Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_053938113.1 WG78_RS12250 acetylornithine transaminase
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_001294205.1:WP_053938113.1 Length = 405 Score = 186 bits (471), Expect = 1e-51 Identities = 136/399 (34%), Positives = 206/399 (51%), Gaps = 42/399 (10%) Query: 29 ERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYI 88 ER E + ++D GR ++D+ G AV + GH PK++A Q T P Sbjct: 20 ERGEGAWLYDAAGRAWLDWLQGWAVNSLGHA-PKLVADTLYQQACTLITPSPAFNNTPAT 78 Query: 89 ELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARA-----ATGRAGVIAFTGAYHGRT 143 +LA+ + D + L +G+EA E A+K+AR G +I FT A+HGRT Sbjct: 79 QLAQWLVDHSCMD---QVFLANTGAEANEGAIKLARKWGRLHKDGAFEIITFTSAFHGRT 135 Query: 144 MMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSED--DSIASIERIFKNDAQPQDI 201 + + +GK PG + P ++ G + + I S+ R+ P + Sbjct: 136 IAAMSASGK-----------PG--WDVYFPPQVPGFPKATLNDIESVRRLIG----PHTV 178 Query: 202 AAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIV 261 I++EP+QGEGG S++F+Q LRALCD+H +LLI DEVQTG GRTG FA + GI Sbjct: 179 G-IMLEPIQGEGGVNAASRAFLQALRALCDEHQLLLIFDEVQTGCGRTGPLFAYQASGIE 237 Query: 262 PDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEKL 321 PD+ T K +G G PIS + KA G GGT+ G+P+ A LAV++ + Sbjct: 238 PDIMTLGKGLGAGVPISALLAKA-ACSVFEHGDQGGTFCGNPLTAAVGLAVMQHVAQPAF 296 Query: 322 LERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRA 381 L A G +L++GL E+ A+ +G+VRG G + AIEL GD E ++ A Sbjct: 297 LANVVARGAQLQSGLIELSARFG-LGEVRGAGLLWAIEL---GD------ERAEAVMRAA 346 Query: 382 REKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAE 420 R+ GL++ + + +R + + A++E GLA+L + Sbjct: 347 RDNGLLINNPRPH--CLRIMPALNTTAAEIETGLALLGK 383 Lambda K H 0.319 0.137 0.393 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: 377 Number of extensions: 26 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: 426 Length of database: 405 Length adjustment: 31 Effective length of query: 395 Effective length of database: 374 Effective search space: 147730 Effective search space used: 147730 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