Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_078429044.1 BK574_RS14105 aminotransferase
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_002019605.1:WP_078429044.1 Length = 401 Score = 308 bits (790), Expect = 1e-88 Identities = 167/394 (42%), Positives = 243/394 (61%), Gaps = 8/394 (2%) Query: 22 FSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQ 81 F+K+ +++S VR++LK+V +VIS AGGLP + FP+E I E +E + ++LQ Sbjct: 5 FAKRVRHLQSSAVRDILKVVAKGNVISFAGGLPDDDLFPLEGIKEAFEETF-RSGKKSLQ 63 Query: 82 YGTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAP 141 Y T+GF PLR L E M+++ + +I++T+GSQQA+DL RV NPGD ++ E P Sbjct: 64 YIETEGFLPLRELLIERMKRKDITSYNSEEILLTTGSQQAIDLFSRVTFNPGDFILTENP 123 Query: 142 TYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGV 201 TYLAALQ F+ YE + + + D GM + L K+++ K K +Y +PTF NPAG Sbjct: 124 TYLAALQVFESYEAKVIPVESDTHGMIEEDLVNKIKKY-----KPKCIYVVPTFSNPAGK 178 Query: 202 TMSEKRRKRLLELASEYDFLIVEDNPYGELRYS-GEPVKPIKAWDDEG-RVMYLGTFSKI 259 S +RRK LL+LA +Y +I ED+PYG++++ E PI ++D EG V+Y TFSK Sbjct: 179 VWSNERRKMLLQLAQKYHVVIFEDDPYGDIQFDQNETYSPIASFDKEGAHVLYTSTFSKT 238 Query: 260 LAPGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYK 319 P R GWIA +IR + AKQ+ DL +N SQ + LD HI N+I+ Y+ Sbjct: 239 AVPALRTGWIAGPHQIIRMMSQAKQANDLHSNSLSQQSLFHLCSNFDLDGHIHNLIDVYR 298 Query: 320 PRRDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFF 379 R + ML LE+ + + P+GGMF W+ L +GI+T +L AV +GVAYVPG F+ Sbjct: 299 SRMNIMLHELEKANLPNMSYVVPKGGMFFWIELDKGINTTELLNLAVERGVAYVPGAPFY 358 Query: 380 AHRDVKNTMRLNFTYVPEEKIREGIKRLAETIKE 413 + +NT+RLN+T+ EK+ +G+K L E IKE Sbjct: 359 VGKGQQNTLRLNYTHSTPEKLEKGMKILTEVIKE 392 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: 426 Number of extensions: 25 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: 401 Length adjustment: 31 Effective length of query: 386 Effective length of database: 370 Effective search space: 142820 Effective search space used: 142820 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