Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate Dsui_3376 Dsui_3376 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__PS:Dsui_3376 Length = 388 Score = 162 bits (410), Expect = 2e-44 Identities = 113/327 (34%), Positives = 162/327 (49%), Gaps = 7/327 (2%) Query: 37 LSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAVDAE-QV 95 LS G PDF + A ++L G YA + G LRQ IA + + G A DAE ++ Sbjct: 35 LSQGFPDFQADRSLFDAVHQAMLDGRNQYAPMTGLPELRQAIAAKVQALYGTAYDAESEI 94 Query: 96 VVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENGFRVQA 155 V AGA AL+ + PGDEVIV P+Y +Y GA+ V +R + ++ Sbjct: 95 TVTAGATQALFTAIAAFAGPGDEVIVFAPVYDSYVPAIETVGAKAVYANLRYPD-YKPDW 153 Query: 156 EEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSELLFDGE 215 EV ALITPRTR + +N+PHNP+G+ L A EALAEL ++ ++ DEVY + F+GE Sbjct: 154 NEVRALITPRTRMIIVNTPHNPTGSLLDAADLEALAELTRDTNIVVLGDEVYEHICFEGE 213 Query: 216 HVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGSPEFIQ 275 H S A P +A R+ ++S K++ +TGW++G+ G AAL A + ++ + Sbjct: 214 HQSLARHPELAARSLIVSSFGKTYHITGWKIGYCYGAAALMAEFRKVHQFNVF-TVHAPS 272 Query: 276 DAACTALEAPLPELEAMREAYRRRRDLVIECLADSP-GLRPLRPDGGMFVMVDIRP---T 331 A A + E YR++RD + LA + L P R D P Sbjct: 273 QVGLAAFMADHSRHLQLAEFYRQKRDFFRQQLAGTKFELLPSRGTYFQLARYDALPGPAA 332 Query: 332 GLSAQAFADRLLDRHGVSVLAGEAFGP 358 L FA L GV+V+ F P Sbjct: 333 DLPDTEFAQWLTREVGVAVIPVSVFYP 359 Lambda K H 0.322 0.136 0.411 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: 361 Number of extensions: 18 Number of successful extensions: 3 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: 393 Length of database: 388 Length adjustment: 31 Effective length of query: 362 Effective length of database: 357 Effective search space: 129234 Effective search space used: 129234 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 (21.9 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