Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate 8500677 DvMF_1425 aspartate carbamoyltransferase catalytic subunit (RefSeq)
Query= curated2:Q3YU98 (334 letters) >FitnessBrowser__Miya:8500677 Length = 325 Score = 84.7 bits (208), Expect = 3e-21 Identities = 88/327 (26%), Positives = 140/327 (42%), Gaps = 35/327 (10%) Query: 6 HKHFLKLLDFTPAELNSLLQLAAKLK-ADKKSGKEEAKLTGKNIALIFEKDSTRTRCSFE 64 HK L + T AEL LL AA+ +++ K+ L GK++ L F + STRT+ SF+ Sbjct: 11 HKDLLDVTQLTRAELFHLLDTAAQFHDINRRPVKKVPTLKGKSVVLFFAEPSTRTKTSFD 70 Query: 65 VAAYDQGARVTYLGPSGSQIGHKESIKDTARVLGRMY-DGIQYRGYGQEIVETLAEYAGV 123 VA A L SGS + ES+KDTA L M D I R + LAE Sbjct: 71 VAGKRLSADTFSLAKSGSSLSKGESLKDTALTLQAMTPDIIVIRHSSSGAAQFLAERLDC 130 Query: 124 PVWN-GLTNEFHPTQLLADLLTMQEHLPGKTFNEMTLVYAGD-ARNNMGNSMLEAAALTG 181 V N G HPTQ L D ++++ + G TF TL+ GD A + + S + + G Sbjct: 131 SVVNAGDGWHAHPTQALLDCYSLRQ-VWGDTFEGRTLLILGDIAHSRVARSNVHLLSSLG 189 Query: 182 LDLRLVAPQACWPEAALVTECRALAQQNGGNITLTEDVAKGVEGADFIYTDVWVSMGEAK 241 + +RL AP+ P A + +T+ + V+G D V + + Sbjct: 190 VKVRLCAPRTLLP-----------AGVHNWPVTIFNRLDDAVQGVD----AVMCLRLQLE 234 Query: 242 EKWAERIALLRDYQVNSKMMQLTGNPEVKFLHCLPAFHDDQTTLGKKMAEEFGLHGGMEV 301 + A + LR+Y CL H ++ ++ G+E+ Sbjct: 235 RQQAGLLPDLREYAQR---------------FCLSPRHLTMAAPSARVLHPGPMNRGLEI 279 Query: 302 TDEVFESAASIVFDQAENRMHTIKAVM 328 + + ++ S++ DQ + T A++ Sbjct: 280 SSVLADAPESLILDQVAAGVATRMAIL 306 Lambda K H 0.317 0.132 0.385 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: 2 Number of HSP's successfully gapped: 1 Length of query: 334 Length of database: 325 Length adjustment: 28 Effective length of query: 306 Effective length of database: 297 Effective search space: 90882 Effective search space used: 90882 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 (21.7 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