Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate Pf6N2E2_2395 Pyoverdin biosynthesis protein PvdH, L-2,4-diaminobutyrate:2-oxoglutarate aminotransferase (EC 2.6.1.76)
Query= BRENDA::Q9SR86 (481 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2395 Length = 470 Score = 189 bits (481), Expect = 1e-52 Identities = 140/454 (30%), Positives = 216/454 (47%), Gaps = 25/454 (5%) Query: 48 PFNYSPPPYDGP---STAEIIAKRREFLSPALFHFYNTPLNIVEAKMQYVFDENGRRYLD 104 P SP P + + + ++A++ S A + PL + AK YV D GR ++D Sbjct: 12 PARVSPAPAETLYQFNESPLLARQSRQESNARSYPRRIPLALKRAKGLYVEDVEGRTFID 71 Query: 105 AFGGIATVSCGHCHPEVVNSVVKQL--KLINHS---TILYLNHTISDFAEALVSTLPGDL 159 G T++ GH HP V+ ++ + L +L H+ T + + D L + L + Sbjct: 72 CLAGAGTLALGHNHPVVIEAIQQVLADELPLHTLDLTTPVKDRFVQDLFGLLPAALAAEA 131 Query: 160 KVVFFTNSGTEANELAMMMARLYTGCNDIVSLRNSYHG---NAAATMGATAQSNWKFNVV 216 K+ F +GT+A E A+ + R TG + ++S + YHG A + MG+ ++ Sbjct: 132 KIQFCGPTGTDAVEAALKLVRTATGRSTVLSFQGGYHGMSQGALSLMGSLGPKKPLGALL 191 Query: 217 QSGVHHAINPDPYRGIFGSDGEK-YASDVHDLIQFGTSGQV-----AGFIGESIQGVGGI 270 +GV P YR FG G +++H L + A I E +QG GG+ Sbjct: 192 SNGVQFMPYPYDYRCPFGLGGVAGVKANLHYLENLLNDPEAGVQLPAAVIVEVVQGEGGV 251 Query: 271 VELAPGYLPAAYDIVRKAGGVCIADEVQSGFARTGTHFWGFQSHGVIPDIVTMAKGIGNG 330 + +L I +AG I DE+QSGF RTG F F+ G+IPD+V ++K IG Sbjct: 252 IPADLDWLRGLRRITEQAGVALIVDEIQSGFGRTGKMF-AFEHAGIIPDVVVLSKAIGGS 310 Query: 331 IPLGAVVTTPEIAGVLSRRSYFNTFGGNPMCTAAGHAVLRVLHEEKLQENANLVGSHLKR 390 +PL VV + L ++ TF GN M AAG AV+R L E L +A +G L Sbjct: 311 LPLAVVVYRDWLDTWLPG-AHAGTFRGNQMAMAAGSAVMRYLQEHALPAHAAAMGERLSE 369 Query: 391 RLTLLKNKYELIGDVRGRGLMLGVEFVKDRDLKTPAKAETLH------LMDQMKEMGVLV 444 L +L+ + +GD+RGRGLMLGVE V +H L + + G+++ Sbjct: 370 HLRILQRDFPQLGDIRGRGLMLGVELVDPTGKPDALGHPPVHAGLAPRLQRECLKRGLIL 429 Query: 445 GKGGFYGNVFRITPPLCFTLSDADFLVDVMDHAM 478 GG G V R PPL T ++ D + ++ A+ Sbjct: 430 ELGGRQGGVVRFLPPLIITKAEIDRVAEIFGRAL 463 Lambda K H 0.320 0.136 0.406 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: 572 Number of extensions: 32 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: 481 Length of database: 470 Length adjustment: 33 Effective length of query: 448 Effective length of database: 437 Effective search space: 195776 Effective search space used: 195776 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 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