Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate GFF3586 Psest_3653 4-aminobutyrate aminotransferase, prokaryotic type
Query= BRENDA::Q3UEG6 (513 letters) >FitnessBrowser__psRCH2:GFF3586 Length = 426 Score = 189 bits (479), Expect = 2e-52 Identities = 137/409 (33%), Positives = 196/409 (47%), Gaps = 35/409 (8%) Query: 84 PLLLHQGHMEWLFDSEGNRYLDFFSGIVTVSVGHCHPKVSAVAKKQIDRLWHTS-SVFFH 142 P+ + D EG ++DF GI ++ GH HPK+ + Q+ +L HT V + Sbjct: 25 PIFADHAKNSSVVDVEGREFIDFAGGIAVLNTGHLHPKIIKAVEDQLHKLTHTCFQVLAY 84 Query: 143 SPMHEYAEKLSALLPEPL-KVIFLVNSGSEANDLAMVMARAHSNHTDIISFRGAYHGCSP 201 P E EK++A +P K LV +GSEA + A+ +ARA + +I+F GAYHG + Sbjct: 85 EPYVELCEKINARVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGAYHGRTM 144 Query: 202 YTLGLTN-VGIYKMEV---PGGIGCQSTMCPDVFRGPWGGIHCRDSPVQTVRDCSCAPDC 257 TLGLT V Y + PGGI C G+ DS R Sbjct: 145 MTLGLTGKVAPYSAGMGLMPGGIFRALYPCAIY------GVSVDDSIASIERI------- 191 Query: 258 CQAKERYIEQFKDTLNTSVATSIAGFFAEPIQGVNGVVQYPKEFLKEAFALVRERGGVCI 317 FK N + IA EP+QG G PK+F+ AL E G + I Sbjct: 192 ----------FK---NDAEPRDIAAIIIEPVQGEGGFNVAPKDFMARLRALCDEHGILLI 238 Query: 318 ADEVQTGFGRLGSHFWGFQTHDVLPDIVTMAKGIGNGFPMAAVVTTPEIAKSLAKRLLHF 377 ADEVQTG GR G+ F+ + V+ D+ T AK +G GFP+A V EI ++A L Sbjct: 239 ADEVQTGAGRTGT-FFAMEQMGVVADLTTFAKSVGGGFPIAGVCGKAEIMDAIAPGGLG- 296 Query: 378 STFGGNPLACAIGSAVLEVIEEENLQRNSQEVGTYMLLKFAKLRDEFDIVGDVRGKGLMV 437 T+ GNPL+CA AVLEV EEE L + V + ++ + +G+VRG G M+ Sbjct: 297 GTYAGNPLSCAAALAVLEVFEEEKLLDRCKAVAERLTTGLKAIQTKHKEIGEVRGLGAMI 356 Query: 438 GIEMVQDKISRQPLPKTEVNQIHEDCKDMGLLVGRGGNFSQTFRIVPPM 486 IE+ +D +P +QI +D GL++ G + R++ P+ Sbjct: 357 AIELFEDGDHARPAAAL-TSQIVARARDKGLILLSCGTYYNVLRVLVPL 404 Lambda K H 0.323 0.137 0.424 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: 479 Number of extensions: 26 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 513 Length of database: 426 Length adjustment: 33 Effective length of query: 480 Effective length of database: 393 Effective search space: 188640 Effective search space used: 188640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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