Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate Ac3H11_3135 Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3135 Length = 394 Score = 163 bits (412), Expect = 9e-45 Identities = 107/343 (31%), Positives = 169/343 (49%), Gaps = 10/343 (2%) Query: 23 RALARVEQG--EEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAE 80 +ALAR G E ++ L++G+PDF P + +AA ++ +G T Y + G ALR+RI+ Sbjct: 23 QALAREVAGTREPMIFLNIGEPDFTAPPLVQEAAARAVHSGATQYTNALGLDALRERISS 82 Query: 81 RHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARV 140 ++ R G V A ++VV AGA AL L+ GDE+++ +P Y A + Sbjct: 83 WYQSRFGVNVPARRIVVTAGASAALQLACLALIESGDEILMPDPSYPCNRHFVSAAEGKA 142 Query: 141 VPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLW 200 V +P + +++ A++V A +TR + L SP NP+G S+ + ++ +HD Sbjct: 143 VLLPTTAAERYQLSADKVRAAWNEKTRGVLLASPSNPTGTSIAPDELRRIHDVVRSHDGI 202 Query: 201 MISDEVYSELLFDGEHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLE 260 + DE+Y L ++ E A + D ++NS SK MTGWR+GW+V P A+ +E Sbjct: 203 TMIDEIYLGLSYEEEFGHTAL--AIDDNIISINSFSKYFNMTGWRLGWMVVPEAMVPVVE 260 Query: 261 NLALCMLYGSPEFIQDAACTALEA-PLPELEAMREAYRRRRDLVIECLADSPGLRPLRPD 319 LA + + Q AA EA + E E R ++ RRD I L P++PD Sbjct: 261 RLAQNLFICASTVSQYAALACFEAESIAEYERRRAEFKARRDFFIPALEKLGLAVPVKPD 320 Query: 320 GGMFVMVDIRPTG-----LSAQAFADRLLDRHGVSVLAGEAFG 357 G + D + FA L+ R ++V G FG Sbjct: 321 GAFYAWADCTQAAQRLGVTGSWDFAFELMRRAHIAVTPGRDFG 363 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: 380 Number of extensions: 24 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 393 Length of database: 394 Length adjustment: 31 Effective length of query: 362 Effective length of database: 363 Effective search space: 131406 Effective search space used: 131406 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