Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate 352902 BT3375 aspartate aminotransferase (NCBI ptt file)
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Btheta:352902 Length = 386 Score = 182 bits (462), Expect = 1e-50 Identities = 112/358 (31%), Positives = 189/358 (52%), Gaps = 12/358 (3%) Query: 32 EEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAVD 91 + ++ ++GDPD I +A ++L G T Y+ G LR+ I+ R++ + + Sbjct: 27 DNVIDFTLGDPDIHPHDKIKEAGCKAILEGRTRYSPNAGLLELREIISSRYKLQYNIEYN 86 Query: 92 -AEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGAC-GARVVPVPVRSEN 149 +++V G LY + +LN GDEVI+ P ++ Y + C G ++ PV S N Sbjct: 87 PTNEIMVTVGGMEGLYLTLLAILNRGDEVIIPAPYWINYVQMVCMCSGEPIITAPV-STN 145 Query: 150 GFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSE 209 + E + ITP+T+A+ LN+P NPSG + + + +A++ + +DL +I+DEVY Sbjct: 146 DLSISIENIRKAITPKTKAIILNTPSNPSGRIISDDSIQQIAQIAIENDLIVITDEVYKT 205 Query: 210 LLFDGEHV-SPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHL----ENLAL 264 LL+D H S + M +RT +NSLSK MTGWR+G++ P+ L + + EN+A Sbjct: 206 LLYDNAHFKSIVTCDKMKERTVVINSLSKEFCMTGWRLGYIAAPSELISVMTMFQENIAA 265 Query: 265 CMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFV 324 C +P Q AA AL M E + RR++++E +A + P G + Sbjct: 266 C----APLPSQYAAIEALRNSEKYSAGMIEEFTLRRNVLLEEVAKIKTITVDAPQGTFYA 321 Query: 325 MVDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLREACRRI 382 M++I+ TGL ++ FA LL++ V+V+ G +G IR+ L ++E +R+ Sbjct: 322 MLNIKSTGLKSEEFAYALLEKEQVAVVPGITYGDCCEDFIRIAFTLDIYKIKEGIQRL 379 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: 320 Number of extensions: 15 Number of successful extensions: 4 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: 386 Length adjustment: 30 Effective length of query: 363 Effective length of database: 356 Effective search space: 129228 Effective search space used: 129228 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