Align arginine deiminase (EC 3.5.3.6) (characterized)
to candidate AZOBR_RS13255 AZOBR_RS13255 arginine deiminase
Query= BRENDA::P13981 (418 letters) >FitnessBrowser__azobra:AZOBR_RS13255 Length = 409 Score = 531 bits (1369), Expect = e-155 Identities = 254/411 (61%), Positives = 321/411 (78%), Gaps = 6/411 (1%) Query: 6 TKLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMRER 65 +++GVHSE GKLR V+VC P LAHQRLTP NC +LLFDDVIWV++A++DH D V KM ER Sbjct: 2 SEVGVHSEVGKLRTVLVCRPSLAHQRLTPGNCHDLLFDDVIWVHEAQKDHHDLVLKMEER 61 Query: 66 GIDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYLIG 125 G++VL++H+LL +T+ +P+A +++LDR++TA++VG+ +R WL+ + R+LA +LIG Sbjct: 62 GVEVLDLHDLLAQTLDDPQARRFVLDRRVTANTVGVAAVEVMRPWLDEMPSRELAVHLIG 121 Query: 126 GVAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMYWPAR 185 G+A DLP + + +L E G + F+LPP+PNT F RD +CWIY GVT NPM+WPAR Sbjct: 122 GIAISDLPDNTVSVLLN---EAFGGTDFVLPPIPNTLFQRDPSCWIYNGVTCNPMFWPAR 178 Query: 186 RQETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGERSS 245 + ETLL A+YKFHP F + F IW+GD D+D ++LEGGDVMPIG GVVLIGMGER++ Sbjct: 179 KPETLLQRAVYKFHPRFRDGGFTIWWGDSDEDFTGASLEGGDVMPIGKGVVLIGMGERTN 238 Query: 246 RQAIGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKEIVPFS 305 RQA+GQV ++LF AA RVI +PKSRAAMHLDTVFSFCDRDLVTVF EVV +I +S Sbjct: 239 RQAVGQVTRALFRNNAASRVIACLMPKSRAAMHLDTVFSFCDRDLVTVFREVVDQIRCYS 298 Query: 306 LRP-DPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNSFAAEREQWDDGNNVVCL 364 P D + +R E + LEVVA++LG +LR+V TGGN++ AEREQWDDGNNVV L Sbjct: 299 AYPLDDEGRF--EVRPEARPLLEVVADALGYSRLRIVGTGGNAYEAEREQWDDGNNVVAL 356 Query: 365 EPGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDP 415 EPGVVV YDRNTYTNTLLRKAGVEVIT+ +ELGRGRGGGHCMTCPI R+P Sbjct: 357 EPGVVVAYDRNTYTNTLLRKAGVEVITVRGAELGRGRGGGHCMTCPIWREP 407 Lambda K H 0.319 0.137 0.414 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: 563 Number of extensions: 19 Number of successful extensions: 3 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: 418 Length of database: 409 Length adjustment: 31 Effective length of query: 387 Effective length of database: 378 Effective search space: 146286 Effective search space used: 146286 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 (21.7 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