Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_086508150.1 BZY95_RS01045 aspartate aminotransferase family protein
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_002151265.1:WP_086508150.1 Length = 404 Score = 238 bits (607), Expect = 2e-67 Identities = 151/406 (37%), Positives = 226/406 (55%), Gaps = 34/406 (8%) Query: 26 VVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYE 85 V+ R E S +WD EGREYIDFAGGIAV + GH HP ++ A+ EQ KL H V E Sbjct: 23 VIPVRGEGSRLWDQEGREYIDFAGGIAVNSLGHCHPVLVKALTEQGNKLWHLS-NVYTNE 81 Query: 86 PYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARA------ATGRAGVIAFTGAY 139 P ++LA+ + +R F K +SG EA E A+K+AR + +++F ++ Sbjct: 82 PSLKLAKTLVERT---FADKAYFCSSGGEANEAALKLARRWAHDNFGEHKHRIVSFYQSF 138 Query: 140 HGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQ 199 HGRT T+ + G+ YS G G +PGGI +HG E +++ S+ + +D Sbjct: 139 HGRTFFTVSVGGQP-KYSQGFGPVPGGI--------VHG--EFNNLDSVRDLINDDT--- 184 Query: 200 DIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLG 259 A+++EP+QGEGG ++ F+Q LR LCD H LLI DEVQTG GRTG+ +A + G Sbjct: 185 --CAVMVEPMQGEGGITPATQEFLQGLRDLCDAHDALLIFDEVQTGVGRTGSLYAYMEYG 242 Query: 260 IVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEE 319 I PD+ T AK++GGGFPI + + A+A G G TY G+ +A A ALA ++ + Sbjct: 243 IEPDILTSAKALGGGFPIGAMLTTDRVAPALAIGTHGSTYGGNALASAVALAAVEHIDTP 302 Query: 320 KLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVV 379 ++L + + + L I KH V ++RG+G ++ E+ +K A+ I+ Sbjct: 303 EVLGGVKQRHDLFREHLEAINRKHGVFREIRGMGLLIGAEM---TPEYKDRAK---DILP 356 Query: 380 RAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDEL 425 A E+GL+ L G NV+R + IP+A + +G+A L + L Sbjct: 357 LAIEEGLMALIAGP--NVLRMAPSLVIPEADIAEGMARLERAIERL 400 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: 438 Number of extensions: 20 Number of successful extensions: 6 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: 404 Length adjustment: 31 Effective length of query: 395 Effective length of database: 373 Effective search space: 147335 Effective search space used: 147335 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