Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate BWI76_RS10245 BWI76_RS10245 aspartate aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Koxy:BWI76_RS10245 Length = 402 Score = 164 bits (416), Expect = 3e-45 Identities = 112/372 (30%), Positives = 185/372 (49%), Gaps = 15/372 (4%) Query: 31 GEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAV 90 G++++ L G+ DF TP I A I++++ T Y V G AL+ IA + R + Sbjct: 32 GKQVINLGEGELDFATPPHISYAGIEAIVHHQTKYTAVSGTAALKTAIAAKFARDNQLRY 91 Query: 91 DAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENG 150 E+++ +GA+ ++ L+ G +VI+ P +V+Y + V VP ++G Sbjct: 92 RPEEIIAGSGAKQLIFNAFLATLDAGQQVIIPAPYWVSYPDMVSLADGEPVIVPCDEQHG 151 Query: 151 FRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAH-DLWMISDEVYSE 209 +++ E++AA +TP TR + LNSP NP+GA ALA++ + + +++D++Y Sbjct: 152 WKLTPEQLAAALTPSTRWLILNSPGNPTGAIYSEPELRALADVLADYPHVLVMADDIYEP 211 Query: 210 LLFDGEH--VSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCML 267 L +D + P + RT T+N +SKSHAMTGWR+G+ GP L A ++ L Sbjct: 212 LRYDNVPFITFAQAAPQLVSRTLTVNGVSKSHAMTGWRLGYAGGPQWLIAAMQILQSQST 271 Query: 268 YGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMVD 327 Q AA AL + +RR V+ +A + GL P G +V + Sbjct: 272 SNPSSISQAAAIAALNHSADFFDGWLHRLDKRRQQVLGMIAATEGLSAGIPQGAFYVFAN 331 Query: 328 -------IRPTGLSAQ---AFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLRE 377 + P G + + A+ LL+ V+VL G AFG G++R+ + L + Sbjct: 332 CQQLIGRVTPGGETLRDDSGLANWLLEHTQVAVLHGSAFG--MPGYLRIAYAVEDGLLAQ 389 Query: 378 ACRRIALCAAEL 389 AC+RIA A+L Sbjct: 390 ACQRIAGACAQL 401 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: 423 Number of extensions: 16 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: 402 Length adjustment: 31 Effective length of query: 362 Effective length of database: 371 Effective search space: 134302 Effective search space used: 134302 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