Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate CCNA_02244 CCNA_02244 aminotransferase class I family protein
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >FitnessBrowser__Caulo:CCNA_02244 Length = 425 Score = 400 bits (1027), Expect = e-116 Identities = 204/400 (51%), Positives = 272/400 (68%), Gaps = 6/400 (1%) Query: 4 DWGNVFAGRVAGMGASEIRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNS 63 DW F+ R++ + ASEIRELLKLL++P+I+SFAGGIPDP FP I + Y+ I Sbjct: 22 DWAGRFSERMSRVRASEIRELLKLLDQPDILSFAGGIPDPGLFPAQEIQKGYDAILADPV 81 Query: 64 GAGGALQYTISEGFTPLREWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEK 123 + ALQY++SEG+ PLR+WI + R G+ G D +++T+GSQQAL+ +GKL + G+ Sbjct: 82 LSRQALQYSVSEGYLPLRQWIAERMTRDGMPCGPDNIMLTAGSQQALDLIGKLFLTKGDT 141 Query: 124 ILVTRPTYLGALQAFSPYEPQYLSVPGDA--EGPDLAAVEAALEQKPKFFYLVPDFQNPN 181 ++V RPTYLGALQAF+ YEP YL +P A +G D AA+ A +P Y VPDF NP Sbjct: 142 VMVARPTYLGALQAFNGYEPAYLDLPETALSQGVDEAALMAGRAPRP-LGYFVPDFANPT 200 Query: 182 GTTISLARREALLDLCAKHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGGKITNV--L 239 G +++LA REALL + + + +VEDAAY ELR+ GE P+++ LD R+GG I N L Sbjct: 201 GVSLTLAEREALLAMADRLDMTLVEDAAYRELRFAGEATPTVLGLDITRSGG-IDNARTL 259 Query: 240 FCGSFSKTMVPALRVGWINGPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQNFDSHIR 299 F G+ SKT+ PALR+GW+ GP VI +LVL+KQ DLH STINQ+V H V++ +D H+ Sbjct: 260 FLGTLSKTLSPALRIGWVCGPKAVIEKLVLLKQGADLHVSTINQMVAHRAVTEGYDQHLH 319 Query: 300 RLRAGYKERRDAMLTALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVA 359 RLR Y + ML AL P GVTW+ PEGGMFVWI+LPEG DG LLARAI++ VA Sbjct: 320 RLRGAYGAKARVMLAALERTMPKGVTWSHPEGGMFVWIDLPEGIDGAALLARAIEEERVA 379 Query: 360 FVPGSAFHADRSGKNTLRLSFSNNNPERIREGIRRLCGLL 399 FVPG+ F A+ N +RLS+S +I EG++RL L+ Sbjct: 380 FVPGAPFFAENQTPNAIRLSYSLPTDAQIEEGVQRLARLI 419 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: 525 Number of extensions: 25 Number of successful extensions: 3 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: 425 Length adjustment: 31 Effective length of query: 373 Effective length of database: 394 Effective search space: 146962 Effective search space used: 146962 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 Jul 25 2024. The underlying query database was built on Jul 25 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