Align Formiminoglutamase (EC 3.5.3.8) (characterized)
to candidate 6939103 Sama_3201 arginase/agmatinase/formiminoglutamase (RefSeq)
Query= reanno::SB2B:6939103 (345 letters) >FitnessBrowser__SB2B:6939103 Length = 345 Score = 687 bits (1773), Expect = 0.0 Identities = 345/345 (100%), Positives = 345/345 (100%) Query: 1 MQHLIIFSAKDMTPILGKRPGETRLGNHFLLPEGPTLVAILESAKAQGARFVLLGVGEDA 60 MQHLIIFSAKDMTPILGKRPGETRLGNHFLLPEGPTLVAILESAKAQGARFVLLGVGEDA Sbjct: 1 MQHLIIFSAKDMTPILGKRPGETRLGNHFLLPEGPTLVAILESAKAQGARFVLLGVGEDA 60 Query: 61 GPRANLGRGGATNAFEAMLKYLVNLQSNRFYRGDDCLLLGQLDFGDLLPGEDADVDALRA 120 GPRANLGRGGATNAFEAMLKYLVNLQSNRFYRGDDCLLLGQLDFGDLLPGEDADVDALRA Sbjct: 61 GPRANLGRGGATNAFEAMLKYLVNLQSNRFYRGDDCLLLGQLDFGDLLPGEDADVDALRA 120 Query: 121 AVAAMDERVIEVASAIMEAGLEPIVIGGGHNNAFGLLMSVKNAFGRPAAAVNLDPHSDFR 180 AVAAMDERVIEVASAIMEAGLEPIVIGGGHNNAFGLLMSVKNAFGRPAAAVNLDPHSDFR Sbjct: 121 AVAAMDERVIEVASAIMEAGLEPIVIGGGHNNAFGLLMSVKNAFGRPAAAVNLDPHSDFR 180 Query: 181 LREGRHSGNGFSYAAASGALDFYHVLGLHELKNSEANLEQLAAFGGSWHTLQQIWVRGEL 240 LREGRHSGNGFSYAAASGALDFYHVLGLHELKNSEANLEQLAAFGGSWHTLQQIWVRGEL Sbjct: 181 LREGRHSGNGFSYAAASGALDFYHVLGLHELKNSEANLEQLAAFGGSWHTLQQIWVRGEL 240 Query: 241 SLDDALKHIGKTLRATGLPVALELDLDAIANMPSSAMTAAGVPLLDAARYISHIARHCDC 300 SLDDALKHIGKTLRATGLPVALELDLDAIANMPSSAMTAAGVPLLDAARYISHIARHCDC Sbjct: 241 SLDDALKHIGKTLRATGLPVALELDLDAIANMPSSAMTAAGVPLLDAARYISHIARHCDC 300 Query: 301 AYLHLAEAAPSCHDSGEDAGLRETGQSLTELVYAYIRGRHLALGA 345 AYLHLAEAAPSCHDSGEDAGLRETGQSLTELVYAYIRGRHLALGA Sbjct: 301 AYLHLAEAAPSCHDSGEDAGLRETGQSLTELVYAYIRGRHLALGA 345 Lambda K H 0.320 0.137 0.405 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: 579 Number of extensions: 11 Number of successful extensions: 1 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: 345 Length of database: 345 Length adjustment: 29 Effective length of query: 316 Effective length of database: 316 Effective search space: 99856 Effective search space used: 99856 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: 49 (23.5 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