Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate GFF835 HP15_814 aspartate aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Marino:GFF835 Length = 416 Score = 181 bits (459), Expect = 3e-50 Identities = 108/352 (30%), Positives = 174/352 (49%), Gaps = 2/352 (0%) Query: 32 EEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAVD 91 ++++ LS+G PD TP ++ A ID+L AG T Y G L + + + +R + + Sbjct: 57 KDVIHLSIGQPDLPTPKHVIDAYIDALNAGQTGYTMDAGLPELLVALRDYYGKRYNRKLT 116 Query: 92 AEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENGF 151 + +++ +GA A+Y + PG + IV +P ++ Y + G V V R+EN Sbjct: 117 RDNILITSGATEAMYLAISATSAPGRQFIVTDPSFLLYAPLIRMNGGEVKFVQTRAENNH 176 Query: 152 RVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSELL 211 ++ +EV + PRT A+ LN+P+NP+GA PR+T E + E C + + +DEVY L+ Sbjct: 177 QLDPDEVIKAMGPRTYALILNNPNNPTGAVYPRSTVETILEECAYRGIQVYADEVYDHLI 236 Query: 212 FDGEHVSPASLPGM-ADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGS 270 FD E + M D ++S SK+++M G RVGWV+ A L + + Sbjct: 237 FDDEDFASVLNCSMDLDNIMCISSFSKTYSMAGLRVGWVIASQAAIKSLRRFHMFTTSVA 296 Query: 271 PEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMVDIRP 330 Q A AL + M + YR RRD V+E + +P + +P G F D+ P Sbjct: 297 NTPSQFAGVAALTGDQQCVRDMVDIYRERRDKVVELVDQTPYMTGYKPGGAFFAFPDL-P 355 Query: 331 TGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLREACRRI 382 + A R+L GV ++ G+AFG +R+ E L EA R+ Sbjct: 356 PHVDGSDLALRMLKETGVCMVPGDAFGEGCTNAVRISFSTTCEKLEEAFDRV 407 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: 403 Number of extensions: 14 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: 416 Length adjustment: 31 Effective length of query: 362 Effective length of database: 385 Effective search space: 139370 Effective search space used: 139370 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