Align [amino group carrier protein]-C-terminal-L-glutamyl-γ-L-lysine aminotransferase (EC 2.6.1.118; EC 2.6.1.124) (characterized)
to candidate Pf6N2E2_2395 Pyoverdin biosynthesis protein PvdH, L-2,4-diaminobutyrate:2-oxoglutarate aminotransferase (EC 2.6.1.76)
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2395 Length = 470 Score = 205 bits (521), Expect = 2e-57 Identities = 128/414 (30%), Positives = 219/414 (52%), Gaps = 49/414 (11%) Query: 12 LTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQL-ENISILSTSFSTP 70 L + + + YV D+EGR ++D G G LGH +P+++E ++ L + + + + +TP Sbjct: 51 LALKRAKGLYVEDVEGRTFIDCLAGAGTLALGHNHPVVIEAIQQVLADELPLHTLDLTTP 110 Query: 71 IKDEMLQALDKVKPDKMDNAMLLN----SGTEAVEAALKTARKITGRKKIIAFKNAFHGR 126 +KD +Q L + P + + +GT+AVEAALK R TGR +++F+ +HG Sbjct: 111 VKDRFVQDLFGLLPAALAAEAKIQFCGPTGTDAVEAALKLVRTATGRSTVLSFQGGYHGM 170 Query: 127 TAGSLSVTWNKKYREPFEPLVGP-VEFLTFN-----------------NIEDLSKIDNET 168 + G+LS+ + ++P L+ V+F+ + N+ L + N+ Sbjct: 171 SQGALSLMGSLGPKKPLGALLSNGVQFMPYPYDYRCPFGLGGVAGVKANLHYLENLLNDP 230 Query: 169 -------AAVIVEPIQGESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWA 221 AAVIVE +QGE GVIPA++++++ L+ TE G LI DEIQ+GFGRTGK++A Sbjct: 231 EAGVQLPAAVIVEVVQGEGGVIPADLDWLRGLRRITEQAGVALIVDEIQSGFGRTGKMFA 290 Query: 222 YKHYNIVPDILTAGKAIGGGFPVSVVFLPDHIANKLEEGDHGSTYGGNPMAMAAVTAACK 281 ++H I+PD++ KAIGG P++VV D + L G H T+ GN MAMAA +A + Sbjct: 291 FEHAGIIPDVVVLSKAIGGSLPLAVVVYRDWLDTWL-PGAHAGTFRGNQMAMAAGSAVMR 349 Query: 282 VIEKENVVEQANQKGQQFSNILVKNLADLKVVREVRGKGLMIGIDIRFQPG--------- 332 +++ + A G++ S L D + ++RG+GLM+G+++ G Sbjct: 350 YLQEHALPAHAAAMGERLSEHLRILQRDFPQLGDIRGRGLMLGVELVDPTGKPDALGHPP 409 Query: 333 -------QVLKYLQEKGILAVKAG--STVIRFLPSYLITYENMEEASNVLREGL 377 ++ + ++G++ G V+RFLP +IT ++ + + L Sbjct: 410 VHAGLAPRLQRECLKRGLILELGGRQGGVVRFLPPLIITKAEIDRVAEIFGRAL 463 Lambda K H 0.317 0.136 0.385 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: 414 Number of extensions: 29 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: 387 Length of database: 470 Length adjustment: 32 Effective length of query: 355 Effective length of database: 438 Effective search space: 155490 Effective search space used: 155490 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 (21.6 bits) S2: 51 (24.3 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