Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate WP_013403486.1 CALHY_RS08135 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >NCBI__GCF_000166355.1:WP_013403486.1 Length = 397 Score = 204 bits (519), Expect = 4e-57 Identities = 128/393 (32%), Positives = 199/393 (50%), Gaps = 15/393 (3%) Query: 1 MRYSDFTQRIAGDGAAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLA 60 M+YS I+ A D + L E GE ++ G+PDFDTP I AAI +++ Sbjct: 1 MKYSQRALNISASPTLAIDSLAKKLK--EAGENVIGFGAGEPDFDTPDNIKYAAISAIVK 58 Query: 61 GNTHYADVRGKRALRQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVI 120 G T Y V G L++ IA+ ++ ++VVV GA+ +L V LLN GDEV+ Sbjct: 59 GYTKYTPVAGISCLKEAIAKYYKENYEVDYSPDEVVVSNGAKHSLMNVFFALLNDGDEVL 118 Query: 121 VAEPMYVTYEAVFGACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGA 180 + P +VTY + G +VV VP E +++ ++ T +T+A+ LNSP NP+G Sbjct: 119 LPSPYWVTYPELIKLAGGKVVVVPTTKEKNYKITLSDLEKYTTSKTKAIVLNSPSNPTGM 178 Query: 181 SLPRATWEALAELCMAHDLWMISDEVYSELLFDG-EHVSPASLPGMA-DRTATLNSLSKS 238 + + E C+ +++++SDE+Y +L++DG +H+S AS+ A + +N +SKS Sbjct: 179 VYTYEELKQIVEFCIEREIFIVSDEIYDKLIYDGKKHISAASINEKAKEFVIVVNGVSKS 238 Query: 239 HAMTGWRVGWVVGPAALCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRR 298 +AMTGWR+G+ + + NL Q AA AL P ++ M + + Sbjct: 239 YAMTGWRIGYTLSNKEFTKIMSNLQSHTTSNPNSIAQYAAYEALVGPQDSVKKMICEFEK 298 Query: 299 RRDLVIECLADSPGLRPLRPDGGMFVMVDIRPTG---------LSAQAFADRLLDRHGVS 349 RRDL+ + D+ L L+P+G ++ VDI SA FA LL+ V+ Sbjct: 299 RRDLIYSLVNDTKFLSALKPEGAFYIWVDISAAVGKSFEGKLIDSANTFAKLLLEVEKVA 358 Query: 350 VLAGEAFGPSAAGHIRLGLVLGAEPLREACRRI 382 V+ E FG HIRL + +RE RI Sbjct: 359 VVPSEGFG--MENHIRLSYATSEKNIREGLERI 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: 339 Number of extensions: 13 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: 397 Length adjustment: 31 Effective length of query: 362 Effective length of database: 366 Effective search space: 132492 Effective search space used: 132492 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 24 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