Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate H281DRAFT_01493 H281DRAFT_01493 aspartate carbamoyltransferase
Query= curated2:P18186 (319 letters) >FitnessBrowser__Burk376:H281DRAFT_01493 Length = 430 Score = 118 bits (295), Expect = 3e-31 Identities = 95/315 (30%), Positives = 154/315 (48%), Gaps = 25/315 (7%) Query: 14 LLTLKDLSEEDINALLAEAGEL----KQNKIQPIFHGKTLAMIFEKSSTRTRVSFEAGMA 69 LL++ S + + AL A + ++ KI + G L +F ++STRTRVSF A Sbjct: 91 LLSVDQFSRDSVEALFRVADIMQPIARRRKISRVLEGAVLGNLFFEASTRTRVSFGAAFC 150 Query: 70 QLGGSALFLSQKDLQ-LGRGETVADTAKVLSGYVDAIMIRTFEHEKVEELAKEADIPVIN 128 +LGGS + + +GE++ DT++V+SGYVDA++IR E V E A+ ++PVIN Sbjct: 151 RLGGSVCDTTGFTFSSMAKGESIYDTSRVMSGYVDALVIRHPEQGSVAEFARATNVPVIN 210 Query: 129 GLTDK-YHPCQALADLLTIKEIKGKL----KGVKVAYIGD---GNNVAHSLMIGCAKMGC 180 G HP QAL DL TI+ +L G +A +GD G V + + G Sbjct: 211 GGDGPGEHPSQALLDLYTIQREFSRLGKIVDGAHIALVGDLKYGRTVHSLVKLLALYRGI 270 Query: 181 DISIASPKGYEVLDEAAEAAKTYALQSGSSVTLTDDPIEAVKDADVIYSDVFTSMGQEAE 240 ++ SP E+ E ++G + T D ++ ADV+Y+ T + +E Sbjct: 271 KFTLISPPMLEMPGYIIEQIS----RNGHVIEQTHDLPTGLRGADVVYA---TRIQKERF 323 Query: 241 EQERLAVFAP-YQVNAALV-SHAKPDYTFLHCLPAHRE---EEVTAEIIDGPNSAVFQQA 295 E + P +Q+N ALV S D +H LP +++ ++ A+F+Q Sbjct: 324 TDESFEGYTPDFQINQALVDSVCGSDTLIMHPLPRDSRPGANDLSVDLNHDSRLAIFRQT 383 Query: 296 ENRLHVQKALLKAIL 310 +N + V+ A+ +L Sbjct: 384 DNGIPVRMAIFAVLL 398 Lambda K H 0.315 0.131 0.361 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: 254 Number of extensions: 17 Number of successful extensions: 3 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: 319 Length of database: 430 Length adjustment: 30 Effective length of query: 289 Effective length of database: 400 Effective search space: 115600 Effective search space used: 115600 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 (21.5 bits) S2: 49 (23.5 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