Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Echvi_2919 Echvi_2919 Ornithine/acetylornithine aminotransferase
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__Cola:Echvi_2919 Length = 393 Score = 220 bits (561), Expect = 5e-62 Identities = 148/406 (36%), Positives = 215/406 (52%), Gaps = 47/406 (11%) Query: 29 ERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYI 88 E+AE ++ +G +YID GI V N GH HPKV+ A+Q+QL K H ++ Y Y+ Sbjct: 24 EKAEGIYMYGPKGEKYIDLISGIGVSNVGHRHPKVLKAIQDQLDKYMH----LMVYGEYV 79 Query: 89 ELAE-EIAKRVPGDFPKK---TLLVTSGSEAVENAVKIARAATGRAGVIAFTGAYHGRTM 144 + + ++AK + PKK LV SGSEAVE A+K+A+ TGR +++ AYHG + Sbjct: 80 QSPQTQLAKALTDTLPKKLDNVYLVNSGSEAVEGALKLAKRYTGRREILSCVNAYHGSSH 139 Query: 145 MTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQDIAAI 204 L + G + A L+PG R L +E D + I ++ AAI Sbjct: 140 GALSVGGNEIFKRAYRPLLPG--IRHL------DFNEPDQLDQIT---------EETAAI 182 Query: 205 IIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPDL 264 ++E VQGE G V +K + + LR CD+ G LLI DE+Q G GRTG F+A + IVPD+ Sbjct: 183 MVETVQGEAGIRVGTKEYFKALRHRCDETGTLLILDEIQAGFGRTGKFWAFQHYDIVPDI 242 Query: 265 TTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGG---TYAGSPIACAAALAVLKVFEEEKL 321 AK +GGG PI IM L G T+ G P++CAAALA + + +EKL Sbjct: 243 VVCAKGMGGGMPIGAFIAPQSIMSVFKNNPLLGHITTFGGHPVSCAAALATIDILRDEKL 302 Query: 322 LERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRA 381 ++ + KA L + H I ++R G M+A++ FE A E++ I+ RA Sbjct: 303 IQHVER-----KANLFKKHLNHPKIQEIRNKGLMMAVK-FE-------AFEVLKPIIDRA 349 Query: 382 REKGLI---LLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDE 424 E G+I L C + +R P+TI D ++EK AI+ + DE Sbjct: 350 IELGIITDWFLFC---EDSMRIAPPLTITDEEIEKACAIILQSIDE 392 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: 384 Number of extensions: 24 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: 393 Length adjustment: 31 Effective length of query: 395 Effective length of database: 362 Effective search space: 142990 Effective search space used: 142990 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 17 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