Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate N515DRAFT_0970 N515DRAFT_0970 transcriptional regulator, GntR family
Query= BRENDA::Q72LL6 (397 letters) >FitnessBrowser__Dyella79:N515DRAFT_0970 Length = 491 Score = 162 bits (410), Expect = 2e-44 Identities = 118/362 (32%), Positives = 169/362 (46%), Gaps = 12/362 (3%) Query: 36 SFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYAPLRAFVAEWIG------V 89 +F GLPA E FP A+ R R +L Y G LR +A+++G V Sbjct: 135 AFRVGLPALEHFPSALWAKLLNRHARAPSTESLVYGDPRGCPLLREAIADYLGAVRAVRV 194 Query: 90 RPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQAFRLQGPRFLTVPAGEEGP 149 +VLITTGSQQ + + LD G LE P Y GA QAF G R + VP +EG Sbjct: 195 DAAQVLITTGSQQGVQICAHALLDAGDRAWLEDPGYPGARQAFGTIGARIVPVPVDQEG- 253 Query: 150 DLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRLLQMVMERGLVVVEDDAYRELY 209 LD E + + R +Y PS Q P G R +LL+ VVEDD E Sbjct: 254 -LDVAEGIRRAPDARLVYTSPSHQFPLGMTLSAARRMQLLRWAARADAWVVEDDYDSEYR 312 Query: 210 FGEARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFAVAHPEALQKLVQAKQGADLH 269 FG + SL L E VIY+G+FSKV+ P LR+ + V + + + D Sbjct: 313 FGGRPVASLQGLDTE---ERVIYVGTFSKVMFPSLRLGYLVVPKDLVGTFAACRDALDTC 369 Query: 270 TPMLNQMLVHELLKEG-FSERLERVRRVYREKAQAMLHALDREVPKEVRYTRPKGGMFVW 328 T L Q+ +++ ++EG F+ + R+R +Y E+ A++ ++ +P+ + + GM + Sbjct: 370 TAALPQLAMNDFIREGHFARHIRRMRVLYAERRAALVASIRTHLPEHLEVIGAEAGMQLV 429 Query: 329 MELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLRLSYATLDREGIAEGVRRLGR 388 LP + L RRA + V+ P P +A L L Y D + E VRRL Sbjct: 430 ALLPPDIDDIALSRRAAQVGVSARPLSPCYAEPPARGGLILGYGGADARALDEAVRRLKS 489 Query: 389 AL 390 L Sbjct: 490 CL 491 Lambda K H 0.320 0.139 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: 489 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: 397 Length of database: 491 Length adjustment: 32 Effective length of query: 365 Effective length of database: 459 Effective search space: 167535 Effective search space used: 167535 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