Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate 3607958 Dshi_1366 aminotransferase class-III (RefSeq)
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__Dino:3607958 Length = 441 Score = 186 bits (471), Expect = 1e-51 Identities = 127/414 (30%), Positives = 201/414 (48%), Gaps = 42/414 (10%) Query: 24 YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ- 82 + + + V G AEG + +D G N GH P +VEA++ QA L P Sbjct: 25 FKSNPRMFVAADGMYYTTAEGRQVLDGTAGLWCCNAGHKRPRIVEAIQAQAAELDYAPAF 84 Query: 83 TLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFA------RAHTGRKKFVAA 136 + P E L I P ++ VF NSG+EA E+ALK A R GR + + Sbjct: 85 QMGHPRAFELANRLVEIAPDGMDHVFYTNSGSEAVESALKIALAYHRARGEAGRTRLIGR 144 Query: 137 MRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDV-----------------EALK 179 RG+ G G +SV R+ F L+ V+ +P+ + + L+ Sbjct: 145 ERGYHGVNFGGISVGGIVNNRKHFGTLLTGVDHLPHTHIPENQWSRGMPELGAHLADDLE 204 Query: 180 RAVD----EETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTG 235 R + E AAVI+EP+ G GV +L+ R+ITQ+ G +LI DE+ TG GR G Sbjct: 205 RIIALHGAETIAAVIVEPMAGSTGVLLPPKGYLQRLRKITQDHGIVLIFDEVITGFGRVG 264 Query: 236 KRFAFEHFGIVPDILTLAKALGGGV-PLGVAVMREEVARSMPKGG-------HGTTFGGN 287 F + FG+ PD++T AK L GV P+G + + + +G HG T+ GN Sbjct: 265 AAFGAQRFGVTPDMITCAKGLTNGVIPMGAVLCGSHIHDAFMQGPENLIELFHGYTYSGN 324 Query: 288 PLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAIPSPK-IREVRGMGLMVGLELKEK 346 P+A AAG+A + L+ RA +L P++ E L ++ + + ++R +GL+ +EL+ Sbjct: 325 PIASAAGLATLETYREDDLFARALDLEPYWQEALHSLKGARHVIDIRNLGLIGAIELEPI 384 Query: 347 AA-----PYIARLEKEHRVLALQAGPTVIRFLPPLVIEKEDLERVVEAVRAVLA 395 + + A L+ + + ++ +I PPL+IE ++R+VE + VLA Sbjct: 385 SGHPTKRAFQAFLDAYDKGVLIRTTGDIIALSPPLIIETAQIDRIVETLGEVLA 438 Lambda K H 0.319 0.137 0.403 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: 403 Number of extensions: 23 Number of successful extensions: 6 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: 395 Length of database: 441 Length adjustment: 32 Effective length of query: 363 Effective length of database: 409 Effective search space: 148467 Effective search space used: 148467 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 Apr 09 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