Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate YP_004142121.1 Mesci_2940 class I and II aminotransferase
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >NCBI__GCF_000185905.1:YP_004142121.1 Length = 402 Score = 415 bits (1067), Expect = e-120 Identities = 209/398 (52%), Positives = 277/398 (69%), Gaps = 5/398 (1%) Query: 7 NVFAGRVAGMGASEIRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAG 66 N+ A R + M ASEIRELLKLL++P+IISFAGGIPDP FP AI AY + + AG Sbjct: 5 NLLASRSSRMKASEIRELLKLLDQPDIISFAGGIPDPALFPAEAIRDAYADVL-GGAEAG 63 Query: 67 GALQYTISEGFTPLREWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILV 126 ALQY +SEG+ PLR W+ +G+ G+ + +TSGSQQAL+++GKL + PG+ LV Sbjct: 64 AALQYQVSEGYLPLRRWLAGQMGKLGVACDEANIFITSGSQQALDYLGKLFLSPGDTALV 123 Query: 127 TRPTYLGALQAFSPYEPQY--LSVPGDAEGPDL-AAVEAALEQKPKFFYLVPDFQNPNGT 183 T PTYLGALQAF+ YEP+Y L+ G PD A AA K KF YLVPDF NP G Sbjct: 124 TWPTYLGALQAFNAYEPRYDRLTPAGGNMTPDAYRAAAAANGGKAKFAYLVPDFANPTGN 183 Query: 184 TISLARREALLDLCAKHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGG-KITNVLFCG 242 T++ +REA+LDL + + ++EDAAY LRY+GE P ++ALD AR+GG L+CG Sbjct: 184 TLNREQREAVLDLAGELDIAVIEDAAYRALRYDGEGEPPILALDCARSGGIDKARTLYCG 243 Query: 243 SFSKTMVPALRVGWINGPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQNFDSHIRRLR 302 SFSK + P +RVGW+ P ++ +LVLMKQA DLH+ +INQ+V+H V F+ + +L Sbjct: 244 SFSKILSPGMRVGWVCAPRHIVEKLVLMKQASDLHSPSINQVVMHRVAEAVFEGQVEKLI 303 Query: 303 AGYKERRDAMLTALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAFVP 362 Y+ERRD +L+AL P GVTW++PEGGMFVW+ LPEG D +LLAR++K+A VAFVP Sbjct: 304 DAYRERRDGLLSALEAHMPEGVTWSRPEGGMFVWVTLPEGADATELLARSVKEARVAFVP 363 Query: 363 GSAFHADRSGKNTLRLSFSNNNPERIREGIRRLCGLLQ 400 G+AF+AD +G+NTLRLSF+ + + EGI RL +L+ Sbjct: 364 GNAFYADGTGRNTLRLSFTLADRRAVSEGIPRLAAILK 401 Lambda K H 0.320 0.138 0.410 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: 538 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: 404 Length of database: 402 Length adjustment: 31 Effective length of query: 373 Effective length of database: 371 Effective search space: 138383 Effective search space used: 138383 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 (21.8 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