Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 207835 DVU2347 acetylornithine aminotransferase
Query= BRENDA::Q9I6M4 (426 letters) >MicrobesOnline__882:207835 Length = 399 Score = 188 bits (477), Expect = 3e-52 Identities = 136/419 (32%), Positives = 207/419 (49%), Gaps = 42/419 (10%) Query: 1 MSKTNESLLKRRQAAVPRGVGQIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLH 60 M+ + E+L R ++ + R G+ +P+ +RAE S +WD EGREYID GIAV + GH H Sbjct: 1 MTTSFEALKNREESLLCRTYGR-YPISVQRAEGSRMWDHEGREYIDLLSGIAVTSLGHCH 59 Query: 61 PKVIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAV 120 P++ + Q KL H + E ++LAE++ + K SG+EA E A+ Sbjct: 60 PELAEVMARQARKLVHVS-NLFYQEEQLDLAEKLLSTL---HCTKAFFCNSGAEANEAAI 115 Query: 121 KIARAATGRAG------VIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPC 174 K+AR R V+ TGA+HGRT+ T+ TG+ + G MP G +A Sbjct: 116 KLARRYMQRVRGVDAHEVVTLTGAFHGRTLATVAATGQE-RFQDGFAPMPAGFRQA---- 170 Query: 175 ELHGVSEDDSIASIERIFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHG 234 E I ++ A A +++E VQGEGG ++ + + + LC + G Sbjct: 171 ------EWGDIDALRA-----AITPATAGVLVEMVQGEGGVRPMTQDYARAVADLCREKG 219 Query: 235 ILLIADEVQTGAGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGG 294 +LL+ DE+QTG RTG F+A + G+ PD+ T AK++ G P+ + E+ G Sbjct: 220 VLLMVDEIQTGLCRTGRFWAHQHYGVEPDIVTSAKALANGLPMGAMMTTDEVAQGFVAGS 279 Query: 295 LGGTYAGSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAK-HKVIGDVRGLG 353 T+ + + A A L + + ++L ER+ AVG R R I AK I +VRG G Sbjct: 280 HATTFGAGALVSSVAAATLDIMKRDRLDERATAVGGRAMERFRAIGAKLPGTIEEVRGYG 339 Query: 354 SMVAIEL-FEGGDTHKPAAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQL 411 M+ I L F G + K ELV++ V T V+R + +TI +A L Sbjct: 340 LMIGIVLTFSGKEVWK---ELVARGFV----------CNNTQEKVLRLVPALTIDEADL 385 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: 365 Number of extensions: 16 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: 399 Length adjustment: 31 Effective length of query: 395 Effective length of database: 368 Effective search space: 145360 Effective search space used: 145360 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