Align (R)-3-amino-2-methylpropionate-pyruvate transaminase (EC 2.6.1.40); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate AO356_28705 AO356_28705 hypothetical protein
Query= BRENDA::Q64565 (512 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28705 Length = 449 Score = 201 bits (511), Expect = 5e-56 Identities = 146/457 (31%), Positives = 220/457 (48%), Gaps = 51/457 (11%) Query: 61 YNHVLEIHKQHLSPVNT---AYFQKPLLLHQGHMEWLFDSEGNRYLDFFSGIVTVGVGHC 117 Y H K+ P+++ A K L++ +G ++ D EG+R LD G+ V VGH Sbjct: 2 YEHYKTAQKKFWHPMSSSAPANRSKTLIIARGDGNYITDIEGHRMLDGVGGLWNVNVGHN 61 Query: 118 HPKVTAVAKKQMDRL--WHTSSVFFHSPMHEYAERLSALLP-EPLKVIFLVNSGSEANDL 174 P V A Q+D L + T H + + AERL+++ E + + + GS+A + Sbjct: 62 RPSVKAAIAAQLDELAYYQTFDGIAHPRVFDLAERLTSMFAQENMARVLFSSGGSDAVET 121 Query: 175 AMVMARAY------SNHTDIISFRGAYHGCSPYTLGLTNVGIYKMKV-PSTIACQSTMCP 227 A+ MAR Y T +S R YHG + G+Y P C P Sbjct: 122 ALKMARQYWIASGEPGRTRFLSLRNGYHGVHVGGTSVGGNGVYHYNHGPLLAGCHLLDTP 181 Query: 228 DVFRGPWGGSHCRDSPVQTVRKCSCAPDGCQAKERYIEQFKDTLNTSVATSIAGFFAEPI 287 ++R PW CRD P + C I Q +D + +IA AEP+ Sbjct: 182 WLYRNPWD---CRD-PEELTAHC-------------IRQLEDQIALLGPQTIAALIAEPV 224 Query: 288 QGVNGVVQYPKEFLKEAFALVRERGGVCIADEVQTGFGR----LGSHFWGFQTHDTMPDI 343 QG GV+ P + K + G + IADEV TGFGR LGS WG PD+ Sbjct: 225 QGAGGVIVPPAHYWKRLREVCDRHGILLIADEVVTGFGRTGCMLGSRGWG-----VAPDV 279 Query: 344 VTMAKGIGNGF-PMAAVVTTPEIASSL------AKHLHHFSTFGGSPLACAIGSAVLEVI 396 + +AKGI G+ PM A V IA ++ + + H T+ G P ACA AVL+++ Sbjct: 280 LCLAKGITAGYIPMGATVFNQRIADAIENGPGFSSVIMHGYTYSGHPTACAAALAVLDIV 339 Query: 397 EEENLQRNSQEVGTYMLLKFAKLRDEFDIVGDVRGKGLMVGIEMVQDKISRQPLPKTE-- 454 E E+L N+ +VG +L + L + + +VG+VRGKGLM+ +++V DK++R+PL Sbjct: 340 EAEDLPGNAGKVGAQLLEQLQPLTERYAVVGEVRGKGLMIAVDLVADKVTREPLDPANGL 399 Query: 455 VNQIHEDCKDMGLLVGRGGNFSQTFRIAPPMRVTKLE 491 ++I E + G+LV GN ++PP+ +T E Sbjct: 400 ASRIAEQARRAGVLVRPIGN---KIVMSPPLTLTSDE 433 Lambda K H 0.322 0.136 0.419 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: 536 Number of extensions: 26 Number of successful extensions: 5 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: 512 Length of database: 449 Length adjustment: 34 Effective length of query: 478 Effective length of database: 415 Effective search space: 198370 Effective search space used: 198370 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: 51 (24.3 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