Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate SMc02262 SMc02262 aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Smeli:SMc02262 Length = 396 Score = 300 bits (767), Expect = 6e-86 Identities = 156/386 (40%), Positives = 227/386 (58%), Gaps = 1/386 (0%) Query: 1 MRYSDFTQRIAGDGAAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLA 60 MRY+ T R+A G+ W +H RA G E++ L++G+PD +++ ++ A Sbjct: 1 MRYASITSRLAELGSGKWTLHTRARQLKASGAELIELTIGEPDLPPDRALLEECQRAMNA 60 Query: 61 GNTHYADVRGKRALRQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVI 120 G Y++ RG+ A+ + E++RRR AV AE ++ G Q AL+AV+ L GD V+ Sbjct: 61 GRYRYSNGRGEPAVVAALTEKYRRRRA-AVTAENILCFPGTQTALFAVMFALAEAGDGVL 119 Query: 121 VAEPMYVTYEAVFGACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGA 180 V +P+Y TYE V + GA V VP+ ENGF ++AE++ +TP R + LN+PHNP+GA Sbjct: 120 VGDPLYATYEGVIRSTGAHPVFVPLNPENGFHMRAEDLEKAVTPECRVLLLNTPHNPTGA 179 Query: 181 SLPRATWEALAELCMAHDLWMISDEVYSELLFDGEHVSPASLPGMADRTATLNSLSKSHA 240 L A+ E+ HDLW++ DEVY EL+FD SP P +A+RT ++S+SKSHA Sbjct: 180 VLTAEEIAAIGEVARRHDLWIVCDEVYEELVFDALFASPFDNPDLAERTVVVSSISKSHA 239 Query: 241 MTGWRVGWVVGPAALCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRR 300 G+R GW VGPA L ++ ML+G FI D AL + MRE+Y RR Sbjct: 240 APGFRSGWAVGPAEFTERLLPISETMLFGQQPFIADMTAYALTHDIDTARQMRESYSRRA 299 Query: 301 DLVIECLADSPGLRPLRPDGGMFVMVDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPSA 360 +I+ LA + G+ L P+ GMF ++D+ TGLS +AFA LL+ GV+V+ G +FG A Sbjct: 300 RRIIDGLAGASGVSVLPPEAGMFALIDVSGTGLSGEAFAWALLEEEGVAVMPGSSFGDKA 359 Query: 361 AGHIRLGLVLGAEPLREACRRIALCA 386 +R+ L + + EACRRIA A Sbjct: 360 RNFLRVSLTVPDAAIEEACRRIAALA 385 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: 469 Number of extensions: 23 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: 396 Length adjustment: 31 Effective length of query: 362 Effective length of database: 365 Effective search space: 132130 Effective search space used: 132130 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