Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate PfGW456L13_2301 Pyoverdin biosynthesis protein PvdH, L-2,4-diaminobutyrate:2-oxoglutarate aminotransferase (EC 2.6.1.76)
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2301 Length = 466 Score = 202 bits (515), Expect = 1e-56 Identities = 138/412 (33%), Positives = 214/412 (51%), Gaps = 47/412 (11%) Query: 78 DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQ-PLHSQELLDPLRAMLAKTLAAL 136 D +G+ FIDCL G G +GH +PVV+ A+Q LA + PLH+ +L P++ + L L Sbjct: 59 DVEGRTFIDCLAGAGTLALGHNHPVVIEAIQQVLADELPLHTLDLTTPVKDRFVQDLFGL 118 Query: 137 TPGKL----KYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATA 192 P L K F +GT++VEAALKL + + G+ T I+ G +HG S GALS Sbjct: 119 LPPALAAEAKIQFCGPTGTDAVEAALKLVR---TATGRSTVISFQGGYHGMSQGALSLMG 175 Query: 193 KSTFRKP----------FMPLLPGFRHVPFG---------NIEAMRTALNECKKTGDDVA 233 +KP FMP +R PFG N+ + LN+ + A Sbjct: 176 SLGPKKPLGALLGSGVQFMPYPYDYR-CPFGLGGAQGVKANLSYLENLLNDPEAGVQLPA 234 Query: 234 AVILEPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQP 293 AVI+E +QGEGGVI +L VR++ ++ G +I+DE+Q+G RTGKMFA EH + P Sbjct: 235 AVIVEVVQGEGGVIPADLDWLRGVRRITEQAGVALIVDEIQSGFARTGKMFAFEHAGIIP 294 Query: 294 DILCLAKALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQ 353 D++ ++KA+GG +P+ + + + + L P H TF GN +A AA A + L+E Sbjct: 295 DVVVMSKAIGGS-LPLAVVVYRDWLDTWL---PGAHAGTFRGNQMAMAAGCAVMRYLVEH 350 Query: 354 NLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVD---------NEIGYNF 404 + A G+ L + R L R++P L + RG+G+++ +E VD + + Sbjct: 351 KVCEHAAAMGERLAEHLRILQRDFPQL-GDIRGRGLMLGVELVDPTGALDAQGHPPAFAR 409 Query: 405 ASEMFRQRVLVAGTL-----NNAKTIRIEPPLTLTIEQCELVIKAARKALAA 451 + + ++ L G + + +R PPL +T Q + V + +ALAA Sbjct: 410 LAPLVQRECLKRGLILELGGRHGAVVRFLPPLVITAAQIDRVAEIFGRALAA 461 Lambda K H 0.320 0.135 0.393 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: 508 Number of extensions: 30 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: 459 Length of database: 466 Length adjustment: 33 Effective length of query: 426 Effective length of database: 433 Effective search space: 184458 Effective search space used: 184458 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: 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