Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate 207114 DVU1655 aminotransferase, classes I and II
Query= BRENDA::Q9HUI9 (393 letters) >MicrobesOnline__882:207114 Length = 388 Score = 177 bits (449), Expect = 5e-49 Identities = 117/358 (32%), Positives = 177/358 (49%), Gaps = 6/358 (1%) Query: 30 QGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTH-YADVRGKRALRQRIAERHRRRSGQ 88 +G +I+ L +GDPD TP I++A +++ H Y G A RQ +A + RR G Sbjct: 31 RGVDIISLGIGDPDMATPGFIIEAMKEAIARPANHQYPSYVGMLAFRQEVANWYDRRFGV 90 Query: 89 AVD-AEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRS 147 ++D A +V+ L G++ + +NPGD V+V P Y Y G G V VP+ Sbjct: 91 SLDPATEVIGLIGSKEGIAHFPFAFINPGDLVLVCTPNYPVYHIATGFAGGEVQFVPLLE 150 Query: 148 ENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVY 207 EN F + + R + + +N P+NP+ A+ P +E L ++C D+ + D Y Sbjct: 151 ENDFLPDLDAIPEDTWKRAKMIFVNYPNNPTAATAPLGFYEKLVDICRRFDVIIAHDTAY 210 Query: 208 SELLFDGEHVSPA--SLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALC 265 +E+ +D ++ P+ S+PG D +SLSK++ MTGWRVG VG L A L + Sbjct: 211 TEIYYDEDNRPPSILSVPGAKDVAIEFHSLSKTYNMTGWRVGMAVGNPTLVAGLGKIKEN 270 Query: 266 MLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVM 325 M G + +Q+A+ AL +R YR+RRD VI L G++ P +V Sbjct: 271 MDSGIFQAVQEASIVALRDGDDFCRELRGIYRQRRDTVINAL-HKAGIQCRVPQATFYVW 329 Query: 326 VDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLREACRRIA 383 + P G ++ F R+L GV V G FG G R+ L + L EA RIA Sbjct: 330 ARV-PQGHTSADFVTRVLQETGVVVTPGNGFGTPGEGFFRISLTVDNARLEEAVSRIA 386 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: 20 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: 388 Length adjustment: 31 Effective length of query: 362 Effective length of database: 357 Effective search space: 129234 Effective search space used: 129234 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