Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate CA265_RS14660 CA265_RS14660 aspartate carbamoyltransferase
Query= BRENDA::Q51742 (315 letters) >FitnessBrowser__Pedo557:CA265_RS14660 Length = 311 Score = 116 bits (290), Expect = 8e-31 Identities = 99/318 (31%), Positives = 159/318 (50%), Gaps = 31/318 (9%) Query: 5 LAGRDLLCLQDYTAEEIWTILETAKMFKIWQKIGKPHRL---LEGKTLAMIFQKPSTRTR 61 L+ R LL ++D +I I ETA FK + I +P + L T+A IF + STRT+ Sbjct: 8 LSTRHLLGIKDINRNDIELIFETADNFK--EVINRPIKKVPSLRDITIANIFFENSTRTK 65 Query: 62 VSFEVAMAHLGGHALYLNAQDLQLRRGETIADTAR-VLSRYVDAIMARVYDHKDVEDLAK 120 +SFE+A L + A + +GET+ DT +LS VD ++ R + L+K Sbjct: 66 LSFELAEKRLSADVVNFAASSSSVSKGETLIDTVNNILSMKVDMVVMRHPYAGAGQFLSK 125 Query: 121 YATVPVIN-GLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGD--GNNVAHSLMIAGTK 177 + ++N G HP QAL D +I +K G + G KVV VGD + VA S ++ + Sbjct: 126 HVKAQIVNAGDGAHEHPTQALLDAFSIRQKLGDVAGKKVVIVGDILHSRVAISNILCLQR 185 Query: 178 LGADVVVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASMGQ 237 LGA+V+V P P ++ + G E H+ +KA+ + DV + Sbjct: 186 LGAEVMVCGPTTLIP---------KHIHQLGVKVE--HNLIKALN-----WCDVANMLRI 229 Query: 238 EAEAEE------RRKIFRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVV 291 + E ++ R+ + +NK ++ + + + MH P +RG E+T DV DS S++ Sbjct: 230 QLERQDIKYFPSLREYAMMYGLNKQILDNLDKEIIVMHPGPINRGVEITSDVADSKQSII 289 Query: 292 WDQAENRLHAQKAVLALV 309 +Q EN + + AVL L+ Sbjct: 290 LEQVENGVAVRMAVLYLL 307 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: 194 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: 311 Length adjustment: 27 Effective length of query: 288 Effective length of database: 284 Effective search space: 81792 Effective search space used: 81792 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