Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate HSERO_RS15115 HSERO_RS15115 aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__HerbieS:HSERO_RS15115 Length = 385 Score = 157 bits (396), Expect = 6e-43 Identities = 113/355 (31%), Positives = 176/355 (49%), Gaps = 12/355 (3%) Query: 37 LSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAVD-AEQV 95 L G PDF +V A ++ G Y + G LR+ IAE+ + G D ++ Sbjct: 33 LGQGFPDFHCDPALVAAVTQAMQEGLNQYPPMAGVPVLREAIAEKVEKLYGHRYDPVSEI 92 Query: 96 VVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSE---NGFR 152 V AGA + V C ++PGDEVIV EP+Y Y G VPV V+ E G+ Sbjct: 93 TVTAGATQGILTSVLCAVHPGDEVIVIEPVYDCYVPAIELAGG--VPVFVQMEVGAQGYS 150 Query: 153 VQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSELLF 212 + ++V A +TP+TR + +N+PHNP+G+ + A ALA++ D+ ++SDEVY +++ Sbjct: 151 IPWDKVKAAVTPKTRMIMVNTPHNPTGSVMRAADVAALADIVRGTDILILSDEVYEHMVY 210 Query: 213 DGE-HVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGSP 271 DG+ H S A P +A+R+ +S K++ +TGW+VG+V PAAL A + ++ Sbjct: 211 DGQPHESLARHPELAERSFINSSFGKTYHVTGWKVGYVAAPAALTAEFRKVHQFNVFTVN 270 Query: 272 EFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMVDIRP- 330 +Q ++ P P L+ + Y+ +RDL LA++ L G F V Sbjct: 271 TPVQYGLAAYMKDPAPYLD-LPAFYQHKRDLFRTGLANT-RFELLPSQGTYFQCVKYGAI 328 Query: 331 TGLSAQAFADRLLDRHGVSVLAGEAF--GPSAAGHIRLGLVLGAEPLREACRRIA 383 + L F L GV+ + AF P +G +R E L+ A R+A Sbjct: 329 SALPEAEFCKWLTSEIGVAAIPVSAFYNTPRESGIVRFCFAKKDETLQLALERLA 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: 348 Number of extensions: 13 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: 385 Length adjustment: 30 Effective length of query: 363 Effective length of database: 355 Effective search space: 128865 Effective search space used: 128865 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