Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate Synpcc7942_2545 Synpcc7942_2545 aspartate aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__SynE:Synpcc7942_2545 Length = 392 Score = 238 bits (607), Expect = 2e-67 Identities = 136/371 (36%), Positives = 205/371 (55%), Gaps = 4/371 (1%) Query: 23 RALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERH 82 +A A +G ++ S G+PDF+TP I AA +L G T Y G+ LR+ IA++ Sbjct: 21 QAKAMKAEGLDVCSFSAGEPDFETPLHIRNAAAQALAEGKTRYGPAAGEPDLREAIAQKL 80 Query: 83 RRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVP 142 R +G A ++V G + +LY ++Q LL+PGDEVI+ P +++Y + G V Sbjct: 81 RADNGLDYQAANILVTNGGKQSLYNLMQVLLDPGDEVIIPAPYWLSYPEMVKLAGGVPVI 140 Query: 143 VPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMI 202 V + +GF++Q +++A ITPRTR + LNSP NP+G R EA+A + AHD W++ Sbjct: 141 VETFASDGFKLQPQQLAGAITPRTRLLVLNSPSNPTGMVYSRQELEAIAPIIEAHDFWVV 200 Query: 203 SDEVYSELLFDG-EHVSPASL-PGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLE 260 SDE+Y ++L+DG +H S SL P +RT N +K+++MTGWRVG++ GP+ L A Sbjct: 201 SDEIYEKILYDGADHHSIGSLSPACFERTLISNGFAKAYSMTGWRVGYLAGPSELIAAAA 260 Query: 261 NLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDG 320 +L F Q A AL+ P + M A+ RR L++ L GL P+G Sbjct: 261 SLQSHSTSNVCTFAQYGAIAALQGPQDCVAEMLAAFTERRQLILNGLNQIAGLSCPIPEG 320 Query: 321 GMFVMVDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLREACR 380 +V VDI TGL + + +LLD+H V+ + G AFG + IRL + + + Sbjct: 321 AFYVFVDISKTGLDSMTYCRQLLDQHQVAAIPGIAFGDDRS--IRLSYATDCQTIEKGLE 378 Query: 381 RIALCAAELLG 391 R+ L LLG Sbjct: 379 RLQLFQNSLLG 389 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: 397 Number of extensions: 23 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: 392 Length adjustment: 31 Effective length of query: 362 Effective length of database: 361 Effective search space: 130682 Effective search space used: 130682 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