 letters) >NCBI__GCF_000019845.1:WP_012385547.1 Length = 451 Score = 172 bits (436), Expect = 2e-47 Identities = 124/390 (31%), Positives = 187/390 (47%), Gaps = 36/390 (9%) Query: 40 EGREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEKFSHTCFMVLGYESYVAVCEKLNQLVP 99 +G+ IDF G V N GH HP++ AA+ E+L++ + + EKL Sbjct: 44 DGKAIIDFNSGYCVHNIGHNHPRLIAALKEELDRSGPAMLQTHVSDLAGELAEKLCARAG 103 Query: 100 GDFAKKSALFTSGSEAVENAIKVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKG 159 G F K +SGSE VE IK ARA+T+R+G++ G+HG T AL+L Sbjct: 104 GRFTKVF-FASSGSEGVETVIKFARAHTERSGILYAADGFHGLTCGALSL---------- 152 Query: 160 MGLMQANVFRAEFPCALHGVSEDDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAAT 219 M ++A F L +E IE + +N AA +LEP+QGEGG Sbjct: 153 ---MSDEFWKAGFGPLLPE-TESVLFDDIEAL-ENKLAAKPFAAFVLEPIQGEGGVRVPA 207 Query: 220 PGFMKRLRELCDREGIMLIADEVQTGAGRTGTFFAMEQMGVAADITTFAKSIAGG-FPLS 278 P ++ + + LC R G + + DEVQTG RTG F A GV D+ AK+++GG P S Sbjct: 208 PDYLIKAQALCRRYGTLFVLDEVQTGFYRTGDFLAAHHFGVEPDMVVLAKAMSGGLIPCS 267 Query: 279 GITGRAEVMDAIGPGGLGG-----TYGGSPLACAAALAVIEVFEEEKLLERSNAIGQTIK 333 + + ++I TY + LA A L +++ E+EKL R+ ++G+ ++ Sbjct: 268 AVLMSDAICNSIYSSLRRAFIHTTTYSENSLAMRAGLTTLDILEDEKLGARAASLGEYLR 327 Query: 334 SAIGELASRYPQIAEVRGLGSMIAIELMEN------------GKPAPEYCPQVLTEA--R 379 + E +Y +AEVRGLG + AIE + K P QV+ + Sbjct: 328 RTLTERLGKYEMVAEVRGLGLLNAIEFRKPRSYLLRIPFETFSKIHPAMFGQVVVMRLFK 387 Query: 380 NRGLILLSCGTYGNVLRILVPITAPDEQIQ 409 + G++ CG L+I P+ DEQI+ Sbjct: 388 DHGILSQICGNNFLTLKIAPPLVVSDEQIE 417 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: 416 Number of extensions: 27 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: 425 Length of database: 451 Length adjustment: 32 Effective length of query: 393 Effective length of database: 419 Effective search space: 164667 Effective search space used: 164667 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: 51 (24.3 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