Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_051678460.1 N746_RS0102210 aspartate carbamoyltransferase catalytic subunit
Query= curated2:O67607 (306 letters) >NCBI__GCF_000711195.1:WP_051678460.1 Length = 349 Score = 67.8 bits (164), Expect = 4e-16 Identities = 80/314 (25%), Positives = 133/314 (42%), Gaps = 30/314 (9%) Query: 3 RDFVDLWDLSPKEAWEIV---KKTLKVKKGEEELGKPLSGKTIALLFTKPSTRTRVSFEV 59 + F+ L L P EI+ + L E + L GKTI LF +PSTRTR +FE+ Sbjct: 19 KHFLTLEGLKPHHLTEILDTAESFLNPHTNEIKKVPLLRGKTIMNLFFEPSTRTRTTFEI 78 Query: 60 GIYQLGGNSLFFQEKELQVSRGEDVRDTARTLSKYVDGVIVRNHSHTWLKEFANFASVPV 119 +L + + +GE + DT L + V HS + F P Sbjct: 79 AEKRLSADVMNLNISASATKKGESLLDTMWNLEAMQADMFVIRHSESGAAHFFAEHVAPH 138 Query: 120 INALT----NMSHPCQILSDVFTLYEHYGEELKNLKVAYVGDGNNVCNTLMVGAGMFGLK 175 ++ L +HP Q + D+FT+ + G ++ +LKVA VGD + ++ + + + L Sbjct: 139 VHVLNAGDGQHAHPTQAMLDMFTIRKLKG-DVFDLKVAIVGD---ILHSRVARSQIQALS 194 Query: 176 LFVATPEGYEPNSYYYKKALEFSKENGGSVELTNNPVESVKDADVVYTDVWVSMGEENKN 235 L E E K + E G V + ++ ++ DVV + + +N+ Sbjct: 195 LL----EAREIRVIGPKTLIPPFPEALG-VHVFHDMEAGLEGVDVV-----IMLRLQNER 244 Query: 236 IE-AFLP--------YQVNEKLLSFAKSSVKVMHCLPAKKGQEITEEVFEKNADFIFTQA 286 ++ A LP Y + E+ L++AK VMH P +G EI V + I Q Sbjct: 245 MQGALLPSEQEYFDLYGLTERRLAYAKPDAIVMHPGPINRGVEIDSAVADGPQSVILQQV 304 Query: 287 ENRLHTQKTLMEFL 300 + + +M + Sbjct: 305 TYGIAVRMAVMSII 318 Lambda K H 0.316 0.133 0.386 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: 178 Number of extensions: 8 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 306 Length of database: 349 Length adjustment: 28 Effective length of query: 278 Effective length of database: 321 Effective search space: 89238 Effective search space used: 89238 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 (21.6 bits) S2: 48 (23.1 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