Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate Ga0059261_3995 Ga0059261_3995 succinylarginine dihydrolase (EC 3.5.3.23)
Query= reanno::MR1:201844 (444 letters) >FitnessBrowser__Korea:Ga0059261_3995 Length = 418 Score = 342 bits (876), Expect = 2e-98 Identities = 200/440 (45%), Positives = 267/440 (60%), Gaps = 29/440 (6%) Query: 1 MKHFEANFDGLVGPTHNYAGLSFGNVASLNNAALVSNPKAAAKQGLQKAKALADLGMIQG 60 M E NFDGL+GP+HNYAGLS GN+A+ N+ VS P+AAA QG+ K +A LG+ QG Sbjct: 1 MPRVEINFDGLIGPSHNYAGLSPGNLAATRNSGAVSQPRAAALQGIAKMRANLALGLTQG 60 Query: 61 MLAPQERPDLNTLRRIGFSGSDAQVLQQAAKTAPALLNACCSASSMWTANAATVSPSADT 120 +L P RPD L + S +DA QA SASSMW ANAATVSP+ DT Sbjct: 61 ILLPHARPDHRWLDSLATSYTDAAAHLQAQ---------ALSASSMWAANAATVSPAPDT 111 Query: 121 RDGKLHFTPANLVDKLHRSIE-PITTGRILTATFNDPHYFYHHNHLPEHNSFGDEGAANH 179 DG+ H T ANLV HRS E P T ++ A ND F H +P FGDEGAANH Sbjct: 112 ADGRCHLTVANLVTMPHRSHEWPGTLAQLRLAFGNDA--FRVHGPVPA--PFGDEGAANH 167 Query: 180 TRLCQEYGHAGVELFVYGQEATNPHAPKPLKFPARQTLEASMAIARLHQLEEDNCVFIQQ 239 RLC E+ GVE+FVYG FPARQ EAS A+AR H L+ +F+QQ Sbjct: 168 MRLCPEHDAPGVEVFVYGVSGG--------PFPARQHREASEAVARRHGLDPARTLFVQQ 219 Query: 240 NPAVIDQGVFHNDVIAVGNQNVLFYHEQAFLNTQAKLDEIKRKLDTELYFIEVPTAKVSI 299 + A I G FHNDV+AV N VLF HEQAF + Q +++R + E+ +EVP + VS+ Sbjct: 220 SEAAIAAGAFHNDVVAVANGRVLFAHEQAFADKQGFYADLRRVMP-EVEIVEVPASAVSL 278 Query: 300 NDAVKSYLFNTQIITLPSGEMAIIAPTDCQENPAVYAYLNELLSLNTPIKQVLYFDVKQS 359 DA+ SYLFN Q++TLPSGE A++ PT+ ++ P+V+A+L ++ N PI+ + DV+QS Sbjct: 279 ADAISSYLFNAQLVTLPSGETALVLPTEARDTPSVWAWLQAHVAGNGPIRHLEVVDVRQS 338 Query: 360 MQNGGGPACLRLRVAMNEREVAAVNQHTLLTDALFTRLNTWVEKHYRDRLSTEDLADPQL 419 M NGGGPACLRLRV + A ++ L+ R+ VE H+ + ++ +++ DP L Sbjct: 339 MANGGGPACLRLRVV---ADPATIDPRFLVDPGKLDRIAALVEMHWPETIAQDEIGDPAL 395 Query: 420 VIE---SRTALDELTQIMKL 436 + +R AL +L I++L Sbjct: 396 IARIEAARAALLDLLGIVEL 415 Lambda K H 0.318 0.132 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: 462 Number of extensions: 14 Number of successful extensions: 6 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: 444 Length of database: 418 Length adjustment: 32 Effective length of query: 412 Effective length of database: 386 Effective search space: 159032 Effective search space used: 159032 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: 51 (24.3 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