Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_013644313.1 METBO_RS03620 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000191585.1:WP_013644313.1 Length = 392 Score = 340 bits (871), Expect = 6e-98 Identities = 175/382 (45%), Positives = 255/382 (66%), Gaps = 8/382 (2%) Query: 32 SEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPL 91 S VRE+LK+ + D+IS AGGLP P+TFP E AE T +LE A+ALQY TT+G+ PL Sbjct: 15 SFVREILKVADEPDIISFAGGLPNPDTFPEEEFAESTSYILENSGAEALQYSTTEGYEPL 74 Query: 92 RLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFK 151 R ++E K + + +I+IT+GSQQ LDL+ +VF+N D V+VE PTYLAALQAF Sbjct: 75 RKLVSERYSKN-GLSVDPKNILITNGSQQGLDLVAKVFLNKDDTVLVEKPTYLAALQAFG 133 Query: 152 YYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRL 211 +EP F IPL ++G+ VD+L +++E KL Y+IP FQNP G++ S ++RK + Sbjct: 134 LFEPNFKSIPLLNDGVDVDVLRSQIEE-----DSPKLFYSIPNFQNPTGISYSLEKRKII 188 Query: 212 LELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAA 271 +L ++ + ++VEDNPYGE+R+ GE + PIK + D + LG+FSK++APG R+GWI A Sbjct: 189 GKLLNQNETILVEDNPYGEIRFMGENLPPIKTFTDNS--ILLGSFSKVVAPGIRLGWIVA 246 Query: 272 EPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEE 331 E + L AKQ+ DL +N FSQ+I Y+ ++ H+ I + YK +RD M++ ++ Sbjct: 247 EDETMHHLVTAKQASDLHSNFFSQMIVHHYLTKYDVEEHLSMIRQMYKDQRDFMVEMIKL 306 Query: 332 FMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTMRLN 391 P+ V++T+PEGGMF+WVTLP + + E+ + VA+VPGEAF++ KNT+RLN Sbjct: 307 HFPDDVKYTQPEGGMFLWVTLPGDMAAMELFERTMEDKVAFVPGEAFYSDDPQKNTLRLN 366 Query: 392 FTYVPEEKIREGIKRLAETIKE 413 F+ KI EGIK++ I+E Sbjct: 367 FSNSNNTKIEEGIKKMGNAIRE 388 Lambda K H 0.318 0.137 0.398 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: 433 Number of extensions: 27 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: 417 Length of database: 392 Length adjustment: 31 Effective length of query: 386 Effective length of database: 361 Effective search space: 139346 Effective search space used: 139346 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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