Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_011779876.1 MVAN_RS13360 aspartate carbamoyltransferase
Query= curated2:O27495 (301 letters) >NCBI__GCF_000015305.1:WP_011779876.1 Length = 315 Score = 113 bits (283), Expect = 5e-30 Identities = 99/321 (30%), Positives = 155/321 (48%), Gaps = 36/321 (11%) Query: 1 MKHLLSVCDM--DNVVDLLDLADDYKEGKIREKI-----LRGKTLAMIFEKSSTRTRVSF 53 MKHLL+ D+ ++ +LD AD ++E + ++ LRG+T+ +F ++STRTRVSF Sbjct: 1 MKHLLTAADLSREDATAILDNADRFREALVGREVKKLPTLRGRTIITMFYENSTRTRVSF 60 Query: 54 EVGAFQMGAQPLYLSASDLQLGRGEPIADTARTL-SRYVDGIMIRAISHSDVVELAG--- 109 EV M A + +S+S + +GE + DTA TL + D ++IR + +LA Sbjct: 61 EVAGKWMSADVINVSSSGSSVAKGESLRDTALTLRAAGADALIIRHPASGAAQQLAAWTL 120 Query: 110 --EASVPVIN-GLTDLEHPCQALADMQTIREKLGGFDG-RLVFVGD--GNNVCHSLLLIT 163 +IN G EHP QAL D TIR++LG +G R+V VGD + V S + + Sbjct: 121 DEHGGPSIINAGDGTHEHPTQALLDALTIRQRLGSVEGKRVVIVGDVLHSRVARSNVALL 180 Query: 164 ATLGMDMDVACPPGYEPDPGIREMAGKIADETGSRIRVIHDPSEAVRGADVVYTDVWVSM 223 TLG ++ + PP P G+ + ++ + + + + AD V + + + Sbjct: 181 HTLGAEVVLVAPPTLLP-VGVADWPVTVSQDIDAELPL----------ADAV---LMLRV 226 Query: 224 GYEDEAEDRLEVFRPYQVNMELME----LAAPEAIFMHCLPAVRGQETTAEVIDGPHSVV 279 E R Y V L E A A+ +H P +RG E V D S V Sbjct: 227 QAERMNGGFFPSSREYSVRYGLSEKRQSRLAEHAVVLHPGPMLRGMEIAYSVADSSQSAV 286 Query: 280 WDQAENRLHAQKAIM-HWLMG 299 Q N +H + A++ H L+G Sbjct: 287 LQQVSNGVHVRMAVLFHLLVG 307 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: 196 Number of extensions: 9 Number of successful extensions: 2 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: 315 Length adjustment: 27 Effective length of query: 274 Effective length of database: 288 Effective search space: 78912 Effective search space used: 78912 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 Sep 24 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