Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_012471180.1 GLOV_RS15575 acetylornithine transaminase
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_000020385.1:WP_012471180.1 Length = 399 Score = 248 bits (634), Expect = 2e-70 Identities = 153/432 (35%), Positives = 231/432 (53%), Gaps = 46/432 (10%) Query: 4 TNESLLKRRQAAVPRGVGQIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKV 63 TN+ ++R + + G+ +P+V R E +WD +G+EY+DF G+AV N GH HPKV Sbjct: 2 TNQQWVERSDKVIMKTYGR-YPIVPVRGEGCRLWDADGKEYLDFLAGVAVNNLGHCHPKV 60 Query: 64 IAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIA 123 + A+Q+Q L H C IELAE + F K SG+EA E A+K+A Sbjct: 61 VKALQDQAATLIH-CSNYYQIPQQIELAELLCSH---SFADKAFFCNSGAEANEAAIKLA 116 Query: 124 RAATG-------RAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCEL 176 R + R G+I ++HGRTM T+ TG+ + R P L Sbjct: 117 RKYSREKHNNPERYGIITAADSFHGRTMATVSATGQEK------------VQRFFDPL-L 163 Query: 177 HGVSED--DSIASIERIFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHG 234 HG + + +A++ A AI++EP+QGEGG + S +MQ +R LCD+H Sbjct: 164 HGFAHVPFNDLAALSA-----AVTPQTCAIMLEPIQGEGGINIPSMEYMQGVRELCDRHQ 218 Query: 235 ILLIADEVQTGAGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGG 294 +LLI DEVQ G GRTG FA E GI PD+ T AK++ GG PI + + E+ + PG Sbjct: 219 LLLILDEVQVGMGRTGKLFAYEHFGITPDIMTLAKALAGGAPIGTMLARDEVAASFVPGT 278 Query: 295 LGGTYAGSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGS 354 G T+ G+P+ AAA+A ++ EE LL R++ +GE L L + +++ + +VRG+G Sbjct: 279 HGSTFGGNPLVTAAAVATVRAILEEGLLNRAEEMGEYLHGELERLGSRYSFVKEVRGIGL 338 Query: 355 MVAIEL-FEGGDTHKPAAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEK 413 M+ + L GGD IV + EKG++L T+ V+RF+ P+T+ ++ + Sbjct: 339 MIGMSLSIPGGD-----------IVKKGHEKGVLLNV--THDTVLRFVPPLTVSKQEVNR 385 Query: 414 GLAILAECFDEL 425 + IL F E+ Sbjct: 386 MIEILESIFKEI 397 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: 423 Number of extensions: 23 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: 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 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