Align arginine deiminase (EC 3.5.3.6) (characterized)
to candidate BPHYT_RS27680 BPHYT_RS27680 arginine deiminase
Query= BRENDA::A7LKB0 (417 letters) >FitnessBrowser__BFirm:BPHYT_RS27680 Length = 405 Score = 493 bits (1270), Expect = e-144 Identities = 247/409 (60%), Positives = 305/409 (74%), Gaps = 7/409 (1%) Query: 8 YGVHSEAGKLRKVMVCAPGLAHKRLTPSNCDELLFDDVIWVDQAKRDHFDFVTKMRERGV 67 +GV+SE G LR VMVC PGLA RLTP+NC ELLFDDV+WV QAK DH+ FV+ M+ERG+ Sbjct: 3 FGVYSEIGTLRTVMVCRPGLAQARLTPANCRELLFDDVLWVSQAKNDHYAFVSAMQERGI 62 Query: 68 DVLEMHNLLTDIVQNPEALKWILDRKITPDTVGVGLTNEVRSWLEGQEPRHLAEFLIGGV 127 +VLEMH+LL DI++ EA W+L K++ V + L+ ++ WL LA L+GG+ Sbjct: 63 EVLEMHDLLADILRGREARDWVLAHKLSAGAVDLELSAQLLPWLREMNAGELATRLLGGI 122 Query: 128 AGQDLPESEGASVVKMYNDYLGHSSFILPPLPNTQFTRDTTCWIYGGVTLNPMYWPARRQ 187 +LP E A +V + S F+L PLPNT FTRD +CWI GV L MYWPARR+ Sbjct: 123 VRAELP-FEPAGLVAQCTE---PSGFLLRPLPNTLFTRDNSCWINDGVALGSMYWPARRE 178 Query: 188 ETLLTTAIYKFHPEFTKADFQVWYGDPDQEHGQATLEGGDVMPIGKGIVLIGMGERTSRQ 247 ETLL+ AIY+FHP FT ++W+GDP+ EHG ATLEGGDVMP+ + +VL+GMGERTS Q Sbjct: 179 ETLLSAAIYRFHPRFT-GGARIWWGDPESEHGGATLEGGDVMPLSRDVVLVGMGERTSPQ 237 Query: 248 AIGQLAQNLFAKGAVEQVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVREIVPFIIR 307 + QLA+ LFA +V+QVI A LP+SR AMHLDTV +FCDRDLVT+FPEVV I +R Sbjct: 238 GVAQLARTLFAHESVKQVIAAQLPRSRGAMHLDTVLTFCDRDLVTIFPEVVDGIRCTSLR 297 Query: 308 PDESKPYGMDVRRENKSFIEVVGEQLGVK-LRVVETGGNSFAAEREQWDDGNNVVALEPG 366 P ++ P +DVR E+ F+EVV LGVK LR V TGG+++ AEREQWDDGNNVVAL PG Sbjct: 298 PSQT-PGKLDVRPESAPFLEVVARALGVKQLRTVATGGDTWEAEREQWDDGNNVVALAPG 356 Query: 367 VVIGYDRNTYTNTLLRKAGIEVITISAGELGRGRGGGHCMTCPIVRDPI 415 VV+ Y+RN YTNTLLRKAG+EVITI +GELGRGRGGGHCMTCPI RDP+ Sbjct: 357 VVVAYNRNVYTNTLLRKAGVEVITIPSGELGRGRGGGHCMTCPIERDPV 405 Lambda K H 0.320 0.139 0.424 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: 536 Number of extensions: 13 Number of successful extensions: 5 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: 417 Length of database: 405 Length adjustment: 31 Effective length of query: 386 Effective length of database: 374 Effective search space: 144364 Effective search space used: 144364 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: 50 (23.9 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