Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate Synpcc7942_0670 Synpcc7942_0670 aspartate carbamoyltransferase catalytic subunit
Query= curated2:A0LUC1 (312 letters) >FitnessBrowser__SynE:Synpcc7942_0670 Length = 338 Score = 85.9 bits (211), Expect = 1e-21 Identities = 100/336 (29%), Positives = 148/336 (44%), Gaps = 31/336 (9%) Query: 3 RHFLADDDLTPSEQAAVLDEAA---RLKKDRYAARPLTGPRSVAVVFEKPSTRTRVSFEV 59 RH L+ D +P E VL AA + + R P + V +F +PSTRTR SFE+ Sbjct: 7 RHILSLADFSPVEYEMVLRTAAGFAEVLQRRNKKVPTLQGQVVTTLFFEPSTRTRSSFEL 66 Query: 60 AITELGGQPVVLDAVGSQLGRGEPIEDTAR---------VLSRYVAAIVLRTFGHDRITT 110 A L + A S L +GE I DTAR ++ R+ A V + + Sbjct: 67 AAKRLSADTINFAASSSSLSKGETILDTARTYLAMGSDIMVVRHAQAGVPQAIARE---- 122 Query: 111 LARYAT-VPVVNALSDAY-HPCQALADLLTI-------RERKGGLDGVRLAYVGD--GNN 159 + R T V V+NA + HP QAL DL TI + G + G ++A VGD + Sbjct: 123 MERLGTEVRVLNAGDGQHEHPSQALLDLFTICSVIQPEQPSLGAIAGKKIAIVGDILHSR 182 Query: 160 VACSLLVAGAMAGLHVTVASPAGYQPPP-AVVARAAEIGEQTGGRVEVVDDPRTAARNAD 218 VA S + + AG V +A+P PP A A G ++++ +A NAD Sbjct: 183 VARSNIWSLTAAGAEVHLAAPPTLLPPEFAQFANTPIPGSGLPRQLQIHWQLESALENAD 242 Query: 219 VLYT-DVWTSMGQEEETAARRRAFAGFTVDDDLLALAADDAIVLHCLPAHRGEEITASVL 277 + T + + + R F + D L + +LH P +RG E+++ ++ Sbjct: 243 FVMTLRLQQERMSQSLLPSLREYHREFGLTRDRLRVCQPSVKLLHPGPVNRGVELSSDLM 302 Query: 278 EGPQ-SAIFDQAENRLHTAKALLSFLLDAAGGRGIP 312 E S I Q N + ALL +L+ AA IP Sbjct: 303 EDESISLIQPQVTNGVAVRMALL-YLIGAAVPAAIP 337 Lambda K H 0.319 0.134 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: 209 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: 312 Length of database: 338 Length adjustment: 28 Effective length of query: 284 Effective length of database: 310 Effective search space: 88040 Effective search space used: 88040 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 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