Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_084544841.1 H566_RS23330 PLP-dependent aminotransferase family protein
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >NCBI__GCF_000482785.1:WP_084544841.1 Length = 525 Score = 150 bits (380), Expect = 6e-41 Identities = 125/379 (32%), Positives = 172/379 (45%), Gaps = 23/379 (6%) Query: 29 ERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAGGALQYTISEGFTPLREWICAYL 88 E EI FAG D D FP R + Q + L Y G LR I YL Sbjct: 132 EHVEIQPFAGQDDDYDGFPFKVWQRLQAR--QWRNARAELLDYDHGGGHPALRRAIADYL 189 Query: 89 G-RRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILVTRPTYLGALQAFSPYEPQYLS 147 R + D+VL+T G+QQ+L+ +LL G+ P Y A + Q Sbjct: 190 RVSRSVNVTPDQVLITPGTQQSLDLCARLLADSGDLAWFENPGYWAAERVLRGNGLQLRP 249 Query: 148 VPGDAEGPDLAAVEAALEQKPKFFYLVPDFQNPNGTTISLARREALLDLCAKHGVPIVED 207 V DAEG LA E + K Y+ P Q P G +SLARR ALL+ A+ G I+ED Sbjct: 250 VAVDAEG--LAPSEDDFATRAKLIYVTPSHQYPTGVVMSLARRRALLEYAARTGAWILED 307 Query: 208 AAYTELRYEGEPIPSMVALDAARNGGKITNVLFCGSFSKTMVPALRVGWINGPAEVINRL 267 E RYEG P+ S+ LD A V++ G+FSK + P LR+G++ P + + Sbjct: 308 DYDAEFRYEGRPVASLQGLDDA------GRVIYMGTFSKVLYPGLRIGYMVVPPAIAADM 361 Query: 268 VLMKQAG--DLHT--STINQIVLHDVVSQN-FDSHIRRLRAGYKERRDAMLTALSEFAPA 322 Q G DLH + Q L + + F SHIRR R Y ERR + + L E Sbjct: 362 ----QTGLYDLHRPGQLLMQAALAEFIQLGYFASHIRRQRQVYAERRQRLTSVLREVLGE 417 Query: 323 GVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAFVPGSAFHADRSG--KNTLRLSF 380 G+ + + GM + + LP G D V LA DA + P S ++ D G + L + + Sbjct: 418 GIELSPVQTGMHLVVYLPAGADDV-ALAEECADAGLNVRPLSRYYLDAPGGRRGGLVIGY 476 Query: 381 SNNNPERIREGIRRLCGLL 399 + I G R+L +L Sbjct: 477 AYVKSPGIEPGARKLGAVL 495 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: 527 Number of extensions: 26 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: 525 Length adjustment: 33 Effective length of query: 371 Effective length of database: 492 Effective search space: 182532 Effective search space used: 182532 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: 51 (24.3 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