Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate Ga0059261_1288 Ga0059261_1288 Aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Korea:Ga0059261_1288 Length = 401 Score = 172 bits (435), Expect = 2e-47 Identities = 113/365 (30%), Positives = 179/365 (49%), Gaps = 7/365 (1%) Query: 23 RALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTH-YADVRGKRALRQRIAER 81 RA AR GE+I+ L +G+PD P ++ + + H Y+ +G LR+ A Sbjct: 23 RAAARAA-GEDIIDLGMGNPDLPPPQHVIDKLCEVAQKPSAHGYSQSKGIPGLRRAQANY 81 Query: 82 HRRRSGQAVDAE-QVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARV 140 + RR G VD E +VVV G++ L ++ + PGD ++ P Y + F GA + Sbjct: 82 YGRRFGVDVDPESEVVVTMGSKEGLASLATAITAPGDVILAPNPSYPIHTFGFIIAGATI 141 Query: 141 VPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLW 200 VP + + E PR + +N P NP+ ++ A +E L + +W Sbjct: 142 RAVPTTPDEHYFESLERAMNFTVPRPSILVVNYPSNPTAETVDLAFYERLVAWAKENKVW 201 Query: 201 MISDEVYSELLFDGE-HVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHL 259 +ISD YSEL +DG+ VS + G D SLSK+++M GWR+G+ VG L A + Sbjct: 202 IISDLAYSELYYDGKPTVSILQVKGAKDVAIEFTSLSKTYSMAGWRIGFAVGNKQLIAAM 261 Query: 260 ENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPD 319 + + YG+ +Q AAC AL P +EA R+ Y +RRD+++E + G P Sbjct: 262 TRVKSYLDYGAFTPVQAAACAALNGPQDIVEANRQLYHKRRDVLVESFGRA-GWDIPAPP 320 Query: 320 GGMFVMVDIRP--TGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLRE 377 MF + P L + F+ +LL V+V G +G + G +R+ +V + LR+ Sbjct: 321 ASMFAWAPLPPALAHLGSLEFSKQLLSHAKVAVAPGVGYGENGEGFVRIAMVENEQRLRQ 380 Query: 378 ACRRI 382 A R + Sbjct: 381 AARNV 385 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: 385 Number of extensions: 15 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: 401 Length adjustment: 31 Effective length of query: 362 Effective length of database: 370 Effective search space: 133940 Effective search space used: 133940 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