Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate GFF3565 HP15_3507 aspartate carbamoyltransferase
Query= curated2:O27495 (301 letters) >FitnessBrowser__Marino:GFF3565 Length = 327 Score = 112 bits (281), Expect = 9e-30 Identities = 95/318 (29%), Positives = 148/318 (46%), Gaps = 34/318 (10%) Query: 1 MKHLLSVCDMDNVV--DLLDLADDYKEGKIRE----KILRGKTLAMIFEKSSTRTRVSFE 54 ++H L++ +D + D+LD AD + E R +LRG+T+ +F +SSTRTR +FE Sbjct: 9 LRHFLTLDGLDRALLTDILDTADSFIEVGERTIKKVPLLRGRTVVNLFFESSTRTRSTFE 68 Query: 55 VGAFQMGAQPLYLSASDLQLGRGEPIADTARTLSRYVDGIMIRAISHSDVVELAGEASVP 114 + A ++ A L L S +GE ++DT L + + S S E+ P Sbjct: 69 LAAKRLSADVLNLDISTSATSKGESLSDTLLNLEAMASDMFVVRHSQSGAPHFIAESVTP 128 Query: 115 ---VIN-GLTDLEHPCQALADMQTIREKLGGFDG-RLVFVGD--GNNVCHSLLLITATLG 167 +IN G HP QA+ DM TIR+ G F+G ++ VGD + V S + LG Sbjct: 129 GVAIINAGDGRHAHPTQAMLDMLTIRQHKGRFEGLKVAIVGDVLHSRVARSQIRALNELG 188 Query: 168 MDMDVACPPGYEPDPGIREMAGKIADETGSRIRVIHDPSEAVRGADVVYTDVWVSMGYED 227 + PG + K + G + +D + ++ DVV + + + Sbjct: 189 AEEVRVIAPG--------TLLPKDVESLGCTVE--YDMTRGMKDLDVV-----IMLRLQK 233 Query: 228 EAED------RLEVFRPYQVNMELMELAAPEAIFMHCLPAVRGQETTAEVIDGPHSVVWD 281 E + E +R Y +N + + LA PE I MH P RG E + V DGP SV+ + Sbjct: 234 ERMEGALLPSEREFYRLYGLNQQKLALAHPECIVMHPGPINRGVEIESAVADGPQSVILN 293 Query: 282 QAENRLHAQKAIMHWLMG 299 Q N + + A+M MG Sbjct: 294 QVTNGIAIRMAVMSMAMG 311 Lambda K H 0.320 0.137 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: 219 Number of extensions: 10 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: 301 Length of database: 327 Length adjustment: 27 Effective length of query: 274 Effective length of database: 300 Effective search space: 82200 Effective search space used: 82200 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: 48 (23.1 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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