Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_025763648.1 X939_RS0112665 aspartate carbamoyltransferase catalytic subunit
Query= BRENDA::Q51742 (315 letters) >NCBI__GCF_000566685.1:WP_025763648.1 Length = 307 Score = 119 bits (297), Expect = 1e-31 Identities = 97/316 (30%), Positives = 157/316 (49%), Gaps = 21/316 (6%) Query: 2 VVSLAGRDLLCLQDYTAEEIWTILETAKMFKIWQKIGKPHRL---LEGKTLAMIFQKPST 58 + L+ R LL +++ +I TILETA FK + I +P + L T+A +F + ST Sbjct: 1 MTKLSVRHLLGIKNLNESDIHTILETATQFK--EVINRPIKKVPSLRDITIANVFFENST 58 Query: 59 RTRVSFEVAMAHLGGHALYLNAQDLQLRRGETIADTAR-VLSRYVDAIMARVYDHKDVED 117 RTR+SFE+A L + ++ +++GET+ DT +L+ VD I+ R Sbjct: 59 RTRLSFELAEKRLSADVVNFSSSGSSVKKGETLLDTVNNILAMKVDMIVMRHSSPGAPHY 118 Query: 118 LAKYATVPVIN-GLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGD--GNNVAHSLMIA 174 LA + + V+N G HP QAL D ++ EK G + G K+ +GD + VA S + Sbjct: 119 LANHISANVVNAGDGTHEHPTQALLDAFSMQEKLGDLAGKKIAIIGDITHSRVALSNIFC 178 Query: 175 GTKLGADVVVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYT-DVWA 233 KLGA+V+V P P ++ E G ++ HD A++ DV + Sbjct: 179 LQKLGAEVMVCGPSTLIP---------KHLGELG--VKISHDVRAALQWCDVANVLRIQL 227 Query: 234 SMGQEAEAEERRKIFRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWD 293 Q R+ + + +NK ++ D + MH P +RG E++ D DS +S++ + Sbjct: 228 ERQQIKYFPSLREYAQFYGINKQMLDEVDKDIVLMHPGPINRGVELSSDAADSHHSIILN 287 Query: 294 QAENRLHAQKAVLALV 309 Q EN + + AVL L+ Sbjct: 288 QVENGVAIRMAVLYLL 303 Lambda K H 0.319 0.134 0.400 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: 183 Number of extensions: 8 Number of successful extensions: 4 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: 315 Length of database: 307 Length adjustment: 27 Effective length of query: 288 Effective length of database: 280 Effective search space: 80640 Effective search space used: 80640 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