Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate CA265_RS07515 CA265_RS07515 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Pedo557:CA265_RS07515 Length = 380 Score = 175 bits (444), Expect = 2e-48 Identities = 115/364 (31%), Positives = 183/364 (50%), Gaps = 13/364 (3%) Query: 30 QGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQA 89 +G I+ LSVG+PDF+TP + AA +L T Y+ V G LRQ I + + + Sbjct: 11 KGINIISLSVGEPDFNTPDHVKNAAKKALDENYTRYSPVPGYPDLRQAIVNKLKTENNLD 70 Query: 90 VDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSEN 149 D Q+VV GA+ +L V+ L++P DEVI+ P +V+Y + + V + E+ Sbjct: 71 YDISQIVVSTGAKQSLSNVILTLIDPDDEVIIPTPYWVSYSEMVTLAEGKSVFIDTDIES 130 Query: 150 GFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAH-DLWMISDEVYS 208 F++ ++ A ITP+++ +SP NP+G+ + AL + H +++++SDE+Y Sbjct: 131 DFKITPAQLEAAITPKSKLFMFSSPCNPTGSVYSKEELAALVAVFEKHPNIYILSDEIYE 190 Query: 209 ELLFDGEHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLY 268 + F +H S A + DR +N SK+ AMTGWR+G++ + A + L Sbjct: 191 HINFVDKHESIAQFDSIKDRVIIVNGFSKAFAMTGWRLGYIAANKEIAAANDKLQGQTTS 250 Query: 269 GSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMVDI 328 G+ Q A A E L + M+EA+ RRR+LV L + PG++ PDG + +I Sbjct: 251 GTCSIAQRAGIVAYEQGLASVLEMKEAFLRRRELVYNLLNEIPGVKTNLPDGAFYFFPEI 310 Query: 329 RPTGLSAQA----------FADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLREA 378 A A LL+ V+ + G++FG + +IRL E L EA Sbjct: 311 SSFFGKKDADGNVIKDSSDLALYLLNVGHVATVGGDSFGNN--NYIRLSYAASDESLVEA 368 Query: 379 CRRI 382 RRI Sbjct: 369 LRRI 372 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: 303 Number of extensions: 12 Number of successful extensions: 2 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: 380 Length adjustment: 30 Effective length of query: 363 Effective length of database: 350 Effective search space: 127050 Effective search space used: 127050 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