Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate 6939514 Sama_3606 aminotransferase, class III; 4-aminobutyrate aminotransferase (RefSeq)
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__SB2B:6939514 Length = 472 Score = 202 bits (514), Expect = 2e-56 Identities = 143/460 (31%), Positives = 230/460 (50%), Gaps = 37/460 (8%) Query: 3 LKPNVKEIPGPKARKVIE------------EHHKYMATTTNDPNEYFLVIERAEGVYWID 50 +K N K +PGPK++ ++E E A +V+ RA+G + D Sbjct: 6 MKMNYK-LPGPKSKAMLERGIPLFRNGLRYEEECKKAARRGYRGASQVVVGRAQGSFVWD 64 Query: 51 VDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAA----GTDYYNPYQVELAKKL 106 +D N +DF +G G +P+++EA+ H A G Y P++ ELA+KL Sbjct: 65 LDDNQYIDFQNGWASNPFGNAHPEIVEAV--------HWAHTRYGFHYDTPHRYELAEKL 116 Query: 107 VEIAPGDIERKVFLSNSGTEANEAALKIAKWSTNRKMFIAFIGAFHGRTHGTMSLTASKP 166 V+I P ++ SGTEA EAA+ +A T R+ I+F +FHG G+ L+ + Sbjct: 117 VQIMPNRALTRINFEISGTEAAEAAVNLALTHTKRRYIISFSSSFHGEALGSKMLSGTSN 176 Query: 167 VQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELINRVIDYIEEYLFEHYVPAEEVA 226 M GV+ PYP P G+ ++ + + YI+ ++ VPA +A Sbjct: 177 -NNHYMEAWSGGVITAPYPYSGEIPAGM----TQEQYVEYCLWYIDNHITSSIVPANNIA 231 Query: 227 GIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQMGMGRTGRMWAIEHFDIVP 286 G+ EP EGG +PPK F + L++L +KH ++I DEV G+GRTG+MWAIEH+D++P Sbjct: 232 GLIIEPGLAEGGNWIPPKRFMQGLRELCNKHDWVMIVDEVLTGLGRTGKMWAIEHYDVIP 291 Query: 287 DIVTVAKALGGGIPIGATIFRADLDFGVSGVH--SNTFGGNTVAAAAALAVIEELQ-NGL 343 D++ K + GGI A I D G + + +T+ G+ A A L +E + + Sbjct: 292 DVLVFGKNISGGIEPCAGIAARDEIMGDNEHYHTGSTYAGSPAACCAGLKTLELYERENI 351 Query: 344 IENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLAWGVEFVK-DRKTKEYATKERGEIVVE 402 +E L + + +++ +Y I+ +VR GL GV FV D K++ E+ Sbjct: 352 VEYVAYLGEIAKGIMQKW-TRYSIVNEVRCNGLLLGVNFVSPDEHQKDWWFAR--EVRSR 408 Query: 403 ALKRGLALLGCGKSAIRLIPPLIISEEEAKMGLDIFEEAI 442 ++ G+ + ++ +RL P L + E + GL I EEAI Sbjct: 409 MMENGVWAINDRQTNVRLYPALNMEESVLREGLAIMEEAI 448 Lambda K H 0.319 0.139 0.410 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: 552 Number of extensions: 28 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: 454 Length of database: 472 Length adjustment: 33 Effective length of query: 421 Effective length of database: 439 Effective search space: 184819 Effective search space used: 184819 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: 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