Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate WP_109968729.1 DK846_RS09685 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >NCBI__GCF_003173355.1:WP_109968729.1 Length = 377 Score = 212 bits (539), Expect = 2e-59 Identities = 126/368 (34%), Positives = 197/368 (53%), Gaps = 8/368 (2%) Query: 15 AAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRAL 74 +A +I +A G +++ LS+G+PDF TPA I A ID+L G THYA +G +L Sbjct: 14 SATIEITDKARRLQASGVDVISLSIGEPDFPTPAHITAACIDALNRGETHYAPGKGIPSL 73 Query: 75 RQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFG 134 I+E+ +G + +QV+V GA+ A+Y + +LNPGDE ++ +P +V+YE Sbjct: 74 LSAISEKIEAENGFSCTNDQVIVTCGAKDAIYEACEAVLNPGDEAVILDPSWVSYEPCIQ 133 Query: 135 ACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELC 194 G V P+ + F+V+ + + I +TR + +NSP NPSG+ L R + ++++C Sbjct: 134 IAGGTPVHHPLHKKT-FQVE-DSLLEKINNKTRMIIVNSPSNPSGSVLNRESLRLVSDIC 191 Query: 195 MAHDLWMISDEVYSELLFDGEHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAA 254 HDL +SDE+Y +L++ H S A PGM DRT T+N SK++AMTGWR+G+ V P Sbjct: 192 QDHDLVALSDEIYEKLVYGQIHFSLAMFPGMVDRTITINGFSKAYAMTGWRLGYAVAPKE 251 Query: 255 LCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLR 314 + ++ + + F A AL+ P + MR + RRR+ V+ L D G+ Sbjct: 252 ILGYMNKVQQHTISHPTTFAMFGAVAALKGPQQCISEMRNEFERRREFVLNRLMDM-GIG 310 Query: 315 PLRPDGGMFVMVDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEP 374 +G + + + S A+R L+ V+V G AF + G IRL + Sbjct: 311 YAPAEGAFYAYLKVDGDDAS---IANRWLEEAHVAVTPGVAF--NTPGWIRLSYAASMDT 365 Query: 375 LREACRRI 382 L EA RI Sbjct: 366 LAEAMNRI 373 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: 379 Number of extensions: 18 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: 377 Length adjustment: 30 Effective length of query: 363 Effective length of database: 347 Effective search space: 125961 Effective search space used: 125961 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 24 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