Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate 3607958 Dshi_1366 aminotransferase class-III (RefSeq)
Query= reanno::Marino:GFF3099 (404 letters) >FitnessBrowser__Dino:3607958 Length = 441 Score = 136 bits (342), Expect = 1e-36 Identities = 111/404 (27%), Positives = 185/404 (45%), Gaps = 42/404 (10%) Query: 27 VRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLSNVMTNEP-AL 85 V +G EGR+ +D G+ GH P +V A+ QA ++ + P A Sbjct: 33 VAADGMYYTTAEGRQVLDGTAGLWCCNAGHKRPRIVEAIQAQAAELDYAPAFQMGHPRAF 92 Query: 86 RLAKTLCDLT--FAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHGRT 143 LA L ++ + VF+ NSG+EA E+A K+A Y + +I + +HG Sbjct: 93 ELANRLVEIAPDGMDHVFYTNSGSEAVESALKIALAYHRARGEAGRTRLIGRERGYHGVN 152 Query: 144 LFTVSVGGQPKYLEGFEPAPGGIHHAEF--------------------NDLESVKKLISK 183 +SVGG + F G+ H +DLE + L Sbjct: 153 FGGISVGGIVNNRKHFGTLLTGVDHLPHTHIPENQWSRGMPELGAHLADDLERIIALHGA 212 Query: 184 EKTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMY 243 E A++VEP+ G GV+ + +LQ LR + ++ +L+FDEV +G GR G + Q + Sbjct: 213 ETIAAVIVEPMAGSTGVLLPPKGYLQRLRKITQDHGIVLIFDEVITGFGRVGAAFGAQRF 272 Query: 244 GVVPDILSSAKGLGGG-FPVAAMLTTAKVAASLGVGT-------HGSTYGGNALACAVAQ 295 GV PD+++ AKGL G P+ A+L + + + G HG TY GN +A A Sbjct: 273 GVTPDMITCAKGLTNGVIPMGAVLCGSHIHDAFMQGPENLIELFHGYTYSGNPIASAAGL 332 Query: 296 RVVDTVSQPEILKGVKARSDKLRKGMMDI-GERYGVFTEVRGAGLLLGCVLTEKWQGKA- 353 ++T + ++ ++ + + G R+ + ++R G L+G + E G Sbjct: 333 ATLETYREDDLFARALDLEPYWQEALHSLKGARHVI--DIRNLG-LIGAIELEPISGHPT 389 Query: 354 ----KDFLNAGLEEGVMVLVAGANVIRLAPSLIIPEPDIELALE 393 + FL+A ++GV++ G ++I L+P LII I+ +E Sbjct: 390 KRAFQAFLDA-YDKGVLIRTTG-DIIALSPPLIIETAQIDRIVE 431 Lambda K H 0.318 0.137 0.406 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: 421 Number of extensions: 23 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: 441 Length adjustment: 32 Effective length of query: 372 Effective length of database: 409 Effective search space: 152148 Effective search space used: 152148 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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