Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate 15560 b1439 fused predicted DNA-binding transcriptional regulator/predicted amino transferase (NCBI)
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >FitnessBrowser__Keio:15560 Length = 468 Score = 175 bits (444), Expect = 2e-48 Identities = 122/386 (31%), Positives = 198/386 (51%), Gaps = 19/386 (4%) Query: 21 IRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAGGALQYTISEGFTPL 80 I ++L+ P ++ FA PDP FP + R+ ++ S + ++ + G L Sbjct: 93 IFDMLQASRDPSVVPFASAFPDPRLFPLQQLNRSLAQV--SKTATAMSVIENLPPGNAEL 150 Query: 81 REWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILVTRPTYLGALQAFSP 140 R+ I +GI DE+++T+G+ +AL + + PG+ ++V P + GALQA Sbjct: 151 RQAIARRYALQGITISPDEIVITAGALEALNLSLQAVTEPGDWVIVENPCFYGALQALER 210 Query: 141 YEPQYLSVPGDA-EGPDLAAVEAALEQKP-KFFYLVPDFQNPNGTTISLARREALLDLCA 198 + LSV D EG DL A+E AL++ P K +L+ + QNP G T++ ++ L+ L Sbjct: 211 LRLKALSVATDVKEGIDLQALELALQEYPVKACWLMTNSQNPLGFTLTPQKKAQLVALLN 270 Query: 199 KHGVPIVEDAAYTELRYEGE-PIPSMVALDAARNGGKITNVLFCGSFSKTMVPALRVGWI 257 ++ V ++ED Y+EL + E P+P A+ + VL C SFSK +VP R+GW+ Sbjct: 271 QYNVTLIEDDVYSELYFGREKPLP-------AKAWDRHDGVLHCSSFSKCLVPGFRIGWV 323 Query: 258 NGP--AEVINRLVLMKQAGDLHTSTINQIVLHDVVS-QNFDSHIRRLRAGYKERRDAMLT 314 A I RL LM L TS+ Q+ L D +S + +D+H+RRLR ER+ Sbjct: 324 AAGKHARKIQRLQLMST---LSTSSPMQLALVDYLSTRRYDAHLRRLRRQLAERKQRAWQ 380 Query: 315 ALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAFVPGSAFHADRSGKN 374 AL + PA V + G F+W+ELPE D +L A+ +++ PG F + Sbjct: 381 ALLRYLPAEVKIHHNDSGYFLWLELPEPLDAGELSLAALTH-HISIAPGKMFSTGENWSR 439 Query: 375 TLRLSFSNNNPERIREGIRRLCGLLQ 400 R + + ER + +++L L+Q Sbjct: 440 FFRFNTAWQWGEREEQAVKQLGKLIQ 465 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: 429 Number of extensions: 22 Number of successful extensions: 5 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: 468 Length adjustment: 32 Effective length of query: 372 Effective length of database: 436 Effective search space: 162192 Effective search space used: 162192 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 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