Align 4-guanidinobutyramide hydrolase; SubName: Full=Carbon-nitrogen hydrolase (characterized, see rationale)
to candidate SMc01962 SMc01962 hypothetical protein
Query= uniprot:A0A291T0X0 (265 letters) >FitnessBrowser__Smeli:SMc01962 Length = 259 Score = 203 bits (517), Expect = 3e-57 Identities = 114/255 (44%), Positives = 155/255 (60%), Gaps = 4/255 (1%) Query: 4 LRTALLQNSGHPGDPAGNLKVLDEAAARAAADGAGLLVTAEMFLTGYAIGGGVRDLAEPA 63 ++ A LQ GD A NL ++ AA A+ +GA LLV E+ +TGY G +R LAEPA Sbjct: 2 MKFAALQMKSIGGDVAANLARIERAAIGASGEGASLLVAPELAITGYGAGEAIRRLAEPA 61 Query: 64 DGPSGRAVADIAAAHGLAILYGYPERHAGAVHNSARLVGADGTELANYRKTHLYGCFERA 123 DG R + I+ G+AI+ G+ E+ A AV+NSA V D + YRK+HLYG +ER+ Sbjct: 62 DGRIVRELGRISLKTGIAIVAGFAEQGADAVYNSAVHVDGDAVPVV-YRKSHLYGDYERS 120 Query: 124 SFTPGETPVVQATVGELTVGILVCYDVEFPENVRAHALAGTDLLLVPTAQMHPFE--FVA 181 FTP E +T G+L+CYDVEFPENVR ALAG D +LVPTA + F+ Sbjct: 121 LFTPAEPSTRLFKHRGVTCGMLICYDVEFPENVRRLALAGADAVLVPTALPAGWSGTFIT 180 Query: 182 ESLIPVRAFESQMYIAYVNRSGPEGEFDFVGLSCLAGPDGATCLRAGRGEE-LLLGDVDP 240 + +I RAFE+Q+++AYVN G + F F GLS +A PDG +AG +E L++ ++DP Sbjct: 181 DHMIQTRAFENQVFVAYVNHCGSDDMFSFAGLSLIASPDGQALAKAGSSDETLIIAEIDP 240 Query: 241 KLLTTSRRINPYLRD 255 + SR N YL D Sbjct: 241 QAFAISRAENTYLMD 255 Lambda K H 0.319 0.138 0.414 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: 193 Number of extensions: 11 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: 265 Length of database: 259 Length adjustment: 25 Effective length of query: 240 Effective length of database: 234 Effective search space: 56160 Effective search space used: 56160 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 (21.7 bits) S2: 47 (22.7 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