Align Formiminoglutamase (EC 3.5.3.8) (characterized)
to candidate 203280 SO4198 arginase family protein (NCBI ptt file)
Query= reanno::SB2B:6939103 (345 letters) >FitnessBrowser__MR1:203280 Length = 271 Score = 358 bits (919), Expect = e-104 Identities = 176/265 (66%), Positives = 210/265 (79%), Gaps = 4/265 (1%) Query: 79 LKYLVNLQSNRFYRGDDCLLLGQLDFGDLL----PGEDADVDALRAAVAAMDERVIEVAS 134 ++ +NLQSNRF G +CL+LGQ+ DL E A + ALRAAV +DERVI + Sbjct: 1 MRQWLNLQSNRFLSGTECLILGQVHTADLQLQVKTDEGASLTALRAAVEQLDERVINIVR 60 Query: 135 AIMEAGLEPIVIGGGHNNAFGLLMSVKNAFGRPAAAVNLDPHSDFRLREGRHSGNGFSYA 194 AI++AGLEPI+IGGGHNNA+GLLM+ + R AAVNLDPHSDFRL EGRHSGNGFSYA Sbjct: 61 AILDAGLEPILIGGGHNNAYGLLMAASAHYQRQVAAVNLDPHSDFRLLEGRHSGNGFSYA 120 Query: 195 AASGALDFYHVLGLHELKNSEANLEQLAAFGGSWHTLQQIWVRGELSLDDALKHIGKTLR 254 A GAL +YHVLGLHELKNSEANL+QL FGG+WH+LQQIW+R E+SL AL+ I L Sbjct: 121 ADRGALGYYHVLGLHELKNSEANLQQLTEFGGTWHSLQQIWIRREISLTQALQEIADKLN 180 Query: 255 ATGLPVALELDLDAIANMPSSAMTAAGVPLLDAARYISHIARHCDCAYLHLAEAAPSCHD 314 T LPVALELD+DAIA MPSSA TAAG+PLLDAA YIS+IA HC CAYLHLAEAAPSCH+ Sbjct: 181 QTALPVALELDVDAIAKMPSSASTAAGIPLLDAAHYISYIASHCPCAYLHLAEAAPSCHE 240 Query: 315 SGEDAGLRETGQSLTELVYAYIRGR 339 +G +AG R+ GQS++EL+YAY++ R Sbjct: 241 AGIEAGFRDVGQSISELIYAYVQAR 265 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: 308 Number of extensions: 10 Number of successful extensions: 2 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: 271 Length adjustment: 27 Effective length of query: 318 Effective length of database: 244 Effective search space: 77592 Effective search space used: 77592 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