Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate PfGW456L13_2943 Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2943 Length = 395 Score = 582 bits (1500), Expect = e-171 Identities = 284/390 (72%), Positives = 327/390 (83%) Query: 1 MRYSDFTQRIAGDGAAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLA 60 MRYS TQRIAGDGAAAW IH RALA EQG ++LLLS+GDPDFDTP PIVQAAI SLLA Sbjct: 1 MRYSALTQRIAGDGAAAWQIHDRALALREQGVDVLLLSIGDPDFDTPQPIVQAAIGSLLA 60 Query: 61 GNTHYADVRGKRALRQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVI 120 G+THY VRG + LR IA HRRRSGQAVDA+ V+V GAQCA+Y+V QCLL+PGDEV+ Sbjct: 61 GDTHYPAVRGSQGLRDSIARHHRRRSGQAVDAQHVIVFPGAQCAVYSVAQCLLDPGDEVL 120 Query: 121 VAEPMYVTYEAVFGACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGA 180 VAEPMYVTYE VFGACGA+VVPVPVRS+NGFRV +VAALITP TRAM LNSP+NPSGA Sbjct: 121 VAEPMYVTYEGVFGACGAKVVPVPVRSQNGFRVDPADVAALITPNTRAMLLNSPNNPSGA 180 Query: 181 SLPRATWEALAELCMAHDLWMISDEVYSELLFDGEHVSPASLPGMADRTATLNSLSKSHA 240 SLP W+ALA LC+ HDLW+ISDEVYSELLF+GEH+SPASLPGMA+RTAT+NSLSKSHA Sbjct: 181 SLPLTAWKALAALCIRHDLWLISDEVYSELLFEGEHISPASLPGMAERTATINSLSKSHA 240 Query: 241 MTGWRVGWVVGPAALCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRR 300 M+GWRVGWV+GP +LC HL NL+LCML+G P+FIQ+AA AL+ LP + MRE YR+RR Sbjct: 241 MSGWRVGWVIGPQSLCEHLVNLSLCMLFGIPDFIQNAAQLALDENLPHVAQMREEYRQRR 300 Query: 301 DLVIECLADSPGLRPLRPDGGMFVMVDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPSA 360 DLV L PG++ +RPDGGMFVMVD+R TGLSAQ FA+RLLD +GVSVLAGEAFGPSA Sbjct: 301 DLVCASLNLCPGIQAIRPDGGMFVMVDVRQTGLSAQHFAERLLDGYGVSVLAGEAFGPSA 360 Query: 361 AGHIRLGLVLGAEPLREACRRIALCAAELL 390 AGHIR+GLV+ L +ACRRI +C +L Sbjct: 361 AGHIRIGLVVDRPKLADACRRIVMCVTNML 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: 643 Number of extensions: 16 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: 395 Length adjustment: 31 Effective length of query: 362 Effective length of database: 364 Effective search space: 131768 Effective search space used: 131768 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