Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate GFF3717 PS417_19025 aspartate aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__WCS417:GFF3717 Length = 401 Score = 195 bits (495), Expect = 2e-54 Identities = 127/366 (34%), Positives = 189/366 (51%), Gaps = 15/366 (4%) Query: 30 QGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQA 89 QG +I+ +VG+PDFDTPA I+ AA ++ G+THY G ALRQ I + ++ + A Sbjct: 30 QGRDIVNFTVGEPDFDTPAHILAAASQAMHNGDTHYTSTTGTLALRQAICLKLQQDNDLA 89 Query: 90 VDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSEN 149 ++VV G + +Y + LN GDEVIV P +V+Y + A V +P Sbjct: 90 YGLDEVVAGCGGKHVIYHALAATLNRGDEVIVHTPYWVSYPDIARLNDATPVIIPGDESL 149 Query: 150 GFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAH-DLWMISDEVYS 208 GF++ + + IT RT+ + LNSP+NPSGA ALA++ H + +++DE+Y Sbjct: 150 GFKLSPDALEQAITARTKWVILNSPNNPSGAVYNETELLALAQVLRRHPHVLIMADEIYE 209 Query: 209 ELLFD-GEHVSPASL-PGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCM 266 ++ HV L P + RT +N SK +AMTGWR+G+ GPA L A + L Sbjct: 210 HFIYGRARHVPLTRLAPDLKPRTLIVNGASKGYAMTGWRLGFGAGPAWLIAAIAKLLSQT 269 Query: 267 LYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMV 326 Q AA A + AMRE Y++RR ++ LAD PGL PDG +V Sbjct: 270 TTCPSSLSQAAAVAAFTGDQAPIAAMREEYQQRRARMLALLADIPGLSCTPPDGAFYVFA 329 Query: 327 DI-------RPTG---LSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLR 376 ++ P G S D LL +G++ ++G A+G S ++RL +E + Sbjct: 330 NVSGLMGKLTPQGDRLDSDTQLVDYLLRDYGLATVSGAAYGMSP--YVRLSFASSSEVIE 387 Query: 377 EACRRI 382 E CRR+ Sbjct: 388 EGCRRL 393 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: 414 Number of extensions: 16 Number of successful extensions: 4 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