Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate 8501474 DvMF_2204 aminotransferase class I and II (RefSeq)
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Miya:8501474 Length = 390 Score = 209 bits (531), Expect = 1e-58 Identities = 133/394 (33%), Positives = 204/394 (51%), Gaps = 20/394 (5%) Query: 1 MRYSDFTQRIAGDGAAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLA 60 MR SD RI A ++ +AL +G +++ L+VG+PDF TP + +AA ++ Sbjct: 1 MRISDRLTRIKPSATLA--VNAKALELKAKGVQVVSLAVGEPDFPTPEHVREAAKTAIDQ 58 Query: 61 GNTHYADVRGKRALRQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVI 120 G T Y V G LRQ + R G E VV G + ALY + QCLLNPGDEV+ Sbjct: 59 GFTRYTQVPGIPELRQAVCGYFARFYGVEAPMEATVVTNGGKQALYNLFQCLLNPGDEVL 118 Query: 121 VAEPMYVTYEAVFGACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGA 180 V P +V+Y A+ G V V +E GF+V EE+ +TP+TR + LNSP NP+GA Sbjct: 119 VPAPYWVSYPALVELAGGVPVFVASPAERGFKVTPEELDRAVTPKTRVLLLNSPSNPTGA 178 Query: 181 SLPRATWEALAELCMAHDLWMISDEVYSELLFDGEHVSPASLPGMAD-------RTATLN 233 RA +A+ E +A DL+++SDE+Y L+++ PA + D A +N Sbjct: 179 CYSRAETDAIMEWAIARDLFVVSDEIYDRLVYE-----PAEAVSVCDWWERHPENVAVVN 233 Query: 234 SLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMR 293 L+K+ AMTGWRVG+ + L + + Q AA AL P +E M+ Sbjct: 234 GLAKTFAMTGWRVGYALAHPDLIKAMTKIQGQSTSNICSVAQKAALAALTGPYDAVEEMK 293 Query: 294 EAYRRRRDLVIECLADSPGLRPLRPDGGMFVMVDIR----PTGLSAQAFADRLLDRHGVS 349 +++RRRRDL ++ PG+ +PDG ++ D+R P + + ++++ V+ Sbjct: 294 KSFRRRRDLAHGIVSSWPGVICPKPDGAFYLFADMRALFTPALPDSASLCTYIMEQANVA 353 Query: 350 VLAGEAFGPSAAGHIRLGLVLGAEPLREACRRIA 383 ++ G AFG A +R + + L A ++A Sbjct: 354 LVPGAAFGDDAC--LRFSYAVSDDTLMIALDKVA 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: 452 Number of extensions: 23 Number of successful extensions: 3 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: 390 Length adjustment: 31 Effective length of query: 362 Effective length of database: 359 Effective search space: 129958 Effective search space used: 129958 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