Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate SMc02413 SMc02413 aminotransferase
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__Smeli:SMc02413 Length = 437 Score = 247 bits (630), Expect = 6e-70 Identities = 154/410 (37%), Positives = 228/410 (55%), Gaps = 25/410 (6%) Query: 45 GVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNPYQVELAK 104 G Y DG LLDFS+ G ++G +P + EA+ + L A+ N V LA+ Sbjct: 30 GAYLTADDGRQLLDFSASWGAASLGHSHPAIREAVGRALSDQAGASYLSSANEACVLLAE 89 Query: 105 KLVEIAPGDIERKVFLSNSGTEANEAALKIAKWSTNRKMFIAFIGAFHGRTHGTMSLTAS 164 KL+ + P +V+ +SG++ANE +I +T R +AF GA+HG T G+M ++ Sbjct: 90 KLLSLVPERARGRVWFGHSGSDANETVARIVVAATGRPRILAFHGAYHGGTIGSMGVSGH 149 Query: 165 KPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELINRVIDYIEEYLFEHYVPAEE 224 Q SR G+ VPYPN Y +P+ + + ++E LF VP EE Sbjct: 150 PAQQGSRA----EGLTLVPYPNSY-------AAGSPEAARDAALAHLER-LFATEVPPEE 197 Query: 225 VAGIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQMGMGRTGRMWAIEHFDI 284 VA F EPIQ +GG +VPP FFK ++ L +HGIL++ DEV++G+GR+GR A EH I Sbjct: 198 VAAFFIEPIQSDGGMLVPPDGFFKAVEALCRRHGILIVSDEVKVGLGRSGRFNAFEHSGI 257 Query: 285 VPDIVTVAKALGGGIPIGA-----TIFRADLDFGVSGVHSNTFGGNTVAAAAALAVIEEL 339 PDIV K LGGG+PI A I + F + VH GN V AAAALAV++ + Sbjct: 258 EPDIVVFGKGLGGGLPISAVVGPEAIMNHSVAFSLQTVH-----GNPVCAAAALAVLQTI 312 Query: 340 Q-NGLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLAWGVEFVKDRKTKEYATKERGE 398 + + LI NA + + RE L+ + ++ +IGDVRG GLA G+E V D ++E A+++ Sbjct: 313 ERDHLILNADRSGKVLREALDRLTARHTLIGDVRGRGLALGIELVTDPASREPASRQAAL 372 Query: 399 IVVEALKRGLAL--LGCGKSAIRLIPPLIISEEEAKMGLDIFEEAIKVVS 446 V A + GL L +G + + L PPL ++ EA+ G+ + +A+ V+ Sbjct: 373 TVYRAFQLGLVLYYVGVQSNVLELTPPLTLTPAEAESGVAMLGQALADVA 422 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: 482 Number of extensions: 27 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: 454 Length of database: 437 Length adjustment: 32 Effective length of query: 422 Effective length of database: 405 Effective search space: 170910 Effective search space used: 170910 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