GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cyclodeaminase in Herbaspirillum seropedicae SmR1

Align Ornithine cyclodeaminase; OCD; EC 4.3.1.12 (characterized)
to candidate HSERO_RS22840 HSERO_RS22840 ornithine cyclodeaminase

Query= SwissProt::Q59701
         (356 letters)



>FitnessBrowser__HerbieS:HSERO_RS22840
          Length = 306

 Score = 67.0 bits (162), Expect = 6e-16
 Identities = 66/221 (29%), Positives = 100/221 (45%), Gaps = 14/221 (6%)

Query: 105 GYPLLLSEMTILTALRTAATSALAAKYLARPNSKTMAIIGNGAQSEFQARAFRAILGIQK 164
           G PL   E   +T LRTAA +A+A   LARP++  +A+IG G Q+     A   +   ++
Sbjct: 85  GAPLCTMEGDAMTGLRTAAATAVACDALARPDAGVLAVIGTGVQARSHIPALLQVRPFKE 144

Query: 165 LRLFDIDTSATRKCARNLTGPGFDIVECGSVAEAVEGADVITTVTADKQFATILSDNH-V 223
           + +     S  +  A  +T          S+ EA   ADV+ TVT   + AT L D   +
Sbjct: 145 VLI--AGRSGQQALAEEVTRTLGVPARMVSIDEAAAQADVLVTVT---RSATPLFDGELL 199

Query: 224 GPGVHINAVGGDCPGKTEISMEVLLR-SDIFVEYPPQTWIE-GDIQQLP----RTHPVTE 277
            PG  + AVG       E+    + R + +FVE+ PQ   E GD+ Q          V E
Sbjct: 200 RPGAFVAAVGASKANVRELDDTAIGRAAALFVEWKPQAQQEAGDLVQCAPGVFDWAQVME 259

Query: 278 LWQVMTGEKTGRVGDRQITMFDSVGFAIED--FSALRYVRA 316
           L Q + G    +     I ++  +G  +ED   + L Y +A
Sbjct: 260 LAQAVDGSMPYQRRPDDIVIYKGIGIGLEDVALAGLAYRKA 300


Lambda     K      H
   0.320    0.137    0.405 

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: 178
Number of extensions: 18
Number of successful extensions: 2
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: 356
Length of database: 306
Length adjustment: 28
Effective length of query: 328
Effective length of database: 278
Effective search space:    91184
Effective search space used:    91184
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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