GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cyclodeaminase in Pseudomonas simiae WCS417

Align ornithine cyclodeaminase (EC 4.3.1.12) (characterized)
to candidate GFF3435 PS417_17585 ornithine cyclodeaminase

Query= BRENDA::Q88H32
         (350 letters)



>FitnessBrowser__WCS417:GFF3435
          Length = 348

 Score =  407 bits (1045), Expect = e-118
 Identities = 208/335 (62%), Positives = 256/335 (76%), Gaps = 1/335 (0%)

Query: 1   MTYFIDVPTMSDLVHDIGVAPFIGELAAALRDDFKRWQAFDKSARVASHSEVGVIELMPV 60
           MT +IDV  +  LV   G+   I E+A  +R D+ RWQ F+K AR+A+HS  GVIELMPV
Sbjct: 1   MTRYIDVNDLCYLVSQKGLQTCITEMAEYIRADYLRWQDFEKCARLANHSPDGVIELMPV 60

Query: 61  ADKSRYAFKYVNGHPANTARNLHTVMAFGVLADVDSGYPVLLSELTIATALRTAATSLMA 120
           +D S YAFKYVNGHP NT   + TVMAFG L DVD+G PVLL+E+T+ TA+RTAATS + 
Sbjct: 61  SDASLYAFKYVNGHPKNTLAGMLTVMAFGALGDVDTGLPVLLAEMTLTTAIRTAATSALV 120

Query: 121 AQALARPNARKMALIGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGL 180
           A+ LAR N+R MALIGNG+QSEFQALAFH  LGI EI  +D D  ATAKL ANLK +  +
Sbjct: 121 ARYLARDNSRSMALIGNGSQSEFQALAFHAMLGITEIRLFDIDAKATAKLAANLKAFPAI 180

Query: 181 TIRRASSVAEAVKGVDIITTVTADKAYATIITPDMLEPGMHLNAVGGDCPGKTELHADVL 240
            +  A SVAEAVKG DI+TTVTADKAYATI+T +M+EPGMHLNAVGGDCPGKTEL   ++
Sbjct: 181 KVILAGSVAEAVKGADIVTTVTADKAYATILTDEMIEPGMHLNAVGGDCPGKTELDRRIV 240

Query: 241 RNARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALED 300
             ARV VEYEPQ+RIEGEIQ +P D PV +LW+V+ G+  GR++  QVT+FDSVGFA+ED
Sbjct: 241 ERARVIVEYEPQSRIEGEIQHMPEDSPVTELWQVINGQQPGRENARQVTLFDSVGFAIED 300

Query: 301 YTVLRYVLQQAEKRGMGTKIDLVPWVEDDPKDLFS 335
           Y+ LRYVL  A+   +G+ ++LVP +  DPKDLF+
Sbjct: 301 YSALRYVLDVAKALDVGSDLELVPDLA-DPKDLFA 334


Lambda     K      H
   0.320    0.134    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: 316
Number of extensions: 4
Number of successful extensions: 1
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: 350
Length of database: 348
Length adjustment: 29
Effective length of query: 321
Effective length of database: 319
Effective search space:   102399
Effective search space used:   102399
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: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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