Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate PfGW456L13_1529 Valine--pyruvate aminotransferase (EC 2.6.1.66)
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1529 Length = 390 Score = 155 bits (392), Expect = 2e-42 Identities = 108/355 (30%), Positives = 162/355 (45%), Gaps = 5/355 (1%) Query: 31 GEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAV 90 G +++ L +G+PDF T PI++A +L AG T Y RG LR+ I+ +++R G + Sbjct: 31 GHDVIHLEIGEPDFTTAEPIIRAGQAALTAGKTRYTAARGIPELREAISGFYQQRYGLNI 90 Query: 91 DAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENG 150 D ++++ G AL L++PG ++A+P Y VPV E Sbjct: 91 DPRRILITPGGSGALLLASALLVDPGKHWLLADPGYPCNRHFLRLVEGAAQLVPVGPEVR 150 Query: 151 FRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSEL 210 +++ + + + SP NP+G L R L+ ++ DE+Y L Sbjct: 151 YQLTPGLIERHWDHDSVGALVASPANPTGTILTRDELAKLSVAIKERHGHLVVDEIYHGL 210 Query: 211 LFDGEHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGS 270 + AS+ + D LNS SK MTGWR+GW+V P A LE LA + + Sbjct: 211 TYG---TDAASVLEVDDSAFVLNSFSKYFGMTGWRLGWLVAPDAAVGELEKLAQNLYISA 267 Query: 271 PEFIQDAACTALE-APLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMVDIR 329 P Q AA E A + LE R + RRRD ++ L + + P+G ++ DI Sbjct: 268 PSMAQHAALACFEPATISILEERRAEFGRRRDYLLPALRELGFGIAVEPEGAFYLYADIS 327 Query: 330 PTGLSAQAFADRLLDRHGVSVLAGEAFGPSAAG-HIRLGLVLGAEPLREACRRIA 383 G A AF L+ V+ G FG AG H+R E L+EA RIA Sbjct: 328 KFGGDAFAFCKHFLETEHVAFTPGLDFGRYQAGHHVRFAYTQNLERLQEAVERIA 382 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: 397 Number of extensions: 20 Number of successful extensions: 5 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