Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate Echvi_4661 Echvi_4661 aspartate carbamoyltransferase
Query= BRENDA::Q51742 (315 letters) >FitnessBrowser__Cola:Echvi_4661 Length = 307 Score = 110 bits (275), Expect = 4e-29 Identities = 97/315 (30%), Positives = 152/315 (48%), Gaps = 21/315 (6%) Query: 5 LAGRDLLCLQDYTAEEIWTILETAKMFKIWQKIGKPHRL---LEGKTLAMIFQKPSTRTR 61 L+ + LL ++ +I I ETA FK + I +P + L T+A +F + STRTR Sbjct: 4 LSTKHLLGIKGLNEADIQLIFETADNFK--EVINRPIKKVPSLRDITIANVFFENSTRTR 61 Query: 62 VSFEVAMAHLGGHALYLNAQDLQLRRGETIADTAR-VLSRYVDAIMARVYDHKDVEDLAK 120 +SFE+A L + ++ + +++GET+ DT +LS VD ++ R L++ Sbjct: 62 LSFELAEKRLSADVINFSSSNSSVKKGETLVDTVNNILSMKVDMVVMRHSSPGAPHFLSQ 121 Query: 121 YATVPVIN-GLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGD--GNNVAHSLMIAGTK 177 ++N G HP QAL D +I EK G + G KV +GD + VA S + K Sbjct: 122 NIDANIVNAGDGTHEHPTQALLDAFSIREKLGDVAGKKVAIIGDILHSRVALSNIFCLQK 181 Query: 178 LGADVVVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYT-DVWASMG 236 LGA+V+V P I + + G EL D KA++ DV + Sbjct: 182 LGAEVMVCGP---------ITLLPKYISSLGVKVEL--DVKKALEWCDVANVLRIQLERQ 230 Query: 237 QEAEAEERRKIFRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWDQAE 296 Q R+ + V+K L+ + + MH P +RG E+ DV DS +S++ +Q E Sbjct: 231 QIKYFPSLREYSLYYGVDKKLLDQLDKEIVIMHPGPINRGVELNSDVADSEHSIILNQVE 290 Query: 297 NRLHAQKAVLALVMG 311 N + + AVL L+ G Sbjct: 291 NGVAVRMAVLYLLAG 305 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: 190 Number of extensions: 7 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: 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 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