Align Formiminoglutamase (EC 3.5.3.8) (characterized)
to candidate 7026581 Shewana3_3724 arginase/agmatinase/formiminoglutamase (RefSeq)
Query= reanno::SB2B:6939103 (345 letters) >FitnessBrowser__ANA3:7026581 Length = 350 Score = 427 bits (1099), Expect = e-124 Identities = 218/345 (63%), Positives = 261/345 (75%), Gaps = 7/345 (2%) Query: 1 MQHLIIFSAKDMTPILGKRPGETRLGN--HFLLPEGPTLVAILESAKAQGARFVLLGVGE 58 M I F+ D+ ++ R GET++G H E P L AIL +AKA GA+F +LGVGE Sbjct: 1 MSEFIPFTQADVASLVSPRAGETKIGQCVHLANHEHP-LEAILATAKAHGAQFAILGVGE 59 Query: 59 DAGPRANLGRGGATNAFEAMLKYLVNLQSNRFYRGDDCLLLGQLDFGDLL----PGEDAD 114 D GPRANLGRGGAT+AF ++ +NLQSNRF G +CL+LGQ+ DL GE A Sbjct: 60 DIGPRANLGRGGATDAFTTSMRQWLNLQSNRFLSGAECLILGQVHTADLQLQAQDGEGAS 119 Query: 115 VDALRAAVAAMDERVIEVASAIMEAGLEPIVIGGGHNNAFGLLMSVKNAFGRPAAAVNLD 174 + LR AV +DERVI + SAI AGLEPIVIGGGHNNA+GLLM+ + R AAVNLD Sbjct: 120 LPHLRQAVEQLDERVISIVSAIQAAGLEPIVIGGGHNNAYGLLMATSAHYQRQVAAVNLD 179 Query: 175 PHSDFRLREGRHSGNGFSYAAASGALDFYHVLGLHELKNSEANLEQLAAFGGSWHTLQQI 234 PHSDFRL EGRHSGNGFSYAA GAL +YHVLGLHELKNSEANL+QL+ FGG+WH+LQQI Sbjct: 180 PHSDFRLLEGRHSGNGFSYAANRGALGYYHVLGLHELKNSEANLQQLSDFGGTWHSLQQI 239 Query: 235 WVRGELSLDDALKHIGKTLRATGLPVALELDLDAIANMPSSAMTAAGVPLLDAARYISHI 294 W+R E+SL +AL+ I L T LPV LELD+DAIA MPSSA TAAG+PLLDAA YIS+I Sbjct: 240 WIRREVSLTEALQEIAGKLNHTALPVGLELDVDAIAKMPSSASTAAGIPLLDAAHYISYI 299 Query: 295 ARHCDCAYLHLAEAAPSCHDSGEDAGLRETGQSLTELVYAYIRGR 339 A HC CAYLHLAEAAPSCH++G +AG R+ GQS++EL+YAY++ R Sbjct: 300 ASHCPCAYLHLAEAAPSCHEAGTEAGFRDVGQSISELIYAYVQAR 344 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: 382 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: 350 Length adjustment: 29 Effective length of query: 316 Effective length of database: 321 Effective search space: 101436 Effective search space used: 101436 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