Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate PP_3721 PP_3721 Arginine--pyruvate transaminase AruH
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__Putida:PP_3721 Length = 396 Score = 213 bits (542), Expect = 8e-60 Identities = 130/380 (34%), Positives = 198/380 (52%), Gaps = 15/380 (3%) Query: 32 RAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKKAIREKF 91 RA A++ E K +++L G+PDFDTP + +AA D++ G T Y + G L++AI + Sbjct: 23 RALALQAEDKDILLLSVGDPDFDTPAPIVEAAIDSLRAGHTHYADVRGKLALRQAIANRH 82 Query: 92 QRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHICEGKPVL 151 ++ +G A D++TV GA+ L+ LDPGDEVI+ P + +Y + C K V Sbjct: 83 RQRSGQAVSADQVTVLAGAQCALYCVAQCILDPGDEVIVAEPMYVTYEAVFGACGAKVVP 142 Query: 152 IACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLRHPHVWL 211 + +GFR+ + ITPRTR + LNSP NPSGA+ A + L E+ + H +WL Sbjct: 143 VPVKPENGFRVCPRDVAERITPRTRALALNSPHNPSGASLPRATWEALAELCVAH-DLWL 201 Query: 212 LVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGPRELIKAM 271 + D++Y ++Y+G V+P L PG+ RT T+N +SK++AMTGWR+G+ G L + Sbjct: 202 ISDEVYSELLYEG-EHVSPGSL-PGMAERTATLNSLSKSHAMTGWRMGWVVGSTALATHL 259 Query: 272 AVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAIDGLDCRVPE 331 + Q A+V AL P L E++++RRDLV L GL P+ Sbjct: 260 ENLALCMLYGLPDFVQDAAVVALEHPLPELDAMREAYRQRRDLVCEQLAGCPGLKALKPD 319 Query: 332 GAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAFGLSP--FFRISYA 389 G + V+ + +G + F YLL+ V+V+ G AFG S R+ Sbjct: 320 GGMF-------VMLDIRETGVSAQA---FADYLLDSQGVSVLAGEAFGPSAAGHIRLGLV 369 Query: 390 TSEAELKEALERIAAACDRL 409 L +A +RIA L Sbjct: 370 LGNEALVDACQRIARCAGEL 389 Lambda K H 0.318 0.134 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: 395 Number of extensions: 21 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: 410 Length of database: 396 Length adjustment: 31 Effective length of query: 379 Effective length of database: 365 Effective search space: 138335 Effective search space used: 138335 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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