Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate 8499593 DvMF_0361 LL-diaminopimelate aminotransferase (RefSeq)
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Miya:8499593 Length = 389 Score = 172 bits (437), Expect = 1e-47 Identities = 114/360 (31%), Positives = 183/360 (50%), Gaps = 9/360 (2%) Query: 30 QGEEILLLSVGDPDFDTPAPIVQAAIDSL-LAGNTHYADVRGKRALRQRIAERHRRRSGQ 88 +G +I+ L +GDPD TP I++A ++ N Y G RQ +A + RR G Sbjct: 31 RGVDIISLGIGDPDMPTPDFIIEAMKKAVERPANHQYPSYVGMLEFRQEVANWYGRRFGV 90 Query: 89 AVDAE-QVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRS 147 ++D + +V+ L G++ + +NPGD V+V P Y Y G G V +P+ Sbjct: 91 SLDPKTEVIGLIGSKEGIAHFPLAFVNPGDLVLVCTPNYPVYHIATGFVGGEVQFIPLVE 150 Query: 148 ENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVY 207 EN + + + A R + + +N P+NP+ A+ PRA +E L +C H++ + D Y Sbjct: 151 ENDYLPDLDAIPAATWDRAKMIFVNYPNNPTAATAPRAFYEKLIGICRKHNVIIAHDTAY 210 Query: 208 SELLFDGEHVSPASL---PGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLAL 264 +E+ +D E+ P S+ G D T +SLSK++ MTGWRVG VG A+L A L + Sbjct: 211 TEVYYD-ENDKPMSILEVEGAKDVTIEFHSLSKTYNMTGWRVGMAVGNASLVAGLGKVKE 269 Query: 265 CMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFV 324 + G + +Q+A+ AL +R YR+RRD+V+ L + G+ P ++ Sbjct: 270 NVDSGIFQAVQEASIVALRDGDDFCRELRGIYRKRRDVVVAAL-NKVGIACRVPTAAFYI 328 Query: 325 MVDIRPTGLSAQA-FADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLREACRRIA 383 + P G + A F +L++ GV + G FG G+ R+ L + + L EA RIA Sbjct: 329 WAKV-PAGYGSSAEFVTAVLEKTGVVLTPGNGFGTPGEGYFRISLTVDTDRLEEAVSRIA 387 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: 352 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: 389 Length adjustment: 31 Effective length of query: 362 Effective length of database: 358 Effective search space: 129596 Effective search space used: 129596 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