Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate Pf1N1B4_205 Pyoverdin biosynthesis protein PvdH, L-2,4-diaminobutyrate:2-oxoglutarate aminotransferase (EC 2.6.1.76)
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_205 Length = 470 Score = 235 bits (599), Expect = 2e-66 Identities = 157/415 (37%), Positives = 225/415 (54%), Gaps = 49/415 (11%) Query: 29 LLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQ-AETLMAMPQTLPTP 87 L + R +G V D EG +IDC+ G G LGH +P V+EA+++ + L L TP Sbjct: 51 LALKRAKGIYVEDVEGRSFIDCLAGAGTLALGHNHPVVIEAIQQVLTDELPLHTLDLTTP 110 Query: 88 MRGEFYRTLTAILPPELNRVFPVN----SGTEANEAALKFARAHTGRKKFVAAMRGFSGR 143 ++ +F + L +LPP L + +GT+A EAALK R TGR ++ G+ G Sbjct: 111 VKDQFVQDLFGLLPPALAAEAKIQFCGPTGTDAVEAALKLVRTATGRSTVLSFQGGYHGM 170 Query: 144 TMGSLSVTWEPKYREPFLPLVEP-VEFIPY--------------------NDVEAL---K 179 + G+LS+ ++P L+ V+F+PY N +E L Sbjct: 171 SQGALSLMGSLGPKKPLGALLSSGVQFMPYPYDYRCPFGLGGAQGVQVNLNYLENLLNDP 230 Query: 180 RAVDEETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFA 239 A + AAVI+E VQGEGGV PA ++LR R IT++ G LI+DEIQ+G RTGK FA Sbjct: 231 EAGVQLPAAVIVEAVQGEGGVIPADLDWLRGLRRITEKAGVALIVDEIQSGFARTGKMFA 290 Query: 240 FEHFGIVPDILTLAKALGGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIR 299 FEH GI+PD++ ++KA+GG +PL V V R+ + +P G H TF GN +AMAAG A +R Sbjct: 291 FEHAGIIPDVVVMSKAIGGSLPLAVVVYRDWLDTWLP-GAHAGTFRGNQMAMAAGSAVMR 349 Query: 300 YLERTRLWERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVGLELKEKAA--------P 349 YL ++ E AA +G E L + P++ ++RG GLM+G+EL + P Sbjct: 350 YLTEHKVCEHAAAMGERLSEHLHILQRDFPQLGDIRGRGLMLGVELVDPTGAPDAQGHPP 409 Query: 350 YIARL------EKEHRVLALQAGPT---VIRFLPPLVIEKEDLERVVEAVRAVLA 395 ARL E R L L+ G V+RFLPPLVI +++RV + +A Sbjct: 410 IFARLAPLVQRECLKRGLILELGGRHGGVVRFLPPLVITAAEIDRVADIFGRAMA 464 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: 499 Number of extensions: 19 Number of successful extensions: 7 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: 470 Length adjustment: 32 Effective length of query: 363 Effective length of database: 438 Effective search space: 158994 Effective search space used: 158994 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: 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