Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate GFF3809 PS417_19505 2,4-diaminobutyrate 4-aminotransferase
Query= curated2:Q976K0 (387 letters) >FitnessBrowser__WCS417:GFF3809 Length = 464 Score = 221 bits (563), Expect = 3e-62 Identities = 142/404 (35%), Positives = 226/404 (55%), Gaps = 49/404 (12%) Query: 12 LTIVKGEGQYVWDISGTKYLDLHTGIGVAFLGHRNRRVIEYLSRQMENIMTLST-SFSTP 70 L + + +G YV D+ G +++D G G LGH + VIE + + + + + L T +TP Sbjct: 45 LALKRAKGLYVEDVEGRRFIDCLAGAGTLALGHNHPVVIEAIQQVLADELPLHTLDLTTP 104 Query: 71 IRDEMLKELDPLKPDKMDNIILLN----SGTEAVEAALKTARKITGRKKIIAFKNSFHGR 126 ++D+ +++L L P + + +GT+AVEAALK R TGR +++F+ +HG Sbjct: 105 VKDQFVQDLFGLLPPALAREAKIQFCGPTGTDAVEAALKLVRTATGRSTVLSFQGGYHGM 164 Query: 127 TAGSLSVTWNKRYREPFEPLM-SPVQFLTY--------------------NNIDELKNID 165 + G+LS+ + ++P L+ + VQFL Y + +D L N Sbjct: 165 SQGALSLMGSLGPKKPLGALLGNGVQFLPYPYDYRCPFGLGGAEGVRVNLHYLDNLLNDP 224 Query: 166 EQ----TAAVIVEPIQGESGVIPANEDFMKALREQTQKVGALLVVDEVQTGFGRTGKVWA 221 E AAVIVE +QGE GVIPA+ D+++ LR T++ G L+VDE+Q+GFGRTGK++A Sbjct: 225 EAGVLLPAAVIVEVVQGEGGVIPADLDWLRGLRRITEQAGVALIVDEIQSGFGRTGKLFA 284 Query: 222 YQHYGIIPDLLTAGKAIGGGFPVSALFLPDWIAEKLEEGDHGSTYGGNPMAMAAVTAASK 281 ++H GIIPD++ KAIGG P++ + DW+ L G H T+ GN MAMAA +A + Sbjct: 285 FEHAGIIPDVVVMSKAIGGSLPLAVVVYRDWLDTWL-PGAHAGTFRGNQMAMAAGSAVMR 343 Query: 282 VLKEDNVVEQASIKGEIFKKILREKLSDLKSVREIRGKGLMIGIEI----------RFPP 331 LK+ ++ A+ GE + LR D + +IRG+GLM+G+E+ PP Sbjct: 344 YLKDHDLAGHAAAMGERLGEHLRILQRDFPHLGDIRGRGLMLGVELVDPNGTLDVQGHPP 403 Query: 332 A---IALKVMQD--ERVLALKAG---STVIRFLAPYMITQSDME 367 +A V ++ +R L L+ G +V+RFL P +IT +++ Sbjct: 404 VHRQLAPLVQRECLKRGLILELGGRHGSVVRFLPPLVITAVEVD 447 Lambda K H 0.318 0.135 0.383 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: 422 Number of extensions: 20 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: 387 Length of database: 464 Length adjustment: 32 Effective length of query: 355 Effective length of database: 432 Effective search space: 153360 Effective search space used: 153360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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