Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate WP_092482996.1 BM299_RS08235 acetylornithine transaminase
Query= uniprot:A1S8Y2 (425 letters) >NCBI__GCF_900115975.1:WP_092482996.1 Length = 396 Score = 230 bits (586), Expect = 7e-65 Identities = 147/401 (36%), Positives = 212/401 (52%), Gaps = 41/401 (10%) Query: 30 RAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEKFSHTCFMVLGYESYVA 89 R E A +WD +GRE++DF GGIAV + GH HP V A+ EQ + H + Y+ Sbjct: 27 RGEGARLWDADGREFLDFVGGIAVNSLGHCHPAVVRAIQEQAARLMHVSNLY-----YIE 81 Query: 90 VCEKLNQLVPGDFAKKSALF-TSGSEAVENAIKVARAYTKRAG------VIAFTSGYHGR 142 +L +L+ + F SG+EA E AIK+AR + K+ +I +HGR Sbjct: 82 PQARLAELLVQNSCCDRVFFCNSGAEANEGAIKLARKWAKKQHGADKYEIITAEKSFHGR 141 Query: 143 TMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVSEDDAMASIERIFKNDAEPSDIA 202 T+AA+ TG+ Y +G + F ++ DA+ ER A Sbjct: 142 TLAAITATGQ-PKYQQGFEPLPPGFKYVPF-------NDPDAL---ER-----AIGPHTC 185 Query: 203 AIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIADEVQTGAGRTGTFFAMEQMGVAA 262 A++LEPVQGEGG YAA ++ +RELCDR G++L+ DEVQ G GRTG F A + V Sbjct: 186 AVMLEPVQGEGGVYAAASEYLAGVRELCDRNGLLLVFDEVQCGLGRTGEFLAYQHYDVEP 245 Query: 263 DITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYGGSPLACAAALAVIEVFEEEKLL 322 DI T AK++ GGFP+ + + V A PG T+GG+PLACAA LA ++ + ++ Sbjct: 246 DIITLAKALGGGFPIGAMLAKETVAAAFAPGDHATTFGGNPLACAAGLAAMQTMLGDGVM 305 Query: 323 ERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIELMENGKPAPEYCPQVLTEARNRG 382 + A+G K + +LA +Y I EVRGLG ++ +EL G ++ R +G Sbjct: 306 QNCRAVGAYFKEKLQDLARKYDFIKEVRGLGLLLGMELNRPG-------GDIVNRCREKG 358 Query: 383 LILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFEAVL 423 L L++C NVLR P+ E++ R LE + EAVL Sbjct: 359 L-LINC-VNNNVLRFTPPLVIGTEEVDRALETV----EAVL 393 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: 380 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: 425 Length of database: 396 Length adjustment: 31 Effective length of query: 394 Effective length of database: 365 Effective search space: 143810 Effective search space used: 143810 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 Apr 09 2024. 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