Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate AZOBR_RS20575 AZOBR_RS20575 aspartate carbamoyltransferase
Query= BRENDA::Q51742 (315 letters) >FitnessBrowser__azobra:AZOBR_RS20575 Length = 320 Score = 109 bits (272), Expect = 1e-28 Identities = 94/309 (30%), Positives = 150/309 (48%), Gaps = 18/309 (5%) Query: 8 RDLLCLQDYTAEEIWTILETAKMF-KIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEV 66 R LL ++ TA EI TIL+ A + + ++ K LL+G+T+ +F + STRTR SFE+ Sbjct: 14 RHLLGIEGLTAGEITTILDLADGYVEQNRQPSKKSSLLDGRTIVNLFFENSTRTRTSFEL 73 Query: 67 AMAHLGGHALYLNAQDLQLRRGETIADTARVL-SRYVDAIMARVYDHKDVEDLAKYATVP 125 A LG + +++ +++GET+ DTA L + ++DA++ R D V+ LA Sbjct: 74 AGKRLGADVINMSSDGSSVKKGETLIDTAMTLNAMHLDALVVRHADSGAVKLLADKVNCS 133 Query: 126 VIN-GLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGD--GNNVAHSLMIAGTKLGADV 182 VIN G HP Q L D + I + G++ G+ V GD + VA S + +GA V Sbjct: 134 VINAGDGHHEHPTQGLLDALAIRRRLGSLDGLIVAICGDILHSRVARSNIHLLNAMGARV 193 Query: 183 VVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASMGQEAE-A 241 V P P + E+ H +KDADV+ + + Sbjct: 194 RVVAPPTLIPSQ-----------IDRLGVEIHHSMATGLKDADVVMMLRLQTERMSGQYV 242 Query: 242 EERRKIFRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDS-PNSVVWDQAENRLH 300 R+ F + ++ + + AKP + MH P +RG E+ +V D S++ DQ E + Sbjct: 243 PSTREYFYFYGLDYEKLAVAKPHAVVMHPGPMNRGVEIDSEVADDLKRSMILDQVELGVA 302 Query: 301 AQKAVLALV 309 + AVL L+ Sbjct: 303 VRMAVLDLL 311 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: 219 Number of extensions: 14 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: 320 Length adjustment: 27 Effective length of query: 288 Effective length of database: 293 Effective search space: 84384 Effective search space used: 84384 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