Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate 8500245 DvMF_1002 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (RefSeq)
Query= BRENDA::A4F7V1 (447 letters) >FitnessBrowser__Miya:8500245 Length = 491 Score = 102 bits (254), Expect = 3e-26 Identities = 128/426 (30%), Positives = 174/426 (40%), Gaps = 50/426 (11%) Query: 37 LDAGDGCRLRDLRDGTEYLDMTMFFSSATLGHGHPGLRTPEFEAALVRAGRVKPSNPDFA 96 + A +G RL D DG YLD + GH HP L A +RA K ++ Sbjct: 53 IGAAEGNRLTDT-DGVSYLDGVSSLWTNVHGHRHPRLD------AAIRAQLDKVAHTTLL 105 Query: 97 TVEQARFAETFRRVAG-DPQ-LPLLFFIDGGTLAVENALKVAFDWKTKVNARKGVAIRGS 154 + E R+A PQ L +F+ D G+ +VE ALK+AF + + A G R + Sbjct: 106 GLGSEPSIELAARLAAIAPQGLTRVFYSDSGSTSVEVALKIAFQFHRQAPAHLGGDARRT 165 Query: 155 RVLHLEKAFHGRSGYTLSLTNTDPSKIRDYPM-FDWPRIPSPAVVPGDDWDDPELLPHER 213 R L L A+HG + ++L P+ FD + SP ER Sbjct: 166 RFLSLRNAYHGDTVGAVALGGMALFHSIYAPLLFDTVKAESPYCYRCPFGRQAGSC--ER 223 Query: 214 VAVEAAEAALRRYGREIACFVYEP-IQGEGGDRHLRPRFLRAVQELCREHDVLTVADEVQ 272 + E R+G E+ V EP +QG G P +LR V+ELC EH V VADEV Sbjct: 224 ECITHMETLFARHGHELCAAVVEPLVQGAAGMLLQPPGWLRRVRELCDEHGVFLVADEVA 283 Query: 273 TG-ALTGRAWAYQALGLEPDLVAFGKRMQVCGVMGGRRVL------EVEENAFREASRIS 325 G TG +A + G+ PD + K G+ GG L E + F Sbjct: 284 VGFGKTGTLFACEQEGVTPDFLCLAK-----GISGGYLPLAATLTTERVHDGFLARHEEL 338 Query: 326 STWGGSLTDMVRATRILEVIESEDLFEHSRQMGELLLGELRALVAEFPSV-----VRDAR 380 T+ T I S D+FE R M E L ++ L A ++ V D R Sbjct: 339 RTFFHGHTYTGNPLACAAAIASLDVFEEERVM-ERLQPKIARLAARLDTLRDLPHVGDIR 397 Query: 381 GRGLMCAISFADPDKRNRA------LAVARDHHRTL--------FLPSGTDSLRCRPPLS 426 RG+M I RNRA LA+ H TL P G D + PPLS Sbjct: 398 QRGVMTGIEMV----RNRATKEAYDLALRVGHRVTLEARRRGVIIRPLG-DVMVLMPPLS 452 Query: 427 VRPEEV 432 + +E+ Sbjct: 453 ITDDEI 458 Lambda K H 0.321 0.137 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: 532 Number of extensions: 32 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 447 Length of database: 491 Length adjustment: 33 Effective length of query: 414 Effective length of database: 458 Effective search space: 189612 Effective search space used: 189612 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 (21.9 bits) S2: 51 (24.3 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