Align 2-deoxy-3-keto-D-ribonoate cleavage enzyme (characterized)
to candidate GFF826 PGA1_c08400 Uncharacterized conserved protein
Query= reanno::WCS417:GFF1426 (310 letters) >FitnessBrowser__Phaeo:GFF826 Length = 305 Score = 165 bits (418), Expect = 1e-45 Identities = 114/328 (34%), Positives = 160/328 (48%), Gaps = 49/328 (14%) Query: 1 MSKNRPVIITCAVTGAIHTPSMSPHLPITAQEIADAAIGAAEAGAAIVHLHARDPNDGRP 60 M+KN V ITCAVTG+ T SPH+P + + IA++AI AA+AGAAIVH H RDP G P Sbjct: 5 MAKN--VFITCAVTGSGSTQDRSPHVPRSPKAIAESAIAAAKAGAAIVHCHVRDPETGAP 62 Query: 61 SQDPALFAEFLPQIKAA-SDVVINITTG-------------------GAPTMGVEERLQP 100 S+D L+ E +I+ + +DVV+N+T G G +G R+ Sbjct: 63 SRDLTLYREVTDRIRESDTDVVLNLTAGMGGDMVFGDTENPLPLNEAGTDMIGATARMAH 122 Query: 101 VMQFKPELASLNMGSMNFGLYEMLNRFTDFKHDWERPYLEESDDRIFRNTFRDITHILNA 160 V + PE+ +L+ G+MNF D + NT + + Sbjct: 123 VAECLPEICTLDCGTMNFA----------------------EADYVMTNTPGMLRAMGQM 160 Query: 161 CAENRTRFEIECYDIGHLYTAAHFLERGLLKPPLFIQSVFGLRGGIGGHPEDLAHMRRTA 220 + + EIE +D GHL+ A ++ G+L P +Q G+ G P DL Sbjct: 161 MTDLGVKPEIEAFDTGHLWFAKELVKEGVLNSPALVQLCMGVPWGA---PNDLNTFMAMV 217 Query: 221 DRLFGSDYVWSILGAGRGQIPLATMGLSMGSNARVGLEDSLWDGPGKLAASNADQVRRIR 280 + + SD+ WS GR Q+ + G N RVGLED+LW G G+L A N V R Sbjct: 218 NNV-PSDWDWSAFSLGRDQMAYVAASVLAGGNVRVGLEDNLWLGKGQL-AENWQLVERAG 275 Query: 281 TVIEALGHRVATPDEAREILGLKGRDQV 308 T+IE +G ++ PDE R LGL R V Sbjct: 276 TIIENMGAKLMGPDEVRAQLGLVKRAPV 303 Lambda K H 0.321 0.138 0.416 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: 282 Number of extensions: 13 Number of successful extensions: 5 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: 310 Length of database: 305 Length adjustment: 27 Effective length of query: 283 Effective length of database: 278 Effective search space: 78674 Effective search space used: 78674 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 (21.9 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