Align arginase (EC 3.5.3.1) (characterized)
to candidate SMc01967 SMc01967 agmatinase
Query= metacyc::MONOMER-14988 (338 letters) >FitnessBrowser__Smeli:SMc01967 Length = 352 Score = 118 bits (295), Expect = 3e-31 Identities = 91/280 (32%), Positives = 140/280 (50%), Gaps = 15/280 (5%) Query: 62 SLLGIPLGHNSSFLQGPAFAPPLIREAIWCGSTNSTTEEGKILDDQRVLTDVGDLPVQEL 121 +++G+P+ + G F P +R G N + D + + D+GD+P + Sbjct: 73 AMIGVPMDLGVTNRPGSRFGPRALRAIERIGPYNHVLGCAPVHDLR--VADIGDVPFRSR 130 Query: 122 RDTGIDDDRLMSTVSESVKLVMDENPLRPLVLGGDHSISYPVVRAVSEKLGGPVDILHLD 181 I + + +S+ ++D L PL +GGDHSI++P+++AV K PV ++H+D Sbjct: 131 YRLEISHEDIEKRISQ----IVDAGVL-PLSVGGDHSITHPILKAVGRKQ--PVGMIHID 183 Query: 182 AHPDIYDAFEGNKYSHASSFARIMEGGYA--RRLLQVGIRSINLEGREQGKRFG--VEQY 237 AH D AF+ K+ H F + G R++Q+GIR E G V Sbjct: 184 AHCDTGGAFDLTKFHHGGPFRNAVLDGVLDPTRVIQIGIRGSAEYLWEFSYESGMTVIHA 243 Query: 238 EMRTFSRDRQFLENLKLGEGVKGVYISVDVDCLDPAFAPGVSHFESGGLSFRDVLNILHN 297 E T +E K G Y+S DVD LDP+FAPG E GGL+ R+VL ++ Sbjct: 244 EEVTGLGIPAIIEKAKKIVGDGPTYLSFDVDSLDPSFAPGTGTPEVGGLTTREVLELIRG 303 Query: 298 LQG-DIVGADVVEYNPQRDTADGMTAMVAAKLVRELAAKM 336 L+G ++VG DVVE PQ DT TA A+++ E+ + M Sbjct: 304 LKGVNLVGGDVVEVAPQYDTTTN-TAHAGAQVLFEILSLM 342 Lambda K H 0.317 0.137 0.387 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: 326 Number of extensions: 21 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: 338 Length of database: 352 Length adjustment: 29 Effective length of query: 309 Effective length of database: 323 Effective search space: 99807 Effective search space used: 99807 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 (21.6 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