Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate 350270 BT0742 aspartate carbamoyltransferase catalytic chain (NCBI ptt file)
Query= curated2:Q72D35 (300 letters) >FitnessBrowser__Btheta:350270 Length = 313 Score = 87.0 bits (214), Expect = 5e-22 Identities = 71/284 (25%), Positives = 124/284 (43%), Gaps = 15/284 (5%) Query: 19 VLERAKEMKDTGYRGRTLEGKVATLIFEKASTRTRISFEVAVRHLGGTTI-FMTPAESQL 77 +LE AK+ + R R L+GKV +F + STRTR+SFE A LG I F P + Sbjct: 20 MLEMAKQFEMNPNR-RLLQGKVVATLFFEPSTRTRLSFETAANRLGARVIGFTDPKATSS 78 Query: 78 GRSEPLRDTARVISRYTDCMIVRTFGQAKIDELASFGSIPVVNALTDEG-HPCQVMSDVL 136 + E L+DT ++S Y D +++R + + + +P+VNA HP Q M D+ Sbjct: 79 SKGETLKDTIMMVSSYADIIVMRHYLEGAARYASEVAPVPIVNAGDGANQHPSQTMLDLY 138 Query: 137 TMYERTPDLSQVRVAWIGD--GNNMANSWIEAAMYFPFELFMAFPEGYEPDRQLLGLALE 194 ++Y+ L + + +GD +S + A +F P+ + + E Sbjct: 139 SIYKTQGTLENLNIFLVGDLKYGRTVHSLLMAMRHFNPTFHFIAPDELKMPEEYKLYCKE 198 Query: 195 AGAKIFLTRDPHMAIDGAHYVNTDVWASMGQEEEQ----KRREAAFKGFCIDGALMGRAH 250 K H + D+ + E+ E + + ++ Sbjct: 199 HQIKYI----EHTEFTEEIIADADILYMTRVQRERFTDLMEYERVKNVYILRNKMLENTR 254 Query: 251 PDAKFMHCLPAHRGEEVTDEVMESPASIVWDQAENRLHMQKAIL 294 P+ + +H LP R E+ +V +P + + QA+N L+ ++AIL Sbjct: 255 PNLRILHPLP--RVNEIAYDVDNNPKAYYFQQAQNGLYAREAIL 296 Lambda K H 0.321 0.135 0.413 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: 170 Number of extensions: 12 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 300 Length of database: 313 Length adjustment: 27 Effective length of query: 273 Effective length of database: 286 Effective search space: 78078 Effective search space used: 78078 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 (21.9 bits) S2: 48 (23.1 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