Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate PfGW456L13_3206 Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3206 Length = 396 Score = 670 bits (1728), Expect = 0.0 Identities = 331/390 (84%), Positives = 361/390 (92%) Query: 1 MRYSDFTQRIAGDGAAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLA 60 MR+SD TQRIAGDGAAAWDIHYRALA EQGE+ILLLSVGDPDFDTP PIVQ AIDSLL Sbjct: 1 MRFSDLTQRIAGDGAAAWDIHYRALALREQGEDILLLSVGDPDFDTPQPIVQGAIDSLLN 60 Query: 61 GNTHYADVRGKRALRQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVI 120 GNTHYA+VRGKRALR+ IA RH++RSGQ+V A+QV VLAGAQCAL++V QC+LNPGDEVI Sbjct: 61 GNTHYAEVRGKRALREAIARRHQQRSGQSVSADQVTVLAGAQCALFSVAQCVLNPGDEVI 120 Query: 121 VAEPMYVTYEAVFGACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGA 180 VAEPMYVTYEAVFGACGA VVPVPVRSENGFRV E+VAA ITPRTRA+ALNSPHNPSGA Sbjct: 121 VAEPMYVTYEAVFGACGAVVVPVPVRSENGFRVLPEDVAARITPRTRALALNSPHNPSGA 180 Query: 181 SLPRATWEALAELCMAHDLWMISDEVYSELLFDGEHVSPASLPGMADRTATLNSLSKSHA 240 SLPR+TW ALAELC+AHDLW+ISDEVYSELLF+GEHVSPASLPGMA+RTATLNSLSKSHA Sbjct: 181 SLPRSTWAALAELCIAHDLWLISDEVYSELLFEGEHVSPASLPGMAERTATLNSLSKSHA 240 Query: 241 MTGWRVGWVVGPAALCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRR 300 MTGWRVGWVV P +L AHLENLALCMLYGSP+FIQDAA ALE+ LPELEAMREAYR+RR Sbjct: 241 MTGWRVGWVVAPPSLAAHLENLALCMLYGSPDFIQDAAVVALESNLPELEAMREAYRQRR 300 Query: 301 DLVIECLADSPGLRPLRPDGGMFVMVDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPSA 360 DLV + LAD PG+R L+PDGGMFVM+DIR TGLSAQAFADRLLDRHGVSVLAGEAFGPSA Sbjct: 301 DLVCDSLADCPGVRALKPDGGMFVMLDIRQTGLSAQAFADRLLDRHGVSVLAGEAFGPSA 360 Query: 361 AGHIRLGLVLGAEPLREACRRIALCAAELL 390 AGHIRLGLV+GAEPLR+AC+RIA CA EL+ Sbjct: 361 AGHIRLGLVVGAEPLRDACQRIARCAQELM 390 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: 671 Number of extensions: 22 Number of successful extensions: 1 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