Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate 3609962 Dshi_3343 aminotransferase class-III (RefSeq)
Query= curated2:Q89RB7 (404 letters) >FitnessBrowser__Dino:3609962 Length = 413 Score = 164 bits (416), Expect = 3e-45 Identities = 130/415 (31%), Positives = 192/415 (46%), Gaps = 51/415 (12%) Query: 7 DYLATETRLGAHN----YEPIGVVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKI 62 D L RL N Y+P + + RGEGVW+WD G RYLDC + V GHCHP++ Sbjct: 3 DLLKRRARLMGPNVPTFYDP-PLHIVRGEGVWLWDAGGRRYLDCYNNVPHV--GHCHPRV 59 Query: 63 LAAMVEQAHRLTLTSRAFHNDQLAPFYEEIAALTGS-----HKVLPMNSGAEAVESAIKS 117 + A+ QA L +R H L + I LTG+ + L + +G+EAV+ A++ Sbjct: 60 VDAIARQARVLNTHTRYLHEGVL----DYIERLTGTMDNGLDQALLVCTGSEAVDVALRM 115 Query: 118 VRKWGYEVKGVPDDQAEIIVCADNFHGRTLGIVGFSTDPETRGHFGPFAPGFRIIP---- 173 R + +I + +HG T + ST R G ++ R++P Sbjct: 116 AR--------AATGKTGLIATDNTYHGNTTAVAQLST---RRPPIGGYSDHVRLVPAPEP 164 Query: 174 ------FGD----AAALEQAITPNTVAFLVEPIQGEAGVIIPPAGYFTKVRELCTANNVM 223 FG AAA + A +V PI G+ P G+ + Sbjct: 165 GTDGAAFGAHVARAAAELETAGHGVAALIVCPIFANEGLPCLPRGFLEPAVAALRTRGGL 224 Query: 224 LVLDEIQTGLGRTGKLL-AEQHEGIEADVTLLGKALAGGFYPVSAVLSNNEVLGTLRPG- 281 L+ DE+Q G GR G + Q GI DV LGK++ G YPV+ V++ E++G R Sbjct: 225 LISDEVQPGFGRLGDVFWGYQALGIAPDVVTLGKSMGNG-YPVAGVVARTEIMGAFREAF 283 Query: 282 QHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGARLLEGLKDIRANTVREVRGRGLM 341 + +TFGG+P+A A A A + VL +EG++ENA R G LE L+ +R + VRG GL Sbjct: 284 GYFNTFGGSPVAAAAAMAVLDVLEDEGLVENAKRVGRYTLERLQALRHPAIDGVRGYGLA 343 Query: 342 LAVEL-----HPEAGRARRYCEALQGKGILAK--DTHGHTIRIAPPLVITSDEVD 389 A++L P A E + + +L H ++I PPL + D Sbjct: 344 FALDLVDTDGAPNTALAAAVTEEAKRRSVLINRIGRDMHILKIRPPLPFAPEHGD 398 Lambda K H 0.319 0.136 0.405 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: 467 Number of extensions: 33 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: 404 Length of database: 413 Length adjustment: 31 Effective length of query: 373 Effective length of database: 382 Effective search space: 142486 Effective search space used: 142486 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: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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