Align Formimidoylglutamase; Formiminoglutamase; Formiminoglutamate hydrolase; N-formimino-L-glutamate formiminohydrolase; EC 3.5.3.8 (characterized)
to candidate WP_036372852.1 MVAN_RS15185 agmatinase
Query= SwissProt::P42068 (319 letters) >NCBI__GCF_000015305.1:WP_036372852.1 Length = 340 Score = 157 bits (398), Expect = 3e-43 Identities = 97/305 (31%), Positives = 155/305 (50%), Gaps = 10/305 (3%) Query: 13 SFKDRDVTKMSDLIATWDGQDIKGPALIGVPLSKSSISHSGASFAPGTIRQALKHSSAYS 72 SF R S+ + +W D+ A++G P + + GA F P IR Y Sbjct: 14 SFGHRPFLTESEQLDSWK-PDV---AVVGAPFDVGTTNRPGARFGPRAIRATAYEPGTYH 69 Query: 73 AELGEHVVSEL-LYDLGDIDIHVTDIVKSHHHIFQTMHALLSDHPDWVPLILGGDNSISY 131 +LG + L + D GD SH +I + +HA+ VP+ILGGD+SI++ Sbjct: 70 MDLGLEIFDWLEVVDFGDAYCPHGQTEVSHRNIRERVHAVADR--GIVPVILGGDHSITW 127 Query: 132 STIKAIAQTKG--TTAVIQFDAHHDVRNTEDGG-PTNGTPFRRLLDEEIIEGQHLIQLGI 188 A+A G ++ FDAH D + +G ++GTP RRL++ + G H +Q+G+ Sbjct: 128 PAATAVADVHGYGNVGIVHFDAHADTADEIEGNLASHGTPMRRLIESGAVPGSHFVQVGL 187 Query: 189 REFSNSQAYEAYAKKHNVNIHTMDMIREKGLIPTIKEILPVVQDKTDFIFISVDMDVLDQ 248 R + Q + + + HTM I E+G + + + K D +++SVD+DVLD Sbjct: 188 RGYWPPQDTFEWMLEQKMTWHTMQEIWERGFKAVMADAVAEALAKADKLYVSVDIDVLDP 247 Query: 249 SHAPGCPAIGPGGLYTDELLEAVKYIAQQPNVAGIEIVEVDPTLDFRDMTSRAAAHVLLH 308 +HAPG PGG+ + +LL V+ + + +V G+++VEV P D ++T AA V+ Sbjct: 248 AHAPGTGTPEPGGITSADLLRMVRQLCHEHDVVGVDVVEVAPAYDHAELTINAAHRVVFE 307 Query: 309 ALKGM 313 AL GM Sbjct: 308 ALAGM 312 Lambda K H 0.318 0.136 0.396 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: 324 Number of extensions: 19 Number of successful extensions: 4 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: 319 Length of database: 340 Length adjustment: 28 Effective length of query: 291 Effective length of database: 312 Effective search space: 90792 Effective search space used: 90792 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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