Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate N515DRAFT_3307 N515DRAFT_3307 glutamate-1-semialdehyde 2,1-aminomutase
Query= curated2:Q5SHH5 (395 letters) >FitnessBrowser__Dyella79:N515DRAFT_3307 Length = 426 Score = 147 bits (371), Expect = 6e-40 Identities = 104/306 (33%), Positives = 152/306 (49%), Gaps = 19/306 (6%) Query: 33 RGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPMRGEF 92 R GA +WD EG YID VG +G +GH +P V EAV+R + ++ P P Sbjct: 37 RADGAYLWDVEGKRYIDYVGSWGPMIVGHNHPRVREAVERAVKDGLSF--GTPCPAEITM 94 Query: 93 YRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSGR------TMG 146 T+T ++ P ++ V VNSGTEA +A++ AR TGR K V + G G Sbjct: 95 AETITRLV-PSVDMVRMVNSGTEATMSAIRLARGATGRSKIVKFEGCYHGHGDSFLVKAG 153 Query: 147 SLSVTWEPKYREPFLP--LVEPVEFIPYNDV---EALKRAVDEETAAVILEPVQGEGGVR 201 S ++T+ P +P + + YND+ EAL + A +I+EPV G Sbjct: 154 SGALTFGVP-TSPGVPKAAADLTLTLAYNDLAAAEALFAEHGADIAGLIIEPVAGNMNCI 212 Query: 202 PATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVP 261 P +L+ R + GALLI DE+ TG R A H+GI PD+ T K +GGG+P Sbjct: 213 PPKDGYLQGLRALCTRHGALLIFDEVMTGF-RVALGGAQAHYGITPDLSTFGKIIGGGMP 271 Query: 262 LGAAVMREEVARSMPKGG---HGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFM 318 +GA R E+ + G T GNP+AMAAG+A + ++ ++R A Sbjct: 272 VGAYGGRRELMEQIAPAGPIYQAGTLSGNPVAMAAGLAMLELIQEAGFYDRLAARTRLLA 331 Query: 319 EKLRAI 324 + L+A+ Sbjct: 332 DGLQAV 337 Lambda K H 0.319 0.137 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: 381 Number of extensions: 22 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: 395 Length of database: 426 Length adjustment: 31 Effective length of query: 364 Effective length of database: 395 Effective search space: 143780 Effective search space used: 143780 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: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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