Align aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized)
to candidate 351931 BT2403 aspartokinase/homoserine dehydrogenase (NCBI ptt file)
Query= reanno::Dyella79:N515DRAFT_4002 (853 letters) >FitnessBrowser__Btheta:351931 Length = 811 Score = 165 bits (417), Expect = 1e-44 Identities = 139/468 (29%), Positives = 232/468 (49%), Gaps = 42/468 (8%) Query: 1 MKFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDAL---KQMCAQEDKGKR 57 MKFGGTSV ++ +++ +V S G V+VVVSAL GITD L +M A D Sbjct: 4 MKFGGTSVGSVNSILSVKRIVESA---GEPVIVVVSALGGITDKLINTSKMAAAGDSAYE 60 Query: 58 VEAARAIAQRHYDLLDHM------QLAVPATLAERLSELAMLAEDGPGAMGELA--WAAL 109 E R I RH +++ + Q+A+ + E L+EL + + G + +L+ + Sbjct: 61 GEF-REIVYRHVEMIKEVIPAGAGQVALQRQIGELLNELKDIFQ-GIYLIRDLSPKTSDT 118 Query: 110 VQAHGELMSSALGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPAL 169 + ++GE +SS + A + A +W D+R + N++ L+ + + Sbjct: 119 IVSYGERLSSIIVAELIDEA----KWFDSRTFIKTEKKHNKHTIDADLTNQL-------V 167 Query: 170 NARLAELGEVFITQGFIARE-AQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMF 228 + +V + GFI+ + G LGRGGSD +A+ A L A +EIWTDV G Sbjct: 168 KEAFHSIPKVSLVPGFISSDKVSGDVTNLGRGGSDYTAAIIAAALDASSLEIWTDVDGFM 227 Query: 229 TANPRQVPGARLLQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGT 288 TA+PR + A + L Y EA E+ + GAKV++P + P+ +P++IK+T P+ GT Sbjct: 228 TADPRVISTAYTISELSYVEATELCNFGAKVVYPPTIYPVCHKNIPIIIKNTFNPDGVGT 287 Query: 289 VIGPEV-REHAPSVKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSA 347 VI E + ++K IS+ +L++++ +GM +G +F ++G+SV L+ A Sbjct: 288 VIKQETSNPQSKAIKGISSINDTSLITVQGLGMVGVIGVNYRIFKALAKNGISVFLVSQA 347 Query: 348 ETNVTVSLDPTENLLDSD-AIAALASDLAKVCRVKVIAP------CAAITLVGRGMR--- 397 + + S+ D+D A L + AK + I+P A + +VG M+ Sbjct: 348 SSENSTSIGVRN--ADADLACEVLNEEFAKEIEMGEISPILAERNLATVAIVGENMKHTP 405 Query: 398 SMLHTLSGVLAEFGQIRVHLISQSSNNLNLTFVVDENVVDDLLPHLHE 445 + L G L G I V +Q ++ N++FVVD + L +H+ Sbjct: 406 GIAGKLFGTLGRNG-INVIACAQGASETNISFVVDSKSLRKSLNVIHD 452 Lambda K H 0.319 0.135 0.398 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: 1205 Number of extensions: 53 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: 853 Length of database: 811 Length adjustment: 42 Effective length of query: 811 Effective length of database: 769 Effective search space: 623659 Effective search space used: 623659 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: 56 (26.2 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