Align Uncharacterized aminotransferase MJ0959; EC 2.6.1.- (characterized, see rationale)
to candidate BPHYT_RS03855 BPHYT_RS03855 alanine--glyoxylate aminotransferase
Query= uniprot:Y959_METJA (385 letters) >FitnessBrowser__BFirm:BPHYT_RS03855 Length = 412 Score = 148 bits (373), Expect = 3e-40 Identities = 114/366 (31%), Positives = 181/366 (49%), Gaps = 10/366 (2%) Query: 9 LLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFL-ITGSGT 67 L+M GP +P V A + VI H ++ + VF T++ L + G G+ Sbjct: 31 LMMGAGPVPIPAAVAKANTI-VINHLGATMVKVIGQVKTMARYVFQTKSKWVLGVAGPGS 89 Query: 68 AAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEIL 127 AAM+MAISN+ G +VL+I G F ER A + + LDV G +A + V E + Sbjct: 90 AAMEMAISNLAWEGTRVLSIKNGFFSERMAEMGRRVGAHVSVLDVADGAVASLDEVAEAI 149 Query: 128 DKYDDIKAVTVVHNETSTGARN-PIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186 + + + VTVV ETS N +K+I + K AL +VD V +L + +D + ID Sbjct: 150 -RRERPEVVTVVQGETSNTVWNYHLKDIAALAKAAGALVVVDAVCTLSTMPLEMDAWGID 208 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIK-KNDDKVGFYLDLLAYKKYYEEKKQTPYTP 245 +TG QK L++ PG++ I S+ AW +K + + LD + ++ YT Sbjct: 209 AVITGGQKGLSSIPGVSLIAFSDAAWTRVKTRTAPNAHWCLDASLAENFWHNAGY-HYTA 267 Query: 246 SVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSAK 305 V+ AL+ AL LV E +E R RH + ++A + G+ A+G++L+A + R +V + Sbjct: 268 PVSGVLALHEALRLVCAETLEKRFARHLKCSQALQEGISALGLKLYAPQACRLNSVVGIE 327 Query: 306 YPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMG-ICGEKEVLATLACVELALK 364 P G+ G +S + + ++G I RIG MG C E + TL + + Sbjct: 328 VPAGLSPGDICGHISRHHQVEISGS---FGLPIVRIGQMGEQCREHNLFRTLHALGRTMV 384 Query: 365 ELGFEV 370 +LG V Sbjct: 385 DLGSAV 390 Lambda K H 0.316 0.135 0.379 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: 339 Number of extensions: 21 Number of successful extensions: 2 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: 385 Length of database: 412 Length adjustment: 31 Effective length of query: 354 Effective length of database: 381 Effective search space: 134874 Effective search space used: 134874 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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