Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 5208066 Shew_0578 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__PV4:5208066 Length = 405 Score = 223 bits (567), Expect = 1e-62 Identities = 150/398 (37%), Positives = 211/398 (53%), Gaps = 36/398 (9%) Query: 26 VVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYE 85 V+ R E S VWD EG E++DFAGGIAV GH HP ++ A++EQ K+ H V+ E Sbjct: 25 VIPVRGEGSRVWDQEGNEFVDFAGGIAVNCLGHCHPALVGALKEQGEKIWHLA-NVMTNE 83 Query: 86 PYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARA-ATGRAG-----VIAFTGAY 139 P + LA K V F +K SG+EA E A+K+AR A + G +IAF A+ Sbjct: 84 PALALA---TKLVEATFAEKVYFANSGAEANEAALKLARRYALDKFGAEKDQIIAFDKAF 140 Query: 140 HGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQ 199 HGRT T+ + G+ YS G G P I + IA++E A+ Sbjct: 141 HGRTFFTVSVGGQAA-YSDGFGPKPQSITHL----------PFNDIAALE------AEVS 183 Query: 200 D-IAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQL 258 D AI++EP+QGEGG F++ +RAL D+H L+I DEVQTG GR G +A + Sbjct: 184 DKTCAIMLEPLQGEGGIIDADPEFLRAVRALADKHNALVIFDEVQTGVGRLGELYAYMRT 243 Query: 259 GIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEE 318 + PD+ T AK++GGGFPI+ + EI + G G TY G+P+ACA AVL V Sbjct: 244 EVTPDILTTAKALGGGFPIAAMLTTTEIASHLKIGTHGSTYGGNPLACAIGNAVLDVVNT 303 Query: 319 EKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIV 378 ++L+ + + L+ GL +I K+ V +VRG G ++ L E + Sbjct: 304 PEVLDGVKRREQLLRDGLNQINEKYHVFTEVRGQGLLLGAVLNEQYQGRS------KDFL 357 Query: 379 VRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLA 416 V +GL+ L G NVIRF + IP+A + +GLA Sbjct: 358 VAGTSEGLMCLIAGP--NVIRFTPSLVIPEADIAEGLA 393 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: 402 Number of extensions: 20 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 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