Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate GFF1996 PGA1_c20300 aminotransferase
Query= SwissProt::P96847 (388 letters) >FitnessBrowser__Phaeo:GFF1996 Length = 382 Score = 340 bits (873), Expect = 3e-98 Identities = 180/385 (46%), Positives = 245/385 (63%), Gaps = 6/385 (1%) Query: 4 RVALRAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLG 63 R + R+ V PF VMDV AA + ++++ GQPS GAP R A A AL + LG Sbjct: 2 RNSSRSNVDPFIVMDVMEAARRAEEAGRHIIHMEVGQPSTGAPVAAREALAKALDHDSLG 61 Query: 64 YSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASP 123 Y+VALG+P LR IA Y + + + P+ VVIT GSSG FLL+F A FD+GDRV + +P Sbjct: 62 YTVALGLPALRKRIAQLYGEWYNVDLNPERVVITPGSSGAFLLSFTALFDSGDRVGIGAP 121 Query: 124 GYPCYRNILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPE 183 GYP YR IL ALG V+I R QP Q L +D L G++VASPANPTGT++ Sbjct: 122 GYPSYRQILHALGLTPVDIETSLDHRLQPVPQDLTGLD--LAGLMVASPANPTGTMLDKP 179 Query: 184 ELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRL 243 +AA+ ISDE+YHG+ Y+ T A + + V+NSFSKY++MTGWR+ Sbjct: 180 AMAALIDAAQGQGAAFISDEIYHGIEYEAKAVT--ALEVTDECYVINSFSKYFSMTGWRV 237 Query: 244 GWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLD 303 GW++VP R V+ + N IC P SQ+AA++A + E +GNLA YA NR+L+L+ Sbjct: 238 GWMVVPEDHVRVVERIAQNMFICAPHASQVAALAAM--DCRDELEGNLAVYARNRALMLE 295 Query: 304 GLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFV 363 GL + G DR+AP DGAFYVYADVS+ T DS AF ++L + GVA+ PG+DFD RG + + Sbjct: 296 GLPKAGFDRIAPPDGAFYVYADVSELTHDSRAFAQEILDEAGVAVTPGLDFDPKRGATTL 355 Query: 364 RISFAGPSGDIEEALRRIGSWLPSQ 388 R S+A + DIEE L R+ +++ ++ Sbjct: 356 RFSYARATADIEEGLTRLAAFMAAR 380 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: 444 Number of extensions: 21 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: 388 Length of database: 382 Length adjustment: 30 Effective length of query: 358 Effective length of database: 352 Effective search space: 126016 Effective search space used: 126016 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