Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate GFF3099 HP15_3042 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__Marino:GFF3099 Length = 404 Score = 219 bits (558), Expect = 1e-61 Identities = 134/401 (33%), Positives = 215/401 (53%), Gaps = 36/401 (8%) Query: 21 GQIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQ 80 G I PV R E S +WD EGRE+ID GGIAV GH HP ++ A+ +Q K+ H Sbjct: 22 GSIIPV---RGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLS-N 77 Query: 81 VLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARA------ATGRAGVIA 134 V+ EP + LA+ + F ++ SG+EA E A K+AR + +I+ Sbjct: 78 VMTNEPALRLAKTLCDLT---FAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIIS 134 Query: 135 FTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKN 194 F ++HGRT+ T+ + G+ Y G PGGI A E + + S++++ Sbjct: 135 FKNSFHGRTLFTVSVGGQP-KYLEGFEPAPGGIHHA----------EFNDLESVKKLISK 183 Query: 195 DAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFA 254 + AI++EP+QGEGG ++F+Q LR LCD++ LL+ DEVQ+G GR+G F+A Sbjct: 184 EKT----CAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYA 239 Query: 255 TEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLK 314 + G+VPD+ + AK +GGGFP++ + A++ ++ G G TY G+ +ACA A V+ Sbjct: 240 YQMYGVVPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVD 299 Query: 315 VFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELV 374 + ++L+ +A ++L+ G+ +I ++ V +VRG G ++ L E Sbjct: 300 TVSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGK------A 353 Query: 375 SKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGL 415 + E+G+++L G NVIR + IP+ +E L Sbjct: 354 KDFLNAGLEEGVMVLVAGA--NVIRLAPSLIIPEPDIELAL 392 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: 465 Number of extensions: 18 Number of successful extensions: 4 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 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