Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Echvi_3848 Echvi_3848 Ornithine/acetylornithine aminotransferase
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__Cola:Echvi_3848 Length = 381 Score = 186 bits (473), Expect = 8e-52 Identities = 129/351 (36%), Positives = 188/351 (53%), Gaps = 37/351 (10%) Query: 17 PRGVGQIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSH 76 P V + V +A ST+WD +G EY+D GG AV++ GH HP ++EQL ++ Sbjct: 3 PFDVYPLIDVTPVKASGSTIWDDQGNEYLDLYGGHAVISIGHSHPHYTKRIKEQLDNIAF 62 Query: 77 TCFQVLAYEPYIELAEEIAKRVP--GDFPKKTL-LVTSGSEAVENAVKIARAATGRAGVI 133 V I + +E+A ++ +P L L SG+EA ENA+K+A TG+ G I Sbjct: 63 YSNSV-----QIPIQKELATKLGQLSGYPDYDLFLCNSGAEANENALKLASFETGKKGFI 117 Query: 134 AFTGAYHGRTMMTLGLTGK---VVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIER 190 AFT +HGRT + LT + P++A G+ H + +D +E Sbjct: 118 AFTKGFHGRTSGAVALTDNPKIIAPFNAHEGV--------------HILPFND----LEA 159 Query: 191 IFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTG 250 + K A IA +I+E +QG GG V +F+ L AL Q+G LI DEVQ+G R+G Sbjct: 160 VEKQLATGT-IAGVIVEGIQGVGGIQVPDPAFLLGLSALTKQYGAKLILDEVQSGYARSG 218 Query: 251 TFFATEQL-GIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAA 309 FFA + + G+ PDL T AK +G GFPI GV E + G LG T+ G+ +ACAAA Sbjct: 219 KFFAHQWVEGLKPDLITVAKGMGNGFPIGGVLISPEF--KASHGLLGTTFGGNHLACAAA 276 Query: 310 LAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIEL 360 LAVL+V +EE L+ + G+ + A L ++ + +VRG G M+ +L Sbjct: 277 LAVLEVIDEENLITAAAENGKAIMAALEKVAG----VTEVRGKGLMIGFDL 323 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: 372 Number of extensions: 22 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 426 Length of database: 381 Length adjustment: 31 Effective length of query: 395 Effective length of database: 350 Effective search space: 138250 Effective search space used: 138250 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