Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_007473232.1 CMTB2_RS01220 glutamate-1-semialdehyde-2,1-aminomutase
Query= curated2:Q7SI94 (388 letters) >NCBI__GCF_000170735.1:WP_007473232.1 Length = 420 Score = 145 bits (366), Expect = 2e-39 Identities = 109/319 (34%), Positives = 161/319 (50%), Gaps = 31/319 (9%) Query: 15 IIKGEGQYVWDEKNNKYLDMHAGHGVAFLGHRNK----VIIDHLKKQMEEISTLSLAFDT 70 I KGEG Y++D + NKYLD G GH +K II+ +KK + S T Sbjct: 32 IEKGEGAYIFDIEGNKYLDYIQSWGPLIFGHCDKDTQNAIIEAVKKGV------SFGAPT 85 Query: 71 PIREEMIKELDELKPEDLDNLFLLNSGSEAVELALKIARKITKRRKIVAFKNSFHGRSMG 130 + E+ KE+ EL P L+ + +NSG+EA A+++AR T + I+ F+ +HG S Sbjct: 86 KVEVELAKEVLELFPH-LNLIRFVNSGTEATMSAIRLARGYTGKDDIIKFEGCYHGHSDS 144 Query: 131 ALSVTWN--KKYREPFEPLIGPVEFLE------YNNVDSLKSITE--DTAAVIVEPVQGE 180 L + + P P + P +F + YN+++S+K E D VI+EP+ G Sbjct: 145 LLVSAGSGAATFGVPSSPGV-PADFTKHTLLAKYNDIESVKKCFENGDVGCVIIEPIAGN 203 Query: 181 GGVIPAKKEFVKSLREVTEKVNALLIIDEVQTGFGRTGKIWAYQHFDIKPDILTAGKAIG 240 ++P +KEF+ LRE+ A+LI DEV +GF R ++ + IK DI+T GK IG Sbjct: 204 MSLVPGEKEFLGELREICNHYGAVLIFDEVMSGF-RASLRGSFDIYGIKADIVTFGKVIG 262 Query: 241 GGFPVSAVFLPNWISEKIEEGD---HGSTYGGNPLAAAAVTAACKVAKS-----EKIAEQ 292 GG PV A I EK+ T GNP+A +A K K +++ ++ Sbjct: 263 GGMPVGAFAGKKEIMEKLSPVGPVYQAGTLSGNPVAMSAGLTVIKKLKENPEIYKELEDK 322 Query: 293 AQKKGELFMRILKEKLEDF 311 A+K E F I KE DF Sbjct: 323 AKKLMEGFSEISKENNIDF 341 Lambda K H 0.317 0.136 0.386 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: 398 Number of extensions: 19 Number of successful extensions: 4 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: 388 Length of database: 420 Length adjustment: 31 Effective length of query: 357 Effective length of database: 389 Effective search space: 138873 Effective search space used: 138873 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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