Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate GFF3829 PGA1_262p02330 putative aspartate aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Phaeo:GFF3829 Length = 395 Score = 307 bits (787), Expect = 3e-88 Identities = 161/383 (42%), Positives = 231/383 (60%), Gaps = 1/383 (0%) Query: 1 MRYSDFTQRIAGDGAAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLA 60 MR +D T+R+AG G A W++H A + G +I+ +++G+PD TP ++Q A +++A Sbjct: 1 MRMTDVTRRLAGLGGAKWEVHLTAREMIAAGADIIEMTIGEPDVPTPEALMQTAGAAMMA 60 Query: 61 GNTHYADVRGKRALRQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVI 120 G T Y+D RG+ LRQ +AER+ +G+A+ + V+ G Q ALYAV+ + GDEV+ Sbjct: 61 GRTGYSDGRGEANLRQTLAERYSASTGRAIGPDNVLCFPGTQTALYAVLMGVAEHGDEVL 120 Query: 121 VAEPMYVTYEAVFGACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGA 180 V +PMY TYE V A GA +VPVP+R E+GFR+QA ++A ITPR+RA+ L +PHNP+G+ Sbjct: 121 VGDPMYATYEGVIRASGADMVPVPLRPEHGFRMQANDIAEKITPRSRAILLTTPHNPTGS 180 Query: 181 SLPRATWEALAELCMAHDLWMISDEVYSELLFD-GEHVSPASLPGMADRTATLNSLSKSH 239 L +A+ L HDLW+ISDEVY +L+FD E VSP + ADR ++S+SKSH Sbjct: 181 ILTVEDLDAIGRLADVHDLWIISDEVYEQLVFDAAEFVSPLARAAFADRVIVVSSISKSH 240 Query: 240 AMTGWRVGWVVGPAALCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRR 299 A G+R GW + A C L L+ ML+G+ FI D A+ P E MR + R Sbjct: 241 AAPGFRSGWCIASKAFCDGLLPLSETMLFGNQPFIADMTEQAVREGSPVAEGMRARFAAR 300 Query: 300 RDLVIECLADSPGLRPLRPDGGMFVMVDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPS 359 + E L LR P+ GMF M+++ TGL A+A LL GV+V+ G +FG S Sbjct: 301 AAKLAERLHRDTALRVHSPEAGMFAMINVAATGLDGDAYAQDLLHSAGVAVMPGSSFGES 360 Query: 360 AAGHIRLGLVLGAEPLREACRRI 382 G +R+ L + + A RI Sbjct: 361 LRGWVRVALTIEDDAFDRALTRI 383 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: 443 Number of extensions: 21 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: 395 Length adjustment: 31 Effective length of query: 362 Effective length of database: 364 Effective search space: 131768 Effective search space used: 131768 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