Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate Pf1N1B4_4553 FIG00959354: hypothetical protein
Query= BRENDA::Q5XPV2 (457 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4553 Length = 956 Score = 93.2 bits (230), Expect = 3e-23 Identities = 87/288 (30%), Positives = 128/288 (44%), Gaps = 31/288 (10%) Query: 165 LERSFHGRSGYTMSLTNTEPSKTARFPKFGWP-RISSPA----LQHPPAEHTG--ANQEA 217 L SFHG+ T+ LT + + F +FG P LQ PA HT + Sbjct: 204 LRGSFHGKLVNTVQLTYGKQYRQP-FARFGLNVEFIDPQQPHQLQELPARHTRHWLTLQW 262 Query: 218 ERRALEAAREAFAAADGMIACFIAEPIQGEGGDNHLSAEFLQAMQRLCHENDALFVLDEV 277 L R+AF+A I + EPIQGEGG +A+F A++RLC+E ++DEV Sbjct: 263 SGEQLLVGRQAFSA----ITAVLLEPIQGEGGIIEFAADFYLALRRLCNEQQCPLIVDEV 318 Query: 278 QSGCGITGTAWAYQQLGLQPDLVAFGKKTQVCGVMGGGRIDEVP--------ENVFAVSS 329 QSG G TGT A LQ D K +GGG + EN F+ Sbjct: 319 QSGFGRTGTFLASSHFNLQGDYYCLSK------ALGGGLMKIAATVIRSSHYENDFSYIH 372 Query: 330 RISSTWGGNLADMVRATRLLETI--ERTQVFDTVVQRGKYFRDGLEDLAARHPSVVTNAR 387 SST+ + A A L + + + V +G+Y + L +L A +P V+ + R Sbjct: 373 --SSTFAEDDASCHIALSALNRLFADDNAMLKDVHNKGEYLKTSLLELKAAYPDVIADVR 430 Query: 388 GRGLMCAVDLPDTRTRNEVLRLMYTEHQVIALPCGGRSLRFRPALTIA 435 GRGL+ +L D + +++ + + G L+F AL +A Sbjct: 431 GRGLLLGFELHDQSGNSSLVQASAQYNDALGYLIAGYLLQFE-ALRVA 477 Lambda K H 0.320 0.135 0.402 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: 815 Number of extensions: 39 Number of successful extensions: 2 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: 457 Length of database: 956 Length adjustment: 38 Effective length of query: 419 Effective length of database: 918 Effective search space: 384642 Effective search space used: 384642 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: 54 (25.4 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