Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate AZOBR_RS11880 AZOBR_RS11880 1-aminocyclopropane-1-carboxylate deaminase
Query= SwissProt::P96847 (388 letters) >FitnessBrowser__azobra:AZOBR_RS11880 Length = 384 Score = 429 bits (1104), Expect = e-125 Identities = 216/381 (56%), Positives = 277/381 (72%), Gaps = 4/381 (1%) Query: 4 RVALRAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLG 63 +V+ R +PPF+VM+V AAAER+ +++++ GQPS GAP+ V AA L + LG Sbjct: 6 KVSKRGAIPPFFVMEVMRAAAEREAAGLEVLHMEVGQPSTGAPKGVLEAAHRMLDADVLG 65 Query: 64 YSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASP 123 Y+ ALGIP LR AIA Y+ R+GI V VV+TTGSSG F L FLA FD GDRVAMASP Sbjct: 66 YTGALGIPALRAAIAGWYRDRYGIDVPERRVVVTTGSSGAFQLGFLAAFDPGDRVAMASP 125 Query: 124 GYPCYRNILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPE 183 YP YR+ L+A+G E VE+P GP+ RFQPT ++L ++DPP++G++VASPANPTGT++ E Sbjct: 126 SYPAYRHTLTAIGVEPVELPTGPEHRFQPTIELLEQLDPPIQGLIVASPANPTGTMLSRE 185 Query: 184 ELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRL 243 EL A+A+WCDA VRL+SDE+YHGL Y P+ A + S +A+VVNSFSKY++MTGWRL Sbjct: 186 ELTALAAWCDAKGVRLVSDEIYHGLTY--GPEAVTAAEVSESALVVNSFSKYFSMTGWRL 243 Query: 244 GWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLD 303 GW++VP L R+V+CL N I P LSQ AAV+AF T E DG++A YA NR LLL Sbjct: 244 GWMIVPDDLIRSVECLAQNLFISAPSLSQAAAVAAF--GCTEELDGHVARYARNRELLLR 301 Query: 304 GLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFV 363 L + G D+LAP DGAFY+YADV++ T DS AFC ++LA+TG+A PG+DFD ARG FV Sbjct: 302 ELPKAGFDKLAPADGAFYIYADVTEMTDDSEAFCKRILAETGIACTPGVDFDPARGLRFV 361 Query: 364 RISFAGPSGDIEEALRRIGSW 384 R SFAG I EA RR+ +W Sbjct: 362 RFSFAGAEETIAEAARRLIAW 382 Lambda K H 0.321 0.136 0.416 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: 499 Number of extensions: 25 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: 388 Length of database: 384 Length adjustment: 30 Effective length of query: 358 Effective length of database: 354 Effective search space: 126732 Effective search space used: 126732 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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