Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate WP_022949042.1 H035_RS0111080 acetylornithine transaminase
Query= uniprot:A1S8Y2 (425 letters) >NCBI__GCF_000421465.1:WP_022949042.1 Length = 389 Score = 225 bits (573), Expect = 2e-63 Identities = 135/402 (33%), Positives = 211/402 (52%), Gaps = 35/402 (8%) Query: 25 PVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEKFSHTCFMVLGY 84 PV R E +WD +G+ Y+D GIAV N GH HP + A+ +Q ++ HT + Sbjct: 13 PVAFSRGEGIWLWDTQGKRYLDAISGIAVCNLGHAHPTLARALCDQSQRLWHTSNLYR-I 71 Query: 85 ESYVAVCEKLNQLVPGDFAKKSALF-TSGSEAVENAIKVARAYTKRAG-----VIAFTSG 138 E A+ E L +L ++ F SG+EA E A+K+ARAY G V+ Sbjct: 72 EPQEALAETLTRLS----GMENVFFCNSGAEANEAALKIARAYGHLQGIDTPRVVVADQS 127 Query: 139 YHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVSEDDAMASIERIFKNDAEP 198 +HGRT+A L+ TG +G + R F + +A+A +E + Sbjct: 128 FHGRTLATLSATGNPR-IQQGFEPLLPGFLRVPF-------GDPNAVAVLE-------DR 172 Query: 199 SDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIADEVQTGAGRTGTFFAMEQM 258 SD+ A+++EP+QGEGG G++ LR LCDR G +L+ DEVQTG GRTG +F + Sbjct: 173 SDVVAVLVEPIQGEGGVRMPPNGYLAELRRLCDRNGWLLMLDEVQTGIGRTGRWFGGQHE 232 Query: 259 GVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYGGSPLACAAALAVIEVFEE 318 V D+ T AKS+ GFP+ + + + + G G T+GG+ L C AL V+ + E+ Sbjct: 233 AVTPDVMTLAKSLGNGFPIGACLAKGKAAEVLTAGRHGSTFGGNFLGCRVALEVLRIIEQ 292 Query: 319 EKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIELMENGKPAPEYCPQVLTEA 378 E L++R+ +G +K A+ R+PQ+ +RG G ++AIEL C ++ EA Sbjct: 293 EGLIDRAARLGDQLKEALAHRLGRHPQVKNIRGRGLILAIEL-------DHPCAHLVPEA 345 Query: 379 RNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFE 420 RGL++ T NVLR+L P+ + Q ++ ++ + + + Sbjct: 346 LERGLLINVTAT--NVLRLLPPLILENSQAEQLVDTLVDLIQ 385 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: 405 Number of extensions: 21 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: 389 Length adjustment: 31 Effective length of query: 394 Effective length of database: 358 Effective search space: 141052 Effective search space used: 141052 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