GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cyclodeaminase in Pseudomonas fluorescens FW300-N2E3

Align ornithine cyclodeaminase (EC 4.3.1.12) (characterized)
to candidate AO353_25185 AO353_25185 ornithine cyclodeaminase

Query= BRENDA::Q88H32
         (350 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25185
          Length = 350

 Score =  405 bits (1041), Expect = e-118
 Identities = 207/334 (61%), Positives = 255/334 (76%), Gaps = 1/334 (0%)

Query: 1   MTYFIDVPTMSDLVHDIGVAPFIGELAAALRDDFKRWQAFDKSARVASHSEVGVIELMPV 60
           MT FIDV   + L   +G+   I E+A  +  D+ RW  FDKS R A+HS  GVIELMP 
Sbjct: 1   MTLFIDVDHAARLFAKVGIRRAIREMATYIEADYSRWAQFDKSPRTANHSADGVIELMPT 60

Query: 61  ADKSRYAFKYVNGHPANTARNLHTVMAFGVLADVDSGYPVLLSELTIATALRTAATSLMA 120
            D  +Y+FKYVNGHP N  R+L TVMAFGVLADV SGYP LLSELT+ TA+RTAATS + 
Sbjct: 61  DDGQQYSFKYVNGHPGNGQRDLLTVMAFGVLADVHSGYPTLLSELTLTTAVRTAATSALV 120

Query: 121 AQALARPNARKMALIGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGL 180
           AQ+LARP A  MA+IGNGAQSEFQA+AFH+ L I EI  +D D  A+ KL  NL  + G+
Sbjct: 121 AQSLARPGASVMAIIGNGAQSEFQAIAFHEMLSIREIRIFDIDRDASLKLKHNLSAFPGI 180

Query: 181 TIRRASSVAEAVKGVDIITTVTADKAYATIITPDMLEPGMHLNAVGGDCPGKTELHADVL 240
            +  +SSV EAVKG  I+TTVTADKAYATI+TP+M+EPGMH+NAVGGDCPGKTELHA++L
Sbjct: 181 EVILSSSVQEAVKGAHIVTTVTADKAYATILTPEMIEPGMHINAVGGDCPGKTELHAEIL 240

Query: 241 RNARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALED 300
           RNAR+ VE+EPQTRIEG+IQQL AD PVV+ +R++ GE  GR++D+QVTVFDSVGFALED
Sbjct: 241 RNARIIVEFEPQTRIEGDIQQLEADSPVVEFFRIVLGEVPGRENDAQVTVFDSVGFALED 300

Query: 301 YTVLRYVLQQAEKRGMGTKIDLVPWVEDDPKDLF 334
           ++ LRY+   A + G+G +I LVP    + KDL+
Sbjct: 301 FSSLRYLHDLAREHGIGERIHLVP-TPANIKDLY 333


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: 330
Number of extensions: 10
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: 350
Length adjustment: 29
Effective length of query: 321
Effective length of database: 321
Effective search space:   103041
Effective search space used:   103041
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