Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate HSERO_RS23240 HSERO_RS23240 omega amino acid--pyruvate aminotransferase
Query= BRENDA::A0A3B6MXE9 (473 letters) >FitnessBrowser__HerbieS:HSERO_RS23240 Length = 442 Score = 173 bits (439), Expect = 9e-48 Identities = 132/422 (31%), Positives = 208/422 (49%), Gaps = 37/422 (8%) Query: 54 NYHPIPMVFSKGEGSHILDPEGNKYIDFLSAYSAVNQGHCHPKVLRALIEQAERLTL--S 111 N+ P + EG H D GN +D + V GH HPK++ A+ + L S Sbjct: 24 NFKAAPRMLVSAEGMHYRDDAGNTILDGTAGLWCVPLGHAHPKIVSAVQKSVATLDYAPS 83 Query: 112 SRAFYNDKFPVFAEYLTSMFG--YDMMLPMNTGAEGVETAIKLARKWGYEKKNIPKNEAL 169 + + F + AE L + G + + +G+E V+TA+K+A + K N + Sbjct: 84 FQLGHPSAFEL-AERLKAYTGNRFGNVFYTGSGSEAVDTALKIALAYHRAKGNATRTR-- 140 Query: 170 IVSCCGCFHGRTLGVISMSCDNDATRGFGP-LVPG--HL--------------KVDFGD- 211 ++ +HG G +S+ + F L+PG HL + ++G Sbjct: 141 LIGRERGYHGVGFGGMSVGGIGGNRKTFSTALLPGVDHLPHTHNLEKNAFTKGEPEYGAH 200 Query: 212 -IDGLEKIFKEH-GDRICGFLFEPIQGEAGVIIPPDGYLKAVRDLCSRHNILMIDDEIQT 269 D LE++ H I + EP+ G GV+IPP GYLK +R++C++H IL+I DE+ T Sbjct: 201 LADELERLVTLHDASNIAAVIVEPVAGSTGVLIPPKGYLKRLREICTKHGILLIFDEVIT 260 Query: 270 GIARTGKMLACDWEDVRPDMVILGKALGAGVVPVSAVLADKDIMLCIKPGE------HGS 323 G R G A D+ DV PD+ K L GVVP+ AV +I G HG Sbjct: 261 GFGRLGTPFASDYFDVEPDIFTTAKGLTNGVVPMGAVFVKPEIHDAFMNGPDGIELFHGY 320 Query: 324 TFGGNPLASAVAVASLKVVKDEGLVERAAELGQEFRDQLQKVQQKFPHIIREIRGRGLLN 383 T+ G+PLA A +ASL+V + EG++E A + F++ + + PH+I ++R GL+ Sbjct: 321 TYSGHPLACAAGLASLEVFQTEGVLENAQAVADYFQEAAHAL-RGLPHVI-DVRTIGLIA 378 Query: 384 AVDLCS-KALYPASAYDICIKLKERGILAKPTHDTIIRLAPPLSISSEELAEASKALSDV 442 ++L S A AYD ++ GIL + T D II L+PPL I+ +++ E L+ + Sbjct: 379 GIELASIPGRVGARAYDAFVRAFNDGILIRVTGD-IIALSPPLIINKQQIDELFGKLAAI 437 Query: 443 LE 444 L+ Sbjct: 438 LK 439 Lambda K H 0.321 0.137 0.409 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: 481 Number of extensions: 25 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: 473 Length of database: 442 Length adjustment: 33 Effective length of query: 440 Effective length of database: 409 Effective search space: 179960 Effective search space used: 179960 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