Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate Ac3H11_1602 Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1602 Length = 408 Score = 218 bits (556), Expect = 2e-61 Identities = 131/366 (35%), Positives = 195/366 (53%), Gaps = 15/366 (4%) Query: 30 QGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQA 89 QG+ +++L +G+PDFDTPA I++AA ++ G THY + G L+ I + + +G Sbjct: 37 QGQPVIVLGLGEPDFDTPAHILEAAQQAMARGETHYTVLDGTAELKAAIQHKFKHYNGLD 96 Query: 90 VDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSEN 149 ++ AGA+ LY + +NPGDEVI+ P + +Y + G V VP N Sbjct: 97 FQLNEITAGAGAKQILYNALMASVNPGDEVILPAPYWTSYADMVLIAGGVPVVVPCTEAN 156 Query: 150 GFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAH-DLWMISDEVYS 208 GFR+ E++ A ITPRTR + +NSP NPSGA+ + E+ H +W+++D++Y Sbjct: 157 GFRITPEQLEAAITPRTRWVFINSPSNPSGAAYSAEQLRPVLEVVERHPQVWLLADDIYE 216 Query: 209 ELLFDGE-HVSPAS-LPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCM 266 +L+DG +PA+ LP + DRT T+N +SK++AMTGWR+G+ GP AL A + + Sbjct: 217 HILYDGRAFATPAAVLPSLRDRTLTVNGVSKAYAMTGWRLGYGAGPKALIAAMAVVQSQA 276 Query: 267 LYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMV 326 Q AA AL P + +A++ RRDLV+ L SPGLR P+G + Sbjct: 277 TSCPSSISQAAAVAALTGPQDVVRERCQAFQDRRDLVVAALNVSPGLRCRVPEGAFYTFA 336 Query: 327 DIR-------PTGLSAQAFAD---RLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLR 376 P GL + AD LL H V+V+ G G A + R+ L+ Sbjct: 337 SCEGALGRTTPGGLLLRTDADFCAYLLREHHVAVVPGGVLG--LAPYFRISYAASTADLQ 394 Query: 377 EACRRI 382 EAC RI Sbjct: 395 EACARI 400 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: 455 Number of extensions: 20 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: 393 Length of database: 408 Length adjustment: 31 Effective length of query: 362 Effective length of database: 377 Effective search space: 136474 Effective search space used: 136474 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